Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007782.1 Hibiscus syriacus cultivar Beakdansim tig00110065_pilon, 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: 3900615
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 19
Found at i:1508553 original size:28 final size:28
Alignment explanation
Indices: 1508494--1508556 Score: 92
Period size: 27 Copynumber: 2.3 Consensus size: 28
1508484 GAGTTTATTA
* *
1508494 AAAAATTTAATTTTTTAAATTTCAAAAT
1 AAAAATTAAAATTTTTAAATTTCAAAAT
*
1508522 -AAAATTAAAATTTTTAAATTTTAAAAT
1 AAAAATTAAAATTTTTAAATTTCAAAAT
1508549 AAAAATTA
1 AAAAATTA
1508557 GAGGGAACTC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 24 0.77
28 7 0.23
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (28 bp):
AAAAATTAAAATTTTTAAATTTCAAAAT
Found at i:1513146 original size:11 final size:11
Alignment explanation
Indices: 1513130--1513154 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1513120 GGAGCTTTGT
1513130 TTTGTAAAATA
1 TTTGTAAAATA
1513141 TTTGTAAAATA
1 TTTGTAAAATA
1513152 TTT
1 TTT
1513155 ATTTATGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (11 bp):
TTTGTAAAATA
Found at i:1519638 original size:26 final size:26
Alignment explanation
Indices: 1519609--1519677 Score: 129
Period size: 26 Copynumber: 2.7 Consensus size: 26
1519599 CGACACATTT
*
1519609 AAAAGTTATTCACATAATCCTTCAAA
1 AAAAGTTATTCACAGAATCCTTCAAA
1519635 AAAAGTTATTCACAGAATCCTTCAAA
1 AAAAGTTATTCACAGAATCCTTCAAA
1519661 AAAAGTTATTCACAGAA
1 AAAAGTTATTCACAGAA
1519678 ACTTTTCATG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.48, C:0.17, G:0.07, T:0.28
Consensus pattern (26 bp):
AAAAGTTATTCACAGAATCCTTCAAA
Found at i:1522217 original size:15 final size:15
Alignment explanation
Indices: 1522197--1522228 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1522187 TGACTAGTAT
1522197 AACATATAGTTACAC
1 AACATATAGTTACAC
1522212 AACATATAGTTACAC
1 AACATATAGTTACAC
1522227 AA
1 AA
1522229 TTAAATGCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.19, G:0.06, T:0.25
Consensus pattern (15 bp):
AACATATAGTTACAC
Found at i:1526439 original size:10 final size:10
Alignment explanation
Indices: 1526424--1526497 Score: 50
Period size: 10 Copynumber: 7.6 Consensus size: 10
1526414 CATTTAATAA
1526424 ATAAACGAAC
1 ATAAACGAAC
1526434 ATAAACGAAC
1 ATAAACGAAC
* *
1526444 ACAAAC-ATAA
1 ATAAACGA-AC
*
1526454 ATGACCACGAAC
1 AT-A-AACGAAC
*
1526466 ATAAATGAAC
1 ATAAACGAAC
1526476 AT----GAAC
1 ATAAACGAAC
1526482 ATAAACGAAC
1 ATAAACGAAC
1526492 ATAAAC
1 ATAAAC
1526498 ATTGGAGACC
Statistics
Matches: 49, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 34 0.69
11 2 0.04
12 5 0.10
13 1 0.02
ACGTcount: A:0.58, C:0.20, G:0.09, T:0.12
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:1526452 original size:16 final size:16
Alignment explanation
Indices: 1526431--1526499 Score: 75
Period size: 16 Copynumber: 4.3 Consensus size: 16
1526421 TAAATAAACG
1526431 AACATAAACGAACACA
1 AACATAAACGAACACA
* * *
1526447 AACATAAATGACCACG
1 AACATAAACGAACACA
* **
1526463 AACATAAATGAACATG
1 AACATAAACGAACACA
*
1526479 AACATAAACGAACATA
1 AACATAAACGAACACA
1526495 AACAT
1 AACAT
1526500 TGGAGACCCT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.58, C:0.20, G:0.09, T:0.13
Consensus pattern (16 bp):
AACATAAACGAACACA
Found at i:1527130 original size:14 final size:14
Alignment explanation
Indices: 1527113--1527158 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
1527103 AATGAACATA
*
1527113 AACAAACATAACCG
1 AACAAACATAAACG
1527127 AACAAACATAAACG
1 AACAAACATAAACG
*
1527141 AACATAAC-TGAACG
1 AACA-AACATAAACG
1527155 AACA
1 AACA
1527159 TAACTGAACG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 26 0.90
15 3 0.10
ACGTcount: A:0.59, C:0.24, G:0.09, T:0.09
Consensus pattern (14 bp):
AACAAACATAAACG
Found at i:1527159 original size:14 final size:14
Alignment explanation
Indices: 1527137--1527168 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
1527127 AACAAACATA
1527137 AACGAACATAACTG
1 AACGAACATAACTG
1527151 AACGAACATAACTG
1 AACGAACATAACTG
1527165 AACG
1 AACG
1527169 TTCAGAAACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.22, G:0.16, T:0.12
Consensus pattern (14 bp):
AACGAACATAACTG
Found at i:1527167 original size:24 final size:24
Alignment explanation
Indices: 1527093--1527161 Score: 93
Period size: 24 Copynumber: 2.9 Consensus size: 24
1527083 GATTGGCTTA
* * *
1527093 AACATAAATGAATGAACATAAACA
1 AACATAACTGAACGAACATAAACG
* *
1527117 AACATAACCGAACAAACATAAACG
1 AACATAACTGAACGAACATAAACG
1527141 AACATAACTGAACGAACATAA
1 AACATAACTGAACGAACATAA
1527162 CTGAACGTTC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.59, C:0.19, G:0.09, T:0.13
Consensus pattern (24 bp):
AACATAACTGAACGAACATAAACG
Found at i:1530574 original size:19 final size:21
Alignment explanation
Indices: 1530534--1530575 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
1530524 TATAAGTGAC
1530534 ATGATTACATGATCACAAGAT
1 ATGATTACATGATCACAAGAT
*
1530555 ATGA-TACATGA-CATAAGAT
1 ATGATTACATGATCACAAGAT
1530574 AT
1 AT
1530576 ATGAAAGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 9 0.45
20 7 0.35
21 4 0.20
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (21 bp):
ATGATTACATGATCACAAGAT
Found at i:1531108 original size:16 final size:17
Alignment explanation
Indices: 1531087--1531120 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1531077 GTGCACAACC
1531087 TCTATAG-ACTCACATA
1 TCTATAGTACTCACATA
*
1531103 TCTATAGTTCTCACATA
1 TCTATAGTACTCACATA
1531120 T
1 T
1531121 GTACATGGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.38
Consensus pattern (17 bp):
TCTATAGTACTCACATA
Found at i:1532961 original size:15 final size:15
Alignment explanation
Indices: 1532941--1532972 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1532931 TGACTAGTAT
1532941 AACATATAGTTACAC
1 AACATATAGTTACAC
1532956 AACATATAGTTACAC
1 AACATATAGTTACAC
1532971 AA
1 AA
1532973 TTAAATGCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.19, G:0.06, T:0.25
Consensus pattern (15 bp):
AACATATAGTTACAC
Found at i:1533276 original size:22 final size:19
Alignment explanation
Indices: 1533244--1533297 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
1533234 TACCCCCACC
*
1533244 ATGGTATCGATACTACTATACT
1 ATGGTACCGATACT-CTAT--T
1533266 ATGGTACCGATACTCTATT
1 ATGGTACCGATACTCTATT
*
1533285 ACGGTACCGATAC
1 ATGGTACCGATAC
1533298 CATTTTTGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 13 0.43
21 4 0.13
22 13 0.43
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (19 bp):
ATGGTACCGATACTCTATT
Found at i:1537874 original size:25 final size:26
Alignment explanation
Indices: 1537832--1537886 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 26
1537822 CTGTAAACAA
**
1537832 TTTATTTTTTGATTATTTATTTACTT
1 TTTATTTTTTGAAAATTTATTTACTT
*
1537858 TTTATTTTTT-AAAATTTATTTATTT
1 TTTATTTTTTGAAAATTTATTTACTT
1537883 TTTA
1 TTTA
1537887 AATTTTATCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 16 0.62
26 10 0.38
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (26 bp):
TTTATTTTTTGAAAATTTATTTACTT
Found at i:1537889 original size:17 final size:18
Alignment explanation
Indices: 1537858--1537894 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1537848 TTATTTACTT
1537858 TTTATTTTTTAAAATTTA
1 TTTATTTTTTAAAATTTA
*
1537876 TTTATTTTTTAAATTTTA
1 TTTATTTTTTAAAATTTA
1537894 T
1 T
1537895 CCTGCTTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTATTTTTTAAAATTTA
Found at i:1537892 original size:25 final size:25
Alignment explanation
Indices: 1537846--1537893 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1537836 TTTTTTGATT
**
1537846 ATTTATTTACTTTTTATTTTTTAAA
1 ATTTATTTACTTTTTAAATTTTAAA
*
1537871 ATTTATTTATTTTTTAAATTTTA
1 ATTTATTTACTTTTTAAATTTTA
1537894 TCCTGCTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (25 bp):
ATTTATTTACTTTTTAAATTTTAAA
Found at i:1539861 original size:35 final size:35
Alignment explanation
Indices: 1539815--1539994 Score: 234
Period size: 35 Copynumber: 5.1 Consensus size: 35
1539805 AAAGATGAAC
* * *
1539815 ACTTGAATCGAAAGTCCGATGCCTCTTTCCGTTCG
1 ACTTGAATCGAAAGTGCGATGCTTCCTTCCGTTCG
1539850 ACTTGAATCGAAAGTGCGATGCTTCCTTCCGTTCG
1 ACTTGAATCGAAAGTGCGATGCTTCCTTCCGTTCG
* * *
1539885 AATTGAATCGAAAGTGCGATGCTTCCTTTCGTTTG
1 ACTTGAATCGAAAGTGCGATGCTTCCTTCCGTTCG
* ** *
1539920 ACTTGAATCAAAAGTATAGATGCTTCATTCCGTTCG
1 ACTTGAATCGAAAGT-GCGATGCTTCCTTCCGTTCG
* * *
1539956 ACTTGAATCGAAAGTTCGATACTTCCTTCTGTTCG
1 ACTTGAATCGAAAGTGCGATGCTTCCTTCCGTTCG
1539991 ACTT
1 ACTT
1539995 TATTCACCTT
Statistics
Matches: 126, Mismatches: 18, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
35 97 0.77
36 29 0.23
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.34
Consensus pattern (35 bp):
ACTTGAATCGAAAGTGCGATGCTTCCTTCCGTTCG
Found at i:1539962 original size:71 final size:71
Alignment explanation
Indices: 1539815--1539994 Score: 231
Period size: 71 Copynumber: 2.6 Consensus size: 71
1539805 AAAGATGAAC
* * * *
1539815 ACTTGAATCGAAAGTCCGATGCCT-CTTTCCGTTCGACTTGAATCGAAAGTGCGATGCTTCCTTC
1 ACTTGAATCGAAAGTCCGATGCTTCCTTTCCGTTCGACTTGAATCAAAAGTGAGATGCTTCATTC
1539879 CGTTCG
66 CGTTCG
* * * *
1539885 AATTGAATCGAAAGTGCGATGCTTCCTTT-CGTTTGACTTGAATCAAAAGTATAGATGCTTCATT
1 ACTTGAATCGAAAGTCCGATGCTTCCTTTCCGTTCGACTTGAATCAAAAGT-GAGATGCTTCATT
1539949 CCGTTCG
65 CCGTTCG
* * *
1539956 ACTTGAATCGAAAGTTCGATACTTCC-TTCTGTTCGACTT
1 ACTTGAATCGAAAGTCCGATGCTTCCTTTCCGTTCGACTT
1539995 TATTCACCTT
Statistics
Matches: 94, Mismatches: 13, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
70 42 0.45
71 52 0.55
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.34
Consensus pattern (71 bp):
ACTTGAATCGAAAGTCCGATGCTTCCTTTCCGTTCGACTTGAATCAAAAGTGAGATGCTTCATTC
CGTTCG
Found at i:1542762 original size:2 final size:2
Alignment explanation
Indices: 1542755--1542787 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1542745 GACCCTAACC
1542755 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 T
1542788 GTTAGAAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1552312 original size:15 final size:15
Alignment explanation
Indices: 1552294--1552358 Score: 112
Period size: 15 Copynumber: 4.3 Consensus size: 15
1552284 CAAGGGTATT
1552294 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
1552309 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
**
1552324 GTAGTCCTTCAAGAC
1 GTAGTCCTTCGGGAC
1552339 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
1552354 GTAGT
1 GTAGT
1552359 GGTCCTACGG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 46 1.00
ACGTcount: A:0.17, C:0.25, G:0.31, T:0.28
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:1558577 original size:20 final size:20
Alignment explanation
Indices: 1558552--1558590 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1558542 AGTATGTCCA
1558552 GGGGGTATCGATTCCCCCTG
1 GGGGGTATCGATTCCCCCTG
1558572 GGGGGTATCGATTCCCCCT
1 GGGGGTATCGATTCCCCCT
1558591 AAAGGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.31, G:0.33, T:0.26
Consensus pattern (20 bp):
GGGGGTATCGATTCCCCCTG
Found at i:1565493 original size:21 final size:20
Alignment explanation
Indices: 1565454--1565491 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1565444 AGTATGTCCA
1565454 GGGGGTATCGATTCCCCCTG
1 GGGGGTATCGATTCCCCCTG
1565474 GGGGGTATCGATTCCCCC
1 GGGGGTATCGATTCCCCC
1565492 CTAAAGGAAA
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:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
GGGGGTATCGATTCCCCCTG
Found at i:1581509 original size:27 final size:27
Alignment explanation
Indices: 1581479--1581534 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
1581469 GAAGGCGTCG
* * *
1581479 AAGACTACAAAATAGAGAATAAGAGAA
1 AAGACTACAAAATAAAAAACAAGAGAA
*
1581506 AAGACTACACAATAAAAAACAAGAGAA
1 AAGACTACAAAATAAAAAACAAGAGAA
1581533 AA
1 AA
1581535 AATGACTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.66, C:0.11, G:0.14, T:0.09
Consensus pattern (27 bp):
AAGACTACAAAATAAAAAACAAGAGAA
Found at i:1583268 original size:25 final size:25
Alignment explanation
Indices: 1583234--1583282 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
1583224 ATTAAGCTTG
*
1583234 CCAGCTAGGCTAGTAGATGGTTATT
1 CCAGCTAGGCTAGTAGACGGTTATT
1583259 CCAGCTAGGCTAGTAGACGGTTAT
1 CCAGCTAGGCTAGTAGACGGTTAT
1583283 AGTTTTATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (25 bp):
CCAGCTAGGCTAGTAGACGGTTATT
Found at i:1584283 original size:21 final size:22
Alignment explanation
Indices: 1584258--1584300 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1584248 GGAAAGGTTG
1584258 GGCATATGGTTAAT-AGATGTT
1 GGCATATGGTTAATAAGATGTT
* *
1584279 GGCATATGTTTGATAAGATGTT
1 GGCATATGGTTAATAAGATGTT
1584301 CACTGGTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.28, C:0.05, G:0.28, T:0.40
Consensus pattern (22 bp):
GGCATATGGTTAATAAGATGTT
Found at i:1586641 original size:274 final size:274
Alignment explanation
Indices: 1586151--1586969 Score: 1318
Period size: 274 Copynumber: 3.0 Consensus size: 274
1586141 TTTTGAAACT
* * *
1586151 GTGGAACTCGTTAATGTATATGATGCGTTGAAGTCTTCTAACTGGAAAGTAGCAGTTCATGCTAA
1 GTGGAACCCGTTAATGTGTATGATGCATTGAAGTCTTCTAACTGGAAAGTAGCAGTTCATGCTAA
1586216 ATTTGATTCTTTACAGCGTAATGGTACATAGATTGTGGTAAAGTTACACCCTACGGTCAGTTGTA
66 A-TTGATTCTTTACAGCGTAATGGTACATAGATTGTGGTAAAGTTACACCCTACGGTCAGTTGTA
1586281 GGGTGTAAGTGGCTTTTTAAACTGAAAACTAATCCAAATGGTTCGGTTCATTGCTACAAGGCTCT
130 GGGTGTAAGTGGCTTTTTAAACTGAAAACTAATCCAAATGGTTCGGTTCATTGCTACAAGGCTCT
1586346 GTTGGTTTCTAAATGATTCTCTCAAGTCCCAGGACATGATTTCATTGGGACCTTTAGTCCAGTGG
195 GTTGGTTTCTAAATGATTCTCTCAAGTCCCAGGACATGATTTCATTGGGACCTTTAGTCCAGTGG
1586411 TTAAGTTTTCCAACA
260 TTAAGTTTTCCAACA
*
1586426 GTGGAACCCGTTAATATGTATGATGCATTGAAGTCTTCTAACTGGAAAGTAGCAGTTCATGCTAA
1 GTGGAACCCGTTAATGTGTATGATGCATTGAAGTCTTCTAACTGGAAAGTAGCAGTTCATGCTAA
1586491 ATTGATTCTTTACAGCGTAATGGTACATAGATTGTGGTAAAGTTACACCCTACGGTCAGTTGTAG
66 ATTGATTCTTTACAGCGTAATGGTACATAGATTGTGGTAAAGTTACACCCTACGGTCAGTTGTAG
*
1586556 GGTGTAAGTGGCTTTTTAAACTGAAAACTAATCCAAATGGTTCGTTTCATTGCTACAAGGCTCTG
131 GGTGTAAGTGGCTTTTTAAACTGAAAACTAATCCAAATGGTTCGGTTCATTGCTACAAGGCTCTG
*
1586621 TTGGTTTCTAAATGATTCTCTCAAGTCCCAGGATATGATTTCATTGGGACCTTTAGTCCAGTGGT
196 TTGGTTTCTAAATGATTCTCTCAAGTCCCAGGACATGATTTCATTGGGACCTTTAGTCCAGTGGT
*
1586686 TAAGTTTTCCAATA
261 TAAGTTTTCCAACA
* * ** *
1586700 GTGGAACCTGTTAATGTGTATGATGCATTGAAGTCTT-TCAATTGGAAAACAGCAGTTCATGTTG
1 GTGGAACCCGTTAATGTGTATGATGCATTGAAGTCTTCT-AACTGGAAAGTAGCAGTTCATGCT-
* * ** * * * * *
1586764 AATTTGATGCTTTACAGTATAATGGTACATGGATTGTGGTAAAGGTACCCCCTAGACGTTTAGTT
64 AAATTGATTCTTTACAGCGTAATGGTACATAGATTGTGGTAAAGTTACACCCT--ACGGTCAGTT
* * *
1586829 GTAAGGTGTAAGTGGCTTTTTAAACTGAAAACTAATCCAGATGGTTCGGTTCATCGCTACAAGGC
127 GTAGGGTGTAAGTGGCTTTTTAAACTGAAAACTAATCCAAATGGTTCGGTTCATTGCTACAAGGC
* * * *
1586894 TCTATTAGTTGCTAAAGGATTCTCTCAAGTCCCAGGACATGATTTCATTGGGACCTTTAGTCC-G
192 TCTGTTGGTTTCTAAATGATTCTCTCAAGTCCCAGGACATGATTTCATTGGGACCTTTAGTCCAG
1586958 ATGGTTAAGTTT
257 -TGGTTAAGTTT
1586970 GCTACACTTC
Statistics
Matches: 508, Mismatches: 31, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
273 1 0.00
274 260 0.51
275 108 0.21
276 1 0.00
277 138 0.27
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.34
Consensus pattern (274 bp):
GTGGAACCCGTTAATGTGTATGATGCATTGAAGTCTTCTAACTGGAAAGTAGCAGTTCATGCTAA
ATTGATTCTTTACAGCGTAATGGTACATAGATTGTGGTAAAGTTACACCCTACGGTCAGTTGTAG
GGTGTAAGTGGCTTTTTAAACTGAAAACTAATCCAAATGGTTCGGTTCATTGCTACAAGGCTCTG
TTGGTTTCTAAATGATTCTCTCAAGTCCCAGGACATGATTTCATTGGGACCTTTAGTCCAGTGGT
TAAGTTTTCCAACA
Found at i:1589845 original size:25 final size:25
Alignment explanation
Indices: 1589817--1589869 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
1589807 CATTCTCCAG
*
1589817 CTTT-TTTTTCTTCACTTTTCTTCTT
1 CTTTCTTTCTCTTCAC-TTTCTTCTT
*
1589842 CTTTCTTTCTCTTCACTTTCTTTTT
1 CTTTCTTTCTCTTCACTTTCTTCTT
1589867 CTT
1 CTT
1589870 CACTTTTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 15 0.60
26 10 0.40
ACGTcount: A:0.04, C:0.26, G:0.00, T:0.70
Consensus pattern (25 bp):
CTTTCTTTCTCTTCACTTTCTTCTT
Found at i:1589879 original size:16 final size:15
Alignment explanation
Indices: 1589817--1589875 Score: 65
Period size: 15 Copynumber: 4.3 Consensus size: 15
1589807 CATTCTCCAG
1589817 CTTT-TTTTTCTTCA
1 CTTTCTTTTTCTTCA
*
1589831 C-TT-TTCTTCTT--
1 CTTTCTTTTTCTTCA
*
1589842 CTTTCTTTCTCTTCA
1 CTTTCTTTTTCTTCA
1589857 CTTTCTTTTTCTTCA
1 CTTTCTTTTTCTTCA
1589872 CTTT
1 CTTT
1589876 TCTTCTTCTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
11 1 0.03
12 2 0.05
13 15 0.41
14 1 0.03
15 18 0.49
ACGTcount: A:0.05, C:0.27, G:0.00, T:0.68
Consensus pattern (15 bp):
CTTTCTTTTTCTTCA
Found at i:1589884 original size:16 final size:16
Alignment explanation
Indices: 1589824--1589884 Score: 55
Period size: 16 Copynumber: 4.2 Consensus size: 16
1589814 CAGCTTTTTT
1589824 TTCTTCACTTTTCTTC
1 TTCTTCACTTTTCTTC
*
1589840 TTC-T---TTCT-TTC
1 TTCTTCACTTTTCTTC
*
1589851 -TCTTCAC-TTTCTTT
1 TTCTTCACTTTTCTTC
1589865 TTCTTCACTTTTCTTC
1 TTCTTCACTTTTCTTC
1589881 TTCT
1 TTCT
1589885 CCTCTTATCA
Statistics
Matches: 34, Mismatches: 4, Indels: 14
0.65 0.08 0.27
Matches are distributed among these distances:
10 2 0.06
11 4 0.12
12 3 0.09
13 2 0.06
14 2 0.06
15 8 0.24
16 13 0.38
ACGTcount: A:0.05, C:0.30, G:0.00, T:0.66
Consensus pattern (16 bp):
TTCTTCACTTTTCTTC
Found at i:1591295 original size:15 final size:15
Alignment explanation
Indices: 1591275--1591318 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
1591265 TACGTGAAGA
1591275 AAAGTGAAGAGAAAG
1 AAAGTGAAGAGAAAG
1591290 AAAGTG-A-AG--A-
1 AAAGTGAAGAGAAAG
1591300 AAAGTGAAGAGAAAG
1 AAAGTGAAGAGAAAG
1591315 AAAG
1 AAAG
1591319 AAGAAGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
10 6 0.25
11 2 0.08
12 2 0.08
13 2 0.08
14 2 0.08
15 10 0.42
ACGTcount: A:0.61, C:0.00, G:0.32, T:0.07
Consensus pattern (15 bp):
AAAGTGAAGAGAAAG
Found at i:1591302 original size:25 final size:25
Alignment explanation
Indices: 1591268--1591341 Score: 121
Period size: 25 Copynumber: 2.9 Consensus size: 25
1591258 ATTCAGATAC
1591268 GTGAAGAAAAGTGAAGAGAAAGAAA
1 GTGAAGAAAAGTGAAGAGAAAGAAA
1591293 GTGAAGAAAAGTGAAGAGAAAGAAA
1 GTGAAGAAAAGTGAAGAGAAAGAAA
* *
1591318 GAAGAAGAAAAGTGAAGAAAAAGA
1 G-TGAAGAAAAGTGAAGAGAAAGA
1591342 TGGGAATGGG
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
25 26 0.57
26 20 0.43
ACGTcount: A:0.62, C:0.00, G:0.31, T:0.07
Consensus pattern (25 bp):
GTGAAGAAAAGTGAAGAGAAAGAAA
Found at i:1592034 original size:20 final size:20
Alignment explanation
Indices: 1592009--1592064 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
1591999 GTCTGACAAT
1592009 GAATCGGTTGAAAACCAGTA
1 GAATCGGTTGAAAACCAGTA
*
1592029 GAATCGATTGAAAACCAGTA
1 GAATCGGTTGAAAACCAGTA
* *
1592049 GAACCGGCTGAAAACC
1 GAATCGGTTGAAAACC
1592065 GATAAAATCG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.16
Consensus pattern (20 bp):
GAATCGGTTGAAAACCAGTA
Found at i:1592113 original size:30 final size:30
Alignment explanation
Indices: 1592049--1592105 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
1592039 AAAACCAGTA
* * *
1592049 GAACCGGCTGAAAACCGATAAAATCGGGGT
1 GAACCAGCTGAAAACCGACAAAACCGGGGT
*
1592079 GAACCAGCTGAAAACCGGCAAAACCGG
1 GAACCAGCTGAAAACCGACAAAACCGG
1592106 TTTGAACCGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.39, C:0.25, G:0.28, T:0.09
Consensus pattern (30 bp):
GAACCAGCTGAAAACCGACAAAACCGGGGT
Found at i:1593822 original size:28 final size:27
Alignment explanation
Indices: 1593792--1593883 Score: 75
Period size: 27 Copynumber: 3.4 Consensus size: 27
1593782 AATTTTTTAA
1593792 AAAATATATATATAAATTAATTATAGT
1 AAAATATATATATAAATTAATTATAGT
* *
1593819 AAAAT-TATAGTAGAATTTAACTTAT--T
1 AAAATATATA-TATAAATTAA-TTATAGT
* **
1593845 AAAAAATATATAATAAAGACAATT-TAGT
1 AAAATATATAT-ATAAA-TTAATTATAGT
1593873 AAAATATATAT
1 AAAATATATAT
1593884 TTCAATAATC
Statistics
Matches: 50, Mismatches: 8, Indels: 13
0.70 0.11 0.18
Matches are distributed among these distances:
26 11 0.22
27 22 0.44
28 17 0.34
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.37
Consensus pattern (27 bp):
AAAATATATATATAAATTAATTATAGT
Found at i:1593824 original size:39 final size:37
Alignment explanation
Indices: 1593744--1593824 Score: 92
Period size: 39 Copynumber: 2.1 Consensus size: 37
1593734 TTATCTTTTT
* *
1593744 AATTTTATAAAAAATATTATATAAATTTTATGAATTTA
1 AATTTTATAAAAAATATTATATAAATTTTAT-AAGTAA
*
1593782 AATTTTTTAAAAAATATATATATAAATTAATTAT-AGTAA
1 AATTTTATAAAAAATAT-TATATAAATT--TTATAAGTAA
1593821 AATT
1 AATT
1593825 ATAGTAGAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
38 16 0.43
39 17 0.46
41 4 0.11
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (37 bp):
AATTTTATAAAAAATATTATATAAATTTTATAAGTAA
Found at i:1595343 original size:2 final size:2
Alignment explanation
Indices: 1595336--1595362 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1595326 CTTTCAAATG
1595336 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 T
1595363 TTTTGGTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1597859 original size:21 final size:20
Alignment explanation
Indices: 1597773--1597930 Score: 95
Period size: 21 Copynumber: 7.8 Consensus size: 20
1597763 AAATGACCAA
**
1597773 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
1597792 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* **
1597812 CAGAATCGCAAATC-AGTTTT
1 CAAAATCGCAACGCGA-TTTT
1597832 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1597853 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1597874 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1597894 CAAGAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
1597915 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1597931 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1597959 original size:20 final size:20
Alignment explanation
Indices: 1597898--1598066 Score: 153
Period size: 20 Copynumber: 8.4 Consensus size: 20
1597888 GATTTTCAAG
* ** *
1597898 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1597918 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1597938 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1597958 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1597978 AATAGCAACGCATATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1597998 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
1598018 AATCGCAAC-TATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1598038 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1598058 AATCACAAC
1 AATCGCAAC
1598067 ACTGAAATTT
Statistics
Matches: 121, Mismatches: 24, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
19 2 0.02
20 117 0.97
21 2 0.02
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1597986 original size:60 final size:60
Alignment explanation
Indices: 1597917--1598047 Score: 169
Period size: 60 Copynumber: 2.2 Consensus size: 60
1597907 GCGAATATGA
*
1597917 AAATCGCAACGCGA-A-CACATAAATCGCAACGCGTATCCGTAAACCGCAACGTGT-ATCCGT
1 AAATCGCAACGC-ATATC-CATAAATCGCAACGCGTATCCGTAAACCGCAAC-TATAATCCGT
* * * *
1597977 AAATAGCAACGCATATCCGTAAATCGCAATGCGTATCCGTAAATCGCAACTATAATCCGT
1 AAATCGCAACGCATATCCATAAATCGCAACGCGTATCCGTAAACCGCAACTATAATCCGT
1598037 AAATCGCAACG
1 AAATCGCAACG
1598048 AGAATCTGTA
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
59 3 0.05
60 58 0.94
61 1 0.02
ACGTcount: A:0.37, C:0.27, G:0.17, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCATATCCATAAATCGCAACGCGTATCCGTAAACCGCAACTATAATCCGT
Found at i:1598798 original size:24 final size:24
Alignment explanation
Indices: 1598759--1598805 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1598749 AAATTTGGTC
1598759 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1598783 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1598806 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1598997 original size:12 final size:12
Alignment explanation
Indices: 1598980--1599004 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1598970 ATATAATTCT
1598980 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1598992 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1599004 G
1 G
1599005 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1601396 original size:72 final size:72
Alignment explanation
Indices: 1601303--1601536 Score: 295
Period size: 72 Copynumber: 3.3 Consensus size: 72
1601293 GCAACGAGAG
1601303 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1601368 AAATGAA
66 AAATGAA
* * *
1601375 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1601440 AAATGAA
66 AAATGAA
* * * * * *
1601447 AATCGCAACGAGAGAATCG-CAATGCGAA-ATGAAAATCGCAATGC-GAAATGAAAATCGCAA--
1 AATCGCAATGCGA-AAT-GAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATG
*
1601507 CG--A-GAG
64 CGAAATGAA
1601513 AATCGCAATGCGGAAATGAAAATC
1 AATCGCAATGC-GAAATGAAAATC
1601537 GCAATGCGAA
Statistics
Matches: 141, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
65 1 0.01
66 17 0.12
67 3 0.02
69 2 0.01
71 16 0.11
72 93 0.66
73 8 0.06
74 1 0.01
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (72 bp):
AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
AAATGAA
Found at i:1601424 original size:53 final size:52
Alignment explanation
Indices: 1601289--1601558 Score: 415
Period size: 53 Copynumber: 5.1 Consensus size: 52
1601279 CGGAAATTAC
*
1601289 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C--AA-GAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
1601336 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1601394 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
1601447 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1601499 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
1601552 AATCGCA
1 AATCGCA
1601559 TTGCGATTCT
Statistics
Matches: 207, Mismatches: 3, Indels: 20
0.90 0.01 0.09
Matches are distributed among these distances:
47 8 0.04
49 1 0.00
50 1 0.00
52 66 0.32
53 115 0.56
55 2 0.01
56 1 0.00
57 2 0.01
58 11 0.05
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:1601564 original size:72 final size:68
Alignment explanation
Indices: 1601270--1601563 Score: 276
Period size: 72 Copynumber: 4.2 Consensus size: 68
1601260 GCATTTGACT
** * * *
1601270 ATCGCAACACGGAAATTACAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAAC-AAG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAAG
1601334 AAA
66 AAA
*
1601337 ATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 ATCGCAATGCGGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAA
*
1601402 CG-AGAGA
61 CGAAGAAA
* * * * *
1601409 ATCGCAATGCGGAAATGAAAATCGCAATGCGA-AAT-GAAAAT-CGCAACGAGAGAATCGCAATG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCG-CAATGCGAAATGA-A-AATCGCAA--
1601471 CGAAATGAAA
61 CG-AA-GAAA
1601481 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAA--CG
1601545 AAATGAAA
63 -AA-GAAA
*
1601553 ATCGCATTGCG
1 ATCGCAATGCG
1601564 ATTCTCTCGT
Statistics
Matches: 189, Mismatches: 19, Indels: 32
0.79 0.08 0.13
Matches are distributed among these distances:
65 7 0.04
66 7 0.04
67 33 0.17
69 4 0.02
70 1 0.01
71 21 0.11
72 108 0.57
73 3 0.02
74 5 0.03
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.14
Consensus pattern (68 bp):
ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAAG
AAA
Found at i:1601578 original size:105 final size:105
Alignment explanation
Indices: 1601289--1601558 Score: 426
Period size: 105 Copynumber: 2.6 Consensus size: 105
1601279 CGGAAATTAC
*
1601289 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCCCAA--C--AA-GAAAATCGCAATGCG
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--C-
*
1601348 GAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
63 G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1601394 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAG
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAG
1601459 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
66 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1601499 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCA
1601559 TTGCGATTCT
Statistics
Matches: 157, Mismatches: 2, Indels: 12
0.92 0.01 0.07
Matches are distributed among these distances:
105 125 0.80
106 16 0.10
108 2 0.01
109 1 0.01
110 2 0.01
111 11 0.07
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (105 bp):
AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAG
AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:1601598 original size:53 final size:52
Alignment explanation
Indices: 1601535--1601650 Score: 160
Period size: 53 Copynumber: 2.2 Consensus size: 52
1601525 GAAATGAAAA
*
1601535 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
** ** **
1601587 TCCGCATTGCGATTTTTATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1601640 TCGCATTGCGA
1 TCGCATTGCGA
1601651 TTTTCATTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
52 11 0.20
53 45 0.80
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.40
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:1601613 original size:19 final size:19
Alignment explanation
Indices: 1601573--1601660 Score: 114
Period size: 19 Copynumber: 4.8 Consensus size: 19
1601563 GATTCTCTCG
1601573 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
*
1601593 TTGCGATTTTTATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1601612 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1601626 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1601645 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1601661 AACATAATGC
Statistics
Matches: 59, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
14 6 0.10
16 7 0.12
17 6 0.10
19 26 0.44
20 14 0.24
ACGTcount: A:0.14, C:0.22, G:0.16, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1601770 original size:14 final size:14
Alignment explanation
Indices: 1601751--1601787 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1601741 CTTCAATTAC
1601751 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1601765 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1601779 ACAAATCAA
1 ACAAATCAA
1601788 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1603753 original size:19 final size:19
Alignment explanation
Indices: 1603711--1603850 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
1603701 TAGTTTACTT
* *
1603711 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TCAAAA
* *
1603731 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATCAAAA
* *
1603750 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATCAAAA
*
1603769 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATCAAAA
*
1603788 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATCAAAA
*
1603807 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAATCAAAA
*
1603821 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATCAAAA
*
1603840 TCGCAATGCGA
1 TCGCAACGCGA
1603851 TTTTGGTTTC
Statistics
Matches: 100, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
14 9 0.09
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 73 0.73
20 12 0.12
ACGTcount: A:0.46, C:0.25, G:0.19, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATCAAAA
Found at i:1603881 original size:14 final size:14
Alignment explanation
Indices: 1603862--1603920 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
1603852 TTTGGTTTCG
1603862 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
1603876 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
1603893 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
1603909 CGTTGCGATTTT
1 CGTTGCGATTTT
1603921 CATTTCGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.29
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1603888 original size:33 final size:33
Alignment explanation
Indices: 1603846--1603969 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
1603836 AAAATCGCAA
*
1603846 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1603879 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
1603912 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
* *
1603945 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
1603970 AAGTAAACTA
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1603900 original size:19 final size:18
Alignment explanation
Indices: 1603846--1603937 Score: 83
Period size: 19 Copynumber: 5.4 Consensus size: 18
1603836 AAAATCGCAA
1603846 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
1603865 TGCGATTTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
1603879 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
1603898 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
1603912 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
1603931 TGCGATT
1 TGCGATT
1603938 CTCTCGTTGC
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 23 0.38
15 1 0.02
16 2 0.03
17 2 0.03
18 2 0.03
19 30 0.50
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:1603947 original size:14 final size:14
Alignment explanation
Indices: 1603895--1603951 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1603885 TTTGGTTTCG
*
1603895 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
1603909 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1603928 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1603942 CGTTGCGATT
1 CGTTGCGATT
1603952 TTAAGTTTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1604153 original size:93 final size:93
Alignment explanation
Indices: 1604017--1604390 Score: 709
Period size: 93 Copynumber: 4.1 Consensus size: 93
1604007 ATGGATTGCA
*
1604017 TTAC-TTCAACCAATAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1604081 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1604109 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1604174 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1604202 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1604267 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1604295 TTACTTTCAACC-AAAGACAAAACAAAGA-AAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
1604358 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1604386 TTACT
1 TTACT
1604391 AAGCAATCTA
Statistics
Matches: 279, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
91 67 0.24
92 20 0.07
93 192 0.69
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:1606106 original size:20 final size:20
Alignment explanation
Indices: 1606075--1606171 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
1606065 TTTTGGTTGA
1606075 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
1606095 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
1606115 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
1606134 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
1606149 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
1606169 AAT
1 AAT
1606172 CGCAACGCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 9 0.15
16 4 0.06
17 2 0.03
19 15 0.24
20 20 0.32
21 12 0.19
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:1606127 original size:21 final size:21
Alignment explanation
Indices: 1606073--1606137 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
1606063 TCTTTTGGTT
1606073 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
1606094 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
1606114 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
1606135 GAA
1 GAA
1606138 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:1606141 original size:14 final size:14
Alignment explanation
Indices: 1606122--1606178 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1606112 GAGAAATGAA
1606122 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1606136 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1606155 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1606169 AATCGCAACG
1 AATCGCAACG
1606179 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1606154 original size:33 final size:33
Alignment explanation
Indices: 1606073--1606195 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
1606063 TCTTTTGGTT
*
1606073 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAAC--GC
1606114 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1606147 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1606180 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1606196 TGCGATTTTG
Statistics
Matches: 81, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
33 50 0.62
35 7 0.09
38 1 0.01
40 1 0.01
41 22 0.27
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1606231 original size:14 final size:14
Alignment explanation
Indices: 1606212--1606268 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1606202 TTTGGTTTCG
1606212 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1606226 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1606245 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1606259 CGTTGCGATT
1 CGTTGCGATT
1606269 TTCATTTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1606244 original size:33 final size:33
Alignment explanation
Indices: 1606196--1606275 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
1606186 AAAATCGCAA
**
1606196 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1606229 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1606262 TGCGATTTTCATTT
1 TGCGATTTTCATTT
1606276 TTCTCGTTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.21, G:0.23, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1606281 original size:21 final size:21
Alignment explanation
Indices: 1606256--1606329 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
1606246 GTTGCGATTC
1606256 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
1606277 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
1606298 TCACGTTGCGATTTTCATTTA
1 TCTCGTTGCGATTTTCATTTT
1606319 TCTCGTTGCGA
1 TCTCGTTGCGA
1606330 CTCTTCTGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.14
21 32 0.73
22 6 0.14
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:1606451 original size:33 final size:33
Alignment explanation
Indices: 1606409--1606479 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1606399 AATACTAACT
1606409 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
1606442 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1606475 TGAAA
1 TGAAA
1606480 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:1606884 original size:20 final size:20
Alignment explanation
Indices: 1606859--1607010 Score: 189
Period size: 20 Copynumber: 7.6 Consensus size: 20
1606849 CTTTAAAAAT
1606859 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1606879 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1606899 CACATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
1606919 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1606939 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
1606959 CGCGTTGTGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1606979 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1606999 CGCGTTGCGATT
1 CGCGTTGCGATT
1607011 CTGGAAAATC
Statistics
Matches: 114, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
20 113 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1607915 original size:27 final size:27
Alignment explanation
Indices: 1607885--1607959 Score: 84
Period size: 27 Copynumber: 2.8 Consensus size: 27
1607875 TTAAAATAAA
1607885 AATAAAATAATTTTAAATTAAGTTAAT
1 AATAAAATAATTTTAAATTAAGTTAAT
1607912 AATAAAAT-ATATTT-AA-TAAGTTAAT
1 AATAAAATAAT-TTTAAATTAAGTTAAT
* *
1607937 ATAAAAAATATTTTTAAAGTTAA
1 A-ATAAAATAATTTTAAA-TTAA
1607960 TATATATAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
25 10 0.25
26 13 0.32
27 14 0.35
29 3 0.08
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (27 bp):
AATAAAATAATTTTAAATTAAGTTAAT
Found at i:1607947 original size:24 final size:24
Alignment explanation
Indices: 1607886--1607973 Score: 81
Period size: 24 Copynumber: 3.5 Consensus size: 24
1607876 TAAAATAAAA
1607886 ATAAAATAAT-TTTAAATTAAGTTAAT
1 ATAAAA-AATATTT-AA-TAAGTTAAT
*
1607912 AATAAAATATATTTAATAAGTTAAT
1 -ATAAAAAATATTTAATAAGTTAAT
*
1607937 ATAAAAAATATTT-TTAAAGTTAAT
1 ATAAAAAATATTTAAT-AAGTTAAT
1607961 ATATATAAAATAT
1 ATA-A-AAAATAT
1607974 CATGAAAATG
Statistics
Matches: 54, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
23 1 0.02
24 23 0.43
25 10 0.19
26 11 0.20
27 9 0.17
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (24 bp):
ATAAAAAATATTTAATAAGTTAAT
Found at i:1607952 original size:26 final size:26
Alignment explanation
Indices: 1607888--1607973 Score: 88
Period size: 26 Copynumber: 3.3 Consensus size: 26
1607878 AAATAAAAAT
* *
1607888 AAAATAATTTTAAATTAAGTTAATA-AT
1 AAAAT-ATTTTTAA-TAAGTTAATATAA
*
1607915 AAAATATATTTAATAAGTTAATATAA
1 AAAATATTTTTAATAAGTTAATATAA
1607941 AAAATATTTTT-A-AAGTTAATATATA
1 AAAATATTTTTAATAAGTTAATATA-A
1607966 TAAAATAT
1 -AAAATAT
1607974 CATGAAAATG
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
24 11 0.21
25 12 0.23
26 24 0.46
27 5 0.10
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (26 bp):
AAAATATTTTTAATAAGTTAATATAA
Found at i:1614562 original size:91 final size:91
Alignment explanation
Indices: 1614404--1614573 Score: 261
Period size: 91 Copynumber: 1.9 Consensus size: 91
1614394 TTGTTTATGA
* *
1614404 TCTTTTATGCAGGCCTTAAACAAATATGTTAAATATTAATTCCATGTCAACTGTTTGACATCTTT
1 TCTTTTATGCAAGCCTTAAACAAATATGTTAAATATTAATTCCATGTCAACTGTTTGACATCATT
1614469 TGTTGCTGTATTTTATGATATTTCAT
66 TGTTGCTGTATTTTATGATATTTCAT
* * * *
1614495 TCTTTTATGTAAGCCTTAAACAAATATGTTAAGTA-TATATTCCTTGTCAACTGTTTTACATCAT
1 TCTTTTATGCAAGCCTTAAACAAATATGTTAAATATTA-ATTCCATGTCAACTGTTTGACATCAT
*
1614559 TTGTTGCTGTTTTTT
65 TTGTTGCTGTATTTT
1614574 TCTTGAAGGT
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
90 2 0.03
91 69 0.97
ACGTcount: A:0.26, C:0.14, G:0.12, T:0.48
Consensus pattern (91 bp):
TCTTTTATGCAAGCCTTAAACAAATATGTTAAATATTAATTCCATGTCAACTGTTTGACATCATT
TGTTGCTGTATTTTATGATATTTCAT
Found at i:1616313 original size:19 final size:19
Alignment explanation
Indices: 1616289--1616327 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1616279 ATTACAACTT
1616289 TTGAAAAACAGTACGATAA
1 TTGAAAAACAGTACGATAA
1616308 TTGAAAAACAGTACGATAA
1 TTGAAAAACAGTACGATAA
1616327 T
1 T
1616328 GTTCATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.51, C:0.10, G:0.15, T:0.23
Consensus pattern (19 bp):
TTGAAAAACAGTACGATAA
Found at i:1616367 original size:2 final size:2
Alignment explanation
Indices: 1616360--1616442 Score: 157
Period size: 2 Copynumber: 41.0 Consensus size: 2
1616350 CAACTTGGTG
1616360 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1616402 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
1616443 GCACCAAATA
Statistics
Matches: 80, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 78 0.98
3 2 0.03
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1618352 original size:13 final size:13
Alignment explanation
Indices: 1618303--1618354 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
1618293 AATGACACTC
* *
1618303 AATGAACGTCATT
1 AATGAGCGTCATA
1618316 AATGAGCGTCATA
1 AATGAGCGTCATA
*
1618329 AAT-ATGTGTCATA
1 AATGA-GCGTCATA
*
1618342 AATGCGCGTCATA
1 AATGAGCGTCATA
1618355 GATTTATGAC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
12 1 0.03
13 31 0.97
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (13 bp):
AATGAGCGTCATA
Found at i:1619676 original size:19 final size:19
Alignment explanation
Indices: 1619652--1619689 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1619642 ATCTAGTAAT
* *
1619652 TTTAAAATTTTGTTTAAAA
1 TTTAAAATTATATTTAAAA
1619671 TTTAAAATTATATTTAAAA
1 TTTAAAATTATATTTAAAA
1619690 AACAAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
TTTAAAATTATATTTAAAA
Found at i:1623493 original size:3 final size:3
Alignment explanation
Indices: 1623485--1623547 Score: 117
Period size: 3 Copynumber: 21.0 Consensus size: 3
1623475 ATGTAATTAG
1623485 ATA ATA 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
*
1623533 ATA ACA ATA ATA ATA
1 ATA ATA ATA ATA ATA
1623548 TTTTTTAGAC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1624020 original size:43 final size:42
Alignment explanation
Indices: 1623831--1624020 Score: 109
Period size: 43 Copynumber: 4.4 Consensus size: 42
1623821 ATAACTTGGT
* * *
1623831 TCCTACGTGATGAGGACGATTGGTTATCTGAGGGTGACACGAC
1 TCCTACGTGATGAGGATGACTGGTTATCT-AGGATGACACGAC
* * *** * *
1623874 TCCTACGTGATAAAGA-GATCTGG-TCGGTA-GATGACACAAT
1 TCCTACGTGATGAGGATGA-CTGGTTATCTAGGATGACACGAC
* * * **
1623914 TCCTACGCGATGAGGAT-AGTAGGCTATCTTTAGGGATGATAACACGGT
1 TCCTACGTGATGAGGATGACT-GGTTATC--TA-GGATG---ACACGAC
* *
1623962 TCTTACGTGAAGAGGATGACTGGTTATCTAGGAATGACACGAC
1 TCCTACGTGATGAGGATGACTGGTTATCTAGG-ATGACACGAC
1624005 TCCTACGTGATGAGGA
1 TCCTACGTGATGAGGA
1624021 GGTCTGGTCG
Statistics
Matches: 107, Mismatches: 27, Indels: 26
0.67 0.17 0.16
Matches are distributed among these distances:
39 1 0.01
40 24 0.22
41 2 0.02
42 4 0.04
43 38 0.36
45 6 0.06
46 5 0.05
48 25 0.23
49 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.26
Consensus pattern (42 bp):
TCCTACGTGATGAGGATGACTGGTTATCTAGGATGACACGAC
Found at i:1624147 original size:131 final size:130
Alignment explanation
Indices: 1623818--1624168 Score: 416
Period size: 131 Copynumber: 2.7 Consensus size: 130
1623808 TTTAGGAAGG
* * *
1623818 ATGATAACTTGGTTCCTACGTGATGAGGACGATTGGTTATCTGAGGGTGACACGACTCCTACGTG
1 ATGATAACATGGTTCCTACGTGATGAGGATGACTGGTTATCT-AGGGTGACACGACTCCTACGTG
* * * * *
1623883 ATAAAGAGATCTGGTCGGTAGATGACACAATTCCTACGCGATGAGGATAGTAGGCTATCTTTAGG
65 ATGAGGAGATCTGGTCGGGAGATGACACAATTCCTACGCGATGAGGACAGTAGGCCATCTTTAGG
*
1623948 G
130 A
* * * *
1623949 ATGATAACACGGTTCTTACGTGAAGAGGATGACTGGTTATCTAGGAATGACACGACTCCTACGTG
1 ATGATAACATGGTTCCTACGTGATGAGGATGACTGGTTATCTAGG-GTGACACGACTCCTACGTG
* * ** * * *
1624014 ATGAGGAGGTCTGGTCGGGGGATGACACGGTTCTTACGTGATGAGGACAGTATGCCATCTTTAGG
65 ATGAGGAGATCTGGTCGGGAGATGACACAATTCCTACGCGATGAGGACAGTAGGCCATCTTTAGG
1624079 A
130 A
* ** * *
1624080 ATGAAAACATGGTTCCTATATGATGAGGATGACTGATTATCTATGGGTGACACGAATCCTACGTG
1 ATGATAACATGGTTCCTACGTGATGAGGATGACTGGTTATCTA-GGGTGACACGACTCCTACGTG
* * *
1624145 ATGAGGATATATGGTTGGG-GATGA
65 ATGAGGAGATCTGGTCGGGAGATGA
1624169 AACTGCTCAT
Statistics
Matches: 185, Mismatches: 33, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
130 8 0.04
131 175 0.95
132 2 0.01
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.27
Consensus pattern (130 bp):
ATGATAACATGGTTCCTACGTGATGAGGATGACTGGTTATCTAGGGTGACACGACTCCTACGTGA
TGAGGAGATCTGGTCGGGAGATGACACAATTCCTACGCGATGAGGACAGTAGGCCATCTTTAGGA
Found at i:1624219 original size:44 final size:42
Alignment explanation
Indices: 1624170--1624487 Score: 146
Period size: 44 Copynumber: 7.6 Consensus size: 42
1624160 TGGGGATGAA
*
1624170 ACTGCTCATACTATGATGAATCTTAGTCATCTAAGGGTGATAAC
1 ACTGCTCATACTATGATGAATCTTGGTCATC-AAGGGT-ATAAC
** * * * *
1624214 ACTGCTCATA-TGCGATGAGTCTTGGTTATCCAGGGT-TGAC
1 ACTGCTCATACTATGATGAATCTTGGTCATCAAGGGTATAAC
* *
1624254 ACAT-CTCCTACGTGATGAGGAGATC-TGG---TC-A-GGTATAAC
1 AC-TGCTCATAC-T-ATGATGA-ATCTTGGTCATCAAGGGTATAAC
*
1624293 ACTGCTCATACTATGATGAATCTTGGTCATCTAAGAGTGATAAC
1 ACTGCTCATACTATGATGAATCTTGGTCATC-AAGGGT-ATAAC
* * * * * *
1624337 ATTGCTCATACTATAATGAATCTTGGTTATCCATGGT-TGAC
1 ACTGCTCATACTATGATGAATCTTGGTCATCAAGGGTATAAC
* * * *
1624378 ACGGCTCCTACGTGATGAGGAGATC-TGG---TCAAGGG-ATGAC
1 ACTGCTCATAC-T-ATGATGA-ATCTTGGTCATCAAGGGTATAAC
*** * * * *
1624418 ACTGCTCATA-TGCAATGAGTCTTGGCCATCTGAGAGTGATAAC
1 ACTGCTCATACTATGATGAATCTTGGTCATC-AAGGGT-ATAAC
* *
1624461 ATTGCTTATACTATGATGAATCTTGGT
1 ACTGCTCATACTATGATGAATCTTGGT
1624488 TATCCATGGT
Statistics
Matches: 200, Mismatches: 47, Indels: 54
0.66 0.16 0.18
Matches are distributed among these distances:
36 5 0.03
37 15 0.08
38 6 0.03
39 12 0.06
40 33 0.17
41 15 0.08
42 8 0.04
43 47 0.23
44 59 0.29
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (42 bp):
ACTGCTCATACTATGATGAATCTTGGTCATCAAGGGTATAAC
Found at i:1624441 original size:124 final size:124
Alignment explanation
Indices: 1624116--1624585 Score: 590
Period size: 124 Copynumber: 3.8 Consensus size: 124
1624106 GGATGACTGA
* * ** * * ** *
1624116 TTATCTATGGGTGACACGAATCCTACGTGATGAGGATATATGGTTGGGGATGAAACTGCTCATAC
1 TTATCCATGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGGGATGACACTGCTCATAC
* * * * * ** *
1624181 TATGATGAATCTTAGTCATCTAAGGGTGATAACACTGCTCATA-TGCGATGAGTCTTGG
66 TACGATGAATCTTGGCCATCTAAGAGTGATAACATTGCTCATACTATGATGAATCTTGG
* ** * *
1624239 TTATCCAGGGTTGACACATCTCCTACGTGATGAGGAGATCTGGTCAGGTATAACACTGCTCATAC
1 TTATCCATGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGGGATGACACTGCTCATAC
* * *
1624304 TATGATGAATCTTGGTCATCTAAGAGTGATAACATTGCTCATACTATAATGAATCTTGG
66 TACGATGAATCTTGGCCATCTAAGAGTGATAACATTGCTCATACTATGATGAATCTTGG
1624363 TTATCCATGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAAGGGATGACACTGCTCATA
1 TTATCCATGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTC-AGGGATGACACTGCTCATA
* * * * *
1624428 -TGCAATGAGTCTTGGCCATCTGAGAGTGATAACATTGCTTATACTATGATGAATCTTGG
65 CTACGATGAATCTTGGCCATCTAAGAGTGATAACATTGCTCATACTATGATGAATCTTGG
*
1624487 TTATCCATGGTTGACACGGCTCCTACATGATGAGGACGAT-TGGTCAGGGATGACACTGCTCATA
1 TTATCCATGGTTGACACGGCTCCTACGTGATGAGGA-GATCTGGTCAGGGATGACACTGCTCATA
*
1624551 -TACGATGAGTCTTGGCCATCTAA-AGGTGATAACAT
65 CTACGATGAATCTTGGCCATCTAAGA-GTGATAACAT
1624586 GGTTCCTACG
Statistics
Matches: 306, Mismatches: 37, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
122 1 0.00
123 141 0.46
124 144 0.47
125 20 0.07
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.30
Consensus pattern (124 bp):
TTATCCATGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGGGATGACACTGCTCATAC
TACGATGAATCTTGGCCATCTAAGAGTGATAACATTGCTCATACTATGATGAATCTTGG
Found at i:1626014 original size:25 final size:24
Alignment explanation
Indices: 1625981--1626049 Score: 84
Period size: 25 Copynumber: 2.8 Consensus size: 24
1625971 TGCGTGTGCC
* *
1625981 TCTTATCTTCTATTTCTTTAATTTT
1 TCTTTTCTTCTTTTTCTTT-ATTTT
* *
1626006 TCTTTTCTTTTTTTTCTTTTTTTT
1 TCTTTTCTTCTTTTTCTTTATTTT
1626030 TCTTTTCTTCTTTTTTCTTT
1 TCTTTTCTTC-TTTTTCTTT
1626050 GTTCTGATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
24 13 0.34
25 25 0.66
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (24 bp):
TCTTTTCTTCTTTTTCTTTATTTT
Found at i:1626026 original size:10 final size:10
Alignment explanation
Indices: 1626002--1626035 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
1625992 ATTTCTTTAA
1626002 TTTTTCTTTTC
1 TTTTT-TTTTC
1626013 -TTTTTTTTC
1 TTTTTTTTTC
1626022 TTTTTTTTTC
1 TTTTTTTTTC
1626032 TTTT
1 TTTT
1626036 CTTCTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 5 0.23
10 17 0.77
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:1626026 original size:15 final size:14
Alignment explanation
Indices: 1626002--1626045 Score: 61
Period size: 14 Copynumber: 3.0 Consensus size: 14
1625992 ATTTCTTTAA
*
1626002 TTTTTCTTTTCTTT
1 TTTTTCTTTTTTTT
1626016 TTTTTCTTTTTTTT
1 TTTTTCTTTTTTTT
1626030 TCTTTTCTTCTTTTTT
1 T-TTTTCTT-TTTTTT
1626046 CTTTGTTCTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 14 0.52
15 7 0.26
16 6 0.22
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTTCTTTTTTTT
Found at i:1626034 original size:24 final size:26
Alignment explanation
Indices: 1625993--1626049 Score: 91
Period size: 25 Copynumber: 2.3 Consensus size: 26
1625983 TTATCTTCTA
1625993 TTTCTTTAATTTTTCTTTTCTT-TTT
1 TTTCTTTAATTTTTCTTTTCTTCTTT
*
1626018 TTTCTTT-TTTTTTCTTTTCTTCTTT
1 TTTCTTTAATTTTTCTTTTCTTCTTT
1626043 TTTCTTT
1 TTTCTTT
1626050 GTTCTGATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 13 0.43
25 17 0.57
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (26 bp):
TTTCTTTAATTTTTCTTTTCTTCTTT
Found at i:1626046 original size:15 final size:14
Alignment explanation
Indices: 1626003--1626049 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 14
1625993 TTTCTTTAAT
1626003 TTTTCTTTTCTTTT-
1 TTTTCTTTT-TTTTC
1626017 TTTTCTTTTTTTTTC
1 TTTTC-TTTTTTTTC
1626032 TTTTCTTCTTTTTTC
1 TTTTCTT-TTTTTTC
1626047 TTT
1 TTT
1626050 GTTCTGATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
14 11 0.37
15 19 0.63
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (14 bp):
TTTTCTTTTTTTTC
Found at i:1626048 original size:10 final size:9
Alignment explanation
Indices: 1626003--1626045 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
1625993 TTTCTTTAAT
1626003 TTTTCTTTTC
1 TTTT-TTTTC
1626013 TTTTTTTTC
1 TTTTTTTTC
1626022 TTTTTTTT-
1 TTTTTTTTC
*
1626030 TCTTTTCTTC
1 T-TTTTTTTC
1626040 TTTTTT
1 TTTTTT
1626046 CTTTGTTCTG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
8 1 0.03
9 23 0.79
10 5 0.17
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:1631840 original size:30 final size:30
Alignment explanation
Indices: 1631805--1631877 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 30
1631795 AATGGATTTA
*
1631805 TTTAGTGACCAAATTATAAATTTGGT-AAAG
1 TTTAGTGACCAAAGTATAAATTT-GTAAAAG
*
1631835 TTTAGTGACCAAAGTATAAATTTTTAAAAG
1 TTTAGTGACCAAAGTATAAATTTGTAAAAG
*
1631865 TTTAGGGACCAAA
1 TTTAGTGACCAAA
1631878 ATGTAATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
29 1 0.03
30 38 0.97
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.34
Consensus pattern (30 bp):
TTTAGTGACCAAAGTATAAATTTGTAAAAG
Found at i:1631886 original size:29 final size:30
Alignment explanation
Indices: 1631805--1631895 Score: 94
Period size: 30 Copynumber: 3.1 Consensus size: 30
1631795 AATGGATTTA
* * ***
1631805 TTTAGTGACCAAATTATAAATTTGGTAAAG
1 TTTAGGGACCAAAATATAAATTTTAAAAAG
* * *
1631835 TTTAGTGACCAAAGTATAAATTTTTAAAAG
1 TTTAGGGACCAAAATATAAATTTTAAAAAG
*
1631865 TTTAGGGACCAAAATGT-AATTTTAAAAAG
1 TTTAGGGACCAAAATATAAATTTTAAAAAG
1631894 TT
1 TT
1631896 ATATATGGGT
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 13 0.25
30 40 0.75
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.36
Consensus pattern (30 bp):
TTTAGGGACCAAAATATAAATTTTAAAAAG
Found at i:1633892 original size:61 final size:61
Alignment explanation
Indices: 1633792--1633906 Score: 178
Period size: 61 Copynumber: 1.9 Consensus size: 61
1633782 AAAAGTGGAT
1633792 ACGACCTTATGTATCATGTCCAGATTAGCACTATAGCGTAAGCTTAGTATAGGTGGTGGGC
1 ACGACCTTATGTATCATGTCCAGATTAGCACTATAGCGTAAGCTTAGTATAGGTGGTGGGC
* * * *
1633853 ACGACCTTATGTGT-ATTGTCCGGATTAGCACTATGGCGTAAGCTTAGTGTAGGT
1 ACGACCTTATGTATCA-TGTCCAGATTAGCACTATAGCGTAAGCTTAGTATAGGT
1633907 TTGGCACTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
60 1 0.02
61 48 0.98
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.31
Consensus pattern (61 bp):
ACGACCTTATGTATCATGTCCAGATTAGCACTATAGCGTAAGCTTAGTATAGGTGGTGGGC
Found at i:1634077 original size:45 final size:45
Alignment explanation
Indices: 1634013--1634194 Score: 249
Period size: 45 Copynumber: 4.0 Consensus size: 45
1634003 GGTAAGCATG
* * * *
1634013 AAAATAAGCTTACAAGCTTATGGAATAAATGGCAAGTGTATTGAT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
* * *
1634058 AAAATAAGTTTTCGAGCTTATGGGATAAATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
*
1634103 AAAATAAGCTTACGAGCTTATGCAATAAATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
* * *
1634148 AAAATAAGCTTACGAGCTTATGGGATAAAAT-ATATGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAAT-AAATGGTAAGTATATTGGT
1634193 AA
1 AA
1634195 GAAAGTTGTA
Statistics
Matches: 121, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
45 117 0.97
46 4 0.03
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.32
Consensus pattern (45 bp):
AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
Found at i:1636136 original size:3 final size:3
Alignment explanation
Indices: 1636128--1636211 Score: 123
Period size: 3 Copynumber: 28.0 Consensus size: 3
1636118 ATGTAATTAG
* * *
1636128 ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA ACA ACA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
1636176 ATA ATA ATA ATA ATA ATA ATA ATA ACA GTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1636212 TTTTTTAGAC
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 73 1.00
ACGTcount: A:0.65, C:0.05, G:0.01, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:1640414 original size:32 final size:32
Alignment explanation
Indices: 1640377--1640488 Score: 116
Period size: 32 Copynumber: 3.5 Consensus size: 32
1640367 TATTAGCAGT
* * *
1640377 GTGTTGTATTCAGATAATGCACAACAGTGTTA
1 GTGTTGTATTCAAATAATACACAACAGTGTCA
* * * *
1640409 GTGTTGCATTCAAATAATTCATAACAATGTCA
1 GTGTTGTATTCAAATAATACACAACAGTGTCA
* * *
1640441 TTGTTGTATTCAAATAATACACAATAGTATCA
1 GTGTTGTATTCAAATAATACACAACAGTGTCA
* *
1640473 GCGTTGTATTAAAATA
1 GTGTTGTATTCAAATA
1640489 TTGTAAAGTA
Statistics
Matches: 64, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 64 1.00
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (32 bp):
GTGTTGTATTCAAATAATACACAACAGTGTCA
Found at i:1641555 original size:28 final size:28
Alignment explanation
Indices: 1641514--1641567 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
1641504 GAACTATATC
1641514 AAATTCTTAGTTTCATACATAATGTTAA
1 AAATTCTTAGTTTCATACATAATGTTAA
*
1641542 AAATTCTTTA-TTTCATACATGATGTT
1 AAATTC-TTAGTTTCATACATAATGTT
1641568 TTCTGCCGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 21 0.88
29 3 0.12
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.46
Consensus pattern (28 bp):
AAATTCTTAGTTTCATACATAATGTTAA
Found at i:1644232 original size:23 final size:23
Alignment explanation
Indices: 1644182--1644238 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
1644172 TGTGAAATGT
1644182 TCTCTGCCTTTATGACACATTTA
1 TCTCTGCCTTTATGACACATTTA
* * *
1644205 TCTCTACCTTTGTGGCACATTT-
1 TCTCTGCCTTTATGACACATTTA
1644227 TGCTCTGCCTTT
1 T-CTCTGCCTTT
1644239 TGGTAGCTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 1 0.03
23 28 0.97
ACGTcount: A:0.14, C:0.28, G:0.12, T:0.46
Consensus pattern (23 bp):
TCTCTGCCTTTATGACACATTTA
Found at i:1647427 original size:36 final size:33
Alignment explanation
Indices: 1647363--1647450 Score: 113
Period size: 36 Copynumber: 2.5 Consensus size: 33
1647353 AATTAAATCA
*
1647363 TTAAACATTACATTAAGGATAAAAACAACGAAC
1 TTAAACATTACATTAAGGATAAAAACAACAAAC
*
1647396 TATGAACATTACATTAAGAAGATAAAAACAACAAAC
1 T-TAAACATTACATTAAG--GATAAAAACAACAAAC
*
1647432 TTAATACATTACGTTAAGG
1 TTAA-ACATTACATTAAGG
1647451 GCATAAATAC
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
33 1 0.02
34 16 0.34
35 2 0.04
36 28 0.60
ACGTcount: A:0.52, C:0.14, G:0.10, T:0.24
Consensus pattern (33 bp):
TTAAACATTACATTAAGGATAAAAACAACAAAC
Found at i:1647457 original size:36 final size:34
Alignment explanation
Indices: 1647363--1647462 Score: 112
Period size: 36 Copynumber: 2.9 Consensus size: 34
1647353 AATTAAATCA
*
1647363 TTAAACATTACATTAA-GGATAAAAACAACGAAC
1 TTAAACATTACATTAAGGGATAAAAACAACAAAC
* *
1647396 TATGAACATTACATTAAGAAGATAAAAACAACAAAC
1 T-TAAACATTACATTAAG-GGATAAAAACAACAAAC
* *
1647432 TTAATACATTACGTTAAGGGCATAAATACAA
1 TTAA-ACATTACATTAAGGG-ATAAAAACAA
1647463 TTAACCATTC
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
33 1 0.02
34 14 0.25
35 3 0.05
36 37 0.67
ACGTcount: A:0.53, C:0.14, G:0.10, T:0.23
Consensus pattern (34 bp):
TTAAACATTACATTAAGGGATAAAAACAACAAAC
Found at i:1648239 original size:33 final size:34
Alignment explanation
Indices: 1648168--1648239 Score: 103
Period size: 36 Copynumber: 2.1 Consensus size: 34
1648158 TAATGTACAT
1648168 TTTTCTGAAATGAAGTGATATATCACAGTTGAAAAG
1 TTTTCTGAAATGAAGTGATATATCACA--TGAAAAG
1648204 TTTTCTGAAATG-AGTTGATATATCAC-TGAAAAG
1 TTTTCTGAAATGAAG-TGATATATCACATGAAAAG
1648237 TTT
1 TTT
1648240 CTGTCACTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
33 10 0.29
35 2 0.06
36 23 0.66
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (34 bp):
TTTTCTGAAATGAAGTGATATATCACATGAAAAG
Found at i:1648365 original size:142 final size:143
Alignment explanation
Indices: 1648116--1648669 Score: 695
Period size: 143 Copynumber: 3.9 Consensus size: 143
1648106 AGTGATATAT
* * * * * * * * * *
1648116 CACTGAAACGTTTCAT-TCATTGCGCATTAAATGGTCAATGAGTAATGTACATTTTTCTGAAATG
1 CACTGAAAAGTTTC-TGCCATTGTGCATTATATGGCCTATGAGAAATGGACTTTTTTCTGATATG
*
1648180 AAGTGATATATCACAGTTGAAAAGTTTTCTGAAATGAGTTGATATATCACTGAAAAGTTTCTGTC
65 AAGTGATATATCACA-CTGAAAAGTTTTCTGAAATGAGTTGATATATCACTGAAAAGTTTCTGTC
*
1648245 ACTGAATTAATTGGG
129 ACCGAATTAATTGGG
* * * *
1648260 CACTGAAAAGTTTCTACCTTTGTGCATTATATGGCCTATGAGAAATGGA-TTTTTTATGGTATGA
1 CACTGAAAAGTTTCTGCCATTGTGCATTATATGGCCTATGAGAAATGGACTTTTTTCTGATATGA
*
1648324 AGTGATATATCACACTGAAAAGTTTTCTGAAATGAGTTGATATATCACTGAAAAGTTTTTGTCAC
66 AGTGATATATCACACTGAAAAGTTTTCTGAAATGAGTTGATATATCACTGAAAAGTTTCTGTCAC
* *
1648389 CAAATTATTTGGG
131 CGAATTAATTGGG
* * ** * * *
1648402 AATTGAAATTTTTCTGCCATTGTGCATTATATGGCCTACGAGAAATGAATGTTTTTTCTGATATG
1 CACTGAAAAGTTTCTGCCATTGTGCATTATATGGCCTATGAGAAATGGA-CTTTTTTCTGATATG
* * *
1648467 AAGTGATATATCA-ACTAAAAAGTTTTCTGAAATGAGTTGATATAACACTGAAGAGTTTCTGTCA
65 AAGTGATATATCACACTGAAAAGTTTTCTGAAATGAGTTGATATATCACTGAAAAGTTTCTGTCA
**
1648531 CCGAATTAATTATG
130 CCGAATTAATTGGG
* * * *
1648545 CACTGAAAAGTTTTTGCCATTGTGCATTATAGGGCCTATGAGAAATGGACATTTTTCTAATATGA
1 CACTGAAAAGTTTCTGCCATTGTGCATTATATGGCCTATGAGAAATGGACTTTTTTCTGATATGA
*
1648610 A-TGGATATATCCCAACTGAAAAGTTTTCT-AAATTGAGTTGATATATCACTGAAAAGTTTC
66 AGT-GATATATCAC-ACTGAAAAGTTTTCTGAAA-TGAGTTGATATATCACTGAAAAGTTTC
1648670 CATCACTTAA
Statistics
Matches: 352, Mismatches: 51, Indels: 14
0.84 0.12 0.03
Matches are distributed among these distances:
141 1 0.00
142 122 0.35
143 127 0.36
144 102 0.29
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.36
Consensus pattern (143 bp):
CACTGAAAAGTTTCTGCCATTGTGCATTATATGGCCTATGAGAAATGGACTTTTTTCTGATATGA
AGTGATATATCACACTGAAAAGTTTTCTGAAATGAGTTGATATATCACTGAAAAGTTTCTGTCAC
CGAATTAATTGGG
Found at i:1651668 original size:3 final size:3
Alignment explanation
Indices: 1651654--1651688 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
1651644 GTTTGGTAAG
1651654 TCT TCAT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TC-T TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1651689 ATTATCCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.03, C:0.31, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:1659337 original size:17 final size:18
Alignment explanation
Indices: 1659305--1659338 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1659295 TTCTATTTCT
1659305 TCATTCTTCTTGTTCTTC
1 TCATTCTTCTTGTTCTTC
*
1659323 TCATT-TTCTTTTTCTT
1 TCATTCTTCTTGTTCTT
1659339 GCTTCTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.06, C:0.24, G:0.03, T:0.68
Consensus pattern (18 bp):
TCATTCTTCTTGTTCTTC
Found at i:1662706 original size:17 final size:17
Alignment explanation
Indices: 1662659--1662714 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
1662649 AACCAAAACA
* * *
1662659 TTGATTGACCTGAACTA
1 TTGACTGACCCGAACTG
* *
1662676 TTGACTTACTCGAACTG
1 TTGACTGACCCGAACTG
*
1662693 TTGACTGACCCGAACCG
1 TTGACTGACCCGAACTG
1662710 TTGAC
1 TTGAC
1662715 CGAATAGAAC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (17 bp):
TTGACTGACCCGAACTG
Found at i:1662746 original size:22 final size:22
Alignment explanation
Indices: 1662702--1662747 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1662692 GTTGACTGAC
*
1662702 CCGAACCGTTGACCGAATAGAA
1 CCGAACCGTTAACCGAATAGAA
*
1662724 CCGAACTGTTAACC-AATATGAA
1 CCGAACCGTTAACCGAATA-GAA
1662746 CC
1 CC
1662748 TATGAAGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.37, C:0.28, G:0.17, T:0.17
Consensus pattern (22 bp):
CCGAACCGTTAACCGAATAGAA
Found at i:1663527 original size:13 final size:13
Alignment explanation
Indices: 1663509--1663556 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
1663499 GTTATAAATC
1663509 TATGACGCGCATT
1 TATGACGCGCATT
* * *
1663522 TATGACACACACT
1 TATGACGCGCATT
**
1663535 TATGACGCTTATT
1 TATGACGCGCATT
1663548 TATGACGCG
1 TATGACGCG
1663557 TAATGCTCAT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:1663724 original size:2 final size:2
Alignment explanation
Indices: 1663717--1663787 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
1663707 TTTCATAAAT
1663717 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
1663759 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
1663788 TGTAGATTGA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1669334 original size:15 final size:15
Alignment explanation
Indices: 1669316--1669346 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1669306 AAATTATAAA
1669316 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
1669331 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
1669346 T
1 T
1669347 CATCGATAAT
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:1673189 original size:2 final size:2
Alignment explanation
Indices: 1673182--1673206 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1673172 TTTACATTCT
1673182 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 T
1673207 TAATGACCTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1676571 original size:19 final size:19
Alignment explanation
Indices: 1676547--1676594 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1676537 ATCTAAGATT
1676547 TGGTCGTAACGTCAAGGTC
1 TGGTCGTAACGTCAAGGTC
1676566 TGGTCGTAACGTCAAGGTC
1 TGGTCGTAACGTCAAGGTC
*
1676585 GGGTC-TAACG
1 TGGTCGTAACG
1676595 CGTTACATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 5 0.18
19 23 0.82
ACGTcount: A:0.21, C:0.21, G:0.33, T:0.25
Consensus pattern (19 bp):
TGGTCGTAACGTCAAGGTC
Found at i:1683334 original size:43 final size:44
Alignment explanation
Indices: 1683249--1683341 Score: 134
Period size: 43 Copynumber: 2.1 Consensus size: 44
1683239 TCCTCATAGG
1683249 GGTATCGATACTAGGGTATTTTTTCAAAACATCGAATACAATTTT
1 GGTATCGATACTAGGGTA-TTTTTCAAAACATCGAATACAATTTT
* * *
1683294 GGTATCGATATTGGGGTA-TTTTCAAAACATCGAATGCAATTTT
1 GGTATCGATACTAGGGTATTTTTCAAAACATCGAATACAATTTT
*
1683337 CGTAT
1 GGTAT
1683342 TGGTACTTAG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
43 28 0.64
45 16 0.36
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (44 bp):
GGTATCGATACTAGGGTATTTTTCAAAACATCGAATACAATTTT
Found at i:1701663 original size:49 final size:46
Alignment explanation
Indices: 1701539--1701664 Score: 119
Period size: 49 Copynumber: 2.7 Consensus size: 46
1701529 TTTCAAAAGA
* * *
1701539 AAAAAAAAAGAAATAGTAAAATAAAAAATGGATAAATGTTAAATTT
1 AAAAAAAAATAAAAAATAAAATAAAAAATGGATAAATGTTAAATTT
* * **
1701585 AAAAAAAAATAAAAAAAATAAAGAAAAAATGAAGA-AAATGTTATTTTTT
1 AAAAAAAAATAAAAAATA-AAATAAAAAATG--GATAAATGTTA-AATTT
* *
1701634 CAAAAGAAATAAAGAAATAAAATAAAAAATG
1 AAAAAAAAATAAA-AAATAAAATAAAAAATG
1701665 TCAAATTTTT
Statistics
Matches: 64, Mismatches: 11, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
46 14 0.22
47 11 0.17
48 8 0.12
49 27 0.42
50 4 0.06
ACGTcount: A:0.68, C:0.01, G:0.10, T:0.21
Consensus pattern (46 bp):
AAAAAAAAATAAAAAATAAAATAAAAAATGGATAAATGTTAAATTT
Found at i:1702315 original size:484 final size:494
Alignment explanation
Indices: 1701363--1702363 Score: 1420
Period size: 484 Copynumber: 2.0 Consensus size: 494
1701353 GATCGATTAC
* *
1701363 AATTGCCCCTAAAAAGTCAAAAATATTAGATTGAAAGATAAATATTAAATAAATCAAAAAGAGAG
1 AATTGCCCCTAAAAAATCAAAAATATTAGATTAAAAGATAAATATTAAATAAATCAAAAAGAGAG
* *
1701428 AGAAAAAGAAAATTAAATTTGGAAAATAAAATAATAAAAGATAAAAATAAAAGTTGTTAAAAGAG
66 AGAAAAAGAAAATTAAATTAGG------AAATAATAAAAGA-AAAAATAAAAGATGTTAAAAGAG
1701493 AGAGATAAAATAAGTTAAGATGAAGAAAATATTAAATTTCAAAAGAAAAAAAAAAGAAATAGTAA
124 AGAGATAAAATAAGTTAAGATGAAGAAAATATTAAATTT----------AAAAAAGAAATAG-AA
*
1701558 AATAAAAAATGGATAAATGTTAAATTTAAAAAAAAATAAAAAAAATAAAGAAAAAATGAAGAAAA
178 AATAAAAAAGGGATAAATGTTAAATTTAAAAAAAAAT--AAAAAATAAAGAAAAAATGAAGAAAA
1701623 TGTTATTTTTTCAAAAGAAATAAAGAAATAAAATAAAAAATGTCAAATTTTTGAAATAATAAAAT
241 TGTTATTTTTTCAAAAGAAATAAAGAAATAAAATAAAAAATGTCAAATTTTTGAAATAATAAAAT
**
1701688 AAAGGAAATAAATAAAACTTAAGGGATCAAATTGGAACAAATTGAAATTTATTGGTCAAATAGAT
306 AAAGGAAATAAATAAAACTTAAGGGATCAAATTCAAACAAATTGAAATTTATTGGTCAAATAGAT
1701753 ACAAAAATGAGCTGCAAGAAATATTAAAAAGGTTAGGGGTTAAACTGCATAAATATAAAAATATA
371 ACAAAAATGAGCTGCAAGAAATATTAAAAAGGTTAGGGGTTAAACTGCATAAATATAAAAATATA
* * * *
1701818 AATAGGTACTAAATTGAAACAATTAAAAATTTCAGAGCCAATTTATAACATGTGACCAA
436 AAAAGGGACTAAATTGAAACAATTAAAAATTTCAAAGCCAATTTATAACAGGTGACCAA
* * *
1701877 AATTGCCCCTAAAAAAT-AAAAACTGTTAGATTAAAATATAAATATTAAATAAATCAAAGAGAGA
1 AATTGCCCCTAAAAAATCAAAAA-TATTAGATTAAAAGATAAATATTAAATAAATCAAAAAGAGA
1701941 GAGAAAAAAGAAAATTAAATTAGG-AA-AATAAAAG-AAAAATAAAAGATGTTAAAAGAGAGAGA
65 GAG-AAAAAGAAAATTAAATTAGGAAATAATAAAAGAAAAAATAAAAGATGTTAAAAGAGAGAGA
*
1702003 TAAAATAAGTTAAGATGAAGAAAATATTAAATTT-TAAAAG-AA-A-AAAATAAAAAAGGGATAA
129 TAAAATAAGTTAAGATGAAGAAAATATTAAATTTAAAAAAGAAATAGAAAATAAAAAAGGGATAA
* * * *
1702064 ATGTTAAATTTAAAAAAAAAT-CAAAATTATGAAAAAATGAAGAAAATGTTATTTTTTCAAAATA
194 ATGTTAAATTTAAAAAAAAATAAAAAATAAAGAAAAAATGAAGAAAATGTTATTTTTTCAAAAGA
** *
1702128 AATAAA-AAATAAAAT-TCAAAT-TC-AATTGTTTGAAATATTAAAATAAAGGAAATAAATAAAA
259 AATAAAGAAATAAAATAAAAAATGTCAAATT-TTTGAAATAATAAAATAAAGGAAATAAATAAAA
* * *
1702189 CTTAAGGGATCAAATTCAAACAAATTGAAATTTA-TGGATCAAATCGATGCAAAAAATGAGTTGC
323 CTTAAGGGATCAAATTCAAACAAATTGAAATTTATTGG-TCAAATAGATAC-AAAAATGAGCTGC
*
1702253 AAGAAATATTAAAAAGGTTAGGGGTTAAATTGCATAAATAT-AAAATATAAAAAGGGACTAAATT
386 AAGAAATATTAAAAAGGTTAGGGGTTAAACTGCATAAATATAAAAATATAAAAAGGGACTAAATT
* *
1702317 GAAACAATTCAAAATTTCAAAGCCAATTTATAACAGGTGATCAA
451 GAAACAATTAAAAATTTCAAAGCCAATTTATAACAGGTGACCAA
1702361 AAT
1 AAT
1702364 GAATTACATA
Statistics
Matches: 454, Mismatches: 28, Indels: 40
0.87 0.05 0.08
Matches are distributed among these distances:
483 7 0.02
484 140 0.31
485 56 0.12
486 9 0.02
487 45 0.10
490 38 0.08
492 1 0.00
493 2 0.00
494 5 0.01
505 61 0.13
507 8 0.02
508 2 0.00
513 5 0.01
514 56 0.12
515 19 0.04
ACGTcount: A:0.57, C:0.05, G:0.13, T:0.25
Consensus pattern (494 bp):
AATTGCCCCTAAAAAATCAAAAATATTAGATTAAAAGATAAATATTAAATAAATCAAAAAGAGAG
AGAAAAAGAAAATTAAATTAGGAAATAATAAAAGAAAAAATAAAAGATGTTAAAAGAGAGAGATA
AAATAAGTTAAGATGAAGAAAATATTAAATTTAAAAAAGAAATAGAAAATAAAAAAGGGATAAAT
GTTAAATTTAAAAAAAAATAAAAAATAAAGAAAAAATGAAGAAAATGTTATTTTTTCAAAAGAAA
TAAAGAAATAAAATAAAAAATGTCAAATTTTTGAAATAATAAAATAAAGGAAATAAATAAAACTT
AAGGGATCAAATTCAAACAAATTGAAATTTATTGGTCAAATAGATACAAAAATGAGCTGCAAGAA
ATATTAAAAAGGTTAGGGGTTAAACTGCATAAATATAAAAATATAAAAAGGGACTAAATTGAAAC
AATTAAAAATTTCAAAGCCAATTTATAACAGGTGACCAA
Found at i:1703340 original size:18 final size:18
Alignment explanation
Indices: 1703314--1703382 Score: 52
Period size: 17 Copynumber: 3.7 Consensus size: 18
1703304 AAAATTAATA
1703314 AAATA-ATAATATATTAT
1 AAATATATAATATATTAT
* *
1703331 AAATATATAATA-AATAA
1 AAATATATAATATATTAT
*
1703348 AAATAAAATAAATAATATTAAT
1 AAAT-ATAT-AAT-ATATT-AT
1703370 ATAATATATAATA
1 A-AATATATAATA
1703383 AAAAAACTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 11
0.70 0.11 0.20
Matches are distributed among these distances:
17 12 0.31
18 9 0.23
19 3 0.08
20 2 0.05
21 5 0.13
22 5 0.13
23 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AAATATATAATATATTAT
Found at i:1703347 original size:33 final size:35
Alignment explanation
Indices: 1703310--1703399 Score: 96
Period size: 40 Copynumber: 2.5 Consensus size: 35
1703300 AAAAAAAATT
1703310 AATAAAATAATAATATATT-ATA-AATATATAATA
1 AATAAAATAATAATATATTAATATAATATATAATA
1703343 AATAAAAATAAAATAAATAATATTAATATAATATATAATA
1 AAT-AAAAT--AAT-AAT-ATATTAATATAATATATAATA
1703383 AA-AAAACTATATAATAT
1 AATAAAA-TA-ATAATAT
1703400 TATATTTTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 15
0.76 0.00 0.24
Matches are distributed among these distances:
33 3 0.06
34 5 0.10
36 5 0.10
37 7 0.15
38 11 0.23
39 4 0.08
40 13 0.27
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (35 bp):
AATAAAATAATAATATATTAATATAATATATAATA
Found at i:1703357 original size:15 final size:15
Alignment explanation
Indices: 1703294--1703362 Score: 59
Period size: 15 Copynumber: 4.4 Consensus size: 15
1703284 GACCTGGACC
*
1703294 AAATAAAAAAAAAAT
1 AAATAAAAATAAAAT
*
1703309 TAAT-AAAATAATAAT
1 AAATAAAAATAA-AAT
* *
1703324 ATATTATAAATATATAAT
1 A-A--ATAAAAATAAAAT
1703342 AAATAAAAATAAAAT
1 AAATAAAAATAAAAT
1703357 AAATAA
1 AAATAA
1703363 TATTAATATA
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
14 6 0.14
15 23 0.55
16 1 0.02
17 1 0.02
18 6 0.14
19 5 0.12
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AAATAAAAATAAAAT
Found at i:1703376 original size:40 final size:38
Alignment explanation
Indices: 1703310--1703388 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 38
1703300 AAAAAAAATT
*
1703310 AATAAAATAATAATATATTATAAATATATAATAAATAAA
1 AATAAAATAATAATATAATATAAATATATAATAAA-AAA
1703349 AATAAAATAAATAATATTAATAT-AATATATAATAAAAAA
1 AATAAAAT-AATAATA-TAATATAAATATATAATAAAAAA
1703388 A
1 A
1703389 CTATATAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
39 12 0.32
40 20 0.54
41 5 0.14
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (38 bp):
AATAAAATAATAATATAATATAAATATATAATAAAAAA
Found at i:1703494 original size:13 final size:13
Alignment explanation
Indices: 1703476--1703502 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1703466 GAAACTATAT
1703476 ATACGTTTTCAAA
1 ATACGTTTTCAAA
1703489 ATACGTTTTCAAA
1 ATACGTTTTCAAA
1703502 A
1 A
1703503 CTATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (13 bp):
ATACGTTTTCAAA
Found at i:1703508 original size:71 final size:68
Alignment explanation
Indices: 1703453--1703758 Score: 323
Period size: 69 Copynumber: 4.3 Consensus size: 68
1703443 ATGTTTCCAA
* *
1703453 AAAAATATTTTAAGAAACTATATATACG-TTTTCAAAATACGTTTTCAAAACTATAT-TATATAC
1 AAAACTATTTTAA-AAACTATATATACGTTTTTCAAAA-ACGTTTTAAAAACTATATAT-TATAC
1703516 GTTTTC
63 GTTTTC
* * *** *
1703522 AAAAACCGTTTTTTAAAAACTATATATTATAAGTTTTTCAAAATTATTTTAAAAATTATATATTA
1 -AAAA-C-TATTTTAAAAAC--TATA-TATACGTTTTTCAAAAACGTTTTAAAAACTATATATTA
*
1703587 CACGTTTTC
60 TACGTTTTC
* * *
1703596 AAAATTATTTTAAAAAACTATATACTATG-TTTTCAAAACCGTTTTAAAAACTATATATTATACG
1 AAAACTATTTT-AAAAACTATATA-TACGTTTTTCAAAAACGTTTTAAAAACTATATATTATACG
1703660 TTTTC
64 TTTTC
* *
1703665 AAAACTATTTTAAAAAACTACATATTATACGTTTTTCAAAACCGTTTT-AAAGCTATATATTATA
1 AAAACTATTTT-AAAAACT--ATA-TATACGTTTTTCAAAAACGTTTTAAAAACTATATATTATA
1703729 CGTTTTC
62 CGTTTTC
1703736 AAAACTATTTTAAAAACTATATA
1 AAAACTATTTTAAAAACTATATA
1703759 GTATATGTTT
Statistics
Matches: 203, Mismatches: 20, Indels: 29
0.81 0.08 0.12
Matches are distributed among these distances:
67 2 0.01
68 3 0.01
69 55 0.27
70 18 0.09
71 48 0.24
72 31 0.15
73 8 0.04
74 28 0.14
75 10 0.05
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (68 bp):
AAAACTATTTTAAAAACTATATATACGTTTTTCAAAAACGTTTTAAAAACTATATATTATACGTT
TTC
Found at i:1703769 original size:35 final size:35
Alignment explanation
Indices: 1703453--1703801 Score: 329
Period size: 35 Copynumber: 9.8 Consensus size: 35
1703443 ATGTTTCCAA
*
1703453 AAAAATATTTTAAGAAAC--TATA-TATACGTTTTC
1 AAAACTATTTTAA-AAACTATATATTATACGTTTTC
*
1703486 AAAA-TACGTTTTCAAAACTATAT-TATATACGTTTTC
1 AAAACTA--TTTTAAAAACTATATAT-TATACGTTTTC
* *
1703522 AAAAACCGTTTTTTAAAAACTATATATTATAAGTTTTTC
1 -AAAA-C-TATTTTAAAAACTATATATTATACG-TTTTC
* * *
1703561 AAAATTATTTTAAAAATTATATATTACACGTTTTC
1 AAAACTATTTTAAAAACTATATATTATACGTTTTC
* *
1703596 AAAATTATTTTAAAAAACTATATACTAT--GTTTTC
1 AAAACTATTTT-AAAAACTATATATTATACGTTTTC
**
1703630 AAAACCGTTTTAAAAACTATATATTATACGTTTTC
1 AAAACTATTTTAAAAACTATATATTATACGTTTTC
*
1703665 AAAACTATTTTAAAAAACTACATATTATACGTTTTTC
1 AAAACTATTTT-AAAAACTATATATTATACG-TTTTC
** *
1703702 AAAACCGTTTT-AAAGCTATATATTATACGTTTTC
1 AAAACTATTTTAAAAACTATATATTATACGTTTTC
* * *
1703736 AAAACTATTTTAAAAACTATATAGTATATGTTTTT
1 AAAACTATTTTAAAAACTATATATTATACGTTTTC
*
1703771 AAAAATAAATTTCCT-AAAACTATATATTATA
1 AAAACT--ATTT--TAAAAACTATATATTATA
1703802 TAATTTCAAA
Statistics
Matches: 263, Mismatches: 31, Indels: 39
0.79 0.09 0.12
Matches are distributed among these distances:
32 2 0.01
33 23 0.09
34 33 0.13
35 74 0.28
36 63 0.24
37 22 0.08
38 38 0.14
39 7 0.03
40 1 0.00
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.42
Consensus pattern (35 bp):
AAAACTATTTTAAAAACTATATATTATACGTTTTC
Found at i:1710796 original size:78 final size:78
Alignment explanation
Indices: 1710690--1710842 Score: 188
Period size: 77 Copynumber: 2.0 Consensus size: 78
1710680 ATATAGTAAG
** *
1710690 TAAACATTAAAAGAATGTAATTTTGATTACAACTCTTTTAAT-TGATATTT-CATTCGGAA-TAA
1 TAAACATTAAAAGAATGTAATTCAGATTACAACTC-TTTAATGT-ATATTTAAATT--GAATTAA
1710752 TTAAATAAGATTTTAAA
62 TTAAATAAGATTTTAAA
* * *
1710769 TAAACATT-AAAGATTGTAATTCAGATTATAAGTCTTTAATGTATATTTAAATTGAATTAATTAA
1 TAAACATTAAAAGAATGTAATTCAGATTACAACTCTTTAATGTATATTTAAATTGAATTAATTAA
1710833 ATAAGATTTT
66 ATAAGATTTT
1710843 TTATTAATTC
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
76 3 0.05
77 29 0.45
78 25 0.38
79 8 0.12
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.42
Consensus pattern (78 bp):
TAAACATTAAAAGAATGTAATTCAGATTACAACTCTTTAATGTATATTTAAATTGAATTAATTAA
ATAAGATTTTAAA
Found at i:1731522 original size:2 final size:2
Alignment explanation
Indices: 1731515--1731562 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1731505 TTTTGATGAG
1731515 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1731557 AT AT AT
1 AT AT AT
1731563 TTGTTTTAGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1735491 original size:20 final size:21
Alignment explanation
Indices: 1735453--1735492 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1735443 ATTTTTTATA
* *
1735453 TTAATGTTTATTTATTTTTGT
1 TTAATGTTTATGTAGTTTTGT
1735474 TTAATG-TTATGTAGTTTTG
1 TTAATGTTTATGTAGTTTTG
1735493 ATAAACTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.20, C:0.00, G:0.15, T:0.65
Consensus pattern (21 bp):
TTAATGTTTATGTAGTTTTGT
Found at i:1735491 original size:21 final size:21
Alignment explanation
Indices: 1735422--1735491 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 21
1735412 TAATTGTAAG
*
1735422 GTTTTTATTTAGTGTTATGTAA
1 GTTTTTATTTAATGTTATGT-A
* *
1735444 TTTTTTATATTAATGTTTATTTA
1 GTTTTTAT-TTAATG-TTATGTA
*
1735467 -TTTTTGTTTAATGTTATGTA
1 GTTTTTATTTAATGTTATGTA
1735487 GTTTT
1 GTTTT
1735492 GATAAACTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
20 6 0.15
21 10 0.25
22 13 0.32
23 6 0.15
24 5 0.12
ACGTcount: A:0.21, C:0.00, G:0.13, T:0.66
Consensus pattern (21 bp):
GTTTTTATTTAATGTTATGTA
Found at i:1739849 original size:105 final size:105
Alignment explanation
Indices: 1739739--1740641 Score: 1527
Period size: 105 Copynumber: 8.6 Consensus size: 105
1739729 TTTGTCGGAT
* * * * *
1739739 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTCGATTCACCTCCTTTTGGGGTGAATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
* *
1739804 GGAACATGCTCTTCTCATTACGAACCTTCTCCTTTAAGAC
66 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
* *
1739844 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCTTTCTACGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
** *
1739909 GGAACATACTCTTCTCATTACGAACCTTCTCCTTTAAGAC
66 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
* *
1739949 GAGTTCTTCTCATTATGAACTTTTCTGGAAATATTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
*
1740014 GGAACAGGCTCTTCTCATTACGAACCTTCTCATTTAGGAC
66 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
1740054 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
* * *
1740119 GGAACAGGCTCTTCTTATTACGAACCTTCTCTTTTAGAAC
66 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
*
1740159 GAGTTCTTCTCATTATGAACTCTTCTGGAAATATTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
*
1740224 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTATAGGAC
66 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
* * *
1740264 GAGTTCTTCTCATTATGAACTCTTCTGGAAATATTGGCTCACCTTCTTCTGCGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
*
1740329 GGAACAGGCTCTTCTCATTACAAACCTTCTCCTTTAGGAC
66 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
1740369 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
*
1740434 GGAACAGGCTCTTCTCATTACAAACCTTCTCCTTTAGGAC
66 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
1740474 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
* *
1740539 GGAACAGGCTCTTCTCATTACGAACCATCTCCTTTAGGAT
66 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
* * * *
1740579 GAGTTCTTCTCATTCTGAACTCTTCTGGAAATGTTGGGTCACCTCCTTTTGTGGTGGATTTGA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGA
1740642 TTGTTGTTGA
Statistics
Matches: 758, Mismatches: 40, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
105 758 1.00
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.36
Consensus pattern (105 bp):
GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
Found at i:1741573 original size:8 final size:8
Alignment explanation
Indices: 1741562--1741670 Score: 86
Period size: 8 Copynumber: 14.0 Consensus size: 8
1741552 TTCATTTTTC
1741562 TTTTCATT
1 TTTTCATT
*
1741570 TTTTCTTT
1 TTTTCATT
*
1741578 TTTTCCTT
1 TTTTCATT
1741586 TTTT--TT
1 TTTTCATT
*
1741592 CTTT--TT
1 TTTTCATT
*
1741598 TTTTCTTTT
1 TTTTC-ATT
*
1741607 TTTTCTTTT
1 TTTTC-ATT
1741616 TTTTCATT
1 TTTTCATT
1741624 TTTTCATTT
1 TTTTCA-TT
*
1741633 TTTTTATT
1 TTTTCATT
1741641 TTTT-A-T
1 TTTTCATT
*
1741647 TTTTCACT
1 TTTTCATT
1741655 TTTTCATT
1 TTTTCATT
1741663 TTTTCATT
1 TTTTCATT
1741671 CATTCTCTTT
Statistics
Matches: 88, Mismatches: 7, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
6 15 0.17
7 2 0.02
8 48 0.55
9 23 0.26
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTCATT
Found at i:1741578 original size:18 final size:17
Alignment explanation
Indices: 1741557--1741650 Score: 100
Period size: 18 Copynumber: 5.3 Consensus size: 17
1741547 CCTTTTTCAT
1741557 TTTTCTTTTCATTTTTTC
1 TTTT-TTTTCATTTTTTC
* *
1741575 TTTTTTTCCTTTTTTTTC
1 TTTTTTTTC-ATTTTTTC
*
1741593 TTTTTTTTTCTTTTTTTTC
1 -TTTTTTTTC-ATTTTTTC
1741612 TTTTTTTTCATTTTTTC
1 TTTTTTTTCATTTTTTC
*
1741629 ATTTTTTTT-ATTTTTTA
1 -TTTTTTTTCATTTTTTC
1741646 TTTTT
1 TTTTT
1741651 CACTTTTTCA
Statistics
Matches: 68, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
16 5 0.07
17 18 0.26
18 28 0.41
19 17 0.25
ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTTTTTTCATTTTTTC
Done.