Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold329
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4121247
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 5938 characters in sequence are not A, C, G, or T
File 2 of 25
Found at i:203103 original size:17 final size:18
Alignment explanation
Indices: 203081--203117 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
203071 AAAATTGCAG
203081 AAAAAAG-AGAAAAAAGA
1 AAAAAAGAAGAAAAAAGA
*
203098 AAAAAAGAAGAAAAATGA
1 AAAAAAGAAGAAAAAAGA
203116 AA
1 AA
203118 GAAGATGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (18 bp):
AAAAAAGAAGAAAAAAGA
Found at i:203403 original size:18 final size:17
Alignment explanation
Indices: 203380--203419 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
203370 TAAAATGAAA
203380 AAAAAAGAAAAGAAAAGG
1 AAAAAAGAAAA-AAAAGG
* *
203398 AAAAAAGAGAAAAATGG
1 AAAAAAGAAAAAAAAGG
203415 AAAAA
1 AAAAA
203420 GTGAAGCTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.03
Consensus pattern (17 bp):
AAAAAAGAAAAAAAAGG
Found at i:204734 original size:91 final size:91
Alignment explanation
Indices: 204587--204917 Score: 502
Period size: 91 Copynumber: 3.6 Consensus size: 91
204577 CACATTTCGG
* * * * *
204587 AATCATATCCCCTTCACCCAACTACTAGATGGTATTGATGCATAACAAAGCTTGATTTCCTTGGG
1 AATCATATCTCCTTCATCCAACCACTAGATGGTATTGATGCATCACAAAGCCTGATTTCCTTGGG
*
204652 GGCAAGGTGTAGCCCACACATTCCCT
66 GGTAAGGTGTAGCCCACACATTCCCT
* * * * **
204678 AGTCATATCTCCTTCATCTAATCACTAGATGGTATTGATGCATTACAAAGCCTGATTTCCTAAGG
1 AATCATATCTCCTTCATCCAACCACTAGATGGTATTGATGCATCACAAAGCCTGATTTCCTTGGG
204743 GGTAAGGTGTAGCCCACACATTCCCT
66 GGTAAGGTGTAGCCCACACATTCCCT
* * *
204769 AATCATATCTCCTTCATCCAACCATTAGTTGGTATTGATGCATCACAAAGCCTAATTTTCC-TGG
1 AATCATATCTCCTTCATCCAACCACTAGATGGTATTGATGCATCACAAAGCCTGA-TTTCCTTGG
*
204833 GGGTAAGGTATAGCCCACACATTCCCT
65 GGGTAAGGTGTAGCCCACACATTCCCT
204860 AATCATATCTCCTTCATCCAACCACTAGATGGTATTGATGCATCACAAAGCCTGATTT
1 AATCATATCTCCTTCATCCAACCACTAGATGGTATTGATGCATCACAAAGCCTGATTT
204918 TCTTCGGGCA
Statistics
Matches: 215, Mismatches: 24, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
90 3 0.01
91 207 0.96
92 5 0.02
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (91 bp):
AATCATATCTCCTTCATCCAACCACTAGATGGTATTGATGCATCACAAAGCCTGATTTCCTTGGG
GGTAAGGTGTAGCCCACACATTCCCT
Found at i:204994 original size:92 final size:91
Alignment explanation
Indices: 204587--204994 Score: 407
Period size: 91 Copynumber: 4.5 Consensus size: 91
204577 CACATTTCGG
* * * * * * * *
204587 AATCATATCCCCTTCACCCAACTACTAGATGGTATTGATGCATAACAAAGCTTGA-TTTCCTTGG
1 AATCATATCTCCTTCATCCAACCACTAGTTGGTATTGATGCATCACAAAGCCTAATTTTCC-TGC
* *
204651 GGGCAAGGTGTAGCCCACACATTCCCT
65 GGGCAAAGTATAGCCCACACATTCCCT
* * * * * *
204678 AGTCATATCTCCTTCATCTAATCACTAGATGGTATTGATGCATTACAAAGCCTGA-TTTCCTAAG
1 AATCATATCTCCTTCATCCAACCACTAGTTGGTATTGATGCATCACAAAGCCTAATTTTCCT--G
* * *
204742 -GGGTAAGGTGTAGCCCACACATTCCCT
64 CGGGCAAAGTATAGCCCACACATTCCCT
* *
204769 AATCATATCTCCTTCATCCAACCATTAGTTGGTATTGATGCATCACAAAGCCTAATTTTCCTGGG
1 AATCATATCTCCTTCATCCAACCACTAGTTGGTATTGATGCATCACAAAGCCTAATTTTCCTGCG
* *
204834 GGTAAGGTATAGCCCACACATTCCCT
66 GGCAAAGTATAGCCCACACATTCCCT
* * *
204860 AATCATATCTCCTTCATCCAACCACTAGATGGTATTGATGCATCACAAAGCCTGATTTT-CTTCG
1 AATCATATCTCCTTCATCCAACCACTAGTTGGTATTGATGCATCACAAAGCCTAATTTTCCTGCG
*
204924 GGCAAAG-ATATCCCGACCATTCATTCCC-
66 GGCAAAGTATAGCCC-A-CA--CATTCCCT
** * * *
204952 AATCATATC-CCTTTCATTTAGCTACTAGTTGATATTGATGCAT
1 AATCATATCTCC-TTCATCCAACCACTAGTTGGTATTGATGCAT
204995 TACATGACCA
Statistics
Matches: 277, Mismatches: 31, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
89 6 0.02
90 11 0.04
91 212 0.77
92 41 0.15
93 7 0.03
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (91 bp):
AATCATATCTCCTTCATCCAACCACTAGTTGGTATTGATGCATCACAAAGCCTAATTTTCCTGCG
GGCAAAGTATAGCCCACACATTCCCT
Found at i:205232 original size:35 final size:35
Alignment explanation
Indices: 205169--205316 Score: 158
Period size: 35 Copynumber: 4.3 Consensus size: 35
205159 AAATTTTCTC
* * * * *
205169 TCAAACTCTTTCCAAT-ATCGTTTAATTGTGTTTAG
1 TCAAACTCTTTCC-ATCATCATTTGATTGTATCTGG
* *
205204 ACAAATTCTTTCCATCATCATTTGATTGTATCTGG
1 TCAAACTCTTTCCATCATCATTTGATTGTATCTGG
* *
205239 TCAAACTCTTTCCATCATCGTTTGATTATATCTGG
1 TCAAACTCTTTCCATCATCATTTGATTGTATCTGG
* * *
205274 TCAAGCTCTTTCCATCATCATTTGACTGTA-CTCG
1 TCAAACTCTTTCCATCATCATTTGATTGTATCTGG
205308 TCAAA-TCTT
1 TCAAACTCTT
205317 ACCCCTCTTG
Statistics
Matches: 95, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
33 4 0.04
34 9 0.09
35 82 0.86
ACGTcount: A:0.24, C:0.22, G:0.11, T:0.43
Consensus pattern (35 bp):
TCAAACTCTTTCCATCATCATTTGATTGTATCTGG
Found at i:205252 original size:70 final size:69
Alignment explanation
Indices: 205169--205316 Score: 174
Period size: 70 Copynumber: 2.1 Consensus size: 69
205159 AAATTTTCTC
* * * * *
205169 TCAAACTCTTTCCAAT-ATCGTTTAATTGTGTTTAGACAAATTCTTTCCATCATCATTTGATTGT
1 TCAAACTCTTTCC-ATCATCGTTTAATTATATCTAGACAAACTCTTTCCATCATCATTTGACTGT
*
205233 ATCTGG
65 A-CTCG
* * * *
205239 TCAAACTCTTTCCATCATCGTTTGATTATATCTGGTCAAGCTCTTTCCATCATCATTTGACTGTA
1 TCAAACTCTTTCCATCATCGTTTAATTATATCTAGACAAACTCTTTCCATCATCATTTGACTGTA
205304 CTCG
66 CTCG
205308 TCAAA-TCTT
1 TCAAACTCTT
205317 ACCCCTCTTG
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
68 4 0.06
69 10 0.15
70 53 0.79
ACGTcount: A:0.24, C:0.22, G:0.11, T:0.43
Consensus pattern (69 bp):
TCAAACTCTTTCCATCATCGTTTAATTATATCTAGACAAACTCTTTCCATCATCATTTGACTGTA
CTCG
Found at i:206600 original size:26 final size:28
Alignment explanation
Indices: 206541--206638 Score: 98
Period size: 28 Copynumber: 3.6 Consensus size: 28
206531 AAAATCAGGA
206541 TTGGAGTATCCCCTCG--GAAATAACGGGG
1 TTGGAGTAT-CCCT-GATGAAATAACGGGG
*
206569 TTGGAGTATCCCTGATG-AA-ACCGGGG
1 TTGGAGTATCCCTGATGAAATAACGGGG
* * *
206595 TTGGAGTGTTCCCTCA-GAAATAACAGGG
1 TTGGAGT-ATCCCTGATGAAATAACGGGG
206623 TTGGAGTATCCCTGAT
1 TTGGAGTATCCCTGAT
206639 TGTTAAAAGT
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
26 15 0.26
27 20 0.35
28 22 0.39
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (28 bp):
TTGGAGTATCCCTGATGAAATAACGGGG
Found at i:206781 original size:52 final size:51
Alignment explanation
Indices: 206622--206788 Score: 183
Period size: 51 Copynumber: 3.3 Consensus size: 51
206612 AAATAACAGG
* *** * *
206622 GTTGGAGTATCCCTGATTGTTAAAAGTCGATGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTAAGAAAAATGGATGTTTTGGAAATAAAATCGGA
* * * * *
206673 GTTTGAGTATCCCCGATTATGGAAAATGGGTGTTTTAGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTAAGAAAAATGGATGTTTTGGAAATAAAATCGGA
* * *
206724 GTTGGAGTATCCCCGATTAAGAAAAAATTGATGTTTTGGAAATGAAA-CCGA
1 GTTGGAGTATCCCCGATTAAG-AAAAATGGATGTTTTGGAAATAAAATCGGA
206775 GATTGGAGTATCCC
1 G-TTGGAGTATCCC
206789 AAGATGAAAA
Statistics
Matches: 97, Mismatches: 17, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
51 65 0.67
52 32 0.33
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTAAGAAAAATGGATGTTTTGGAAATAAAATCGGA
Found at i:209087 original size:20 final size:21
Alignment explanation
Indices: 209062--209156 Score: 110
Period size: 20 Copynumber: 4.7 Consensus size: 21
209052 AAAATGCCTG
*
209062 AATGTATCGATACATTGTAA-
1 AATGTATCGATACAATGTAAC
*
209082 AATGTATCGATATAA--TAAGC
1 AATGTATCGATACAATGTAA-C
*
209102 AATGTATCGATACAATGCAA-
1 AATGTATCGATACAATGTAAC
*
209122 AATGTATCGGTACAATG-AAC
1 AATGTATCGATACAATGTAAC
209142 AATGTATCGATACAA
1 AATGTATCGATACAA
209157 ATTGTCAAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
18 3 0.05
19 2 0.03
20 57 0.89
22 2 0.03
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (21 bp):
AATGTATCGATACAATGTAAC
Found at i:209124 original size:40 final size:40
Alignment explanation
Indices: 209062--209156 Score: 138
Period size: 40 Copynumber: 2.4 Consensus size: 40
209052 AAAATGCCTG
* * *
209062 AATGTATCGATACATTGTAAAATGTATCGATATAAT-AAGC
1 AATGTATCGATACAATGCAAAATGTATCGATACAATGAA-C
*
209102 AATGTATCGATACAATGCAAAATGTATCGGTACAATGAAC
1 AATGTATCGATACAATGCAAAATGTATCGATACAATGAAC
209142 AATGTATCGATACAA
1 AATGTATCGATACAA
209157 ATTGTCAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 48 0.96
41 2 0.04
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (40 bp):
AATGTATCGATACAATGCAAAATGTATCGATACAATGAAC
Found at i:209241 original size:20 final size:21
Alignment explanation
Indices: 209192--209248 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
209182 CAGTTGCCCA
* *
209192 GAATGTATCGATATAATGAGC
1 GAATGTATCGATACAATGAAC
*
209213 GACTGTATCGATACAATGAAC
1 GAATGTATCGATACAATGAAC
209234 -AATGTATCGATACAA
1 GAATGTATCGATACAA
209249 ATTATCAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 14 0.44
21 18 0.56
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.26
Consensus pattern (21 bp):
GAATGTATCGATACAATGAAC
Found at i:209998 original size:42 final size:42
Alignment explanation
Indices: 209946--210036 Score: 112
Period size: 42 Copynumber: 2.1 Consensus size: 42
209936 AGGATAAAGG
*
209946 GAAAAAGGAAAACGAAA-CGCATCCTGCTCTTTGAGGACAAAA
1 GAAAAAGGAAAAC-AAAGCGCATCCTGCTCTTTAAGGACAAAA
* * **
209988 GAAAGAGGAAAACAAAGTGTGTCCTGCTCTTTAAGGACAAAA
1 GAAAAAGGAAAACAAAGCGCATCCTGCTCTTTAAGGACAAAA
210030 GAGAAAA
1 GA-AAAA
210037 TAAGGGAATG
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
41 3 0.07
42 35 0.85
43 3 0.07
ACGTcount: A:0.46, C:0.15, G:0.23, T:0.15
Consensus pattern (42 bp):
GAAAAAGGAAAACAAAGCGCATCCTGCTCTTTAAGGACAAAA
Found at i:210106 original size:42 final size:43
Alignment explanation
Indices: 209967--210116 Score: 173
Period size: 42 Copynumber: 3.5 Consensus size: 43
209957 ACGAAACGCA
* *
209967 TCCTGCTCTTTGA-GGACAAAAGAAAGAGGAAAACAAAGTGTG
1 TCCTGCTCTTTGAGGGACAAAAGAGAGAGGAAAATAAAGTGTG
* * ** *
210009 TCCTGCTCTTT-AAGGACAAAAGAGAAAATAAGGGAATGAAGTGTG
1 TCCTGCTCTTTGAGGGACAAAAGAGAGAGGAA---AATAAAGTGTG
*
210054 TCCTGCTCTTTGAGGGA-AAAAGAGAGAGGAAAATAAAGTGCG
1 TCCTGCTCTTTGAGGGACAAAAGAGAGAGGAAAATAAAGTGTG
210096 TCCTGCTCTTTGA-GGACAAAA
1 TCCTGCTCTTTGAGGGACAAAA
210117 AAGTGCCACT
Statistics
Matches: 90, Mismatches: 12, Indels: 12
0.79 0.11 0.11
Matches are distributed among these distances:
41 4 0.04
42 51 0.57
45 31 0.34
46 4 0.04
ACGTcount: A:0.38, C:0.14, G:0.27, T:0.21
Consensus pattern (43 bp):
TCCTGCTCTTTGAGGGACAAAAGAGAGAGGAAAATAAAGTGTG
Found at i:210184 original size:61 final size:58
Alignment explanation
Indices: 210082--210265 Score: 203
Period size: 61 Copynumber: 3.1 Consensus size: 58
210072 AAAGAGAGAG
* ** * *
210082 GAAAATAAAGTGCGTCCTGCTCTTTGAGGACAAAAAAGTGCCACTAACTCGTGTGGGCTTT
1 GAAAAAAAAG-GCGTCCTGCTCTTTGAGGAC--GGAAGTGCCACCAACTTGTGTGGGCTTT
* *
210143 GAAAAAGAAAGGCGTCCTGCTCTTTAATGACTGGAAGGTGCCACCAACTTGTGTGGGCTTT
1 GAAAAA-AAAGGCGTCCTGCTCTTTGAGGAC-GGAA-GTGCCACCAACTTGTGTGGGCTTT
*
210204 GCAAAGAAAAA-GCATCCTGCTCTTTGAGGACGG-AGTGCCACCAACTTGTGTGGGCTTT
1 G-AAA-AAAAAGGCGTCCTGCTCTTTGAGGACGGAAGTGCCACCAACTTGTGTGGGCTTT
210262 -AAAA
1 GAAAA
210266 GATGTCATGC
Statistics
Matches: 108, Mismatches: 11, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
55 1 0.01
56 3 0.03
58 24 0.22
59 1 0.01
60 4 0.04
61 63 0.58
62 10 0.09
63 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.25
Consensus pattern (58 bp):
GAAAAAAAAGGCGTCCTGCTCTTTGAGGACGGAAGTGCCACCAACTTGTGTGGGCTTT
Found at i:210428 original size:53 final size:53
Alignment explanation
Indices: 210317--210430 Score: 133
Period size: 53 Copynumber: 2.1 Consensus size: 53
210307 GTCCTACTCT
* * * *
210317 TTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTCGAAATGCATCCTGCTC
1 TTGAGGACTAGGAAGGGCCACCAACTTGTGTGGGCTTCAAAATG-ATCATGCTC
* *
210371 TTGAGGAC-AGGAAGGGCCACCGACTTGTGTGGGCTTTAAAGATG-TCATGCTC
1 TTGAGGACTAGGAAGGGCCACCAACTTGTGTGGGCTTCAAA-ATGATCATGCTC
210423 GTTGAGGA
1 -TTGAGGA
210431 ATAAAAGGGT
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
52 7 0.13
53 34 0.65
54 11 0.21
ACGTcount: A:0.22, C:0.20, G:0.32, T:0.25
Consensus pattern (53 bp):
TTGAGGACTAGGAAGGGCCACCAACTTGTGTGGGCTTCAAAATGATCATGCTC
Found at i:210459 original size:145 final size:147
Alignment explanation
Indices: 210149--210503 Score: 462
Period size: 145 Copynumber: 2.4 Consensus size: 147
210139 CTTTGAAAAA
* * * *
210149 GAAAG-GCGTCCTGCTCTTTAATGACT-GGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGAA
1 GAAAGAGCGTCCTACTCTTTGAGGACTGGGAA-GTGCCACCAACTTGTGTGGGCGTT-C---G-A
*
210212 AAAGCATCCTGCTCTTTGAGGACGGAGTGCCACCAACTTGTGTGGGCTTTAAAAGATGTCATGCT
60 AAAGCATCCTGCTCTTTGAGGACGGAGGGCCACCAACTTGTGTGGGCTTTAAAAGATGTCATGCT
* *
210277 CTTTGAGGACTAAAGGGTGAAAG
125 CGTTGAGGAATAAAGGGTGAAAG
*
210300 G-AAGAGCGTCCTACTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGC-TTCGAAATGCA
1 GAAAGAGCGTCCTACTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCGTTCGAAAAGCA
*
210363 TCCTGCTC-TTGAGGACAGGAAGGGCCACCGACTTGTGTGGGCTTT-AAAGATGTCATGCTCGTT
66 TCCTGCTCTTTGAGGAC-GG-AGGGCCACCAACTTGTGTGGGCTTTAAAAGATGTCATGCTCGTT
210426 GAGGAATAAAAGGGTG-AAG
129 GAGGAAT-AAAGGGTGAAAG
*
210445 GAAAGAGCGT-CTACTCGTTGAGGACTGGGAAGTG-C-CC-ACTTGTGTGGGCGTTCGAAAAG
1 GAAAGAGCGTCCTACTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCGTTCGAAAAG
210504 GCCAAAAATC
Statistics
Matches: 187, Mismatches: 10, Indels: 22
0.85 0.05 0.10
Matches are distributed among these distances:
142 12 0.06
143 10 0.05
144 9 0.05
145 66 0.35
146 40 0.21
149 1 0.01
150 5 0.03
151 40 0.21
152 4 0.02
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (147 bp):
GAAAGAGCGTCCTACTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCGTTCGAAAAGCA
TCCTGCTCTTTGAGGACGGAGGGCCACCAACTTGTGTGGGCTTTAAAAGATGTCATGCTCGTTGA
GGAATAAAGGGTGAAAG
Found at i:210719 original size:61 final size:60
Alignment explanation
Indices: 210538--210962 Score: 371
Period size: 61 Copynumber: 7.1 Consensus size: 60
210528 ACTAAAAAAA
* *
210538 AAAATGCCACCAACTTGTG-GGGCTGT----G-AAAGGCGTCCTGGCTCTTTGAGGACTGG
1 AAAATGCCACCAACTTGTGTGGGCTTTAAAGGAAAAGGCATCCT-GCTCTTTGAGGACTGG
* * * *
210593 AAAATGCCACCAACTCGTGTAGGC-TTAAAGAGAAAA-GCATCCTGCTCTTTGAGGGAGTAG
1 AAAATGCCACCAACTTGTGTGGGCTTTAAAG-GAAAAGGCATCCTGCTCTTTGA-GGACTGG
* *
210653 AAAATG-CACCAACGTGTGTGGGGATTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGACTGG
1 AAAATGCCACCAACTTGTGT-GGGCTTT-AAAGGAAAAGGCATCCTGCTCTTTGAGGACTGG
* * *
210714 AAAATGCCCCCAACTTGTGTGGGCTTTAAAAGGAAAAAG-AGTCCTGCTCTTTGAGGACTAGA
1 AAAATGCCACCAACTTGTGTGGGCTTT-AAAGGAAAAGGCA-TCCTGCTCTTTGAGGACT-GG
*** *
210776 AAAAGTGCCACCAACTTGTGTGGGAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCTTTGAGGAC
1 AAAA-TGCCACCAACTTGTGTGGG--CTT-TAAAGG----AAAAGGCATCCTGCTCTTTGAGGAC
*
210841 T-C
58 TGG
*
210843 AAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGCATCCTGCTCTTTGAGGACTGG
1 AAA-ATGCCACCAACTTGTGTGGGCTTTAAAGGAAAAGGCATCCTGCTCTTTGAGGACTGG
** * * *
210899 AAGGTGCCACCAACTTGTGTAGGCTTTAAAAGGAAAAGGCGTCTTGCTCTTTGAGGACT-G
1 AAAATGCCACCAACTTGTGTGGGCTTT-AAAGGAAAAGGCATCCTGCTCTTTGAGGACTGG
210959 AAAA
1 AAAA
210963 GTGAAAGGAG
Statistics
Matches: 305, Mismatches: 33, Indels: 59
0.77 0.08 0.15
Matches are distributed among these distances:
55 66 0.22
56 5 0.02
59 20 0.07
60 26 0.09
61 79 0.26
62 36 0.12
63 18 0.06
64 1 0.00
65 8 0.03
66 1 0.00
67 22 0.07
69 23 0.08
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.25
Consensus pattern (60 bp):
AAAATGCCACCAACTTGTGTGGGCTTTAAAGGAAAAGGCATCCTGCTCTTTGAGGACTGG
Found at i:210857 original size:130 final size:122
Alignment explanation
Indices: 210686--210918 Score: 306
Period size: 130 Copynumber: 1.8 Consensus size: 122
210676 ATTTAAAAGG
* *
210686 AAAAGGCATCCTGCTCTTTGAGGACTGGAAAATGCCCCCAACTTGTGTGGGCTTTAAAAGGAAAA
1 AAAAGGCATCCTGCTCTTTGAGGACTGCAAAATGCCACCAACTTGTGTGGGCTTTAAAAGG----
*
210751 AGAGTCCTGCTCTTTGAGGACTAGAAAAAGTGCCACCAACTTGTGTGGGAACTTGTGTGGGCTTT
62 -CA-TCCTGCTCTTTGAGGACT-G-AAAAGTGCCACCAACTTGTGTGGGAACTTGTGTGGGCTTT
* * *
210816 AAAAGGCGTCCTGCTCTTTGAGGACT-CAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCAT
1 AAAAGGCATCCTGCTCTTTGAGGACTGCAAA-ATGCCACCAACTTGTGTGGGCTTTAAAAGGCAT
* *
210880 CCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGT
65 CCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGT
210919 AGGCTTTAAA
Statistics
Matches: 94, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
122 19 0.20
123 1 0.01
124 18 0.19
125 1 0.01
129 3 0.03
130 52 0.55
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (122 bp):
AAAAGGCATCCTGCTCTTTGAGGACTGCAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCATC
CTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGAACTTGTGTGGGCTTT
Found at i:210884 original size:55 final size:55
Alignment explanation
Indices: 210800--210931 Score: 219
Period size: 55 Copynumber: 2.4 Consensus size: 55
210790 CTTGTGTGGG
*
210800 AACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCTTTGAGGACTCAAAGGTGCCACC
1 AACTTGTGTGGGCTTTAAAAGGCATCCTGCTCTTTGAGGACTCAAAGGTGCCACC
* **
210855 AACTTGTGTGGGCTTTGAAAGGCATCCTGCTCTTTGAGGACTGGAAGGTGCCACC
1 AACTTGTGTGGGCTTTAAAAGGCATCCTGCTCTTTGAGGACTCAAAGGTGCCACC
*
210910 AACTTGTGTAGGCTTTAAAAGG
1 AACTTGTGTGGGCTTTAAAAGG
210932 AAAAGGCGTC
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 71 1.00
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (55 bp):
AACTTGTGTGGGCTTTAAAAGGCATCCTGCTCTTTGAGGACTCAAAGGTGCCACC
Found at i:211960 original size:10 final size:10
Alignment explanation
Indices: 211957--211998 Score: 68
Period size: 10 Copynumber: 4.2 Consensus size: 10
211947 TTTTTCTTTG
211957 TTTTGTTTTT
1 TTTTGTTTTT
211967 TTTTG-TTTT
1 TTTTGTTTTT
211976 TTTTGTTTTT
1 TTTTGTTTTT
211986 TTTTGGTTTTT
1 TTTT-GTTTTT
211997 TT
1 TT
211999 GAAAAAGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.30
10 13 0.43
11 8 0.27
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (10 bp):
TTTTGTTTTT
Found at i:211965 original size:15 final size:14
Alignment explanation
Indices: 211946--211979 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
211936 CTTTTCTCTC
211946 TTTTTTCTTTGTTT
1 TTTTTTCTTTGTTT
*
211960 TGTTTTTTTTTGTTT
1 T-TTTTTCTTTGTTT
211975 TTTTT
1 TTTTT
211980 GTTTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.00, C:0.03, G:0.09, T:0.88
Consensus pattern (14 bp):
TTTTTTCTTTGTTT
Found at i:211988 original size:9 final size:9
Alignment explanation
Indices: 211946--211999 Score: 63
Period size: 9 Copynumber: 5.8 Consensus size: 9
211936 CTTTTCTCTC
*
211946 TTTTTTCTT
1 TTTTTTGTT
*
211955 TGTTTTGTTT
1 TTTTTTG-TT
211965 TTTTTTGTT
1 TTTTTTGTT
211974 TTTTTTGTTT
1 TTTTTTG-TT
*
211984 TTTTTTGGT
1 TTTTTTGTT
211993 TTTTTTG
1 TTTTTTG
212000 AAAAAGAATG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
9 22 0.56
10 17 0.44
ACGTcount: A:0.00, C:0.02, G:0.13, T:0.85
Consensus pattern (9 bp):
TTTTTTGTT
Found at i:211990 original size:19 final size:19
Alignment explanation
Indices: 211946--211999 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
211936 CTTTTCTCTC
* *
211946 TTTTTTCTTTGTTTTGTTT
1 TTTTTTGTTTTTTTTGTTT
211965 TTTTTTGTTTTTTTTGTTT
1 TTTTTTGTTTTTTTTGTTT
*
211984 TTTTTTGGTTTTTTTG
1 TTTTTTGTTTTTTTTG
212000 AAAAAGAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.00, C:0.02, G:0.13, T:0.85
Consensus pattern (19 bp):
TTTTTTGTTTTTTTTGTTT
Found at i:222310 original size:4 final size:4
Alignment explanation
Indices: 222301--222325 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
222291 TGATATAACA
222301 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
222326 CCTCAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:224579 original size:76 final size:77
Alignment explanation
Indices: 224483--224680 Score: 249
Period size: 76 Copynumber: 2.5 Consensus size: 77
224473 CCGATTATAG
* * * *
224483 AAAATAGATGTTTCAAAAATAATATCGGGATTGGAGTATCCTCTCAGAAATAACGGGGTTGGAGT
1 AAAATTGATGTTTTAGAAATAA-ATCGGGATTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGT
224548 ATCCCTG-A-TGA
65 ATCCCTGAAGTGA
* * *
224559 AAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTGTCCCCTCAGAAATAACGGGGTTGGAGT
1 AAAATTGATGTTTTAGAAAT-AAATCGGGATTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGT
224624 ATCCCTGAATGTGA
65 ATCCCTGAA-GTGA
* *
224638 AAAATTGATGTTTTGGAAATTAAATC-GGAGTTGAAGTATCCCC
1 AAAATTGATGTTTTAGAAA-TAAATCGGGA-TTGGAGTATCCCC
224681 GATTATGGAA
Statistics
Matches: 104, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
76 62 0.60
77 3 0.03
78 2 0.02
79 36 0.35
80 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (77 bp):
AAAATTGATGTTTTAGAAATAAATCGGGATTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTA
TCCCTGAAGTGA
Found at i:224775 original size:52 final size:51
Alignment explanation
Indices: 224616--224785 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
224606 AAATAACGGG
* * ** *
224616 GTTGGAGTATCCCTGAATGTGAAAAATTGATGTTTTGGAAATTAAATCGGA
1 GTTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATAAAATCGGA
* * * * * *
224667 GTTGAAGTATCCCCGATTATGGAAAATGGGTGTTTTAGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATAAAATCGGA
* *
224718 GTTGGAGTATCCCCGATTAAGAAAAAATTGATGTTTTGGAAATGAAA-CCGA
1 GTTGGAGTATCCCCGATTAAG-AAAAATTGATGTTTTGGAAATAAAATCGGA
224769 GATTGGAGTATCCCCGA
1 G-TTGGAGTATCCCCGA
224786 GATGAAAAAT
Statistics
Matches: 100, Mismatches: 17, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
51 65 0.65
52 35 0.35
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.29
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATAAAATCGGA
Found at i:227106 original size:20 final size:19
Alignment explanation
Indices: 227081--227244 Score: 139
Period size: 20 Copynumber: 7.8 Consensus size: 19
227071 AAAATGCCTG
227081 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGA-C
*
227101 AATGTATCGATACAATGCAA
1 AATGTATCGATACAATG-AC
*
227121 AATGTATCGATACATCTGGGTAAACCC
1 AATGTATCGATACA-AT--G---A--C
*
227148 AGAATGTATCGATACAATGCAA
1 --AATGTATCGATACAATG-AC
227170 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGA-C
*
227190 AATGTATAGATACAATGAAC
1 AATGTATCGATACAATG-AC
*
227210 AATGTATCGATACAATAAAC
1 AATGTATCGATACAAT-GAC
227230 AATGTATCGATACAA
1 AATGTATCGATACAA
227245 ATTGTGAAAA
Statistics
Matches: 120, Mismatches: 11, Indels: 26
0.76 0.07 0.17
Matches are distributed among these distances:
19 1 0.01
20 97 0.81
21 3 0.03
23 1 0.01
24 1 0.01
25 1 0.01
26 1 0.01
28 1 0.01
29 14 0.12
ACGTcount: A:0.43, C:0.15, G:0.16, T:0.25
Consensus pattern (19 bp):
AATGTATCGATACAATGAC
Found at i:227129 original size:40 final size:40
Alignment explanation
Indices: 227081--227244 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
227071 AAAATGCCTG
227081 AATGTATCGATACAATGAGCAATGTATCGATACAATGCAA
1 AATGTATCGATACAATGAGCAATGTATCGATACAATGCAA
* *
227121 AATGTATCGATACATCTGGGTAAACCCAGAATGTATCGATACAATGCAA
1 AATGTATCGATACA-AT--G---A-GC--AATGTATCGATACAATGCAA
*
227170 AATGTATCGATACAATGAGCAATGTATAGATACAATG-AA
1 AATGTATCGATACAATGAGCAATGTATCGATACAATGCAA
* *
227209 CAATGTATCGATACAATAAACAATGTATCGATACAA
1 -AATGTATCGATACAATGAGCAATGTATCGATACAA
227245 ATTGTGAAAA
Statistics
Matches: 106, Mismatches: 8, Indels: 20
0.79 0.06 0.15
Matches are distributed among these distances:
39 2 0.02
40 62 0.58
41 1 0.01
42 1 0.01
43 2 0.02
46 2 0.02
47 1 0.01
48 1 0.01
49 34 0.32
ACGTcount: A:0.43, C:0.15, G:0.16, T:0.25
Consensus pattern (40 bp):
AATGTATCGATACAATGAGCAATGTATCGATACAATGCAA
Found at i:227612 original size:49 final size:49
Alignment explanation
Indices: 227520--227635 Score: 150
Period size: 49 Copynumber: 2.4 Consensus size: 49
227510 CTATATTGAA
* *
227520 GTTAGGACCTAGTCAAA-T-TCTTTTTCACCTAGTTTGACTGTATTGGC
1 GTTAGGACTTGGTCAAACTCTCTTTTTCACCTAGTTTGACTGTATTGGC
* *
227567 GTTA-GACTTGGTCAAACTCTCTTTTTCACCCTTA-TTTGATTGTATTTGC
1 GTTAGGACTTGGTCAAACTCTCTTTTTCA-CC-TAGTTTGACTGTATTGGC
227616 GTTAGGACTTGGTCAAACTC
1 GTTAGGACTTGGTCAAACTC
227636 CTTGCATCAT
Statistics
Matches: 60, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
46 10 0.17
47 5 0.08
48 9 0.15
49 19 0.32
50 17 0.28
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.41
Consensus pattern (49 bp):
GTTAGGACTTGGTCAAACTCTCTTTTTCACCTAGTTTGACTGTATTGGC
Found at i:228034 original size:84 final size:84
Alignment explanation
Indices: 227907--228348 Score: 460
Period size: 84 Copynumber: 5.2 Consensus size: 84
227897 TTGTCGGCTT
* * ** *
227907 AGTCCTCGATCAACCTCTCATCCATTGTTTACCTG-CTGGCTTAGTCCCCGATAAACCCATTACC
1 AGTCTTCGATCAACCT-TCATCCATTGTTTACTTGTC-GGCTTAGTCCTTGGTAAACCCATTACC
* ** * *
227971 TTTACAATAACCTGTTAGCTC
64 CTTACGGTGACCTATTAGCTC
* * * * * *
227992 AGTCTCCGATCAACCTTCATCCATTGATTACTTGTCGACTTAGTCCCTAGTAAACCTATTACCCT
1 AGTCTTCGATCAACCTTCATCCATTGTTTACTTGTCGGCTTAGTCCTTGGTAAACCCATTACCCT
*
228057 TACGG-GAACCTATTAGGTC
66 TACGGTG-ACCTATTAGCTC
** * * ** * *
228076 AGT-TTTTAGTCAACTTTCATCCATAGTTTACTTGTCAACATAGTCCTTGGTAAACCCATTGCCC
1 AGTCTTCGA-TCAACCTTCATCCATTGTTTACTTGTCGGCTTAGTCCTTGGTAAACCCATTACCC
* * *
228140 TTATGGTGACCTGTCAGCTC
65 TTACGGTGACCTATTAGCTC
*
228160 AGTCTTCGGTCAACCTTCATCCATTGTTTACTTGTCGGCTTAGTCCTTGGTAAACCCATTACCCT
1 AGTCTTCGATCAACCTTCATCCATTGTTTACTTGTCGGCTTAGTCCTTGGTAAACCCATTACCCT
* * *
228225 TACGATGACCTATCAGCTT
66 TACGGTGACCTATTAGCTC
* * * * *
228244 AGTCTCCTG-TCAACCTTCATCCATTATTTACCTATCGGCTCAGTCCTTGGTAAACCCATTACCC
1 AGTCTTC-GATCAACCTTCATCCATTGTTTACTTGTCGGCTTAGTCCTTGGTAAACCCATTACCC
*
228308 TTACGGTGACCTATTAGCTA
65 TTACGGTGACCTATTAGCTC
*
228328 AATCTTCGATCAACCTTCATC
1 AGTCTTCGATCAACCTTCATC
228349 TACTATTTAC
Statistics
Matches: 296, Mismatches: 54, Indels: 15
0.81 0.15 0.04
Matches are distributed among these distances:
83 3 0.01
84 274 0.93
85 19 0.06
ACGTcount: A:0.23, C:0.29, G:0.14, T:0.34
Consensus pattern (84 bp):
AGTCTTCGATCAACCTTCATCCATTGTTTACTTGTCGGCTTAGTCCTTGGTAAACCCATTACCCT
TACGGTGACCTATTAGCTC
Found at i:228384 original size:252 final size:253
Alignment explanation
Indices: 227898--228363 Score: 541
Period size: 252 Copynumber: 1.8 Consensus size: 253
227888 CTCGTTAACT
* *
227898 TGTCGGCTTAGTCCTCGATCAACCTCTCATCCATTGTTTACCTGCTGGCTTAGTCCCCGATAAAC
1 TGTCAGCTCAGTCCTCGATCAACCTCTCATCCATTGTTTACCTGCTGGCTTAGTCCCCGATAAAC
* * * * *
227963 CCATTACCTTTACAATAACCTGTTAGCTCAGTCTCCGATCAACCTTCATCCATTGATTACTTGTC
66 CCATTACCCTTACAATAACCTATCAGCTCAGTCTCCGATCAACCTTCATCCATTGATTACCTATC
* * * * * ** *
228028 GACTTAGTCCCTAGTAAACCTATTACCCTTACGGGAACCTATTAGGTCAGTTTTTAGTCAACTTT
131 GACTCAGTCCCTAGTAAACCCATTACCCTTACGGGAACCTATTAGCTAAATTTCGAGTCAACCTT
* * * *
228093 CATCCATAGTTTACTTGTCAACATAGTCCTTGGTAAACCCATTGCCCTTATGGTGACC
196 CATCCATAGTTTACCTATCAACATAGTCCTCGATAAACCCATTGCCCTTATGGTGACC
* * * ** *
228151 TGTCAGCTCAGTCTTCGGTCAACCT-TCATCCATTGTTTACTTG-TCGGCTTAGTCCTTGGTAAA
1 TGTCAGCTCAGTCCTCGATCAACCTCTCATCCATTGTTTACCTGCT-GGCTTAGTCCCCGATAAA
* * *
228214 CCCATTACCCTTACGATGACCTATCAGCTTAGTCTCCTG-TCAACCTTCATCCATT-ATTTACCT
65 CCCATTACCCTTACAATAACCTATCAGCTCAGTCTCC-GATCAACCTTCATCCATTGA-TTACCT
* * *
228277 ATCGGCTCAGTCCTTGGTAAACCCATTACCCTTACGGTG-ACCTATTAGCTAAATCTTCGA-TCA
128 ATCGACTCAGTCCCTAGTAAACCCATTACCCTTACGG-GAACCTATTAGCTAAAT-TTCGAGTCA
*
228340 ACCTTCATCTACTA-TTTACCTATC
191 ACCTTCATCCA-TAGTTTACCTATC
228364 GTCTCAGTTC
Statistics
Matches: 177, Mismatches: 30, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
251 2 0.01
252 147 0.83
253 28 0.16
ACGTcount: A:0.23, C:0.29, G:0.14, T:0.35
Consensus pattern (253 bp):
TGTCAGCTCAGTCCTCGATCAACCTCTCATCCATTGTTTACCTGCTGGCTTAGTCCCCGATAAAC
CCATTACCCTTACAATAACCTATCAGCTCAGTCTCCGATCAACCTTCATCCATTGATTACCTATC
GACTCAGTCCCTAGTAAACCCATTACCCTTACGGGAACCTATTAGCTAAATTTCGAGTCAACCTT
CATCCATAGTTTACCTATCAACATAGTCCTCGATAAACCCATTGCCCTTATGGTGACC
Found at i:228638 original size:42 final size:40
Alignment explanation
Indices: 228549--228726 Score: 117
Period size: 42 Copynumber: 4.3 Consensus size: 40
228539 CAAGTATTTC
** * * * *
228549 CTTTTATATTTTGTTGACTTGTCAGTCTAATCTCGATCAACT
1 CTTTTATCCTTTGTTGACTTGTCACT-TAGTCTCGGT-AAAT
* *
228591 TTTTTATCCTTTGTTTACTTGTCAACTTAGTCTCGAGTAAAT
1 CTTTTATCCTTTGTTGACTTGTC-ACTTAGTCTCG-GTAAAT
* * * * *
228633 CTTTTATCCATTATTGACTT-TCAGTTCAGTCTCGGTCAAC
1 CTTTTATCCTTTGTTGACTTGTCACTT-AGTCTCGGTAAAT
* * * *
228673 CTTTTATCCCTTGCTGACCTGTTGC-CTTGGTCTCGGGTAAAT
1 CTTTTATCCTTTGTTGACTTG-T-CACTTAGTCTC-GGTAAAT
228715 CTTTTATCCTTT
1 CTTTTATCCTTT
228727 TAGTCCCGGT
Statistics
Matches: 105, Mismatches: 24, Indels: 14
0.73 0.17 0.10
Matches are distributed among these distances:
40 23 0.22
41 14 0.13
42 64 0.61
43 4 0.04
ACGTcount: A:0.18, C:0.22, G:0.13, T:0.47
Consensus pattern (40 bp):
CTTTTATCCTTTGTTGACTTGTCACTTAGTCTCGGTAAAT
Found at i:229290 original size:169 final size:168
Alignment explanation
Indices: 228824--229344 Score: 710
Period size: 168 Copynumber: 3.1 Consensus size: 168
228814 CCGTTAATCT
* * * *
228824 TTTATCCTTT-ATTACCCA-TCGGCCCAGTCCC-AGGTAAATCCTTTATCCCTCGTTGACTTGTC
1 TTTATCCTTTGTTTACCCAGTCGACTCAGTCCCGA-GTAAATCTTTTATCCCTCGTTGACTTGTC
* * * *
228886 GATTTAATCTCGATCAACTTTTTATCCTTCATTCACCTATCGGCTTGGTCCCAGGTACTTCCCTT
65 GATTTAATCCCGATTAACTTTTTATCCTTCATTCACCTGTCGGCTTGGTCCCA-GTACTTCCTTT
*
228951 TATCTTTTGTTGACTTGTCGGTCCAATCTCGATCAACTTC
129 TATCTTTTGTTGACTTGTCAGTCCAATCTCGATCAACTTC
* ** * *
228991 TTCATCCTTTGTTTACCC-GTCGACGT-AGTCTGGGGTAAATCTTGTATCCCTCGTTGACTTGTC
1 TTTATCCTTTGTTTACCCAGTCGAC-TCAGTCCCGAGTAAATCTTTTATCCCTCGTTGACTTGTC
* * *
229054 GGTTTAATCCTGATTAACTTTTTATCCTTCATTCACATGTCGGCTTGGTCCCAAGTACTTCCTTT
65 GATTTAATCCCGATTAACTTTTTATCCTTCATTCACCTGTCGGCTTGGTCCC-AGTACTTCCTTT
*
229119 TATCTTTTGTTGACTTGTCAGTCCAATCCCGATCAACTTC
129 TATCTTTTGTTGACTTGTCAGTCCAATCTCGATCAACTTC
** *
229159 TTTATCCTTTGTTTACCCAGTCGACTCAGTCCCGAGTAAATCTTTTATCTTTCGTTGACTTGACG
1 TTTATCCTTTGTTTACCCAGTCGACTCAGTCCCGAGTAAATCTTTTATCCCTCGTTGACTTGTCG
* * * * *
229224 ATTTAATCCCAATTAACTTTTTATCTTTTATTCACCTGTCGGCTTGGTCCCGACTACTTTCTTTT
66 ATTTAATCCCGATTAACTTTTTATCCTTCATTCACCTGTCGGCTTGGTCCC-AGTACTTCCTTTT
* *
229289 ATCTTTTATTGACTTGTCAATCCAATCTCGATCAACTTC
130 ATCTTTTGTTGACTTGTCAGTCCAATCTCGATCAACTTC
229328 TTTATCCTTTGTTTACC
1 TTTATCCTTTGTTTACC
229345 TGTTGGCTTA
Statistics
Matches: 309, Mismatches: 38, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
167 9 0.03
168 153 0.50
169 147 0.48
ACGTcount: A:0.18, C:0.26, G:0.13, T:0.42
Consensus pattern (168 bp):
TTTATCCTTTGTTTACCCAGTCGACTCAGTCCCGAGTAAATCTTTTATCCCTCGTTGACTTGTCG
ATTTAATCCCGATTAACTTTTTATCCTTCATTCACCTGTCGGCTTGGTCCCAGTACTTCCTTTTA
TCTTTTGTTGACTTGTCAGTCCAATCTCGATCAACTTC
Found at i:229371 original size:84 final size:82
Alignment explanation
Indices: 228736--229458 Score: 405
Period size: 84 Copynumber: 8.7 Consensus size: 82
228726 TTAGTCCCGG
* * * ** * * *
228736 TCAAC-TTTTATCCCTTATTTACTTGTTAGCTTAGTCCCAAGTAAATCTCTTATCCTTTGTTGA-
1 TCAACTTTTTATCCTTTGTTTACCTGTCGGCTTAGT-CCAGGTAAATCTTTTATCTTTTGTTGAC
* ** *
228799 TTCATTAGTTCAATCCCG-
65 TT-GTCGGTTCAATCTCGA
* * ** ** * ** *
228817 TTAA-TCTTTTATCCTTT-ATTACCCATCGGCCCAGTCCCAGGTAAATCCTTTATCCCTCGTTGA
1 TCAACT-TTTTATCCTTTGTTTACCTGTCGGCTTAGT-CCAGGTAAATCTTTTATCTTTTGTTGA
* *
228880 CTTGTCGATTTAATCTCGA
64 CTTGTCGGTTCAATCTCGA
** * * * ** *
228899 TCAACTTTTTATCCTTCATTCACCTATCGGCTTGGTCCCAGGTACTTCCCTTTATCTTTTGTTGA
1 TCAACTTTTTATCCTTTGTTTACCTGTCGGCTTAGT-CCAGGTAAAT-CTTTTATCTTTTGTTGA
*
228964 CTTGTCGGTCCAATCTCGA
64 CTTGTCGGTTCAATCTCGA
* * * * ** * ** *
228983 TCAACTTCTTCATCCTTTGTTTACCCGTCGACGTAGTCTGGGGTAAATCTTGTATCCCTCGTTGA
1 TCAACTT-TTTATCCTTTGTTTACCTGTCGGCTTAGTC-CAGGTAAATCTTTTATCTTTTGTTGA
*
229048 CTTGTCGGTTTAATC-CTGA
64 CTTGTCGGTTCAATCTC-GA
* ** * * * * **
229067 TTAACTTTTTATCCTTCATTCACATGTCGGCTTGGTCCCAAGTACTTCCTTTTATCTTTTGTTGA
1 TCAACTTTTTATCCTTTGTTTACCTGTCGGCTTAGT-CCAGGTAAAT-CTTTTATCTTTTGTTGA
* * *
229132 CTTGTCAGTCCAATCCCGA
64 CTTGTCGGTTCAATCTCGA
* * * * *
229151 TCAACTTCTTTATCCTTTGTTTACCCAGTCGACTCAGTCCCGAGTAAATCTTTTATCTTTCGTTG
1 TCAACTT-TTTATCCTTTGTTTA-CCTGTCGGCTTAGTCCAG-GTAAATCTTTTATCTTTTGTTG
* * * * *
229216 ACTTGACGATTTAATCCCAA
63 ACTTGTCGGTTCAATCTCGA
* * * * * * * ** *
229236 TTAACTTTTTATCTTTTATTCACCTGTCGGCTTGGTCCCGACTACTTTCTTTTATCTTTTATTGA
1 TCAACTTTTTATCCTTTGTTTACCTGTCGGCTTAGTCCAG-GTA-AATCTTTTATCTTTTGTTGA
** *
229301 CTTGTCAATCCAATCTCGA
64 CTTGTCGGTTCAATCTCGA
* ** *
229320 TCAACTTCTTTATCCTTTGTTTACCTGTTGGCTTAGTCCTAGGTAAATCTTTTATCAATTGTTAA
1 TCAACTT-TTTATCCTTTGTTTACCTGTCGGCTTAGTCC-AGGTAAATCTTTTATCTTTTGTTGA
* * *
229385 CTCGTCGGTTCAGTCTCGG
64 CTTGTCGGTTCAATCTCGA
* * * * * *
229404 TCAACCTTTTATCCCTTGCTTACCTGTTGGCTTGGTCCCGAGTAAATCTTTTATC
1 TCAACTTTTTATCCTTTGTTTACCTGTCGGCTTAGTCCAG-GTAAATCTTTTATC
229459 CTTTCAGTCT
Statistics
Matches: 479, Mismatches: 143, Indels: 38
0.73 0.22 0.06
Matches are distributed among these distances:
81 45 0.09
82 26 0.05
83 106 0.22
84 185 0.39
85 103 0.22
86 14 0.03
ACGTcount: A:0.19, C:0.25, G:0.14, T:0.42
Consensus pattern (82 bp):
TCAACTTTTTATCCTTTGTTTACCTGTCGGCTTAGTCCAGGTAAATCTTTTATCTTTTGTTGACT
TGTCGGTTCAATCTCGA
Found at i:229374 original size:42 final size:41
Alignment explanation
Indices: 229328--229462 Score: 123
Period size: 42 Copynumber: 3.2 Consensus size: 41
229318 GATCAACTTC
*
229328 TTTATCCTTTGTTTACCTGTTGGCTTAGTCCTAGGTAAATCT
1 TTTATCCTTTG-TTACCTGTTGGCTTAGTCCTCGGTAAATCT
** * * * *
229370 TTTATCAATTGTTAACTCGTCGG-TTCAGT-CTCGGTCAACCT
1 TTTATCCTTTGTTACCT-GTTGGCTT-AGTCCTCGGTAAATCT
* *
229411 TTTATCCCTTGCTTACCTGTTGGCTTGGTCC-CGAGTAAATCT
1 TTTATCCTTTG-TTACCTGTTGGCTTAGTCCTCG-GTAAATCT
229453 TTTATCCTTT
1 TTTATCCTTT
229463 CAGTCTCAGT
Statistics
Matches: 72, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
41 33 0.46
42 39 0.54
ACGTcount: A:0.16, C:0.23, G:0.16, T:0.44
Consensus pattern (41 bp):
TTTATCCTTTGTTACCTGTTGGCTTAGTCCTCGGTAAATCT
Found at i:229515 original size:67 final size:68
Alignment explanation
Indices: 229393--229529 Score: 177
Period size: 67 Copynumber: 2.0 Consensus size: 68
229383 AACTCGTCGG
* * ** * * *
229393 TTCAGTCTCGGTCAACCTTTTATCCCTTGCTTACCTGTTGGCTTGGTCCCGAGTAAATCTTTTAT
1 TTCAGTCTCAGTCAACCTTTTATCCCTTACTTACCTGTCAGCTTAGTCCCAAGTAAATCTCTTAT
229458 CCT
66 CCT
* * *
229461 TTCAGTCTCAGTCAA-CTTTTATCCCTTATTTACTTGTCAGCTTAGTCCTAAGTAAATCTCTTAT
1 TTCAGTCTCAGTCAACCTTTTATCCCTTACTTACCTGTCAGCTTAGTCCCAAGTAAATCTCTTAT
229525 CCT
66 CCT
229528 TT
1 TT
229530 ATTGATTTGT
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
67 45 0.76
68 14 0.24
ACGTcount: A:0.18, C:0.26, G:0.12, T:0.43
Consensus pattern (68 bp):
TTCAGTCTCAGTCAACCTTTTATCCCTTACTTACCTGTCAGCTTAGTCCCAAGTAAATCTCTTAT
CCT
Found at i:229540 original size:42 final size:40
Alignment explanation
Indices: 229478--229591 Score: 120
Period size: 41 Copynumber: 2.8 Consensus size: 40
229468 TCAGTCAACT
*
229478 TTTATCCCTTATTTACTTGTCAGCTTAGTCCTAAGTAAATC
1 TTTATCCTTTATTTACTTGTCAGCTTAGTCC-AAGTAAATC
* * * * * * *
229519 TCTTATCCTTTATTGATTTGTCAGTTTAATCCCATTTAATC
1 T-TTATCCTTTATTTACTTGTCAGCTTAGTCCAAGTAAATC
*
229560 TTTCATCCTTTGTTTACTTGTCAGCTTAGTCC
1 TTT-ATCCTTTATTTACTTGTCAGCTTAGTCC
229592 CATGTGAATC
Statistics
Matches: 58, Mismatches: 13, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
40 2 0.03
41 31 0.53
42 25 0.43
ACGTcount: A:0.20, C:0.22, G:0.10, T:0.48
Consensus pattern (40 bp):
TTTATCCTTTATTTACTTGTCAGCTTAGTCCAAGTAAATC
Found at i:229570 original size:41 final size:42
Alignment explanation
Indices: 229476--229613 Score: 118
Period size: 42 Copynumber: 3.3 Consensus size: 42
229466 TCTCAGTCAA
* * * * * * *
229476 CTTTTATCCCTTATTTACTTGTCAGCTTAGTCCTAAGTAAAT
1 CTTTCATCCTTTATTGACTTGTCAGCTTAATCCCATGTGAAT
* * *
229518 CTCTT-ATCCTTTATTGATTTGTCAGTTTAATCCCAT-TTAAT
1 CT-TTCATCCTTTATTGACTTGTCAGCTTAATCCCATGTGAAT
* * *
229559 CTTTCATCCTTTGTTTACTTGTCAGCTTAGTCCCATGTGAAT
1 CTTTCATCCTTTATTGACTTGTCAGCTTAATCCCATGTGAAT
*
229601 CCTTCTATCCTTT
1 CTTTC-ATCCTTT
229614 TTGTCGCAAT
Statistics
Matches: 77, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
40 2 0.03
41 32 0.42
42 34 0.44
43 9 0.12
ACGTcount: A:0.20, C:0.23, G:0.09, T:0.48
Consensus pattern (42 bp):
CTTTCATCCTTTATTGACTTGTCAGCTTAATCCCATGTGAAT
Found at i:230648 original size:97 final size:97
Alignment explanation
Indices: 230518--230727 Score: 361
Period size: 97 Copynumber: 2.2 Consensus size: 97
230508 AAAAAAAACG
*
230518 GGGTTGGAGTATCCCCTCGAAGGAATGGGGTTGGAGTGTCCCCGATGATGACAATTTAAGCGAGA
1 GGGTTGGAGTATCCCCTCGAAGGAATGGGGTTGGAGTGTCCCCAATGATGACAATTTAAGCGAGA
230583 ATAAGATTTGAATCTTGACAAGTTTAAAAGC-
66 ATAAGATTTGAATCTTGACAAGTTTAAAAGCA
* *
230614 GAGGTTAGAGTATCCCCTC-AGAGGAATGGGGTTGGAGTGTTCCCAATGATGACAATTTAAGCGA
1 G-GGTTGGAGTATCCCCTCGA-AGGAATGGGGTTGGAGTGTCCCCAATGATGACAATTTAAGCGA
230678 GAATAAGATTTGAATCTTGACAAGTTTAAAAGCA
64 GAATAAGATTTGAATCTTGACAAGTTTAAAAGCA
230712 GGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCC
230728 GAGGAATAAA
Statistics
Matches: 107, Mismatches: 4, Indels: 5
0.92 0.03 0.04
Matches are distributed among these distances:
96 2 0.02
97 104 0.97
98 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.29, T:0.26
Consensus pattern (97 bp):
GGGTTGGAGTATCCCCTCGAAGGAATGGGGTTGGAGTGTCCCCAATGATGACAATTTAAGCGAGA
ATAAGATTTGAATCTTGACAAGTTTAAAAGCA
Found at i:234413 original size:13 final size:13
Alignment explanation
Indices: 234395--234419 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
234385 CATTTTATGG
234395 TGTATCGATACAA
1 TGTATCGATACAA
234408 TGTATCGATACA
1 TGTATCGATACA
234420 TACTGTGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:234435 original size:32 final size:33
Alignment explanation
Indices: 234372--234439 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
234362 CGTTACAGGC
**
234372 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
*
234405 CAATGTATCGATACATACTGT-GTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
234437 CAA
1 CAA
234440 GTTTGGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (33 bp):
CAATGTATCGATACATACTATGGTGTATCGATA
Found at i:234535 original size:33 final size:33
Alignment explanation
Indices: 234493--234558 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
234483 TCTTTTTGAA
234493 GTATCGATACAATGCAACAGGTATCGATACAAT
1 GTATCGATACAATGCAACAGGTATCGATACAAT
** * *
234526 GTATCGATACTGTGCCACATGTATCGATACAAT
1 GTATCGATACAATGCAACAGGTATCGATACAAT
234559 TAAATGTGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (33 bp):
GTATCGATACAATGCAACAGGTATCGATACAAT
Found at i:239069 original size:13 final size:13
Alignment explanation
Indices: 239051--239108 Score: 62
Period size: 13 Copynumber: 4.0 Consensus size: 13
239041 CAATTTTTTG
239051 TGTATCGATACAT
1 TGTATCGATACAT
239064 TGTATCGATACATACTTT
1 TGTATCGATAC--A---T
239082 GTGTATCGATACAT
1 -TGTATCGATACAT
239096 TGTATCGATACAT
1 TGTATCGATACAT
239109 ACTTTGTGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 24 0.62
14 1 0.03
15 1 0.03
17 1 0.03
18 1 0.03
19 11 0.28
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.40
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:239088 original size:19 final size:19
Alignment explanation
Indices: 239064--239126 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
239054 ATCGATACAT
239064 TGTATCGATACATACTTTG
1 TGTATCGATACATACTTTG
239083 TGTATCGATAC--A---T-
1 TGTATCGATACATACTTTG
239096 TGTATCGATACATACTTTG
1 TGTATCGATACATACTTTG
239115 TGTATCGATACA
1 TGTATCGATACA
239127 AGTTTGGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
15 1 0.03
17 1 0.03
18 1 0.03
19 23 0.61
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.40
Consensus pattern (19 bp):
TGTATCGATACATACTTTG
Found at i:239088 original size:32 final size:32
Alignment explanation
Indices: 239031--239126 Score: 165
Period size: 32 Copynumber: 3.0 Consensus size: 32
239021 TACAAGCCAA
**
239031 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATAC-ATACTTTGTGTATCGATACAT
239064 TGTATCGATACATACTTTGTGTATCGATACAT
1 TGTATCGATACATACTTTGTGTATCGATACAT
239096 TGTATCGATACATACTTTGTGTATCGATACA
1 TGTATCGATACATACTTTGTGTATCGATACA
239127 AGTTTGGCTA
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 50 0.82
33 11 0.18
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.42
Consensus pattern (32 bp):
TGTATCGATACATACTTTGTGTATCGATACAT
Found at i:239869 original size:21 final size:21
Alignment explanation
Indices: 239828--239871 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
239818 CTCCCCTTTA
* *
239828 TCTCCCCCTTTTATTAATAAT
1 TCTCCCCCTTTAATCAATAAT
239849 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCTTTAATCAA-TAAT
239870 TC
1 TC
239872 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.02, T:0.41
Consensus pattern (21 bp):
TCTCCCCCTTTAATCAATAAT
Found at i:241687 original size:13 final size:13
Alignment explanation
Indices: 241669--241707 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
241659 ATAATCCCCC
*
241669 TGTATCGATACAG
1 TGTATCGATACAA
241682 TGTATCGATACAA
1 TGTATCGATACAA
241695 TGTATCGATACAA
1 TGTATCGATACAA
241708 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:243786 original size:15 final size:15
Alignment explanation
Indices: 243766--243797 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
243756 ATTTCGTTTG
*
243766 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
243781 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
243796 GA
1 GA
243798 ACACTTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.22, G:0.16, T:0.47
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:252568 original size:13 final size:13
Alignment explanation
Indices: 252552--252608 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
252542 CATTTTATCG
252552 TGTATCGATACAA
1 TGTATCGATACAA
*
252565 TGTATCAATACATACTA
1 TGTATCGATAC--A--A
252582 TGTGTATCGATACAA
1 --TGTATCGATACAA
252597 TGTATCGATACA
1 TGTATCGATACA
252609 TACTGTGTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 22 0.61
15 2 0.06
17 2 0.06
19 10 0.28
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:252570 original size:20 final size:20
Alignment explanation
Indices: 252532--252570 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
252522 TACAGGCCAA
* *
252532 TGTATCGATACATTTTATCG
1 TGTATCGATACAATGTATCG
252552 TGTATCGATACAATGTATC
1 TGTATCGATACAATGTATC
252571 AATACATACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.41
Consensus pattern (20 bp):
TGTATCGATACAATGTATCG
Found at i:252592 original size:32 final size:32
Alignment explanation
Indices: 252529--252628 Score: 155
Period size: 32 Copynumber: 3.1 Consensus size: 32
252519 CGTTACAGGC
**
252529 CAATGTATCGATACATTTTATCGTGTATCGATA
1 CAATGTATCGATACATACTAT-GTGTATCGATA
*
252562 CAATGTATCAATACATACTATGTGTATCGATA
1 CAATGTATCGATACATACTATGTGTATCGATA
*
252594 CAATGTATCGATACATACTGTGTGTATCGATA
1 CAATGTATCGATACATACTATGTGTATCGATA
252626 CAA
1 CAA
252629 GTTTGGCTAC
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
32 44 0.71
33 18 0.29
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATACTATGTGTATCGATA
Found at i:252621 original size:19 final size:18
Alignment explanation
Indices: 252565--252627 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
252555 ATCGATACAA
*
252565 TGTATCAATACATACTATG
1 TGTATCGATACATACT-TG
252584 TGTATCGATACA-A----
1 TGTATCGATACATACTTG
252597 TGTATCGATACATACTGTG
1 TGTATCGATACATACT-TG
252616 TGTATCGATACA
1 TGTATCGATACA
252628 AGTTTGGCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 12 0.32
14 1 0.03
18 1 0.03
19 23 0.62
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (18 bp):
TGTATCGATACATACTTG
Found at i:252724 original size:33 final size:33
Alignment explanation
Indices: 252682--252744 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
252672 TCTTTTTGAA
252682 GTATCGATACAATGCAACAGGTATCGATACAAT
1 GTATCGATACAATGCAACAGGTATCGATACAAT
** *
252715 GTATCGATACTGTGCAACATGTATCGATAC
1 GTATCGATACAATGCAACAGGTATCGATAC
252745 TTTTTAGGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (33 bp):
GTATCGATACAATGCAACAGGTATCGATACAAT
Found at i:253538 original size:134 final size:133
Alignment explanation
Indices: 253380--253749 Score: 525
Period size: 132 Copynumber: 2.8 Consensus size: 133
253370 TTCAAACATC
* *
253380 AATTCATCAAATATTATTATTTATTTCGA-ATTAATTTAGTTTTAAAAAATTCATTCA-TTTCTA
1 AATTTATCAAATATTATTATTTATTTC-ATATTAATTTAGTTTTCAAAAATTCATTCATTTTC-A
* *
253443 TGAATTTTGAATTTTTTCTTGAAATTTCCTTTTCTTCAAAAAACAGAGTTTTCTTGGTTTTTGAT
64 TGATTTTTTAATTTTTTCTTGAAATTTCCTTTT-TTCAAAAAACAGAGTTTTCTTGGTTTTTGAT
253508 TTTTAA
128 TTTTAA
* *
253514 AATTTATCAAATATTATTATTTATTTCATATTAATTCAATTTTCAAAAATTCATTCATTTTCATG
1 AATTTATCAAATATTATTATTTATTTCATATTAATTTAGTTTTCAAAAATTCATTCATTTTCATG
* *** * *
253579 ATTTCTTTATTTTTTTCTTGAAATTTCCCTTTTTTC---AAGGGGATTTTTTTTGGTTTTTGATT
66 ATTT-TTTAATTTTTTCTTGAAATTT-CCTTTTTTCAAAAAACAGAGTTTTCTTGGTTTTTGATT
253641 TTTAA
129 TTTAA
*
253646 AATTTATCAAATATTATTATTTATTTCATATTAATCTAGTTTTCAAAAATTCATTCATTTTCATG
1 AATTTATCAAATATTATTATTTATTTCATATTAATTTAGTTTTCAAAAATTCATTCATTTTCATG
*
253711 ATTTTTTAATTTTTTCTTGAAATTTTTCTTTTTTCAAAA
66 ATTTTTTAATTTTTTCTTGAAA-TTTCCTTTTTTCAAAA
253750 TACGGTATTT
Statistics
Matches: 211, Mismatches: 17, Indels: 16
0.86 0.07 0.07
Matches are distributed among these distances:
131 25 0.12
132 95 0.45
133 1 0.00
134 58 0.27
135 26 0.12
136 6 0.03
ACGTcount: A:0.30, C:0.10, G:0.06, T:0.55
Consensus pattern (133 bp):
AATTTATCAAATATTATTATTTATTTCATATTAATTTAGTTTTCAAAAATTCATTCATTTTCATG
ATTTTTTAATTTTTTCTTGAAATTTCCTTTTTTCAAAAAACAGAGTTTTCTTGGTTTTTGATTTT
TAA
Found at i:254340 original size:2 final size:2
Alignment explanation
Indices: 254333--254371 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
254323 AGACCTTTTG
254333 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
254372 TCCGTTACTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:255598 original size:9 final size:9
Alignment explanation
Indices: 255586--255628 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
255576 AAGAAAAACA
255586 AAAAAAAAG
1 AAAAAAAAG
255595 AAAAAAAAG
1 AAAAAAAAG
255604 AAAAGAAAA-
1 AAAA-AAAAG
* *
255613 ATAAAAATG
1 AAAAAAAAG
255622 AAAAAAA
1 AAAAAAA
255629 GTGTGCAATG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
8 3 0.10
9 22 0.76
10 4 0.14
ACGTcount: A:0.86, C:0.00, G:0.09, T:0.05
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:255604 original size:25 final size:27
Alignment explanation
Indices: 255576--255628 Score: 76
Period size: 25 Copynumber: 2.0 Consensus size: 27
255566 TCCTCTAAAT
255576 AAGAAAA-ACAAAA-AAAAA-GAAAAAA
1 AAGAAAAGA-AAAATAAAAATGAAAAAA
255601 AAGAAAAGAAAAATAAAAATGAAAAAA
1 AAGAAAAGAAAAATAAAAATGAAAAAA
255628 A
1 A
255629 GTGTGCAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 11 0.44
26 6 0.24
27 8 0.32
ACGTcount: A:0.85, C:0.02, G:0.09, T:0.04
Consensus pattern (27 bp):
AAGAAAAGAAAAATAAAAATGAAAAAA
Found at i:255607 original size:14 final size:13
Alignment explanation
Indices: 255585--255628 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
255575 TAAGAAAAAC
255585 AAAAAAAAAGAAA
1 AAAAAAAAAGAAA
255598 AAAAAGAAAAGAAA
1 AAAAA-AAAAGAAA
* *
255612 AATAAAAATGAAA
1 AAAAAAAAAGAAA
255625 AAAA
1 AAAA
255629 GTGTGCAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 15 0.56
14 12 0.44
ACGTcount: A:0.86, C:0.00, G:0.09, T:0.05
Consensus pattern (13 bp):
AAAAAAAAAGAAA
Found at i:255688 original size:18 final size:16
Alignment explanation
Indices: 255650--255688 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
255640 AAAAAAATGC
*
255650 AGAAAAAGAGAAAAAA
1 AGAAAAAAAGAAAAAA
255666 AGAAAAAAAGAAGAAAA
1 AGAAAAAAAGAA-AAAA
255683 ATGAAA
1 A-GAAA
255689 GAAGATGAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 11 0.55
17 5 0.25
18 4 0.20
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (16 bp):
AGAAAAAAAGAAAAAA
Found at i:257501 original size:91 final size:91
Alignment explanation
Indices: 257169--257499 Score: 511
Period size: 91 Copynumber: 3.6 Consensus size: 91
257159 CACATTTCGG
* * * * * *
257169 AATCATATCCCCTTCAACCAACTATTAGATGGTATTGATGCATAACAAAGCTTGATTTCCTTGGG
1 AATCATATCTCCTTCATCCAACCACTAGATGGTATTGATGCATCACAAAGCCTGATTTCCTTGGG
*
257234 GGCAAGGTGTAGCCCACACATTCCCT
66 GGTAAGGTGTAGCCCACACATTCCCT
* * * *
257260 AGTCATATCTCCTTCATCTAACCACTAGATGGTATTGATGCATTACAAAGCCTGATTTCCTTAGG
1 AATCATATCTCCTTCATCCAACCACTAGATGGTATTGATGCATCACAAAGCCTGATTTCCTTGGG
*
257325 GGTAAGGTGCAGCCCACACATTCCCT
66 GGTAAGGTGTAGCCCACACATTCCCT
* *
257351 AATCATATCTCTTTCATCCAACCATTAGATGGTATTGATGCATCACAAAGCCTGATTTTCC-TGG
1 AATCATATCTCCTTCATCCAACCACTAGATGGTATTGATGCATCACAAAGCCTGA-TTTCCTTGG
*
257415 GGGTAAGGTATAGCCCACACATTCCCT
65 GGGTAAGGTGTAGCCCACACATTCCCT
257442 AATCATATCTCCTTCATCCAACCACTAGATGGTATTGATGCATCACAAAGCCTGATTT
1 AATCATATCTCCTTCATCCAACCACTAGATGGTATTGATGCATCACAAAGCCTGATTT
257500 TCTTTGGGCA
Statistics
Matches: 218, Mismatches: 21, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
90 3 0.01
91 210 0.96
92 5 0.02
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (91 bp):
AATCATATCTCCTTCATCCAACCACTAGATGGTATTGATGCATCACAAAGCCTGATTTCCTTGGG
GGTAAGGTGTAGCCCACACATTCCCT
Found at i:257837 original size:35 final size:35
Alignment explanation
Indices: 257793--257882 Score: 135
Period size: 35 Copynumber: 2.5 Consensus size: 35
257783 TAGACAAATT
* *
257793 TTTTCCATCATTATTTGATTGCATTTGGTCAAACTC
1 TTTT-CATCATCATTTGACTGCATTTGGTCAAACTC
*
257829 TTTTCATCATCATTTGACTGTATTTGGTCAAACTC
1 TTTTCATCATCATTTGACTGCATTTGGTCAAACTC
*
257864 TTTCCATCATCATTTGACT
1 TTTTCATCATCATTTGACT
257883 ATACTCGATC
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 46 0.92
36 4 0.08
ACGTcount: A:0.22, C:0.21, G:0.10, T:0.47
Consensus pattern (35 bp):
TTTTCATCATCATTTGACTGCATTTGGTCAAACTC
Found at i:257895 original size:35 final size:35
Alignment explanation
Indices: 257821--257899 Score: 106
Period size: 35 Copynumber: 2.3 Consensus size: 35
257811 TTGCATTTGG
* * * * *
257821 TCAAACTCTTTTCATCATCATTTGACTGTATTTGG
1 TCAAACTCTTTCCATCATCATTTGACTATACTCGA
257856 TCAAACTCTTTCCATCATCATTTGACTATACTCGA
1 TCAAACTCTTTCCATCATCATTTGACTATACTCGA
257891 TCAAA-TCTT
1 TCAAACTCTT
257900 ACCCTTCTTG
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
34 4 0.10
35 35 0.90
ACGTcount: A:0.27, C:0.24, G:0.08, T:0.42
Consensus pattern (35 bp):
TCAAACTCTTTCCATCATCATTTGACTATACTCGA
Found at i:257937 original size:60 final size:60
Alignment explanation
Indices: 257873--258005 Score: 144
Period size: 60 Copynumber: 2.2 Consensus size: 60
257863 CTTTCCATCA
* * *
257873 TCATTTGACTATACTC-GATCAAATCTTAC-CCTTCTTGACTATATTCCGTCAAGTCTTTCC
1 TCATTTGACTATACTCAG-TCAAATCTCACTCCTT-TTGACTATATTCCGTCAAGACCTTCC
* * * * *
257933 TCATTTAACTGTACTCAGTCAAATCTCACTCCTTTTGATTGTATTCGGTCAAGACCTTCC
1 TCATTTGACTATACTCAGTCAAATCTCACTCCTTTTGACTATATTCCGTCAAGACCTTCC
**
257993 TTGTTTGACTATA
1 TCATTTGACTATA
258006 TTGGCATTAA
Statistics
Matches: 59, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
60 54 0.92
61 5 0.08
ACGTcount: A:0.23, C:0.26, G:0.11, T:0.41
Consensus pattern (60 bp):
TCATTTGACTATACTCAGTCAAATCTCACTCCTTTTGACTATATTCCGTCAAGACCTTCC
Found at i:258057 original size:47 final size:46
Alignment explanation
Indices: 257989--258219 Score: 205
Period size: 47 Copynumber: 4.9 Consensus size: 46
257979 GGTCAAGACC
* *
257989 TTCCTTGTTTGACTATATTGGCATTAAGACCTAGTCAAACTCTTTT
1 TTCCTTGTTTAACTGTATTGGCATTAAGACCTAGTCAAACTCTTTT
* * * *
258035 TTCCTCTGTTTAACTGTATTGGCGTTAGGACATGGTCAAACTCTTTT
1 TTCCT-TGTTTAACTGTATTGGCATTAAGACCTAGTCAAACTCTTTT
* * ** * *
258082 TCACCTTGTTTAACTGTATTAGTGTT-AGACCTGGTCAAACTCTCTCT
1 T-TCCTTGTTTAACTGTATTGGCATTAAGACCTAGTCAAACTCT-TTT
* * * *
258129 TTCACTCTCATTTAACTGTATTGGCATTAGGACTTAGTCAAACTCCTTTC
1 TTC-CT-T-GTTTAACTGTATTGGCATTAAGACCTAGTCAAACT-CTTTT
* * * *
258179 ATCATTGTTTGACTGTATTGGCATT-AGTCCTAGTCAAACTC
1 TTCCTTGTTTAACTGTATTGGCATTAAGACCTAGTCAAACTC
258220 CTTTCCTCTT
Statistics
Matches: 148, Mismatches: 29, Indels: 17
0.76 0.15 0.09
Matches are distributed among these distances:
45 1 0.01
46 33 0.22
47 76 0.51
48 5 0.03
49 16 0.11
50 15 0.10
51 2 0.01
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.41
Consensus pattern (46 bp):
TTCCTTGTTTAACTGTATTGGCATTAAGACCTAGTCAAACTCTTTT
Found at i:258159 original size:96 final size:93
Alignment explanation
Indices: 258015--258228 Score: 254
Period size: 96 Copynumber: 2.3 Consensus size: 93
258005 ATTGGCATTA
* * * * *
258015 AGACCTAGTCAAACTCTTTTTTCCTCTGTTTAACTGTATTGGCGTTAGGACATGGTCAAACTCTT
1 AGACCTAGTCAAACTCTTCTTTCCTCTATTTAACTGTATTGGCATTAGGACATAGTCAAACTC-C
*
258080 TTTCA-CCTTGTTTAACTGTATTAGTGTT
65 TTTCATCATTGTTTAACTGTATTAGTGTT
* *
258108 AGACCTGGTCAAACTCTCTCTTTCACTCTCATTTAACTGTATTGGCATTAGGACTTAGTCAAACT
1 AGACCTAGTCAAACTCT-TCTTTC-CTCT-ATTTAACTGTATTGGCATTAGGACATAGTCAAACT
* * **
258173 CCTTTCATCATTGTTTGACTGTATTGGCATT
63 CCTTTCATCATTGTTTAACTGTATTAGTGTT
*
258204 AGTCCTAGTCAAACTC--CTTTCCTCT
1 AGACCTAGTCAAACTCTTCTTTCCTCT
258229 TTGCCGGATG
Statistics
Matches: 103, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
92 4 0.04
93 21 0.20
94 5 0.05
95 9 0.09
96 64 0.62
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.41
Consensus pattern (93 bp):
AGACCTAGTCAAACTCTTCTTTCCTCTATTTAACTGTATTGGCATTAGGACATAGTCAAACTCCT
TTCATCATTGTTTAACTGTATTAGTGTT
Found at i:258604 original size:84 final size:84
Alignment explanation
Indices: 258453--258921 Score: 487
Period size: 84 Copynumber: 5.6 Consensus size: 84
258443 TAGTCCTCGG
* * * * *
258453 TCAACCTTTCATCCATTGTTTACCTATCAGCTTAGTCCCTGGTAAACCCATTACCCTTACGGTGA
1 TCAACC-TTCATCCATTATTTACCTGTCGGCTTAGTCCCTAGTAAACCCATTACCCTTACGATGA
258518 CCTATCAGCTCAGTCTCCGA
65 CCTATCAGCTCAGTCTCCGA
* * * * * *
258538 TCAACCTTCATCCATTGTTTACTTGTCGGCTTAGTCCCTAGTAAACCTATTACCTTTATGAAGAC
1 TCAACCTTCATCCATTATTTACCTGTCGGCTTAGTCCCTAGTAAACCCATTACCCTTACGATGAC
* * *
258603 CTATTAGC-CTAGTCTCTGG
66 CTATCAGCTC-AGTCTCCGA
* * * * * * * *
258622 TTAACCTTCATCCATTGTTAACATGACCGCATT-GTCCCTCGTAAACCCATTACCCTTA-TAGTG
1 TCAACCTTCATCCATTATTTACCTGTCGGC-TTAGTCCCTAGTAAACCCATTACCCTTACGA-TG
* *
258685 ACCTGTCAGCTCAGTCTCCGG
64 ACCTATCAGCTCAGTCTCCGA
* * * * * * * *
258706 CCAACTTTCGTCTATTATTTACTTGTTGGCTTAGTCCTTAGTAAACCCATTACCCTTACGGTGAC
1 TCAACCTTCATCCATTATTTACCTGTCGGCTTAGTCCCTAGTAAACCCATTACCCTTACGATGAC
258771 CTATCAGCTCAGTCTCCGA
66 CTATCAGCTCAGTCTCCGA
* * * * *
258790 TCAACCTTCATCCATTATTTACCTGTCGACTTAAT-CCTCGGTAAACTCATTACCCTTACAATGA
1 TCAACCTTCATCCATTATTTACCTGTCGGCTTAGTCCCT-AGTAAACCCATTACCCTTACGATGA
* *
258854 CCTATCAACTTAGTCTCCGA
65 CCTATCAGCTCAGTCTCCGA
* * *
258874 TCAACCTTTATCCATTATTTACCTATCGGCTCAGTCCCTAGTAAACCC
1 TCAACCTTCATCCATTATTTACCTGTCGGCTTAGTCCCTAGTAAACCC
258922 CTTCTCTTCT
Statistics
Matches: 312, Mismatches: 64, Indels: 17
0.79 0.16 0.04
Matches are distributed among these distances:
83 6 0.02
84 294 0.94
85 12 0.04
ACGTcount: A:0.23, C:0.30, G:0.12, T:0.34
Consensus pattern (84 bp):
TCAACCTTCATCCATTATTTACCTGTCGGCTTAGTCCCTAGTAAACCCATTACCCTTACGATGAC
CTATCAGCTCAGTCTCCGA
Found at i:258898 original size:41 final size:41
Alignment explanation
Indices: 258769--258900 Score: 106
Period size: 41 Copynumber: 3.2 Consensus size: 41
258759 CCTTACGGTG
* * *
258769 ACCTATCAGCTCAGTCTCCGATCAACCTTCATCCATTATTT
1 ACCTATCAACTTAGTCTCCGATCAACCTTTATCCATTATTT
* * * * * * * * *
258810 ACCTGTCGACTTAATC-CTCGGTAAACTCATTA-CCCTTACAATG
1 ACCTATCAACTTAGTCTC-CGATCAAC-CTTTATCCATT--ATTT
258853 ACCTATCAACTTAGTCTCCGATCAACCTTTATCCATTATTT
1 ACCTATCAACTTAGTCTCCGATCAACCTTTATCCATTATTT
258894 ACCTATC
1 ACCTATC
258901 GGCTCAGTCC
Statistics
Matches: 64, Mismatches: 21, Indels: 12
0.66 0.22 0.12
Matches are distributed among these distances:
40 1 0.02
41 30 0.47
42 7 0.11
43 25 0.39
44 1 0.02
ACGTcount: A:0.27, C:0.32, G:0.08, T:0.34
Consensus pattern (41 bp):
ACCTATCAACTTAGTCTCCGATCAACCTTTATCCATTATTT
Found at i:258944 original size:84 final size:85
Alignment explanation
Indices: 258299--258971 Score: 411
Period size: 84 Copynumber: 8.0 Consensus size: 85
258289 TTTTTCATCT
* * * *
258299 TTGTTTACCTATCGGCTTCGTCCCTGGTAAACCCA-TA-CCTTTTTGGTGACCTATCAACTTAGT
1 TTGTTTACCTATCGGCTTAGTCCCTAGTAAACCCATTACCCTTCTTGGTGACCTATCAACTCAGT
*
258362 CTCCGATCAACCTCTT-TCTTA
66 CTCCGATCAACCT-TTATC-CA
* * * * * * * * * * ** *
258383 TTGTTTACCTATCGGGC-CAGTCTC-AGGGTCAATCCTTTATCC--CTTGTTAACTTGTTGACTT
1 TTGTTTACCTATC-GGCTTAGTCCCTA--GTAAACCCATTACCCTTCTTGGTGACCTATCAACTC
*
258444 AGTC-CTCGGTCAACCTTTCATCCA
63 AGTCTC-CGATCAACCTTT-ATCCA
* * *
258468 TTGTTTACCTATCAGCTTAGTCCCTGGTAAACCCATTACCCTTAC--GGTGACCTATCAGCTCAG
1 TTGTTTACCTATCGGCTTAGTCCCTAGTAAACCCATTACCCTT-CTTGGTGACCTATCAACTCAG
*
258531 TCTCCGATCAACCTTCATCCA
65 TCTCCGATCAACCTTTATCCA
* * * ** * *
258552 TTGTTTACTTGTCGGCTTAGTCCCTAGTAAACCTATTA-CCTT-TATGAAGACCTATTAGC-CTA
1 TTGTTTACCTATCGGCTTAGTCCCTAGTAAACCCATTACCCTTCT-TGGTGACCTATCAACTC-A
* * * *
258614 GTCTCTGGTTAACCTTCATCCA
64 GTCTCCGATCAACCTTTATCCA
* * * * * * * *
258636 TTGTTAACATGA-CCGCATT-GTCCCTCGTAAACCCATTACCCTT-ATAGTGACCTGTCAGCTCA
1 TTGTTTACCT-ATCGGC-TTAGTCCCTAGTAAACCCATTACCCTTCTTGGTGACCTATCAACTCA
** * *
258698 GTCTCCGGCCAA-CTTTCGTCTA
64 GTCTCCGATCAACCTTT-ATCCA
* * * * * *
258720 TTATTTACTTGTTGGCTTAGTCCTTAGTAAACCCATTACCCTTAC--GGTGACCTATCAGCTCAG
1 TTGTTTACCTATCGGCTTAGTCCCTAGTAAACCCATTACCCTT-CTTGGTGACCTATCAACTCAG
*
258783 TCTCCGATCAACCTTCATCCA
65 TCTCCGATCAACCTTTATCCA
* * * * * * ** *
258804 TTATTTACCTGTCGACTTAAT-CCTCGGTAAACTCATTACCCTTAC--AATGACCTATCAACTTA
1 TTGTTTACCTATCGGCTTAGTCCCT-AGTAAACCCATTACCCTT-CTTGGTGACCTATCAACTCA
258866 GTCTCCGATCAACCTTTATCCA
64 GTCTCCGATCAACCTTTATCCA
* * * * *
258888 TTATTTACCTATCGGCTCAGTCCCTAGTAAACCCCTT-CTCTTCTTGGTGACTTATCAACTCAGT
1 TTGTTTACCTATCGGCTTAGTCCCTAGTAAACCCATTACCCTTCTTGGTGACCTATCAACTCAGT
*
258952 CTCCGGTCAACTTCTTTATC
66 CTCCGATCAAC--CTTTATC
258972 GTTTACTTAC
Statistics
Matches: 452, Mismatches: 103, Indels: 66
0.73 0.17 0.11
Matches are distributed among these distances:
82 1 0.00
83 16 0.04
84 332 0.73
85 88 0.19
86 12 0.03
87 3 0.01
ACGTcount: A:0.22, C:0.30, G:0.13, T:0.35
Consensus pattern (85 bp):
TTGTTTACCTATCGGCTTAGTCCCTAGTAAACCCATTACCCTTCTTGGTGACCTATCAACTCAGT
CTCCGATCAACCTTTATCCA
Found at i:258952 original size:252 final size:252
Alignment explanation
Indices: 258482--258964 Score: 600
Period size: 252 Copynumber: 1.9 Consensus size: 252
258472 TTACCTATCA
*
258482 GCTTAGTCCCTGGTAAACCCATTACCCTTACGGTGACCTATCAGCTCAGTCTCCGATCAACCTTC
1 GCTTAGTCCCTAGTAAACCCATTACCCTTACGGTGACCTATCAGCTCAGTCTCCGATCAACCTTC
* * * * * * * *
258547 ATCCATTGTTTACTTGTCGGCTTAGTCCCTAGTAAACCTATTACCTTTATGAAGACCTATTAGCC
66 ATCCATTATTTACCTGTCGACTTAATCCCTAGTAAACCTATTACCCTTATCAAGACCTATCAACC
* * * * * *
258612 TAGTCTCTGGTTAACCTTCATCCATTGTTAACATGACCGCATTGTCCCTCGTAAACCCATTACCC
131 TAGTCTCCGATCAACCTTCATCCATTATTAACATGACCGCATAGTCCCTAGTAAACCCATTACCC
* *
258677 TTATAGTGACCTGTCAGCTCAGTCTCCGGCCAACTTTCGTCTATTATTTACTTGTTG
196 TTATAGTGACCTATCAACTCAGTCTCCGGCCAACTTTCGTCTATTATTTACTTGTTG
*
258734 GCTTAGTCCTTAGTAAACCCATTACCCTTACGGTGACCTATCAGCTCAGTCTCCGATCAACCTTC
1 GCTTAGTCCCTAGTAAACCCATTACCCTTACGGTGACCTATCAGCTCAGTCTCCGATCAACCTTC
*
258799 ATCCATTATTTACCTGTCGACTTAAT-CCTCGGTAAA-CTCATTACCCTTA-CAATGACCTATCA
66 ATCCATTATTTACCTGTCGACTTAATCCCT-AGTAAACCT-ATTACCCTTATCAA-GACCTATCA
* * * * * *
258861 ACTTAGTCTCCGATCAACCTTTATCCATTATTTACCT-ATCGGC-TCAGTCCCTAGTAAACCCCT
128 ACCTAGTCTCCGATCAACCTTCATCCATTATTAACATGA-CCGCAT-AGTCCCTAGTAAACCCAT
* * * * *
258924 T-CTCTTCTTGGTGACTTATCAACTCAGTCTCCGGTCAACTT
191 TACCCTT-ATAGTGACCTATCAACTCAGTCTCCGGCCAACTT
258965 CTTTATCGTT
Statistics
Matches: 195, Mismatches: 30, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
251 13 0.07
252 182 0.93
ACGTcount: A:0.23, C:0.30, G:0.13, T:0.34
Consensus pattern (252 bp):
GCTTAGTCCCTAGTAAACCCATTACCCTTACGGTGACCTATCAGCTCAGTCTCCGATCAACCTTC
ATCCATTATTTACCTGTCGACTTAATCCCTAGTAAACCTATTACCCTTATCAAGACCTATCAACC
TAGTCTCCGATCAACCTTCATCCATTATTAACATGACCGCATAGTCCCTAGTAAACCCATTACCC
TTATAGTGACCTATCAACTCAGTCTCCGGCCAACTTTCGTCTATTATTTACTTGTTG
Found at i:259916 original size:84 final size:83
Alignment explanation
Indices: 259371--260006 Score: 373
Period size: 84 Copynumber: 7.6 Consensus size: 83
259361 TTAATCTTTC
** * * * ** * * *
259371 ATCCTTTGTTTACCCGTCAGCCTAGTCCTAAGTAAATCCGTTATCCCTTGTTGACTTGTCGGTTT
1 ATCCTTTGTTTACCTATCGGCTTAGTCCTAGGTAAATCTTTTATCCTTTGTTGACTTGTCGATTC
* *
259436 AATCTCGGTCAAATTTTT
66 AATCTCGATCAACTTTTT
** * * * * ** * *
259454 ATCCTTCATTCACCTATCGACTTGGTCCCAGGTACTTCTTTTTATCTTTTGTTGACTTGTCGATC
1 ATCCTTTGTTTACCTATCGGCTTAGTCCTAGGTAAATC-TTTTATCCTTTGTTGACTTGTCGATT
*
259519 CAATCTCGATCAACTTCTTC
65 CAATCTCGATCAACTT-TTT
* * ** * * ** * *
259539 ATCCTTTGTTTACCCATCGACCCAGT-CTCGAGTAAATCCTTTATCCTTTAATGATTTGTCGGTT
1 ATCCTTTGTTTACCTATCGGCTTAGTCCTAG-GTAAATCTTTTATCCTTTGTTGACTTGTCGATT
* * *
259603 TAATCCCAATCAACTTTTT
65 CAATCTCGATCAACTTTTT
** * * * * * ** *
259622 ATCCTTCATTCACTTATCGGCTTGGTCTTGGGTACTTCTCTTTATCTTTTGTTGACTTGTC-AGT
1 ATCCTTTGTTTACCTATCGGCTTAGTCCTAGGTAAATCT-TTTATCCTTTGTTGACTTGTCGA-T
* *
259686 CCAATCTCGGTCAA-TATCTTT
64 TCAATCTCGATCAACT-T-TTT
* * * * ** * * **
259707 ATCCTTTTTTTACCCATAGGCCTAGTCCCGGGTAAATCCTTTATCCCTCATTGACTTGTC-AGTT
1 ATCCTTTGTTTACCTATCGGCTTAGTCCTAGGTAAATCTTTTATCCTTTGTTGACTTGTCGA-TT
* * *
259771 TAATCCCGATCAACTTTTC
65 CAATCTCGATCAACTTTTT
* * * * * *** * *
259790 ATCCTTTATTCACTTATCAGCTTGGTCCTAGGTGCTTCCTTTTATCTTTTGTTGACTTGTCGATC
1 ATCCTTTGTTTACCTATCGGCTTAGTCCTAGGTAAAT-CTTTTATCCTTTGTTGACTTGTCGATT
259855 CAATCTCGATCAACTTCTTT
65 CAATCTCGATCAACTT-TTT
* * *
259875 ATCCTTTGTTTACCTATTGGCTTAGTCCTAGGTAAATCTTTTATCCATTGTTGACTCGTC-AGTT
1 ATCCTTTGTTTACCTATCGGCTTAGTCCTAGGTAAATCTTTTATCCTTTGTTGACTTGTCGA-TT
* * * *
259939 CAGTTTCGGTCAACGTTTT
65 CAATCTCGATCAACTTTTT
* * * * * * *
259958 ATCCCTTGCTTAGCTGTTGGCTTGGTCCCAGGTAAATCTTTTATCCTTT
1 ATCCTTTGTTTACCTATCGGCTTAGTCCTAGGTAAATCTTTTATCCTTT
260007 CAGTCCTGGT
Statistics
Matches: 403, Mismatches: 137, Indels: 26
0.71 0.24 0.05
Matches are distributed among these distances:
83 122 0.30
84 194 0.48
85 87 0.22
ACGTcount: A:0.18, C:0.25, G:0.14, T:0.43
Consensus pattern (83 bp):
ATCCTTTGTTTACCTATCGGCTTAGTCCTAGGTAAATCTTTTATCCTTTGTTGACTTGTCGATTC
AATCTCGATCAACTTTTT
Found at i:259938 original size:168 final size:167
Alignment explanation
Indices: 259365--259938 Score: 697
Period size: 168 Copynumber: 3.4 Consensus size: 167
259355 TCCCATTTAA
* * * * *
259365 TCTTTCATCCTTTGTTTACCCGTCAGCCTAGTCCTAAGTAAATCCGTTATCCCTTGTTGACTTGT
1 TCTTT-ATCCTTTGTTTACCCATCGGCCTAGTCCTAGGTAAATCCTTTATCCCTTATTGACTTGT
* * * * * * *
259430 CGGTTTAATCTCGGTCAAATTTTTATCCTTCATTCACCTATCGACTTGGTCCCAGGTACTTCTTT
65 CAGTTTAATCCCGATCAACTTTTTATCCTTCATTCACTTATCG-CTTGGTCCTAGGTACTTCCTT
259495 TTATCTTTTGTTGACTTGTCGATCCAATCTCGATCAACT
129 TTATCTTTTGTTGACTTGTCGATCCAATCTCGATCAACT
* * * * * * *
259534 TCTTCATCCTTTGTTTACCCATCGACCCAGT-CTCGAGTAAATCCTTTATCCTTTAATGATTTGT
1 TCTTTATCCTTTGTTTACCCATCGGCCTAGTCCTAG-GTAAATCCTTTATCCCTTATTGACTTGT
* * * *
259598 CGGTTTAATCCCAATCAACTTTTTATCCTTCATTCACTTATCGGCTTGGTCTTGGGTACTT-CTC
65 CAGTTTAATCCCGATCAACTTTTTATCCTTCATTCACTTATC-GCTTGGTCCTAGGTACTTCCT-
*
259662 TTTATCTTTTGTTGACTTGTC-AGTCCAATCTCGGTCAA-T
128 TTTATCTTTTGTTGACTTGTCGA-TCCAATCTCGATCAACT
* * ** *
259701 ATCTTTATCCTTTTTTTACCCATAGGCCTAGTCCCGGGTAAATCCTTTATCCCTCATTGACTTGT
1 -TCTTTATCCTTTGTTTACCCATCGGCCTAGTCCTAGGTAAATCCTTTATCCCTTATTGACTTGT
* * *
259766 CAGTTTAATCCCGATCAACTTTTCATCCTTTATTCACTTATCAGCTTGGTCCTAGGTGCTTCCTT
65 CAGTTTAATCCCGATCAACTTTTTATCCTTCATTCACTTATC-GCTTGGTCCTAGGTACTTCCTT
259831 TTATCTTTTGTTGACTTGTCGATCCAATCTCGATCAACT
129 TTATCTTTTGTTGACTTGTCGATCCAATCTCGATCAACT
* * * * * * *
259870 TCTTTATCCTTTGTTTACCTATTGGCTTAGTCCTAGGTAAATCTTTTATCCATTGTTGACTCGTC
1 TCTTTATCCTTTGTTTACCCATCGGCCTAGTCCTAGGTAAATCCTTTATCCCTTATTGACTTGTC
259935 AGTT
66 AGTT
259939 CAGTTTCGGT
Statistics
Matches: 343, Mismatches: 53, Indels: 19
0.83 0.13 0.05
Matches are distributed among these distances:
167 5 0.01
168 327 0.95
169 11 0.03
ACGTcount: A:0.18, C:0.25, G:0.13, T:0.43
Consensus pattern (167 bp):
TCTTTATCCTTTGTTTACCCATCGGCCTAGTCCTAGGTAAATCCTTTATCCCTTATTGACTTGTC
AGTTTAATCCCGATCAACTTTTTATCCTTCATTCACTTATCGCTTGGTCCTAGGTACTTCCTTTT
ATCTTTTGTTGACTTGTCGATCCAATCTCGATCAACT
Found at i:260069 original size:67 final size:68
Alignment explanation
Indices: 259946--260073 Score: 172
Period size: 67 Copynumber: 1.9 Consensus size: 68
259936 GTTCAGTTTC
* * * *
259946 GGTCAACGTTTTATCCCTTGCTTAGCTGTTGGCTTGGTCCCAGGTAAATCTTTTATCCTTTCAGT
1 GGTCAACGTTTTATCCCTTGCTTAGCTGTCGGCTTAGTCCCAAGTAAATCTCTTATCCTTTCAGT
260011 CCT
66 CCT
*
260014 GGTCAAC-TTTTATCCCTTGTTTA-CTTGTCGGCTTAGTCCCAAGTAAAT-TCCTTATCCTTT
1 GGTCAACGTTTTATCCCTTGCTTAGC-TGTCGGCTTAGTCCCAAGTAAATCT-CTTATCCTTT
260074 GTTGATTCGT
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
66 2 0.04
67 44 0.83
68 7 0.13
ACGTcount: A:0.16, C:0.25, G:0.16, T:0.42
Consensus pattern (68 bp):
GGTCAACGTTTTATCCCTTGCTTAGCTGTCGGCTTAGTCCCAAGTAAATCTCTTATCCTTTCAGT
CCT
Found at i:261651 original size:166 final size:163
Alignment explanation
Indices: 261137--261694 Score: 692
Period size: 166 Copynumber: 3.4 Consensus size: 163
261127 TTCAAATATC
* * **
261137 AATTCATCAAATATTATTATTTATTTCATATTAATTCAGTTTTAAAAATTCATTCATTTCCATGA
1 AATTCATCAAATATCATTATTTATTTCATATTAATTCAGTTTTAAAAATTCATTCATTTTCATTC
** ** * * *
261202 ATTTTGAATTTTTTCTAAAAATTTCCTTTTTTCAAATATGGAGTTTTGTACTCCGTAAATTTTTT
66 ATTTTTTATTTTTTCTTGAAATTTCCTTTTTTCAAATATAGTGTTTTCTACTCCGTAAATTTTTT
* * ** *
261267 -TCAAGGGGATTTTTCTAGGTTTTTGATTTCTAA
131 CT-AAGAGGATTTTTCTTGGTTTTCAATTTTTAA
* * * * *
261300 AATTCATCCAATATTATTATTTATTTTATATTAATTTAGTTTTCAAAAATTTATTCATTTTCATT
1 AATTCATCAAATATCATTATTTATTTCATATTAATTCAGTTTT-AAAAATTCATTCATTTTCATT
* * *
261365 CATTTTTTATTTTTTCTTGGAATTTCCTTTTTTCAAAAATACGGTTTTTTCTACTCCGTAAATTT
65 CATTTTTTATTTTTTCTTGAAATTTCCTTTTTTCAAATATA--GTGTTTTCTACTCCGTAAATTT
261430 TTTC-AAGAGGATTTTTCTTGGTTTTCAATTTTTAA
128 TTTCTAAGAGGATTTTTCTTGGTTTTCAATTTTTAA
* ** *
261465 AATTCATCAAATATCATTATTTATTTTATATTAATTCTTTTTTCAAAAATTCATTCACTTTCATT
1 AATTCATCAAATATCATTATTTATTTCATATTAATTCAGTTTT-AAAAATTCATTCATTTTCATT
*
261530 CATTTTTTATTTTTTCTTTGAAATTTCTCTTTTTTCGAAATATAGTGTTTTCTACTTCGTAAATT
65 CATTTTTTATTTTTTC-TTGAAATTTC-CTTTTTTC-AAATATAGTGTTTTCTACTCCGTAAATT
*
261595 TTTTCTAA-AGGATTTTTCTTGGTTTTCAATTTTTAG
127 TTTTCTAAGAGGATTTTTCTTGGTTTTCAATTTTTAA
** * *
261631 AATTTGTCAAACATCATTATTTGA-TTCATATTAATTCAGTTTTAAAAAGTTAATTCATTTTCAT
1 AATTCATCAAATATCATTATTT-ATTTCATATTAATTCAGTTTTAAAAA-TTCATTCATTTTCAT
261695 GAGTTTTGGA
Statistics
Matches: 343, Mismatches: 42, Indels: 17
0.85 0.10 0.04
Matches are distributed among these distances:
163 40 0.12
164 51 0.15
165 105 0.31
166 130 0.38
167 11 0.03
168 6 0.02
ACGTcount: A:0.28, C:0.11, G:0.07, T:0.53
Consensus pattern (163 bp):
AATTCATCAAATATCATTATTTATTTCATATTAATTCAGTTTTAAAAATTCATTCATTTTCATTC
ATTTTTTATTTTTTCTTGAAATTTCCTTTTTTCAAATATAGTGTTTTCTACTCCGTAAATTTTTT
CTAAGAGGATTTTTCTTGGTTTTCAATTTTTAA
Found at i:261710 original size:166 final size:164
Alignment explanation
Indices: 261137--261809 Score: 691
Period size: 166 Copynumber: 4.1 Consensus size: 164
261127 TTCAAATATC
* * *
261137 AATTCATCAAATATTATTATTTATTTCATATTAATTCAGTTTT-AAAAATTCATTCATTTCCATG
1 AATTCATCAAATATCATTATTTATTTCATATTAATTCAGTTTTCAAAAATTCATTCATTTTCATT
* * ** * * *
261201 AATTTTGAATTTTTTCTAAAAATTTCCTTTTTTCAAATATGGAGTTTTGTACTCCGTAAATTTTT
66 CATTTTGTATTTTTTCTTGAAATTTCCTTTTTTCAAATATAGTGTTTTCTACTCCGTAAATTTTT
* * ** *
261266 T-TCAAGGGGATTTTTCTAGGTTTTTGATTTCTAA
131 TCT-AAGAGGATTTTTCTTGGTTTTCAATTTTTAA
* * * * *
261300 AATTCATCCAATATTATTATTTATTTTATATTAATTTAGTTTTCAAAAATTTATTCATTTTCATT
1 AATTCATCAAATATCATTATTTATTTCATATTAATTCAGTTTTCAAAAATTCATTCATTTTCATT
* * * *
261365 CATTTTTTATTTTTTCTTGGAATTTCCTTTTTTCAAAAATACGGTTTTTTCTACTCCGTAAATTT
66 CATTTTGTATTTTTTCTTGAAATTTCCTTTTTTCAAATATA--GTGTTTTCTACTCCGTAAATTT
261430 TTTC-AAGAGGATTTTTCTTGGTTTTCAATTTTTAA
129 TTTCTAAGAGGATTTTTCTTGGTTTTCAATTTTTAA
* ** *
261465 AATTCATCAAATATCATTATTTATTTTATATTAATTCTTTTTTCAAAAATTCATTCACTTTCATT
1 AATTCATCAAATATCATTATTTATTTCATATTAATTCAGTTTTCAAAAATTCATTCATTTTCATT
* *
261530 CATTTTTTATTTTTTCTTTGAAATTTCTCTTTTTTCGAAATATAGTGTTTTCTACTTCGTAAATT
66 CATTTTGTATTTTTTC-TTGAAATTTC-CTTTTTTC-AAATATAGTGTTTTCTACTCCGTAAATT
*
261595 TTTTCTAA-AGGATTTTTCTTGGTTTTCAATTTTTAG
128 TTTTCTAAGAGGATTTTTCTTGGTTTTCAATTTTTAA
** * *
261631 AATTTGTCAAACATCATTATTTGA-TTCATATTAATTCAGTTTT-AAAAAGTTAATTCATTTTCA
1 AATTCATCAAATATCATTATTT-ATTTCATATTAATTCAGTTTTCAAAAA-TTCATTCATTTTCA
* * * * * * * * * *
261694 -TGAGTTTTGGATTTTTTTGTTGAAATTCCCCTTTTTTTAAGAAACCA-AGTTTTCTTCTCTGT-
64 TTCA-TTTTGTA-TTTTTTCTTGAAATT-TCCTTTTTTCAA-ATA-TAGTGTTTTCTACTCCGTA
* * * **
261756 AATTTTTT-TAGGGGGATTTTTCTTTGTTTAAAATTTTTAA
124 AATTTTTTCTAAGAGGATTTTTCTTGGTTTTCAATTTTTAA
* *
261796 AATGCATCTAATAT
1 AATTCATCAAATAT
261810 TTTCATTGAA
Statistics
Matches: 429, Mismatches: 65, Indels: 30
0.82 0.12 0.06
Matches are distributed among these distances:
163 40 0.09
164 53 0.12
165 149 0.35
166 162 0.38
167 19 0.04
168 6 0.01
ACGTcount: A:0.28, C:0.11, G:0.08, T:0.53
Consensus pattern (164 bp):
AATTCATCAAATATCATTATTTATTTCATATTAATTCAGTTTTCAAAAATTCATTCATTTTCATT
CATTTTGTATTTTTTCTTGAAATTTCCTTTTTTCAAATATAGTGTTTTCTACTCCGTAAATTTTT
TCTAAGAGGATTTTTCTTGGTTTTCAATTTTTAA
Found at i:261762 original size:331 final size:328
Alignment explanation
Indices: 261137--261876 Score: 753
Period size: 331 Copynumber: 2.2 Consensus size: 328
261127 TTCAAATATC
*
261137 AATTCATCAAATATTATTATTTATTTCATATTAATTCAGTTTTAAAAATTCATTCATTTCCATGA
1 AATTCATCAAATATCATTATTTATTTCATATTAATTCAGTTTTAAAAATTCATTCATTTCCATGA
* *
261202 ATTTTGAATTTTTTCTAAAAATTTCCTTTTTTCAAATATGGAGTTTTGTACTCCGTAAATTTTTT
66 ATTTTGAATTTTTTCTAAAAATTTCCTTTTTTCAAATATAGAGTTTTCTACTCCGTAAATTTTTT
* ** * * * *
261267 TCAAGGGGATTTTTCTAGGTTTTTGATTTCTAAAATTCATCCAATATTATTATTTATTTTATATT
131 TCAAGAGGATTTTTCTAGGTTTTCAATTTCTAAAATTCATCAAACATCATTATTTATTTCATATT
* * ** * *
261332 AATTTAGTTTTCAAAAATTTATTCATTTTCATTCATTTTTTATTTTTTCTTGGAATTTCCTTTTT
196 AATTCAGTTTTCAAAAATTAATTCATTTTCATTCATTTTGGATTTTTTCTTGAAATTCCCTTTTT
**** **
261397 TCAAAAATACGGTTTTTTCTACTCCGTAAATTTTTTCAAGAGGATTTTTCTTGGTTTTCAATTTT
261 TCAAAAATACCAAGTTTTCTACTCCGTAAATTTTTTCAAGAGGATTTTTCTTGGTTTAAAATTTT
261462 TAA
326 TAA
* **
261465 AATTCATCAAATATCATTATTTATTTTATATTAATTCTTTTTTCAAAAATTCATTCACTTT-CAT
1 AATTCATCAAATATCATTATTTATTTCATATTAATTCAGTTTT-AAAAATTCATTCA-TTTCCAT
** ** ** * *
261529 TCATTTTTTATTTTTTCTTTGAAATTTCTCTTTTTTCGAAATATAGTGTTTTCTACTTCGTAAA-
64 GAATTTTGAATTTTTTC-TAAAAATTTC-CTTTTTTC-AAATATAGAGTTTTCTACTCCGTAAAT
* * * **
261593 TTTTTTCTAA-AGGATTTTTCTTGGTTTTCAATTTTTAGAATTTGTCAAACATCATTATTTGA-T
126 TTTTTTC-AAGAGGATTTTTCTAGGTTTTCAATTTCTAAAATTCATCAAACATCATTATTT-ATT
* *
261656 TCATATTAATTCAGTTTT-AAAAAGTTAATTCATTTTCA-TGAGTTTTGGATTTTTTTGTTGAAA
189 TCATATTAATTCAGTTTTCAAAAA-TTAATTCATTTTCATTCA-TTTTGGA-TTTTTTCTTGAAA
* * * * * * * *
261719 TTCCCCTTTTTTTAAGAA-ACCAAGTTTTCTTCTCTGT-AATTTTTTTAGGGGGATTTTTCTTTG
251 TT-CCCTTTTTTCAAAAATACCAAGTTTTCTACTCCGTAAATTTTTTCAAGAGGATTTTTCTTGG
261782 TTTAAAATTTTTAA
315 TTTAAAATTTTTAA
* * * * ** ** * *
261796 AATGCATCTAATAT-TTTCATTGAACTCCCATTAATTCAGTTTTTAAAAAATTCAATT-TTTTTC
1 AATTCATCAAATATCATT-ATTTATTTCATATTAATTCAG-TTTT-AAAAATTC-ATTCATTTCC
261859 ATGAATTTTGAATTTTTT
62 ATGAATTTTGAATTTTTT
261877 TGCATATATT
Statistics
Matches: 332, Mismatches: 65, Indels: 26
0.78 0.15 0.06
Matches are distributed among these distances:
328 39 0.12
329 29 0.09
330 20 0.06
331 151 0.45
332 78 0.23
333 15 0.05
ACGTcount: A:0.28, C:0.11, G:0.08, T:0.53
Consensus pattern (328 bp):
AATTCATCAAATATCATTATTTATTTCATATTAATTCAGTTTTAAAAATTCATTCATTTCCATGA
ATTTTGAATTTTTTCTAAAAATTTCCTTTTTTCAAATATAGAGTTTTCTACTCCGTAAATTTTTT
TCAAGAGGATTTTTCTAGGTTTTCAATTTCTAAAATTCATCAAACATCATTATTTATTTCATATT
AATTCAGTTTTCAAAAATTAATTCATTTTCATTCATTTTGGATTTTTTCTTGAAATTCCCTTTTT
TCAAAAATACCAAGTTTTCTACTCCGTAAATTTTTTCAAGAGGATTTTTCTTGGTTTAAAATTTT
TAA
Found at i:262378 original size:20 final size:19
Alignment explanation
Indices: 262353--262415 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 19
262343 ACTGAAAAAG
*
262353 AAGGAAAAAGAGAAAAGAAA
1 AAGGAAAAA-AAAAAAGAAA
*
262373 AAGGAAGAAAACAAAAGAAAA
1 AAGGAA-AAAAAAAAAG-AAA
262394 AGAGAGAAAAAAAAAAAGAAA
1 A-AG-GAAAAAAAAAAAGAAA
262415 A
1 A
262416 CTCTCAACCA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
20 12 0.32
21 11 0.30
22 11 0.30
23 3 0.08
ACGTcount: A:0.78, C:0.02, G:0.21, T:0.00
Consensus pattern (19 bp):
AAGGAAAAAAAAAAAGAAA
Found at i:277377 original size:20 final size:20
Alignment explanation
Indices: 277352--277544 Score: 144
Period size: 20 Copynumber: 9.8 Consensus size: 20
277342 TTTTCACAAT
277352 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
277372 TTGTATCGATACATTTTGGGTTTACCCGGA
1 TTGTATCGATACA--TT--G-TT---C--A
277402 -TGTATCGATACATT-TTGCA
1 TTGTATCGATACATTGTT-CA
*
277421 TTGTATCGATACATTGCTCA
1 TTGTATCGATACATTGTTCA
277441 -TGTATCGATACA----T--
1 TTGTATCGATACATTGTTCA
*
277454 TTGTATCGATACATTGCTCA
1 TTGTATCGATACATTGTTCA
277474 TTGTATCGATACA-T-TT--
1 TTGTATCGATACATTGTTCA
*
277490 TTGTATCGATACATTGCTCA
1 TTGTATCGATACATTGTTCA
277510 TTGTATCGATACATT-TTACA
1 TTGTATCGATACATTGTT-CA
*
277530 ATGTATCGATACATT
1 TTGTATCGATACATT
277545 CAGGCATTTT
Statistics
Matches: 143, Mismatches: 6, Indels: 48
0.73 0.03 0.24
Matches are distributed among these distances:
14 12 0.08
15 1 0.01
16 13 0.09
17 1 0.01
18 3 0.02
19 15 0.10
20 73 0.51
21 2 0.01
22 2 0.01
23 2 0.01
24 1 0.01
25 2 0.01
27 2 0.01
28 1 0.01
29 12 0.08
30 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.42
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:277460 original size:14 final size:14
Alignment explanation
Indices: 277441--277468 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
277431 ACATTGCTCA
277441 TGTATCGATACATT
1 TGTATCGATACATT
277455 TGTATCGATACATT
1 TGTATCGATACATT
277469 GCTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (14 bp):
TGTATCGATACATT
Found at i:277476 original size:53 final size:50
Alignment explanation
Indices: 277402--277504 Score: 145
Period size: 53 Copynumber: 2.0 Consensus size: 50
277392 TTTACCCGGA
*
277402 TGTATCGATACATTTTGCATTGTATCGATACATTGCTCATGTATCGATACATT
1 TGTATCGATACATTCTGCATTGTATCGATACATT--T-ATGTATCGATACATT
*
277455 TGTATCGATACATTGCT-CATTGTATCGATACATTTTTGTATCGATACATT
1 TGTATCGATACATT-CTGCATTGTATCGATACATTTATGTATCGATACATT
277505 GCTCATTGTA
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
50 14 0.30
51 1 0.02
53 31 0.66
54 1 0.02
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.43
Consensus pattern (50 bp):
TGTATCGATACATTCTGCATTGTATCGATACATTTATGTATCGATACATT
Found at i:277500 original size:36 final size:36
Alignment explanation
Indices: 277402--277544 Score: 193
Period size: 36 Copynumber: 3.8 Consensus size: 36
277392 TTTACCCGGA
277402 TGTATCGATACATTTTGCATTGTATCGATACATTGCTCA-
1 TGTATCGATACA-TTT---TTGTATCGATACATTGCTCAT
277441 TGTATCGATACA--TTTGTATCGATACATTGCTCAT
1 TGTATCGATACATTTTTGTATCGATACATTGCTCAT
277475 TGTATCGATACATTTTTGTATCGATACATTGCTCAT
1 TGTATCGATACATTTTTGTATCGATACATTGCTCAT
277511 TGTATCGATACATTTTACAATGTATCGATACATT
1 TGTATCGATACATTTT----TGTATCGATACATT
277545 CAGGCATTTT
Statistics
Matches: 97, Mismatches: 0, Indels: 13
0.88 0.00 0.12
Matches are distributed among these distances:
33 20 0.21
34 12 0.12
36 39 0.40
39 12 0.12
40 14 0.14
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (36 bp):
TGTATCGATACATTTTTGTATCGATACATTGCTCAT
Found at i:279976 original size:36 final size:36
Alignment explanation
Indices: 279929--279997 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
279919 CGATTTACCG
**
279929 CAATCGGGGATACTCCAACTTTGATTTTATTTTTCA
1 CAATCGGGGATACTCCAACCCTGATTTTATTTTTCA
279965 CAATCGGGGATACTCCAACCCTGATTTTATTTT
1 CAATCGGGGATACTCCAACCCTGATTTTATTTT
279998 CGAAACACCG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (36 bp):
CAATCGGGGATACTCCAACCCTGATTTTATTTTTCA
Found at i:286208 original size:61 final size:61
Alignment explanation
Indices: 286110--286975 Score: 756
Period size: 61 Copynumber: 14.5 Consensus size: 61
286100 TAGCCCTTCT
* * ** *
286110 AGTCCTCAAAGAGCAGGACACCTTTTT-CTTTTCAAGCCCACATGAGTTGGTGGCACATTTC
1 AGTCCTCAAAGAGCAGGAC-GCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
286171 AGTCCTCAAAGAGCTGGACGCTTTTTCCTTCTGAAGCCCACACAAGTTGGTGGCACC-TTC
1 AGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * *
286231 TAGTCCTCAAAGAGCAGGAGGTCGTTTTCTTTTTAAAGCCCACACAAGTTGGTGGAACCCTTT-
1 -AGTCCTCAAAGAGCAGGACG-CTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTTC
* * * * *
286294 AGTCCTCAAAGAGCAGGACACCTTTTT-CTTTTCAAGCCCACACGAGTTGGTGGTACATTTC
1 AGTCCTCAAAGAGCAGGAC-GCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * ** * * *
286355 AGTCCTTAAAGAGTAGGACATTTTTTCCTTCTGAAA-CCCACACAAGTTAGTGGCACCTTCC
1 AGTCCTCAAAGAGCAGGACGCTTTTTCCTT-TTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * *
286416 AGTCCTCAAAGAGCAGGACGTCTTTTT-TTTTTCAAAGCCCATACAAGTTGGTGGCACCCTCC
1 AGTCCTCAAAGAGCAGGACG-CTTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
* * * *
286478 AATCCTCAAAGAGTAGGACG-TCTTTTCCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTT
1 AGTCCTCAAAGAGCAGGACGCT-TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * * *
286539 AGTCCTCAAAGAGTAGGATGC-----CC-CTCAAAGCCCACACAAGTTAGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * ** *
286594 AGTCCTCAAAGATCAAGACG------CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTT
1 AGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
286649 AGTCCTCAAAGAGCAGGACG-----T-CTTTTATAGCCCACACAAGTTGGTGGCACTTTTTT
1 AGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTTC
* *
286705 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTC
1 AGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * *
286765 TAATCCTCAAAGAGCAGGA-----TGT-CTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 -AGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
* * * * * *
286821 AAGTCCTCAAAGAGCAGGATGCTTTCTCCTTTTAAAGACCACTCGAGTTGGTGGCACCTTCC
1 -AGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * * * *
286883 AGTCCTCAAAGAGCAGGACGCCTTTT-CTTTTCAAAGCCCGCACGAGTTGGTGGTACTTTTT
1 AGTCCTCAAAGAGCAGGACGCTTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
* * * *
286944 AGTCTTCAAAGAGCATGACGCCTTTTCTTTTT
1 AGTCCTCAAAGAGCAGGACGCTTTTTCCTTTT
286976 CTCCTTTGTC
Statistics
Matches: 674, Mismatches: 96, Indels: 69
0.80 0.11 0.08
Matches are distributed among these distances:
54 2 0.00
55 147 0.22
56 47 0.07
60 29 0.04
61 283 0.42
62 160 0.24
63 4 0.01
64 2 0.00
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (61 bp):
AGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
Found at i:286331 original size:123 final size:120
Alignment explanation
Indices: 286104--286975 Score: 729
Period size: 123 Copynumber: 7.3 Consensus size: 120
286094 CCCTTTTAGC
* * * ** *
286104 CCTTCTAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAGCCCACATGAGTTGGTGGCACATT
1 CCTTCTAGTCCTCAAAGAGCAGGAC-GCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT
* * * * *
286169 TCAGTCCTCAAAGAGCTGGACGCTTTTTC-CTTCTGAAGCCCACACAAGTTGGTGGCA
65 T-AGTCCTCAAAGAGCAGGACACCTTTTCTTTTC-AAAGCCCACACAAGTTGGTGGCA
* * *
286226 CCTTCTAGTCCTCAAAGAGCAGGAGGTCGTTTTCTTTTTAAAGCCCACACAAGTTGGTGGAACCC
1 CCTTCTAGTCCTCAAAGAGCAGGACG-C-TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CC
* *
286291 TTTAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTC-AAGCCCACACGAGTTGGTGGTA
63 TTTAGTCCTCAAAGAGCAGGACACC-TTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
* * * ** * *
286349 CATT-TCAGTCCTTAAAGAGTAGGACATTTTTTCCTTCTGAAA-CCCACACAAGTTAGTGGCACC
1 CCTTCT-AGTCCTCAAAGAGCAGGAC-GCTTTTCCTT-TTAAAGCCCACACAAGTTGGTGGCACC
* * * * *
286412 TTCCAGTCCTCAAAGAGCAGGACGTCTTTTTTTTTTCAAAGCCCATACAAGTTGGTGGCA
63 TT-TAGTCCTCAAAGAGCAGGAC-ACCTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
* * * * *
286472 CCCTCCAATCCTCAAAGAGTAGGACGTCTTTTCCTCTTAAAGCCCACACAAGTTGGTGGCACCTT
1 CCTTCTAGTCCTCAAAGAGCAGGACG-CTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC-T
* ** * *
286537 TTAGTCCTCAAAGAGTAGGATGCC----C--CTCAAAGCCCACACAAGTTAGTGGCA
64 TTAGTCCTCAAAGAGCAGGACACCTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
* * * **
286588 CCTT-TCAGTCCTCAAAGATCAAGACG-----CCTTTCAAAGCCCACACAAGTTGGTGGCATTTT
1 CCTTCT-AGTCCTCAAAGAGCAGGACGCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CCT
* *
286647 TTAGTCCTCAAAGAGCAGG--A-C--GTCTTTT-ATAGCCCACACAAGTTGGTGGCA
64 TTAGTCCTCAAAGAGCAGGACACCTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
* * **
286698 CTTTTTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCATTT
1 C-CTTCTAGTCCTCAAAGAGCAGGACG-CTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCT
* *
286763 TCTAATCCTCAAAGAGCAGG--A---TGTC-TTTCAAAGCCCACACAAGTTGGTGGCA
64 T-TAGTCCTCAAAGAGCAGGACACCTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
** * * * * *
286815 TTTTCCAAGTCCTCAAAGAGCAGGATGCTTTCTCCTTTTAAAGACCACTCGAGTTGGTGGCACCT
1 CCTT-CTAGTCCTCAAAGAGCAGGACGCTTT-TCCTTTTAAAGCCCACACAAGTTGGTGGCACCT
* * * * *
286880 TCCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTCAAAGCCCGCACGAGTTGGTGGTA
64 T-TAGTCCTCAAAGAGCAGGACACCTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
* * * * *
286938 CTTTTTAGTCTTCAAAGAGCATGACGCCTTTTCTTTTT
1 CCTTCTAGTCCTCAAAGAGCAGGACG-CTTTTCCTTTT
286976 CTCCTTTGTC
Statistics
Matches: 614, Mismatches: 95, Indels: 82
0.78 0.12 0.10
Matches are distributed among these distances:
107 1 0.00
109 1 0.00
110 68 0.11
111 21 0.03
112 1 0.00
116 56 0.09
117 136 0.22
121 4 0.01
122 109 0.18
123 203 0.33
124 11 0.02
125 3 0.00
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (120 bp):
CCTTCTAGTCCTCAAAGAGCAGGACGCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
AGTCCTCAAAGAGCAGGACACCTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:286422 original size:184 final size:181
Alignment explanation
Indices: 286103--286901 Score: 759
Period size: 184 Copynumber: 4.5 Consensus size: 181
286093 CCCCTTTTAG
* *
286103 CCCTTCTAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAGCCCACATGAGTTGGTGGCACAT
1 CCCTT-TAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTAAAGCCCACACGAGTTGGTGGCACAT
* *
286168 TTCAGTCCTCAAAGAGCT-GGACGCTTTTTCCTTCTG-AAGCCCACACAAGTTGGTGGCACCTTC
65 TTCAGTCCTCAAAGAG-TAGGACACTTTTTCCTTCTGAAAGCCCACACAAGTTAGTGGCACCTTC
* * *
286231 TAGTCCTCAAAGAGCAGGAGGTCGTTTTCTTTTTAAAGCCCACACAAGTTGGTGGAA
129 CAGTCCTCAAAGAGCAGGA-GTCG---TCTTTTCAAAGCCCACACAAGTTGGTGGCA
* *
286288 CCCTTTAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAGCCCACACGAGTTGGTGGTACATT
1 CCCTTTAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTAAAGCCCACACGAGTTGGTGGCACATT
* *
286353 TCAGTCCTTAAAGAGTAGGACATTTTTTCCTTCTGAAA-CCCACACAAGTTAGTGGCACCTTCCA
66 TCAGTCCTCAAAGAGTAGGACACTTTTTCCTTCTGAAAGCCCACACAAGTTAGTGGCACCTTCCA
* * *
286417 GTCCTCAAAGAGCAGGACGTCTTTTTTTTTTCAAAGCCCATACAAGTTGGTGGCA
131 GTCCTCAAAGAGCAGGA-GTC---GTCTTTTCAAAGCCCACACAAGTTGGTGGCA
** * * ** * * * *
286472 CCCTCCAATCCTCAAAGAGTAGGACGTCTTTTCCTCTTAAAGCCCACACAAGTTGGTGGCACCTT
1 CCCTTTAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTAAAGCCCACACGAGTTGGTGGCACATT
* * * * *
286537 TTAGTCCTCAAAGAGTAGG--A----TGCC-CCTCAAAGCCCACACAAGTTAGTGGCACCTTTCA
66 TCAGTCCTCAAAGAGTAGGACACTTTTTCCTTCTGAAAGCCCACACAAGTTAGTGGCACCTTCCA
* * *
286595 GTCCTCAAAGATCA--AGACG-CCTTTCAAAGCCCACACAAGTTGGTGGCA
131 GTCCTCAAAGAGCAGGAGTCGTCTTTTCAAAGCCCACACAAGTTGGTGGCA
*** * * * *
286643 TTTTTTAGTCCTCAAAGAGCAGG--A-C---GTCTTTTATAGCCCACACAAGTTGGTGGCACTTT
1 CCCTTTAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTAAAGCCCACACGAGTTGGTGGCAC-AT
* * * * * * ** *
286702 TTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTT-TTAAAGCCCACACAAGTTGGTGGCATTTTCT
65 TTCAGTCCTCAAAGAGTAGGACACTTTTTCCTTCTGAAAGCCCACACAAGTTAGTGGCACCTTCC
*
286766 AATCCTCAAAGAGCAGGA-T-GTC-TTTCAAAGCCCACACAAGTTGGTGGCA
130 AGTCCTCAAAGAGCAGGAGTCGTCTTTTCAAAGCCCACACAAGTTGGTGGCA
* ** * * *
286815 --TTTTCCAAGTCCTCAAAGAGCAGGA-TGCTTTCTCCTTTTAAAGACCACTCGAGTTGGTGGCA
1 CCCTTT---AGTCCTCAAAGAGCAGGACACCTTT-TTCTTTTAAAGCCCACACGAGTTGGTGGCA
* * *
286877 CCTTCCAGTCCTCAAAGAGCAGGAC
62 CATTTCAGTCCTCAAAGAGTAGGAC
286902 GCCTTTTCTT
Statistics
Matches: 515, Mismatches: 73, Indels: 59
0.80 0.11 0.09
Matches are distributed among these distances:
165 27 0.05
166 20 0.04
168 1 0.00
170 4 0.01
171 42 0.08
172 69 0.13
173 18 0.03
174 1 0.00
175 3 0.01
176 1 0.00
177 5 0.01
178 62 0.12
179 25 0.05
182 1 0.00
183 1 0.00
184 228 0.44
185 7 0.01
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.28
Consensus pattern (181 bp):
CCCTTTAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTAAAGCCCACACGAGTTGGTGGCACATT
TCAGTCCTCAAAGAGTAGGACACTTTTTCCTTCTGAAAGCCCACACAAGTTAGTGGCACCTTCCA
GTCCTCAAAGAGCAGGAGTCGTCTTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:286598 original size:55 final size:55
Alignment explanation
Indices: 286447--286965 Score: 369
Period size: 55 Copynumber: 9.0 Consensus size: 55
286437 CTTTTTTTTT
* ** * * *
286447 TCAAAGCCCATACAAGTTGGTGGCACCCTCCAATCCTCAAAGAGTAGGACGTCTTTTCCTC
1 TCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACG-C----CC-C
* * *
286508 TTAAAGCCCACACAAGTTGGTGGCACCTTTT-AGTCCTCAAAGAGTAGGATGCCCC
1 TCAAAGCCCACACAAGTTGGTGGCA-CTTTTCAGTCCTCAAAGAGCAGGACGCCCC
* * * * **
286563 TCAAAGCCCACACAAGTTAGTGGCACCTTTCAGTCCTCAAAGATCAAGACGCCTT
1 TCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCCC
* * * **
286618 TCAAAGCCCACACAAGTTGGTGGCATTTTTTAGTCCTCAAAGAGCAGGACGTCTT
1 TCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCCC
* * *
286673 TTATAGCCCACACAAGTTGGTGGCACTTTTTTAGTCCTCAAAGAGCAGGACGCCTTTTCC
1 TCAAAGCCCACACAAGTTGGTGGCAC-TTTTCAGTCCTCAAAGAGCAGGACGCC----CC
* * * * **
286733 TTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCTAATCCTCAAAGAGCAGGATGTCTT
1 --TCAAAGCCCACACAAGTTGGTGGCACTTTTC-AGTCCTCAAAGAGCAGGACGCCCC
*
286790 TCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAAGTCCTCAAAGAGCAGGATGCTTTCTCC
1 TCAAAGCCCACACAAGTTGGTGGCACTTTT-C-AGTCCTCAAAGAGCAGGACGC---C-CC
* * * * * * *
286850 TTTTAAAGACCACTCGAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCTTT
1 --TCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCC----C--C
* * * * * *
286913 TCAAAGCCCGCACGAGTTGGTGGTACTTTTTAGTCTTCAAAGAGCATGACGCC
1 TCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCC
286966 TTTTCTTTTT
Statistics
Matches: 375, Mismatches: 60, Indels: 46
0.78 0.12 0.10
Matches are distributed among these distances:
54 4 0.01
55 141 0.38
56 48 0.13
58 1 0.00
59 1 0.00
60 5 0.01
61 125 0.33
62 48 0.13
63 2 0.01
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27
Consensus pattern (55 bp):
TCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCCC
Found at i:286729 original size:28 final size:28
Alignment explanation
Indices: 286643--286730 Score: 79
Period size: 28 Copynumber: 3.1 Consensus size: 28
286633 GTTGGTGGCA
*
286643 TTTTTTAGTCCTCAAAGAGCAGGACGTC
1 TTTTTTAGTCCTCAAAGAGCAGGACGCC
* * * * ** **
286671 TTTTATAGCCCACACA-AGTTGGTGGCAC
1 TTTTTTAGTCCTCAAAGAGCAGGACGC-C
286699 TTTTTTAGTCCTCAAAGAGCAGGACGCC
1 TTTTTTAGTCCTCAAAGAGCAGGACGCC
286727 TTTT
1 TTTT
286731 CCTTTTAAAG
Statistics
Matches: 41, Mismatches: 17, Indels: 4
0.66 0.27 0.06
Matches are distributed among these distances:
27 5 0.12
28 30 0.73
29 6 0.15
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (28 bp):
TTTTTTAGTCCTCAAAGAGCAGGACGCC
Found at i:287101 original size:42 final size:42
Alignment explanation
Indices: 287024--287126 Score: 113
Period size: 42 Copynumber: 2.4 Consensus size: 42
287014 TTCTTTTCCT
* *
287024 TTTTGTCCTTAAAGAGCAGGATGCACTTTGTTTTCC-TATTTC
1 TTTTGTCCTCAAAGAGCAGGA-GCACTTTGGTTTCCTTATTTC
*
287066 TTTTGTCCTCAAAGAGCAGGA-CACATTTCGGTTTCCTTTTTTC
1 TTTTGTCCTCAAAGAGCAGGAGCAC-TTT-GGTTTCCTTATTTC
*
287109 CTTTGTCCTCGAAA-AGCA
1 TTTTGTCCTC-AAAGAGCA
287127 TGACGTACTC
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
40 3 0.06
41 3 0.06
42 26 0.49
43 18 0.34
44 3 0.06
ACGTcount: A:0.20, C:0.22, G:0.17, T:0.41
Consensus pattern (42 bp):
TTTTGTCCTCAAAGAGCAGGAGCACTTTGGTTTCCTTATTTC
Found at i:287863 original size:20 final size:20
Alignment explanation
Indices: 287838--287892 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
287828 TTTTCACAAT
287838 TTGTATCGATACATTGT-TCA
1 TTGTATCGATACATT-TCTCA
287858 TTGTATCGATACATTTCTCA
1 TTGTATCGATACATTTCTCA
*
287878 TTGTATTGATACATT
1 TTGTATCGATACATT
287893 CTGGGTTTAC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 32 0.97
ACGTcount: A:0.25, C:0.15, G:0.13, T:0.47
Consensus pattern (20 bp):
TTGTATCGATACATTTCTCA
Found at i:287948 original size:20 final size:20
Alignment explanation
Indices: 287908--288006 Score: 65
Period size: 20 Copynumber: 4.7 Consensus size: 20
287898 TTTACTCGGA
* *
287908 TGTATCAATACATTTTGCAT
1 TGTATCGATACATTTTACAT
287928 TGTATCGATACATTTCTCATTACAT
1 TGTATCGATACA--T-T--TTACAT
* * *
287953 TGCATCGATACATTGCT-CGT
1 TGTATCGATACATT-TTACAT
* * *
287973 TGTTTTGATACATTTTACAA
1 TGTATCGATACATTTTACAT
287993 TGTATCGATACATT
1 TGTATCGATACATT
288007 CAGGCATTTT
Statistics
Matches: 59, Mismatches: 14, Indels: 12
0.69 0.16 0.14
Matches are distributed among these distances:
19 1 0.02
20 37 0.63
21 1 0.02
22 2 0.03
23 2 0.03
25 16 0.27
ACGTcount: A:0.27, C:0.17, G:0.12, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATTTTACAT
Found at i:290358 original size:51 final size:50
Alignment explanation
Indices: 290301--290412 Score: 147
Period size: 51 Copynumber: 2.2 Consensus size: 50
290291 ATTTTTCATC
* * * *
290301 TCGGGGATACTCCAACTTC-GATTTTATTTCTAAAGCATCGATTTATCGCAA
1 TCGGGGATACTCCAAC-TCGGATTTTATTTCCAAA-CACCAATTTATCACAA
*
290352 TCGGGGATACTCCAACTCGGATTTTATTTCCAAACACCAATTTTTCACAA
1 TCGGGGATACTCCAACTCGGATTTTATTTCCAAACACCAATTTATCACAA
290402 T-GGGGATACTC
1 TCGGGGATACTC
290413 TAACCCCGTT
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
49 10 0.18
50 15 0.27
51 30 0.55
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (50 bp):
TCGGGGATACTCCAACTCGGATTTTATTTCCAAACACCAATTTATCACAA
Found at i:290462 original size:28 final size:28
Alignment explanation
Indices: 290403--290473 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 28
290393 TTTTCACAAT
* *
290403 GGGGATACTCTAACCCCGTTATTTCGTC
1 GGGGATACTCTAACCCCGTTATTCCGTA
290431 GGGGATACTCTAACCCCGTTATGTCCG-A
1 GGGGATACTCTAACCCCGTTAT-TCCGTA
*
290459 GGGGATACTCCAACC
1 GGGGATACTCTAACC
290474 TCGTCTTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
28 36 0.92
29 3 0.08
ACGTcount: A:0.21, C:0.30, G:0.24, T:0.25
Consensus pattern (28 bp):
GGGGATACTCTAACCCCGTTATTCCGTA
Found at i:290609 original size:108 final size:106
Alignment explanation
Indices: 290354--290630 Score: 276
Period size: 108 Copynumber: 2.6 Consensus size: 106
290344 TATCGCAATC
* *
290354 GGGGATACTCCAA-CTCGGATTTTATTTCCAAACA-CCAA-TTTTTCACAATGGGGATACTCTAA
1 GGGGATACTCCAACCTC-GATTTTATTTCTAAA-ATCCAATTTTTTCACAATGGGGATACTCCAA
* * * *
290416 CCCCGTTATTTCGTCGGGGATACTCTAACCCCGTTATGTCCGA
64 CCCCATTATGTCATCGGGGATACTCCAACCCCGTTATGTCCGA
* *** * * *
290459 GGGGATACTCCAACCTCG-TCTTTATATCTAAAATATTGATTTTTTCATAATCGGGGGTATTCCA
1 GGGGATACTCCAACCTCGAT-TTTATTTCTAAAAT-CCAATTTTTTCACAAT-GGGGATACTCCA
* * * *
290523 ACCCCATTATGTCATCGGGGATACTCCAATCTCGTTATTTTCGA
63 ACCCCATTATGTCATCGGGGATACTCCAACCCCGTTATGTCCGA
* * *
290567 GGGGATACTTCAACCTTGATTTTATTTCTAAAATGCCAA-TTTTTCACAATCAGGGATACTCCAA
1 GGGGATACTCCAACCTCGATTTTATTTCTAAAAT-CCAATTTTTTCACAAT-GGGGATACTCCAA
290631 TTCCAATGTT
Statistics
Matches: 137, Mismatches: 28, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
104 2 0.01
105 24 0.18
106 4 0.03
107 31 0.23
108 75 0.55
109 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (106 bp):
GGGGATACTCCAACCTCGATTTTATTTCTAAAATCCAATTTTTTCACAATGGGGATACTCCAACC
CCATTATGTCATCGGGGATACTCCAACCCCGTTATGTCCGA
Found at i:292708 original size:43 final size:44
Alignment explanation
Indices: 292660--292780 Score: 140
Period size: 43 Copynumber: 2.8 Consensus size: 44
292650 AAAACCCCAT
* *
292660 AATGTATCGATACAATGAACAT-TGTATCGATACATATCCTCAA
1 AATGTATCGATACAATCAACATACGTATCGATACATATCCTCAA
* *
292703 AATGTATCGATAC-ATCTACCTACGTATCGATACATATCCTCAA
1 AATGTATCGATACAATCAACATACGTATCGATACATATCCTCAA
* * * * *
292746 TATGTATTGATAC-ATCTACTTATGTATCGATACAT
1 AATGTATCGATACAATCAACATACGTATCGATACAT
292781 TTTTTTTATA
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
42 5 0.07
43 64 0.93
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.34
Consensus pattern (44 bp):
AATGTATCGATACAATCAACATACGTATCGATACATATCCTCAA
Found at i:292712 original size:23 final size:22
Alignment explanation
Indices: 292682--292760 Score: 83
Period size: 23 Copynumber: 3.6 Consensus size: 22
292672 CAATGAACAT
292682 TGTATCGATACATATCCTCAAAA
1 TGTATCGATACATATCCTC-AAA
*
292705 TGTATCGATACATCTACCT---A
1 TGTATCGATACATAT-CCTCAAA
*
292725 CGTATCGATACATATCCTCAATA
1 TGTATCGATACATATCCTCAA-A
*
292748 TGTATTGATACAT
1 TGTATCGATACAT
292761 CTACTTATGT
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
19 3 0.07
20 14 0.30
23 26 0.57
24 3 0.07
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.34
Consensus pattern (22 bp):
TGTATCGATACATATCCTCAAA
Found at i:292731 original size:20 final size:20
Alignment explanation
Indices: 292704--292780 Score: 82
Period size: 20 Copynumber: 3.7 Consensus size: 20
292694 TATCCTCAAA
292704 ATGTATCGATACATCTACCT
1 ATGTATCGATACATCTACCT
* * *
292724 ACGTATCGATACATATCCTCAAT
1 ATGTATCGATACATCTAC-C--T
* *
292747 ATGTATTGATACATCTACTT
1 ATGTATCGATACATCTACCT
292767 ATGTATCGATACAT
1 ATGTATCGATACAT
292781 TTTTTTTATA
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
20 29 0.64
21 1 0.02
23 15 0.33
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATCTACCT
Found at i:295426 original size:21 final size:21
Alignment explanation
Indices: 295400--295441 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
295390 TTTCATCCTA
295400 TTTTATAAATTTTGTGTTTTC
1 TTTTATAAATTTTGTGTTTTC
**
295421 TTTTATATTTTTTGTGTTTTC
1 TTTTATAAATTTTGTGTTTTC
295442 AAAATATAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.05, G:0.10, T:0.71
Consensus pattern (21 bp):
TTTTATAAATTTTGTGTTTTC
Found at i:298908 original size:166 final size:163
Alignment explanation
Indices: 298736--299044 Score: 424
Period size: 166 Copynumber: 1.9 Consensus size: 163
298726 TAATTTATAG
*
298736 TAAATCAATTTTGAAAAATCCATTTATTTTCATAAGTTTTTCA-TTTTTTCTTTAAAATTCTCCT
1 TAAATCAATTTTGAAAAATCCATTTATTTTCATAAGTTGTTCATTTTTTTC-TTAAAATTCTCCT
* * * * * *
298800 GTTTCTAAAAAATTGAGTTTTGTATTCTATAAATATTTTTGAAGGGGATTTTTCTCGATTT-AAA
65 -ATT-TAAAAAATTGAGTTTTCTATTCCATAAAT-GTTTTCAA-AGGATTTTTCTCGATTTAAAA
298864 TTTTTAAAATTCATCTAACATTACCATTAGACTCCTTT
126 TTTTTAAAATTCATCTAACATTACCATTAGACTCCTTT
* * * * *
298902 TAAATCAATTTTGAAAAATTCTTTTATTTTTATAAGTTGTTCATTTTTTTCTTCAAATTTTCCTA
1 TAAATCAATTTTGAAAAATCCATTTATTTTCATAAGTTGTTCATTTTTTTCTTAAAATTCTCCTA
* * *
298967 TTTGAAAAATTGAGTTTTCTATTCCATAAATGTTTTCAAAGGATTTTTCTTGGTTTAAAATTTTT
66 TTTAAAAAATTGAGTTTTCTATTCCATAAATGTTTTCAAAGGATTTTTCTCGATTTAAAATTTTT
299032 AAAATTCATCTAA
131 AAAATTCATCTAA
299045 TATTGTCATT
Statistics
Matches: 126, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
162 14 0.11
163 27 0.21
164 26 0.21
165 2 0.02
166 50 0.40
167 7 0.06
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.50
Consensus pattern (163 bp):
TAAATCAATTTTGAAAAATCCATTTATTTTCATAAGTTGTTCATTTTTTTCTTAAAATTCTCCTA
TTTAAAAAATTGAGTTTTCTATTCCATAAATGTTTTCAAAGGATTTTTCTCGATTTAAAATTTTT
AAAATTCATCTAACATTACCATTAGACTCCTTT
Found at i:299584 original size:12 final size:12
Alignment explanation
Indices: 299567--299609 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
299557 TTTAGGAAGT
299567 GAAAAAAAGAGA
1 GAAAAAAAGAGA
299579 GAAAAAATAGA-A
1 GAAAAAA-AGAGA
299591 G-AAAAAAGAGA
1 GAAAAAAAGAGA
299602 GAAAAAAA
1 GAAAAAAA
299610 TTAAGCCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 3 0.11
11 7 0.25
12 15 0.54
13 3 0.11
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (12 bp):
GAAAAAAAGAGA
Found at i:299585 original size:11 final size:11
Alignment explanation
Indices: 299569--299608 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
299559 TAGGAAGTGA
299569 AAAAAAGAGAG
1 AAAAAAGAGAG
*
299580 AAAAAATAGAAG
1 AAAAAAGAG-AG
299592 AAAAAAGAGAG
1 AAAAAAGAGAG
299603 AAAAAA
1 AAAAAA
299609 ATTAAGCCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 16 0.62
12 10 0.38
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.03
Consensus pattern (11 bp):
AAAAAAGAGAG
Found at i:300816 original size:140 final size:141
Alignment explanation
Indices: 300520--300822 Score: 371
Period size: 142 Copynumber: 2.1 Consensus size: 141
300510 CATTTTTTAT
* * ** * *
300520 ATTTCTATTATTCCTATGGTTATCTGTAGAGGTATAGACATCTTCAAAACTTTTCGTATCTTTTC
1 ATTTCTAATATTCTTATGGTTATCCATAGAGGTATAGAAATCTTCAAAACTTTTCATATCTTTTC
** * * * *
300585 AGTTCTTTATTAAGGTACAAAATAATTTTTTTTAGAAATTAAAAATTAAATAAAATTGATTATCT
66 AGTTCTCCATTAAGATACAAAATAA-TTATTTTAGAAATTAAAAATTAAATAAAATTGAATATCG
300650 TAATTTTTCAAG
130 TAATTTTTCAAG
* * * *
300662 ATTTCTATTGTTCTTATGGTTATCCATAGGGGTATAGAAATTTTCAAAACTTTTCATATCTTTTT
1 ATTTCTAATATTCTTATGGTTATCCATAGAGGTATAGAAATCTTCAAAACTTTTCATATC-TTTT
* *
300727 C-GATTCTCCA-TAATATACAAAATGA-TATTTTAGAAATTAAAAATTAAATAAAAATT-AATAT
65 CAG-TTCTCCATTAAGATACAAAATAATTATTTTAGAAATTAAAAATTAAAT-AAAATTGAATAT
300788 CGTAATTTTTCAAG
128 CGTAATTTTTCAAG
*
300802 ATTTGTAATATTCTTATGGTT
1 ATTTCTAATATTCTTATGGTT
300823 TGCTTTTCCT
Statistics
Matches: 139, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
140 58 0.42
141 6 0.04
142 65 0.47
143 10 0.07
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (141 bp):
ATTTCTAATATTCTTATGGTTATCCATAGAGGTATAGAAATCTTCAAAACTTTTCATATCTTTTC
AGTTCTCCATTAAGATACAAAATAATTATTTTAGAAATTAAAAATTAAATAAAATTGAATATCGT
AATTTTTCAAG
Found at i:302785 original size:157 final size:154
Alignment explanation
Indices: 302354--302957 Score: 557
Period size: 156 Copynumber: 3.9 Consensus size: 154
302344 ATGTTCAAAG
* * * *
302354 AAAATTACAAAAAAGCCCCTA-AGATATACCTTCGACGTAGAAGTA-CCCA-ATACCCCTAAAAG
1 AAAATTACAAAAATGCCCCTAGAG-TATACCTTCGACGTAAAAGTATCTCATA-ACCCCTAAAGG
* ** * * *
302416 ACTTAAAAAGGATTCCAAATA-GGATGAACCTATCCTAAATA-CATACCTTTGGCAAAAAAGC-G
64 ACTTAAAAA-GACTATAAA-AGGGATGAACCTATCCTAAATATC-CACCTTCGGCATAAAAGCAG
302478 AACCTGGTGATAACCTAAGACTTAGTTCTAA
126 -ACCTGGTGATAACCTAAGAC-TAGTTCTAA
* * *
302509 AAAATTATC-AAAATGCCCTTATAGGTATACCTTCGACGTAAAAGTATCTCATTAA-TCCTAAAG
1 AAAATTA-CAAAAATGCCCCTAGA-GTATACCTTCGACGTAAAAGTATCTCA-TAACCCCTAAAG
* * * * * *
302572 AACATAAAAGGACTATAAAAAGGG-TGAACTTATCCTAAATACCCACCTTCGACATAAAAGCAGG
63 GACTTAAAAAGACTAT-AAAAGGGATGAACCTATCCTAAATATCCACCTTCGGCATAAAAGCA-G
*
302636 ACCTGGTGATGACCTAAGAGCTAGTTCT-A
126 ACCTGGTGATAACCTAAGA-CTAGTTCTAA
* * *
302665 AAAATTACAAAAATGCCCCTACGAGTATACCTTCGACATAAAAGTATCTCGACAA-CCTTAAAGG
1 AAAATTACAAAAATGCCCCTA-GAGTATACCTTCGACGTAAAAGTATCTC-ATAACCCCTAAAGG
* * * *
302729 ATTTAAAAAGACTCATAAAAGGGATGAACCTATCCTAAATATCTACCTTAGGCATAAAAGTAGAC
64 ACTTAAAAAGACT-ATAAAAGGGATGAACCTATCCTAAATATCCACCTTCGGCATAAAAGCAGAC
* * * * * *
302794 TTGGTGACAACCTAGGACTCGATTTTGA
128 CTGGTGATAACCTAAGACTAG-TTCTAA
* * * * * * *
302822 AAAATTACGAAAATACCCTTAGGGGATACCTTCGACGTGAAAGTATTCTAAT-ACCCCTAAAGGA
1 AAAATTACAAAAATGCCCCTAGAGTATACCTTCGACGTAAAAGTA-TCTCATAACCCCTAAAGGA
* * *
302886 CTTAAAAAGAACTATAAAAGGAATTAAGCTATCCTAAATATCCACCTTCGGCATAAAAGCAGACC
65 CTTAAAAAG-ACTATAAAAGGGATGAACCTATCCTAAATATCCACCTTCGGCATAAAAGCAGACC
*
302951 CGGTGAT
129 TGGTGAT
302958 TATCTAGGAT
Statistics
Matches: 367, Mismatches: 60, Indels: 43
0.78 0.13 0.09
Matches are distributed among these distances:
155 22 0.06
156 232 0.63
157 109 0.30
158 3 0.01
159 1 0.00
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.24
Consensus pattern (154 bp):
AAAATTACAAAAATGCCCCTAGAGTATACCTTCGACGTAAAAGTATCTCATAACCCCTAAAGGAC
TTAAAAAGACTATAAAAGGGATGAACCTATCCTAAATATCCACCTTCGGCATAAAAGCAGACCTG
GTGATAACCTAAGACTAGTTCTAA
Found at i:302921 original size:313 final size:310
Alignment explanation
Indices: 302354--302957 Score: 688
Period size: 313 Copynumber: 1.9 Consensus size: 310
302344 ATGTTCAAAG
* * * *
302354 AAAATTACAAAAAAGCCCCTAAGATATACCTTCGACGTAGAAGTACCCAATACCCCTAAAAGACT
1 AAAATTACAAAAAAGCCCCTAAGATATACCTTCGACATAAAAGTACCCAACAACCCTAAAAGACT
* * * *
302419 TAAAAAGGATTCCAAATAGGATGAACCTATCCTAAATACATACCTTTGGCAAAAAAGCGAACCTG
66 TAAAAAGGACTCCAAAAAGGATGAACCTATCCTAAATACATACCTTAGGCAAAAAAGAGAACCTG
* * * *
302484 GTGATAACCTAAGACTTAGTTCTAAAAAATTATCAAAATGCCCTTATAGGTATACCTTCGACGTA
131 GTGACAACCTAAGACTGAGTTCTAAAAAATTATCAAAATACCCTTATAGGGATACCTTCGACGTA
* * * *
302549 AAAGTATCTCATTAATCCTAAAGAACATAAAAGGACTATAAAAAGGGTGAACTTATCCTAAATAC
196 AAAGTATCTCAATAACCCTAAAGAACATAAAAGAACTATAAAAAGGATGAACTTATCCTAAATAC
*
302614 CCACCTTCGACATAAAAGCAGGACCTGGTGATGACCTAAGAGCTAGTTCTA
261 CCACCTTCGACATAAAAGCA-GACCCGGTGATGACCTAAGAGCTAGTTCTA
* * * * * *
302665 AAAATTACAAAAATGCCCCTACGAGTATACCTTCGACATAAAAGTATCTCGACAACCTTAAAGGA
1 AAAATTACAAAAAAGCCCCTAAGA-TATACCTTCGACATAAAAGTA-CCCAACAACCCTAAAAGA
* *
302730 TTTAAAAA-GACT-CATAAAAGGGATGAACCTATCCTAAATATC-TACCTTAGGCATAAAAGTAG
64 CTTAAAAAGGACTCCA-AAAA-GGATGAACCTATCCTAAATA-CATACCTTAGGCAAAAAAG-AG
* * * * *
302792 -ACTTGGTGACAACCTAGGACTCGA-TTTTGAAAAATTA-CGAAAATACCCTTA-GGGGATACCT
125 AACCTGGTGACAACCTAAGACT-GAGTTCTAAAAAATTATC-AAAATACCCTTATAGGGATACCT
* * * * *
302853 TCGACGTGAAAGTAT-TCTAATACCCCTAAAGGACTTAAAAAGAACTAT-AAAAGGAATTAAGC-
188 TCGACGTAAAAGTATCTC-AATAACCCTAAAGAACAT-AAAAGAACTATAAAAAGG-ATGAA-CT
* *
302915 TATCCTAAATATCCACCTTCGGCATAAAAGCAGACCCGGTGAT
249 TATCCTAAATACCCACCTTCGACATAAAAGCAGACCCGGTGAT
302958 TATCTAGGAT
Statistics
Matches: 244, Mismatches: 37, Indels: 23
0.80 0.12 0.08
Matches are distributed among these distances:
311 26 0.11
312 77 0.32
313 137 0.56
314 4 0.02
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.24
Consensus pattern (310 bp):
AAAATTACAAAAAAGCCCCTAAGATATACCTTCGACATAAAAGTACCCAACAACCCTAAAAGACT
TAAAAAGGACTCCAAAAAGGATGAACCTATCCTAAATACATACCTTAGGCAAAAAAGAGAACCTG
GTGACAACCTAAGACTGAGTTCTAAAAAATTATCAAAATACCCTTATAGGGATACCTTCGACGTA
AAAGTATCTCAATAACCCTAAAGAACATAAAAGAACTATAAAAAGGATGAACTTATCCTAAATAC
CCACCTTCGACATAAAAGCAGACCCGGTGATGACCTAAGAGCTAGTTCTA
Found at i:303677 original size:148 final size:150
Alignment explanation
Indices: 303466--303752 Score: 343
Period size: 148 Copynumber: 1.9 Consensus size: 150
303456 TTTCACATGT
* *
303466 TTAATTTAATTTTTCTTAAAAAGTGTCATTTCATAACTTGATGGAAACCCGCCAAAATACGAAAA
1 TTAATTTAATTTTTCTTAAAAAGTGTCATTTCATAACTTAATGGAAACCCGCAAAAATACGAAAA
* * * * *
303531 -ATTTTGAAATCTTTTAATACCCCTACGGATACCCATAGGAATATAAAAGA-TTAAAAACGATTA
66 GATTTTAAAATATTTT-ATACCCCTACAGATAACCATA-GAATATAAAAGACTTAAAAACAATTA
303594 ATATTTATTTTAGTGAGGGGAG
129 ATATTTATTTTAGTGAGGGGAG
* **
303616 TTAATTTAATTATTTC-TAAAAA-T-TCATTTCATACCTTAATGGGTACCCG-AAAATATACGAA
1 TTAATTTAATT-TTTCTTAAAAAGTGTCATTTCATAACTTAATGGAAACCCGCAAAA-ATACGAA
* * * * *
303677 AAGTTTTTTAAAATATTTTATACCCCTATAGATAAGCATAGAATATAAAAGACTTGAAAATAATT
64 AAG-ATTTTAAAATATTTTATACCCCTACAGATAACCATAGAATATAAAAGACTTAAAAACAATT
*
303742 ACTATTTATTT
128 AATATTTATTT
303753 ATATTTCGGA
Statistics
Matches: 116, Mismatches: 16, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
147 3 0.03
148 43 0.37
149 37 0.32
150 29 0.25
151 4 0.03
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (150 bp):
TTAATTTAATTTTTCTTAAAAAGTGTCATTTCATAACTTAATGGAAACCCGCAAAAATACGAAAA
GATTTTAAAATATTTTATACCCCTACAGATAACCATAGAATATAAAAGACTTAAAAACAATTAAT
ATTTATTTTAGTGAGGGGAG
Found at i:304171 original size:162 final size:161
Alignment explanation
Indices: 303744--304202 Score: 674
Period size: 162 Copynumber: 2.8 Consensus size: 161
303734 AAATAATTAC
* *
303744 TATTTATTTATATTTCGGAAAAAAAATCATTTCGTACCTTAAT-GAATACCCGAAAAGATACGAA
1 TATTTATTTAT-TTT-TG-AAAAAAATCATTTCGTACCTTAATAG-ATACTCGAAAAGATACGAA
* * * *
303808 AAGTTTTTGAAATCTTTTATACCCTTACGAATACCCATAAGAATATAAAAGATTAAAGATGATCA
62 AAGTTTTTGAAATCTTTTATACCCTTACGGATACCCATAGGAATATAAAAGTTTAAAAATGATCA
* *
303873 ATATTTGTTGTAGTTAATGAAGGGTGAATTAATAT
127 ATATTTGTTGTAATTAACGAAGGGTGAATTAATAT
*
303908 TATTTATTTATTTTTGAAAAAAATCATTTCGTACCTTAATAGATACTCGAAAAGATATGAAAAGT
1 TATTTATTTATTTTTGAAAAAAATCATTTCGTACCTTAATAGATACTCGAAAAGATACGAAAAGT
** * *
303973 TTTTGAAATCTTTTATACCCTTATAGATAACCATAGGTATATAAAAGTTTTAAAAATGATCAATA
66 TTTTGAAATCTTTTATACCCTTACGGATACCCATAGGAATATAAAAG-TTTAAAAATGATCAATA
304038 TTTGTTGTAATTAACG-AGGAGTGAATTTAATAT
130 TTTGTTGTAATTAACGAAGG-GTGAA-TTAATAT
304071 TATTTATTTATTTTTGAAAAAAATCATTTCGTACCTTAATAGATACTCGAAAAGATACGAAAAG-
1 TATTTATTTATTTTTGAAAAAAATCATTTCGTACCTTAATAGATACTCGAAAAGATACGAAAAGT
* *
304135 TTTTAAAATCTTTTATACTCC-TACGGATACCCATAGGAATATAAAAGATTTAAAAATGATTAAT
66 TTTTGAAATCTTTTATAC-CCTTACGGATACCCATAGGAATATAAAAG-TTTAAAAATGATCAAT
304199 ATTT
129 ATTT
304203 AAAATATATA
Statistics
Matches: 269, Mismatches: 21, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
161 89 0.33
162 94 0.35
163 75 0.28
164 11 0.04
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (161 bp):
TATTTATTTATTTTTGAAAAAAATCATTTCGTACCTTAATAGATACTCGAAAAGATACGAAAAGT
TTTTGAAATCTTTTATACCCTTACGGATACCCATAGGAATATAAAAGTTTAAAAATGATCAATAT
TTGTTGTAATTAACGAAGGGTGAATTAATAT
Found at i:305027 original size:11 final size:11
Alignment explanation
Indices: 305013--305052 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
305003 TTTTCTCTAT
305013 TTTTCTTTCTC
1 TTTTCTTTCTC
305024 TTTTCTTTCTTC
1 TTTTCTTTC-TC
*
305036 TTTTTTTCTCTC
1 TTTTCTT-TCTC
305048 TTTTC
1 TTTTC
305053 AGCTGAGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 9 0.36
12 14 0.56
13 2 0.08
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTTCTTTCTC
Found at i:305912 original size:169 final size:166
Alignment explanation
Indices: 305698--306173 Score: 679
Period size: 169 Copynumber: 2.8 Consensus size: 166
305688 TGGGATTTTG
*
305698 AGGAAAAAATCCAAAACTTATGAAAATGAATTTATTTTATAAAACTAAATTAATATGAAATAAAT
1 AGGAAAAAATCCAAAACTTATGAAAATGAATTTATTTTTTAAAACTAAATTAATATGAAATAAAT
* * * * *
305763 AATGACATTTTATGAATTTTAAAAATTAAAAATTAAGAAAAATCCTCTCAAAAGAATTTACGGAG
66 AATGATATTTGATGAATTTTAAAAATTAAAAATTAAGAAAAATCCCCTCAAAAAAAATTACGGAG
*
305828 TAGAAAACACT-GTATTTTGAAAAAAAAAAAAGGAATTTCA
131 TAGAAAACACTCGTA---TG--AAAAAAAAAAGGAATTTAA
* *
305868 AGG-AAAAATCCAAAACTTATGAAAATGAATTTATTTTTTAAAACTGAATTAATCTGAAATAAAT
1 AGGAAAAAATCCAAAACTTATGAAAATGAATTTATTTTTTAAAACTAAATTAATATGAAATAAAT
* *
305932 AATGATATTTGATAAATTTTAAAAATTAAAAATTAAGAAAAATCCCCTCGAAAAAAATTACGGAG
66 AATGATATTTGATGAATTTTAAAAATTAAAAATTAAGAAAAATCCCCTCAAAAAAAATTACGGAG
* *
305997 TAGAAAACA-TCGTATGTAAAAAAAAGGGAATTTAA
131 TAGAAAACACTCGTATGAAAAAAAAAAGGAATTTAA
** * * * *
306032 AGGAAAAAAATAAAAAACTCATGAAAATAAATTTATTTTTTAAAACTCAATTAATATTAAATAAA
1 AGG-AAAAAATCCAAAACTTATGAAAATGAATTTATTTTTTAAAACTAAATTAATATGAAATAAA
* *
306097 TAATGATATTTGATGAATTTTATAAATTAAAAATTAAGAAAAATCCCCACAAAAAAAAATTACGG
65 TAATGATATTTGATGAATTTTAAAAATTAAAAATTAAGAAAAATCCCCTC-AAAAAAAATTACGG
306162 AGTAGAAAACAC
129 AGTAGAAAACAC
306174 CCCGTAATAC
Statistics
Matches: 277, Mismatches: 24, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
164 19 0.07
166 102 0.37
167 24 0.09
168 1 0.00
169 128 0.46
170 3 0.01
ACGTcount: A:0.53, C:0.08, G:0.10, T:0.29
Consensus pattern (166 bp):
AGGAAAAAATCCAAAACTTATGAAAATGAATTTATTTTTTAAAACTAAATTAATATGAAATAAAT
AATGATATTTGATGAATTTTAAAAATTAAAAATTAAGAAAAATCCCCTCAAAAAAAATTACGGAG
TAGAAAACACTCGTATGAAAAAAAAAAGGAATTTAA
Found at i:308446 original size:167 final size:164
Alignment explanation
Indices: 308256--308878 Score: 671
Period size: 167 Copynumber: 3.8 Consensus size: 164
308246 TTTTTTCTCT
* ** * * *
308256 GTAAATTTTTTCGGGAGGATTTTTCTTAATTTTTAATTTTTAAAATTCATCAAATATTTTTATTT
1 GTAAATTTTTTTGGGAGGATTTTTCTTGGTTTTCAATTTTTAAAATTCATCAAA-ATTATCATTT
* * *
308321 ATTTCATATTAATTCAGTTTTTAAAAATTCATTCATTTTCTTGAGCTTTTGATTTGTTTCCTTGA
65 ATTTCATATTAATTCAGTTTTCAAAAATTCATTCATTTTCATGAGTTTTTGATTT-TTTCCTTGA
* *
308386 AATTTTTCTTTTTTTGAAATACGATATTTTTTACTTC
129 AA-TTTTCTTTTTTTGAAATACGATGTTTTCTACTTC
308423 GTAAATTTTTTTGGG-GAGATTTTTCTTGGTTTTCAATTTTTAAAATTCATCAAAAATTATCATT
1 GTAAATTTTTTTGGGAG-GATTTTTCTTGGTTTTCAATTTTTAAAATTCATC-AAAATTATCATT
* ** * *
308487 TATTCCATATTAATTTTGTTTTCAAAAATTCATTCATTTTCATTCA-TTTTTGATTTTTTTCTTG
64 TATTTCATATTAATTCAGTTTTCAAAAATTCATTCATTTTCA-TGAGTTTTTGATTTTTTCCTTG
* *
308551 AAA-CTTCTTTTTTTCGAAATA-TAGTGTTTTCTAC-TC
128 AAATTTTCTTTTTTT-GAAATACGA-TGTTTTCTACTTC
* *
308587 TGTAAATTTTTTTGGGAGGATTTTTTTTGGTTTTCAATTTTTAAAATTCATCAAACATTATCCTT
1 -GTAAATTTTTTTGGGAGGATTTTTCTTGGTTTTCAATTTTTAAAATTCATCAAA-ATTATCATT
* * * * * *
308652 TATTTTACATTAATTCATTTTTCAAAAATTCATTCATTTTCATGAGTTTTTAAGTTTTTCCCTTA
64 TATTTCATATTAATTCAGTTTTCAAAAATTCATTCATTTTCATGAGTTTTTGA-TTTTTTCCTTG
* * * *
308717 AAACTTCTCTTTTTTCGAAATACGGTGTTTTCTACTCC
128 AAA-TTTTCTTTTTTTGAAATACGATGTTTTCTACTTC
* ** * *
308755 GCAAATTTTTTCAAGGA-AATTTTTCTTGGTTTTGAATTTTTAAAA--CATC---A-T-T-ATTT
1 GTAAATTTTTT-TGGGAGGATTTTTCTTGGTTTTCAATTTTTAAAATTCATCAAAATTATCATTT
* * * *
308811 ATTTCATATTAATTCGGTTTTCAAAAATTCATTCATCTTCATGAGTTTTTGCATTTTTGCTTTGA
65 ATTTCATATTAATTCAGTTTTCAAAAATTCATTCATTTTCATGAGTTTTTG-ATTTTTTCCTTGA
308876 AAT
129 AAT
308879 CCCTATTTTC
Statistics
Matches: 387, Mismatches: 53, Indels: 42
0.80 0.11 0.09
Matches are distributed among these distances:
157 1 0.00
158 59 0.15
159 2 0.01
160 1 0.00
161 1 0.00
164 18 0.05
165 116 0.30
166 23 0.06
167 149 0.39
168 17 0.04
ACGTcount: A:0.26, C:0.12, G:0.09, T:0.53
Consensus pattern (164 bp):
GTAAATTTTTTTGGGAGGATTTTTCTTGGTTTTCAATTTTTAAAATTCATCAAAATTATCATTTA
TTTCATATTAATTCAGTTTTCAAAAATTCATTCATTTTCATGAGTTTTTGATTTTTTCCTTGAAA
TTTTCTTTTTTTGAAATACGATGTTTTCTACTTC
Found at i:308630 original size:332 final size:323
Alignment explanation
Indices: 308252--308852 Score: 792
Period size: 332 Copynumber: 1.8 Consensus size: 323
308242 AGATTTTTTT
* * * *
308252 CTCTGTAAATTTTTTCGGGAGGATTTTTCTTAATTTTTAATTTTTAAAATTCATCAAATATTTTT
1 CTCTGTAAATTTTTTCGGGAGGATTTTTCTTAATTTTCAATTTTTAAAATTCATCAAACATTATC
* * * *
308317 ATTTATTTCATATTAATTCAGTTTTT-AAAAATTCATTCATTTTCTTGAGCTTTTGA-TTTGTTT
66 ATTTATTTCACATTAATTCA-TTTTTCAAAAATTCATTCATTTTCATGAGCTTTTAAGTTT-TTC
* * * * * * * *** *
308380 CCTTGAAATTTTTCTTTTTTTGAAATACGATATTTTTTACTTCGTAAATTTTTTTGGGGAGATTT
129 CCTTAAAACTTCTCTTTTTTCGAAATACGATATTTTCTACTCCGCAAATTTTTTCAAGGAAATTT
**
308445 TTCTTGGTTTTCAATTTTTAAAATTCATCAAAAATTATCATTTATTCCATATTAATTTTGTTTTC
194 TTCTTGGTTTTCAATTTTTAAAA--CATC----A-T-T-ATTTATTCCATATTAATTCGGTTTTC
*
308510 AAAAATTCATTCATTTTCATTCATTTTTGATTTTTTTCTTGAAACTTCTTTTTTTCGAAATATAG
250 AAAAATTCATTCATCTTCATTCATTTTTGATTTTTTTCTTGAAACTTCTTTTTTTCGAAATATAG
308575 TGTTTTCTA
315 TGTTTTCTA
* * **
308584 CTCTGTAAATTTTTTTGGGAGGATTTTTTTTGGTTTTCAATTTTTAAAATTCATCAAACATTATC
1 CTCTGTAAATTTTTTCGGGAGGATTTTTCTTAATTTTCAATTTTTAAAATTCATCAAACATTATC
* * *
308649 CTTTATTTTACATTAATTCATTTTTCAAAAATTCATTCATTTTCATGAGTTTTTAAGTTTTTCCC
66 ATTTATTTCACATTAATTCATTTTTCAAAAATTCATTCATTTTCATGAGCTTTTAAGTTTTTCCC
* *
308714 TTAAAACTTCTCTTTTTTCGAAATACGGTGTTTTCTACTCCGCAAATTTTTTCAAGGAAATTTTT
131 TTAAAACTTCTCTTTTTTCGAAATACGATATTTTCTACTCCGCAAATTTTTTCAAGGAAATTTTT
* *
308779 CTTGGTTTTGAATTTTTAAAACATCATTATTTATTTCATATTAATTCGGTTTTCAAAAATTCATT
196 CTTGGTTTTCAATTTTTAAAACATCATTATTTATTCCATATTAATTCGGTTTTCAAAAATTCATT
308844 CATCTTCAT
261 CATCTTCAT
308853 GAGTTTTTGC
Statistics
Matches: 234, Mismatches: 33, Indels: 13
0.84 0.12 0.05
Matches are distributed among these distances:
323 42 0.18
324 1 0.00
325 1 0.00
326 1 0.00
330 4 0.02
331 5 0.02
332 177 0.76
333 3 0.01
ACGTcount: A:0.27, C:0.12, G:0.08, T:0.53
Consensus pattern (323 bp):
CTCTGTAAATTTTTTCGGGAGGATTTTTCTTAATTTTCAATTTTTAAAATTCATCAAACATTATC
ATTTATTTCACATTAATTCATTTTTCAAAAATTCATTCATTTTCATGAGCTTTTAAGTTTTTCCC
TTAAAACTTCTCTTTTTTCGAAATACGATATTTTCTACTCCGCAAATTTTTTCAAGGAAATTTTT
CTTGGTTTTCAATTTTTAAAACATCATTATTTATTCCATATTAATTCGGTTTTCAAAAATTCATT
CATCTTCATTCATTTTTGATTTTTTTCTTGAAACTTCTTTTTTTCGAAATATAGTGTTTTCTA
Found at i:308905 original size:158 final size:156
Alignment explanation
Indices: 308315--308908 Score: 484
Period size: 165 Copynumber: 3.6 Consensus size: 156
308305 TCAAATATTT
* * *
308315 TTATTTATTTCATATTAATTCAGTTTTTAAAAATTCATTCATTTTCTTGAGCTTTTGATTTGTTT
1 TTATTTATTTCATATTAATTCAGTTTTCAAAAATTCATTCATTTTCATGAGTTTTTGA-TT-TTT
* * * * * * * * *
308380 CCTTGAAATTTTTCTTTTTTTGAAATA-CGATATTTTTTACTTCGTAAATTTTTT-TGGGGAGAT
64 CTTTGAAA--TCTCTTTTTTCGAAATATCG-TGTTTTCTACTCCGCAAATTTTTTAAGGAGA-AT
*
308443 TTTTCTTGGTTTTCAATTTTTAAAATTCATCAAAAA
125 TTTTCTTGGTTTTCAATTTTTAAAA-TCAT---ACA
* ** *
308479 TTATCATTTATTCCATATTAATTTTGTTTTCAAAAATTCATTCATTTTCATTCA-TTTTTGATTT
1 -T-T-ATTTATTTCATATTAATTCAGTTTTCAAAAATTCATTCATTTTCA-TGAGTTTTTGATTT
* * * * ** *
308543 TTTTCTTGAAA-CTTCTTTTTTTCGAAATATAGTGTTTTCTACTCTGTAAATTTTTTTGGGAGGA
62 TTCT-TTGAAATC-TC-TTTTTTCGAAATATCGTGTTTTCTACTCCGCAAATTTTTTAAGGAGAA
*
308607 TTTTTTTTGGTTTTCAATTTTTAAAATTCATCAAACA
124 TTTTTCTTGGTTTTCAATTTTTAAAA-TCAT---ACA
* * * *
308644 TTATCCTTTATTTTACATTAATTCATTTTTCAAAAATTCATTCATTTTCATGAGTTTTTAAGTTT
1 TTA---TTTATTTCATATTAATTCAGTTTTCAAAAATTCATTCATTTTCATGAGTTTTTGA-TTT
* *
308709 TTCCCTTAAAACTTCTCTTTTTTCGAAATA-CGGTGTTTTCTACTCCGCAAATTTTTTCAAGGA-
62 TT-CTTTGAAA--TCTCTTTTTTCGAAATATC-GTGTTTTCTACTCCGCAAATTTTTT-AAGGAG
*
308772 AATTTTTCTTGGTTTTGAATTTTTAAAA-CAT-CA
122 AATTTTTCTTGGTTTTCAATTTTTAAAATCATACA
* *
308805 TTATTTATTTCATATTAATTCGGTTTTCAAAAATTCATTCATCTTCATGAGTTTTTGCATTTTTG
1 TTATTTATTTCATATTAATTCAGTTTTCAAAAATTCATTCATTTTCATGAGTTTTTG-ATTTTT-
* * * *
308870 CTTTGAAATCCCTATTTTCTCAAAAAATCGAGTTTTCTA
64 CTTTGAAATCTCT-TTTT-TCGAAATATCGTGTTTTCTA
308909 TTCCATAAAT
Statistics
Matches: 353, Mismatches: 53, Indels: 53
0.77 0.12 0.12
Matches are distributed among these distances:
156 4 0.01
157 4 0.01
158 74 0.21
159 2 0.01
161 5 0.01
162 1 0.00
163 1 0.00
164 5 0.01
165 119 0.34
166 23 0.07
167 107 0.30
168 7 0.02
169 1 0.00
ACGTcount: A:0.26, C:0.13, G:0.09, T:0.52
Consensus pattern (156 bp):
TTATTTATTTCATATTAATTCAGTTTTCAAAAATTCATTCATTTTCATGAGTTTTTGATTTTTCT
TTGAAATCTCTTTTTTCGAAATATCGTGTTTTCTACTCCGCAAATTTTTTAAGGAGAATTTTTCT
TGGTTTTCAATTTTTAAAATCATACA
Found at i:308935 original size:158 final size:156
Alignment explanation
Indices: 308256--308958 Score: 529
Period size: 167 Copynumber: 4.3 Consensus size: 156
308246 TTTTTTCTCT
* ** * *
308256 GTAAATTTTTTCGGGAGGATTTTTCTTAATTTTTAATTTTTAAAATTCATCAAATATTTTTATTT
1 GTAAATTTTTTCGGGGGGATTTTTCTTGGTTTTAAATTTTTAAAA-TCAT---ACA---TTATTT
* * * *
308321 ATTTCATATTAATTCAGTTTTTAAAAATTCATTCATTTTCTTGAGCTTTTGATTTGTTTCCTTGA
59 ATTTCATATTAATTCAGTTTTCAAAAATTCATTCATTTTCATGAGTTTTTGA-TT-TTTCTTTGA
* * * * *
308386 AATTTTTCTTTTTTTGAAATA-CGATATTTTTTACTTC
122 AA--TCTCTTTTTTCGAAATATCG-TGTTTTCTACTCC
* * * *
308423 GTAAATTTTTTTGGGGAGATTTTTCTTGGTTTTCAATTTTTAAAATTCATCAAAAATTATCATTT
1 GTAAATTTTTTCGGGGGGATTTTTCTTGGTTTTAAATTTTTAAAA-TCAT---ACA-T-T-ATTT
* ** * *
308488 ATTCCATATTAATTTTGTTTTCAAAAATTCATTCATTTTCATTCA-TTTTTGATTTTTTTCTTGA
59 ATTTCATATTAATTCAGTTTTCAAAAATTCATTCATTTTCA-TGAGTTTTTGATTTTTCT-TTGA
* *
308552 AA-CTTCTTTTTTTCGAAATATAGTGTTTTCTACTCT
122 AATC-TC-TTTTTTCGAAATATCGTGTTTTCTACTCC
* * * *
308588 GTAAATTTTTTTGGGAGGATTTTTTTTGGTTTTCAATTTTTAAAATTCATCAAACATTATCCTTT
1 GTAAATTTTTTCGGGGGGATTTTTCTTGGTTTTAAATTTTTAAAA-TCAT---ACATTA---TTT
* * * * * *
308653 ATTTTACATTAATTCATTTTTCAAAAATTCATTCATTTTCATGAGTTTTTAAGTTTTTCCCTTAA
59 ATTTCATATTAATTCAGTTTTCAAAAATTCATTCATTTTCATGAGTTTTTGA-TTTTT-CTTTGA
308718 AACTTCTCTTTTTTCGAAATA-CGGTGTTTTCTACTCC
122 AA--TCTCTTTTTTCGAAATATC-GTGTTTTCTACTCC
* ** ** *
308755 GCAAATTTTTTCAAGGAAATTTTTCTTGGTTTTGAATTTTTAAAA-CAT-CATTATTTATTTCAT
1 GTAAATTTTTTCGGGGGGATTTTTCTTGGTTTTAAATTTTTAAAATCATACATTATTTATTTCAT
* * *
308818 ATTAATTCGGTTTTCAAAAATTCATTCATCTTCATGAGTTTTTGCATTTTTGCTTTGAAATCCCT
66 ATTAATTCAGTTTTCAAAAATTCATTCATTTTCATGAGTTTTTG-ATTTTT-CTTTGAAATCTCT
* * * *
308883 ATTTTCTCAAAAAATCGAGTTTTCTATTCC
129 -TTTT-TCGAAATATCGTGTTTTCTACTCC
* * * *
308913 ATAAATATTTTCGGGGGGA-TTTTCTTTGGTCTAAAATTTTTAAAAT
1 GTAAATTTTTTCGGGGGGATTTTTC-TTGGTTTTAAATTTTTAAAAT
308959 GTACCTACTA
Statistics
Matches: 440, Mismatches: 73, Indels: 54
0.78 0.13 0.10
Matches are distributed among these distances:
156 4 0.01
157 9 0.02
158 106 0.24
159 2 0.00
161 5 0.01
162 1 0.00
163 1 0.00
164 5 0.01
165 125 0.28
166 20 0.05
167 157 0.36
168 4 0.01
169 1 0.00
ACGTcount: A:0.27, C:0.12, G:0.09, T:0.52
Consensus pattern (156 bp):
GTAAATTTTTTCGGGGGGATTTTTCTTGGTTTTAAATTTTTAAAATCATACATTATTTATTTCAT
ATTAATTCAGTTTTCAAAAATTCATTCATTTTCATGAGTTTTTGATTTTTCTTTGAAATCTCTTT
TTTCGAAATATCGTGTTTTCTACTCC
Found at i:311126 original size:154 final size:154
Alignment explanation
Indices: 310839--311244 Score: 428
Period size: 154 Copynumber: 2.6 Consensus size: 154
310829 CCTTCATGTC
* *
310839 TATAGTCCTTTTTAAGTCCTTTAGGGGTATCGGG-TACTTTCACGTCGAAGGTATCCCCTAAGGG
1 TATAGTCCTTTTTAAGTCC-TTAGGGGTATCGGGATACTTTCACTTCGAAGGTATCCCCTAGGGG
* * * *
310903 CATTTTCATAATTTTTCATAACCGAGTCCTAGGCATTCACTAGGTCTACTTTCATGTCGAAGGTA
65 CATTTTTATAATTTTT-ATAACCGAGTCCTAGGCATTCACCAGGCCTACTTTCATGCCGAAGGTA
310968 GGTATTTAGAATAGGTTCACC-C-CA
129 GGTATTTAGAATAGGTTCACCTCTCA
* * *
310992 TCTAGTGCTTTTTAAGTCCTTCAGGGGTATCGGGATACTTTCACTTCGAAGGTATCTCCTAGGGG
1 TATAGTCCTTTTTAAGTCCTT-AGGGGTATCGGGATACTTTCACTTCGAAGGTATCCCCTAGGGG
* ** * * * * *
311057 CATTTTTGTAATTCTTTA-AAGTTGAGTCTTAGG-TTATCACCGGGCCTATTTTTATGCCGAAGG
65 CATTTTTATAATT-TTTATAA-CCGAGTCCTAGGCAT-TCACCAGGCCTACTTTCATGCCGAAGG
* * **
311120 TGGGTATTTAGGATAGGTTCACCTCTTT
127 TAGGTATTTAGAATAGGTTCACCTCTCA
* * * * *
311148 TATAGTCCTTTTTAAGTCCCTTAGGGTTTTCAGGATACTTTCA-TGTTGAAAGTATCCCCTAGGG
1 TATAGTCCTTTTTAAGT-CCTTAGGGGTATCGGGATACTTTCACT-TCGAAGGTATCCCCTAGGG
* * *
311212 ACATTTTTATAATTTTTTAGAACCTAGTCCTAG
64 GCATTTTTATAA-TTTTTATAACCGAGTCCTAG
311245 ATAACCACCG
Statistics
Matches: 207, Mismatches: 35, Indels: 19
0.79 0.13 0.07
Matches are distributed among these distances:
152 2 0.01
153 32 0.15
154 90 0.43
155 5 0.02
156 70 0.34
157 8 0.04
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.38
Consensus pattern (154 bp):
TATAGTCCTTTTTAAGTCCTTAGGGGTATCGGGATACTTTCACTTCGAAGGTATCCCCTAGGGGC
ATTTTTATAATTTTTATAACCGAGTCCTAGGCATTCACCAGGCCTACTTTCATGCCGAAGGTAGG
TATTTAGAATAGGTTCACCTCTCA
Found at i:314971 original size:81 final size:80
Alignment explanation
Indices: 314832--314989 Score: 203
Period size: 81 Copynumber: 2.0 Consensus size: 80
314822 AATTTTTAAA
* * * * * * * *
314832 TTTTTCACTTCTAAAATATCGAATTTTTCATCATTGGGATACTCTAATCCCACTATTTTCTAGGG
1 TTTTTCACTTCTAAAACATCAAAATTTTCACCATCGGGATACTCTAACCCCACTATTTTCGAGGA
314897 GATACTCCAACCTCG
66 GATACTCCAACCTCG
314912 TTTTT-ACTTCTAAAACCATCAAAATTTTCACCATCGAGGATACTCTAACCCCA-TCATTTTCGA
1 TTTTTCACTTCTAAAA-CATCAAAATTTTCACCATCG-GGATACTCTAACCCCACT-ATTTTCGA
314975 GGAGATACTCCAACC
63 GGAGATACTCCAACC
314990 CCATCATTTT
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
79 10 0.15
80 21 0.31
81 36 0.54
ACGTcount: A:0.29, C:0.26, G:0.10, T:0.35
Consensus pattern (80 bp):
TTTTTCACTTCTAAAACATCAAAATTTTCACCATCGGGATACTCTAACCCCACTATTTTCGAGGA
GATACTCCAACCTCG
Found at i:314984 original size:28 final size:27
Alignment explanation
Indices: 314945--315045 Score: 123
Period size: 28 Copynumber: 3.7 Consensus size: 27
314935 ATTTTCACCA
*
314945 TCGA-GGATACTCTAACCCCATCATTT
1 TCGAGGGATACTCCAACCCCATCATTT
314971 TCGAGGAGATACTCCAACCCCATCATTT
1 TCGAGG-GATACTCCAACCCCATCATTT
* * *
314999 TCGAAGGGATACTCTAATCCCATTATTT
1 TCG-AGGGATACTCCAACCCCATCATTT
*
315027 TTGAGGGAATACTCCAACC
1 TCGAGGG-ATACTCCAACC
315046 TCATTTTTAC
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
26 4 0.06
27 5 0.08
28 52 0.81
29 3 0.05
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.29
Consensus pattern (27 bp):
TCGAGGGATACTCCAACCCCATCATTT
Found at i:315019 original size:137 final size:137
Alignment explanation
Indices: 314867--315125 Score: 346
Period size: 137 Copynumber: 1.9 Consensus size: 137
314857 TTTCATCATT
* * *
314867 GGGATACTCTAATCCCACTATTTTCT-AGGGGATACTCCAACCTCGTTTTTACTTCTAAAACCAT
1 GGGATACTCTAATCCCACTATTTT-TGAGGGAATACTCCAACCTCATTTTTACTTCCAAAACCAT
*
314931 CAAAATTTTCACCATCGAGGA-TAC-TCTAACCCCATCATTT-TCGAGGAGATACTCCAACCCCA
65 CAAAATTTTCACCAT-AAGGAGTACTTC-AACCCCATCATTTCT-GAGGAGATACTCCAACCCCA
314993 TCATTTTCGAA
127 TCATTTTCGAA
* **
315004 GGGATACTCTAATCCCATTATTTTTGAGGGAATACTCCAACCTCATTTTTACTTCCAAAAGTATC
1 GGGATACTCTAATCCCACTATTTTTGAGGGAATACTCCAACCTCATTTTTACTTCCAAAACCATC
* * * * *
315069 AAATTTTTTATCATAAGGAGTACTTCAACCCCATCATTTCTGAGGGGATACTTCAAC
66 AAAATTTTCACCATAAGGAGTACTTCAACCCCATCATTTCTGAGGAGATACTCCAAC
315126 TCCGTTTTTA
Statistics
Matches: 106, Mismatches: 12, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
136 5 0.05
137 98 0.92
138 3 0.03
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.32
Consensus pattern (137 bp):
GGGATACTCTAATCCCACTATTTTTGAGGGAATACTCCAACCTCATTTTTACTTCCAAAACCATC
AAAATTTTCACCATAAGGAGTACTTCAACCCCATCATTTCTGAGGAGATACTCCAACCCCATCAT
TTTCGAA
Found at i:315114 original size:81 final size:78
Alignment explanation
Indices: 315017--315234 Score: 201
Period size: 79 Copynumber: 2.7 Consensus size: 78
315007 ATACTCTAAT
* * * * *
315017 CCCATTATTTTTGAGGGAATACTCCAACCTCATTTTTACTTCCAAAAGTATCAAATTTTTTATCA
1 CCCATCATTTCTGAGGGGATACT-CAACCTCATTTTTACTTCCAAAA-TAT-AAATATTTTACCA
* *
315082 TAAGGAG-TACTTCAAC
63 T-AGGAGATACTGCAAA
* * **
315098 CCCATCATTTCTGAGGGGATACTTCAA-CTCCGTTTTTATTTCCAAAATATTGATATTTTACCAT
1 CCCATCATTTCTGAGGGGATAC-TCAACCT-CATTTTTACTTCCAAAATATAAATATTTTACCAT
* *
315162 TGGGGATACTGCAAA
64 AGGAGATACTGCAAA
* *
315177 CCCATCATTTCTAAGGGGATACTTAACC-CTATTTTTACTTCCAAAATATTAAA-ATTTT
1 CCCATCATTTCTGAGGGGATACTCAACCTC-ATTTTTACTTCCAAAATA-TAAATATTTT
315235 CATCTCGGGA
Statistics
Matches: 112, Mismatches: 19, Indels: 15
0.77 0.13 0.10
Matches are distributed among these distances:
77 1 0.01
78 27 0.24
79 41 0.37
80 5 0.04
81 37 0.33
82 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.38
Consensus pattern (78 bp):
CCCATCATTTCTGAGGGGATACTCAACCTCATTTTTACTTCCAAAATATAAATATTTTACCATAG
GAGATACTGCAAA
Found at i:316607 original size:18 final size:19
Alignment explanation
Indices: 316577--316614 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
316567 ATTATTATTA
316577 TTATTATTATATAA-AAAT
1 TTATTATTATATAATAAAT
316595 TTATATATT-TATAATAAAT
1 TTAT-TATTATATAATAAAT
316614 T
1 T
316615 AAACACATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTATTATTATATAATAAAT
Found at i:316713 original size:9 final size:9
Alignment explanation
Indices: 316699--316771 Score: 85
Period size: 9 Copynumber: 7.7 Consensus size: 9
316689 TTCTTCCATA
*
316699 TTTCTTTTC
1 TTTCTTTTT
316708 TTTCTTTTT
1 TTTCTTTTT
316717 TTTCTTTTT
1 TTTCTTTTT
316726 TTTCCTTTTT
1 TTT-CTTTTT
316736 TTTCTTTTT
1 TTTCTTTTT
316745 CTTT-TTTTT
1 -TTTCTTTTT
316754 TTTACCTTTTT
1 TTT--CTTTTT
316765 CTTTCTT
1 -TTTCTT
316772 AATAAACCAA
Statistics
Matches: 57, Mismatches: 1, Indels: 11
0.83 0.01 0.16
Matches are distributed among these distances:
8 3 0.05
9 31 0.54
10 15 0.26
11 5 0.09
12 3 0.05
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:316722 original size:18 final size:19
Alignment explanation
Indices: 316699--316771 Score: 98
Period size: 19 Copynumber: 3.8 Consensus size: 19
316689 TTCTTCCATA
316699 TTTC-TTTTCTTTCTTTTT
1 TTTCTTTTTCTTTCTTTTT
316717 TTTCTTTTT-TTTCCTTTTT
1 TTTCTTTTTCTTT-CTTTTT
316736 TTTCTTTTTCTTT-TTTTT
1 TTTCTTTTTCTTTCTTTTT
316754 TTTACCTTTTTCTTTCTT
1 TTT--CTTTTTCTTTCTT
316772 AATAAACCAA
Statistics
Matches: 49, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
18 15 0.31
19 19 0.39
20 13 0.27
21 2 0.04
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTCTTTTTCTTTCTTTTT
Found at i:317545 original size:19 final size:19
Alignment explanation
Indices: 317518--317560 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
317508 CTAAGCAACC
317518 AAAAAAGAAAAAAGAGAA-
1 AAAAAAGAAAAAAGAGAAG
*
317536 AAAAATAGAAAAAATAGAAG
1 AAAAA-AGAAAAAAGAGAAG
317556 AAAAA
1 AAAAA
317561 GGGAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.23
19 12 0.55
20 5 0.23
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (19 bp):
AAAAAAGAAAAAAGAGAAG
Found at i:317578 original size:9 final size:9
Alignment explanation
Indices: 317518--317559 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
317508 CTAAGCAACC
317518 AAAAA-AGA
1 AAAAATAGA
*
317526 AAAAAGAGAA
1 AAAAATAG-A
317536 AAAAATAGA
1 AAAAATAGA
317545 AAAAATAGA
1 AAAAATAGA
317554 AGAAAA
1 A-AAAA
317560 AGGGAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
8 5 0.17
9 13 0.43
10 12 0.40
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (9 bp):
AAAAATAGA
Done.