Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold761
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: 32122
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Found at i:1984 original size:19 final size:20
Alignment explanation
Indices: 1941--1991 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
1931 TACAGGCTAA
**
1941 TGTATCGATACATTTTTTGG
1 TGTATCGATACATACTTTGG
1961 TGTATCGATACATACTTT-G
1 TGTATCGATACATACTTTGG
1980 TGTATCGATACA
1 TGTATCGATACA
1992 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATACTTTGG
Found at i:6061 original size:79 final size:77
Alignment explanation
Indices: 5955--6156 Score: 219
Period size: 78 Copynumber: 2.6 Consensus size: 77
5945 AAAAATTTAA
* * *
5955 TATTTTGGAGATAAAGAT-AGGGTTGGAGTATCCTTTCAAAAATAAT-GAGGCTAGAGTATCCCC
1 TATTTTGGAAATAAA-ATCGGGGTTGGAGTATCCCTT-AAAAATAATAG-GGCTAGAGTA-CCCC
*
6018 AATTCTGGAAAATCGG
62 AATTATGGAAAATCGG
* * * * *
6034 TGTTTTGGAAATAAAATCGGGGTTGGAGTATCCCCTTAGAAATAATAGGGTTGGAGTACCCCGAT
1 TATTTTGGAAATAAAATCGGGGTTGGAGTAT-CCCTTAAAAATAATAGGGCTAGAGTACCCCAAT
*
6099 TATGGAAAATTGG
65 TATGGAAAATCGG
* * *
6112 TATTTTAGAAATAAAATCGGGGTTAGAGTATCCCCTAGAAAATAA
1 TATTTTGGAAATAAAATCGGGGTTGGAGTATCCCTTA-AAAATAA
6157 CGGGGTTGGA
Statistics
Matches: 104, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
77 5 0.05
78 53 0.51
79 41 0.39
80 5 0.05
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (77 bp):
TATTTTGGAAATAAAATCGGGGTTGGAGTATCCCTTAAAAATAATAGGGCTAGAGTACCCCAATT
ATGGAAAATCGG
Found at i:6141 original size:78 final size:79
Alignment explanation
Indices: 6008--6174 Score: 239
Period size: 78 Copynumber: 2.1 Consensus size: 79
5998 AATGAGGCTA
* * * *
6008 GAGTATCCCCAATTCTGGAAAATCGGTGTTTTGGAAATAAAATCGGGGTTGGAGTATCCCCTTAG
1 GAGTATCCCCAATTATGGAAAATCGGTATTTTAGAAATAAAATCGGGGTTAGAGTATCCCC-TAG
*
6073 -AAATAATAGGGTTG
65 AAAATAACAGGGTTG
* *
6087 GAGTA-CCCCGATTATGGAAAATTGGTATTTTAGAAATAAAATCGGGGTTAGAGTATCCCCTAGA
1 GAGTATCCCCAATTATGGAAAATCGGTATTTTAGAAATAAAATCGGGGTTAGAGTATCCCCTAGA
*
6151 AAATAACGGGGTTG
66 AAATAACAGGGTTG
6165 GAGTATCCCC
1 GAGTATCCCC
6175 TAGAAAATAA
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
77 3 0.04
78 66 0.85
79 9 0.12
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.28
Consensus pattern (79 bp):
GAGTATCCCCAATTATGGAAAATCGGTATTTTAGAAATAAAATCGGGGTTAGAGTATCCCCTAGA
AAATAACAGGGTTG
Found at i:6160 original size:28 final size:28
Alignment explanation
Indices: 6129--6202 Score: 139
Period size: 28 Copynumber: 2.6 Consensus size: 28
6119 GAAATAAAAT
*
6129 CGGGGTTAGAGTATCCCCTAGAAAATAA
1 CGGGGTTGGAGTATCCCCTAGAAAATAA
6157 CGGGGTTGGAGTATCCCCTAGAAAATAA
1 CGGGGTTGGAGTATCCCCTAGAAAATAA
6185 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
6203 GATTGTGAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCTAGAAAATAA
Found at i:6271 original size:107 final size:107
Alignment explanation
Indices: 6051--6388 Score: 477
Period size: 107 Copynumber: 3.2 Consensus size: 107
6041 GAAATAAAAT
** * *
6051 CGGGGTTGGAGTATCCCCTTAG-AAATAATAGGGTTGGAGTA-CCCCGATTATGGAAAATTGGTA
1 CGGGGTTGGAGTATCCCC-TAGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTA
* *
6114 TTTTAGAAATAAAA-TCGGGGTTAGAGTATCCCCTAGAAAATAA
65 TTTTGGAAATAAAACT-GGGGTTAGAGTATCCCCTCGAAAATAA
* * *
6157 CGGGGTTGGAGTATCCCCTAGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAACTGATGT
1 CGGGGTTGGAGTATCCCCTAGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTAT
* *
6222 TTTGGAAATAAAACTGGGGTTGGAGTATTCCCTCGAAAATAA
66 TTTGGAAATAAAACTGGGGTTAGAGTATCCCCTCGAAAATAA
* * * *
6264 CGAGGTTGGAGTATTCCCTCGAAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATTGGTAT
1 CGGGGTTGGAGTATCCCCTAGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTAT
6329 TTTGGAAATAAAACTGGGGTTAGAGTATCCCCTC-AGAAATAA
66 TTTGGAAATAAAACTGGGGTTAGAGTATCCCCTCGA-AAATAA
*
6371 TGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
6389 GATTGTAAAA
Statistics
Matches: 205, Mismatches: 23, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
105 3 0.01
106 36 0.18
107 165 0.80
108 1 0.00
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (107 bp):
CGGGGTTGGAGTATCCCCTAGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTAT
TTTGGAAATAAAACTGGGGTTAGAGTATCCCCTCGAAAATAA
Found at i:6272 original size:28 final size:28
Alignment explanation
Indices: 6239--6305 Score: 134
Period size: 28 Copynumber: 2.4 Consensus size: 28
6229 ATAAAACTGG
6239 GGTTGGAGTATTCCCTCGAAAATAACGA
1 GGTTGGAGTATTCCCTCGAAAATAACGA
6267 GGTTGGAGTATTCCCTCGAAAATAACGA
1 GGTTGGAGTATTCCCTCGAAAATAACGA
6295 GGTTGGAGTAT
1 GGTTGGAGTAT
6306 CCCCGATTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.27
Consensus pattern (28 bp):
GGTTGGAGTATTCCCTCGAAAATAACGA
Found at i:6329 original size:79 final size:75
Alignment explanation
Indices: 6254--6465 Score: 244
Period size: 79 Copynumber: 2.7 Consensus size: 75
6244 GAGTATTCCC
* * *
6254 TCGAAAATAACGAGGTTGGAGTATTCCCTCGAAAATAACGAGGTTGGAGTATCCCCGATTGTGAA
1 TCGAAAATAACGAGGTTAGAGTATCCCCTC-AAAATAACGAGGTTGGAGTATCCCCGATTGTAAA
6319 AAATTGGTATTT
65 AAATTGGTA-TT
* * * * *
6331 TGGAAATAAAACTGGGGTTAGAGTATCCCCTCAGAAATAATGGGGTTGGAGTATCCCCGATTGTA
1 TCGAAA-ATAAC-GAGGTTAGAGTATCCCCTCA-AAATAACGAGGTTGGAGTATCCCCGATTGTA
*
6396 AAAAATTGGTGTT
63 AAAAATTGGTATT
* *
6409 TTGAAAATAAAACCGAGTTTAGAGTATCCCCTCAAAAATAACGAGGTTGGAGTATCC
1 TCGAAAAT--AA-CGAGGTTAGAGTATCCCCTC-AAAATAACGAGGTTGGAGTATCC
6466 TCTCAGAAAT
Statistics
Matches: 113, Mismatches: 15, Indels: 12
0.81 0.11 0.09
Matches are distributed among these distances:
77 6 0.05
78 12 0.11
79 93 0.82
80 2 0.02
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (75 bp):
TCGAAAATAACGAGGTTAGAGTATCCCCTCAAAATAACGAGGTTGGAGTATCCCCGATTGTAAAA
AATTGGTATT
Found at i:6411 original size:186 final size:187
Alignment explanation
Indices: 6157--6651 Score: 660
Period size: 186 Copynumber: 2.6 Consensus size: 187
6147 TAGAAAATAA
* * * * *
6157 CGGGGTTGGAGTATCCCCTAGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAACTGATGT
1 CGGGGTTAGAGTATCCCCTAGAAAATAATGGGGTTGGAGTATCCCCGATTGTAAAAAAATGGTGT
*
6222 TTTGGAAATAAAACTGGGGTTGGAGTATTCCCTCGAAAATAACGAGGTTGGAGTATTCC-CTC-G
66 TTTGGAAATAAAACTGGGGTTGGAGTATCCCCTC-AAAATAACGAGGTTGGAGTATTCCTCTCAG
** * *
6285 AAAATAACGAGGTTGGAGTATCCCCGATTGTG-AAAAATTGGTATTTTGGAAATAAAAC
130 -AAATAACGAAATTAGAGTATCCCCGATTGTGAAAAAATTGATATTTTGGAAATAAAAC
* *
6343 TGGGGTTAGAGTATCCCCTCAG-AAATAATGGGGTTGGAGTATCCCCGATTGTAAAAAATTGGTG
1 CGGGGTTAGAGTATCCCCT-AGAAAATAATGGGGTTGGAGTATCCCCGATTGTAAAAAAATGGTG
* * * * *
6407 TTTTGAAAATAAAACCGAGTTTAGAGTATCCCCTCAAAAATAACGAGGTTGGAGTA-TCCTCTCA
65 TTTTGGAAATAAAACTGGGGTTGGAGTATCCCCTC-AAAATAACGAGGTTGGAGTATTCCTCTCA
* *
6471 GAAATAACGAAATTAGAGTATCCCCGATTTTGAAAAAATTGATGTTTTGGAAATAAAAC
129 GAAATAACGAAATTAGAGTATCCCCGATTGTGAAAAAATTGATATTTTGGAAATAAAAC
* * *
6530 CGGGGTTAGAGTATCCCCTTGAAAATAAT-GGGTTAGAGTATCCCCGATTGTGAAAAAAATGGTA
1 CGGGGTTAGAGTATCCCCTAGAAAATAATGGGGTTGGAGTATCCCCGATTGT-AAAAAAATGGTG
* * *
6594 TTTTGGAAATAAAACTAGTGTTGGAGATATCCCCTCAGAAATAACGGGGTTGGAGTAT
65 TTTTGGAAATAAAACTGGGGTTGGAG-TATCCCCTCA-AAATAACGAGGTTGGAGTAT
6652 CCCCGATTGT
Statistics
Matches: 268, Mismatches: 32, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
185 3 0.01
186 156 0.58
187 82 0.31
188 27 0.10
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.28
Consensus pattern (187 bp):
CGGGGTTAGAGTATCCCCTAGAAAATAATGGGGTTGGAGTATCCCCGATTGTAAAAAAATGGTGT
TTTGGAAATAAAACTGGGGTTGGAGTATCCCCTCAAAATAACGAGGTTGGAGTATTCCTCTCAGA
AATAACGAAATTAGAGTATCCCCGATTGTGAAAAAATTGATATTTTGGAAATAAAAC
Found at i:6461 original size:28 final size:28
Alignment explanation
Indices: 6427--6495 Score: 93
Period size: 28 Copynumber: 2.5 Consensus size: 28
6417 AAAACCGAGT
**
6427 TTAGAGTATCCCCTCAAAAATAACGAGG
1 TTAGAGTATCCCCTCAAAAATAACGAAA
* * *
6455 TTGGAGTATCCTCTCAGAAATAACGAAA
1 TTAGAGTATCCCCTCAAAAATAACGAAA
6483 TTAGAGTATCCCC
1 TTAGAGTATCCCC
6496 GATTTTGAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (28 bp):
TTAGAGTATCCCCTCAAAAATAACGAAA
Found at i:6462 original size:107 final size:107
Alignment explanation
Indices: 6345--6574 Score: 309
Period size: 107 Copynumber: 2.1 Consensus size: 107
6335 AATAAAACTG
* *** * *
6345 GGGTTAGAGTATCCCCTCAGAAATAATGGGGTTGGAGTATCCCCGATTGT-AAAAAATTGGTGTT
1 GGGTTAGAGTATCCCCTCAGAAATAACGAAATTAGAGTATCCCCGATTGTGAAAAAATTGATGTT
*
6409 TTGAAAATAAAACCGAGTTTAGAGTATCCCCTCAAAAATAAC
66 TTGAAAATAAAACCGAGGTTAGAGTATCCCCTCAAAAATAAC
* * *
6451 GAGGTTGGAGTATCCTCTCAGAAATAACGAAATTAGAGTATCCCCGATTTTGAAAAAATTGATGT
1 G-GGTTAGAGTATCCCCTCAGAAATAACGAAATTAGAGTATCCCCGATTGTGAAAAAATTGATGT
* * ** *
6516 TTTGGAAATAAAACCGGGGTTAGAGTATCCCCTTGAAAATAAT
65 TTTGAAAATAAAACCGAGGTTAGAGTATCCCCTCAAAAATAAC
6559 GGGTTAGAGTATCCCC
1 GGGTTAGAGTATCCCC
6575 GATTGTGAAA
Statistics
Matches: 105, Mismatches: 17, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
106 1 0.01
107 54 0.51
108 50 0.48
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (107 bp):
GGGTTAGAGTATCCCCTCAGAAATAACGAAATTAGAGTATCCCCGATTGTGAAAAAATTGATGTT
TTGAAAATAAAACCGAGGTTAGAGTATCCCCTCAAAAATAAC
Found at i:6667 original size:159 final size:157
Alignment explanation
Indices: 6453--6837 Score: 430
Period size: 159 Copynumber: 2.5 Consensus size: 157
6443 AAAATAACGA
* *** * *
6453 GGTTGGAGTATCCTCTCAGAAATAACGAAATTAGAGTATCCCCGATTTTGAAAAAATTGATGTTT
1 GGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTG-AAAAATTGATGTTT
* * * * *
6518 TGGAAATAAAACCGGGGTT-AGAGTATCCCCTTGAAAATAATG-GGTTAGAGTATCCCCGATTGT
65 TGGAAATAAAACCGAGGTTGA-AGTATACCCTCG-AAATAACGAGGTTAGAGTATCCCCGATTAT
*
6581 GAAAAAAATGGTATTTTGGAAATAAAA-CTAG
128 G-AAAAAATAGTATTTTGGAAATAAAATC-AG
*
6612 TGTTGGAGATATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATT-AGTGTT
1 GGTTGGAG-TATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGA-TGTT
* * *
6676 TTGAAAATAAAATCGAGGTTGAAGTATACCCTCGAAATAACGAGGTTGGAGTATCCCCGATTATG
64 TTGGAAATAAAACCGAGGTTGAAGTATACCCTCGAAATAACGAGGTTAGAGTATCCCCGATTATG
* *
6741 AAAAATTAGTATTTTGGAAATAAAATCGG
129 AAAAAATAGTATTTTGGAAATAAAATCAG
* * * *
6770 GGTTGGAGTTTCCCCT------TAACAGGGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTT
1 GGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTT
*
6829 AGAAATAAA
66 GGAAATAAA
6838 GACATGAATG
Statistics
Matches: 195, Mismatches: 25, Indels: 20
0.81 0.10 0.08
Matches are distributed among these distances:
151 46 0.24
157 7 0.04
158 39 0.20
159 66 0.34
160 37 0.19
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (157 bp):
GGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTT
GGAAATAAAACCGAGGTTGAAGTATACCCTCGAAATAACGAGGTTAGAGTATCCCCGATTATGAA
AAAATAGTATTTTGGAAATAAAATCAG
Found at i:6731 original size:78 final size:78
Alignment explanation
Indices: 6450--6837 Score: 398
Period size: 78 Copynumber: 5.0 Consensus size: 78
6440 TCAAAAATAA
* ** * *
6450 CGAGGTTGGAGTATCCTCTCAGAAATAACGAAATTAGAGTATCCCCGATTTTGAAAAAATT-GAT
1 CGAGGTTGGAGTATCCCCTC-GAAATAACGAGGTTGGAGTATCCCCGATTGTG-AAAAATTAG-T
*
6514 GTTTTGGAAATAAAAC
63 GTTTTGGAAATAAAAT
* * * * * * * *
6530 CGGGGTTAGAGTATCCCCTTGAAAATAATG-GGTTAGAGTATCCCCGATTGTGAAAAAAATGGTA
1 CGAGGTTGGAGTATCCCCTCG-AAATAACGAGGTTGGAGTATCCCCGATTGTG-AAAAATTAGTG
6594 TTTTGGAAATAAAA-
64 TTTTGGAAATAAAAT
* *
6608 CTAGTGTTGGAGATATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGT
1 CGAG-GTTGGAG-TATCCCCTC-GAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATTAGT
*
6673 GTTTTGAAAATAAAAT
63 GTTTTGGAAATAAAAT
* * * *
6689 CGAGGTTGAAGTATACCCTCGAAATAACGAGGTTGGAGTATCCCCGATTATGAAAAATTAGTATT
1 CGAGGTTGGAGTATCCCCTCGAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTT
6754 TTGGAAATAAAAT
66 TTGGAAATAAAAT
* * * *
6767 CGGGGTTGGAGTTTCCCCT-----TAAC-AGGGTTGGAGTATCCCCGATTGTGGAAAATTGGTGT
1 CGAGGTTGGAGTATCCCCTCGAAATAACGA-GGTTGGAGTATCCCCGATTGTGAAAAATTAGTGT
*
6826 TTTAGAAATAAA
65 TTTGGAAATAAA
6838 GACATGAATG
Statistics
Matches: 264, Mismatches: 36, Indels: 23
0.82 0.11 0.07
Matches are distributed among these distances:
72 1 0.00
73 45 0.17
78 71 0.27
79 56 0.21
80 66 0.25
81 25 0.09
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (78 bp):
CGAGGTTGGAGTATCCCCTCGAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTT
TTGGAAATAAAAT
Found at i:10021 original size:75 final size:74
Alignment explanation
Indices: 9842--10023 Score: 186
Period size: 75 Copynumber: 2.4 Consensus size: 74
9832 AAAGGAAGGG
* * * * * * * **
9842 GCATCTTGCTCTTTGAGGACAAATGAAAAGGAGCACATCTTGCTCTTCGAGGATAAAGGAAATGA
1 GCATCTTGCTCTTTGAGGACAAAGGAAAAAGAGCACATCCTACTCTACGAAGAGAAAGGAAAAAA
*
9907 GAACGAAAT
66 GAAAGAAAT
** * * *
9916 GGGTCCTGCTCCTTGAGGACAAAGGAAAAAAGAGTACATCCTACTCTACGAAGAGAAAGGAAAAA
1 GCATCTTGCTCTTTGAGGACAAAGG-AAAAAGAGCACATCCTACTCTACGAAGAGAAAGGAAAAA
*
9981 AGGAAATAATAT
65 A-GAAAGAA-AT
9993 GCATCTTGCTCTTTGAGGACAAA-GAAAAAGA
1 GCATCTTGCTCTTTGAGGACAAAGGAAAAAGA
10024 AGGAAATTAA
Statistics
Matches: 85, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
74 20 0.24
75 38 0.45
76 6 0.07
77 21 0.25
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.20
Consensus pattern (74 bp):
GCATCTTGCTCTTTGAGGACAAAGGAAAAAGAGCACATCCTACTCTACGAAGAGAAAGGAAAAAA
GAAAGAAAT
Found at i:10126 original size:59 final size:59
Alignment explanation
Indices: 10037--10660 Score: 691
Period size: 59 Copynumber: 10.5 Consensus size: 59
10027 AAATTAAAGC
* *
10037 GCGTCCTACTCTTTGGGGACT-AGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAA
1 GCGTCCTACTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAA
* ** *
10096 GCGTCCTGCTCTTTGAGGACCAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAA
1 GCGTCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAA
* * * * * *
10155 GCATCTTGCTCTTTGAAGACTGGAAGGTGCTACCAACTTGTGTGGGCTTTGAAAGGAAA
1 GCGTCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAA
* * * * * *
10214 GCATCCTACTTTTTGAGGACTGGAAGGTGCTACCAACTTGTGTAGGCTTTGTAAGGAAA
1 GCGTCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAA
* * * *
10273 ACGTCCTACTCTTTGAAGACTGAGAGGTGCGACCAACTTGTGTGGGCTTTGAAAGGAAA
1 GCGTCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAA
* *
10332 ACGTCCTACTCTTTGAGGACTGGAAGGTGCCACCAACTTATGTGTGGGCTTTGAAAGGAAA
1 GCGTCCTACTCTTTGAGGACTGAAAGGTGCCACCAAC-T-TGTGTGGGCTTTGAAAGGAAA
* * * * * *
10393 ACGTCCTGCTCTTTGAGGATTGGAAGGTGCCACCAACTTGTATAGGCTTTGAAAGGAAAA
1 GCGTCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGG-AAA
* * * * * * * * *
10453 GGCATCCTGCTTTTTAAGCACT-AACAAGTGCCACAAACTTGTGT-GGCTTTAAAAAGAAAA
1 -GCGTCCTACTCTTTGAGGACTGAA-AGGTGCCACCAACTTGTGTGGGCTTT-GAAAGGAAA
* * * *
10513 GGTGTCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAGAA
1 -GCGTCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGA-AA
* *
10574 G-G-CACTACTCTTTGAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTGAATGGAAA
1 GCGTC-CTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAA
*
10632 GGGCATCCTACTCTTTGAGGACTGAAAGG
1 --GCGTCCTACTCTTTGAGGACTGAAAGG
10661 ATAAAAGCTT
Statistics
Matches: 488, Mismatches: 62, Indels: 28
0.84 0.11 0.05
Matches are distributed among these distances:
58 3 0.01
59 303 0.62
60 58 0.12
61 123 0.25
62 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (59 bp):
GCGTCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAA
Found at i:14456 original size:52 final size:51
Alignment explanation
Indices: 14371--14494 Score: 212
Period size: 52 Copynumber: 2.4 Consensus size: 51
14361 ATATGAAAAG
* *
14371 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAA
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
*
14422 TTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA
1 -TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
14474 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
14495 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 21 0.30
52 48 0.70
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
Found at i:14507 original size:51 final size:51
Alignment explanation
Indices: 14371--14514 Score: 202
Period size: 52 Copynumber: 2.8 Consensus size: 51
14361 ATATGAAAAG
*
14371 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
14423 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA-
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
14474 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
14515 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
50 2 0.02
51 34 0.40
52 48 0.57
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:14521 original size:13 final size:13
Alignment explanation
Indices: 14503--14527 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14493 CAAAGATCAG
14503 TGTATCGATACAA
1 TGTATCGATACAA
14516 TGTATCGATACA
1 TGTATCGATACA
14528 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:14605 original size:33 final size:33
Alignment explanation
Indices: 14568--14634 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
14558 AGTAGCTTAA
14568 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
14601 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
14634 A
1 A
14635 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:14608 original size:13 final size:13
Alignment explanation
Indices: 14590--14614 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14580 CAAAAAAATA
14590 TGTATCGATACAT
1 TGTATCGATACAT
14603 TGTATCGATACA
1 TGTATCGATACA
14615 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:15750 original size:49 final size:49
Alignment explanation
Indices: 15633--15958 Score: 441
Period size: 49 Copynumber: 6.7 Consensus size: 49
15623 AAAATGATGT
* * *
15633 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G--AAGGTGC
*
15685 CGATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* * * * *
15734 CAATGTGCTGAGTCAAGGCCAGCTACATTGGATTTAAAGATAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
15783 CAATATGCTGATTCAAGGCCAGCTATA-TGGACTT--A-AT---GGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* * *
15825 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGTAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
*
15874 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* *
15923 CAATATGGTGATTCAAGGCCAGCTATATTGGGCTTA
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
15959 GAAGGGTTGC
Statistics
Matches: 245, Mismatches: 22, Indels: 17
0.86 0.08 0.06
Matches are distributed among these distances:
42 31 0.13
43 7 0.03
45 3 0.01
46 2 0.01
48 6 0.02
49 158 0.64
51 1 0.00
52 37 0.15
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (49 bp):
CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
Found at i:15935 original size:140 final size:140
Alignment explanation
Indices: 15680--15950 Score: 461
Period size: 140 Copynumber: 1.9 Consensus size: 140
15670 AGATGGAAAA
* *
15680 GGTGCCGATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGA
1 GGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATATGCTGA
*
15745 GTCAAGGCCAGCTACATTGGATTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATA
66 GTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATA
15810 TGGACTTAAT
131 TGGACTTAAT
* * *
15820 GGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGTAGGTGCCAATATGCTGA
1 GGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATATGCTGA
* * *
15885 TTCAAGGCCAGCTATATTGGACTTAAAGATAAAGGTGCCAATATGGTGATTCAAGGCCAGCTATA
66 GTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATA
15950 T
131 T
15951 TGGGCTTAGA
Statistics
Matches: 122, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
140 122 1.00
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (140 bp):
GGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATATGCTGA
GTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATA
TGGACTTAAT
Found at i:15985 original size:30 final size:30
Alignment explanation
Indices: 15951--16039 Score: 96
Period size: 30 Copynumber: 3.0 Consensus size: 30
15941 CCAGCTATAT
*
15951 TGGGCTTAGAAGGGTTGCCACCGACTTGTG
1 TGGGCTTAGAAGGGTTGCCACTGACTTGTG
*
15981 TGGGCTTTGGAAAAGGG-TGCCACTGA-TT-TG
1 TGGGC-TT--AGAAGGGTTGCCACTGACTTGTG
*
16011 TGGGCTTTGAA-GGTTGCCACTGACTTGTG
1 TGGGCTTAGAAGGGTTGCCACTGACTTGTG
16040 GGCTTTCGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
26 2 0.04
27 11 0.22
28 2 0.04
29 4 0.08
30 12 0.24
31 4 0.08
32 8 0.16
33 6 0.12
ACGTcount: A:0.17, C:0.17, G:0.36, T:0.30
Consensus pattern (30 bp):
TGGGCTTAGAAGGGTTGCCACTGACTTGTG
Found at i:16031 original size:27 final size:27
Alignment explanation
Indices: 15951--16045 Score: 100
Period size: 27 Copynumber: 3.3 Consensus size: 27
15941 CCAGCTATAT
* *
15951 TGGGCTTAGAAGGGTTGCCACCGACTTGTG
1 TGGGCTTTGAA-GGTTGCCACTGA-TT-TG
*
15981 TGGGCTTTGGAAAAGGGTGCCACTGATTTG
1 TGGGCTTT-G--AAGGTTGCCACTGATTTG
*
16011 TGGGCTTTGAAGGTTGCCACTGACTTG
1 TGGGCTTTGAAGGTTGCCACTGATTTG
16038 TGGGCTTT
1 TGGGCTTT
16046 CGAAAAAAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
27 24 0.42
29 1 0.02
30 17 0.30
31 3 0.05
32 10 0.18
33 2 0.04
ACGTcount: A:0.16, C:0.17, G:0.36, T:0.32
Consensus pattern (27 bp):
TGGGCTTTGAAGGTTGCCACTGATTTG
Found at i:16059 original size:57 final size:60
Alignment explanation
Indices: 15951--16078 Score: 163
Period size: 57 Copynumber: 2.2 Consensus size: 60
15941 CCAGCTATAT
* * *** * *
15951 TGGGCTTAGAAGGGTTGCCACCGACTTGTGTGGGCTTTGGAAAAGGGTGCCACTGATTTG
1 TGGGCTTTGAAGGGTTGCCACCGACTTGTGTGGGCTTTCGAAAAAAATGCCACCGACTTG
*
16011 TGGGCTTTGAA-GGTTGCCACTGAC-T-TGTGGGCTTTCGAAAAAAATGCCACCGACTTG
1 TGGGCTTTGAAGGGTTGCCACCGACTTGTGTGGGCTTTCGAAAAAAATGCCACCGACTTG
16068 TGGGCTTTGAA
1 TGGGCTTTGAA
16079 AAAAATGCCA
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
57 37 0.62
58 1 0.02
59 12 0.20
60 10 0.17
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (60 bp):
TGGGCTTTGAAGGGTTGCCACCGACTTGTGTGGGCTTTCGAAAAAAATGCCACCGACTTG
Found at i:16066 original size:30 final size:29
Alignment explanation
Indices: 15979--16104 Score: 139
Period size: 30 Copynumber: 4.3 Consensus size: 29
15969 CACCGACTTG
*** *
15979 TGTGGGCTTTGGAAAAGGGTGCCACTGATT
1 TGTGGGCTTT-GAAAAAAATGCCACTGACT
***
16009 TGTGGGCTTTG--AAGGTTGCCACTGACT
1 TGTGGGCTTTGAAAAAAATGCCACTGACT
*
16036 TGTGGGCTTTCGAAAAAAATGCCACCGACT
1 TGTGGGCTTT-GAAAAAAATGCCACTGACT
16066 TGTGGGCTTTGAAAAAAATGCCACTGACT
1 TGTGGGCTTTGAAAAAAATGCCACTGACT
*
16095 TGTGGACTTT
1 TGTGGGCTTT
16105 TGAAGGGTGA
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
27 24 0.28
28 1 0.01
29 28 0.33
30 32 0.38
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.30
Consensus pattern (29 bp):
TGTGGGCTTTGAAAAAAATGCCACTGACT
Found at i:16107 original size:30 final size:30
Alignment explanation
Indices: 16025--16108 Score: 134
Period size: 29 Copynumber: 2.8 Consensus size: 30
16015 CTTTGAAGGT
*
16025 TGCCACTGACTTGTGGGCTTTCGAAAAAAA
1 TGCCACTGACTTGTGGGCTTTTGAAAAAAA
*
16055 TGCCACCGACTTGTGGGC-TTTGAAAAAAA
1 TGCCACTGACTTGTGGGCTTTTGAAAAAAA
*
16084 TGCCACTGACTTGTGGACTTTTGAA
1 TGCCACTGACTTGTGGGCTTTTGAA
16109 GGGTGATGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 26 0.53
30 23 0.47
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (30 bp):
TGCCACTGACTTGTGGGCTTTTGAAAAAAA
Found at i:17554 original size:1 final size:1
Alignment explanation
Indices: 17550--17664 Score: 95
Period size: 1 Copynumber: 115.0 Consensus size: 1
17540 CCGGACCCCC
* * * * * * * * *
17550 TTTTTTGTTTTTGTTTGTTTTTTTATTGTTTTTGTTTTTTTTTTTGTTTTTTTTGTTTTTTTGTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
** ** **
17615 TTTTTTTTTTGGTTTTTCATTTTTTTCGTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
17665 GGAGGACGCC
Statistics
Matches: 88, Mismatches: 26, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 88 1.00
ACGTcount: A:0.02, C:0.02, G:0.10, T:0.87
Consensus pattern (1 bp):
T
Found at i:17580 original size:21 final size:20
Alignment explanation
Indices: 17550--17665 Score: 107
Period size: 19 Copynumber: 5.8 Consensus size: 20
17540 CCGGACCCCC
17550 TTTTTTGTTTTTGTTTGTTT
1 TTTTTTGTTTTTGTTTGTTT
17570 TTTTATTGTTTTTG-TT-TTT
1 TTTT-TTGTTTTTGTTTGTTT
17589 TTTTTTGTTTTT-TTTGTTT
1 TTTTTTGTTTTTGTTTGTTT
* *
17608 TTTTGTTTTTTTTTTTTGGTTT
1 TTTT-TTGTTTTTGTTT-GTTT
* *
17630 TTCATTT-TTTTCGTTT-TTT
1 TT-TTTTGTTTTTGTTTGTTT
* *
17649 TTTTTTTTTTTTTTTTG
1 TTTTTTGTTTTTGTTTG
17666 GAGGACGCCG
Statistics
Matches: 80, Mismatches: 7, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
18 13 0.16
19 26 0.32
20 13 0.16
21 19 0.24
22 8 0.10
23 1 0.01
ACGTcount: A:0.02, C:0.02, G:0.10, T:0.86
Consensus pattern (20 bp):
TTTTTTGTTTTTGTTTGTTT
Found at i:17581 original size:9 final size:9
Alignment explanation
Indices: 17550--17664 Score: 112
Period size: 9 Copynumber: 12.4 Consensus size: 9
17540 CCGGACCCCC
17550 TTTTTTGTT
1 TTTTTTGTT
17559 TTTGTTTGTTT
1 TTT-TTTG-TT
17570 TTTTATTGTT
1 TTTT-TTGTT
17580 TTTGTTT-TT
1 TTT-TTTGTT
17589 TTTTTTGTT
1 TTTTTTGTT
17598 TTTTTTG-T
1 TTTTTTGTT
17606 TTTTTTGTT
1 TTTTTTGTT
*
17615 TTTTTTTTT
1 TTTTTTGTT
*
17624 TGGTTTTTCATT
1 T--TTTTT-GTT
*
17636 TTTTTCGTT
1 TTTTTTGTT
17645 TTTTTT-TT
1 TTTTTTGTT
17653 TTTTTT-TT
1 TTTTTTGTT
17661 TTTT
1 TTTT
17665 GGAGGACGCC
Statistics
Matches: 92, Mismatches: 5, Indels: 19
0.79 0.04 0.16
Matches are distributed among these distances:
8 25 0.27
9 34 0.37
10 16 0.17
11 14 0.15
12 3 0.03
ACGTcount: A:0.02, C:0.02, G:0.10, T:0.87
Consensus pattern (9 bp):
TTTTTTGTT
Found at i:17595 original size:29 final size:28
Alignment explanation
Indices: 17550--17664 Score: 130
Period size: 29 Copynumber: 4.1 Consensus size: 28
17540 CCGGACCCCC
*
17550 TTTTTTG--TTTTTGTTTGTTTTTTTAT
1 TTTTTTGTTTTTTTTTTTGTTTTTTTAT
*
17576 TGTTTTTGTTTTTTTTTTTGTTTTTTTTGT
1 T-TTTTTGTTTTTTTTTTTG-TTTTTTTAT
* *
17606 TTTTTTGTTTTTTTTTTTTGGTTTTTCAT
1 TTTTTTG-TTTTTTTTTTTGTTTTTTTAT
17635 TTTTTTCGTTTTTTTTTTT-TTTTTTT-T
1 TTTTTT-GTTTTTTTTTTTGTTTTTTTAT
17662 TTT
1 TTT
17665 GGAGGACGCC
Statistics
Matches: 76, Mismatches: 7, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
26 1 0.01
27 10 0.13
28 5 0.07
29 38 0.50
30 22 0.29
ACGTcount: A:0.02, C:0.02, G:0.10, T:0.87
Consensus pattern (28 bp):
TTTTTTGTTTTTTTTTTTGTTTTTTTAT
Found at i:17605 original size:38 final size:35
Alignment explanation
Indices: 17550--17664 Score: 140
Period size: 38 Copynumber: 3.1 Consensus size: 35
17540 CCGGACCCCC
17550 TTTTTTGTTTTTGTTTGTTTTTTTATTGTTTTTGTTTTT
1 TTTTTTGTTTTT-TTTGTTTTTTT-TT-TTTTT-TTTTT
17589 TTTTTTGTTTTTTTTGTTTTTTTGTTTTTTTTTTTT
1 TTTTTTGTTTTTTTTGTTTTTTT-TTTTTTTTTTTT
** *
17625 GGTTTTTCATTTTTTTCGTTTTTTTTTTTTTTTTTTT
1 --TTTTTTGTTTTTTTTGTTTTTTTTTTTTTTTTTTT
17662 TTT
1 TTT
17665 GGAGGACGCC
Statistics
Matches: 70, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
35 3 0.04
36 5 0.07
37 17 0.24
38 33 0.47
39 12 0.17
ACGTcount: A:0.02, C:0.02, G:0.10, T:0.87
Consensus pattern (35 bp):
TTTTTTGTTTTTTTTGTTTTTTTTTTTTTTTTTTT
Found at i:27372 original size:10 final size:10
Alignment explanation
Indices: 27357--27383 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
27347 ATGTATCAAG
27357 CAAAAACAAA
1 CAAAAACAAA
27367 CAAAAACAAA
1 CAAAAACAAA
27377 CAAAAAC
1 CAAAAAC
27384 TTAGTTAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (10 bp):
CAAAAACAAA
Found at i:31606 original size:52 final size:51
Alignment explanation
Indices: 31521--31644 Score: 212
Period size: 52 Copynumber: 2.4 Consensus size: 51
31511 ATATGAAAAG
* *
31521 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAA
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
*
31572 TTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA
1 -TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
31624 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
31645 AGATCAGTGT
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 21 0.30
52 48 0.70
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
Found at i:31670 original size:13 final size:13
Alignment explanation
Indices: 31652--31676 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31642 ACAAGATCAG
31652 TGTATCGATACAA
1 TGTATCGATACAA
31665 TGTATCGATACA
1 TGTATCGATACA
31677 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:31754 original size:33 final size:33
Alignment explanation
Indices: 31717--31783 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
31707 AGTAGCTTAA
31717 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
31750 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
31783 A
1 A
31784 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:31757 original size:13 final size:13
Alignment explanation
Indices: 31739--31763 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31729 CAAAAAAATA
31739 TGTATCGATACAT
1 TGTATCGATACAT
31752 TGTATCGATACA
1 TGTATCGATACA
31764 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Done.