Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold440
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: 457504
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.30
Warning! 43543 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:537 original size:31 final size:32
Alignment explanation
Indices: 490--556 Score: 109
Period size: 31 Copynumber: 2.1 Consensus size: 32
480 AGCAGAAATT
490 AATAGAAGCGGTACCATCTTAGCAGCAAAAACC
1 AATAGAA-CGGTACCATCTTAGCAGCAAAAACC
*
523 AATAGAA-GGTACCATCTTAGCTGCAAAAACC
1 AATAGAACGGTACCATCTTAGCAGCAAAAACC
554 AAT
1 AAT
557 TAAAATTCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
31 26 0.79
33 7 0.21
ACGTcount: A:0.43, C:0.22, G:0.16, T:0.18
Consensus pattern (32 bp):
AATAGAACGGTACCATCTTAGCAGCAAAAACC
Found at i:1177 original size:17 final size:17
Alignment explanation
Indices: 1155--1192 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
1145 GAATCCGAAT
1155 GTCTGCCCACCTTCTCC
1 GTCTGCCCACCTTCTCC
1172 GTCTGCCCACCTTCTCC
1 GTCTGCCCACCTTCTCC
1189 GTCT
1 GTCT
1193 TCTCTGTCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.05, C:0.50, G:0.13, T:0.32
Consensus pattern (17 bp):
GTCTGCCCACCTTCTCC
Found at i:2107 original size:83 final size:83
Alignment explanation
Indices: 2015--2181 Score: 307
Period size: 83 Copynumber: 2.0 Consensus size: 83
2005 AAATCTATTA
*
2015 AATTTCATTTCACGAAACGGCTATGTTTTATTCAATTTTTCAAATATTATTTGCGGCGTTTTTTA
1 AATTTCATTTCACGAAACGGCTACGTTTTATTCAATTTTTCAAATATTATTTGCGGCGTTTTTTA
*
2080 CAAAAACGCCACTAAATT
66 AAAAAACGCCACTAAATT
*
2098 AATTTCATTTCACGAAACGGCTCCGTTTTATTCAATTTTTCAAATATTATTTGCGGCGTTTTTTA
1 AATTTCATTTCACGAAACGGCTACGTTTTATTCAATTTTTCAAATATTATTTGCGGCGTTTTTTA
2163 AAAAAACGCCACTAAATT
66 AAAAAACGCCACTAAATT
2181 A
1 A
2182 TTTATATTTA
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 81 1.00
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.40
Consensus pattern (83 bp):
AATTTCATTTCACGAAACGGCTACGTTTTATTCAATTTTTCAAATATTATTTGCGGCGTTTTTTA
AAAAAACGCCACTAAATT
Found at i:2774 original size:32 final size:31
Alignment explanation
Indices: 2713--2774 Score: 72
Period size: 32 Copynumber: 1.9 Consensus size: 31
2703 ATTCCTAACC
* *
2713 CATAAGCCCTAAATCCCCCTTAACTCTTAAAG
1 CATAAACCCTAAA-CCCCCTAAACTCTTAAAG
2745 CATAAACCCTAAA-CCCCTAAATCTCCTTAA
1 CATAAACCCTAAACCCCCTAAA-CT-CTTAA
2775 CCCCTAAAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
30 7 0.27
31 2 0.08
32 17 0.65
ACGTcount: A:0.37, C:0.35, G:0.03, T:0.24
Consensus pattern (31 bp):
CATAAACCCTAAACCCCCTAAACTCTTAAAG
Found at i:2784 original size:39 final size:40
Alignment explanation
Indices: 2719--2796 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 40
2709 AACCCATAAG
* *
2719 CCCTAAATCCCCCTTAACTCTTAAAGCATAAACCCTAAAC
1 CCCTAAATCCCCCTTAACCCCTAAAGCATAAACCCTAAAC
* *
2759 CCCTAAAT-CTCCTTAACCCCTAAAGCATAACCCCTAAA
1 CCCTAAATCCCCCTTAACCCCTAAAGCATAAACCCTAAA
2797 AAAATTTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 26 0.76
40 8 0.24
ACGTcount: A:0.37, C:0.38, G:0.03, T:0.22
Consensus pattern (40 bp):
CCCTAAATCCCCCTTAACCCCTAAAGCATAAACCCTAAAC
Found at i:3580 original size:31 final size:32
Alignment explanation
Indices: 3514--3588 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 32
3504 TAACCCATAT
* * *
3514 ATAACCCCTAAATCCCCTTTAACCCTTAAAGC
1 ATAACCCCTAAATCCCCTCTAACCCCTAAACC
* *
3546 ATAAACCCTAAA-CTCCTCTAACCCCTAAACC
1 ATAACCCCTAAATCCCCTCTAACCCCTAAACC
3577 ATAACCCCTAAA
1 ATAACCCCTAAA
3589 AAATTTTATT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 26 0.70
32 11 0.30
ACGTcount: A:0.39, C:0.39, G:0.01, T:0.21
Consensus pattern (32 bp):
ATAACCCCTAAATCCCCTCTAACCCCTAAACC
Found at i:4597 original size:114 final size:114
Alignment explanation
Indices: 4396--4947 Score: 570
Period size: 114 Copynumber: 4.9 Consensus size: 114
4386 ATTTTAAATC
* * * * * * *
4396 CCTGAGCATTAGCGGCGCTTT-TTTAAAAACGCCGCTAAAACCC-CAACAGTTCAGAAAACGACG
1 CCTGAGCATTAGCGGCGCTTTCTATAAAAGCGCCGCTAAATCCCTGAA-AGCTCGGGAAACGACG
* * * *
4459 TCGTTGGGCTTAGGTTTTTAGCGGCGCTTTCACAAAAACGCCGCTAAAAA
65 TCGTTGCGCTTAGGTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGA
* * * * * * *
4509 CATGAGCATTAGCGGCGCTTTCTATAAAAGCGCCACTAAAGCCCTGAAAGGTGGGGAGACGACAT
1 CCTGAGCATTAGCGGCGCTTTCTATAAAAGCGCCGCTAAATCCCTGAAAGCTCGGGAAACGACGT
4574 CGTTGCGC-TAGGTTTTTTTGCGGCGC-TTCCCTAAAAACGCCGCTAAAGA
66 CGTTGCGCTTAGG-TTTTTTGCGGCGCTTTCCC-AAAAACGCCGCTAAAGA
** ** * *
4623 CCTGAGTTTTAGCGGCGAATTCTAT-AAAGCGCCGCTAAATCCCTAAAAAGCTCGGGAAACGTCG
1 CCTGAGCATTAGCGGCGCTTTCTATAAAAGCGCCGCTAAATCCCT-GAAAGCTCGGGAAACGACG
* *
4687 TCGTTGCGCTTAGTTTTTTTGCGGCGCTTTCCCACAAACGCCGCTAAAGA
65 TCGTTGCGCTTAGGTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGA
* * * * *
4737 CCTGAGCATTAGCGGCGC-TT-TACTAAAA-CACCGCTAAATTCAC-GAAAGCTCAGAAAACGGC
1 CCTGAGCATTAGCGGCGCTTTCTA-TAAAAGCGCCGCTAAA-TCCCTGAAAGCTCGGGAAACGAC
* * * *
4798 GTTGTTGGGCTTATGTTTTTTGCGGCGCTTTCCTAAAAACGCCGCTAAAG-
64 GTCGTTGCGCTTAGGTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGA
** ** * * * *
4848 CCTTGAGCATTAGCGGCGCTTAAT-TAAAAATGCTGCTAAATCCCCGAATGCTCGGGAAACGGCG
1 CC-TGAGCATTAGCGGCGCTTTCTATAAAAGCGCCGCTAAATCCCTGAAAGCTCGGGAAACGACG
4912 TCGTTGCGC-TAGGTTTTTTGCGGCGCTTTCCCAAAA
65 TCGTTGCGCTTAGGTTTTTTGCGGCGCTTTCCCAAAA
4948 TCGCTGGTAA
Statistics
Matches: 366, Mismatches: 58, Indels: 31
0.80 0.13 0.07
Matches are distributed among these distances:
111 2 0.01
112 109 0.30
113 88 0.24
114 157 0.43
115 10 0.03
ACGTcount: A:0.26, C:0.25, G:0.24, T:0.25
Consensus pattern (114 bp):
CCTGAGCATTAGCGGCGCTTTCTATAAAAGCGCCGCTAAATCCCTGAAAGCTCGGGAAACGACGT
CGTTGCGCTTAGGTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGA
Found at i:5409 original size:4 final size:4
Alignment explanation
Indices: 5400--5434 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
5390 ATATTCCTTT
5400 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTA
5435 TTATATTACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (4 bp):
TTAA
Found at i:6828 original size:20 final size:20
Alignment explanation
Indices: 6776--6824 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
6766 ATGCGATGAC
* * * *
6776 TATATCAAACAAATAAAATT
1 TATATAAAATAAACAAAATG
6796 TATATAAAATAAACAAAATG
1 TATATAAAATAAACAAAATG
6816 TATA-AAAAT
1 TATATAAAAT
6825 TAAAATTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (20 bp):
TATATAAAATAAACAAAATG
Found at i:7199 original size:8 final size:8
Alignment explanation
Indices: 7186--7224 Score: 69
Period size: 8 Copynumber: 4.9 Consensus size: 8
7176 ACCACTACAT
7186 AAGAATCC
1 AAGAATCC
7194 AAGAATCC
1 AAGAATCC
7202 AAGAATCC
1 AAGAATCC
7210 AAGAATCC
1 AAGAATCC
*
7218 AACAATC
1 AAGAATC
7225 ATTCTTATTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.51, C:0.26, G:0.10, T:0.13
Consensus pattern (8 bp):
AAGAATCC
Found at i:9632 original size:21 final size:21
Alignment explanation
Indices: 9608--9655 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
9598 CGACTGTGGC
* *
9608 GGAGGACTAGCAGCTGGGGGT
1 GGAGGACTAACAGCTGAGGGT
*
9629 GGAGGACTAACAGGTGAGGGT
1 GGAGGACTAACAGCTGAGGGT
9650 GGAGGA
1 GGAGGA
9656 TATAAGGATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.25, C:0.10, G:0.52, T:0.12
Consensus pattern (21 bp):
GGAGGACTAACAGCTGAGGGT
Found at i:18614 original size:8 final size:8
Alignment explanation
Indices: 18601--18639 Score: 69
Period size: 8 Copynumber: 4.9 Consensus size: 8
18591 TGCACCACAT
18601 AAGAATCC
1 AAGAATCC
18609 AAGAATCC
1 AAGAATCC
18617 AAGAATCC
1 AAGAATCC
18625 AAGAATCC
1 AAGAATCC
*
18633 AACAATC
1 AAGAATC
18640 ATTCTTATTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.51, C:0.26, G:0.10, T:0.13
Consensus pattern (8 bp):
AAGAATCC
Found at i:26205 original size:324 final size:324
Alignment explanation
Indices: 25585--26215 Score: 987
Period size: 324 Copynumber: 1.9 Consensus size: 324
25575 GGCTAAGATC
* * * *
25585 AATGTTTTGGGAATTGAGTTGAGAAGGTATATCTCCGCTAATGATGTTATGTCTTAGATCAAGCT
1 AATGTTTTGGGAATTGAGTTGAGAAGGAATATCTCCACTAATGATGTTATGGCTTAGATCAAGCA
* *
25650 GGTATAGAGATAAGCCACCAATTTGCAGGGGAATCCTTCCACTCAAGTTATTTTTTGCCAAAATT
66 GGTATAGAGATAAGCCACCAATTTGCAGGGGAATCCTTCCACTCAAGTTATTGTTTGCCAAAACT
* * * * * *
25715 AAGTACATTAAATTTGACAAATTACCAATTTGAGTTGGAATGGGTCCACTCAATTTGTTTTCTGA
131 AAGCACATTAAATTTGACAAATTACCAATCTGAGATGGAATGGGGCCACTAAATTTGTTGTCTGA
* * *
25780 AAGATCTAAGTGTTCCAGGGCTTTCAGATTCTCAATTTCATGGGGTATGGGACCTTCCAAAAGAT
196 AAGATCTAAGTGATCCAGGGCTTTCAAACTCTCAATTTCATGGGGTATGGGACCTTCCAAAAGAT
* *
25845 TCGAAGCAATGAATAGATACCGCAAATTGTGTAAATGAAATAGAGATGAAGACATGGAATTGGA
261 TCGAAGCAATGAATAGATACCACAAATTGGGTAAATGAAATAGAGATGAAGACATGGAATTGGA
25909 AATGTTTTGGGAATTGAGTTGAGAAGGAATATCTCCACTAATGATGTTATGGCTTAGATCAAGCA
1 AATGTTTTGGGAATTGAGTTGAGAAGGAATATCTCCACTAATGATGTTATGGCTTAGATCAAGCA
*
25974 GGTATAGAGATAAGCCACCAATTTGCTGGGGAATCCTTCCACTCAAGTTATTGTTTGCCAAAACT
66 GGTATAGAGATAAGCCACCAATTTGCAGGGGAATCCTTCCACTCAAGTTATTGTTTGCCAAAACT
**
26039 AAGCATGTTAAATTTGACAAATTACCAATCTGAGATGGAATGGGGCCACTAAATTTGTTGTCTGA
131 AAGCACATTAAATTTGACAAATTACCAATCTGAGATGGAATGGGGCCACTAAATTTGTTGTCTGA
*
26104 GAGATCTAAGT-ATCGCAGGG-TATTCAAACTCTCAATTTCATGGGGTATGGGACCTTCCAAAAG
196 AAGATCTAAGTGATC-CAGGGCT-TTCAAACTCTCAATTTCATGGGGTATGGGACCTTCCAAAAG
* * * * * *
26167 ATTTGAAGCCATGGATAGATGCCATAAATTGGGTAAATGAAGTAGAGAT
259 ATTCGAAGCAATGAATAGATACCACAAATTGGGTAAATGAAATAGAGAT
26216 AAAGGGATTG
Statistics
Matches: 278, Mismatches: 27, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
323 3 0.01
324 275 0.99
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.30
Consensus pattern (324 bp):
AATGTTTTGGGAATTGAGTTGAGAAGGAATATCTCCACTAATGATGTTATGGCTTAGATCAAGCA
GGTATAGAGATAAGCCACCAATTTGCAGGGGAATCCTTCCACTCAAGTTATTGTTTGCCAAAACT
AAGCACATTAAATTTGACAAATTACCAATCTGAGATGGAATGGGGCCACTAAATTTGTTGTCTGA
AAGATCTAAGTGATCCAGGGCTTTCAAACTCTCAATTTCATGGGGTATGGGACCTTCCAAAAGAT
TCGAAGCAATGAATAGATACCACAAATTGGGTAAATGAAATAGAGATGAAGACATGGAATTGGA
Found at i:32193 original size:41 final size:41
Alignment explanation
Indices: 32147--32252 Score: 176
Period size: 41 Copynumber: 2.6 Consensus size: 41
32137 ATCACTTAAT
*
32147 GATCACCAGCACTTAGCCTGCTAGGCTTATAACCTGATTCA
1 GATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCA
* * *
32188 TATCACCGGCACTTAGCCTACTAGGCTTATAGCCTGATTCA
1 GATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCA
32229 GATCACCGGCACTTAGCCTGCTAG
1 GATCACCGGCACTTAGCCTGCTAG
32253 ACGTAAAGTC
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (41 bp):
GATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCA
Found at i:32276 original size:41 final size:41
Alignment explanation
Indices: 32148--32308 Score: 155
Period size: 41 Copynumber: 3.9 Consensus size: 41
32138 TCACTTAATG
* * * *
32148 ATCACCAGCACTTAGCCTGCTAGGCTTATAA-CCTGATTCAT
1 ATCACCGGCACTTAGCCTGCTAGACGTA-AAGCCTGAATCAT
* * * * * *
32189 ATCACCGGCACTTAGCCTACTAGGCTTATAGCCTGATTCAG
1 ATCACCGGCACTTAGCCTGCTAGACGTAAAGCCTGAATCAT
* *
32230 ATCACCGGCACTTAGCCTGCTAGACGTAAAGTCTGAAACAT
1 ATCACCGGCACTTAGCCTGCTAGACGTAAAGCCTGAATCAT
* * *
32271 TTCACCGGCA-TCAAGCCTGCTAGACGTAAAGTCTGAAT
1 ATCACCGGCACT-TAGCCTGCTAGACGTAAAGCCTGAAT
32309 TATCTCATTG
Statistics
Matches: 103, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
40 2 0.02
41 101 0.98
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (41 bp):
ATCACCGGCACTTAGCCTGCTAGACGTAAAGCCTGAATCAT
Found at i:37307 original size:19 final size:20
Alignment explanation
Indices: 37280--37327 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
37270 TAAATTTACG
*
37280 ATCATTTTGTTTC-A-TTTC
1 ATCATTTTGTTGCGATTTTC
37298 ATCGATTTTGTTGCGATTTTC
1 ATC-ATTTTGTTGCGATTTTC
37319 ATCATTTTG
1 ATCATTTTG
37328 CTTTATAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 3 0.12
19 9 0.35
20 7 0.27
21 7 0.27
ACGTcount: A:0.17, C:0.15, G:0.12, T:0.56
Consensus pattern (20 bp):
ATCATTTTGTTGCGATTTTC
Found at i:38143 original size:15 final size:15
Alignment explanation
Indices: 38123--38151 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
38113 ACATAAGGAT
38123 ATGAGGAAAGGATCA
1 ATGAGGAAAGGATCA
38138 ATGAGGAAAGGATC
1 ATGAGGAAAGGATC
38152 GATGTCTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.07, G:0.34, T:0.14
Consensus pattern (15 bp):
ATGAGGAAAGGATCA
Found at i:42118 original size:42 final size:42
Alignment explanation
Indices: 42071--42238 Score: 237
Period size: 42 Copynumber: 4.0 Consensus size: 42
42061 CAAACAAAAA
* *
42071 CGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTTTTTACAAG
1 CGCCGCTAAAGAACATGTTCTTTAGTGGCGTTTTTTTACAAG
*
42113 CGCCGCTAAAGAACATGTTCTTTAGTGGCGTTTTTCTACAAG
1 CGCCGCTAAAGAACATGTTCTTTAGTGGCGTTTTTTTACAAG
* * *
42155 CGCCGCTAAAGAACATGTTCTTTAGTGTCATTTTTTTTACAAA
1 CGCCGCTAAAGAACATGTTCTTTAGTGGC-GTTTTTTTACAAG
* * * *
42198 CGCCGCGAAAGAATATGTTCTTTAGTGGCGCTTTTATACAA
1 CGCCGCTAAAGAACATGTTCTTTAGTGGCGTTTTTTTACAA
42239 AAACGCCACT
Statistics
Matches: 112, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
42 76 0.68
43 36 0.32
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.35
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGTTCTTTAGTGGCGTTTTTTTACAAG
Found at i:42219 original size:85 final size:84
Alignment explanation
Indices: 42071--42238 Score: 246
Period size: 85 Copynumber: 2.0 Consensus size: 84
42061 CAAACAAAAA
* * *
42071 CGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTTTTTACAAGCGCCGCTAAAGAACATGTTCTTT
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTACAAACGCCGCGAAAGAACATGTTCTTT
* *
42136 AGTGGCGTTTTTCTACAAG
66 AGTGGCGCTTTTATACAAG
* * * *
42155 CGCCGCTAAAGAACATGTTCTTTAGTGTCATTTTTTTTACAAACGCCGCGAAAGAATATGTTCTT
1 CGCCGCTAAAGAACATGTTCTTTAGCGGC-GTTTTTTTACAAACGCCGCGAAAGAACATGTTCTT
42220 TAGTGGCGCTTTTATACAA
65 TAGTGGCGCTTTTATACAA
42239 AAACGCCACT
Statistics
Matches: 74, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
84 26 0.35
85 48 0.65
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.35
Consensus pattern (84 bp):
CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTACAAACGCCGCGAAAGAACATGTTCTTT
AGTGGCGCTTTTATACAAG
Found at i:42322 original size:14 final size:14
Alignment explanation
Indices: 42299--42332 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
42289 GCCCTCCTGT
*
42299 AGCAAAAATTCAAA
1 AGCAACAATTCAAA
42313 AGCAACAATTCAAA
1 AGCAACAATTCAAA
42327 AGCAAC
1 AGCAAC
42333 CAATAGTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.59, C:0.21, G:0.09, T:0.12
Consensus pattern (14 bp):
AGCAACAATTCAAA
Found at i:42624 original size:21 final size:21
Alignment explanation
Indices: 42556--42626 Score: 88
Period size: 21 Copynumber: 3.4 Consensus size: 21
42546 TTTTGCTCTG
* *
42556 CTCTACTTCTCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
*
42577 CTCCGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* * *
42598 CGCTGCTTCCCTCGCTTCCGC
1 CTCTGCTTCCCTCGCTGCAGC
42619 CTCTGCTT
1 CTCTGCTT
42627 TAAGTTGTAG
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.04, C:0.48, G:0.17, T:0.31
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:77434 original size:5 final size:5
Alignment explanation
Indices: 77390--77418 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
77380 TTATTTATTA
77390 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
77419 TTATATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:84758 original size:18 final size:18
Alignment explanation
Indices: 84723--84782 Score: 54
Period size: 18 Copynumber: 3.5 Consensus size: 18
84713 TCATACTGTT
* * *
84723 TTTATTTTTAAAAATTTA
1 TTTAATTTTAATATTTTA
*
84741 TTTAATTTTGATATTTTA
1 TTTAATTTTAATATTTTA
84759 TTT--TTTTAATATTTT-
1 TTTAATTTTAATATTTTA
*
84774 TATAATTTT
1 TTTAATTTT
84783 TAAAATATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
15 2 0.06
16 11 0.32
17 4 0.12
18 17 0.50
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (18 bp):
TTTAATTTTAATATTTTA
Found at i:88102 original size:25 final size:26
Alignment explanation
Indices: 88046--88108 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 26
88036 AGAAACATGA
*
88046 AAAATATATTATATAAAAAATGACAT
1 AAAATATAATATATAAAAAATGACAT
* *
88072 ATAATAGTAATATAT-AAAAATGA-TT
1 AAAATA-TAATATATAAAAAATGACAT
88097 AAAATAATAATA
1 AAAAT-ATAATA
88109 CCCAGTAGGA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
25 10 0.32
26 14 0.45
27 7 0.23
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.32
Consensus pattern (26 bp):
AAAATATAATATATAAAAAATGACAT
Found at i:88179 original size:4 final size:4
Alignment explanation
Indices: 88170--88194 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
88160 TAATAGAACT
88170 AGTA AGTA AGTA AGTA AGTA AGTA A
1 AGTA AGTA AGTA AGTA AGTA AGTA A
88195 AAGACTAATA
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:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (4 bp):
AGTA
Found at i:88702 original size:19 final size:20
Alignment explanation
Indices: 88673--88713 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
88663 TTCATTTTTC
88673 AAAACGAAAAGAAAAAAAAT
1 AAAACGAAAAGAAAAAAAAT
*
88693 AAAA-GAAAAGAAAAATAAT
1 AAAACGAAAAGAAAAAAAAT
88712 AA
1 AA
88714 TAAAAACAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.80, C:0.02, G:0.10, T:0.07
Consensus pattern (20 bp):
AAAACGAAAAGAAAAAAAAT
Found at i:94481 original size:110 final size:110
Alignment explanation
Indices: 94227--94514 Score: 418
Period size: 110 Copynumber: 2.6 Consensus size: 110
94217 TTGGCTATTC
* *
94227 GGTTAAATGAGAAAAATCGACACCCAACACCTTAGGGCACGTTTTCTCGAATTTCCCAAATGCAA
1 GGTTGAATGAGAAAAATCGACACCCAACACCTTAGGGCACG-TTTCTCGAATTTCCCAAACGCAA
* * * *
94292 AACATTGCCTTATTTCTAAAATTTTTTAAAGGATATTTAGCCATTT
65 AACATTGCCTTATTTCGAAAAGTTTTAAAAGGATATTAAGCCATTT
* * * *
94338 GGTTGAACGAGAAAAATCGACATCCATCACCTTAGGGCACGTTCTCTCAAATTTCCCAAACGCAA
1 GGTTGAATGAGAAAAATCGACACCCAACACCTTAGGGCACGTT-TCTCGAATTTCCCAAACGCAA
94403 AACATTGCCTTATTT-GAAAAGTTTTAAAAGGATATTAAGCCATTT
65 AACATTGCCTTATTTCGAAAAGTTTTAAAAGGATATTAAGCCATTT
* *
94448 GGTTGAATGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTCCTCGAATTT-CCAAACGTCA
1 GGTTGAATGAGAAAAATCGACACCCAACACCTTAGGGCACGTTT-CTCGAATTTCCCAAACG-CA
94512 AAA
64 AAA
94515 ACGAATAATA
Statistics
Matches: 159, Mismatches: 15, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
109 8 0.05
110 80 0.50
111 71 0.45
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (110 bp):
GGTTGAATGAGAAAAATCGACACCCAACACCTTAGGGCACGTTTCTCGAATTTCCCAAACGCAAA
ACATTGCCTTATTTCGAAAAGTTTTAAAAGGATATTAAGCCATTT
Found at i:94916 original size:3 final size:3
Alignment explanation
Indices: 94902--94946 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
94892 AAATGGAAAT
* *
94902 ATA ATG ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
94947 TGGGTAACAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:95918 original size:21 final size:23
Alignment explanation
Indices: 95874--95919 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
95864 TATAGCCGAA
*
95874 TGCTACTGCTTTTGTTGTCTTGTT
1 TGCTACTGC-TTTCTTGTCTTGTT
95898 TGCTACTG-TTTCTTG-CTTGTT
1 TGCTACTGCTTTCTTGTCTTGTT
95919 T
1 T
95920 CTTTCTTTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
22 6 0.29
24 8 0.38
ACGTcount: A:0.04, C:0.17, G:0.20, T:0.59
Consensus pattern (23 bp):
TGCTACTGCTTTCTTGTCTTGTT
Found at i:96781 original size:129 final size:129
Alignment explanation
Indices: 96551--97918 Score: 2025
Period size: 129 Copynumber: 10.6 Consensus size: 129
96541 TTGTGGTAGA
* * ** *
96551 TTTAATCCGAC-CTACTGCAACTTCAGAG-GTATAGGATTCATTAT-TTTAATCCGCTCCACTGC
1 TTTAATCCG-CTCCACTGCAACTTCAGAGAG-ATAGGATTGATT-TCTTTCGTCTGCTCCACTGC
* * *
96613 AACTTCAGGGAGATAGGATTGGATGTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGGG
63 AACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTG
96678 GT
128 GT
* * *
96680 TTTAATCCGCTCCTCTGTAACTTCAGAGAGATAGGATTGATTTCTTTCGTCTTCTCCACTGCAAC
1 TTTAATCCGCTCCACTGCAACTTCAGAGAGATAGGATTGATTTCTTTCGTCTGCTCCACTGCAAC
*
96745 TTCAGGGAGATAAGACTGTATGTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGT
66 TTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGT
* * * * * *
96809 TTTTATCCGTTCCACTACAACTTCAGGGAGATAGGATTGATTTCTTTTGTCTGCTCCATTGCAAC
1 TTTAATCCGCTCCACTGCAACTTCAGAGAGATAGGATTGATTTCTTTCGTCTGCTCCACTGCAAC
* *
96874 TTCAGGGAGATAAGGCTGGATGTGACCTGCTCTACTGCAACTTCAGAGAGATAAGATCTAG-GGT
66 TTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCT-GTGGT
* * * *
96938 TTTAATCCGCTCCTCTGCAACTTCAGTGGGATAAGATTGATTTCTTTCGTCTGCTCCACTGCAAC
1 TTTAATCCGCTCCACTGCAACTTCAGAGAGATAGGATTGATTTCTTTCGTCTGCTCCACTGCAAC
* *
97003 TTCAGGGAGATAAGACTGGATGTGACCTGCTCTACTGCAACTTCAGAGAGATAAGATATGTGGT
66 TTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGT
* *
97067 TTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTGATTTCTTTCGTCTGCTCCACTGCAAC
1 TTTAATCCGCTCCACTGCAACTTCAGAGAGATAGGATTGATTTCTTTCGTCTGCTCCACTGCAAC
* * * *
97132 TTCAGGGAGATAATACTGTATGTGATCTGCTCTACAGCAACTTCAGAGAGATAAGATCTATGGT
66 TTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGT
* * *
97196 TTTAATCCGCTCCACTACAACTTCA-AGGAGATGGGATTGATTTCTTTTGTCTGCTCCACTGCAA
1 TTTAATCCGCTCCACTGCAACTTCAGA-GAGATAGGATTGATTTCTTTCGTCTGCTCCACTGCAA
* *
97260 CTTCAGGGAGATAAGACTGGATGTGACCTGCTCTACTGCAACTTCAGAGGGATAAGATCTGTGGT
65 CTTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGT
* * * *
97325 TTTAATCCGCTCTACTGCAACTTCAGGGATATAGGATTGATTTCTTTCGTCTGCTCCACTGTAAC
1 TTTAATCCGCTCCACTGCAACTTCAGAGAGATAGGATTGATTTCTTTCGTCTGCTCCACTGCAAC
* * *
97390 TTTAGGGAGATAAGCCTGTATGTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGT
66 TTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGT
* * *
97454 TTTAATCCGCTCCACTACAACTTCA-AGGAGATGGGATTGATTTCTTTTGTCTGCTCCACTGCAA
1 TTTAATCCGCTCCACTGCAACTTCAGA-GAGATAGGATTGATTTCTTTCGTCTGCTCCACTGCAA
* * * *
97518 CTTTAGGGAGATAAGCCTGTATGTGATCTGCTCTACTGCAACTTCAGAGGGATAAGATCTGTGGT
65 CTTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGT
97583 TTTAATCCGCTCCACTGCAACTTCAG-GAAGATAGGATTGATTTCTTTCGTCTGCTCCACTGCAA
1 TTTAATCCGCTCCACTGCAACTTCAGAG-AGATAGGATTGATTTCTTTCGTCTGCTCCACTGCAA
* * **
97647 CTTTAGGGAGATAAGCCTTTATGTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGT
65 CTTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGT
* * * *
97712 TTTAATCCGCTCCACTACAACTTCA-AGGAGATGGGATTGATTTCTTTTGTTTGCTCCACTGCAA
1 TTTAATCCGCTCCACTGCAACTTCAGA-GAGATAGGATTGATTTCTTTCGTCTGCTCCACTGCAA
* * *
97776 CTTCAGAGAGATAAGACTGGATGTGACCTACTCTA-TGCAACTTCAGAGAGATAAGATCTGTGGT
65 CTTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGT
* *
97840 TTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTTCGTCTGCTCCACTGCAAC
1 TTTAATCCGCTCCACTGCAACTTCAGAGAGATAGGATTGATTTCTTTCGTCTGCTCCACTGCAAC
97905 TTCAGGGAGATAAG
66 TTCAGGGAGATAAG
97919 GTTTGAAATT
Statistics
Matches: 1126, Mismatches: 100, Indels: 27
0.90 0.08 0.02
Matches are distributed among these distances:
128 104 0.09
129 1019 0.90
130 3 0.00
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (129 bp):
TTTAATCCGCTCCACTGCAACTTCAGAGAGATAGGATTGATTTCTTTCGTCTGCTCCACTGCAAC
TTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGT
Found at i:97943 original size:46 final size:44
Alignment explanation
Indices: 96604--97960 Score: 245
Period size: 44 Copynumber: 31.5 Consensus size: 44
96594 TTTTAATCCG
* * *
96604 CTCCACTGCAACTTCAGGGAGATAGGATTGGA---TGT-GATCTG
1 CTCCACTGCAACTTCAGGGAGATAGGATTGAATTCTTTCG-TCTA
* * * *** ** **
96645 CTCTACTGCAACTTCAGAGAGATAAGATCTGGGGT-TTTAATCCG
1 CTCCACTGCAACTTCAGGGAGATAGGAT-TGAATTCTTTCGTCTA
* * * * *
96689 CTCCTCTGTAACTTCAGAGAGATAGGATTGATTTCTTTCGTCTT
1 CTCCACTGCAACTTCAGGGAGATAGGATTGAATTCTTTCGTCTA
* * * * *
96733 CTCCACTGCAACTTCAGGGAGATAAGACTG---TATGT-GATCTG
1 CTCCACTGCAACTTCAGGGAGATAGGATTGAATTCTTTCG-TCTA
* * * ** * **
96774 CTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTT-TTT-ATCCG
1 CTCCACTGCAACTTCAGGGAGATAGGAT-TG-AATTCTTTCGTCTA
* * * * *
96818 TTCCACTACAACTTCAGGGAGATAGGATTGATTTCTTTTGTCTG
1 CTCCACTGCAACTTCAGGGAGATAGGATTGAATTCTTTCGTCTA
* * * * ** *
96862 CTCCATTGCAACTTCAGGGAGATAAGG-CTGGA-TGTGAC--CTG
1 CTCCACTGCAACTTCAGGGAGAT-AGGATTGAATTCTTTCGTCTA
* * * ** ** **
96903 CTCTACTGCAACTTCAGAGAGATAAGATCT-AGGGT-TTTAATCCG
1 CTCCACTGCAACTTCAGGGAGATAGGAT-TGA-ATTCTTTCGTCTA
* * * *
96947 CTCCTCTGCAACTTCAGTGG-GATAAGATTGATTTCTTTCGTCTG
1 CTCCACTGCAACTTCAG-GGAGATAGGATTGAATTCTTTCGTCTA
* * * * ** *
96991 CTCCACTGCAACTTCAGGGAGATAAGACTGGA-TGTGAC--CTG
1 CTCCACTGCAACTTCAGGGAGATAGGATTGAATTCTTTCGTCTA
* * * *** ** **
97032 CTCTACTGCAACTTCAGAGAGATAAGATATGTGGT-TTTAATCCG
1 CTCCACTGCAACTTCAGGGAGATAGGAT-TGAATTCTTTCGTCTA
* * *
97076 CTCCACTGTAACTTCAGGGAGATAGGATTGATTTCTTTCGTCTG
1 CTCCACTGCAACTTCAGGGAGATAGGATTGAATTCTTTCGTCTA
* * * *
97120 CTCCACTGCAACTTCAGGGAGATA--A-T-ACTGTATGT-GATCTG
1 CTCCACTGCAACTTCAGGGAGATAGGATTGAAT-TCTTTCG-TCTA
* * * * ** **
97161 CTCTACAGCAACTTCAGAGAGATAAGATCT--ATGGT-TTTAATCCG
1 CTCCACTGCAACTTCAGGGAGATAGGAT-TGAAT--TCTTTCGTCTA
* * * * * *
97205 CTCCACTACAACTTCAAGGAGATGGGATTGATTTCTTTTGTCTG
1 CTCCACTGCAACTTCAGGGAGATAGGATTGAATTCTTTCGTCTA
* * * * ** *
97249 CTCCACTGCAACTTCAGGGAGATAAGACTGGA-TGTGAC--CTG
1 CTCCACTGCAACTTCAGGGAGATAGGATTGAATTCTTTCGTCTA
* * *** ** **
97290 CTCTACTGCAACTTCAGAGG-GATAAGATCTGTGGT-TTTAATCCG
1 CTCCACTGCAACTTCAG-GGAGATAGGAT-TGAATTCTTTCGTCTA
* * * *
97334 CTCTACTGCAACTTCAGGGATATAGGATTGATTTCTTTCGTCTG
1 CTCCACTGCAACTTCAGGGAGATAGGATTGAATTCTTTCGTCTA
* * * ** * * *
97378 CTCCACTGTAACTTTAGGGAGATAAGCCTG---TATGT-GATCTG
1 CTCCACTGCAACTTCAGGGAGATAGGATTGAATTCTTTCG-TCTA
* * * *** ** **
97419 CTCTACTGCAACTTCAGAGAGATAAGATCTGTGGT-TTTAATCCG
1 CTCCACTGCAACTTCAGGGAGATAGGAT-TGAATTCTTTCGTCTA
* * * * * *
97463 CTCCACTACAACTTCAAGGAGATGGGATTGATTTCTTTTGTCTG
1 CTCCACTGCAACTTCAGGGAGATAGGATTGAATTCTTTCGTCTA
* * ** * * *
97507 CTCCACTGCAACTTTAGGGAGATAAGCCTG---TATGT-GATCTG
1 CTCCACTGCAACTTCAGGGAGATAGGATTGAATTCTTTCG-TCTA
* * *** ** **
97548 CTCTACTGCAACTTCAGAGG-GATAAGATCTGTGGT-TTTAATCCG
1 CTCCACTGCAACTTCAG-GGAGATAGGAT-TGAATTCTTTCGTCTA
* * *
97592 CTCCACTGCAACTTCAGGAAGATAGGATTGATTTCTTTCGTCTG
1 CTCCACTGCAACTTCAGGGAGATAGGATTGAATTCTTTCGTCTA
* * ** * * *
97636 CTCCACTGCAACTTTAGGGAGATAAGCCT---TTATGT-GATCTG
1 CTCCACTGCAACTTCAGGGAGATAGGATTGAATTCTTTCG-TCTA
* * * *** ** **
97677 CTCTACTGCAACTTCAGAGAGATAAGATCTGTGGT-TTTAATCCG
1 CTCCACTGCAACTTCAGGGAGATAGGAT-TGAATTCTTTCGTCTA
* * * * * * *
97721 CTCCACTACAACTTCAAGGAGATGGGATTGATTTCTTTTGTTTG
1 CTCCACTGCAACTTCAGGGAGATAGGATTGAATTCTTTCGTCTA
* * * * * **
97765 CTCCACTGCAACTTCAGAGAGATAAGACTGGA-TGTGAC--CTA
1 CTCCACTGCAACTTCAGGGAGATAGGATTGAATTCTTTCGTCTA
* * * *** ** *
97806 CTCTA-TGCAACTTCAGAGAGATAAGATCTGTGGT-TTTAATCCA
1 CTCCACTGCAACTTCAGGGAGATAGGAT-TGAATTCTTTCGTCTA
* *
97849 CTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTTCGTCTG
1 CTCCACTGCAACTTCAGGGAGATAGGATTGAATTCTTTCGTCTA
*
97893 CTCCACTGCAACTTCAGGGAGATAAGGTTTGAAATTC-TTCGGTCTA
1 CTCCACTGCAACTTCAGGGAGAT-AGGATTG-AATTCTTTC-GTCTA
* *
97939 CTCCACTGTAACCTCAGGGAGA
1 CTCCACTGCAACTTCAGGGAGA
97961 ATAGACCTGA
Statistics
Matches: 971, Mismatches: 266, Indels: 153
0.70 0.19 0.11
Matches are distributed among these distances:
40 30 0.03
41 258 0.27
42 26 0.03
43 54 0.06
44 552 0.57
45 22 0.02
46 29 0.03
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGGAGATAGGATTGAATTCTTTCGTCTA
Found at i:98040 original size:85 final size:82
Alignment explanation
Indices: 97938--98221 Score: 275
Period size: 85 Copynumber: 3.3 Consensus size: 82
97928 TCTTCGGTCT
97938 ACTCCACTGTAACCTCAGGGAGAATAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAGAGAT
1 ACTCCACTGTAACCTCAGGGAG-ATAGACCT-AT-CGATCTACTCTGCTGTAACTTCAGAGAGAT
98003 AAGATCCTTGATTTTAATCC
63 AAGATCCTTGATTTTAATCC
* * * ** *
98023 ACTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTTGATCTGCTCCACTGTAA-TCTCAGGG
1 ACTCCACTGTAACCTCAGGGAGATA-GA--CCTATC---GATCTACTCTGCTGTAACT-TCAGAG
** * *
98087 AGATAAGAT-CTCTGGCTTCAATCT
59 AGATAAGATCCT-TGATTTTAATCC
* *
98111 GCTCCACTGTAACCTCAGGGAGATAAGACCTAATATGATCTACTCTGCTGTAACTTCAGAGAGAT
1 ACTCCACTGTAACCTCAGGGAGAT-AGACCT-AT-CGATCTACTCTGCTGTAACTTCAGAGAGAT
*
98176 AAGATCCTTTATTTTAATCC
63 AAGATCCTTGATTTTAATCC
* * * *
98196 GCTCTACTGTGACTTCAGGGAGATAG
1 ACTCCACTGTAACCTCAGGGAGATAG
98222 GATAGTGTCT
Statistics
Matches: 160, Mismatches: 26, Indels: 27
0.75 0.12 0.13
Matches are distributed among these distances:
84 5 0.03
85 80 0.50
86 7 0.04
87 7 0.04
88 60 0.38
89 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (82 bp):
ACTCCACTGTAACCTCAGGGAGATAGACCTATCGATCTACTCTGCTGTAACTTCAGAGAGATAAG
ATCCTTGATTTTAATCC
Found at i:98072 original size:44 final size:44
Alignment explanation
Indices: 98024--98313 Score: 204
Period size: 44 Copynumber: 6.7 Consensus size: 44
98014 TTTTAATCCA
* * **
98024 CTCCACTGTAATCTCAGGGAGATAGGAT-TACTATCTTTGATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCT-CTAGCTTCAATCTG
*
98068 CTCCACTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCTCTAGCTTCAATCTG
* * * *
98112 CTCCACTGTAACCTCAGGGAGATAAGA-C-CTA-ATAT-GATCTA
1 CTCCACTGTAATCTCAGGGAGATAAGATCTCTAGCT-TCAATCTG
** * * * * *
98153 CTCTGCTGTAA-CTTCAGAGAGATAAGATCCTTTA-TTTTAATCCG
1 CTCCACTGTAATC-TCAGGGAGATAAGAT-CTCTAGCTTCAATCTG
* * * ** *
98197 CTCTACTGTGA-CTTCAGGGAGATAGGAT-AGT-GTCTTCGATCTG
1 CTCCACTGTAATC-TCAGGGAGATAAGATCTCTAG-CTTCAATCTG
* * * *
98240 CTCCGCTGTAATCTCAGGGAAATAAGATCTCTGGCTTCAATTTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCTCTAGCTTCAATCTG
* *
98284 CTCCACTGTGACCTCAGGGAGATAAGATCT
1 CTCCACTGTAATCTCAGGGAGATAAGATCT
98314 GAAATATTCA
Statistics
Matches: 193, Mismatches: 41, Indels: 24
0.75 0.16 0.09
Matches are distributed among these distances:
40 1 0.01
41 27 0.14
42 4 0.02
43 30 0.16
44 129 0.67
45 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (44 bp):
CTCCACTGTAATCTCAGGGAGATAAGATCTCTAGCTTCAATCTG
Found at i:98183 original size:173 final size:172
Alignment explanation
Indices: 97763--98315 Score: 658
Period size: 173 Copynumber: 3.2 Consensus size: 172
97753 TTCTTTTGTT
* * * * * *
97763 TGCTCCACTGCAACTTCAGAGAGATAAGA-CTGGATGTGACCTACTCT-ATGCAACTTCAGAGAG
1 TGCTCCACTGTAACCTCAGGGAGATAAGACCT-GATGTGATCTACTCTGCTGTAACTTCAGAGAG
* * *
97826 ATAAGAT-CTGTGGTTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTTCG-
65 ATAAGATCCT-TGATTTTAATCCACTCCACTGTAACTTCAGGGAGATAGGATT-ATATCTTT-GA
* * * **
97889 TCTGCTCCACTGCAA-CTTCAGGGAGATAAGGT-T-TGAAATTCTTCGGTC
127 TCTGCTCCACTGTAATC-TCAGGGAGATAAGATCTCTG----GCTTCAATC
* *
97937 TACTCCACTGTAACCTCAGGGAGA-ATAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAGAG
1 TGCTCCACTGTAACCTCAGGGAGATA-AGACCTGATGTGATCTACTCTGCTGTAACTTCAGAGAG
98001 ATAAGATCCTTGATTTTAATCCACTCCACTGTAA-TCTCAGGGAGATAGGATTACTATCTTTGAT
65 ATAAGATCCTTGATTTTAATCCACTCCACTGTAACT-TCAGGGAGATAGGATTA-TATCTTTGAT
98065 CTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATC
128 CTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATC
* *
98110 TGCTCCACTGTAACCTCAGGGAGATAAGACCTAATATGATCTACTCTGCTGTAACTTCAGAGAGA
1 TGCTCCACTGTAACCTCAGGGAGATAAGACCTGATGTGATCTACTCTGCTGTAACTTCAGAGAGA
* * * * * *
98175 TAAGATCCTTTATTTTAATCCGCTCTACTGTGACTTCAGGGAGATAGGA-TAGTGTCTTCGATCT
66 TAAGATCCTTGATTTTAATCCACTCCACTGTAACTTCAGGGAGATAGGATTA-TATCTTTGATCT
* * *
98239 GCTCCGCTGTAATCTCAGGGAAATAAGATCTCTGGCTTCAATT
130 GCTCCACTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATC
* *
98282 TGCTCCACTGTGACCTCAGGGAGATAAGATCTGA
1 TGCTCCACTGTAACCTCAGGGAGATAAGACCTGA
98316 AATATTCATT
Statistics
Matches: 334, Mismatches: 33, Indels: 26
0.85 0.08 0.07
Matches are distributed among these distances:
172 83 0.25
173 109 0.33
174 41 0.12
175 95 0.28
176 4 0.01
177 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (172 bp):
TGCTCCACTGTAACCTCAGGGAGATAAGACCTGATGTGATCTACTCTGCTGTAACTTCAGAGAGA
TAAGATCCTTGATTTTAATCCACTCCACTGTAACTTCAGGGAGATAGGATTATATCTTTGATCTG
CTCCACTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATC
Found at i:99701 original size:21 final size:21
Alignment explanation
Indices: 99677--99722 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
99667 TTCTTTCTTC
*
99677 TTTTTGTTTTTTTTATTTTAA
1 TTTTTGATTTTTTTATTTTAA
*
99698 TTTTTGATTTTTTTATTTTCA
1 TTTTTGATTTTTTTATTTTAA
99719 TTTT
1 TTTT
99723 GACTTTGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.13, C:0.02, G:0.04, T:0.80
Consensus pattern (21 bp):
TTTTTGATTTTTTTATTTTAA
Found at i:100450 original size:93 final size:95
Alignment explanation
Indices: 100309--100498 Score: 321
Period size: 93 Copynumber: 2.0 Consensus size: 95
100299 TATGAATAAT
100309 TATTTATACAATATGATTATGAATGAATGACGTGGAAGAAAATCTAAAAGAATGAAATAATCAGA
1 TATTTATACAATATGATTATGAAT--ATGACGTGGAAGAAAATCTAAAAGAATGAAATAATCAGA
* *
100374 AATAATTATTTAAAAAGAATGAAAGAATATTG
64 AATAATTATTCAAAAAGAATGAAAGAACATTG
*
100406 TATTTATACAATATGATTATGAAT-T-ATGTGGAAGAAAATCTAAAAGAATGAAATAATCAGAAA
1 TATTTATACAATATGATTATGAATATGACGTGGAAGAAAATCTAAAAGAATGAAATAATCAGAAA
100469 TAATTATTCAAAAAGAATGAAAGAACATTG
66 TAATTATTCAAAAAGAATGAAAGAACATTG
100499 GCTCAAAAAG
Statistics
Matches: 90, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
93 65 0.72
94 1 0.01
97 24 0.27
ACGTcount: A:0.52, C:0.05, G:0.15, T:0.29
Consensus pattern (95 bp):
TATTTATACAATATGATTATGAATATGACGTGGAAGAAAATCTAAAAGAATGAAATAATCAGAAA
TAATTATTCAAAAAGAATGAAAGAACATTG
Found at i:104179 original size:3 final size:3
Alignment explanation
Indices: 104102--104160 Score: 109
Period size: 3 Copynumber: 19.7 Consensus size: 3
104092 AAATGGAAAT
*
104102 ATA ATG ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
104150 ATA ATA ATA AT
1 ATA ATA ATA AT
104161 GGTAACATTA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:105127 original size:21 final size:23
Alignment explanation
Indices: 105083--105128 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
105073 TATAGCCGAA
*
105083 TGCTACTGCTTTTGTTGTCTTGTT
1 TGCTACTGC-TTTCTTGTCTTGTT
105107 TGCTACTG-TTTCTTG-CTTGTT
1 TGCTACTGCTTTCTTGTCTTGTT
105128 T
1 T
105129 CTTTCTTTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
22 6 0.29
24 8 0.38
ACGTcount: A:0.04, C:0.17, G:0.20, T:0.59
Consensus pattern (23 bp):
TGCTACTGCTTTCTTGTCTTGTT
Found at i:113193 original size:12 final size:12
Alignment explanation
Indices: 113178--113204 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
113168 CTCTTTTTCC
113178 TTTTTCTTTTGT
1 TTTTTCTTTTGT
113190 TTTTTCTTTTGT
1 TTTTTCTTTTGT
113202 TTT
1 TTT
113205 CTTTTCACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.85
Consensus pattern (12 bp):
TTTTTCTTTTGT
Found at i:135749 original size:38 final size:38
Alignment explanation
Indices: 135698--135775 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
135688 TACCAGGAAA
*
135698 ACCAAATGGGACAAAACCTCGGTTAAGGGAAAAATAGT
1 ACCAAATGGGACAAAACCTCGGTTAAGGGAAAAAGAGT
*
135736 ACCAAATGGGACAAAATCTCGGTTAAGGGAAAAAGAGT
1 ACCAAATGGGACAAAACCTCGGTTAAGGGAAAAAGAGT
135774 AC
1 AC
135776 AATGCGTGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.45, C:0.15, G:0.24, T:0.15
Consensus pattern (38 bp):
ACCAAATGGGACAAAACCTCGGTTAAGGGAAAAAGAGT
Found at i:147691 original size:29 final size:27
Alignment explanation
Indices: 147608--147693 Score: 97
Period size: 25 Copynumber: 3.1 Consensus size: 27
147598 TTAAAATGAC
147608 TTTATATAAAAATAAACAAAATTTATAAA
1 TTTATAT-AAAATAAACAAAA-TTATAAA
*
147637 ATTATATAAAATCAAAC-AAA-TA-AAA
1 TTTATATAAAAT-AAACAAAATTATAAA
147662 TTTATATAAAAGTAAACAAAATGTATAAA
1 TTTATATAAAA-TAAACAAAAT-TATAAA
147691 TTT
1 TTT
147694 TAATTTTATC
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
25 17 0.35
26 6 0.12
28 10 0.20
29 16 0.33
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (27 bp):
TTTATATAAAATAAACAAAATTATAAA
Found at i:152956 original size:5 final size:5
Alignment explanation
Indices: 152927--152982 Score: 60
Period size: 5 Copynumber: 11.0 Consensus size: 5
152917 AAATATCTCA
* * *
152927 AAAAT AAATT AAAA- ACAAAA AAACAT AACAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT A-AAAT AAA-AT AAAAT AAAAT AAAAT AAAAT AAAAT
152978 AAAAT
1 AAAAT
152983 TGGTTAAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
4 1 0.02
5 38 0.88
6 4 0.09
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:153885 original size:21 final size:22
Alignment explanation
Indices: 153845--153885 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
153835 ATGTAAAAAT
* *
153845 AATTTTCCATCTTCTTTTTTAA
1 AATTATCCATCTTCTATTTTAA
153867 AATTATCCA-CTTCTATTTT
1 AATTATCCATCTTCTATTTT
153886 GATTACATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.24, C:0.20, G:0.00, T:0.56
Consensus pattern (22 bp):
AATTATCCATCTTCTATTTTAA
Found at i:156285 original size:76 final size:76
Alignment explanation
Indices: 156091--156302 Score: 253
Period size: 76 Copynumber: 2.8 Consensus size: 76
156081 GACGTGCCCT
* * * * *
156091 GCACTAGTCGAATAAATCGACAAAGATTTGCACCCAAAGCTCGTCAGATTAACTGACGGTATTAA
1 GCACTAGTCGAATAAATCGACAAAGATTTGCGCCCAGAGCTAGTCAGATAAACTGACGATATTAA
* *
156156 TTGTGTGCCCA
66 CTGTGTACCCA
* * * *
156167 GCACTAGTCGAATAAATTGACAAAGATTTGTGCCCAGTGCTAGTCGGATAAACTGACGATATTAA
1 GCACTAGTCGAATAAATCGACAAAGATTTGCGCCCAGAGCTAGTCAGATAAACTGACGATATTAA
*
156232 CTGTGTACTCA
66 CTGTGTACCCA
* * * * * * *
156243 TCACTAGTCGAATAAACCGACAAAGATTTACGCTCAGCGCTAGTAAGATAAACCGACGAT
1 GCACTAGTCGAATAAATCGACAAAGATTTGCGCCCAGAGCTAGTCAGATAAACTGACGAT
156303 CACATACATA
Statistics
Matches: 114, Mismatches: 22, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
76 114 1.00
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (76 bp):
GCACTAGTCGAATAAATCGACAAAGATTTGCGCCCAGAGCTAGTCAGATAAACTGACGATATTAA
CTGTGTACCCA
Found at i:157433 original size:106 final size:106
Alignment explanation
Indices: 157242--157783 Score: 755
Period size: 106 Copynumber: 5.1 Consensus size: 106
157232 TCAAAAAACA
* * * * * *
157242 TACTTTGAAGTTTTAAAAGGATATTTGGCTATTTGGTCAACCAAGAAATCAAAACTCAGCACGTT
1 TACTTTGAAATTTTAAAAGGATATTTGGCTATTTGGTCAAACGAGAAATCGAAACCCAGCACATT
* *
157307 AGGGCACGCTTTCTCAAATTTCCAAATGCAAAATATTGCCT
66 AGGGCACGTTTTCTCGAATTTCCAAATGCAAAATATTGCCT
* * *
157348 CACTTTGAAATTTTAGAAGGATATTTGGTTATTTGGTCAAACGAGAAATCGAAACCCAGCACATT
1 TACTTTGAAATTTTAAAAGGATATTTGGCTATTTGGTCAAACGAGAAATCGAAACCCAGCACATT
* *
157413 AGGGTACATTTTCTCGAATTTCCAAATGCAAAATATTGCCT
66 AGGGCACGTTTTCTCGAATTTCCAAATGCAAAATATTGCCT
* * *
157454 TACTTTGAAATTTTAAAAGGATATTTGGTTATTTGGTCGAACGAGAAATTGAAACCCAGCACATT
1 TACTTTGAAATTTTAAAAGGATATTTGGCTATTTGGTCAAACGAGAAATCGAAACCCAGCACATT
* *
157519 AGGGCATG-TTTCTCGAATTTGCAAATGCAAAATATTGCCT
66 AGGGCACGTTTTCTCGAATTTCCAAATGCAAAATATTGCCT
** *
157559 TACTTTGAAATTTTAAAAGGATATTTGGCTATTTGGTTGAACGAAAAAATCGAAACCCAGCACAT
1 TACTTTGAAATTTTAAAAGGATATTTGGCTATTTGGTCAAACG-AGAAATCGAAACCCAGCACAT
* * *
157624 TAGGGCACGTTTTCTCGAATTTCTAAACG-AAAACATTGCCT
65 TAGGGCACGTTTTCTCGAATTTCCAAATGCAAAATATTGCCT
* * * * * *
157665 TATTTTGAAATTTTTAAAAAGATATTTAGCTATTTGGTTGAACAAGAAAAATCGAAACCCAGCAC
1 TACTTTGAAA-TTTTAAAAGGATATTTGGCTATTTGG-TCAA-ACGAGAAATCGAAACCCAGCAC
*
157730 ATTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAATATTGCCT
63 ATTAGGGCACGTTTTCTCGAATTTCCAAATGCAAAATATTGCCT
157774 TACTTTGAAA
1 TACTTTGAAA
157784 ACTTTTCTTT
Statistics
Matches: 391, Mismatches: 39, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
105 72 0.18
106 206 0.53
107 40 0.10
108 51 0.13
109 22 0.06
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Consensus pattern (106 bp):
TACTTTGAAATTTTAAAAGGATATTTGGCTATTTGGTCAAACGAGAAATCGAAACCCAGCACATT
AGGGCACGTTTTCTCGAATTTCCAAATGCAAAATATTGCCT
Found at i:157868 original size:15 final size:15
Alignment explanation
Indices: 157844--157874 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
157834 AATAAATATG
*
157844 ATAATGTGAACAAAA
1 ATAATATGAACAAAA
157859 ATAATATGAACAAAA
1 ATAATATGAACAAAA
157874 A
1 A
157875 CAAATAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.06, G:0.10, T:0.19
Consensus pattern (15 bp):
ATAATATGAACAAAA
Found at i:158816 original size:13 final size:14
Alignment explanation
Indices: 158798--158826 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
158788 AGGAAACCCC
158798 TTTAGT-TTTTTTT
1 TTTAGTCTTTTTTT
158811 TTTAGTCTTTTTTT
1 TTTAGTCTTTTTTT
158825 TT
1 TT
158827 GAACCTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.07, C:0.03, G:0.07, T:0.83
Consensus pattern (14 bp):
TTTAGTCTTTTTTT
Found at i:159297 original size:6 final size:6
Alignment explanation
Indices: 159288--159328 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
159278 AAATAAAATT
159288 CTAAAA CTAAAA CTAAAA CTAAAA CTAAAA CTAAAA CTAAA
1 CTAAAA CTAAAA CTAAAA CTAAAA CTAAAA CTAAAA CTAAA
159329 GTCTAAAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.66, C:0.17, G:0.00, T:0.17
Consensus pattern (6 bp):
CTAAAA
Found at i:159706 original size:18 final size:18
Alignment explanation
Indices: 159685--159731 Score: 69
Period size: 17 Copynumber: 2.7 Consensus size: 18
159675 TTTGGTCTAC
*
159685 TGTTTTGTTTTGGGTTTT
1 TGTTTTGTTTTGGGTATT
159703 TG-TTTGTTTTGGGTATT
1 TGTTTTGTTTTGGGTATT
*
159720 TGTTTTTTTTTG
1 TGTTTTGTTTTG
159732 ACTATTTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 16 0.62
18 10 0.38
ACGTcount: A:0.02, C:0.00, G:0.26, T:0.72
Consensus pattern (18 bp):
TGTTTTGTTTTGGGTATT
Found at i:160554 original size:45 final size:44
Alignment explanation
Indices: 160456--160617 Score: 166
Period size: 45 Copynumber: 3.6 Consensus size: 44
160446 ATTTTAATCC
* * *
160456 GCTCCACTGCAACTTCAAGGAGAT-AGGATTAG-TATCTTCAACTT
1 GCTCCACTGCAACTTCAGGGAGATAAGG-TTTGTTATCTTCATC-T
*
160500 GCTCTACTGCAACTTCAGGGAGATAAGGTTTGTTATCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGGTTTGTTATCTTCA-TCT
** * * *
160545 GCTCCACTGCAACTTCAGGGAGATAAGACTTGTTATGGTGTGATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGGTTTGTTAT-CT-TCATCT
* *
160591 GCTCTACTGCAACTTCAGAGAGATAAG
1 GCTCCACTGCAACTTCAGGGAGATAAG
160618 ATCTGTAGCT
Statistics
Matches: 101, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
44 25 0.25
45 45 0.45
46 29 0.29
47 2 0.02
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.30
Consensus pattern (44 bp):
GCTCCACTGCAACTTCAGGGAGATAAGGTTTGTTATCTTCATCT
Found at i:160898 original size:128 final size:129
Alignment explanation
Indices: 160733--161028 Score: 400
Period size: 128 Copynumber: 2.3 Consensus size: 129
160723 AATAAAGTCT
**
160733 GATGTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCATCATTTTAATTTGCT-TCACTGC
1 GATGTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCATCATTTTAATCCGCTCT-ACTGC
* * * *
160797 AACTTCAG-GAAGATAGGATTAGTTTCTTCAATCTGATCCAGTGCAACTTCAGGGAGATAAGATT
65 AACATCAGAG-AGATAGGATTAGTTTCTTCAATCTGACCCACTGCAACTTCAGGGAGATAAGACT
160861 G
129 G
** ** *
160862 GATGTGATCTGCT-TACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCTACTGCG
1 GATGTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCATCATTTTAATCCGCTCTACTGCA
* ** *
160926 ACATCAGAGAGATAGGATTGGTTTCTTCTGTCTGCCCCACTGCAACTTCAGGGAGATAAGACTG
66 ACATCAGAGAGATAGGATTAGTTTCTTCAATCTGACCCACTGCAACTTCAGGGAGATAAGACTG
* *
160990 GATGCGATCTGCTCTACTGCAAATTCAGAGAGATAAGAT
1 GATGTGATCTGCTCTACTGCAACTTCAGAGAGATAAGAT
161029 TGATAATTTA
Statistics
Matches: 147, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
128 108 0.73
129 39 0.27
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (129 bp):
GATGTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCATCATTTTAATCCGCTCTACTGCA
ACATCAGAGAGATAGGATTAGTTTCTTCAATCTGACCCACTGCAACTTCAGGGAGATAAGACTG
Found at i:161010 original size:41 final size:41
Alignment explanation
Indices: 160838--161027 Score: 141
Period size: 44 Copynumber: 4.5 Consensus size: 41
160828 TCTGATCCAG
* * *
160838 TGCAACTTCAGGGAGATAAGATTGGATGTGATCTGCT-TAC
1 TGCAACTTCAGAGAGATAAGACTGGATGCGATCTGCTCTAC
* *** *
160878 TGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCTAC
1 TGCAACTTCAGAGAGATAAGA-C--TGGATGCGATCTGCTCTAC
* * * * * * * *
160922 TGCGACATCAGAGAGATAGGATTGGTTTCTTCTG-TCTGCCCCAC
1 TGCAACTTCAGAGAGATAAGACTGG---ATGC-GATCTGCTCTAC
*
160966 TGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTAC
1 TGCAACTTCAGAGAGATAAGACTGGATGCGATCTGCTCTAC
*
161007 TGCAAATTCAGAGAGATAAGA
1 TGCAACTTCAGAGAGATAAGA
161028 TTGATAATTT
Statistics
Matches: 114, Mismatches: 27, Indels: 17
0.72 0.17 0.11
Matches are distributed among these distances:
40 21 0.18
41 32 0.28
43 11 0.10
44 50 0.44
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (41 bp):
TGCAACTTCAGAGAGATAAGACTGGATGCGATCTGCTCTAC
Found at i:161245 original size:100 final size:100
Alignment explanation
Indices: 161115--162849 Score: 2208
Period size: 100 Copynumber: 17.4 Consensus size: 100
161105 CAATGTCGGG
* ** * * * *
161115 GAAGTAAGAGTCGTTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACT
1 GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACC
161180 GTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGA
66 GTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGA
* * * * **
161215 GAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCAGGGAAACAGGATTTGCC
1 GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACC
* *
161280 GTTGTAGCTTCAATTTGTTCCACTGCACCGCCAGG
66 GTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGA
161315 GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACC
1 GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACC
* *
161380 GTTGTAGCTTCAATCTGTTCCATTGCACCGCCAGG
66 GTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGA
* * * * * *
161415 GAAGTAAGATTCACCGTAGTGGCTTTAATCATTTTAATTGCAATGTCGGGGAAACAAGATTCGCC
1 GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACC
* * * *
161480 GTTGTAGCTTCAATTTGTTGCACTGCACTGCCAAA
66 GTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGA
* *
161515 GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTTATC
1 GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACC
* * *
161580 GTTGTAGTTTCAATCTATTCCATTGCACCGCCA-A
66 GTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGA
* * * *
161614 GGAAGTAAGATTCGCCGTTGTGACTTCAATCTTTTTAATTGTAATGTCGGGGAAACAAGATTCAT
1 -GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCAC
* * *
161679 CGTTTTAGCTTCAATCTGTCCCACTGCACCGCTAG-
65 CGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGA
* * **
161714 GAAGGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTTGC
1 GAA-GTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCAC
*
161779 CGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGT
65 CGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGA
* * ** * *
161815 GAAGTAAGATTCGCCATTGTGGCTTCAATGTTTTTAATTGCAATGTCTAGGAAACAAGATTCACT
1 GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACC
* *
161880 GTTGTAGCTTCAATCTGTTCCACTACACTGCCA-A
66 GTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGA
* ** * * * *
161914 GGAAGTAAGATTTGTTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGC
1 -GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCAC
*
161979 TGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGA
65 CGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGA
* * * * * * **
162015 GAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTCAATTACAATGTCAGGGAAACAGGATTTGCC
1 GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACC
* *
162080 GTTGTAGCTTCAATTTGTTCCACTGCACCGCCAGG
66 GTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGA
* *
162115 GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCACC
1 GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACC
* * *
162180 GTTGTAGCTTCAATTTGTTCCATTGCACCGCCAGG
66 GTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGA
* * * * * *
162215 GAAGTAAGATTCACCGTAGTGGCTTTAATCCTTTTAATTGCAATGTCGGGGAAACAAGATTCGCC
1 GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACC
* * * *
162280 GTTGTAGCTTCAATTTGTTGCACTGCACTGCCAAA
66 GTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGA
* * *
162315 GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGCAAGATTTATC
1 GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACC
* * * *
162380 GTTGTAGTTTCAATCTATTCCATTGCACTGCCA-A
66 GTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGA
* * *
162414 GGAAGTAAGATTCGCCGTTGTGACTTCAATCTTTTTAATTGTAATGTCGGGGAAACAAGATTCAC
1 -GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCAC
* * *
162479 CGTTTTAGCTTCAATCTGTCCCACTGCACCGCTAGA
65 CGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGA
* * **
162515 -AAGGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTTGC
1 GAA-GTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCAC
* *
162579 CGTTGTAGCTTCAATCTGTTCCACTGCACCACCAGT
65 CGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGA
* * ** *
162615 GAAGTAAGATTCGCCATTGTGGCTTCAATGTTTTTAATTGCAATGTCTAGGAAACAAGATTCACC
1 GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACC
* *
162680 GTTGTAGCTTCAATCTGTTCCACTACACTGCCA-A
66 GTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGA
* ** * * * **
162714 GGAAGTAAGATTTGTTGTTGTAGCTTCAATC-TTTTAACTGTAATGTCGGGGAAGCAAGATTCGT
1 -GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCAC
* * * ** *
162778 TGTTATAGTTTCAATCTGTTCCACTATACTGCCA-A
65 CGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGA
* *
162813 TGAAGTAAGATTCGCTGTTGTAGCTTCAATCTTTTTA
1 -GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTA
162850 GGGGGACAGG
Statistics
Matches: 1418, Mismatches: 205, Indels: 24
0.86 0.12 0.01
Matches are distributed among these distances:
99 92 0.06
100 1319 0.93
101 7 0.00
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (100 bp):
GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACC
GTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGA
Found at i:163318 original size:132 final size:132
Alignment explanation
Indices: 162847--163297 Score: 628
Period size: 132 Copynumber: 3.4 Consensus size: 132
162837 TTCAATCTTT
* * * *
162847 TTAGGGGGACAGGATCTATAATCTTCAACCTACTCCACTGCTGCTCAGAAAGATAAGGTTTGTGA
1 TTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGAGAGATAAGGTTTGTGG
* * * *
162912 CTGAAATCTGCTTCCCTACTACCTCGGGAAGATAAGATTCACCGTCTTTGATCTGCT---CTACT
66 CTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTTCGATTTGCTCCACTACT
162974 AC
131 AC
* * * * *
162976 TTAGGGAGATAGGACCTGCAATCTTCAACCTACTCCACTGCTGCTCAAAGAGAT-AGGATTGGTG
1 TTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGAGAGATAAGG-TTTGTG
*
163040 GCTTAAATC-GTCTTCCCTACTACCTTGGGAAGATAGGATTCACCGTCTTCGATTTGCTCCACTA
65 GCTTAAATCTG-CTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTTCGATTTGCTCCACTA
163104 CTTA-
129 C-TAC
**
163108 TTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACAACTGCTCATG-GAGATAAGGTTTGTG
1 TTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCA-GAGAGATAAGGTTTGTG
* *
163172 GCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTAACCATCTTCGATTTGCTCCACTAC
65 GCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTTCGATTTGCTCCACTAC
*
163237 TGC
130 TAC
* *
163240 TTAGGGAGACAGGATCTGCAATCTTTAACCTACTCCACTGCTGCTCAGAGAGATAAGG
1 TTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGAGAGATAAGG
163298 CTAGTTTTTT
Statistics
Matches: 282, Mismatches: 29, Indels: 19
0.85 0.09 0.06
Matches are distributed among these distances:
128 4 0.01
129 102 0.36
131 2 0.01
132 168 0.60
133 6 0.02
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.29
Consensus pattern (132 bp):
TTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGAGAGATAAGGTTTGTGG
CTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTTCGATTTGCTCCACTACT
AC
Found at i:163980 original size:19 final size:19
Alignment explanation
Indices: 163938--163984 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
163928 TTGGAGAACT
**
163938 TAATGCAAATGATGTCATG
1 TAATGCAAATGATGAAATG
163957 TAATGCAAATGCATGAAATG
1 TAATGCAAATG-ATGAAATG
163977 -AATGCAAA
1 TAATGCAAA
163985 ACAGATGTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 19 0.76
20 6 0.24
ACGTcount: A:0.45, C:0.11, G:0.19, T:0.26
Consensus pattern (19 bp):
TAATGCAAATGATGAAATG
Found at i:165678 original size:106 final size:106
Alignment explanation
Indices: 165487--165922 Score: 658
Period size: 106 Copynumber: 4.1 Consensus size: 106
165477 TCAAAAAACA
* * * * * *
165487 TACTTTGAAGTTTTAAGAGGATATTTGGCTATTTGGTC-AACCAAGAAATCAAAACTCAGCACGT
1 TACTTTGAAATTTTAAAAGGATATTTGGCTATTTGGTCGAA-CGAGAAATCGAAACCCAGCACAT
* * *
165551 TAGGGCACGCTTTCTCAAATTTCTAAATGCAAAATATTGCCT
65 TAGGGCACGTTTTCTCGAATTTCCAAATGCAAAATATTGCCT
* * * *
165593 CACTTTGAAATTTTAGAAGGATATTTGGTTATTTGGTCGAACGAGAAACCGAAACCCAGCACATT
1 TACTTTGAAATTTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACATT
*
165658 AGGGTACGTTTTCTCGAATTTCCAAATGCAAAATATTGCCT
66 AGGGCACGTTTTCTCGAATTTCCAAATGCAAAATATTGCCT
*
165699 TACTTTGAAATTTTAAAAGGATATTTGGTTATTTGGTCGAACGAGAAATCGAAACCCAGCACATT
1 TACTTTGAAATTTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACATT
165764 AGGGCACGTTTTCTCGAATTTCCAAATGCAAAATATTGCCT
66 AGGGCACGTTTTCTCGAATTTCCAAATGCAAAATATTGCCT
* *
165805 TACTTTGAAATTTTAAAAGGATATTTGGCTATTTGGTCGAACGAAAAAAATCGAAACTCAGCACA
1 TACTTTGAAATTTTAAAAGGATATTTGGCTATTTGGTCGAACG--AGAAATCGAAACCCAGCACA
* * *
165870 TTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAATATTGCGT
64 TTAGGGCACGTTTTCTCGAATTTCCAAATGCAAAATATTGCCT
165913 TACTTTGAAA
1 TACTTTGAAA
165923 AATTTTCCTT
Statistics
Matches: 303, Mismatches: 24, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
106 233 0.77
107 2 0.01
108 68 0.22
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (106 bp):
TACTTTGAAATTTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACATT
AGGGCACGTTTTCTCGAATTTCCAAATGCAAAATATTGCCT
Found at i:166125 original size:9 final size:8
Alignment explanation
Indices: 166089--166207 Score: 59
Period size: 9 Copynumber: 13.8 Consensus size: 8
166079 TAAGTATGAA
166089 AATAATAGT
1 AATAATA-T
*
166098 ACATAATAA
1 A-ATAATAT
166107 AATAATAT
1 AATAATAT
166115 AATATATAT
1 AATA-ATAT
*
166124 AAAAAGGTA-
1 AATAA--TAT
166133 AATAGATAT
1 AATA-ATAT
166142 -ATAA-ACT
1 AATAATA-T
166149 AATACA-AT
1 AATA-ATAT
166157 AATAATACCT
1 AATAATA--T
166167 -ATAATAAT
1 AATAAT-AT
166175 AATAATAAT
1 AATAAT-AT
166184 AATAATAAT
1 AATAAT-AT
166193 AATAATAAT
1 AATAAT-AT
166202 AATAAT
1 AATAAT
166208 CAATAACATA
Statistics
Matches: 92, Mismatches: 4, Indels: 28
0.74 0.03 0.23
Matches are distributed among these distances:
6 1 0.01
7 3 0.03
8 26 0.28
9 51 0.55
10 11 0.12
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.31
Consensus pattern (8 bp):
AATAATAT
Found at i:166162 original size:3 final size:3
Alignment explanation
Indices: 166154--166213 Score: 86
Period size: 3 Copynumber: 19.7 Consensus size: 3
166144 AAACTAATAC
*
166154 AAT AAT AAT ACCT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
166199 AAT AAT AAT CAAT AA
1 AAT AAT AAT -AAT AA
166214 CATAACAAGA
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
2 1 0.02
3 47 0.90
4 4 0.08
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:166964 original size:13 final size:14
Alignment explanation
Indices: 166946--166974 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
166936 AGGAAACACC
166946 TTTAGT-TTTTTTT
1 TTTAGTCTTTTTTT
166959 TTTAGTCTTTTTTT
1 TTTAGTCTTTTTTT
166973 TT
1 TT
166975 GAACCTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.07, C:0.03, G:0.07, T:0.83
Consensus pattern (14 bp):
TTTAGTCTTTTTTT
Found at i:170787 original size:144 final size:143
Alignment explanation
Indices: 170589--171030 Score: 559
Period size: 144 Copynumber: 3.1 Consensus size: 143
170579 GGGAGTGGGC
* * * * * * * *
170589 CCAA-AAGCATATTGGAGGATAGATCCAGTGTAACCAAATTCGTTAGCCTACCAATTTCTTGTGG
1 CCAACAAGCATATTAGAAGATAGATCCAATGTAATCAAATTTGTCAGTCTCCCAATTTCTTGTGG
170653 AATGGATCCATTAAGTTGGTTATGC-TGAAGGAGCAACGACCCTAGATTGGTTACATTGTTGACA
66 AATGGATCCATTAAGTTGGTT-TGCATGAAGGAGCAACGACCCTAGATTGGTTA-ATTGTTGACA
170717 GAAGATGGGATTGGA
129 GAAGATGGGATTGGA
*
170732 CCAACAAGCATATTAAAAGATAGATCCAATGTAATCAAATTTGTCAGTCTCCCAATTTCTTGTGG
1 CCAACAAGCATATTAGAAGATAGATCCAATGTAATCAAATTTGTCAGTCTCCCAATTTCTTGTGG
* * * * * ** * *
170797 AATGGGTCCATTAAGTTGGTTTCCATAAAGAACCAACGATGCAAGATTGGTCAAGTTGTTGACAG
66 AATGGATCCATTAAGTTGGTTTGCATGAAGGAGCAACGACCCTAGATTGGTTAA-TTGTTGACAG
170862 AAGATGGGATTGGA
130 AAGATGGGATTGGA
* *
170876 CCAACAAG-ATTATTAGAAGATAGATTCAATGTAATCAAATTTGTCAGTCTCCCAATTTCTCGTG
1 CCAACAAGCA-TATTAGAAGATAGATCCAATGTAATCAAATTTGTCAGTCTCCCAATTTCTTGTG
* ** * * * *
170940 GAATGGATCCATTAAGTTGG-TTGCCTTGAAGGAGCAACGACTGTAGATTAGTTAGGTTGGTGAT
65 GAATGGATCCATTAAGTTGGTTTG-CATGAAGGAGCAACGACCCTAGATTGGTTA-ATTGTTGAC
171004 AGAAGATGGGATTGGA
128 AGAAGATGGGATTGGA
171020 CCAACAAGCAT
1 CCAACAAGCAT
171031 GTTGCTTGAG
Statistics
Matches: 256, Mismatches: 36, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
143 10 0.04
144 245 0.96
145 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.29
Consensus pattern (143 bp):
CCAACAAGCATATTAGAAGATAGATCCAATGTAATCAAATTTGTCAGTCTCCCAATTTCTTGTGG
AATGGATCCATTAAGTTGGTTTGCATGAAGGAGCAACGACCCTAGATTGGTTAATTGTTGACAGA
AGATGGGATTGGA
Found at i:176659 original size:6 final size:6
Alignment explanation
Indices: 176645--176678 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
176635 GCTTCTTGCC
*
176645 CTTGTAG CTTGAG CTTGAG CTCGAG CTTGAG CTT
1 CTTG-AG CTTGAG CTTGAG CTTGAG CTTGAG CTT
176679 TATTTGCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
6 21 0.84
7 4 0.16
ACGTcount: A:0.15, C:0.21, G:0.29, T:0.35
Consensus pattern (6 bp):
CTTGAG
Found at i:180610 original size:17 final size:17
Alignment explanation
Indices: 180588--180640 Score: 97
Period size: 17 Copynumber: 3.1 Consensus size: 17
180578 NNNNNNNNNN
*
180588 AAAGATATGGGTATTAG
1 AAAGATATGGGTATCAG
180605 AAAGATATGGGTATCAG
1 AAAGATATGGGTATCAG
180622 AAAGATATGGGTATCAG
1 AAAGATATGGGTATCAG
180639 AA
1 AA
180641 TCTGAGATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.43, C:0.04, G:0.28, T:0.25
Consensus pattern (17 bp):
AAAGATATGGGTATCAG
Found at i:183882 original size:24 final size:24
Alignment explanation
Indices: 183848--183896 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
183838 CATTAGTTCC
* *
183848 TTTAATTATTTCTATATACT-ATTA
1 TTTAATGATTTATAT-TACTAATTA
183872 TTTAATGATTTATATTACTAATTA
1 TTTAATGATTTATATTACTAATTA
183896 T
1 T
183897 AGTAAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.57
Consensus pattern (24 bp):
TTTAATGATTTATATTACTAATTA
Found at i:187821 original size:18 final size:18
Alignment explanation
Indices: 187798--187844 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
187788 AAACATGAGT
* *
187798 TGAGCTCGCAACTTTCAA
1 TGAGCTTGCAACTTTAAA
187816 TGAGCTTGCAACTTTAAA
1 TGAGCTTGCAACTTTAAA
187834 TGAGCTTGCAA
1 TGAGCTTGCAA
187845 GTGTAGAGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (18 bp):
TGAGCTTGCAACTTTAAA
Found at i:197818 original size:22 final size:22
Alignment explanation
Indices: 197790--197834 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
197780 TAAAACAGGT
* *
197790 CTTTAGCGGCGTTTTTTTATGC
1 CTTTAGCGGCGCTTTTTAATGC
197812 CTTTAGCGGCGCTTTTTAATGC
1 CTTTAGCGGCGCTTTTTAATGC
197834 C
1 C
197835 GCTAAAAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.44
Consensus pattern (22 bp):
CTTTAGCGGCGCTTTTTAATGC
Found at i:198019 original size:43 final size:42
Alignment explanation
Indices: 197922--198232 Score: 345
Period size: 43 Copynumber: 7.3 Consensus size: 42
197912 TTATTTCTAT
* * *
197922 AAACGCCGCTATAGAGCAAGACCTTTAGTGGCGC-TTTTCCAC
1 AAACGCCGCTATAGA-TAGGACCTTTAGCGGCGCTTTTTCCAC
* * *
197964 AAACGTCACTATAGAGTAGGACCTTTAGCAGCGCTTTTTCCAC
1 AAACGCCGCTATAGA-TAGGACCTTTAGCGGCGCTTTTTCCAC
* * * *
198007 AAACGCCGCTATAGAGCAGGACCTTTAACGGCTCTTTTTGCAC
1 AAACGCCGCTATAGA-TAGGACCTTTAGCGGCGCTTTTTCCAC
* * * * **
198050 AAATGCCACTATAGACCAGGACCTTTAGCGACGCTTTTTATAC
1 AAACGCCGCTATAGA-TAGGACCTTTAGCGGCGCTTTTTCCAC
* *
198093 AAACGCCGCTATAGATCAGGACCTTTAGTGGCGCTTTTCCCAC
1 AAACGCCGCTATAGAT-AGGACCTTTAGCGGCGCTTTTTCCAC
** *
198136 CTACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGAT-AGGACCTTTAGCGGCGCTTTTTCCAC
* *
198179 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTACCAC
1 AAACGCCGCTATAGAT-AGGACCTTTAGCGGCGCTTTTTCCAC
198222 AAACGCCGCTA
1 AAACGCCGCTA
198233 AAAACATATC
Statistics
Matches: 231, Mismatches: 36, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
42 28 0.12
43 203 0.88
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (42 bp):
AAACGCCGCTATAGATAGGACCTTTAGCGGCGCTTTTTCCAC
Found at i:198159 original size:129 final size:128
Alignment explanation
Indices: 197922--198232 Score: 390
Period size: 129 Copynumber: 2.4 Consensus size: 128
197912 TTATTTCTAT
* * * * * *
197922 AAACGCCGCTATAGAGCAAGACCTTTAGTGGCGCTTTTCCACAAACGTCACTATAGAGTAGGACC
1 AAACGCCACTATAGACCAAGACCTTTAGCGGCGCTTTTACACAAACGCCGCTATAGAGTAGGACC
* * **
197987 TTTAGCAGCGCTTTTTCCACAAACGCCGCTATAGAGCAGGACCTTTAACGGCTCTTTTTGCAC
66 TTTAGCAGCGCTTTTCCCACAAACGCCGCTATAGAGCAGGACCTTTAACGGCGCTTTTCCCAC
* * * *
198050 AAATGCCACTATAGACCAGGACCTTTAGCGACGCTTTTTATACAAACGCCGCTATAGA-TCAGGA
1 AAACGCCACTATAGACCAAGACCTTTAGCGGCGC-TTTTACACAAACGCCGCTATAGAGT-AGGA
** ** * *
198114 CCTTTAGTGGCGCTTTTCCCACCTACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
64 CCTTTAGCAGCGCTTTTCCCACAAACGCCGCTATAGAGCAGGACCTTTAACGGCGCTTTTCCCAC
* *
198179 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTACCACAAACGCCGCTA
1 AAACGCCACTATAGACCAAGACCTTTAGCGGCGCTTTTA-CACAAACGCCGCTA
198233 AAAACATATC
Statistics
Matches: 154, Mismatches: 26, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
128 34 0.22
129 120 0.78
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (128 bp):
AAACGCCACTATAGACCAAGACCTTTAGCGGCGCTTTTACACAAACGCCGCTATAGAGTAGGACC
TTTAGCAGCGCTTTTCCCACAAACGCCGCTATAGAGCAGGACCTTTAACGGCGCTTTTCCCAC
Found at i:198232 original size:86 final size:85
Alignment explanation
Indices: 197922--198228 Score: 391
Period size: 86 Copynumber: 3.6 Consensus size: 85
197912 TTATTTCTAT
* *
197922 AAACGCCGCTATAGAGCAAGACCTTTAGTGGCGCTTTTCCACAAACGTCACTATAGAGT-AGGAC
1 AAACGCCGCTATAGAGCAAGACCTTTAGCGGCGCTTTTCCACAAACGCCACTATAGA-TCAGGAC
*
197986 CTTTAGCAGCGCTTTTTCCAC
65 CTTTAGCGGCGCTTTTTCCAC
* * * * * *
198007 AAACGCCGCTATAGAGCAGGACCTTTAACGGCTCTTTTTGCACAAATGCCACTATAGACCAGGAC
1 AAACGCCGCTATAGAGCAAGACCTTTAGCGGCGC-TTTTCCACAAACGCCACTATAGATCAGGAC
* **
198072 CTTTAGCGACGCTTTTTATAC
65 CTTTAGCGGCGCTTTTTCCAC
* * * ** *
198093 AAACGCCGCTATAGATCAGGACCTTTAGTGGCGCTTTTCCCACCTACGCCGCTATAGATCAGGAC
1 AAACGCCGCTATAGAGCAAGACCTTTAGCGGCGCTTTT-CCACAAACGCCACTATAGATCAGGAC
*
198158 CTTTAGCGGCGCTTTTCCCAC
65 CTTTAGCGGCGCTTTTTCCAC
*
198179 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTACCACAAACGCC
1 AAACGCCGCTATAGAGCAAGACCTTTAGCGGCGCTTTT-CCACAAACGCC
198229 GCTAAAAACA
Statistics
Matches: 188, Mismatches: 31, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
85 34 0.18
86 154 0.82
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (85 bp):
AAACGCCGCTATAGAGCAAGACCTTTAGCGGCGCTTTTCCACAAACGCCACTATAGATCAGGACC
TTTAGCGGCGCTTTTTCCAC
Found at i:202925 original size:82 final size:84
Alignment explanation
Indices: 202834--203075 Score: 339
Period size: 89 Copynumber: 2.8 Consensus size: 84
202824 CCAAACCACA
202834 AACCCCTAAATC-TTATTTAATATATAAATTAGAAAACACTAATTAATCTAAATCCTAAACCCTA
1 AACCCCTAAA-CATTATTTAATATATAAATTA-AAAACACTAATTAATCTAAATCCTAAACCCTA
* * *
202898 ACCTTAGCCTGAAT-C-A-CT
64 ACCTGACCCTAAATCCAACCT
202916 AACCCCTAAACATTATTTAATATATAAATTAAAAAGCACTAATTAATCTAAATCCTAAACCCTAA
1 AACCCCTAAACATTATTTAATATATAAATTAAAAA-CACTAATTAATCTAAATCCTAAACCCTAA
*
202981 CCCGACCCTAAATCCCTAACCCCT
65 CCTGACCCTAAAT-CC-AA--CCT
*
203005 AACCCCTAAACATTATTTAATATATAAATTAAAACACACTAATTAATCTAAACCCTAAACCCTAA
1 AACCCCTAAACATTATTTAATATATAAATTAAAA-ACACTAATTAATCTAAATCCTAAACCCTAA
203070 CCTGAC
65 CCTGAC
203076 GCCGAATCCA
Statistics
Matches: 144, Mismatches: 6, Indels: 13
0.88 0.04 0.08
Matches are distributed among these distances:
81 5 0.03
82 67 0.47
84 1 0.01
86 1 0.01
89 69 0.48
90 1 0.01
ACGTcount: A:0.44, C:0.26, G:0.02, T:0.28
Consensus pattern (84 bp):
AACCCCTAAACATTATTTAATATATAAATTAAAAACACTAATTAATCTAAATCCTAAACCCTAAC
CTGACCCTAAATCCAACCT
Found at i:203175 original size:14 final size:15
Alignment explanation
Indices: 203158--203191 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
203148 CTTAAATCAA
203158 AATCTCTAA-TCCAT
1 AATCTCTAATTCCAT
*
203172 AATCCCTAATTCCAT
1 AATCTCTAATTCCAT
203187 AATCT
1 AATCT
203192 ATAAACCTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.35, C:0.29, G:0.00, T:0.35
Consensus pattern (15 bp):
AATCTCTAATTCCAT
Found at i:203744 original size:41 final size:41
Alignment explanation
Indices: 203687--203795 Score: 173
Period size: 41 Copynumber: 2.6 Consensus size: 41
203677 NNNNNNNNNN
203687 GCGCTTCTTCAAAAACGCCGCTAAAGATCTGAGCATTAGCA
1 GCGCTTCTTCAAAAACGCCGCTAAAGATCTGAGCATTAGCA
**
203728 GCGCTTCTTCAAAAACGCCGCTAAAGATCTGAGCATTAGTG
1 GCGCTTCTTCAAAAACGCCGCTAAAGATCTGAGCATTAGCA
* *
203769 GCGCTTTTTTTAAAAACGCCGCTAAAG
1 GCGC-TTCTTCAAAAACGCCGCTAAAG
203796 CCCTGAAAGG
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
41 43 0.68
42 20 0.32
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (41 bp):
GCGCTTCTTCAAAAACGCCGCTAAAGATCTGAGCATTAGCA
Found at i:225063 original size:16 final size:16
Alignment explanation
Indices: 225032--225062 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
225022 TTTAGGACTG
225032 CTATTTTTAATGTTTT
1 CTATTTTTAATGTTTT
225048 CTATTTTT-ATGTTTT
1 CTATTTTTAATGTTTT
225063 TTTTATTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.16, C:0.06, G:0.06, T:0.71
Consensus pattern (16 bp):
CTATTTTTAATGTTTT
Found at i:225963 original size:17 final size:17
Alignment explanation
Indices: 225916--225974 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
225906 TCACCTAATA
*
225916 GAGCTTGCACCTTTGTT
1 GAGCTTGCACCTTTGGT
* *
225933 GA-CATCGCAGCTTTGGT
1 GAGC-TTGCACCTTTGGT
*
225950 GAGCTTGCATCTTTGGGT
1 GAGCTTGCACCTTT-GGT
225968 GAGCTTG
1 GAGCTTG
225975 TAAATGTGTG
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
16 1 0.03
17 22 0.65
18 11 0.32
ACGTcount: A:0.14, C:0.20, G:0.31, T:0.36
Consensus pattern (17 bp):
GAGCTTGCACCTTTGGT
Found at i:228202 original size:18 final size:19
Alignment explanation
Indices: 228160--228203 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
228150 ACCGGACCGG
*
228160 CGAACTCCCTAAATTTGGT
1 CGAACTCTCTAAATTTGGT
*
228179 -GTACTCTCTAAATTT-GT
1 CGAACTCTCTAAATTTGGT
228196 CGAACTCT
1 CGAACTCT
228204 TCAGGAATGG
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (19 bp):
CGAACTCTCTAAATTTGGT
Found at i:231926 original size:32 final size:30
Alignment explanation
Indices: 231885--231962 Score: 104
Period size: 32 Copynumber: 2.5 Consensus size: 30
231875 TTTTGATGCA
*
231885 TTTTATAATTTTTAAAAAATTTTACAATTTTT
1 TTTTATAATTTTTAAAAAA-TTTA-AATATTT
*
231917 TTTTCTAATTTTTAATAAAATTTAAATATTT
1 TTTTATAATTTTTAA-AAAATTTAAATATTT
231948 TTTTAT-ATTTTTAAA
1 TTTTATAATTTTTAAA
231963 TAGTGTTATT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
29 1 0.02
30 8 0.19
31 11 0.26
32 18 0.43
33 4 0.10
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (30 bp):
TTTTATAATTTTTAAAAAATTTAAATATTT
Found at i:235244 original size:2 final size:2
Alignment explanation
Indices: 235239--235263 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
235229 CAAAAAAATA
235239 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
235264 AGACATGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:236014 original size:30 final size:30
Alignment explanation
Indices: 235979--236060 Score: 96
Period size: 29 Copynumber: 2.8 Consensus size: 30
235969 AACCAAAAAT
* *
235979 ACAAGCCAAAAATGTAAACCAAAGTGACGG
1 ACAAGCCAAAAATGTAAGCCAAAGTGACGA
*
236009 ACAAGCCAAAGAA--TAAGCCAAAGTGGCGA
1 ACAAGCCAAA-AATGTAAGCCAAAGTGACGA
* *
236038 ACAAACCAAAAGTGTAAGCCAAA
1 ACAAGCCAAAAATGTAAGCCAAA
236061 ATGGTAGACA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
28 1 0.02
29 22 0.50
30 19 0.43
31 2 0.05
ACGTcount: A:0.51, C:0.21, G:0.20, T:0.09
Consensus pattern (30 bp):
ACAAGCCAAAAATGTAAGCCAAAGTGACGA
Found at i:240721 original size:23 final size:22
Alignment explanation
Indices: 240695--240749 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
240685 AAAATAGTGG
*
240695 GAAAAAAAACAAGAAAATAGCAA
1 GAAAAAAAACAAGAAAATAAC-A
* *
240718 GAAAAAGAAC-AGCAAATAACA
1 GAAAAAAAACAAGAAAATAACA
*
240739 GTAAAAAAACA
1 GAAAAAAAACA
240750 GTTGGTTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 9 0.35
22 8 0.31
23 9 0.35
ACGTcount: A:0.71, C:0.11, G:0.13, T:0.05
Consensus pattern (22 bp):
GAAAAAAAACAAGAAAATAACA
Found at i:240749 original size:21 final size:21
Alignment explanation
Indices: 240697--240750 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
240687 AATAGTGGGA
*
240697 AAAAAAACAAGAAAATAGCAAG
1 AAAAAAAC-AGAAAATAACAAG
*
240719 AAAAAGAACAGCAAATAAC-AG
1 AAAAA-AACAGAAAATAACAAG
240740 TAAAAAAACAG
1 -AAAAAAACAG
240751 TTGGTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 7 0.25
22 18 0.64
23 3 0.11
ACGTcount: A:0.70, C:0.11, G:0.13, T:0.06
Consensus pattern (21 bp):
AAAAAAACAGAAAATAACAAG
Found at i:241448 original size:29 final size:30
Alignment explanation
Indices: 241416--241477 Score: 90
Period size: 31 Copynumber: 2.1 Consensus size: 30
241406 GTTTCACGTG
*
241416 TATAATT-ATATCAAATTAAAATTCATATA
1 TATAATTAATATCAAATCAAAATTCATATA
*
241445 TATAATTACATATTAAATCAAAATTCATATA
1 TATAATTA-ATATCAAATCAAAATTCATATA
241476 TA
1 TA
241478 ATTTTAAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 7 0.24
31 22 0.76
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (30 bp):
TATAATTAATATCAAATCAAAATTCATATA
Found at i:241478 original size:29 final size:28
Alignment explanation
Indices: 241416--241480 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 28
241406 GTTTCACGTG
*
241416 TATAATTATATCAAATTAAAATTCATATA
1 TATAATTATATCAAATCAAAATTCA-ATA
*
241445 TATAATTACATATTAAATCAAAATTC-ATA
1 TATAATT--ATATCAAATCAAAATTCAATA
241474 TATAATT
1 TATAATT
241481 TTAAGATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 17 0.53
31 15 0.47
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.42
Consensus pattern (28 bp):
TATAATTATATCAAATCAAAATTCAATA
Found at i:248402 original size:20 final size:20
Alignment explanation
Indices: 248377--248415 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
248367 CCAAACACAT
**
248377 AATATTCATTTAATATTATA
1 AATATTCAAATAATATTATA
248397 AATATTCAAATAATATTAT
1 AATATTCAAATAATATTAT
248416 TTAAATAGTT
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:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (20 bp):
AATATTCAAATAATATTATA
Found at i:248496 original size:155 final size:156
Alignment explanation
Indices: 248213--248525 Score: 619
Period size: 155 Copynumber: 2.0 Consensus size: 156
248203 TCTTTAAAAT
248213 AAACACATAATTATTCATTTAATATTATAAATATTCAAATAATATTATTTAAATAGTTATAATTT
1 AAACACATAATTATTCATTTAATATTATAAATATTCAAATAATATTATTTAAATAGTTATAATTT
248278 TTTTTTCAAAAAATCAAATAATATAACTTTTAATTAATTACACCCATTCATTTATTGTTATTGGA
66 TTTTTTCAAAAAATCAAATAATATAACTTTTAATTAATTACACCCATTCATTTATTGTTATTGGA
248343 ACACTATAAATATTTGAAAATGTTCC
131 ACACTATAAATATTTGAAAATGTTCC
248369 AAACACATAA-TATTCATTTAATATTATAAATATTCAAATAATATTATTTAAATAGTTATAATTT
1 AAACACATAATTATTCATTTAATATTATAAATATTCAAATAATATTATTTAAATAGTTATAATTT
248433 TTTTTTCAAAAAATCAAATAATATAACTTTTAATTAATTACACCCATTCATTTATTGTTATTGGA
66 TTTTTTCAAAAAATCAAATAATATAACTTTTAATTAATTACACCCATTCATTTATTGTTATTGGA
248498 ACACTATAAATATTTGAAAATGTTCC
131 ACACTATAAATATTTGAAAATGTTCC
248524 AA
1 AA
248526 CAATCTCCCC
Statistics
Matches: 157, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
155 147 0.94
156 10 0.06
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.42
Consensus pattern (156 bp):
AAACACATAATTATTCATTTAATATTATAAATATTCAAATAATATTATTTAAATAGTTATAATTT
TTTTTTCAAAAAATCAAATAATATAACTTTTAATTAATTACACCCATTCATTTATTGTTATTGGA
ACACTATAAATATTTGAAAATGTTCC
Found at i:257707 original size:2 final size:2
Alignment explanation
Indices: 257702--257862 Score: 322
Period size: 2 Copynumber: 80.5 Consensus size: 2
257692 ATATAGGGTT
257702 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
257744 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
257786 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
257828 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 T
257863 GACATTTTTA
Statistics
Matches: 159, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 159 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:258799 original size:37 final size:36
Alignment explanation
Indices: 258728--258799 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 36
258718 GGAGCGCATC
*
258728 AGTCAGAATAGATCCAAAAGGCTGATGAATTGAATT
1 AGTCAGAATAGATCCAAAAGGCTGATGAACTGAATT
258764 AGTCAGAATAGATCCGAAAAGGCT-ATTGAACTGAAT
1 AGTCAGAATAGATCC-AAAAGGCTGA-TGAACTGAAT
258800 AGAGTTTACT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
36 16 0.48
37 17 0.52
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.24
Consensus pattern (36 bp):
AGTCAGAATAGATCCAAAAGGCTGATGAACTGAATT
Found at i:261482 original size:15 final size:15
Alignment explanation
Indices: 261456--261492 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
261446 TGCCTGAAAG
261456 CATGATGGAGTCTGTA
1 CATGA-GGAGTCTGTA
*
261472 CATGAGGAGTCTGTG
1 CATGAGGAGTCTGTA
261487 CATGAG
1 CATGAG
261493 TTGCATAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.24, C:0.14, G:0.35, T:0.27
Consensus pattern (15 bp):
CATGAGGAGTCTGTA
Found at i:261984 original size:30 final size:30
Alignment explanation
Indices: 261950--262032 Score: 78
Period size: 30 Copynumber: 2.8 Consensus size: 30
261940 TATATGTATC
* * * *
261950 TGGATGCCCTTGTGGTTATTTAATGATGTG
1 TGGATGCCCTTATGGCTATCTAATGATGTA
* *
261980 TGGATGCCTTTATGGCTATCTATTGATGTA
1 TGGATGCCCTTATGGCTATCTAATGATGTA
* *
262010 TGGATG-GCTCTGTGGCTATCTAA
1 TGGATGCCCT-TATGGCTATCTAA
262033 GTCAAGTGGA
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
29 1 0.02
30 41 0.98
ACGTcount: A:0.18, C:0.13, G:0.28, T:0.41
Consensus pattern (30 bp):
TGGATGCCCTTATGGCTATCTAATGATGTA
Found at i:266286 original size:29 final size:30
Alignment explanation
Indices: 266235--266308 Score: 80
Period size: 29 Copynumber: 2.4 Consensus size: 30
266225 CAAATTTTGT
266235 TATATATATACATAAATACATTTTCATAATA
1 TATATATATACAT-AATACATTTTCATAATA
* * *
266266 TATATATGTACAT-ATATATTTTTATAACT-
1 TATATATATACATAATACATTTTCATAA-TA
266295 TATTATATATACAT
1 TA-TATATATACAT
266309 TCATACATAC
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
29 14 0.38
30 11 0.30
31 12 0.32
ACGTcount: A:0.43, C:0.08, G:0.01, T:0.47
Consensus pattern (30 bp):
TATATATATACATAATACATTTTCATAATA
Found at i:266380 original size:29 final size:27
Alignment explanation
Indices: 266326--266382 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
266316 TACGTACTCA
* * *
266326 TATATATATTTTATATATTTTGTAATT
1 TATATACATTTTATATATTATATAATT
266353 TATATACATGTTTATATATCTATATAATT
1 TATATACAT-TTTATATAT-TATATAATT
266382 T
1 T
266383 TACATTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 8 0.32
28 9 0.36
29 8 0.32
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (27 bp):
TATATACATTTTATATATTATATAATT
Found at i:266816 original size:109 final size:109
Alignment explanation
Indices: 266631--266952 Score: 504
Period size: 109 Copynumber: 3.0 Consensus size: 109
266621 ATCCTTTTAA
* * *
266631 AAAAAATTCAAAGTAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAGCGTGCCCTAATGTGCTG
1 AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTG
266696 GGTTTCGATTTTTCTCGTTCGACCAAATAGCCAAATATCCTTTC
66 GGTTTCGATTTTTCTCGTTCGACCAAATAGCCAAATATCCTTTC
* *
266740 AAAAATTTCAAAATAAGGCAATGTTTTGTGTTTGGAAATTCGAGAAAACGTGCCCTAATATGCTG
1 AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTG
* * *
266805 GGTTTCAATTTTTCTCGTTCGAACAAATAGCCAAATATCCTTTT
66 GGTTTCGATTTTTCTCGTTCGACCAAATAGCCAAATATCCTTTC
* * * * *
266849 AGAAATTTTAAAATAAGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACATGCTCTAATGTGCTG
1 AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTG
*
266914 GGTTTCGA--TTTCTCGTTGGACCAAATAGCCAAATATCCT
66 GGTTTCGATTTTTCTCGTTCGACCAAATAGCCAAATATCCT
266953 CTTAAATCTT
Statistics
Matches: 195, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
107 29 0.15
109 166 0.85
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (109 bp):
AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTG
GGTTTCGATTTTTCTCGTTCGACCAAATAGCCAAATATCCTTTC
Found at i:271045 original size:9 final size:9
Alignment explanation
Indices: 271033--271135 Score: 71
Period size: 9 Copynumber: 10.4 Consensus size: 9
271023 GTATTTAATT
271033 AATTTTAAA
1 AATTTTAAA
271042 AATTTTAAA
1 AATTTTAAA
*
271051 AATATATAAAA
1 AAT-T-TTAAA
271062 ATTATTTTAAA
1 A--ATTTTAAA
271073 AATTTTAAA
1 AATTTTAAA
*
271082 AATATTAAA
1 AATTTTAAA
*
271091 ATTATTTAAA
1 AAT-TTTAAA
*
271101 AATGTGTAAA
1 AAT-TTTAAA
* *
271111 CATTATAAAAA
1 AATT-T-TAAA
271122 ATATTTTAAA
1 A-ATTTTAAA
271132 AATT
1 AATT
271136 AATTAAATGC
Statistics
Matches: 73, Mismatches: 13, Indels: 16
0.72 0.13 0.16
Matches are distributed among these distances:
9 34 0.47
10 19 0.26
11 14 0.19
12 4 0.05
13 2 0.03
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (9 bp):
AATTTTAAA
Found at i:271069 original size:31 final size:31
Alignment explanation
Indices: 271029--271135 Score: 141
Period size: 31 Copynumber: 3.5 Consensus size: 31
271019 ATCAGTATTT
271029 AATTAATTTTAAAAATTTTAAAAATATATAAA
1 AATT-ATTTTAAAAATTTTAAAAATATATAAA
271061 AATTATTTTAAAAATTTTAAAAATAT-T-AA
1 AATTATTTTAAAAATTTTAAAAATATATAAA
* *
271090 AATTA-TTTAAAAATGTGTAAACAT-TATAAA
1 AATTATTTTAAAAAT-TTTAAAAATATATAAA
*
271120 AAATATTTTAAAAATT
1 AATTATTTTAAAAATT
271136 AATTAAATGC
Statistics
Matches: 68, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
28 10 0.15
29 15 0.22
30 8 0.12
31 31 0.46
32 4 0.06
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (31 bp):
AATTATTTTAAAAATTTTAAAAATATATAAA
Found at i:271101 original size:50 final size:49
Alignment explanation
Indices: 271037--271134 Score: 117
Period size: 50 Copynumber: 2.0 Consensus size: 49
271027 TTAATTAATT
**
271037 TTAAAAATTTTAAAAATATATAAAAATTATTTTAAAA-ATTTTAAAAATA
1 TTAAAAATTTTAAAAATATATAAAAATTA-TAAAAAATATTTTAAAAATA
* * * *
271086 TTAAAATTATTTAAAAATGTGTAAACATTATAAAAAATATTTTAAAAAT
1 TTAAAAAT-TTTAAAAATATATAAAAATTATAAAAAATATTTTAAAAAT
271135 TAATTAAATG
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
49 12 0.29
50 29 0.71
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (49 bp):
TTAAAAATTTTAAAAATATATAAAAATTATAAAAAATATTTTAAAAATA
Found at i:273576 original size:31 final size:31
Alignment explanation
Indices: 273541--273599 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
273531 CCCTAGTGAA
*
273541 TTAAATAAAAACTTTTGAATAGTTTAGTTAC
1 TTAAATAAAAACTTTTGAATAATTTAGTTAC
*
273572 TTAAATGAAAACTTTTGAATAATTTAGT
1 TTAAATAAAAACTTTTGAATAATTTAGT
273600 GACCAAATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.05, G:0.10, T:0.42
Consensus pattern (31 bp):
TTAAATAAAAACTTTTGAATAATTTAGTTAC
Found at i:274312 original size:31 final size:31
Alignment explanation
Indices: 274251--274307 Score: 77
Period size: 28 Copynumber: 1.9 Consensus size: 31
274241 TTTAACATTT
274251 AAAAATTCAAAAAATATAAAAATTATTTTAA
1 AAAAATTCAAAAAATATAAAAATTATTTTAA
274282 AAAAATT---AAAATATAAAAGA-TATTTT
1 AAAAATTCAAAAAATATAAAA-ATTATTTT
274308 TTTAATATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
28 17 0.68
29 1 0.04
31 7 0.28
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (31 bp):
AAAAATTCAAAAAATATAAAAATTATTTTAA
Found at i:279106 original size:18 final size:18
Alignment explanation
Indices: 279083--279118 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
279073 GAATGACTCA
279083 TATTTCAGAGACAATCTC
1 TATTTCAGAGACAATCTC
*
279101 TATTTCAGAGATAATCTC
1 TATTTCAGAGACAATCTC
279119 CTAGTTAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.36
Consensus pattern (18 bp):
TATTTCAGAGACAATCTC
Found at i:284209 original size:20 final size:19
Alignment explanation
Indices: 284184--284233 Score: 82
Period size: 20 Copynumber: 2.6 Consensus size: 19
284174 AATACAAAAT
284184 AATTCAAAATAATTTTCAAA
1 AATTCAAAATAATTTTC-AA
284204 AATTCAAAATAATTTTCAA
1 AATTCAAAATAATTTTCAA
*
284223 AACTCAAAATA
1 AATTCAAAATA
284234 TTTATAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (19 bp):
AATTCAAAATAATTTTCAA
Found at i:284224 original size:12 final size:10
Alignment explanation
Indices: 284169--284217 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
284159 TCTCTCTCAA
*
284169 CAAAA-AATA
1 CAAAATAATT
284178 CAAAATAATT
1 CAAAATAATT
284188 CAAAATAATTTT
1 CAAAATAA--TT
284200 C-AAA-AATT
1 CAAAATAATT
284208 CAAAATAATT
1 CAAAATAATT
284218 TTCAAAACTC
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
8 3 0.09
9 8 0.24
10 17 0.50
11 3 0.09
12 3 0.09
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (10 bp):
CAAAATAATT
Found at i:288010 original size:109 final size:106
Alignment explanation
Indices: 287873--288072 Score: 346
Period size: 109 Copynumber: 1.9 Consensus size: 106
287863 TTGAGCTCAC
287873 TAACTTGTGGAACTTATGATGTGTATAAGATTTCATAAATTCATGAGTATATTGATAATGAAATT
1 TAACTTGTGGAACTTATGATGTGTATAAGATTTCATAAATTCATG-G-ATA-TGATAATGAAATT
287938 ATGCATCATTTTATAAAAATTGAGTTTAAGATTTCATAAATTCA
63 ATGCATCATTTTATAAAAATTGAGTTTAAGATTTCATAAATTCA
* * *
287982 TAACTTGTGGGACTTATGATGTGTATAAGATTTCATAAATTCATGGGTATGGTAATGAAATTATG
1 TAACTTGTGGAACTTATGATGTGTATAAGATTTCATAAATTCATGGATATGATAATGAAATTATG
288047 CATCATTTTATAAAAATTGAGTTTAA
66 CATCATTTTATAAAAATTGAGTTTAA
288073 AAAAAAGGTA
Statistics
Matches: 88, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
106 41 0.47
107 2 0.02
108 1 0.01
109 44 0.50
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.40
Consensus pattern (106 bp):
TAACTTGTGGAACTTATGATGTGTATAAGATTTCATAAATTCATGGATATGATAATGAAATTATG
CATCATTTTATAAAAATTGAGTTTAAGATTTCATAAATTCA
Found at i:292617 original size:23 final size:23
Alignment explanation
Indices: 292591--292636 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
292581 TTCAAGTTGT
292591 ACGAAGCTATTCAATACTAAGTC
1 ACGAAGCTATTCAATACTAAGTC
292614 ACGAAGCTATTCAATACTAAGTC
1 ACGAAGCTATTCAATACTAAGTC
292637 GTGATACAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.26
Consensus pattern (23 bp):
ACGAAGCTATTCAATACTAAGTC
Found at i:303043 original size:15 final size:15
Alignment explanation
Indices: 303024--303080 Score: 96
Period size: 15 Copynumber: 3.8 Consensus size: 15
303014 TTGACTTGCT
*
303024 ATCTTTTGATTTTTC
1 ATCTTTTGATTTGTC
*
303039 GTCTTTTGATTTGTC
1 ATCTTTTGATTTGTC
303054 ATCTTTTGATTTGTC
1 ATCTTTTGATTTGTC
303069 ATCTTTTGATTT
1 ATCTTTTGATTT
303081 TTCGCCATTG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 39 1.00
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.63
Consensus pattern (15 bp):
ATCTTTTGATTTGTC
Found at i:303047 original size:30 final size:30
Alignment explanation
Indices: 303013--303077 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
303003 GACTTCATGC
* *
303013 TTTGACTTG-CTATCTTTTGATTTTTCGTCT
1 TTTGACTTGTC-ATCTTTTGATTTGTCATCT
*
303043 TTTGATTTGTCATCTTTTGATTTGTCATCT
1 TTTGACTTGTCATCTTTTGATTTGTCATCT
303073 TTTGA
1 TTTGA
303078 TTTTTCGCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 30 0.97
31 1 0.03
ACGTcount: A:0.12, C:0.14, G:0.14, T:0.60
Consensus pattern (30 bp):
TTTGACTTGTCATCTTTTGATTTGTCATCT
Found at i:303602 original size:29 final size:28
Alignment explanation
Indices: 303543--303603 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
303533 CATTTCCAAA
**
303543 AAAAATTACGGAAATGGGCCATTTTGTT
1 AAAAATTACGGAAATGGGCCATTTTCCT
*
303571 AAAAATTACTGGAAA-GGGTCGATTTTCCT
1 AAAAATTAC-GGAAATGGG-CCATTTTCCT
303600 AAAA
1 AAAA
303604 CGTGCTGAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 12 0.43
29 16 0.57
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (28 bp):
AAAAATTACGGAAATGGGCCATTTTCCT
Found at i:303783 original size:32 final size:30
Alignment explanation
Indices: 303722--303784 Score: 72
Period size: 32 Copynumber: 2.0 Consensus size: 30
303712 GGCCAATTAG
* * *
303722 GGTTTAGGTTTTTTTTATTTTAAGTGTTTA
1 GGTTTAGGTTTATTTAATTTTAAGGGTTTA
*
303752 GGTTTAGGGTTATATTTAATTTTTAGGGTTTA
1 GGTTTA-GGTT-TATTTAATTTTAAGGGTTTA
303784 G
1 G
303785 AGGTTCTGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 6 0.22
31 4 0.15
32 17 0.63
ACGTcount: A:0.19, C:0.00, G:0.24, T:0.57
Consensus pattern (30 bp):
GGTTTAGGTTTATTTAATTTTAAGGGTTTA
Found at i:303843 original size:29 final size:29
Alignment explanation
Indices: 303786--303867 Score: 103
Period size: 29 Copynumber: 2.8 Consensus size: 29
303776 AGGGTTTAGA
303786 GGTTCTGAAAAAAATAA-TTTGTACAGGATG
1 GGTTCTG-AAAAAATAATTTTG-ACAGGATG
**
303816 GGTTCTGAAAAAATAATTTTGAGGGGATG
1 GGTTCTGAAAAAATAATTTTGACAGGATG
* *
303845 GGTTTTGAAGAAATAATTTTGAC
1 GGTTCTGAAAAAATAATTTTGAC
303868 GAGATGAGTT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 35 0.76
30 11 0.24
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.33
Consensus pattern (29 bp):
GGTTCTGAAAAAATAATTTTGACAGGATG
Found at i:313517 original size:24 final size:25
Alignment explanation
Indices: 313479--313540 Score: 97
Period size: 25 Copynumber: 2.5 Consensus size: 25
313469 ATTTTTGTCT
* *
313479 TTTTTTTTCACCCAACTATCTTGGA
1 TTTTTTGTCACCAAACTATCTTGGA
313504 TTTTTTGTCACCAAACTATCTTGGA
1 TTTTTTGTCACCAAACTATCTTGGA
*
313529 TTTTTGGTCACC
1 TTTTTTGTCACC
313541 TAAAACCCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.19, C:0.23, G:0.11, T:0.47
Consensus pattern (25 bp):
TTTTTTGTCACCAAACTATCTTGGA
Found at i:316012 original size:57 final size:57
Alignment explanation
Indices: 315924--316032 Score: 184
Period size: 57 Copynumber: 1.9 Consensus size: 57
315914 AATTCGGATT
*
315924 ACCCGTCCGGGCTAAATCTATTTTCCACATATTCTTCGGGAGGGCTATATCAAGATC
1 ACCCGTCCGGGATAAATCTATTTTCCACATATTCTTCGGGAGGGCTATATCAAGATC
*
315981 ACCCGTCCGGGATAGATCT-TTTTCACACATATTCTTCGGGAGGGCTATATCA
1 ACCCGTCCGGGATAAATCTATTTTC-CACATATTCTTCGGGAGGGCTATATCA
316033 GGATAGGATC
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
56 5 0.10
57 44 0.90
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (57 bp):
ACCCGTCCGGGATAAATCTATTTTCCACATATTCTTCGGGAGGGCTATATCAAGATC
Found at i:330020 original size:20 final size:20
Alignment explanation
Indices: 329995--330032 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
329985 GTAAAAATAT
329995 CAAATTTGTTGAGTAATTAC
1 CAAATTTGTTGAGTAATTAC
330015 CAAATTTGTTGAGTAATT
1 CAAATTTGTTGAGTAATT
330033 TTCTGCATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.08, G:0.16, T:0.42
Consensus pattern (20 bp):
CAAATTTGTTGAGTAATTAC
Found at i:330926 original size:8 final size:8
Alignment explanation
Indices: 330877--330934 Score: 63
Period size: 7 Copynumber: 7.8 Consensus size: 8
330867 CAGTTTTAAC
330877 ATTTTATTA
1 ATTTTA-TA
330886 A-TTTATA
1 ATTTTATA
330893 A-TTTAT-
1 ATTTTATA
330899 ATTTTAT-
1 ATTTTATA
330906 ATTTTAT-
1 ATTTTATA
330913 ATTTTATA
1 ATTTTATA
330921 ATTTTATA
1 ATTTTATA
*
330929 AATTTA
1 ATTTTA
330935 AAAAGATTAA
Statistics
Matches: 46, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
6 1 0.02
7 27 0.59
8 17 0.37
9 1 0.02
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
ATTTTATA
Found at i:336692 original size:2 final size:2
Alignment explanation
Indices: 336685--336713 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
336675 TGTTGGGTTT
336685 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 T
336714 GCAGGAAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:339094 original size:15 final size:16
Alignment explanation
Indices: 339068--339098 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
339058 AAATTTGATT
339068 TAAAATATACCAAAAA
1 TAAAATATACCAAAAA
339084 TAAAA-ATACCAAAAA
1 TAAAATATACCAAAAA
339099 CTAATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.71, C:0.13, G:0.00, T:0.16
Consensus pattern (16 bp):
TAAAATATACCAAAAA
Found at i:342543 original size:18 final size:18
Alignment explanation
Indices: 342520--342555 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
342510 TGATGGTAGG
342520 ACAACAGAATTCGTTTCC
1 ACAACAGAATTCGTTTCC
342538 ACAACAGAATTCGTTTCC
1 ACAACAGAATTCGTTTCC
342556 GGTGATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.28, G:0.11, T:0.28
Consensus pattern (18 bp):
ACAACAGAATTCGTTTCC
Found at i:347418 original size:14 final size:14
Alignment explanation
Indices: 347399--347426 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
347389 ATATTAATCA
347399 AAAGTTATAAAAGT
1 AAAGTTATAAAAGT
347413 AAAGTTATAAAAGT
1 AAAGTTATAAAAGT
347427 GTATGTTTCA
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:0.57, C:0.00, G:0.14, T:0.29
Consensus pattern (14 bp):
AAAGTTATAAAAGT
Found at i:348352 original size:22 final size:19
Alignment explanation
Indices: 348309--348353 Score: 54
Period size: 22 Copynumber: 2.2 Consensus size: 19
348299 ATATTTTTTT
*
348309 AAAAATTATAAAAATTTCA
1 AAAAATTATAAAAAGTTCA
348328 AAAAATATATAAAGAAAGTTCA
1 AAAAAT-TAT-AA-AAAGTTCA
348350 AAAA
1 AAAA
348354 TTAAAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 6 0.27
20 3 0.14
21 2 0.09
22 11 0.50
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.24
Consensus pattern (19 bp):
AAAAATTATAAAAAGTTCA
Found at i:348983 original size:21 final size:21
Alignment explanation
Indices: 348954--349002 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
348944 ATAGAATTCA
*
348954 ATTTAATAACTAAAAATAAAT
1 ATTTAATAAATAAAAATAAAT
* * *
348975 ATTTGATAAATAAAATTAATT
1 ATTTAATAAATAAAAATAAAT
348996 A-TTAATA
1 ATTTAATA
349003 TTTTTATAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (21 bp):
ATTTAATAAATAAAAATAAAT
Found at i:353792 original size:14 final size:15
Alignment explanation
Indices: 353770--353807 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
353760 CAATCAAACA
353770 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
353784 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
353799 ACAGAAAAT
1 CCAGAAAAT
353808 TAAAACATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:353834 original size:34 final size:35
Alignment explanation
Indices: 353774--353841 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 35
353764 CAAACACCAG
*
353774 AAAATATTTTCCAGTAAATCATTTTACAGAAAATT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAATT
* * *
353809 AAAACATTTTCCCG-AAATTATTTTACGGAAAAT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAT
353842 ATTTTACTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.35
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAATT
Found at i:356775 original size:3 final size:3
Alignment explanation
Indices: 356767--356793 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
356757 TTTAGCAATT
356767 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
356794 AAACCCTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:364697 original size:17 final size:16
Alignment explanation
Indices: 364672--364726 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
364662 TATTGGTTTC
*
364672 TTGTGTTGTTGCTGGTT
1 TTGTTTTGTTGC-GGTT
*
364689 TTGTTTTGTTTCGGTT
1 TTGTTTTGTTGCGGTT
* * *
364705 TTTTTTTTTTGAGGTT
1 TTGTTTTGTTGCGGTT
364721 TTGTTT
1 TTGTTT
364727 AAGCATTAGC
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
16 21 0.68
17 10 0.32
ACGTcount: A:0.02, C:0.04, G:0.25, T:0.69
Consensus pattern (16 bp):
TTGTTTTGTTGCGGTT
Found at i:373533 original size:15 final size:17
Alignment explanation
Indices: 373515--373560 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 17
373505 TTGCCATAAA
373515 AATATTTAAAA-AA-AT
1 AATATTTAAAATAAGAT
*
373530 AATATTCAAAATAAGAT
1 AATATTTAAAATAAGAT
*
373547 AATTATTTTAAATA
1 AA-TATTTAAAATA
373561 TCTCTACATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
15 10 0.40
16 2 0.08
17 4 0.16
18 9 0.36
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (17 bp):
AATATTTAAAATAAGAT
Done.