Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013603.1 Corchorus capsularis cultivar CVL-1 contig13624, whole genome shotgun sequence
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: 87927
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:35 original size:3 final size:3
Alignment explanation
Indices: 22--61 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
12 ATATATATAT
*
22 ATA ACA ATA ATA ATA ATA ATAA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA
62 GAATAAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:48 original size:16 final size:16
Alignment explanation
Indices: 27--59 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
17 TATATATAAC
27 AATAATAATAATAATA
1 AATAATAATAATAATA
43 AATAATAATAATAATA
1 AATAATAATAATAATA
59 A
1 A
60 TAGAATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AATAATAATAATAATA
Found at i:2019 original size:47 final size:47
Alignment explanation
Indices: 1950--2045 Score: 156
Period size: 47 Copynumber: 2.0 Consensus size: 47
1940 AAGACAATAT
* * *
1950 ATACAGAAAATTATTGTTGAAAAATCTCCTACATTTTTTACAAGGTG
1 ATACAAAAAATTATTATTGAAAAATCTCCTACATTTTTTACAAAGTG
*
1997 ATACAAAAAATTATTATTGAAAAATCTCCTATATTTTTTACAAAGTG
1 ATACAAAAAATTATTATTGAAAAATCTCCTACATTTTTTACAAAGTG
2044 AT
1 AT
2046 TCAACTCTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (47 bp):
ATACAAAAAATTATTATTGAAAAATCTCCTACATTTTTTACAAAGTG
Found at i:4258 original size:24 final size:24
Alignment explanation
Indices: 4213--4258 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
4203 TATCGATGAG
* * *
4213 TGAAGATCTGCCAAATTGTAGACT
1 TGAAAATCTGCCAAACTATAGACT
4237 TGAAAATCTGCCAAACTATAGA
1 TGAAAATCTGCCAAACTATAGA
4259 AATAAATTAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.26
Consensus pattern (24 bp):
TGAAAATCTGCCAAACTATAGACT
Found at i:4814 original size:47 final size:49
Alignment explanation
Indices: 4711--4814 Score: 126
Period size: 47 Copynumber: 2.2 Consensus size: 49
4701 TAATATACAT
* * *
4711 ATGACATTCAAATCAATCAATCAATCTAATAGTATTTTAATTTGATCAA
1 ATGACATTCAAACCAATCAATCAATCTAATAATATTTTAATTAGATCAA
* * *
4760 AT--TATTCAAACCAATCAATCAATCTAATAATA-TTTGATTAGA-CAC
1 ATGACATTCAAACCAATCAATCAATCTAATAATATTTTAATTAGATCAA
4805 ATGACATTCA
1 ATGACATTCA
4815 GGGACACATG
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
45 4 0.09
46 8 0.17
47 32 0.70
49 2 0.04
ACGTcount: A:0.43, C:0.16, G:0.06, T:0.35
Consensus pattern (49 bp):
ATGACATTCAAACCAATCAATCAATCTAATAATATTTTAATTAGATCAA
Found at i:6437 original size:41 final size:40
Alignment explanation
Indices: 6300--6447 Score: 179
Period size: 40 Copynumber: 3.7 Consensus size: 40
6290 AACAAGAAAA
* * * * *
6300 GTAAATAACACCTTCTGGTGAGGAAGGACAAGACAGGAAT
1 GTAAACAACACCTTCCGATGGGGAAGGACAAAACAGGAAT
* * *
6340 GTAGACAACACCTTCCGGTGGGGAAGGGCAAAACAGGAAT
1 GTAAACAACACCTTCCGATGGGGAAGGACAAAACAGGAAT
* * *
6380 GTAAACAACACTTTCCGATAGGGAAGGACAAAACGGGAAAT
1 GTAAACAACACCTTCCGATGGGGAAGGACAAAACAGG-AAT
*
6421 TTAAACAACACCTTCCGATGGGGAAGG
1 GTAAACAACACCTTCCGATGGGGAAGG
6448 GCATGATGCG
Statistics
Matches: 92, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
40 65 0.71
41 27 0.29
ACGTcount: A:0.39, C:0.18, G:0.28, T:0.16
Consensus pattern (40 bp):
GTAAACAACACCTTCCGATGGGGAAGGACAAAACAGGAAT
Found at i:6601 original size:33 final size:32
Alignment explanation
Indices: 6561--6668 Score: 135
Period size: 33 Copynumber: 3.3 Consensus size: 32
6551 AGCATAAGTG
*
6561 ACCGGCCACGCGACTTGGAGATGCCCGCGCAAC
1 ACCGGCCACGCGACATGGAGATGCCCG-GCAAC
* *
6594 ACCGGCCATGCGACATGGAGATGCCCGGCCATC
1 ACCGGCCACGCGACATGGAGATGCCCGG-CAAC
** *
6627 ACCGGCCACGCGACATGGCCATGCCCGGCCAC
1 ACCGGCCACGCGACATGGAGATGCCCGGCAAC
6659 ACCCGGCCAC
1 A-CCGGCCAC
6669 ATGACTCGGC
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
32 4 0.06
33 61 0.94
ACGTcount: A:0.20, C:0.43, G:0.29, T:0.08
Consensus pattern (32 bp):
ACCGGCCACGCGACATGGAGATGCCCGGCAAC
Found at i:6680 original size:33 final size:32
Alignment explanation
Indices: 6581--6705 Score: 108
Period size: 33 Copynumber: 3.8 Consensus size: 32
6571 CGACTTGGAG
* *** **
6581 ATGCCCGCGCAACACCGGCCATGCGACATGGAG
1 ATGCCCG-GCCACACCGGCCACATGACATGGCC
**
6614 ATGCCCGGCCATCACCGGCCACGCGACATGGCC
1 ATGCCCGGCCA-CACCGGCCACATGACATGGCC
6647 ATGCCCGGCCACACCCGGCCACATGAC-TCGGCC
1 ATGCCCGGCCACA-CCGGCCACATGACAT-GGCC
* *
6680 ATGCCCCGCCACAACCGGCCATATGA
1 ATGCCCGGCCAC-ACCGGCCACATGA
6706 TCCTTTAGCT
Statistics
Matches: 80, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
32 6 0.08
33 73 0.91
34 1 0.01
ACGTcount: A:0.22, C:0.43, G:0.26, T:0.10
Consensus pattern (32 bp):
ATGCCCGGCCACACCGGCCACATGACATGGCC
Found at i:7649 original size:17 final size:18
Alignment explanation
Indices: 7608--7641 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
7598 ACCTTATTGA
7608 AAAATTC-AAAAATTCAG
1 AAAATTCAAAAAATTCAG
7625 AAAATTCAAAAAATTCA
1 AAAATTCAAAAAATTCA
7642 TAAATTCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.62, C:0.12, G:0.03, T:0.24
Consensus pattern (18 bp):
AAAATTCAAAAAATTCAG
Found at i:7651 original size:8 final size:8
Alignment explanation
Indices: 7607--7649 Score: 59
Period size: 8 Copynumber: 5.1 Consensus size: 8
7597 CACCTTATTG
7607 AAAAATTC
1 AAAAATTC
7615 AAAAATTC
1 AAAAATTC
7623 AGAAAATTC
1 A-AAAATTC
7632 AAAAAATTC
1 -AAAAATTC
*
7641 ATAAATTC
1 AAAAATTC
7649 A
1 A
7650 TAGCCGATTC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
8 17 0.53
9 14 0.44
10 1 0.03
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (8 bp):
AAAAATTC
Found at i:9195 original size:33 final size:33
Alignment explanation
Indices: 9158--9231 Score: 105
Period size: 33 Copynumber: 2.2 Consensus size: 33
9148 GTTTGCGAAA
9158 ATACTAAACCTAATTT-GAGTGTTGGATGTGATG
1 ATACTAAACCTAATTTAG-GTGTTGGATGTGATG
**
9191 ATACTAAACCTAATTTAGGTGTTGTTTGTGATG
1 ATACTAAACCTAATTTAGGTGTTGGATGTGATG
*
9224 AAACTAAA
1 ATACTAAA
9232 TCTGTTTTGG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 36 0.97
34 1 0.03
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.36
Consensus pattern (33 bp):
ATACTAAACCTAATTTAGGTGTTGGATGTGATG
Found at i:9302 original size:33 final size:30
Alignment explanation
Indices: 9255--9337 Score: 94
Period size: 30 Copynumber: 2.7 Consensus size: 30
9245 CTAATTGTGA
* *
9255 TGAAAACAAATCTGTTTTGGTTGATCATAGCAT
1 TGAAAATAATTCTGTTTTGGTTG---ATAGCAT
* * *
9288 TGCAAATAATTCTGTTTTGGTTGATGGTAT
1 TGAAAATAATTCTGTTTTGGTTGATAGCAT
9318 TGAAAATAATTCTGTTTTGG
1 TGAAAATAATTCTGTTTTGG
9338 GTGAGAAGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
30 24 0.55
33 20 0.45
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.42
Consensus pattern (30 bp):
TGAAAATAATTCTGTTTTGGTTGATAGCAT
Found at i:11143 original size:33 final size:32
Alignment explanation
Indices: 11095--11198 Score: 118
Period size: 33 Copynumber: 3.2 Consensus size: 32
11085 TAAGTGACCA
*
11095 GCCACGCGACTTGGAGATGCCCGCGCAACACCG
1 GCCACGCGACATGGAGATGCCCG-GCAACACCG
* * *
11128 GCCATGCGACATGGAGATGCGCGGCCATCACCG
1 GCCACGCGACATGGAGATGCCCGG-CAACACCG
** *
11161 GCCACGCGACATGGCCATGCCCGGCCACACCCG
1 GCCACGCGACATGGAGATGCCCGGCAACA-CCG
11194 GCCAC
1 GCCAC
11199 ATGACTTGGC
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
32 4 0.07
33 55 0.93
ACGTcount: A:0.20, C:0.41, G:0.30, T:0.09
Consensus pattern (32 bp):
GCCACGCGACATGGAGATGCCCGGCAACACCG
Found at i:11209 original size:33 final size:32
Alignment explanation
Indices: 11111--11235 Score: 106
Period size: 33 Copynumber: 3.8 Consensus size: 32
11101 CGACTTGGAG
* *** **
11111 ATGCCCGCGCAACACCGGCCATGCGACATGGAG
1 ATGCCCG-GCCACACCGGCCACATGACATGGCC
* **
11144 ATGCGCGGCCATCACCGGCCACGCGACATGGCC
1 ATGCCCGGCCA-CACCGGCCACATGACATGGCC
*
11177 ATGCCCGGCCACACCCGGCCACATGACTTGGCC
1 ATGCCCGGCCACA-CCGGCCACATGACATGGCC
* *
11210 ATGCCCCGCCACAACCGGCCATATGA
1 ATGCCCGGCCAC-ACCGGCCACATGA
11236 TCCGTTAGCT
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
32 5 0.06
33 72 0.92
34 1 0.01
ACGTcount: A:0.22, C:0.42, G:0.26, T:0.10
Consensus pattern (32 bp):
ATGCCCGGCCACACCGGCCACATGACATGGCC
Found at i:13138 original size:290 final size:290
Alignment explanation
Indices: 12618--13196 Score: 1113
Period size: 290 Copynumber: 2.0 Consensus size: 290
12608 TGTGAAACTA
12618 GTTTGGATTGTGGGCAGCCGTATTGCTCCTTTCCATGCTTCAAAATGATGATGCCTTTATTCTTC
1 GTTTGGATTGTGGGCAGCCGTATTGCTCCTTTCCATGCTTCAAAATGATGATGCCTTTATTCTTC
12683 ACATGTCACCATATTAAGAACCAACCAAAAACAAGTACTTCACCTAAGGGTTTTTCAAGCCAAAA
66 ACATGTCACCATATTAAGAACCAACCAAAAACAAGTACTTCACCTAAGGGTTTTTCAAGCCAAAA
*
12748 TATTTTACTAACATGTGTCAAGTGAATGATGGATGGTCATCAACACATGTCAAGCCATGAGAGGT
131 TATTTGACTAACATGTGTCAAGTGAATGATGGATGGTCATCAACACATGTCAAGCCATGAGAGGT
* *
12813 GCTTGCTTCCACATAAGCTTCATGTTGGTGAGGTGCTTGCTTGGCTCCAACGTGGCTAACTTGGT
196 GCTTGCTTCCACATAAGCTTCATGTTGGTGAGGTGCTAGCTTGGCTCCAACATGGCTAACTTGGT
**
12878 TTCACTCAACGTGACATGTCATCAAAGCTT
261 CCCACTCAACGTGACATGTCATCAAAGCTT
12908 GTTTGGATTGTGGGCAGCCGTATTGCTCCTTTCCATGCTTCAAAATGATGATGCCTTTATTCTTC
1 GTTTGGATTGTGGGCAGCCGTATTGCTCCTTTCCATGCTTCAAAATGATGATGCCTTTATTCTTC
12973 ACATGTCACCATATTAAGAACCAACCAAAAACAAGTACTTCACCTAAGGGTTTTTCAAGCCAAAA
66 ACATGTCACCATATTAAGAACCAACCAAAAACAAGTACTTCACCTAAGGGTTTTTCAAGCCAAAA
13038 TATTTGACTAACATGTGTCAAGTGAATGATGGATGGTCATCAACACATGTCAAGCCATGAGAGGT
131 TATTTGACTAACATGTGTCAAGTGAATGATGGATGGTCATCAACACATGTCAAGCCATGAGAGGT
13103 GCTTGCTTCCACATAAGCTTCATGTTGGTGAGGTGCTAGCTTGGCTCCAACATGGCTAACTTGGT
196 GCTTGCTTCCACATAAGCTTCATGTTGGTGAGGTGCTAGCTTGGCTCCAACATGGCTAACTTGGT
13168 CCCACTCAACGTGACATGTCATCAAAGCT
261 CCCACTCAACGTGACATGTCATCAAAGCT
13197 AGGTGCTCAC
Statistics
Matches: 284, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
290 284 1.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (290 bp):
GTTTGGATTGTGGGCAGCCGTATTGCTCCTTTCCATGCTTCAAAATGATGATGCCTTTATTCTTC
ACATGTCACCATATTAAGAACCAACCAAAAACAAGTACTTCACCTAAGGGTTTTTCAAGCCAAAA
TATTTGACTAACATGTGTCAAGTGAATGATGGATGGTCATCAACACATGTCAAGCCATGAGAGGT
GCTTGCTTCCACATAAGCTTCATGTTGGTGAGGTGCTAGCTTGGCTCCAACATGGCTAACTTGGT
CCCACTCAACGTGACATGTCATCAAAGCTT
Found at i:13410 original size:41 final size:41
Alignment explanation
Indices: 13287--14098 Score: 802
Period size: 41 Copynumber: 19.1 Consensus size: 41
13277 TCCCGTGTCA
*
13287 CAAACTAGGAAAACTAAACAACACCTTCCGATGGGGAAGGG
1 CAAACTGGGAAAACTAAACAACACCTTCCGATGGGGAAGGG
* *
13328 CAAACTGGGAAATGTAGACTTAGACAACACCTTCCGGTGGGGAAGGG
1 CAAACTGGG-AA---A-AC-TAAACAACACCTTCCGATGGGGAAGGG
13375 CAAACTGGGAAAACTAAACAACACCTTCCGATGGGGAAGGG
1 CAAACTGGGAAAACTAAACAACACCTTCCGATGGGGAAGGG
* * *
13416 CAAACTGGGAAATGTAGACTTAGACAACACCTTCCGGTGGGGAAGGA
1 CAAACTGGG-AA---A-AC-TAAACAACACCTTCCGATGGGGAAGGG
*
13463 AAAACTGGGAAAACTAAACAACACCTTCCGATGGGGAAGGG
1 CAAACTGGGAAAACTAAACAACACCTTCCGATGGGGAAGGG
*
13504 CAAACT-GG-AAACTTAAACAACACCTTCCGGTGGGGAAGGG
1 CAAACTGGGAAAAC-TAAACAACACCTTCCGATGGGGAAGGG
*
13544 CAAACT-GG-AAACTTAAACAACACCTTCCGGTGGGGAAGGG
1 CAAACTGGGAAAAC-TAAACAACACCTTCCGATGGGGAAGGG
* *
13584 CAAACTAGGG--AACTTAAATAAAACCTTCCGATGGGGAAGGG
1 CAAACT-GGGAAAAC-TAAACAACACCTTCCGATGGGGAAGGG
* *
13625 CAAACTGGGAAAACTATGAAATTAAACAACACCTTCCGGTGAGGAA-GG
1 CAAACTGGGAAAAC--------TAAACAACACCTTCCGATGGGGAAGGG
* *
13673 CAGACTGTG-AAACTTAAACAACACCTTCCGATGGGGAAGGG
1 CAAACTGGGAAAAC-TAAACAACACCTTCCGATGGGGAAGGG
* * *
13714 CAAATTGGG-AAACTTAAACAACACCTTCCGGTGGGGAATGG
1 CAAACTGGGAAAAC-TAAACAACACCTTCCGATGGGGAAGGG
*
13755 CAAACTGGGAAAACTAAACAACACCTTCCAATGGGGAAGGG
1 CAAACTGGGAAAACTAAACAACACCTTCCGATGGGGAAGGG
* * * *
13796 CAAATTGAG-AAACTAAACAACACCTTTCGGTGGGGAAGGG
1 CAAACTGGGAAAACTAAACAACACCTTCCGATGGGGAAGGG
* * *
13836 CGAACTGGG-AAACTAAACAACACCTTCCGGTGAGGAAGGG
1 CAAACTGGGAAAACTAAACAACACCTTCCGATGGGGAAGGG
*
13876 CAAACTGGGAATAAGCAGCTAAACAACACCTTCCGATGAGGAAGGG
1 CAAACTGGG-A-AA--A-CTAAACAACACCTTCCGATGGGGAAGGG
* ** *
13922 CCAACTGGG-AATTTAAACAACACCTTCCGATGAGGAAGGG
1 CAAACTGGGAAAACTAAACAACACCTTCCGATGGGGAAGGG
* *
13962 CAAATTGGGAATAGGCAACTAAACAACACCTTCCGATGAGGAAGGG
1 CAAACTGGG-A-A---AACTAAACAACACCTTCCGATGGGGAAGGG
* * ** *
14008 CAAACTGGGAATAGTAAACAACTTCTTCCGATGAGGAAGGG
1 CAAACTGGGAAAACTAAACAACACCTTCCGATGGGGAAGGG
* * *
14049 CAAACTGGGAATAAGCAACTAGACAACACATTCCGGTGGGGAAGGG
1 CAAACTGGG---AA--AACTAAACAACACCTTCCGATGGGGAAGGG
14095 CAAA
1 CAAA
14099 TTAGGAATTT
Statistics
Matches: 662, Mismatches: 66, Indels: 81
0.82 0.08 0.10
Matches are distributed among these distances:
39 4 0.01
40 205 0.31
41 217 0.33
42 17 0.03
43 7 0.01
44 3 0.00
45 4 0.01
46 105 0.16
47 70 0.11
48 9 0.01
49 21 0.03
ACGTcount: A:0.37, C:0.20, G:0.27, T:0.15
Consensus pattern (41 bp):
CAAACTGGGAAAACTAAACAACACCTTCCGATGGGGAAGGG
Found at i:13436 original size:88 final size:84
Alignment explanation
Indices: 13287--14098 Score: 815
Period size: 88 Copynumber: 9.5 Consensus size: 84
13277 TCCCGTGTCA
* *
13287 CAAACTAGGAAAACTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAATGTAGACTTAGA
1 CAAACTGGGAAAACTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGG-AA--TA-ACTTAAA
*
13352 CAACACCTTCCGGTGGGGAAGGG
62 CAACACCTTCCGATGGGGAAGGG
*
13375 CAAACTGGGAAAACTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAATGTAGACTTAGA
1 CAAACTGGGAAAACTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGG-AA--TA-ACTTAAA
* *
13440 CAACACCTTCCGGTGGGGAAGGA
62 CAACACCTTCCGATGGGGAAGGG
*
13463 AAAACTGGGAAAACTAAACAACACCTTCCGATGGGGAAGGGCAAACT-GG-A-AACTTAAACAAC
1 CAAACTGGGAAAACTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAATAACTTAAACAAC
*
13525 ACCTTCCGGTGGGGAAGGG
66 ACCTTCCGATGGGGAAGGG
* *
13544 CAAACT-GG-AAACTTAAACAACACCTTCCGGTGGGGAAGGGCAAACTAGGG---AACTTAAATA
1 CAAACTGGGAAAAC-TAAACAACACCTTCCGATGGGGAAGGGCAAACT-GGGAATAACTTAAACA
*
13604 AAACCTTCCGATGGGGAAGGG
64 ACACCTTCCGATGGGGAAGGG
* * * *
13625 CAAACTGGGAAAACTATGAAATTAAACAACACCTTCCGGTGAGGAA-GGCAGACTGTG-A-AACT
1 CAAACTGGGAAAAC--------TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAATAACT
13687 TAAACAACACCTTCCGATGGGGAAGGG
58 TAAACAACACCTTCCGATGGGGAAGGG
* * *
13714 CAAATTGGG-AAACTTAAACAACACCTTCCGGTGGGGAATGGCAAACTGGGAA-AAC-TAAACAA
1 CAAACTGGGAAAAC-TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAATAACTTAAACAA
*
13776 CACCTTCCAATGGGGAAGGG
65 CACCTTCCGATGGGGAAGGG
* * * * *
13796 CAAATTGAG-AAACTAAACAACACCTTTCGGTGGGGAAGGGCGAACTGGG-A-AAC-TAAACAAC
1 CAAACTGGGAAAACTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAATAACTTAAACAAC
* *
13857 ACCTTCCGGTGAGGAAGGG
66 ACCTTCCGATGGGGAAGGG
* *
13876 CAAACTGGGAATAAGCAGCTAAACAACACCTTCCGATGAGGAAGGGCCAACTGGGAAT---TTAA
1 CAAACTGGG-A-AA--A-CTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAATAACTTAA
*
13938 ACAACACCTTCCGATGAGGAAGGG
61 ACAACACCTTCCGATGGGGAAGGG
* * *
13962 CAAATTGGGAATAGGCAACTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAT-A-GTAA
1 CAAACTGGG-A-A---AACTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAATAACTTAA
** *
14025 ACAACTTCTTCCGATGAGGAAGGG
61 ACAACACCTTCCGATGGGGAAGGG
* * *
14049 CAAACTGGGAATAAGCAACTAGACAACACATTCCGGTGGGGAAGGGCAAA
1 CAAACTGGG---AA--AACTAAACAACACCTTCCGATGGGGAAGGGCAAA
14099 TTAGGAATTT
Statistics
Matches: 649, Mismatches: 45, Indels: 61
0.86 0.06 0.08
Matches are distributed among these distances:
79 4 0.01
80 69 0.11
81 124 0.19
82 52 0.08
83 10 0.02
85 2 0.00
86 110 0.17
87 69 0.11
88 139 0.21
89 46 0.07
90 24 0.04
ACGTcount: A:0.37, C:0.20, G:0.27, T:0.15
Consensus pattern (84 bp):
CAAACTGGGAAAACTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAATAACTTAAACAAC
ACCTTCCGATGGGGAAGGG
Found at i:14106 original size:46 final size:46
Alignment explanation
Indices: 13687--14141 Score: 366
Period size: 46 Copynumber: 10.6 Consensus size: 46
13677 CTGTGAAACT
* * *
13687 TAAACAACACCTTCCGATGGGGAAGGGCAAATTGGG-A-AA-C--T
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATAAGCAAC
* * *
13728 TAAACAACACCTTCCGGTGGGGAATGGCAAACTGGG---AA--AAC
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATAAGCAAC
* * * *
13769 TAAACAACACCTTCCAATGGGGAAGGGCAAA-T-----TGAGAAAC
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATAAGCAAC
* * * *
13809 TAAACAACACCTTTCGGTGGGGAAGGGCGAACTGGG----A--AAC
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATAAGCAAC
* *
13849 TAAACAACACCTTCCGGTGAGGAAGGGCAAACTGGGAATAAGCAGC
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATAAGCAAC
* *
13895 TAAACAACACCTTCCGATGAGGAAGGGCCAACTGGGAAT------T
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATAAGCAAC
* *
13935 TAAACAACACCTTCCGATGAGGAAGGGCAAATTGGGAATAGGCAAC
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATAAGCAAC
13981 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAT-AG----
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATAAGCAAC
**
14022 TAAACAACTTCTTCCGATGAGGAAGGGCAAACTGGGAATAAGCAAC
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATAAGCAAC
* * * * * * **
14068 TAGACAACACATTCCGGTGGGGAAGGGCAAATTAGGAATTTGACAAC
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATAAG-CAAC
* *
14115 TAGACAACACCTTCAGACTG-GGAAGGG
1 TAAACAACACCTTCCGA-TGAGGAAGGG
14142 TAAAACCGAA
Statistics
Matches: 347, Mismatches: 39, Indels: 50
0.80 0.09 0.11
Matches are distributed among these distances:
38 1 0.00
40 106 0.31
41 99 0.29
42 3 0.01
44 1 0.00
45 1 0.00
46 109 0.31
47 25 0.07
48 2 0.01
ACGTcount: A:0.37, C:0.20, G:0.27, T:0.16
Consensus pattern (46 bp):
TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATAAGCAAC
Found at i:14138 original size:47 final size:46
Alignment explanation
Indices: 14042--14141 Score: 112
Period size: 47 Copynumber: 2.2 Consensus size: 46
14032 CTTCCGATGA
* * *
14042 GGAAGGGCAAACTGGGAATAAGCAACTAGACAACACATTCCGGTGG
1 GGAAGGGCAAACTAGGAATAAGCAACTAGACAACACATTCAGCTGG
* ** *
14088 GGAAGGGCAAATTAGGAATTTGACAACTAGACAACACCTTCAGACT-G
1 GGAAGGGCAAACTAGGAATAAG-CAACTAGACAACACATTCAG-CTGG
14135 GGAAGGG
1 GGAAGGG
14142 TAAAACCGAA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
46 18 0.40
47 26 0.58
48 1 0.02
ACGTcount: A:0.37, C:0.18, G:0.30, T:0.15
Consensus pattern (46 bp):
GGAAGGGCAAACTAGGAATAAGCAACTAGACAACACATTCAGCTGG
Found at i:15445 original size:21 final size:21
Alignment explanation
Indices: 15419--15461 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
15409 GTTTCTGCTC
15419 GCTGACTTTCCCTTGAAAATG
1 GCTGACTTTCCCTTGAAAATG
15440 GCTGACTTTCCCTTGAAAATG
1 GCTGACTTTCCCTTGAAAATG
15461 G
1 G
15462 TTATAATGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (21 bp):
GCTGACTTTCCCTTGAAAATG
Found at i:22425 original size:33 final size:33
Alignment explanation
Indices: 22383--22455 Score: 137
Period size: 33 Copynumber: 2.2 Consensus size: 33
22373 GTGGGGAACG
*
22383 TAAGGGCGGCACCTCTCCCTAATCGTAAAGCCA
1 TAAGGGCGGCACCTCTCCCTAATCCTAAAGCCA
22416 TAAGGGCGGCACCTCTCCCTAATCCTAAAGCCA
1 TAAGGGCGGCACCTCTCCCTAATCCTAAAGCCA
22449 TAAGGGC
1 TAAGGGC
22456 AGCATAAACA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.27, C:0.33, G:0.22, T:0.18
Consensus pattern (33 bp):
TAAGGGCGGCACCTCTCCCTAATCCTAAAGCCA
Found at i:30736 original size:11 final size:10
Alignment explanation
Indices: 30718--30751 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
30708 GAAGTTCGTG
30718 TTTTGAAGAT
1 TTTTGAAGAT
30728 TTCTTGAAGAT
1 TT-TTGAAGAT
30739 ATTTTGAAGAT
1 -TTTTGAAGAT
30750 TT
1 TT
30752 GAAGACAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (10 bp):
TTTTGAAGAT
Found at i:33084 original size:178 final size:179
Alignment explanation
Indices: 32785--33135 Score: 677
Period size: 178 Copynumber: 2.0 Consensus size: 179
32775 ATTCCATCAT
32785 AGACCAATGAAAATTCAAGTGCATACTCAACCAAAATTTGTATTTCCATCCTATCAATGAAACAA
1 AGACCAATGAAAATTCAAGTGCATACTCAACCAAAATTTGTATTTCCATCCTATCAATGAAACAA
32850 AATAATAACCACCAAAGATTTTAAATAAGCTCAAAGGTGAAAACAAGTCTTAAA-TTTTTTTGGG
66 AATAATAACCACCAAAGATTTTAAATAAGCTCAAAGGTGAAAACAAGTCTTAAATTTTTTTTGGG
*
32914 GCTACTAGCCCATCACATCCCCCACTAGTGCTTTTTAAATGATGTAAAA
131 GCTACTAGCCCATCACATCCCCCACTAGTGCTTATTAAATGATGTAAAA
*
32963 AGACCAATGAAAATTCAAGTGCATACTCAACCAAAATTTGTATTTCCATCCTATCAATGAGACAA
1 AGACCAATGAAAATTCAAGTGCATACTCAACCAAAATTTGTATTTCCATCCTATCAATGAAACAA
33028 AATAATAACCACCAAAGATTTTAAATAAGCTCAAAGGTGAAAACAAGTCTTAAATTTTTTTTGGG
66 AATAATAACCACCAAAGATTTTAAATAAGCTCAAAGGTGAAAACAAGTCTTAAATTTTTTTTGGG
33093 GCTACTAGCCCATCACATCCCCCACTAGTGCTTATTAAATGAT
131 GCTACTAGCCCATCACATCCCCCACTAGTGCTTATTAAATGAT
33136 TTGTATAATT
Statistics
Matches: 170, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
178 118 0.69
179 52 0.31
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.28
Consensus pattern (179 bp):
AGACCAATGAAAATTCAAGTGCATACTCAACCAAAATTTGTATTTCCATCCTATCAATGAAACAA
AATAATAACCACCAAAGATTTTAAATAAGCTCAAAGGTGAAAACAAGTCTTAAATTTTTTTTGGG
GCTACTAGCCCATCACATCCCCCACTAGTGCTTATTAAATGATGTAAAA
Found at i:35824 original size:23 final size:23
Alignment explanation
Indices: 35793--35868 Score: 75
Period size: 23 Copynumber: 3.4 Consensus size: 23
35783 GTTTCTGGGG
*
35793 CTCCTCGCTGGTGGCAAGGTGAC
1 CTCCCCGCTGGTGGCAAGGTGAC
** * *
35816 CTCCCCGCTCATGTCAAGG-G-G
1 CTCCCCGCTGGTGGCAAGGTGAC
* *
35837 CTCCCTGCTGGTGGCAAGCTGAC
1 CTCCCCGCTGGTGGCAAGGTGAC
35860 CTCCCCGCT
1 CTCCCCGCT
35869 CACGGCAAGC
Statistics
Matches: 39, Mismatches: 12, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
21 14 0.36
22 2 0.05
23 23 0.59
ACGTcount: A:0.12, C:0.38, G:0.29, T:0.21
Consensus pattern (23 bp):
CTCCCCGCTGGTGGCAAGGTGAC
Found at i:35854 original size:21 final size:21
Alignment explanation
Indices: 35789--35854 Score: 53
Period size: 21 Copynumber: 3.0 Consensus size: 21
35779 CTAAGTTTCT
35789 GGGGCT-CCTCGCTGGTGGCAA
1 GGGGCTCCCT-GCTGGTGGCAA
* * ** *
35810 GGTGACCTCCCCGCTCATGTCAA
1 GG-G-GCTCCCTGCTGGTGGCAA
35833 GGGGCTCCCTGCTGGTGGCAA
1 GGGGCTCCCTGCTGGTGGCAA
35854 G
1 G
35855 CTGACCTCCC
Statistics
Matches: 32, Mismatches: 10, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
21 16 0.50
22 2 0.06
23 12 0.38
24 2 0.06
ACGTcount: A:0.12, C:0.32, G:0.36, T:0.20
Consensus pattern (21 bp):
GGGGCTCCCTGCTGGTGGCAA
Found at i:44993 original size:21 final size:21
Alignment explanation
Indices: 44949--44994 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
44939 CAGCGGCACA
* *
44949 TGGGTGCTCAAGCCAACAGGC
1 TGGGTGCTCAAGCAAACAGCC
* *
44970 TGGGTGCTCAGGCAAAGAGCC
1 TGGGTGCTCAAGCAAACAGCC
44991 TGGG
1 TGGG
44995 CGCCCACCCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.22, C:0.24, G:0.39, T:0.15
Consensus pattern (21 bp):
TGGGTGCTCAAGCAAACAGCC
Found at i:45146 original size:19 final size:20
Alignment explanation
Indices: 45108--45146 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
45098 GCTTGGTCCC
* *
45108 TTTGCTTCCAAATTTCAATT
1 TTTGCTACCAAATCTCAATT
45128 TTTGCTACCAAA-CTCAATT
1 TTTGCTACCAAATCTCAATT
45147 CCAACTTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.28, C:0.23, G:0.05, T:0.44
Consensus pattern (20 bp):
TTTGCTACCAAATCTCAATT
Found at i:62273 original size:22 final size:22
Alignment explanation
Indices: 62247--62317 Score: 88
Period size: 22 Copynumber: 3.2 Consensus size: 22
62237 CAAGGCGGAG
*
62247 TTTCAAGCGTCTTAGGGTAGAA
1 TTTCAAGCGTCTTAGGGTAGAC
* * * *
62269 TTTCAGGTGTCTAAGGGTTGAC
1 TTTCAAGCGTCTTAGGGTAGAC
*
62291 TTTCAAGCGTCTTAGGGCAGAC
1 TTTCAAGCGTCTTAGGGTAGAC
62313 TTTCA
1 TTTCA
62318 GGTGTCTAAG
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.34
Consensus pattern (22 bp):
TTTCAAGCGTCTTAGGGTAGAC
Found at i:62492 original size:59 final size:59
Alignment explanation
Indices: 62400--63420 Score: 851
Period size: 60 Copynumber: 17.0 Consensus size: 59
62390 TCGGGGCAGA
* * * * *
62400 CTTTCAAGCATTAGTTTGCCACGGACTGGCCTACTTCAGTGCCGACCACAGATTGGTCT
1 CTTTCAAGTATCAGTTGGCCACAGACTGGCCTACTTCAGTGTCGACCACAGATTGGTCT
* * *
62459 CTTTCATGTATCAGTTGGCCACAGACTGGCCTACTTCAATGTCGACCAAAGATTGGTCT
1 CTTTCAAGTATCAGTTGGCCACAGACTGGCCTACTTCAGTGTCGACCACAGATTGGTCT
* * ** *
62518 TTTTCAA-TCATGAGTTGGCCATGGACTGGCCTAGTTCAGTGTCGACCACAGATTGGTCT
1 CTTTCAAGT-ATCAGTTGGCCACAGACTGGCCTACTTCAGTGTCGACCACAGATTGGTCT
* * * * *
62577 CTTTCAAGCATGAGTTGGCCAC-GAACTGGCCTACTTCAGTATCGGCCAACAGAATGGTCT
1 CTTTCAAGTATCAGTTGGCCACAG-ACTGGCCTACTTCAGTGTCGACC-ACAGATTGGTCT
* * * * *
62637 CTTTCAAGTATCAGTCGGCCACGGAATGGCCTACTTCAGTATCGACCACATATTGGTCT
1 CTTTCAAGTATCAGTTGGCCACAGACTGGCCTACTTCAGTGTCGACCACAGATTGGTCT
* * *
62696 CTTTCAAGTATCAGTTGGCCACGGACTGGCCTACTTCAGTGTCGACCACAAATTGATCT
1 CTTTCAAGTATCAGTTGGCCACAGACTGGCCTACTTCAGTGTCGACCACAGATTGGTCT
* *
62755 CTTTTAAGTATCAGTTGGCCACAGACTGGCCTACTTCAGTGTCGACCACGGATTGGTCT
1 CTTTCAAGTATCAGTTGGCCACAGACTGGCCTACTTCAGTGTCGACCACAGATTGGTCT
* *** * * * * * *
62814 CTTTCAAATATCAGCATCAACCACAGATTGGTCTCTTTTAAGTATCAGT-T-GGCCGCGGACTGG
1 CTTTCAAGTATCAG--TTGGCCACAGACTGG-C-C---T-ACT-TCAGTGTCGACCACAGATTGG
62877 -C-
57 TCT
* * * * * **
62878 CTTCTTAAGTGTC-GAT---CACAGATTGGTCTGTTTCAAGTATCAGCATCGACCACAGATTGGT
1 CTT-TCAAGTATCAGTTGGCCACAGACTGGCCTACTTC-AG--T--G--TCGACCACAGATTGGT
62939 CT
58 CT
* *
62941 ATTTCAAGTATCAGTTGGCCACAGACTGGCCTATTTCAGTGTCGACCACAGATTGGTCT
1 CTTTCAAGTATCAGTTGGCCACAGACTGGCCTACTTCAGTGTCGACCACAGATTGGTCT
* * * * *
63000 CTTTCAAGTATCAGTTGGCTACGGACTAGCCTACTTCAAGTATTGACCACAGATTGGTCT
1 CTTTCAAGTATCAGTTGGCCACAGACTGGCCTACTTC-AGTGTCGACCACAGATTGGTCT
* * * * * * ** *
63060 CTTTCAGGTATTAGTTGGCTACGGACTGGCCAACTTCAAGTGTTGACTGCGGATTGGTCT
1 CTTTCAAGTATCAGTTGGCCACAGACTGGCCTACTTC-AGTGTCGACCACAGATTGGTCT
* * ** * * * ***
63120 CTTTCAGGTATTAGTTGGCTGCATACTAGCCTACTTCAAGTGTTGACCGTGGATTGGTCT
1 CTTTCAAGTATCAGTTGGCCACAGACTGGCCTACTTC-AGTGTCGACCACAGATTGGTCT
* * * *
63180 CTTT-AAGGTATTAGTTGGCTACAGACTAGCCTACTTCAAGTGTTGACCACAGATTGGTCT
1 CTTTCAA-GTATCAGTTGGCCACAGACTGGCCTACTTC-AGTGTCGACCACAGATTGGTCT
* * * * * *
63240 CTTTCAGGTATTAGTTGGCTACGGACTGGCCTACTTCAAGTGTTGACCACGGATTGGTCT
1 CTTTCAAGTATCAGTTGGCCACAGACTGGCCTACTTC-AGTGTCGACCACAGATTGGTCT
* * * * * *
63300 CTTTCATGTATTAGTTGGCTACAGACTAGCCTACTTCAAGTG-CTAACCACAGATTGGTAT
1 CTTTCAAGTATCAGTTGGCCACAGACTGGCCTACTTC-AGTGTC-GACCACAGATTGGTCT
* * * ** * * *
63360 CTTTCAGGTATTAGTTGGCTATGGACTAGCCTACTTCAATGTCGATCACAGATTGGTCT
1 CTTTCAAGTATCAGTTGGCCACAGACTGGCCTACTTCAGTGTCGACCACAGATTGGTCT
63419 CT
1 CT
63421 CTTTCATTTT
Statistics
Matches: 812, Mismatches: 115, Indels: 70
0.81 0.12 0.07
Matches are distributed among these distances:
52 2 0.00
53 3 0.00
54 1 0.00
55 1 0.00
57 1 0.00
58 2 0.00
59 347 0.43
60 370 0.46
61 23 0.03
62 9 0.01
63 6 0.01
64 4 0.00
65 9 0.01
66 26 0.03
67 3 0.00
68 5 0.01
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.32
Consensus pattern (59 bp):
CTTTCAAGTATCAGTTGGCCACAGACTGGCCTACTTCAGTGTCGACCACAGATTGGTCT
Found at i:62850 original size:93 final size:93
Alignment explanation
Indices: 62740--63013 Score: 422
Period size: 93 Copynumber: 2.9 Consensus size: 93
62730 TTCAGTGTCG
* * *
62740 ACCACAAATTGATCTCTTTTAAGTATCAGTTGGCCACAGACTGGCCTACTTCAGTGTCGACCACG
1 ACCACAGATTGGTCTCTTTTAAGTATCAGTTGGCCACAGACTGGCCTACTTCAGTGTCGACCACA
*
62805 GATTGGTCTCTTTCAAATATCAGCATCA
66 GATTGGTCTCTTTCAAGTATCAGCATCA
* * * * *
62833 ACCACAGATTGGTCTCTTTTAAGTATCAGTTGGCCGCGGACTGGCCTTCTTAAGTGTCGATCACA
1 ACCACAGATTGGTCTCTTTTAAGTATCAGTTGGCCACAGACTGGCCTACTTCAGTGTCGACCACA
* *
62898 GATTGGTCTGTTTCAAGTATCAGCATCG
66 GATTGGTCTCTTTCAAGTATCAGCATCA
* * *
62926 ACCACAGATTGGTCTATTTCAAGTATCAGTTGGCCACAGACTGGCCTATTTCAGTGTCGACCACA
1 ACCACAGATTGGTCTCTTTTAAGTATCAGTTGGCCACAGACTGGCCTACTTCAGTGTCGACCACA
62991 GATTGGTCTCTTTCAAGTATCAG
66 GATTGGTCTCTTTCAAGTATCAG
63014 TTGGCTACGG
Statistics
Matches: 161, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 161 1.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.31
Consensus pattern (93 bp):
ACCACAGATTGGTCTCTTTTAAGTATCAGTTGGCCACAGACTGGCCTACTTCAGTGTCGACCACA
GATTGGTCTCTTTCAAGTATCAGCATCA
Found at i:62975 original size:32 final size:32
Alignment explanation
Indices: 62795--63014 Score: 147
Period size: 34 Copynumber: 7.1 Consensus size: 32
62785 CTACTTCAGT
* * *
62795 GTCGACCACGGATTGGTCTCTTTCAAATATCA
1 GTCGACCACAGATTGGTCTATTTCAAGTATCA
* * *
62827 GCATCAACCACAGATTGGTCTCTTTTAAGTATCA
1 G--TCGACCACAGATTGGTCTATTTCAAGTATCA
* * * * * *
62861 GTTGGCCGCGGACTGGCCT-TCTT-AAG--T--
1 GTCGACCACAGATTGGTCTAT-TTCAAGTATCA
* *
62888 GTCGATCACAGATTGGTCTGTTTCAAGTATCA
1 GTCGACCACAGATTGGTCTATTTCAAGTATCA
62920 GCATCGACCACAGATTGGTCTATTTCAAGTATCA
1 G--TCGACCACAGATTGGTCTATTTCAAGTATCA
* * * *
62954 GTTGGCCACAGACTGGCCTATTTC-AG--T--
1 GTCGACCACAGATTGGTCTATTTCAAGTATCA
*
62981 GTCGACCACAGATTGGTCTCTTTCAAGTATCA
1 GTCGACCACAGATTGGTCTATTTCAAGTATCA
63013 GT
1 GT
63015 TGGCTACGGA
Statistics
Matches: 143, Mismatches: 29, Indels: 32
0.70 0.14 0.16
Matches are distributed among these distances:
27 33 0.23
28 6 0.04
29 2 0.01
30 2 0.01
31 6 0.04
32 36 0.25
34 58 0.41
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (32 bp):
GTCGACCACAGATTGGTCTATTTCAAGTATCA
Found at i:62989 original size:152 final size:150
Alignment explanation
Indices: 62625--63070 Score: 479
Period size: 152 Copynumber: 2.9 Consensus size: 150
62615 GTATCGGCCA
* * *
62625 ACAGAATGGTCTCTTTCAAGTATCAGTCGGCCACGGAATGGCCTACTTCAGTATCGACCACATAT
1 ACAGAATGGTCTATTTCAAGTATCAGTCGGCCACGGAATGGCCTATTTCAGTATCGACCACAGAT
* * *
62690 TGGTCTCTTTCAAGTATCAGTTGGCCACGGACTGGCCTACTTCAGTGTCGACCACAAATTGATCT
66 TGGTCTCTTTCAAGTATCAGTTGGCCACGGACTGGCCTACTTAAGTGTCGACCACAGATTGGTCT
* * *
62755 CTTTTAAGTATCAGTTGGCC
131 CTTTCAAGTATCAGTCGACC
* * * * * * * *
62775 ACAGACTGGCCTACTTC-AG--T--GTCGACCACGGATTGGTCTCTTTCAAATATCAGCATCAAC
1 ACAGAATGGTCTATTTCAAGTATCAGTCGGCCACGGAATGG-C-C--T---ATTTCAGTATCGAC
* * * *
62835 CACAGATTGGTCTCTTTTAAGTATCAGTTGGCCGCGGACTGGCCTTCTTAAGTGTCGATCACAGA
59 CACAGATTGGTCTCTTTCAAGTATCAGTTGGCCACGGACTGGCCTACTTAAGTGTCGACCACAGA
*
62900 TTGGTCTGTTTCAAGTATCAGCATCGACC
124 TTGGTCTCTTTCAAGTATCAG--TCGACC
* * * * *
62929 ACAGATTGGTCTATTTCAAGTATCAGTTGGCCACAGACTGGCCTATTTCAGTGTCGACCACAGAT
1 ACAGAATGGTCTATTTCAAGTATCAGTCGGCCACGGAATGGCCTATTTCAGTATCGACCACAGAT
* * * *
62994 TGGTCTCTTTCAAGTATCAGTTGGCTACGGACTAGCCTACTTCAAGTATTGACCACAGATTGGTC
66 TGGTCTCTTTCAAGTATCAGTTGGCCACGGACTGGCCTACTT-AAGTGTCGACCACAGATTGGTC
*
63059 TCTTTCAGGTAT
130 TCTTTCAAGTAT
63071 TAGTTGGCTA
Statistics
Matches: 238, Mismatches: 43, Indels: 27
0.77 0.14 0.09
Matches are distributed among these distances:
145 14 0.06
146 1 0.00
147 2 0.01
149 3 0.01
150 13 0.05
152 140 0.59
153 29 0.12
154 18 0.08
155 3 0.01
157 2 0.01
158 1 0.00
159 12 0.05
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (150 bp):
ACAGAATGGTCTATTTCAAGTATCAGTCGGCCACGGAATGGCCTATTTCAGTATCGACCACAGAT
TGGTCTCTTTCAAGTATCAGTTGGCCACGGACTGGCCTACTTAAGTGTCGACCACAGATTGGTCT
CTTTCAAGTATCAGTCGACC
Found at i:63245 original size:28 final size:28
Alignment explanation
Indices: 63214--63305 Score: 78
Period size: 28 Copynumber: 3.1 Consensus size: 28
63204 ACTAGCCTAC
*
63214 TTCAAGTGTTGACCACAGATTGGTCTCT
1 TTCAAGTGTTGACCACGGATTGGTCTCT
* * * * *
63242 TTCAGGTATTAGTTGGCTACGGACTGGCCTAC-
1 TTCA---AGT-GTTGACCACGGATTGGTCT-CT
63274 TTCAAGTGTTGACCACGGATTGGTCTCT
1 TTCAAGTGTTGACCACGGATTGGTCTCT
63302 TTCA
1 TTCA
63306 TGTATTAGTT
Statistics
Matches: 47, Mismatches: 11, Indels: 12
0.67 0.16 0.17
Matches are distributed among these distances:
27 1 0.02
28 23 0.49
29 2 0.04
31 2 0.04
32 18 0.38
33 1 0.02
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.35
Consensus pattern (28 bp):
TTCAAGTGTTGACCACGGATTGGTCTCT
Found at i:64085 original size:13 final size:13
Alignment explanation
Indices: 64067--64091 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
64057 GGAAAGGGGA
64067 AAAAAGAAAAAGG
1 AAAAAGAAAAAGG
64080 AAAAAGAAAAAG
1 AAAAAGAAAAAG
64092 AAGTTTATAG
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:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAGG
Found at i:66684 original size:36 final size:36
Alignment explanation
Indices: 66644--66717 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
66634 AATTAAAAAA
66644 AGCAAAGTACTTAAATCAGGGTAATTAAGTAAAAGC
1 AGCAAAGTACTTAAATCAGGGTAATTAAGTAAAAGC
*
66680 AGCAAAGTACTTAATTCAGGGTAATTAAGTAAAAGC
1 AGCAAAGTACTTAAATCAGGGTAATTAAGTAAAAGC
66716 AG
1 AG
66718 TTAAAGAACT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.46, C:0.11, G:0.20, T:0.23
Consensus pattern (36 bp):
AGCAAAGTACTTAAATCAGGGTAATTAAGTAAAAGC
Found at i:66780 original size:39 final size:39
Alignment explanation
Indices: 66729--67082 Score: 396
Period size: 39 Copynumber: 9.3 Consensus size: 39
66719 TAAAGAACTG
*
66729 AATTTCAAGGAAATTACGTAAAAGAAGACTGACTGACTT
1 AATTTCAAGGAAATTAGGTAAAAGAAGACTGACTGACTT
* * *
66768 AATTTCACGGAAATTAGGTCAAAGAAGATTGACTGACTT
1 AATTTCAAGGAAATTAGGTAAAAGAAGACTGACTGACTT
66807 AATTTCAAGGAAATTAGGTAAAAAGAAGACTGACTGACTT
1 AATTTCAAGGAAATTAGGT-AAAAGAAGACTGACTGACTT
* * * *
66847 AATTTCAAAGATATTAAGTAAAAGAATACTGACTGACTT
1 AATTTCAAGGAAATTAGGTAAAAGAAGACTGACTGACTT
* * *
66886 AATTTGAAAGAAATTAGGT-AAA-AAGA-AGACTGACTT
1 AATTTCAAGGAAATTAGGTAAAAGAAGACTGACTGACTT
* *
66922 AATTTCAAGGAAATTAGGTAAAAGAGGACTAACTGACTT
1 AATTTCAAGGAAATTAGGTAAAAGAAGACTGACTGACTT
*
66961 AGTTTCAAGGAAATTAGGTAAAAGAAGACTG---G-CTT
1 AATTTCAAGGAAATTAGGTAAAAGAAGACTGACTGACTT
* * * *
66996 AATTTCAAGGAAGGAAATTAGG-CAAAGAA-A--GACCGCCCT
1 AATTTC----AAGGAAATTAGGTAAAAGAAGACTGACTGACTT
67035 AATTTCAAGGAAATTAGGTAAAAGAAGACTG---G-CTT
1 AATTTCAAGGAAATTAGGTAAAAGAAGACTGACTGACTT
67070 AATTTCAAGGAAA
1 AATTTCAAGGAAA
67083 GAAATTAGGG
Statistics
Matches: 270, Mismatches: 29, Indels: 36
0.81 0.09 0.11
Matches are distributed among these distances:
35 36 0.13
36 34 0.13
37 8 0.03
38 13 0.05
39 145 0.54
40 34 0.13
ACGTcount: A:0.44, C:0.11, G:0.20, T:0.25
Consensus pattern (39 bp):
AATTTCAAGGAAATTAGGTAAAAGAAGACTGACTGACTT
Found at i:66871 original size:79 final size:78
Alignment explanation
Indices: 66729--67082 Score: 396
Period size: 79 Copynumber: 4.7 Consensus size: 78
66719 TAAAGAACTG
* * *
66729 AATTTCAAGGAAATTACGTAAAAGAAGACTGACTGACTTAATTTCACGGAAATTAGGTCAAAGAA
1 AATTTCAAGGAAATTAGGTAAAAGAAGACTGACTGACTTAATTTCAAGGAAATTAGGTAAAAGAA
*
66794 GATTGACTGACTT
66 GACTGACTGACTT
* * *
66807 AATTTCAAGGAAATTAGGTAAAAAGAAGACTGACTGACTTAATTTCAAAGATATTAAGTAAAAGA
1 AATTTCAAGGAAATTAGGT-AAAAGAAGACTGACTGACTTAATTTCAAGGAAATTAGGTAAAAGA
*
66872 ATACTGACTGACTT
65 AGACTGACTGACTT
* * * *
66886 AATTTGAAAGAAATTAGGT-AAA-AAGA-AGACTGACTTAATTTCAAGGAAATTAGGTAAAAGAG
1 AATTTCAAGGAAATTAGGTAAAAGAAGACTGACTGACTTAATTTCAAGGAAATTAGGTAAAAGAA
*
66948 GACTAACTGACTT
66 GACTGACTGACTT
* *
66961 AGTTTCAAGGAAATTAGGTAAAAGAAGACTG---G-CTTAATTTCAAGGAAGGAAATTAGG-CAA
1 AATTTCAAGGAAATTAGGTAAAAGAAGACTGACTGACTTAATTTC----AAGGAAATTAGGTAAA
* * *
67021 AGAA-A--GACCGCCCT
62 AGAAGACTGACTGACTT
67035 AATTTCAAGGAAATTAGGTAAAAGAAGACTG---G-CTTAATTTCAAGGAAA
1 AATTTCAAGGAAATTAGGTAAAAGAAGACTGACTGACTTAATTTCAAGGAAA
67083 GAAATTAGGG
Statistics
Matches: 240, Mismatches: 28, Indels: 24
0.82 0.10 0.08
Matches are distributed among these distances:
70 7 0.03
74 54 0.22
75 59 0.25
76 8 0.03
77 12 0.05
78 31 0.13
79 69 0.29
ACGTcount: A:0.44, C:0.11, G:0.20, T:0.25
Consensus pattern (78 bp):
AATTTCAAGGAAATTAGGTAAAAGAAGACTGACTGACTTAATTTCAAGGAAATTAGGTAAAAGAA
GACTGACTGACTT
Found at i:67066 original size:74 final size:74
Alignment explanation
Indices: 66729--67120 Score: 288
Period size: 74 Copynumber: 5.2 Consensus size: 74
66719 TAAAGAACTG
* *
66729 AATTTCAAGGAAATTACGTAAAAGAAGACTGACTGACTTAATTTC-ACG---GAAATTAGGTCAA
1 AATTTCAAGGAAATTAGGTAAAAGAAGACTG---G-CTTAATTTCAAGGAAAGAAATTAGG-CAA
* *
66790 AGAAGATTGACTGACTT
61 AGAA-A--GACCGACCT
* **
66807 AATTTCAAGGAAATTAGGTAAAAAGAAGACTGACTGACTTAATTTC----AAAGATATTAAGTAA
1 AATTTCAAGGAAATTAGGT-AAAAGAAGACTG---G-CTTAATTTCAAGGAAAGAAATT-AGGCA
* *
66868 AAGAATACTGACTGACTT
60 AAGAA-A--GACCGACCT
* * * *
66886 AATTTGAAAGAAATTAGGTAAAAAGAAGACTGACTTAATTTCAA-G---GAAATTAGGTAAAAGA
1 AATTTCAAGGAAATTAGGT-AAAAGAAGACTGGCTTAATTTCAAGGAAAGAAATTAGG-CAAAGA
* *
66947 GGACTA-ACTGACTT
64 --A--AGACCGACCT
* *
66961 AGTTTCAAGGAAATTAGGTAAAAGAAGACTGGCTTAATTTCAAGGAAGGAAATTAGGCAAAGAAA
1 AATTTCAAGGAAATTAGGTAAAAGAAGACTGGCTTAATTTCAAGGAAAGAAATTAGGCAAAGAAA
*
67026 GACCGCCCT
66 GACCGACCT
*
67035 AATTTCAAGGAAATTAGGTAAAAGAAGACTGGCTTAATTTCAAGGAAAGAAATTAGGGAAAGAAA
1 AATTTCAAGGAAATTAGGTAAAAGAAGACTGGCTTAATTTCAAGGAAAGAAATTAGGCAAAGAAA
* * *
67100 GTCTGACTT
66 GACCGACCT
67109 AATTTCAAGGAA
1 AATTTCAAGGAA
67121 GGAAATTAGG
Statistics
Matches: 271, Mismatches: 26, Indels: 38
0.81 0.08 0.11
Matches are distributed among these distances:
73 1 0.00
74 109 0.40
75 46 0.17
77 6 0.02
78 29 0.11
79 78 0.29
80 2 0.01
ACGTcount: A:0.44, C:0.10, G:0.20, T:0.25
Consensus pattern (74 bp):
AATTTCAAGGAAATTAGGTAAAAGAAGACTGGCTTAATTTCAAGGAAAGAAATTAGGCAAAGAAA
GACCGACCT
Found at i:67087 original size:113 final size:113
Alignment explanation
Indices: 66738--67141 Score: 345
Period size: 113 Copynumber: 3.5 Consensus size: 113
66728 GAATTTCAAG
* *
66738 GAAATTACGTAAAAGAAGACTGACTGACTTAATTTC----ACGGAAATTAGGTCAAAGAAGATTG
1 GAAATTAGGTAAAAGAA-A--GACTGACTTAATTTCAAGGAAGGAAATTAGGT-AAAGAA-A--G
* *
66799 ACTGACTTAATTTCAAGGAAATTAGGTAAAAAGAAGACTGACTGACTTAATTTC---AAA
59 ACCGACCTAATTTCAAGGAAATTAGGT-AAAAGAAGACTG---G-CTTAATTTCAAGAAA
* * * * *
66856 GATATTAAGTAAAAGAATACTGACTGACTTAATTT----GAAAGAAATTAGGTAAAAAGAAGACT
1 GAAATTAGGTAAAAGAA-A--GACTGACTTAATTTCAAGGAAGGAAATTAGGTAAAGA-AAGACC
* * * *
66917 GACTTAATTTCAAGGAAATTAGGTAAAAGAGGACTAACTGACTTAGTTTCAAG---
62 GACCTAATTTCAAGGAAATTAGGTAAAAGA--A--GACTGGCTTAATTTCAAGAAA
* * *
66970 GAAATTAGGTAAAAG-AAGACTGGCTTAATTTCAAGGAAGGAAATTAGGCAAAGAAAGACCGCCC
1 GAAATTAGGTAAAAGAAAGACTGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAAGACCGACC
67034 TAATTTCAAGGAAATTAGGTAAAAGAAGACTGGCTTAATTTCAAGGAAA
66 TAATTTCAAGGAAATTAGGTAAAAGAAGACTGGCTTAATTTCAA-GAAA
* *
67083 GAAATTAGG-GAAAGAAAGTCTGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAAGAC
1 GAAATTAGGTAAAAGAAAGACTGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAAGAC
67142 TAAGGCACAT
Statistics
Matches: 243, Mismatches: 25, Indels: 41
0.79 0.08 0.13
Matches are distributed among these distances:
109 14 0.06
110 14 0.06
111 1 0.00
112 5 0.02
113 84 0.35
114 43 0.18
115 28 0.12
116 1 0.00
117 5 0.02
118 48 0.20
ACGTcount: A:0.45, C:0.10, G:0.21, T:0.24
Consensus pattern (113 bp):
GAAATTAGGTAAAAGAAAGACTGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAAGACCGACC
TAATTTCAAGGAAATTAGGTAAAAGAAGACTGGCTTAATTTCAAGAAA
Found at i:67110 original size:39 final size:39
Alignment explanation
Indices: 66967--67142 Score: 220
Period size: 39 Copynumber: 4.6 Consensus size: 39
66957 ACTTAGTTTC
66967 AAGGAAATTAGGTAAA-AGAAGACTGGCTTAATTTCAAGG
1 AAGGAAATTAGGTAAAGA-AAGACTGGCTTAATTTCAAGG
* * * *
67006 AAGGAAATTAGGCAAAGAAAGACCGCCCTAATTTC----
1 AAGGAAATTAGGTAAAGAAAGACTGGCTTAATTTCAAGG
67041 AAGGAAATTAGGTAAA-AGAAGACTGGCTTAATTTCAAGG
1 AAGGAAATTAGGTAAAGA-AAGACTGGCTTAATTTCAAGG
* * * *
67080 AAAGAAATTAGGGAAAGAAAGTCTGACTTAATTTCAAGG
1 AAGGAAATTAGGTAAAGAAAGACTGGCTTAATTTCAAGG
67119 AAGGAAATTAGGTAAAGAAAGACT
1 AAGGAAATTAGGTAAAGAAAGACT
67143 AAGGCACATG
Statistics
Matches: 115, Mismatches: 15, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
34 1 0.01
35 29 0.25
39 83 0.72
40 2 0.02
ACGTcount: A:0.45, C:0.10, G:0.24, T:0.21
Consensus pattern (39 bp):
AAGGAAATTAGGTAAAGAAAGACTGGCTTAATTTCAAGG
Found at i:67264 original size:32 final size:33
Alignment explanation
Indices: 67171--67297 Score: 211
Period size: 33 Copynumber: 3.8 Consensus size: 33
67161 CAGGGAAGGA
*
67171 AATTAAGTAGAATAAAAGAACTTAATTCAGCGT
1 AATTAAGTAGAATAAAAGAACTTAATTCAGGGT
67204 AATTAAGTAGAATAAAAGAACTTAATTCAGGGT
1 AATTAAGTAGAATAAAAGAACTTAATTCAGGGT
67237 AATTAAGTAGAATAAAAG-ACTTAATTCAGGGT
1 AATTAAGTAGAATAAAAGAACTTAATTCAGGGT
67269 AATTAAGTAGAATCAATTAAGAACTTAAT
1 AATTAAGTAGAAT-AA--AAGAACTTAAT
67298 CTAAAAAGAG
Statistics
Matches: 89, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
32 27 0.30
33 52 0.58
35 3 0.03
36 7 0.08
ACGTcount: A:0.49, C:0.07, G:0.16, T:0.28
Consensus pattern (33 bp):
AATTAAGTAGAATAAAAGAACTTAATTCAGGGT
Found at i:67274 original size:65 final size:68
Alignment explanation
Indices: 67171--67297 Score: 215
Period size: 65 Copynumber: 1.9 Consensus size: 68
67161 CAGGGAAGGA
67171 AATTAAGTAGAATAAAAGAACTTAATTCAGCGTAATTAAGTAGAAT-AA-AAGAACTTAATTCAG
1 AATTAAGTAGAATAAAAGAACTTAATTCAGCGTAATTAAGTAGAATCAATAAGAACTTAATTCAG
67234 GGT
66 GGT
*
67237 AATTAAGTAGAATAAAAG-ACTTAATTCAGGGTAATTAAGTAGAATCAATTAAGAACTTAAT
1 AATTAAGTAGAATAAAAGAACTTAATTCAGCGTAATTAAGTAGAATCAA-TAAGAACTTAAT
67298 CTAAAAAGAG
Statistics
Matches: 57, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
65 26 0.46
66 20 0.35
68 11 0.19
ACGTcount: A:0.49, C:0.07, G:0.16, T:0.28
Consensus pattern (68 bp):
AATTAAGTAGAATAAAAGAACTTAATTCAGCGTAATTAAGTAGAATCAATAAGAACTTAATTCAG
GGT
Found at i:75319 original size:49 final size:49
Alignment explanation
Indices: 75247--75387 Score: 201
Period size: 49 Copynumber: 2.9 Consensus size: 49
75237 CAGGATGGGA
* *
75247 ATTTCTCCCAAAATACTCATAGTATTCATCAAGAGGGGCACCAGTGGCC
1 ATTTCTCCCAAAGTACTCATAGTAGTCATCAAGAGGGGCACCAGTGGCC
* *
75296 ATTTCTCCCAAAGTACTCATAGTAGTCATCAAGAGGGGCACTAGTTGCC
1 ATTTCTCCCAAAGTACTCATAGTAGTCATCAAGAGGGGCACCAGTGGCC
* * ** *
75345 GTTTCTCCCAAAGTGCTCATAAAAGCCATCAAGAGGGGCACCA
1 ATTTCTCCCAAAGTACTCATAGTAGTCATCAAGAGGGGCACCA
75388 ATCCTGTTCC
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 82 1.00
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.23
Consensus pattern (49 bp):
ATTTCTCCCAAAGTACTCATAGTAGTCATCAAGAGGGGCACCAGTGGCC
Found at i:78599 original size:22 final size:22
Alignment explanation
Indices: 78573--78661 Score: 72
Period size: 22 Copynumber: 4.0 Consensus size: 22
78563 CCTTTCTTCA
*
78573 AAGCGTTTCAAGGCAGACTTTC
1 AAGCGTCTCAAGGCAGACTTTC
* * *
78595 AAGCGTCTCAGGGTAGAATTTC
1 AAGCGTCTCAAGGCAGACTTTC
* * **
78617 AGGTGTCT-AAGGGTTGACTTTC
1 AAGCGTCTCAA-GGCAGACTTTC
* *
78639 AAGCGTCTCACGACAGACTTTC
1 AAGCGTCTCAAGGCAGACTTTC
78661 A
1 A
78662 GGTGTCTAAG
Statistics
Matches: 50, Mismatches: 15, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
21 1 0.02
22 48 0.96
23 1 0.02
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.28
Consensus pattern (22 bp):
AAGCGTCTCAAGGCAGACTTTC
Found at i:78661 original size:44 final size:44
Alignment explanation
Indices: 78588--78672 Score: 134
Period size: 44 Copynumber: 1.9 Consensus size: 44
78578 TTTCAAGGCA
* **
78588 GACTTTCAAGCGTCTCAGGGTAGAATTTCAGGTGTCTAAGGGTT
1 GACTTTCAAGCGTCTCACGACAGAATTTCAGGTGTCTAAGGGTT
*
78632 GACTTTCAAGCGTCTCACGACAGACTTTCAGGTGTCTAAGG
1 GACTTTCAAGCGTCTCACGACAGAATTTCAGGTGTCTAAGG
78673 ATTGGTCTCT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (44 bp):
GACTTTCAAGCGTCTCACGACAGAATTTCAGGTGTCTAAGGGTT
Found at i:78848 original size:59 final size:59
Alignment explanation
Indices: 78744--79413 Score: 750
Period size: 59 Copynumber: 11.3 Consensus size: 59
78734 TTGGGGTATA
* * * *
78744 CTTTCAAGCATTAGTTGGCCACGGACTGGCCTACTTCAGTGTCGACCACATATTGGTCT
1 CTTTCAAGTATCAGTTGGCCACAGACTGGCCTACTTCAGTGTCGACCACAGATTGGTCT
* * * *
78803 CTTTAAAGTATCAGTTGGCCACAGCCTGGCCTACTTCAATGTCGACCACATATTGGTCT
1 CTTTCAAGTATCAGTTGGCCACAGACTGGCCTACTTCAGTGTCGACCACAGATTGGTCT
* * * *
78862 CTTTCAAGCATGAGTTGGCCACGGATTGGCCTACTTCAGTGTCGACCACAGATTGGTCT
1 CTTTCAAGTATCAGTTGGCCACAGACTGGCCTACTTCAGTGTCGACCACAGATTGGTCT
* * *
78921 CTTTCAAG-ATTGAGTTGGCCACGGATTGGCCTACTTCAGTGTCGACCACAGATTGGTCT
1 CTTTCAAGTA-TCAGTTGGCCACAGACTGGCCTACTTCAGTGTCGACCACAGATTGGTCT
* * *
78980 CTTTCAAGTATGAGTTGGCCAC-GAACTGGCCTACTTCAGTATCGATCACAGATTGGTCT
1 CTTTCAAGTATCAGTTGGCCACAG-ACTGGCCTACTTCAGTGTCGACCACAGATTGGTCT
*
79039 CTTTCAAGTATCAGTTGGCCACAGACTCGCCTACTTCAGTGTCGACCACAGATTGGTCT
1 CTTTCAAGTATCAGTTGGCCACAGACTGGCCTACTTCAGTGTCGACCACAGATTGGTCT
* * *
79098 CTTTCAAGTATCAGTTGGCCACAGATTGGCCTACTTCAGTGTCGACCACGGATTAGTCT
1 CTTTCAAGTATCAGTTGGCCACAGACTGGCCTACTTCAGTGTCGACCACAGATTGGTCT
* * * *** * * * *
79157 CTTTTAAATATCAGGTGGCCTTGGACTGGCCTACTTCAAGTATTGACCACGGATTGATCT
1 CTTTCAAGTATCAGTTGGCCACAGACTGGCCTACTTC-AGTGTCGACCACAGATTGGTCT
* ** * * ** * *
79217 CTTTCAGGTATTTGTTGGCTACGGACTGGCCTACTTCAAGTGTTAACCGCGGATTGGTCT
1 CTTTCAAGTATCAGTTGGCCACAGACTGGCCTACTTC-AGTGTCGACCACAGATTGGTCT
* * * ** * * * *
79277 CTTTCAGGTATTAGTTGGCTACAGACTAACCTACTTCAATTGTTGACCGCGGATTGGTCT
1 CTTTCAAGTATCAGTTGGCCACAGACTGGCCTACTTC-AGTGTCGACCACAGATTGGTCT
* * * * * *
79337 CTTTCAGGTATTAGTTGTCTACAGACTAGCCTACTTCAGGTGTTGACCACAGATTGGTCT
1 CTTTCAAGTATCAGTTGGCCACAGACTGGCCTACTTCA-GTGTCGACCACAGATTGGTCT
* *
79397 CTTTCAGGTATTAGTTG
1 CTTTCAAGTATCAGTTG
79414 TGATCGAGCT
Statistics
Matches: 545, Mismatches: 60, Indels: 11
0.88 0.10 0.02
Matches are distributed among these distances:
58 2 0.00
59 352 0.65
60 191 0.35
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.32
Consensus pattern (59 bp):
CTTTCAAGTATCAGTTGGCCACAGACTGGCCTACTTCAGTGTCGACCACAGATTGGTCT
Found at i:79063 original size:32 final size:32
Alignment explanation
Indices: 79026--79126 Score: 106
Period size: 32 Copynumber: 3.3 Consensus size: 32
79016 CAGTATCGAT
79026 CACAGATTGGTCTCTTTCAAGTATCAGTTGGC
1 CACAGATTGGTCTCTTTCAAGTATCAGTTGGC
* * * * *
79058 CACAGACTCGCCTAC-TTC-AG--T--GTCGAC
1 CACAGATTGGTCT-CTTTCAAGTATCAGTTGGC
79085 CACAGATTGGTCTCTTTCAAGTATCAGTTGGC
1 CACAGATTGGTCTCTTTCAAGTATCAGTTGGC
79117 CACAGATTGG
1 CACAGATTGG
79127 CCTACTTCAG
Statistics
Matches: 52, Mismatches: 10, Indels: 14
0.68 0.13 0.18
Matches are distributed among these distances:
26 1 0.02
27 17 0.33
28 2 0.04
29 1 0.02
30 1 0.02
31 2 0.04
32 27 0.52
33 1 0.02
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.30
Consensus pattern (32 bp):
CACAGATTGGTCTCTTTCAAGTATCAGTTGGC
Found at i:80071 original size:11 final size:11
Alignment explanation
Indices: 80055--80080 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
80045 GTTCCTGCCC
80055 AATTTCCAGGA
1 AATTTCCAGGA
80066 AATTTCCAGGA
1 AATTTCCAGGA
80077 AATT
1 AATT
80081 CTAGAAGTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (11 bp):
AATTTCCAGGA
Found at i:81046 original size:12 final size:13
Alignment explanation
Indices: 81005--81049 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
80995 AATTATTGTT
81005 TGCTTTATTAATC
1 TGCTTTATTAATC
*
81018 TGCTTTATTAATT
1 TGCTTTATTAATC
81031 TGCTTTA-TAATC
1 TGCTTTATTAATC
81043 TGCTTTA
1 TGCTTTA
81050 GATTTAGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.22, C:0.13, G:0.09, T:0.56
Consensus pattern (13 bp):
TGCTTTATTAATC
Found at i:81057 original size:6 final size:6
Alignment explanation
Indices: 81046--81072 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
81036 TATAATCTGC
81046 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
81073 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:81411 original size:32 final size:32
Alignment explanation
Indices: 81367--81427 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
81357 TTGTTTTTGA
*
81367 TTTTCCGTTTTTTCTAAAAAAAAAAAAAAGTT
1 TTTTCCGATTTTTCTAAAAAAAAAAAAAAGTT
*
81399 TTTTCCGATTTTTCTAAATAAAAAAAAAA
1 TTTTCCGATTTTTCTAAAAAAAAAAAAAA
81428 TTTCCGTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.39
Consensus pattern (32 bp):
TTTTCCGATTTTTCTAAAAAAAAAAAAAAGTT
Done.