Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008426.1 Hibiscus syriacus cultivar Beakdansim tig00111210_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: 4445546
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 18
Found at i:1837810 original size:197 final size:198
Alignment explanation
Indices: 1837368--1837865 Score: 571
Period size: 197 Copynumber: 2.5 Consensus size: 198
1837358 GTGAAAGGGC
1837368 ATCATAATAACAATTTATAACAAATATTAATTTCTCAATAT-AAAAAATTATGACAAATAATATT
1 ATCATAATAACAATTTATAACAAATATTAATTTCT-AATATAAAAAAATTATGACAAATAATATT
** * * * *
1837432 -TTTTTCAATAACAAAATTGTAACAAATTTATTTATTTATTTACAATAATACTGTAAATATAGTC
65 CTTTCACAATAAC-AAATTGTAACAAATTTA--TA--TAGTTACAATAAAAATGTAAATATAATC
* * *
1837496 AAAATAAAAATTTATGTGAAATTTATTTCGTCACAATATTTTCTCAAAATAAAAACTTTCGACAA
125 AAAATAAAAAGTTATGTCAAATTTATTTCATCACAATATTTTCTCAAAATAAAAACTTTCGACAA
* *
1837561 ATTTGTTTT
190 ATTTATTTA
* * * * *
1837570 GTCATAATAACAATTTATAACAAATACTAATTTCTCA-ATAAAAAAATTATGACAAACAACATTC
1 ATCATAATAACAATTTATAACAAATATTAATTTCTAATATAAAAAAATTATGACAAATAATATTC
* * *
1837634 TTTCACAATAACAAATTGCAACAAATTTATATAGTTACAATAACAAAT-TAAATTTAATTAAAAT
66 TTTCACAATAACAAATTGTAACAAATTTATATAGTTACAATAA-AAATGTAAATATAATCAAAAT
* * *
1837698 AAAAAGTTATGTCAAATTTATTT-ATCTCAATATTTTGTCAAAA-ATAAAA-TTT-GTCATAATT
130 AAAAAGTTATGTCAAATTTATTTCATCACAATATTTTCTCAAAATA-AAAACTTTCGACA-AATT
1837759 TATTTA
193 TATTTA
* * * *
1837765 ATCAAAATAAAAATTTATAACAAATATTAATTTCTAAATATAAAAAAATTGTGACAAGTAATATT
1 ATCATAATAACAATTTATAACAAATATTAATTTCT-AATATAAAAAAATTATGACAAATAATATT
* * * * *
1837830 CTTTCAGAATAATACATTGTAACAAAATTATTTAGT
65 CTTTCACAATAACAAATTGTAACAAATTTATATAGT
1837866 CGCAGAAAAA
Statistics
Matches: 252, Mismatches: 37, Indels: 19
0.82 0.12 0.06
Matches are distributed among these distances:
194 3 0.01
195 43 0.17
196 22 0.09
197 97 0.38
198 2 0.01
199 2 0.01
200 2 0.01
201 38 0.15
202 43 0.17
ACGTcount: A:0.48, C:0.10, G:0.05, T:0.38
Consensus pattern (198 bp):
ATCATAATAACAATTTATAACAAATATTAATTTCTAATATAAAAAAATTATGACAAATAATATTC
TTTCACAATAACAAATTGTAACAAATTTATATAGTTACAATAAAAATGTAAATATAATCAAAATA
AAAAGTTATGTCAAATTTATTTCATCACAATATTTTCTCAAAATAAAAACTTTCGACAAATTTAT
TTA
Found at i:1839576 original size:19 final size:20
Alignment explanation
Indices: 1839533--1839578 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
1839523 TAATATGATG
* * *
1839533 GAAATTAATGTTTGAGTGTT
1 GAAATTGATGTTAGAATGTT
1839553 GAAATTGATGTTAGAATG-T
1 GAAATTGATGTTAGAATGTT
1839572 GAAATTG
1 GAAATTG
1839579 GATTATTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.39
Consensus pattern (20 bp):
GAAATTGATGTTAGAATGTT
Found at i:1841062 original size:30 final size:30
Alignment explanation
Indices: 1841026--1841130 Score: 122
Period size: 30 Copynumber: 3.5 Consensus size: 30
1841016 TGGTACTATG
*
1841026 GTGTGTAAGGACACTTCGTACAATATTATA
1 GTGTGTAAGGACACTTCGTACAATATTGTA
* * *
1841056 GTGTGTAAGGACACTTAGCACAACATTGTA
1 GTGTGTAAGGACACTTCGTACAATATTGTA
* * * *
1841086 GTGTGTAAGGTCAC-TCAGTGCAATACTGTG
1 GTGTGTAAGGACACTTC-GTACAATATTGTA
1841116 GTGTGTAAGGACACT
1 GTGTGTAAGGACACT
1841131 CAATGTATAT
Statistics
Matches: 61, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
29 1 0.02
30 60 0.98
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (30 bp):
GTGTGTAAGGACACTTCGTACAATATTGTA
Found at i:1841637 original size:18 final size:21
Alignment explanation
Indices: 1841614--1841660 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 21
1841604 TTATTATAGT
1841614 TAGTATTAAAA-AAAT-TTA-
1 TAGTATTAAAATAAATATTAC
1841632 TAGTA-TAAAATAAATATTAC
1 TAGTATTAAAATAAATATTAC
1841652 TA-TATTAAA
1 TAGTATTAAA
1841661 TTATATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 5 0.20
18 9 0.36
19 5 0.20
20 6 0.24
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.38
Consensus pattern (21 bp):
TAGTATTAAAATAAATATTAC
Found at i:1844914 original size:20 final size:19
Alignment explanation
Indices: 1844868--1844906 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1844858 GCTCAACAAT
1844868 AAAGGATCGATCCTTTTTG
1 AAAGGATCGATCCTTTTTG
*
1844887 AAAAGATCGATCCTTTTTG
1 AAAGGATCGATCCTTTTTG
1844906 A
1 A
1844907 GAGGGATCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (19 bp):
AAAGGATCGATCCTTTTTG
Found at i:1851769 original size:29 final size:29
Alignment explanation
Indices: 1851734--1851803 Score: 140
Period size: 29 Copynumber: 2.4 Consensus size: 29
1851724 AGTTCAAAAT
1851734 ATAACACATCAAGAACCTTGACAAGCAAA
1 ATAACACATCAAGAACCTTGACAAGCAAA
1851763 ATAACACATCAAGAACCTTGACAAGCAAA
1 ATAACACATCAAGAACCTTGACAAGCAAA
1851792 ATAACACATCAA
1 ATAACACATCAA
1851804 AACTAATACT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.53, C:0.24, G:0.09, T:0.14
Consensus pattern (29 bp):
ATAACACATCAAGAACCTTGACAAGCAAA
Found at i:1855378 original size:25 final size:25
Alignment explanation
Indices: 1855350--1855410 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
1855340 ACATGATTGT
* *
1855350 TTTATCTGCTTTCAATTATGACTGA
1 TTTATCTGATTTCAATTATGAATGA
*
1855375 TTTATCTGATTTGAATTATGAATGA
1 TTTATCTGATTTCAATTATGAATGA
*
1855400 TTTATATGATT
1 TTTATCTGATT
1855411 AAAATAATGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.28, C:0.08, G:0.13, T:0.51
Consensus pattern (25 bp):
TTTATCTGATTTCAATTATGAATGA
Found at i:1855420 original size:25 final size:25
Alignment explanation
Indices: 1855367--1855420 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
1855357 GCTTTCAATT
* * ** *
1855367 ATGACTGATTTATCTGATTTGAATT
1 ATGAATGATTTATATGATTAAAATA
1855392 ATGAATGATTTATATGATTAAAATA
1 ATGAATGATTTATATGATTAAAATA
1855417 ATGA
1 ATGA
1855421 TTTTTGTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.04, G:0.15, T:0.43
Consensus pattern (25 bp):
ATGAATGATTTATATGATTAAAATA
Found at i:1859286 original size:30 final size:31
Alignment explanation
Indices: 1859252--1859313 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
1859242 ATTTTTAGTT
*
1859252 GCACTGTA-TTAATTATTGTTCTTACATGTA
1 GCACTGTATTTAATTATTGTTCTCACATGTA
*
1859282 GCACTGTATTTAATTATTGTTCTCACTTGTA
1 GCACTGTATTTAATTATTGTTCTCACATGTA
1859313 G
1 G
1859314 GTTTATTTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 8 0.28
31 21 0.72
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.47
Consensus pattern (31 bp):
GCACTGTATTTAATTATTGTTCTCACATGTA
Found at i:1866582 original size:26 final size:26
Alignment explanation
Indices: 1866553--1866603 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
1866543 ATATTAGCCT
*
1866553 TGAAC-CCAAAAATGACCAGAATAACA
1 TGAACTCC-AAAATAACCAGAATAACA
1866579 TGAACTCCAAAATAACCAGAATAAC
1 TGAACTCCAAAATAACCAGAATAAC
1866604 CCTGAGTACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 21 0.91
27 2 0.09
ACGTcount: A:0.53, C:0.24, G:0.10, T:0.14
Consensus pattern (26 bp):
TGAACTCCAAAATAACCAGAATAACA
Found at i:1867701 original size:60 final size:60
Alignment explanation
Indices: 1867632--1867784 Score: 161
Period size: 60 Copynumber: 2.6 Consensus size: 60
1867622 AGGGTTGATC
* * * *
1867632 CATTT-CTTTGTGC-TTAGGGTAAGTTCTTATGGACCTTAGGGCACTC-CACTCAGGTGGA-T
1 CATTTGCTTTGTGCATT-GGGTAAGTTCTTATGGACCTAACGACACTCTC-CCCAGGT-GACT
* ** * * *
1867691 CGTTTGCTTTGCACATTGGTTAAGTCCTTATGAACCTAACGACACTCTCCCCAGGTGACT
1 CATTTGCTTTGTGCATTGGGTAAGTTCTTATGGACCTAACGACACTCTCCCCAGGTGACT
1867751 CATTTGCTTTGTGCATTGGGTAAGTTCTTATGGA
1 CATTTGCTTTGTGCATTGGGTAAGTTCTTATGGA
1867785 TCTGCAGGTA
Statistics
Matches: 74, Mismatches: 16, Indels: 7
0.76 0.16 0.07
Matches are distributed among these distances:
59 6 0.08
60 65 0.88
61 3 0.04
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.36
Consensus pattern (60 bp):
CATTTGCTTTGTGCATTGGGTAAGTTCTTATGGACCTAACGACACTCTCCCCAGGTGACT
Found at i:1875713 original size:26 final size:26
Alignment explanation
Indices: 1875684--1875734 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
1875674 AAATTATCCT
1875684 TGAAC-CTAAAAATGACCAAAATAACA
1 TGAACTCT-AAAATGACCAAAATAACA
*
1875710 TGAACTCTAAAATGACCAGAATAAC
1 TGAACTCTAAAATGACCAAAATAAC
1875735 CCTAAGTACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 21 0.91
27 2 0.09
ACGTcount: A:0.53, C:0.20, G:0.10, T:0.18
Consensus pattern (26 bp):
TGAACTCTAAAATGACCAAAATAACA
Found at i:1878532 original size:26 final size:26
Alignment explanation
Indices: 1878503--1878552 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
1878493 AAATTACCCT
*
1878503 TGAAC-CCAAAAATGACCAGAATAACA
1 TGAACTCC-AAAATAACCAGAATAACA
1878529 TGAACTCCAAAATAACCAGAATAA
1 TGAACTCCAAAATAACCAGAATAA
1878553 ACCCGAGTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.54, C:0.22, G:0.10, T:0.14
Consensus pattern (26 bp):
TGAACTCCAAAATAACCAGAATAACA
Found at i:1879649 original size:60 final size:59
Alignment explanation
Indices: 1879578--1879758 Score: 161
Period size: 60 Copynumber: 3.0 Consensus size: 59
1879568 GGGAGGCTCA
* **
1879578 TTTACTTTGCACTTAGGGTAAGTTCTTATGGACCTGGGGGCACTCCCCTCAGGTGGATCT
1 TTTATTTTGCACTT-GGGTAAGTTCTTATGGACCTGAAGGCACTCCCCTCAGGTGGATCT
* * * * *
1879638 TTTATTTTGCACATTGGGTAAG-TCTTTATGAACCT-AACGACATTCTCCTCAGGTGGTTCAT
1 TTTATTTTGCAC-TTGGGTAAGTTC-TTATGGACCTGAA-GGCACTCCCCTCAGGTGGATC-T
** * * * *
1879699 TTGCTTTGTGCA-TTGGGTAAGTTCTTATGGAGCTGAAGGTACCCCCCTCAGGTGGCTCT
1 TTTATTT-TGCACTTGGGTAAGTTCTTATGGACCTGAAGGCACTCCCCTCAGGTGGATCT
1879758 T
1 T
1879759 ACACTTCAGC
Statistics
Matches: 96, Mismatches: 18, Indels: 15
0.74 0.14 0.12
Matches are distributed among these distances:
59 4 0.04
60 76 0.79
61 12 0.12
62 4 0.04
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.36
Consensus pattern (59 bp):
TTTATTTTGCACTTGGGTAAGTTCTTATGGACCTGAAGGCACTCCCCTCAGGTGGATCT
Found at i:1897075 original size:30 final size:30
Alignment explanation
Indices: 1897039--1897096 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
1897029 ATAGGTAACA
*
1897039 AAGTCCCATACTAAATCAGGACGGGGAATG
1 AAGTCCCATACAAAATCAGGACGGGGAATG
* *
1897069 AAGTCCCATACAAAATCATGATGGGGAA
1 AAGTCCCATACAAAATCAGGACGGGGAA
1897097 AAAAGTCTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.40, C:0.19, G:0.24, T:0.17
Consensus pattern (30 bp):
AAGTCCCATACAAAATCAGGACGGGGAATG
Found at i:1897103 original size:30 final size:30
Alignment explanation
Indices: 1897038--1897103 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
1897028 AATAGGTAAC
* *
1897038 AAAGTCCCATACTAAATCAGGACGGGGAAT
1 AAAGTCCCATACAAAATCAGGACGGGGAAA
* * *
1897068 GAAGTCCCATACAAAATCATGATGGGGAAA
1 AAAGTCCCATACAAAATCAGGACGGGGAAA
1897098 AAAGTC
1 AAAGTC
1897104 TAATGCAGAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.42, C:0.18, G:0.23, T:0.17
Consensus pattern (30 bp):
AAAGTCCCATACAAAATCAGGACGGGGAAA
Found at i:1903363 original size:2 final size:2
Alignment explanation
Indices: 1903356--1903380 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1903346 AAAGATAACA
1903356 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1903381 CTCAAGTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1903634 original size:30 final size:30
Alignment explanation
Indices: 1903600--1903715 Score: 117
Period size: 30 Copynumber: 3.9 Consensus size: 30
1903590 AATCATAATG
* *
1903600 GGGAACAAAGTCTCATACAGAATCAGAACA
1 GGGAACGAAGTCCCATACAGAATCAGAACA
* *
1903630 GGGAATGAAGTCCCATTCAGAATCA-AGACA
1 GGGAACGAAGTCCCATACAGAATCAGA-ACA
* * * * * * *
1903660 GGGAATGGAGTCCTATGCAGAATGAGGATA
1 GGGAACGAAGTCCCATACAGAATCAGAACA
1903690 GGGAACGAAGTCCCATACAGAATCAG
1 GGGAACGAAGTCCCATACAGAATCAG
1903716 GAATGCATCA
Statistics
Matches: 69, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
29 1 0.01
30 68 0.99
ACGTcount: A:0.40, C:0.18, G:0.27, T:0.16
Consensus pattern (30 bp):
GGGAACGAAGTCCCATACAGAATCAGAACA
Found at i:1905920 original size:18 final size:17
Alignment explanation
Indices: 1905879--1905925 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
1905869 CTCGTACTGG
1905879 GAGTATCGATACTCTAC
1 GAGTATCGATACTCTAC
* *
1905896 CAGTATCGATACTCTCAT
1 GAGTATCGATACTCT-AC
*
1905914 GAGTATCAATAC
1 GAGTATCGATAC
1905926 AAATATAGCT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 14 0.56
18 11 0.44
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (17 bp):
GAGTATCGATACTCTAC
Found at i:1909983 original size:35 final size:35
Alignment explanation
Indices: 1909890--1910012 Score: 196
Period size: 35 Copynumber: 3.5 Consensus size: 35
1909880 TAGTAAATCA
*
1909890 TCCGTTCTAGTTGAATCGAAAGTGCGATGCTTCCT
1 TCCGTTCTACTTGAATCGAAAGTGCGATGCTTCCT
1909925 T-CGTT-TCACTTGAATCGAAAGTGCGATGCTTCCT
1 TCCGTTCT-ACTTGAATCGAAAGTGCGATGCTTCCT
*
1909959 TCCGTTCTACTTTAATCGAAAGTGCGATGCTTCCT
1 TCCGTTCTACTTGAATCGAAAGTGCGATGCTTCCT
*
1909994 TCCGTTCTACTTTAATCGA
1 TCCGTTCTACTTGAATCGA
1910013 CTTTTTTTAG
Statistics
Matches: 83, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
33 1 0.01
34 31 0.37
35 50 0.60
36 1 0.01
ACGTcount: A:0.20, C:0.24, G:0.19, T:0.37
Consensus pattern (35 bp):
TCCGTTCTACTTGAATCGAAAGTGCGATGCTTCCT
Found at i:1911595 original size:19 final size:19
Alignment explanation
Indices: 1911567--1911603 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1911557 ACATTAACGA
* *
1911567 TGCATGTTCTAGAATGCAC
1 TGCATATTCTACAATGCAC
1911586 TGCATATTCTACAATGCA
1 TGCATATTCTACAATGCA
1911604 TATTTCAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (19 bp):
TGCATATTCTACAATGCAC
Found at i:1911676 original size:5 final size:5
Alignment explanation
Indices: 1911668--1911762 Score: 154
Period size: 5 Copynumber: 18.2 Consensus size: 5
1911658 AACATGCACC
1911668 ATATT ATATT ATATT ATATT ATATTAT ATATT ATATT ATATT ATATTAT
1 ATATT ATATT ATATT ATATT ATA-T-T ATATT ATATT ATATT ATA-T-T
1911717 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT A
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT A
1911763 ATGCGCTTGC
Statistics
Matches: 86, Mismatches: 0, Indels: 8
0.91 0.00 0.09
Matches are distributed among these distances:
5 74 0.86
6 4 0.05
7 8 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATATT
Found at i:1911700 original size:22 final size:22
Alignment explanation
Indices: 1911672--1911760 Score: 164
Period size: 22 Copynumber: 4.1 Consensus size: 22
1911662 TGCACCATAT
1911672 TATATTATATTATATTATATTA
1 TATATTATATTATATTATATTA
1911694 TATATTATATTATATTATATTA
1 TATATTATATTATATTATATTA
1911716 TATATTATATTATATTATA-T-
1 TATATTATATTATATTATATTA
1911736 TATATTATATTATATTATATTA
1 TATATTATATTATATTATATTA
1911758 TAT
1 TAT
1911761 TAATGCGCTT
Statistics
Matches: 65, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
20 19 0.29
21 2 0.03
22 44 0.68
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TATATTATATTATATTATATTA
Found at i:1911802 original size:18 final size:18
Alignment explanation
Indices: 1911763--1911815 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
1911753 TATTATATTA
** *
1911763 ATGCGCTTGCGTATGTGT
1 ATGCGCTTGCGTATACGC
1911781 ATGCGCTTGCGTATACGC
1 ATGCGCTTGCGTATACGC
* *
1911799 ATGCGCATGCATATACG
1 ATGCGCTTGCGTATACG
1911816 TTGTATATGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.19, C:0.23, G:0.28, T:0.30
Consensus pattern (18 bp):
ATGCGCTTGCGTATACGC
Found at i:1914005 original size:18 final size:18
Alignment explanation
Indices: 1913982--1914021 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
1913972 ATTGCATTTG
1913982 AACCTAAGATTAGTTAGT
1 AACCTAAGATTAGTTAGT
1914000 AACCTAAGATTAGTTAGT
1 AACCTAAGATTAGTTAGT
1914018 AACC
1 AACC
1914022 AAACAAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (18 bp):
AACCTAAGATTAGTTAGT
Found at i:1914503 original size:2 final size:2
Alignment explanation
Indices: 1914494--1914546 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
1914484 TATCATTAAC
1914494 TA TA -A 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
1914535 TA TA TA TA TA TA
1 TA TA TA TA TA TA
1914547 ATTGATTCTT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1915179 original size:20 final size:21
Alignment explanation
Indices: 1915140--1915180 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
1915130 CACACTGAAT
1915140 GCTGAATGGTTCATCATTCAGC
1 GCTGAATGGTTCA-CATTCAGC
1915162 GCTGAATGGTTC-CATTCAG
1 GCTGAATGGTTCACATTCAG
1915181 AGCCAAACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.37
22 12 0.63
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (21 bp):
GCTGAATGGTTCACATTCAGC
Found at i:1916445 original size:30 final size:29
Alignment explanation
Indices: 1916410--1916488 Score: 72
Period size: 29 Copynumber: 2.7 Consensus size: 29
1916400 TTACAATGCA
* *
1916410 TAAAGTTCAGTGATTAAATTGAAAATA-AT
1 TAAAGTTCAGTGATTAAATT-AAAAGAGAG
* *
1916439 TAAAAGTAT-AGTGAGTAAAATAAAAGAGAG
1 T-AAAGT-TCAGTGATTAAATTAAAAGAGAG
*
1916469 TAAAGTTCAATGATTAAATT
1 TAAAGTTCAGTGATTAAATT
1916489 TGTAATTTAT
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
28 1 0.03
29 20 0.51
30 17 0.44
31 1 0.03
ACGTcount: A:0.51, C:0.03, G:0.16, T:0.30
Consensus pattern (29 bp):
TAAAGTTCAGTGATTAAATTAAAAGAGAG
Found at i:1919307 original size:28 final size:29
Alignment explanation
Indices: 1919276--1919345 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
1919266 AATTGCAATA
* *
1919276 ATAAATAT-AAAAGATTAGAGATCTA-AAT
1 ATAAATATAAAAAG-TTAAAGACCTATAAT
*
1919304 ATAAATATAAAAAGTTAAAGACCTATATT
1 ATAAATATAAAAAGTTAAAGACCTATAAT
1919333 ATAAATATAAAAA
1 ATAAATATAAAAA
1919346 AATTGAGAGC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 17 0.46
29 20 0.54
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.29
Consensus pattern (29 bp):
ATAAATATAAAAAGTTAAAGACCTATAAT
Found at i:1925388 original size:18 final size:20
Alignment explanation
Indices: 1925341--1925388 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 20
1925331 ATCCTATAGA
1925341 GAGTATCGATACTCCACCCT
1 GAGTATCGATACTCCACCCT
* *
1925361 GGGTAT--ATACT-TACCC-
1 GAGTATCGATACTCCACCCT
1925377 GAGTATCGATAC
1 GAGTATCGATAC
1925389 CAAATTTGGC
Statistics
Matches: 23, Mismatches: 3, Indels: 6
0.72 0.09 0.19
Matches are distributed among these distances:
16 5 0.22
17 4 0.17
18 9 0.39
20 5 0.22
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (20 bp):
GAGTATCGATACTCCACCCT
Found at i:1934490 original size:26 final size:27
Alignment explanation
Indices: 1934428--1934490 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 27
1934418 TTTTAATTTT
* *
1934428 TAATTTATATTACATATTATATTATAA
1 TAATTTATATTACATATAATATTACAA
* *
1934455 TAATGT-TATTATATATAATATT-CAA
1 TAATTTATATTACATATAATATTACAA
*
1934480 TTATTTATATT
1 TAATTTATATT
1934491 TAATTTTATT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
25 6 0.21
26 18 0.62
27 5 0.17
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (27 bp):
TAATTTATATTACATATAATATTACAA
Found at i:1935206 original size:7 final size:7
Alignment explanation
Indices: 1935190--1935263 Score: 86
Period size: 6 Copynumber: 10.9 Consensus size: 7
1935180 TTCATGTTTG
1935190 AAAA-AA
1 AAAAGAA
1935196 AAAAGAA
1 AAAAGAA
1935203 AAAAG-A
1 AAAAGAA
1935209 AAAA-AA
1 AAAAGAA
1935215 AAAA-AA
1 AAAAGAA
1935221 AAAAG-A
1 AAAAGAA
1935227 AAAAGAAGA
1 AAAAG-A-A
1935236 AAAAGAA
1 AAAAGAA
1935243 GAAAAGAA
1 -AAAAGAA
1935251 AAAAGAA
1 AAAAGAA
1935258 AAAAGA
1 AAAAGA
1935264 TTAAAAATTT
Statistics
Matches: 61, Mismatches: 0, Indels: 13
0.82 0.00 0.18
Matches are distributed among these distances:
6 26 0.43
7 21 0.34
8 8 0.13
9 6 0.10
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:1935222 original size:24 final size:24
Alignment explanation
Indices: 1935190--1935261 Score: 101
Period size: 24 Copynumber: 3.0 Consensus size: 24
1935180 TTCATGTTTG
1935190 AAAAAAAAAAGAAAAAAGAAAAAA
1 AAAAAAAAAAGAAAAAAGAAAAAA
*
1935214 AAAAAAAAAA-AGAAAAAGAAGAAA
1 AAAAAAAAAAGA-AAAAAGAAAAAA
* *
1935238 AAGAAGAAAAGAAAAAAGAAAAAA
1 AAAAAAAAAAGAAAAAAGAAAAAA
1935262 GATTAAAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
23 1 0.02
24 40 0.95
25 1 0.02
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (24 bp):
AAAAAAAAAAGAAAAAAGAAAAAA
Found at i:1935270 original size:1 final size:1
Alignment explanation
Indices: 1935190--1935261 Score: 63
Period size: 1 Copynumber: 72.0 Consensus size: 1
1935180 TTCATGTTTG
* * * * * * * *
1935190 AAAAAAAAAAGAAAAAAGAAAAAAAAAAAAAAAAAGAAAAAGAAGAAAAAGAAGAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
1935255 GAAAAAA
1 AAAAAAA
1935262 GATTAAAAAT
Statistics
Matches: 53, Mismatches: 18, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (1 bp):
A
Found at i:1935357 original size:18 final size:19
Alignment explanation
Indices: 1935336--1935374 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
1935326 CTCCAGTTAG
*
1935336 TTATTTTTTAAGTAT-TAT
1 TTATTTTTTAAATATATAT
1935354 TTATTTTTTAAATATATAT
1 TTATTTTTTAAATATATAT
1935373 TT
1 TT
1935375 TTAAAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (19 bp):
TTATTTTTTAAATATATAT
Found at i:1936468 original size:26 final size:26
Alignment explanation
Indices: 1936432--1936483 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
1936422 GCGTCTTTGA
1936432 ACCGGCGGTCAGCGGAAAGTATTAGC
1 ACCGGCGGTCAGCGGAAAGTATTAGC
1936458 ACCGGCGGTCAGCGGAAAGTATTAGC
1 ACCGGCGGTCAGCGGAAAGTATTAGC
1936484 GCCAATAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.23, G:0.35, T:0.15
Consensus pattern (26 bp):
ACCGGCGGTCAGCGGAAAGTATTAGC
Found at i:1939360 original size:17 final size:17
Alignment explanation
Indices: 1939334--1939366 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
1939324 TTTTGTTTTT
1939334 AATTTATTTAAGTATTTA
1 AATTTATTTAA-TATTTA
1939352 AATTT-TTTAATATTT
1 AATTTATTTAATATTT
1939367 TATTTAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
AATTTATTTAATATTTA
Found at i:1939368 original size:17 final size:19
Alignment explanation
Indices: 1939329--1939368 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
1939319 TAATATTTTG
*
1939329 TTTTTAATTTATTTAAGTA
1 TTTTAAATTTATTTAAGTA
1939348 -TTTAAATTT-TTTAA-TA
1 TTTTAAATTTATTTAAGTA
1939364 TTTTA
1 TTTTA
1939369 TTTAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
16 2 0.11
17 9 0.47
18 8 0.42
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (19 bp):
TTTTAAATTTATTTAAGTA
Found at i:1941682 original size:33 final size:34
Alignment explanation
Indices: 1941645--1941718 Score: 82
Period size: 34 Copynumber: 2.2 Consensus size: 34
1941635 TAATACTTAC
1941645 TTTATTTCATT-AATTTGGTTGGA-TTTATT-TTAA
1 TTTATTTCATTAAATTT-GTTGGACTTT-TTGTTAA
**
1941678 TTTATTTTGTTAAATTTGTTGGACTTTTTGTTAA
1 TTTATTTCATTAAATTTGTTGGACTTTTTGTTAA
*
1941712 TGTATTT
1 TTTATTT
1941719 TGGTTAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
33 17 0.49
34 18 0.51
ACGTcount: A:0.22, C:0.03, G:0.14, T:0.62
Consensus pattern (34 bp):
TTTATTTCATTAAATTTGTTGGACTTTTTGTTAA
Found at i:1941712 original size:34 final size:34
Alignment explanation
Indices: 1941656--1941732 Score: 95
Period size: 34 Copynumber: 2.2 Consensus size: 34
1941646 TTATTTCATT
*
1941656 AATTTGGTTGGATTTATTTTAATTTATTTT-GTTA
1 AATTT-GTTGGATTTATTTTAATGTATTTTGGTTA
1941690 AATTTGTTGGACTTT-TTGTTAATGTATTTTGGTTA
1 AATTTGTTGGA-TTTATT-TTAATGTATTTTGGTTA
*
1941725 ATTTTGTT
1 AATTTGTT
1941733 TATTACCATT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
33 8 0.21
34 19 0.50
35 11 0.29
ACGTcount: A:0.21, C:0.01, G:0.17, T:0.61
Consensus pattern (34 bp):
AATTTGTTGGATTTATTTTAATGTATTTTGGTTA
Found at i:1941762 original size:35 final size:32
Alignment explanation
Indices: 1941727--1941807 Score: 83
Period size: 35 Copynumber: 2.3 Consensus size: 32
1941717 TTTGGTTAAT
1941727 TTTGTT-TATTACCATTTAATATCAGTTATTGTAA
1 TTTGTTATATTACCATTTAATA-C--TTATTGTAA
1941761 TTTGTTTATCATTTACCATTTAATACTTATTGTAA
1 TTTG-TTAT-A-TTACCATTTAATACTTATTGTAA
*
1941796 GTTTGTTGTATT
1 -TTTGTTATATT
1941808 TAAAATTATA
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
33 2 0.05
34 5 0.12
35 14 0.34
36 5 0.12
37 2 0.05
38 13 0.32
ACGTcount: A:0.26, C:0.09, G:0.10, T:0.56
Consensus pattern (32 bp):
TTTGTTATATTACCATTTAATACTTATTGTAA
Found at i:1951937 original size:21 final size:21
Alignment explanation
Indices: 1951913--1951956 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 21
1951903 TACAGTGTAA
*
1951913 AGTATTATCGGTACCCCTTGG
1 AGTATTATCGATACCCCTTGG
1951934 AG---TATCGATACCCCTTGG
1 AGTATTATCGATACCCCTTGG
1951952 AGTAT
1 AGTAT
1951957 CGATACCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 6
0.73 0.04 0.23
Matches are distributed among these distances:
18 17 0.89
21 2 0.11
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.32
Consensus pattern (21 bp):
AGTATTATCGATACCCCTTGG
Found at i:1951945 original size:18 final size:18
Alignment explanation
Indices: 1951918--1951963 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
1951908 TGTAAAGTAT
*
1951918 TATCGGTACCCCTTGGAG
1 TATCGATACCCCTTGGAG
1951936 TATCGATACCCCTTGGAG
1 TATCGATACCCCTTGGAG
1951954 TATCGATACC
1 TATCGATACC
1951964 TATTTTGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (18 bp):
TATCGATACCCCTTGGAG
Found at i:1952980 original size:19 final size:19
Alignment explanation
Indices: 1952956--1953007 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
1952946 AATGCATTTG
1952956 ATGCATCGATGCACAAGAC
1 ATGCATCGATGCACAAGAC
1952975 ATGCATCGATGCACAAGAC
1 ATGCATCGATGCACAAGAC
*
1952994 ATGTATCGATGCAC
1 ATGCATCGATGCAC
1953008 TCAGGCTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (19 bp):
ATGCATCGATGCACAAGAC
Found at i:1961720 original size:10 final size:10
Alignment explanation
Indices: 1961705--1961734 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1961695 ATTGATCAAA
1961705 AAGAAGAAAC
1 AAGAAGAAAC
1961715 AAGAAGAAAC
1 AAGAAGAAAC
*
1961725 AACAAGAAAC
1 AAGAAGAAAC
1961735 TATAATCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.70, C:0.13, G:0.17, T:0.00
Consensus pattern (10 bp):
AAGAAGAAAC
Found at i:1965781 original size:54 final size:54
Alignment explanation
Indices: 1965708--1966197 Score: 600
Period size: 54 Copynumber: 9.3 Consensus size: 54
1965698 TTTGCATATG
* * * * *
1965708 TAGTGCCGATAC-GATAATTCACAAACTCATTATG-ATTACGTTGGGTTACACACA
1 TAGTGCCAATACAGA-AATTCATAAACTCATTATGAATTTC-TTAGGTTGCACACA
* * * *
1965762 TAGTACCAATACGGAAATTCATCAACTTATTATGAATTTCTTAGGTTGCACACA
1 TAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCTTAGGTTGCACACA
*
1965816 TAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCTTAGGTTGTACACA
1 TAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCTTAGGTTGCACACA
* *
1965870 TAGTGCCAATAC-GAAATTCAT-AACTTATTATGAATTTCTTAGGTTGCACATA
1 TAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCTTAGGTTGCACACA
* * *
1965922 TAGT-CC----C-G--ATAC-GAAACTCATT-TGACTTTCTTAGGTTGCACACA
1 TAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCTTAGGTTGCACACA
*
1965966 TAGTGCAAATAC-GAAAATTCATAAACTCATTATGAATTTCTTAGGTTGCACACA
1 TAGTGCCAATACAG-AAATTCATAAACTCATTATGAATTTCTTAGGTTGCACACA
*
1966020 TAGTGCCAATACAG-AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACA
1 TAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCTTAGGTTGCACACA
* * *
1966073 TAGTGACAATACAGAAATTCATAAACAT-ATTATGAATTTCTTAAGCTGCACACA
1 TAGTGCCAATACAGAAATTCATAAAC-TCATTATGAATTTCTTAGGTTGCACACA
* * * * *
1966127 TAATGTCAATACGGAAATTCATAAACTTATTATGAATTTCTTAGGTTGTACACA
1 TAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCTTAGGTTGCACACA
1966181 TAGTGCCAATACAGAAA
1 TAGTGCCAATACAGAAA
1966198 ATCCAATACA
Statistics
Matches: 380, Mismatches: 39, Indels: 34
0.84 0.09 0.08
Matches are distributed among these distances:
44 24 0.06
45 11 0.03
47 2 0.01
49 2 0.01
51 2 0.01
52 35 0.09
53 70 0.18
54 226 0.59
55 8 0.02
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (54 bp):
TAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCTTAGGTTGCACACA
Found at i:1972823 original size:54 final size:53
Alignment explanation
Indices: 1972697--1973227 Score: 723
Period size: 54 Copynumber: 9.9 Consensus size: 53
1972687 TTCTATGGTT
* * * * * **
1972697 TTGCACACGTAGTGCCGATACGGTAATTCACAAACTCATTATGAATTACGTGGGG
1 TTGCACACATAGTGCCAATAC-GAAATTCATAAACTCATTATGAATTTC-TTAGG
* *
1972752 TTGCACATATAGTGCCAATACAGAAATTCATAATCTCATTATGAATTTCTTAGG
1 TTGCACACATAGTGCCAATAC-GAAATTCATAAACTCATTATGAATTTCTTAGG
1972806 TTGCACACATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAGG
1 TTGCACACATAGTGCCAATACG-AAATTCATAAACTCATTATGAATTTCTTAGG
*
1972860 TTGCACACATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTTGG
1 TTGCACACATAGTGCCAATACG-AAATTCATAAACTCATTATGAATTTCTTAGG
*
1972914 TTG-ACACATAGTGCCAATACGAAAATTCATAAACTCATTATAAATTT-TTAGG
1 TTGCACACATAGTGCCAATACG-AAATTCATAAACTCATTATGAATTTCTTAGG
* *
1972966 TTGCACACATAGTGTCAATACGAAAATTCATAAACTTATTAT-AATTTCTTAGG
1 TTGCACACATAGTGCCAATACG-AAATTCATAAACTCATTATGAATTTCTTAGG
* *
1973019 TTGCACACATAGTGCCAATTAGGAAATTCATAAACTTATTATGAATTTCTTAGG
1 TTGCACACATAGTGCCAA-TACGAAATTCATAAACTCATTATGAATTTCTTAGG
* * *
1973073 TTGCACACATAGTGCCAATAAGGAAATTCATAAACTTATTATAAATTTCTTAGG
1 TTGCACACATAGTGCCAAT-ACGAAATTCATAAACTCATTATGAATTTCTTAGG
* *
1973127 TTGCACACATAGTGCCAATACGGAAATTCATTAACTTATTATGAATTTCTTAGG
1 TTGCACACATAGTGCCAATAC-GAAATTCATAAACTCATTATGAATTTCTTAGG
* *
1973181 TTACACTCATAGTGCCAATACGGAAATTCAT-AACT-A-TATGAATTTCT
1 TTGCACACATAGTGCCAATAC-GAAATTCATAAACTCATTATGAATTTCT
1973228 AGTTACACAT
Statistics
Matches: 444, Mismatches: 25, Indels: 18
0.91 0.05 0.04
Matches are distributed among these distances:
51 11 0.02
52 13 0.03
53 127 0.29
54 252 0.57
55 41 0.09
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (53 bp):
TTGCACACATAGTGCCAATACGAAATTCATAAACTCATTATGAATTTCTTAGG
Found at i:1976310 original size:14 final size:14
Alignment explanation
Indices: 1976291--1976320 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1976281 TTCAAAGGGA
*
1976291 TAATTGTGATTGGG
1 TAATTGTAATTGGG
1976305 TAATTGTAATTGGG
1 TAATTGTAATTGGG
1976319 TA
1 TA
1976321 GGATCGGCAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.30, T:0.43
Consensus pattern (14 bp):
TAATTGTAATTGGG
Found at i:1979435 original size:26 final size:26
Alignment explanation
Indices: 1979381--1979433 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
1979371 AATAATCCCG
*
1979381 AATATTTAATTTAAATTAATTAAATA
1 AATATTTAATTTAAATTAAATAAATA
*
1979407 AATATTTAA-TTAATTTGAAAT-AATA
1 AATATTTAATTTAAATT-AAATAAATA
1979432 AA
1 AA
1979434 ATCCCTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 12 0.50
26 12 0.50
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (26 bp):
AATATTTAATTTAAATTAAATAAATA
Found at i:1988290 original size:12 final size:12
Alignment explanation
Indices: 1988257--1988309 Score: 65
Period size: 12 Copynumber: 4.5 Consensus size: 12
1988247 ATATACAAAT
*
1988257 ACCTAACTC-TC
1 ACCTAAATCTTC
*
1988268 ACCTAACTCTTC
1 ACCTAAATCTTC
1988280 ACC-AAATTCTTC
1 ACCTAAA-TCTTC
1988292 ACCTAAATCTTC
1 ACCTAAATCTTC
1988304 ACCTAA
1 ACCTAA
1988310 CTAAATTGAT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
11 11 0.29
12 24 0.63
13 3 0.08
ACGTcount: A:0.32, C:0.38, G:0.00, T:0.30
Consensus pattern (12 bp):
ACCTAAATCTTC
Found at i:1991908 original size:31 final size:31
Alignment explanation
Indices: 1991871--1991935 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
1991861 AAGTCTTTAG
*
1991871 TTTCTTCAATCGTCACGACTATGTGCTCAAA
1 TTTCTTCAATCGTCACGACTATATGCTCAAA
1991902 TTTCTTCAATCGTCACGACTATATGCTCAAA
1 TTTCTTCAATCGTCACGACTATATGCTCAAA
1991933 TTT
1 TTT
1991936 GGGATCCAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.26, C:0.25, G:0.11, T:0.38
Consensus pattern (31 bp):
TTTCTTCAATCGTCACGACTATATGCTCAAA
Found at i:1992902 original size:12 final size:12
Alignment explanation
Indices: 1992869--1992923 Score: 76
Period size: 12 Copynumber: 4.7 Consensus size: 12
1992859 ATATAAAAAT
1992869 ACCTAACTC-TC
1 ACCTAACTCTTC
1992880 ACCTAACTCTTC
1 ACCTAACTCTTC
* *
1992892 ATCTAATTCTTC
1 ACCTAACTCTTC
*
1992904 ACCTAACTCTTT
1 ACCTAACTCTTC
1992916 ACCTAACT
1 ACCTAACT
1992924 AAATTGATGT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
11 9 0.24
12 29 0.76
ACGTcount: A:0.27, C:0.36, G:0.00, T:0.36
Consensus pattern (12 bp):
ACCTAACTCTTC
Found at i:1996063 original size:65 final size:64
Alignment explanation
Indices: 1995946--1996154 Score: 203
Period size: 65 Copynumber: 3.2 Consensus size: 64
1995936 TTTCAAAGTG
* * * * * ** *
1995946 ATGCACCGATGCACCAATCCATGCATCGATGCACCATGGAATAAATTG-AACATCGAATGCATTC
1 ATGCATCGATGCA-CTAGCCATGCATCGATGCACTATGG-CTATTTTGAAACATCGAATGCATTT
1996010 C
64 C
* * *
1996011 ATGCATCGATGCACATA-CTATTCATCGATGCACT-TAGAG-T-TTTATGAAAACATCGAATGGA
1 ATGCATCGATGCAC-TAGCCATGCATCGATGCACTAT-G-GCTATTT-TG-AAACATCGAATGCA
*
1996072 TTTG
61 TTTC
1996076 ATGCATCGATGCACTAGCCATGCATCGATGCACTATGGCTATTTTGAAACATCGAATGCATTTC
1 ATGCATCGATGCACTAGCCATGCATCGATGCACTATGGCTATTTTGAAACATCGAATGCATTTC
*
1996140 ATGAATCGATGCACT
1 ATGCATCGATGCACT
1996155 CTTAGTGAAC
Statistics
Matches: 119, Mismatches: 15, Indels: 21
0.77 0.10 0.14
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 49 0.41
65 61 0.51
66 4 0.03
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (64 bp):
ATGCATCGATGCACTAGCCATGCATCGATGCACTATGGCTATTTTGAAACATCGAATGCATTTC
Found at i:2001632 original size:23 final size:22
Alignment explanation
Indices: 2001561--2001641 Score: 92
Period size: 23 Copynumber: 3.6 Consensus size: 22
2001551 ACACTTAACA
2001561 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCA-CCC-TTGAAT
* * *
2001585 GTGCATCGATTCACCATT-AAG
1 GTGCATCGATGCACCCTTGAAT
*
2001606 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATGCAC-CCTTGAAT
2001629 GTGCATCGATGCA
1 GTGCATCGATGCA
2001642 TAAGGCCATG
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
21 14 0.30
22 5 0.11
23 16 0.34
24 12 0.26
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.27
Consensus pattern (22 bp):
GTGCATCGATGCACCCTTGAAT
Found at i:2018665 original size:21 final size:22
Alignment explanation
Indices: 2018626--2018666 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2018616 AACTAGGGTT
*
2018626 TATTCTCTACCCAATATTAGGG
1 TATTCTCTACCCAAGATTAGGG
2018648 TATTCTCTA-CCAAGATTAG
1 TATTCTCTACCCAAGATTAG
2018667 TTTTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (22 bp):
TATTCTCTACCCAAGATTAGGG
Found at i:2034764 original size:27 final size:28
Alignment explanation
Indices: 2034711--2034766 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
2034701 GGTTTAGGTT
* * * *
2034711 TTATATATTTATTTTGTTTGTATTATTA
1 TTATATATTTACTTTGTATATAATATTA
2034739 TTATATA-TTACTTTGTATATAATATTA
1 TTATATATTTACTTTGTATATAATATTA
2034766 T
1 T
2034767 AGCATGATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 17 0.71
28 7 0.29
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.62
Consensus pattern (28 bp):
TTATATATTTACTTTGTATATAATATTA
Found at i:2041339 original size:38 final size:36
Alignment explanation
Indices: 2041297--2041373 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
2041287 TTGGGTGTTG
*
2041297 TTTCTCTCGAAACAAAATGTCGTCTCACTTGAGACATT
1 TTTCTCTCAAAAC-AAAT-TCGTCTCACTTGAGACATT
* ** *
2041335 TTTCTCTTAAAACAAATTTTTTTCACTTGAGACATT
1 TTTCTCTCAAAACAAATTCGTCTCACTTGAGACATT
2041371 TTT
1 TTT
2041374 TTCGGAACAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
36 19 0.56
37 4 0.12
38 11 0.32
ACGTcount: A:0.29, C:0.19, G:0.09, T:0.43
Consensus pattern (36 bp):
TTTCTCTCAAAACAAATTCGTCTCACTTGAGACATT
Found at i:2041340 original size:18 final size:18
Alignment explanation
Indices: 2041319--2041373 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
2041309 CAAAATGTCG
2041319 TCTCACTTGAGACATTTT
1 TCTCACTTGAGACATTTT
* *
2041337 TCT--CTTAAAACAAATTTT
1 TCTCACTTGAGAC--ATTTT
*
2041355 TTTCACTTGAGACATTTT
1 TCTCACTTGAGACATTTT
2041373 T
1 T
2041374 TTCGGAACAA
Statistics
Matches: 28, Mismatches: 5, Indels: 8
0.68 0.12 0.20
Matches are distributed among these distances:
16 6 0.21
18 16 0.57
20 6 0.21
ACGTcount: A:0.27, C:0.18, G:0.07, T:0.47
Consensus pattern (18 bp):
TCTCACTTGAGACATTTT
Found at i:2041521 original size:16 final size:17
Alignment explanation
Indices: 2041492--2041530 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
2041482 TTTCAAAGTT
2041492 ATTTTTCTTAAAAACAA
1 ATTTTTCTTAAAAACAA
2041509 ATTTTTCTTAAAAACAA
1 ATTTTTCTTAAAAACAA
2041526 ATTTT
1 ATTTT
2041531 GTTTCACTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (17 bp):
ATTTTTCTTAAAAACAA
Found at i:2041559 original size:38 final size:37
Alignment explanation
Indices: 2041509--2041687 Score: 139
Period size: 37 Copynumber: 5.2 Consensus size: 37
2041499 TTAAAAACAA
* *
2041509 ATTTTTCT-TAAAAACAAATTTTGTTTCACTTGAGTC
1 ATTTTTCTCTTAAAACAAATTTTGTTTCACTTGAGAC
2041545 ATTTTTCTCTTAAAACAAATTTTGTTTCACTTGAGAC
1 ATTTTTCTCTTAAAACAAATTTTGTTTCACTTGAGAC
** ** * **
2041582 ATTTTTCT-TTGGAAC-AA--TAATTTCA---AAGTT
1 ATTTTTCTCTTAAAACAAATTTTGTTTCACTTGAGAC
* * * * *
2041612 GTTTTTCT-TAAAAATAAATTTTGTCTCGCTTGAGAC
1 ATTTTTCTCTTAAAACAAATTTTGTTTCACTTGAGAC
*
2041648 ATTTTTCTCTT-AAAC--ATTTTGTTTCACTTGAGAT
1 ATTTTTCTCTTAAAACAAATTTTGTTTCACTTGAGAC
2041682 ATTTTT
1 ATTTTT
2041688 ATCTCAAACA
Statistics
Matches: 108, Mismatches: 27, Indels: 18
0.71 0.18 0.12
Matches are distributed among these distances:
30 12 0.11
31 2 0.02
33 10 0.09
34 22 0.20
35 2 0.02
36 25 0.23
37 35 0.32
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.49
Consensus pattern (37 bp):
ATTTTTCTCTTAAAACAAATTTTGTTTCACTTGAGAC
Found at i:2041617 original size:120 final size:120
Alignment explanation
Indices: 2041404--2041633 Score: 356
Period size: 120 Copynumber: 1.9 Consensus size: 120
2041394 GTTGTTTTCT
*
2041404 AAATTTTATCTCACTTGAGACATTTTTCTCTTAAAACAAATTTCTCTTCACTTGAGTCATTTTTC
1 AAATTTTATCTCACTTGAGACATTTTTCTCTTAAAACAAATTTCTCTTCACTTGAGACATTTTTC
2041469 TTCGGAACACAAATTTCAAAGTTATTTTTCTTAAAAACAAATTTTTCTTAAAAAC
66 TTCGGAACACAAATTTCAAAGTTATTTTTCTTAAAAACAAATTTTTCTTAAAAAC
* * * *
2041524 AAATTTTGTTTCACTTGAGTCATTTTTCTCTTAAAACAAATTT-TGTTTCACTTGAGACATTTTT
1 AAATTTTATCTCACTTGAGACATTTTTCTCTTAAAACAAATTTCT-CTTCACTTGAGACATTTTT
* * *
2041588 CTTTGGAACA-ATAATTTCAAAGTTGTTTTTCTTAAAAATAAATTTT
65 CTTCGGAACACA-AATTTCAAAGTTATTTTTCTTAAAAACAAATTTT
2041634 GTCTCGCTTG
Statistics
Matches: 100, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
119 2 0.02
120 98 0.98
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.45
Consensus pattern (120 bp):
AAATTTTATCTCACTTGAGACATTTTTCTCTTAAAACAAATTTCTCTTCACTTGAGACATTTTTC
TTCGGAACACAAATTTCAAAGTTATTTTTCTTAAAAACAAATTTTTCTTAAAAAC
Found at i:2041669 original size:34 final size:35
Alignment explanation
Indices: 2041628--2041720 Score: 98
Period size: 34 Copynumber: 2.7 Consensus size: 35
2041618 CTTAAAAATA
* *
2041628 AATTTTGTCTCGCTTGAGACATTTTTCTCTTAAAC
1 AATTTTGTCTCGCTTGAGACATTTTTATCTCAAAC
* * *
2041663 -ATTTTGTTTCACTTGAGATATTTTTATCTCAAAC
1 AATTTTGTCTCGCTTGAGACATTTTTATCTCAAAC
** *
2041697 AAGCATCGTCTCGCTTGAGACATT
1 AA-TTTTGTCTCGCTTGAGACATT
2041721 CTCCCAAATT
Statistics
Matches: 45, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
34 29 0.64
35 1 0.02
36 15 0.33
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.43
Consensus pattern (35 bp):
AATTTTGTCTCGCTTGAGACATTTTTATCTCAAAC
Found at i:2041892 original size:36 final size:36
Alignment explanation
Indices: 2041830--2041938 Score: 155
Period size: 36 Copynumber: 3.0 Consensus size: 36
2041820 CTTTGAATAT
2041830 GTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACA
1 GTTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACA
* *
2041867 GTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGATA
1 GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
* * * *
2041903 GTTTCCCTTAAAACAGACTTTGTCTCGCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
2041939 TTTTTCTCAC
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
36 51 0.80
37 13 0.20
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.37
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
Found at i:2042041 original size:74 final size:74
Alignment explanation
Indices: 2041909--2042064 Score: 192
Period size: 74 Copynumber: 2.1 Consensus size: 74
2041899 GATAGTTTCC
* * * *
2041909 CTTAAAACAGACTTTGTCTCGCTTGAGACATTTTTCTCACAAAAAAACATTTCGTTTCA-TTACA
1 CTTAAAACAGACTTTGTCTCGCTTAAGACATTTTACTCACAAAAAAACATTTCATTTCACTCA-A
*
2041973 TATTATTTTT
65 AATTATTTTT
* *
2041983 CTTAAAACATACTTTGTCTCGCTTAAGACATTTTACTCA-AAACAAGA-ATATTCATTTCACTCA
1 CTTAAAACAGACTTTGTCTCGCTTAAGACATTTTACTCACAAA-AAAACAT-TTCATTTCACTCA
*
2042046 AAATTGTTTTT
64 AAATTATTTTT
2042057 CTTAAAAC
1 CTTAAAAC
2042065 CAAAATTTAT
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
73 5 0.07
74 64 0.90
75 2 0.03
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.40
Consensus pattern (74 bp):
CTTAAAACAGACTTTGTCTCGCTTAAGACATTTTACTCACAAAAAAACATTTCATTTCACTCAAA
ATTATTTTT
Found at i:2042304 original size:53 final size:52
Alignment explanation
Indices: 2042155--2042346 Score: 208
Period size: 52 Copynumber: 3.7 Consensus size: 52
2042145 TAAGACTTTT
* * * *
2042155 AGAAACTAAGCATGATTTTCAGGGGTTTCTCGATGTTTTCAAATGAACTTGAA
1 AGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATGTTTTCAAATGAA-TTTAA
* * * *
2042208 AGAAGCTAAACCTAATTTT-AGGGGTTTCTTAATGTTTTTAAATGAATTTCAA
1 AGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTT-AA
* * * * * *
2042260 AGAAATTAAGCCTAATTTTTAGGGATTTCTTGATATTTTCAAATGAGTGTT-T
1 AGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATGTTTTCAAATGAAT-TTAA
*
2042312 AGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATG
1 AGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATG
2042347 ATGATTTTTA
Statistics
Matches: 114, Mismatches: 22, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
51 2 0.02
52 72 0.63
53 38 0.33
54 2 0.02
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (52 bp):
AGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTAA
Found at i:2042576 original size:42 final size:41
Alignment explanation
Indices: 2042447--2042576 Score: 111
Period size: 42 Copynumber: 3.1 Consensus size: 41
2042437 TTTTGTTAAG
*
2042447 TAAGTCTTTCGAGCAAGATGAGTAAGTCCTTCGGGCCAT-CA
1 TAAGTCTTTCGAGCAAGATGA-TAAGTCCTTCGGGCTATCCA
* * * * * ** *
2042488 GTAAGTCTTTCAAGCATGATGCTTAAATTCTTTAGG-TCATCTA
1 -TAAGTCTTTCGAGCAAGATG-ATAAGTCCTTCGGGCT-ATCCA
*
2042531 TAAGTTTTTTCGAGCAAGATGATAAGTCCTTCGGGCTATCCA
1 TAAG-TCTTTCGAGCAAGATGATAAGTCCTTCGGGCTATCCA
2042573 TAAG
1 TAAG
2042577 ACCTTCGGGC
Statistics
Matches: 65, Mismatches: 18, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
42 50 0.77
43 15 0.23
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (41 bp):
TAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCTATCCA
Found at i:2043067 original size:22 final size:22
Alignment explanation
Indices: 2043042--2043090 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
2043032 CTCTCTAGTT
*
2043042 TTTTAAAG-TTTTCTCTTTTTAC
1 TTTTAAAGTTTTTCCCTTTTT-C
*
2043064 TTTTCAAGTTTTTCCCTTTTTC
1 TTTTAAAGTTTTTCCCTTTTTC
2043086 TTTTA
1 TTTTA
2043091 TTTTCAAGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.14, C:0.16, G:0.04, T:0.65
Consensus pattern (22 bp):
TTTTAAAGTTTTTCCCTTTTTC
Found at i:2043736 original size:9 final size:9
Alignment explanation
Indices: 2043696--2043748 Score: 63
Period size: 9 Copynumber: 5.8 Consensus size: 9
2043686 ATTCTTATTT
2043696 TTATTTTAA
1 TTATTTTAA
*
2043705 TTACTTTTAT
1 TTA-TTTTAA
2043715 TTA-TTTAA
1 TTATTTTAA
*
2043723 TTATTTTTA
1 TTATTTTAA
2043732 TTATTTTAA
1 TTATTTTAA
2043741 TATATTTT
1 T-TATTTT
2043749 TACCAAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
8 7 0.19
9 16 0.43
10 14 0.38
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (9 bp):
TTATTTTAA
Found at i:2043739 original size:18 final size:18
Alignment explanation
Indices: 2043696--2043750 Score: 76
Period size: 18 Copynumber: 3.0 Consensus size: 18
2043686 ATTCTTATTT
*
2043696 TTATTTTAATTACTTTTA
1 TTATTTTAATTATTTTTA
2043714 TT-TATTTAATTATTTTTA
1 TTAT-TTTAATTATTTTTA
2043732 TTATTTTAATATATTTTTA
1 TTATTTTAAT-TATTTTTA
2043751 CCAAAATTCC
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
17 1 0.03
18 23 0.70
19 9 0.27
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (18 bp):
TTATTTTAATTATTTTTA
Found at i:2050795 original size:105 final size:105
Alignment explanation
Indices: 2050613--2051007 Score: 574
Period size: 105 Copynumber: 3.7 Consensus size: 105
2050603 GGATAAACCG
* * * **
2050613 ATCAACATTTCCATAAGAGTTCAAAATGAGAAGAACTTGTCCTAAAGGAGAAAGTTTGTAATGAG
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATGAG
* *
2050678 AAGAACTTGTTCCTTTCAAATTCACCCCCGAAGGTGGTGA
66 AAGAACTTGTTCCTTTCAAATCCACCCCCGAAGGAGGTGA
* * *
2050718 ATCAATATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAGGTTCGTAATGAG
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATGAG
* * ***
2050783 AAGAGCATGTTCCTTTCAAATCCACCATAGAAGGAGGTGA
66 AAGAACTTGTTCCTTTCAAATCCACCCCCGAAGGAGGTGA
* *
2050823 AACAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCTTAAAGGAGAAAGTTCATAATGAG
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATGAG
*
2050888 AAGAACTTGTTCCTTTCAAATCCACCCCCAGAAGAAGGTGA
66 AAGAACTTGTTCCTTTCAAATCCACCCCC-GAAGGAGGTGA
* *
2050929 ATCAACATTTCCTGAAGAGTTCATAATGAGAAGAACTCGTTCTAAAGGAGAAGAAGTTCATAATG
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAG-A-AAGTTCATAATG
*
2050994 AAAAGAACTTGTTC
64 AGAAGAACTTGTTC
2051008 AACCTTAGCT
Statistics
Matches: 258, Mismatches: 29, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
105 176 0.68
106 56 0.22
107 1 0.00
108 25 0.10
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (105 bp):
ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATGAG
AAGAACTTGTTCCTTTCAAATCCACCCCCGAAGGAGGTGA
Found at i:2051007 original size:20 final size:19
Alignment explanation
Indices: 2050947--2051008 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 19
2050937 TTCCTGAAGA
2050947 GTTCATAATGAGAAGAACT
1 GTTCATAATGAGAAGAACT
*
2050966 CGTTC-TAAAGGAGAAGAA--
1 -GTTCAT-AATGAGAAGAACT
*
2050984 GTTCATAATGAAAAGAACTT
1 GTTCATAATGAGAAGAAC-T
2051004 GTTCA
1 GTTCA
2051009 ACCTTAGCTC
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
17 13 0.38
18 1 0.03
19 1 0.03
20 19 0.56
ACGTcount: A:0.42, C:0.11, G:0.21, T:0.26
Consensus pattern (19 bp):
GTTCATAATGAGAAGAACT
Found at i:2051102 original size:137 final size:136
Alignment explanation
Indices: 2050944--2051292 Score: 565
Period size: 137 Copynumber: 2.5 Consensus size: 136
2050934 CATTTCCTGA
*
2050944 AGAGTTCATAATGAGAAGAACTCGTTCTAAAGGAGAAGAAGTTCATAATGAAAAGAACTTGTTCA
1 AGAGTTCATAATGAGAAGAACTCGTTCTAAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
*
2051009 ACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCTCACTCGAGGGCTCAACATTT
66 ACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCTCACTCGAGGGATCAACATTT
*
2051074 TTAGTGG
131 TCAGT-G
* * *
2051081 AGAGTTCATAATGAGAAGAACTTGTCCTAAAGGAAAAGAAGTTCATAATGAGAAGAACTTGTTCA
1 AGAGTTCATAATGAGAAGAACTCGTTCTAAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
*
2051146 ACCTTAGCTCGATTCATTGCATATGGAGTTGAATCAGCAACACCTCACTCGAGGGATCAACATTT
66 ACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCTCACTCGAGGGATCAACATTT
2051211 TCAGTG
131 TCAGTG
* *
2051217 AGAGTTCACAATGAGAAAAACTCG-TCTGATAAGGGAGAAGAAGTTCATAATGAGAAGAACTTGT
1 AGAGTTCATAATGAGAAGAACTCGTTCT-A-AA-GGAGAAGAAGTTCATAATGAGAAGAACTTGT
*
2051281 TCGACCTTAGCT
63 TCAACCTTAGCT
2051293 TATTTCCATC
Statistics
Matches: 196, Mismatches: 13, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
135 2 0.01
136 23 0.12
137 130 0.66
138 41 0.21
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (136 bp):
AGAGTTCATAATGAGAAGAACTCGTTCTAAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
ACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCTCACTCGAGGGATCAACATTT
TCAGTG
Found at i:2054274 original size:105 final size:105
Alignment explanation
Indices: 2054092--2054481 Score: 538
Period size: 105 Copynumber: 3.7 Consensus size: 105
2054082 GGATAAACCG
* * * *
2054092 ATCAACATTTCCATAAGAGTTCAAAATGAGAAGAACTTGTCCTAAAGGAGAAAGTTTGTAATGAG
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCGTAATGAG
* *
2054157 AAGAACTTGTTCCTTTCAAATTCACCCCCGAAGGTGGTGA
66 AAGAACTTGTTCCTTTCAAATCCACCCCCGAAGGAGGTGA
* *
2054197 ATCAATATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAGGTTCGTAATGAG
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCGTAATGAG
* * ***
2054262 AAGAGCATGTTCCTTTCAAATCCACCATAGAAGGAGGTGA
66 AAGAACTTGTTCCTTTCAAATCCACCCCCGAAGGAGGTGA
* * *
2054302 AACAACATTTCCAGAAGAGTTCAT-ATGAGAAGAACTCGTCTTAAAGGAGAAAGTTCAT-ATGAG
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCGTAATGAG
*
2054365 AAGAACTTGTTCCTTTC-AATCCACCCCCAGAAGAAGGTGA
66 AAGAACTTGTTCCTTTCAAATCCACCCCC-GAAGGAGGTGA
* *
2054405 ATCAACATTTCCTGAAGAGTTCATAATGAGAAGAACTCGTTCTAAAGGAGAAGAAGTTC--AATG
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAG-A-AAGTTCGTAATG
*
2054468 AAAAGAACTTGTTC
64 AGAAGAACTTGTTC
2054482 AACCTTAGCT
Statistics
Matches: 251, Mismatches: 29, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
102 8 0.03
103 52 0.21
104 54 0.22
105 131 0.52
106 6 0.02
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.25
Consensus pattern (105 bp):
ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCGTAATGAG
AAGAACTTGTTCCTTTCAAATCCACCCCCGAAGGAGGTGA
Found at i:2054683 original size:127 final size:129
Alignment explanation
Indices: 2054420--2054751 Score: 426
Period size: 127 Copynumber: 2.5 Consensus size: 129
2054410 CATTTCCTGA
*
2054420 AGAGTTCATAATGAGAAGAACTCGTTCTAAAGGAGAAGAAGTTCAATGAAAAGAACTTGTTCAAC
1 AGAGTTCATAATGAGAAGAACTCG-TCTAAAGGAGAAGAAGTTCAATGAGAAGAA-TTGTTCAAC
* * *
2054485 CTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCTCACTCGAGGGCTCAACATTTTA
64 CTTAGCTCGATT-ATC-CATATGCAG-TGAATCAGCAACACCTCACTCGAGGGATCAACATTTCA
*
2054550 GTGG
126 GCGG
* *
2054554 AGAGTTCATAATGAGAAGAACTTGTCCTAAAGGAAAAGAAGTTCATAATGAGAAGAATTGTTCAA
1 AGAGTTCATAATGAGAAGAACTCGT-CTAAAGGAGAAGAAGTTC--AATGAGAAGAATTGTTCAA
2054619 CCTTAGCTCGA-T-T-CAT-TGCA-TGAATCAGCAACACCTCACTCGAGGGATCAACATTTCAGC
63 CCTTAGCTCGATTATCCATATGCAGTGAATCAGCAACACCTCACTCGAGGGATCAACATTTCAGC
2054679 GG
128 GG
* * *
2054681 AGAGTTCACAATGAGAA-AACTCGTCTGATAAGGGAGAAGAAGTTCAATGAGAAGAACTGTTC-G
1 AGAGTTCATAATGAGAAGAACTCGTCT-A-AA-GGAGAAGAAGTTCAATGAGAAGAATTGTTCAA
2054744 CCTTAGCT
63 CCTTAGCT
2054752 TATTGCCATC
Statistics
Matches: 180, Mismatches: 12, Indels: 21
0.85 0.06 0.10
Matches are distributed among these distances:
125 10 0.06
126 23 0.13
127 57 0.32
128 12 0.07
129 3 0.02
130 3 0.02
132 1 0.01
133 1 0.01
134 41 0.23
135 19 0.11
136 10 0.06
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (129 bp):
AGAGTTCATAATGAGAAGAACTCGTCTAAAGGAGAAGAAGTTCAATGAGAAGAATTGTTCAACCT
TAGCTCGATTATCCATATGCAGTGAATCAGCAACACCTCACTCGAGGGATCAACATTTCAGCGG
Found at i:2057004 original size:6 final size:6
Alignment explanation
Indices: 2056995--2057022 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2056985 TATGGCATGC
2056995 TAAAGA TAAAGA TAAAGA TAAAGA TAAA
1 TAAAGA TAAAGA TAAAGA TAAAGA TAAA
2057023 ACTTTGGAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.14, T:0.18
Consensus pattern (6 bp):
TAAAGA
Found at i:2059238 original size:41 final size:41
Alignment explanation
Indices: 2059188--2059279 Score: 98
Period size: 40 Copynumber: 2.3 Consensus size: 41
2059178 TTTGTAAACC
* * *
2059188 AAACACCACTAAATGACAACTATATTGC-GATGTTTACGCAA
1 AAACGCCACTAAAGGACAACTATATTGCAG-CGTTTACGCAA
* * *
2059229 AAACGCCACT-ACGGATAACTCTATTGCAGCGTTTACGCAA
1 AAACGCCACTAAAGGACAACTATATTGCAGCGTTTACGCAA
*
2059269 AAATGCCACTA
1 AAACGCCACTA
2059280 CTGGATAACT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
40 32 0.76
41 10 0.24
ACGTcount: A:0.38, C:0.25, G:0.14, T:0.23
Consensus pattern (41 bp):
AAACGCCACTAAAGGACAACTATATTGCAGCGTTTACGCAA
Found at i:2059255 original size:40 final size:42
Alignment explanation
Indices: 2059205--2059297 Score: 138
Period size: 40 Copynumber: 2.3 Consensus size: 42
2059195 ACTAAATGAC
* *
2059205 AACTATATTGCGA-TGTTTACGCAAAAACGCCACTAC-GGAT
1 AACTCTATTGCGAGCGTTTACGCAAAAACGCCACTACTGGAT
*
2059245 AACTCTATTGC-AGCGTTTACGCAAAAATGCCACTACTGGAT
1 AACTCTATTGCGAGCGTTTACGCAAAAACGCCACTACTGGAT
2059286 AACTCTATTGCG
1 AACTCTATTGCG
2059298 GCATTTTTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
39 1 0.02
40 31 0.66
41 15 0.32
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (42 bp):
AACTCTATTGCGAGCGTTTACGCAAAAACGCCACTACTGGAT
Found at i:2061110 original size:41 final size:41
Alignment explanation
Indices: 2061046--2061204 Score: 214
Period size: 41 Copynumber: 3.9 Consensus size: 41
2061036 GTTTATACAA
**
2061046 AAAAACACCACTATTGATT-ACACTATTGTGGCGTTTGT-T
1 AAAAACACCACTATTGATTAACACTATTACGGCGTTTGTCT
* *
2061085 AAAAAACGCCACTATTGATTAACACTATTACGGCGTTTATCT
1 -AAAAACACCACTATTGATTAACACTATTACGGCGTTTGTCT
* *
2061127 AAAAACACCACTATTGATTATCACTATTACGGTGTTTGTCT
1 AAAAACACCACTATTGATTAACACTATTACGGCGTTTGTCT
* * *
2061168 AAAAACGCCACTATTGATTATCACTATTGCGGCGTTT
1 AAAAACACCACTATTGATTAACACTATTACGGCGTTT
2061205 CAGGAATAAA
Statistics
Matches: 106, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
40 18 0.17
41 87 0.82
42 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (41 bp):
AAAAACACCACTATTGATTAACACTATTACGGCGTTTGTCT
Found at i:2061131 original size:81 final size:82
Alignment explanation
Indices: 2061046--2061204 Score: 250
Period size: 82 Copynumber: 2.0 Consensus size: 82
2061036 GTTTATACAA
**
2061046 AAAAACACCACTATTGATTA-CACTATTGTGGCGTTTGT-TAAAAAACGCCACTATTGATTAACA
1 AAAAACACCACTATTGATTATCACTATTACGGCGTTTGTCT-AAAAACGCCACTATTGATTAACA
2061109 CTATTACGGCGTTTATCT
65 CTATTACGGCGTTTATCT
* *
2061127 AAAAACACCACTATTGATTATCACTATTACGGTGTTTGTCTAAAAACGCCACTATTGATTATCAC
1 AAAAACACCACTATTGATTATCACTATTACGGCGTTTGTCTAAAAACGCCACTATTGATTAACAC
*
2061192 TATTGCGGCGTTT
66 TATTACGGCGTTT
2061205 CAGGAATAAA
Statistics
Matches: 71, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
81 20 0.28
82 50 0.70
83 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (82 bp):
AAAAACACCACTATTGATTATCACTATTACGGCGTTTGTCTAAAAACGCCACTATTGATTAACAC
TATTACGGCGTTTATCT
Found at i:2061392 original size:41 final size:42
Alignment explanation
Indices: 2061302--2061393 Score: 98
Period size: 41 Copynumber: 2.2 Consensus size: 42
2061292 CAAAATTTAT
* * *
2061302 ACTCTATTACGGCATTTGTGGTATAAACGCCACTAATTTACC
1 ACTCTATTACGGCATTTGTGGTAAAAACGCCACTAATGTACA
* * * *
2061344 ACCCTATTGCGGCATTT-TTGTAAAAACGCCGCTATATGT-CA
1 ACTCTATTACGGCATTTGTGGTAAAAACGCCACTA-ATGTACA
2061385 ACTCTATTA
1 ACTCTATTA
2061394 TAGCGTTTTT
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
41 22 0.55
42 18 0.45
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (42 bp):
ACTCTATTACGGCATTTGTGGTAAAAACGCCACTAATGTACA
Found at i:2063316 original size:29 final size:30
Alignment explanation
Indices: 2063265--2063326 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
2063255 AAATTTTATC
* ** *
2063265 TAGTGACTAAAGTGTAAGTTTTGA-AGGTT
1 TAGTGACTAAAGTATAAACTTTGACAAGTT
*
2063294 TAGTGGCTAAAGTATAAACTTTGACAAGTT
1 TAGTGACTAAAGTATAAACTTTGACAAGTT
2063324 TAG
1 TAG
2063327 GGACCAAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 20 0.74
30 7 0.26
ACGTcount: A:0.34, C:0.06, G:0.24, T:0.35
Consensus pattern (30 bp):
TAGTGACTAAAGTATAAACTTTGACAAGTT
Found at i:2070929 original size:29 final size:30
Alignment explanation
Indices: 2070896--2070957 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
2070886 CAAATTTGTC
* **
2070896 TAGTGACTAAAGTGTAAGTTTTG-AAAGTT
1 TAGTGACTAAAGTATAAACTTTGAAAAGTT
*
2070925 TAGTGGCTAAAGTATAAACTTTGAAAAGTT
1 TAGTGACTAAAGTATAAACTTTGAAAAGTT
2070955 TAG
1 TAG
2070958 GGATTGAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 19 0.68
30 9 0.32
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.35
Consensus pattern (30 bp):
TAGTGACTAAAGTATAAACTTTGAAAAGTT
Found at i:2077194 original size:90 final size:89
Alignment explanation
Indices: 2077074--2077250 Score: 291
Period size: 90 Copynumber: 2.0 Consensus size: 89
2077064 TAATCCCGAA
* *
2077074 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAATCCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAA-CCCTAATATGAT
*
2077139 TAGGGTAACTTGGATATAAAAGGAT
65 TAGCGTAACTTGGATATAAAAGGAT
* *
2077164 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGATATAATAAAACCCTAATATGATT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAACCCTAATATGATT
*
2077229 AGCGTAACTTGGCTATAAAAGG
66 AGCGTAACTTGGATATAAAAGG
2077251 GTGTGTTAGG
Statistics
Matches: 81, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 33 0.41
90 48 0.59
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (89 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAACCCTAATATGATT
AGCGTAACTTGGATATAAAAGGAT
Found at i:2078040 original size:2 final size:2
Alignment explanation
Indices: 2078033--2078062 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
2078023 CGTAAGAATG
2078033 TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
2078063 GTTTGTTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2082565 original size:18 final size:18
Alignment explanation
Indices: 2082542--2082579 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
2082532 TGAGCTAGAA
2082542 AAGTTCGAAGCAAGACAC
1 AAGTTCGAAGCAAGACAC
2082560 AAGTTCGAAGCAAGACAC
1 AAGTTCGAAGCAAGACAC
2082578 AA
1 AA
2082580 TAGCTGATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.11
Consensus pattern (18 bp):
AAGTTCGAAGCAAGACAC
Found at i:2084066 original size:90 final size:89
Alignment explanation
Indices: 2083967--2084132 Score: 287
Period size: 90 Copynumber: 1.9 Consensus size: 89
2083957 ATTTAATTTC
*
2083967 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCCTAATATGATTAGGATAAGTT
1 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-CCCTAATATGATTAGGATAACTT
2084032 GGATATAAAAGGATTATTAAATACT
65 GGATATAAAAGGATTATTAAATACT
* *
2084057 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCTTAATATGATTAGGGTAACTTG
1 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAGGATAACTTG
*
2084122 GCTATAAAAGG
66 GATATAAAAGG
2084133 GTGTGTTAGG
Statistics
Matches: 72, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 31 0.43
90 41 0.57
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.36
Consensus pattern (89 bp):
AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAGGATAACTTG
GATATAAAAGGATTATTAAATACT
Found at i:2097591 original size:83 final size:83
Alignment explanation
Indices: 2097497--2097661 Score: 258
Period size: 83 Copynumber: 2.0 Consensus size: 83
2097487 AACATCATAT
* * * * *
2097497 TTTAAGTCTTTTCGATTTGGTCACATATTGATGTATGGTTTCTGTTCTTTTATTTTACATTTCAT
1 TTTAAGTCTTTTCAAATTGGTCACATATTGATGGATGGTTTCGGTTCTTTTATTTTACATTTCAG
2097562 CATGCCATGATTGAATAA
66 CATGCCATGATTGAATAA
* * *
2097580 TTTAAGTCTTTTCAAATTGGTCACATATTTATGGATGGTTTCGGTTCTTTTATTTTGCATTTCGG
1 TTTAAGTCTTTTCAAATTGGTCACATATTGATGGATGGTTTCGGTTCTTTTATTTTACATTTCAG
2097645 CATGCCATGATTGAATA
66 CATGCCATGATTGAATA
2097662 TTTGTAATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
83 74 1.00
ACGTcount: A:0.22, C:0.13, G:0.16, T:0.48
Consensus pattern (83 bp):
TTTAAGTCTTTTCAAATTGGTCACATATTGATGGATGGTTTCGGTTCTTTTATTTTACATTTCAG
CATGCCATGATTGAATAA
Found at i:2105342 original size:16 final size:18
Alignment explanation
Indices: 2105321--2105359 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2105311 TGTGTACCCT
2105321 AAATATA-AA-AAAACAA
1 AAATATAGAATAAAACAA
*
2105337 AAATATAGAATAAAATAA
1 AAATATAGAATAAAACAA
2105355 AAATA
1 AAATA
2105360 AATAACTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 2 0.10
18 11 0.55
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.18
Consensus pattern (18 bp):
AAATATAGAATAAAACAA
Found at i:2107398 original size:203 final size:204
Alignment explanation
Indices: 2107046--2107451 Score: 733
Period size: 203 Copynumber: 2.0 Consensus size: 204
2107036 CAGTGGTGGT
2107046 ATAATTAAGTTTTGTTTCATTAAGGGTACGACTAACACAATAAATGACATGGAAGATTTTACCTT
1 ATAATTAAGTTTTGTTTCATTAAGGGTACGACTAACACAATAAATGACATGGAAGATTTTACCTT
*
2107111 TTATTTGCCCTAGCACTGCCCCTACCGCATAGTCACTTGCATCACACATCAGCTCAAAAGGAGCA
66 TTATTTGCCCTAGCACTGCCCCTACCGCATAGTCACTTGCATCACACATCACCTCAAAAGGAGCA
* * * * *
2107176 TCCCAGTCATGTGGTAAAACAATTAGTGCCGAGGTGAGTTTTTTCTTCA-ATCAATGATTGCGTT
131 TCCCAGTCAGGTAGTAAAACAATTAGTACCGAGGTGAGTTTTTTCTTCAGATCAATAAATGCGTT
2107240 GTGGCATTC
196 GTGGCATTC
2107249 ATAATTAAGTTTTGTTTCATTAAGGGTACGACTAACACAATAAATGACATGGAAGATTTTACCTT
1 ATAATTAAGTTTTGTTTCATTAAGGGTACGACTAACACAATAAATGACATGGAAGATTTTACCTT
2107314 TTATTTGCCCTAGCACTGCCCCTACCGCATAGTCACTTGCATCACACATCACCTCAAAAGGAGCA
66 TTATTTGCCCTAGCACTGCCCCTACCGCATAGTCACTTGCATCACACATCACCTCAAAAGGAGCA
* *
2107379 TCCCAGTCAGGTAGTAAAACAATTGGTACCGAGGTGAGTTTTTTCTTCAGATCAGTAAATGCGTT
131 TCCCAGTCAGGTAGTAAAACAATTAGTACCGAGGTGAGTTTTTTCTTCAGATCAATAAATGCGTT
2107444 GTGGCATT
196 GTGGCATT
2107452 AATTGTTGAA
Statistics
Matches: 194, Mismatches: 8, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
203 174 0.90
204 20 0.10
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (204 bp):
ATAATTAAGTTTTGTTTCATTAAGGGTACGACTAACACAATAAATGACATGGAAGATTTTACCTT
TTATTTGCCCTAGCACTGCCCCTACCGCATAGTCACTTGCATCACACATCACCTCAAAAGGAGCA
TCCCAGTCAGGTAGTAAAACAATTAGTACCGAGGTGAGTTTTTTCTTCAGATCAATAAATGCGTT
GTGGCATTC
Found at i:2118648 original size:14 final size:14
Alignment explanation
Indices: 2118629--2118669 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
2118619 AGTGCTTCAA
2118629 CTTTTCTTTCTTTT
1 CTTTTCTTTCTTTT
2118643 CTTTTCTTAT-TTTT
1 CTTTTCTT-TCTTTT
*
2118657 GTTTTC-TTCTTTT
1 CTTTTCTTTCTTTT
2118670 TGAGTGCTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
12 1 0.04
13 5 0.21
14 17 0.71
15 1 0.04
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.78
Consensus pattern (14 bp):
CTTTTCTTTCTTTT
Found at i:2118692 original size:25 final size:24
Alignment explanation
Indices: 2118658--2118708 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
2118648 CTTATTTTTG
*
2118658 TTTTCTTCTTTTTGAGTGCTTGAAT
1 TTTTCTTC-TTTTGAGTGCTTCAAT
2118683 TTTTCTTCTTTTGAGTGCTTCAAT
1 TTTTCTTCTTTTGAGTGCTTCAAT
2118707 TT
1 TT
2118709 CTTTGTTGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 17 0.68
25 8 0.32
ACGTcount: A:0.12, C:0.14, G:0.14, T:0.61
Consensus pattern (24 bp):
TTTTCTTCTTTTGAGTGCTTCAAT
Found at i:2119792 original size:2 final size:2
Alignment explanation
Indices: 2119630--2119776 Score: 83
Period size: 2 Copynumber: 75.5 Consensus size: 2
2119620 TATTTTTTAG
*
2119630 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A- AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* ** * * * * * * *
2119670 AG GC AT AT AT -T AT TT TT GA- AA AT AT AT AGT TT TT TT AA AT AT
1 AT AT AT AT AT AT AT AT AT -AT AT AT AT AT A-T AT AT AT AT AT AT
* * *
2119712 AT AT AT AT AT AT AT AT AC AC AT AA AT AT -T AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2119752 AT -T GAA AT AT AT AT AT AT AT AT AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT A
2119777 GTTTTTTTAA
Statistics
Matches: 115, Mismatches: 20, Indels: 20
0.74 0.13 0.13
Matches are distributed among these distances:
1 7 0.06
2 107 0.93
3 1 0.01
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2119828 original size:11 final size:11
Alignment explanation
Indices: 2119814--2119895 Score: 56
Period size: 9 Copynumber: 8.1 Consensus size: 11
2119804 ATAAGGATAT
2119814 TATATATATTA
1 TATATATATTA
2119825 TATATA-A-TA
1 TATATATATTA
*
2119834 TATATCGTATTA
1 TATAT-ATATTA
2119846 TA-ATATA--A
1 TATATATATTA
* *
2119854 TATTTATGTTA
1 TATATATATTA
2119865 TATAT-TATTA
1 TATATATATTA
2119875 -ATAT-TATTA
1 TATATATATTA
2119884 TAT-TATTATTA
1 TATATA-TATTA
2119895 T
1 T
2119896 TATTAATGTT
Statistics
Matches: 56, Mismatches: 6, Indels: 18
0.70 0.08 0.22
Matches are distributed among these distances:
8 3 0.05
9 20 0.36
10 9 0.16
11 20 0.36
12 4 0.07
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.55
Consensus pattern (11 bp):
TATATATATTA
Found at i:2119882 original size:3 final size:3
Alignment explanation
Indices: 2119862--2119917 Score: 60
Period size: 3 Copynumber: 18.7 Consensus size: 3
2119852 AATATTTATG
* * *
2119862 TTA TATA TTA TTA ATA TTA TTA -TA TTA TTA TTA TTA TTA ATG TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
2119907 TTA TTT TTA TT
1 TTA TTA TTA TT
2119918 TTTGTTTTGT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
2 2 0.05
3 38 0.88
4 3 0.07
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:2119887 original size:17 final size:17
Alignment explanation
Indices: 2119865--2119900 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
2119855 ATTTATGTTA
2119865 TATATTATTAATATTAT
1 TATATTATTAATATTAT
*
2119882 TATATTATTATTATTAT
1 TATATTATTAATATTAT
2119899 TA
1 TA
2119901 ATGTTATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TATATTATTAATATTAT
Found at i:2119893 original size:14 final size:14
Alignment explanation
Indices: 2119810--2119910 Score: 57
Period size: 14 Copynumber: 7.1 Consensus size: 14
2119800 GTGTATAAGG
2119810 ATATT-ATATATATT
1 ATATTAATAT-TATT
*
2119824 ATATATAATATATATC
1 ATAT-TAATAT-TATT
* * *
2119840 GTATT-ATAATATA
1 ATATTAATATTATT
* *
2119853 ATATTTATGTTATAT
1 ATATTAATATTAT-T
2119868 ATTATTAATATTATT
1 A-TATTAATATTATT
*
2119883 ATATTATTATTA-T
1 ATATTAATATTATT
*
2119896 -TATTAATGTTATT
1 ATATTAATATTATT
2119909 AT
1 AT
2119911 TTTTATTTTT
Statistics
Matches: 67, Mismatches: 13, Indels: 14
0.71 0.14 0.15
Matches are distributed among these distances:
12 9 0.13
13 9 0.13
14 23 0.34
15 5 0.07
16 21 0.31
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (14 bp):
ATATTAATATTATT
Found at i:2120727 original size:24 final size:24
Alignment explanation
Indices: 2120700--2120756 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
2120690 ATTGGAATCC
2120700 AATTCCATCAAGAGAGGGAAAGTA
1 AATTCCATCAAGAGAGGGAAAGTA
*
2120724 AATTCCATCAAGGGAGGGAAAGTA
1 AATTCCATCAAGAGAGGGAAAGTA
2120748 AATTCCATC
1 AATTCCATC
2120757 CATAACATGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.42, C:0.16, G:0.23, T:0.19
Consensus pattern (24 bp):
AATTCCATCAAGAGAGGGAAAGTA
Found at i:2121069 original size:33 final size:32
Alignment explanation
Indices: 2120995--2121085 Score: 121
Period size: 32 Copynumber: 2.8 Consensus size: 32
2120985 TTTTATTTCG
* * *
2120995 GGTCGGGTTTGTTTAAGTTTAATATTCAGGTC
1 GGTCGGGTTTTTTTAAGTGTGATATTCAGGTC
**
2121027 GGTCGGGTTTTTTTAAGTGTGATATTTGGGTC
1 GGTCGGGTTTTTTTAAGTGTGATATTCAGGTC
2121059 TGGTCGGG-TTTTTTAAGTGTGATATTC
1 -GGTCGGGTTTTTTTAAGTGTGATATTC
2121086 GCCTCGGGTT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
32 45 0.87
33 7 0.13
ACGTcount: A:0.15, C:0.08, G:0.31, T:0.46
Consensus pattern (32 bp):
GGTCGGGTTTTTTTAAGTGTGATATTCAGGTC
Found at i:2121099 original size:33 final size:31
Alignment explanation
Indices: 2120992--2121102 Score: 116
Period size: 32 Copynumber: 3.4 Consensus size: 31
2120982 TTTTTTTATT
* *
2120992 TCGGGTCGGGTTTGTTTAAGTTTAATATTCAGG
1 TCGGGTCGGGTTT-TTTAAGTGTGATATTC-GG
*
2121025 TC-GGTCGGGTTTTTTTAAGTGTGATATTTGGG
1 TCGGGTCGGG-TTTTTTAAGTGTGATA-TTCGG
* *
2121057 TCTGGTCGGGTTTTTTAAGTGTGATATTCGCC
1 TCGGGTCGGGTTTTTTAAGTGTGATATTCG-G
2121089 TCGGGTTCGGGTTT
1 TCGGG-TCGGGTTT
2121103 AGGGTGAAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
31 3 0.04
32 42 0.63
33 22 0.33
ACGTcount: A:0.13, C:0.11, G:0.32, T:0.44
Consensus pattern (31 bp):
TCGGGTCGGGTTTTTTAAGTGTGATATTCGG
Found at i:2126440 original size:3 final size:3
Alignment explanation
Indices: 2126432--2126457 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2126422 GAATTGGGTT
2126432 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
2126458 CCCTAATGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:2130982 original size:4 final size:4
Alignment explanation
Indices: 2130973--2130997 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2130963 TTAATTCAAG
2130973 CAAA CAAA CAAA CAAA CAAA CAAA C
1 CAAA CAAA CAAA CAAA CAAA CAAA C
2130998 CAATAAAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.72, C:0.28, G:0.00, T:0.00
Consensus pattern (4 bp):
CAAA
Found at i:2139132 original size:16 final size:16
Alignment explanation
Indices: 2139094--2139132 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
2139084 TATATTGAAT
*
2139094 TCTCAACTTGTACATC
1 TCTCAAGTTGTACATC
2139110 TCTCAAGTTGTACATC
1 TCTCAAGTTGTACATC
2139126 TCTCAAG
1 TCTCAAG
2139133 CTTCACCCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.26, C:0.28, G:0.10, T:0.36
Consensus pattern (16 bp):
TCTCAAGTTGTACATC
Found at i:2143725 original size:21 final size:21
Alignment explanation
Indices: 2143701--2143755 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
2143691 CGATGAACAA
2143701 TATCGATACTGATGCAATTAG
1 TATCGATACTGATGCAATTAG
2143722 TATCGATACTGATGCAATTAG
1 TATCGATACTGATGCAATTAG
2143743 TATCGATACTGAT
1 TATCGATACTGAT
2143756 TGTATCGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.35
Consensus pattern (21 bp):
TATCGATACTGATGCAATTAG
Found at i:2143773 original size:36 final size:36
Alignment explanation
Indices: 2143721--2143791 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
2143711 GATGCAATTA
* *
2143721 GTATCGATACTGATGCAATTAGTATCGATACTGATT
1 GTATCGAAACTAATGCAATTAGTATCGATACTGATT
* *
2143757 GTATCGAAACTAATGCAATTGGTATCGATATTGAT
1 GTATCGAAACTAATGCAATTAGTATCGATACTGAT
2143792 GTGTGTATCG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (36 bp):
GTATCGAAACTAATGCAATTAGTATCGATACTGATT
Found at i:2149957 original size:5 final size:6
Alignment explanation
Indices: 2149909--2149939 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
2149899 AAGTATAATT
2149909 TAAAAA TAATAAA TAAAAA TAAAAA TAAAAA
1 TAAAAA TAA-AAA TAAAAA TAAAAA TAAAAA
2149940 GGGAAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
TAAAAA
Found at i:2150027 original size:18 final size:18
Alignment explanation
Indices: 2150006--2150048 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
2149996 GTTGTTTTTA
2150006 AAATAAAAGATAAA-AATT
1 AAATAAAAGA-AAATAATT
2150024 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAATAATT
2150042 AAATAAA
1 AAATAAA
2150049 TAATCTATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 3 0.12
18 21 0.88
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAATAATT
Found at i:2152782 original size:11 final size:11
Alignment explanation
Indices: 2152766--2152797 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
2152756 AAAGTTCGCT
2152766 GAAAATAAAAC
1 GAAAATAAAAC
*
2152777 GAAAATAAAAT
1 GAAAATAAAAC
2152788 GAAAATAAAA
1 GAAAATAAAA
2152798 AATATAACGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.75, C:0.03, G:0.09, T:0.12
Consensus pattern (11 bp):
GAAAATAAAAC
Found at i:2155778 original size:37 final size:39
Alignment explanation
Indices: 2155724--2155820 Score: 99
Period size: 37 Copynumber: 2.5 Consensus size: 39
2155714 ATAATAAAAT
* * * *
2155724 AAAATAACTAATTATAAT-TTAA-AAATAAAAAAATAAA
1 AAAATAAATAATAATAATAATAATAAATAAAAAAAGAAA
* *
2155761 AAAATAAATAATAATAATAATAATAAATAAGAAAGGAAA
1 AAAATAAATAATAATAATAATAATAAATAAAAAAAGAAA
*
2155800 ATAATAAAATAATAAATAATA
1 AAAAT-AAATAAT-AATAATA
2155821 GTAGTAAAGA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
37 16 0.33
38 3 0.06
39 16 0.33
40 7 0.14
41 7 0.14
ACGTcount: A:0.71, C:0.01, G:0.03, T:0.25
Consensus pattern (39 bp):
AAAATAAATAATAATAATAATAATAAATAAAAAAAGAAA
Found at i:2159442 original size:21 final size:21
Alignment explanation
Indices: 2159416--2159455 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2159406 CAGAACCCCA
*
2159416 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
2159437 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
2159456 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:2159484 original size:19 final size:20
Alignment explanation
Indices: 2159438--2159497 Score: 68
Period size: 19 Copynumber: 2.9 Consensus size: 20
2159428 TTCCCCTGTG
2159438 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TC-AA
2159461 GGGGGAATCGGTTCCCTC-A
1 GGGGGAATCGGTTCCCTCAA
* *
2159480 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
2159498 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.17, C:0.27, G:0.35, T:0.22
Consensus pattern (20 bp):
GGGGGAATCGGTTCCCTCAA
Found at i:2168288 original size:25 final size:25
Alignment explanation
Indices: 2168254--2168304 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
2168244 CCTCAAATAA
2168254 TCATTCACTTCTCGAATTCTTTTGT
1 TCATTCACTTCTCGAATTCTTTTGT
2168279 TCATTCACTTCTCGAATTCTTTTGT
1 TCATTCACTTCTCGAATTCTTTTGT
2168304 T
1 T
2168305 TTTCTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.16, C:0.24, G:0.08, T:0.53
Consensus pattern (25 bp):
TCATTCACTTCTCGAATTCTTTTGT
Found at i:2168384 original size:16 final size:15
Alignment explanation
Indices: 2168344--2168384 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
2168334 TACTTTTCTC
*
2168344 TTTTATCTTTTACTT
1 TTTTCTCTTTTACTT
*
2168359 TTTTCGCTTTTACTT
1 TTTTCTCTTTTACTT
2168374 ATTTTCTCTTT
1 -TTTTCTCTTT
2168385 AAGTGCTAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.10, C:0.17, G:0.02, T:0.71
Consensus pattern (15 bp):
TTTTCTCTTTTACTT
Found at i:2171743 original size:21 final size:18
Alignment explanation
Indices: 2171686--2171727 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2171676 TGAGAAAAAA
* **
2171686 AATTTCTAATTCATGGTT
1 AATTTCTGATTCAAAGTT
2171704 AATTTCTGATTCAAAGTT
1 AATTTCTGATTCAAAGTT
2171722 AATTTC
1 AATTTC
2171728 CTCGAATTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.48
Consensus pattern (18 bp):
AATTTCTGATTCAAAGTT
Found at i:2179031 original size:14 final size:14
Alignment explanation
Indices: 2179005--2179037 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2178995 TATAAAAAAA
2179005 TTAC-TTTTATCTT
1 TTACTTTTTATCTT
*
2179018 TTACTTTTTCTCTT
1 TTACTTTTTATCTT
2179032 TTACTT
1 TTACTT
2179038 ATTTTCTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.70
Consensus pattern (14 bp):
TTACTTTTTATCTT
Found at i:2179626 original size:16 final size:16
Alignment explanation
Indices: 2179601--2179634 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2179591 AGAAGTTTGA
2179601 TTCAACTTTACTTCCT
1 TTCAACTTTACTTCCT
* *
2179617 TTCAATTTTACTTTCT
1 TTCAACTTTACTTCCT
2179633 TT
1 TT
2179635 AGTTTTAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.24, G:0.00, T:0.59
Consensus pattern (16 bp):
TTCAACTTTACTTCCT
Found at i:2182501 original size:867 final size:867
Alignment explanation
Indices: 2181313--2183046 Score: 3306
Period size: 867 Copynumber: 2.0 Consensus size: 867
2181303 GTCTAGCTTG
2181313 CACAAAGTAACTTGAATCGTTCCCAATAATTATATAATGACTACTCCATTTATTTGTTGAACTCC
1 CACAAAGTAACTTGAATCGTTCCCAATAATTATATAATGACTACTCCATTTATTTGTTGAACTCC
* *
2181378 TAAGATTTTTGTTCTTAATTCACTCGCTTTTGTTGCAGGGAAAAACATGTCAAGAAAAAGACGAG
66 TAAGATTTTTGTTCTTAATTCACTCACTTTTATTGCAGGGAAAAACATGTCAAGAAAAAGACGAG
2181443 TCATATCAGCTCATGTATTAACTTATGAGGTAAATAAAACAACCAATCTTTAGCTGAGTCTACTA
131 TCATATCAGCTCATGTATTAACTTATGAGGTAAATAAAACAACCAATCTTTAGCTGAGTCTACTA
*
2181508 AAGAAAAAGGGAAAGCATAGAGTTTAATTTGATCATCATCAGTTTCATGCTAGAGAAAACTAGAT
196 AAGAAAAAGGGAAAACATAGAGTTTAATTTGATCATCATCAGTTTCATGCTAGAGAAAACTAGAT
2181573 GAAACTCAGTAAGATGCTTGTGAGGACTTTCGTTGGGTAGTCCACGGTAAGTAGGTAGAAGATGA
261 GAAACTCAGTAAGATGCTTGTGAGGACTTTCGTTGGGTAGTCCACGGTAAGTAGGTAGAAGATGA
* *
2181638 ATCAAACCCGTTTTTAGCTCAAATAGTGTCTCTCCACGAGGGAATGCAATGTAAAGTGGTTGTTC
326 ATCAAACCCGTTTTTAGCTCAAATAGTGTCTCTCCACGAGGGAATGCAATGCAAAATGGTTGTTC
2181703 GATAGTTGCCACAACTAATTCTCATATTGTTTGTTGATCCATTAGAATCAGTTTCTTGAAGTCTT
391 GATAGTTGCCACAACTAATTCTCATATTGTTTGTTGATCCATTAGAATCAGTTTCTTGAAGTCTT
2181768 CTTCATCGTCAAAAAAGTTTTTGGCGTCCAAAGGTATCTCCGGATTATAATCGAATTGCTGTGAT
456 CTTCATCGTCAAAAAAGTTTTTGGCGTCCAAAGGTATCTCCGGATTATAATCGAATTGCTGTGAT
2181833 TATTATTGTTGTTGTTGTTGTCTCCTTTCTTGTAGTGTGCATGAGCATATTCTTCGGGCTAGTCC
521 TATTATTGTTGTTGTTGTTGTCTCCTTTCTTGTAGTGTGCATGAGCATATTCTTCGGGCTAGTCC
2181898 TTCGATCTTAGGTACCCAATCTGTTAGTTCACCTGGATACGTCCTGGTCATAAATCAAAACAAAT
586 TTCGATCTTAGGTACCCAATCTGTTAGTTCACCTGGATACGTCCTGGTCATAAATCAAAACAAAT
2181963 TTAATAAGTAATTTTTAGTGATCCCCAACAATGACACCAATTTGACAAGCGTCGTAATTATCAAA
651 TTAATAAGTAATTTTTAGTGATCCCCAACAATGACACCAATTTGACAAGCGTCGTAATTATCAAA
*
2182028 TAATTAACCCTTTTTCTCGGATAATTATGCTAAGAACGTAATATAGAGAAGAAAGGTGTTGGTTC
716 TAATTAACCCTTTTTCTCGAATAATTATGCTAAGAACGTAATATAGAGAAGAAAGGTGTTGGTTC
*
2182093 ACAGGGATTCAGTAATTTCTAATATAAATCTGAATTGATCTTTAACGAAGAAATCTGTAAAACAA
781 ACAGGGATTCAGTAATTTCTAATATAAATCTAAATTGATCTTTAACGAAGAAATCTGTAAAACAA
2182158 GAAAATTCACTATAGCAAAAGT
846 GAAAATTCACTATAGCAAAAGT
**
2182180 CACAAAGTGTCTTGAATCGTTCCCAATAATTATATAATGACTACTCCATTTATTTGTTGAACTCC
1 CACAAAGTAACTTGAATCGTTCCCAATAATTATATAATGACTACTCCATTTATTTGTTGAACTCC
2182245 TAAGATTTTTGTTCTTAATTCACTCACTTTTATTGCAGGGAAAAACATGTCAAGAAAAAGACGAG
66 TAAGATTTTTGTTCTTAATTCACTCACTTTTATTGCAGGGAAAAACATGTCAAGAAAAAGACGAG
2182310 TCATATCAGCTCATGTATTAACTTATGAGGTAAATAAAACAACCAATCTTTAGCTGAGTCTACTA
131 TCATATCAGCTCATGTATTAACTTATGAGGTAAATAAAACAACCAATCTTTAGCTGAGTCTACTA
* *
2182375 AAGAAAAAGGGAAAACATGGAGTTTAATTTGATCATCATCGGTTTCATGCTAGAGAAAACTAGAT
196 AAGAAAAAGGGAAAACATAGAGTTTAATTTGATCATCATCAGTTTCATGCTAGAGAAAACTAGAT
2182440 GAAACTCAGTAAGATGCTTGTGAGGACTTTCGTTGGGTAGTCCACGGTAAGTAGGTAGAAGATGA
261 GAAACTCAGTAAGATGCTTGTGAGGACTTTCGTTGGGTAGTCCACGGTAAGTAGGTAGAAGATGA
*
2182505 ATCAAACCCGTTTTTAGCTCAAATAGTGTCTCTCCGCGAGGGAATGCAATGCAAAATGGTTGTTC
326 ATCAAACCCGTTTTTAGCTCAAATAGTGTCTCTCCACGAGGGAATGCAATGCAAAATGGTTGTTC
* *
2182570 GATAGTTGCCGCAGCTAATTCTCATATTGTTTGTTGATCCATTAGAATCAGTTTCTTGAAGTCTT
391 GATAGTTGCCACAACTAATTCTCATATTGTTTGTTGATCCATTAGAATCAGTTTCTTGAAGTCTT
* *
2182635 CTTCATTGTCAAAAAAGTTTTTGGCGTCCAAAGGTATCTCCGGATTATAATCGAATTGTTGTGAT
456 CTTCATCGTCAAAAAAGTTTTTGGCGTCCAAAGGTATCTCCGGATTATAATCGAATTGCTGTGAT
*
2182700 TATTATTGTTGTTGTTGTTGTCTCCTTTCTTGTAGTGTGCATGAGCATATTCTTCGGGCTAGTGC
521 TATTATTGTTGTTGTTGTTGTCTCCTTTCTTGTAGTGTGCATGAGCATATTCTTCGGGCTAGTCC
*
2182765 TTCGATCTTAGGTACCCAATCTGTTAGTTCACCTGGATATGTCCTGGTCATAAATCAAAACAAAT
586 TTCGATCTTAGGTACCCAATCTGTTAGTTCACCTGGATACGTCCTGGTCATAAATCAAAACAAAT
2182830 TTAATAAGTAATTTTTAGTGATCCCCAACAATGACACCAATTTGACAAGCGTCGTAATTATCAAA
651 TTAATAAGTAATTTTTAGTGATCCCCAACAATGACACCAATTTGACAAGCGTCGTAATTATCAAA
2182895 TAATTAACCCTTTTTCTCGAATAATTATGCTAAGAACGTAATATAGAGAAGAAAGGTGTTGGTTC
716 TAATTAACCCTTTTTCTCGAATAATTATGCTAAGAACGTAATATAGAGAAGAAAGGTGTTGGTTC
2182960 ACAGGGATTCAGTAATTTCTAATATAAATCTAAATTGATCTTTAACGAAGAAATCTGTAAAACAA
781 ACAGGGATTCAGTAATTTCTAATATAAATCTAAATTGATCTTTAACGAAGAAATCTGTAAAACAA
2183025 GAAAATTCACTATAGCAAAAGT
846 GAAAATTCACTATAGCAAAAGT
2183047 GTTCTGTTGG
Statistics
Matches: 849, Mismatches: 18, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
867 849 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Consensus pattern (867 bp):
CACAAAGTAACTTGAATCGTTCCCAATAATTATATAATGACTACTCCATTTATTTGTTGAACTCC
TAAGATTTTTGTTCTTAATTCACTCACTTTTATTGCAGGGAAAAACATGTCAAGAAAAAGACGAG
TCATATCAGCTCATGTATTAACTTATGAGGTAAATAAAACAACCAATCTTTAGCTGAGTCTACTA
AAGAAAAAGGGAAAACATAGAGTTTAATTTGATCATCATCAGTTTCATGCTAGAGAAAACTAGAT
GAAACTCAGTAAGATGCTTGTGAGGACTTTCGTTGGGTAGTCCACGGTAAGTAGGTAGAAGATGA
ATCAAACCCGTTTTTAGCTCAAATAGTGTCTCTCCACGAGGGAATGCAATGCAAAATGGTTGTTC
GATAGTTGCCACAACTAATTCTCATATTGTTTGTTGATCCATTAGAATCAGTTTCTTGAAGTCTT
CTTCATCGTCAAAAAAGTTTTTGGCGTCCAAAGGTATCTCCGGATTATAATCGAATTGCTGTGAT
TATTATTGTTGTTGTTGTTGTCTCCTTTCTTGTAGTGTGCATGAGCATATTCTTCGGGCTAGTCC
TTCGATCTTAGGTACCCAATCTGTTAGTTCACCTGGATACGTCCTGGTCATAAATCAAAACAAAT
TTAATAAGTAATTTTTAGTGATCCCCAACAATGACACCAATTTGACAAGCGTCGTAATTATCAAA
TAATTAACCCTTTTTCTCGAATAATTATGCTAAGAACGTAATATAGAGAAGAAAGGTGTTGGTTC
ACAGGGATTCAGTAATTTCTAATATAAATCTAAATTGATCTTTAACGAAGAAATCTGTAAAACAA
GAAAATTCACTATAGCAAAAGT
Found at i:2183906 original size:22 final size:22
Alignment explanation
Indices: 2183876--2183917 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2183866 GTTTTTCTGC
*
2183876 TTTCGAATAGAAAAATAATATT
1 TTTCAAATAGAAAAATAATATT
*
2183898 TTTCAAATAGGAAAATAATA
1 TTTCAAATAGAAAAATAATA
2183918 GCTTTTGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.05, G:0.10, T:0.33
Consensus pattern (22 bp):
TTTCAAATAGAAAAATAATATT
Found at i:2193575 original size:44 final size:43
Alignment explanation
Indices: 2193501--2193656 Score: 161
Period size: 44 Copynumber: 3.6 Consensus size: 43
2193491 TTTTGTGTTC
* ** *
2193501 TTTAGCGGCATTTGTA-ACAAAAAACGCCGCTATATACCATACAT
1 TTTA-CGGCATTTGTATCCAAAAAATACCGCTATATACCAGAC-T
* * * *
2193545 TTTATGGCATTTGTATCCTAAAAATACCGCTATATAACAGACC
1 TTTACGGCATTTGTATCCAAAAAATACCGCTATATACCAGACT
* *
2193588 TTTAGCGGCGTTTGTATCCAAAAAATGCCGCTATATACCAGATCT
1 TTTA-CGGCATTTGTATCCAAAAAATACCGCTATATACCAGA-CT
* *
2193633 TTTGCGGCATTTGTATCCGAAAAA
1 TTTACGGCATTTGTATCCAAAAAA
2193657 CACCATGAAT
Statistics
Matches: 92, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
43 14 0.15
44 74 0.80
45 4 0.04
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (43 bp):
TTTACGGCATTTGTATCCAAAAAATACCGCTATATACCAGACT
Found at i:2202294 original size:13 final size:13
Alignment explanation
Indices: 2202276--2202316 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
2202266 GTCATAAATC
*
2202276 TATGACGCGTATT
1 TATGACGCGCATT
*
2202289 TATGACACGCATT
1 TATGACGCGCATT
*
2202302 TATGACGAGCATT
1 TATGACGCGCATT
2202315 TA
1 TA
2202317 GCGTCATTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:2208105 original size:29 final size:29
Alignment explanation
Indices: 2208052--2208134 Score: 94
Period size: 29 Copynumber: 2.9 Consensus size: 29
2208042 ACAGTGGCCG
** **
2208052 TAGGTCGCCATGCACTCCCAACGACCTCC
1 TAGGTCGCCATGCACTCCCGGCGACCAAC
* *
2208081 TAGGTCGCCATGCACGCCCGGCGACCAAG
1 TAGGTCGCCATGCACTCCCGGCGACCAAC
* *
2208110 GAGGTCGCCATGCACTCGCGGCGAC
1 TAGGTCGCCATGCACTCCCGGCGAC
2208135 ATCCCCTGCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.19, C:0.40, G:0.28, T:0.13
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCCGGCGACCAAC
Done.