Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr3
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: 36364294
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2168405 characters in sequence are not A, C, G, or T
File 26 of 91
Found at i:8778779 original size:57 final size:57
Alignment explanation
Indices: 8778708--8778822 Score: 167
Period size: 57 Copynumber: 2.0 Consensus size: 57
8778698 AATTTGCTTG
* * *
8778708 TTGGTCATCCAATTTGTGTATAAATAAATTAAGATAATTTAGAGATAAAATTCAAAT
1 TTGGTCATCCAATTTGTCTATAAATAAATTAAGATAATTTAGAAATAAAACTCAAAT
* * * *
8778765 TTGGTCATCTAATTTTTCTCTAAATAAATTAAGATAATTTAGAAATAATACTCAAAT
1 TTGGTCATCCAATTTGTCTATAAATAAATTAAGATAATTTAGAAATAAAACTCAAAT
8778822 T
1 T
8778823 CAGCCAATCA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 51 1.00
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.39
Consensus pattern (57 bp):
TTGGTCATCCAATTTGTCTATAAATAAATTAAGATAATTTAGAAATAAAACTCAAAT
Found at i:8779366 original size:13 final size:14
Alignment explanation
Indices: 8779348--8779378 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
8779338 TACATATAAG
8779348 TTAACCATTAGCT-
1 TTAACCATTAGCTC
8779361 TTAACCATTAGCTC
1 TTAACCATTAGCTC
8779375 TTAA
1 TTAA
8779379 TTCATACACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.39
Consensus pattern (14 bp):
TTAACCATTAGCTC
Found at i:8781494 original size:73 final size:73
Alignment explanation
Indices: 8781398--8781596 Score: 229
Period size: 73 Copynumber: 2.7 Consensus size: 73
8781388 GAAGATGGCC
* * * *
8781398 GATTCAGAAGCAGAGACAACTTAATCGACTAAGAAACATTGTTAGTCGACTGAGAGCTTACAGTT
1 GATTCAGAAACAGAGATAACTTAATCGACTAAGAAACATTGTTAGTCGACTAAGAGCTTACAGCT
*
8781463 AGAAACTG
66 AAAAACTG
* * ** **
8781471 GATTTAGAGACAGAGATAACTTAATCGACTAAG-AAGTTTGGTTAGTCGACTAAGAGCTTATTGC
1 GATTCAGAAACAGAGATAACTTAATCGACTAAGAAACATT-GTTAGTCGACTAAGAGCTTACAGC
8781535 TAAAAACTG
65 TAAAAACTG
* * * * * *
8781544 GGTTCAGAAACAAAGATGACTTAATTGACTAAGAAGCATAGTTAGTCGACTAA
1 GATTCAGAAACAGAGATAACTTAATCGACTAAGAAACATTGTTAGTCGACTAA
8781597 AAGTATTCTA
Statistics
Matches: 103, Mismatches: 21, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
72 4 0.04
73 97 0.94
74 2 0.02
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.26
Consensus pattern (73 bp):
GATTCAGAAACAGAGATAACTTAATCGACTAAGAAACATTGTTAGTCGACTAAGAGCTTACAGCT
AAAAACTG
Found at i:8800345 original size:23 final size:22
Alignment explanation
Indices: 8800311--8800361 Score: 75
Period size: 23 Copynumber: 2.3 Consensus size: 22
8800301 CAATTTAATA
*
8800311 AATGCTATGCAATGCAAAGTAG
1 AATGCAATGCAATGCAAAGTAG
*
8800333 TATGCANATGCAATGCAAAGTAG
1 AATGCA-ATGCAATGCAAAGTAG
8800356 AATGCA
1 AATGCA
8800362 TGTGATAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 4 0.16
23 21 0.84
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.22
Consensus pattern (22 bp):
AATGCAATGCAATGCAAAGTAG
Found at i:8803206 original size:20 final size:20
Alignment explanation
Indices: 8803180--8803225 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
8803170 AATCTTACAT
* *
8803180 TTTTTCACTTGTTTCCTTGAA
1 TTTTACACTT-TTCCCTTGAA
8803201 TTTTCACACTTTTCCCTTGAA
1 TTTT-ACACTTTTCCCTTGAA
8803222 TTTT
1 TTTT
8803226 TCCACCTAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.15, C:0.22, G:0.07, T:0.57
Consensus pattern (20 bp):
TTTTACACTTTTCCCTTGAA
Found at i:8803227 original size:22 final size:22
Alignment explanation
Indices: 8803185--8803225 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
8803175 TACATTTTTT
*
8803185 CACTTGTTTCCTTGAATTTTCA
1 CACTTGTTCCCTTGAATTTTCA
8803207 CACTT-TTCCCTTGAATTTT
1 CACTTGTTCCCTTGAATTTT
8803226 TCCACCTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.17, C:0.24, G:0.07, T:0.51
Consensus pattern (22 bp):
CACTTGTTCCCTTGAATTTTCA
Found at i:8811156 original size:22 final size:22
Alignment explanation
Indices: 8811131--8811174 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
8811121 TTTAGAACAA
*
8811131 CTTTAAACCCAAAAGCTCTGAT
1 CTTTAAAACCAAAAGCTCTGAT
8811153 CTTTAAAACCAAAAGCTCTGAT
1 CTTTAAAACCAAAAGCTCTGAT
8811175 ACCAATGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.25, G:0.09, T:0.27
Consensus pattern (22 bp):
CTTTAAAACCAAAAGCTCTGAT
Found at i:8819587 original size:38 final size:40
Alignment explanation
Indices: 8819497--8819599 Score: 147
Period size: 38 Copynumber: 2.6 Consensus size: 40
8819487 ACCCGACTCA
**
8819497 TGTACATCCCCCCACATTGTGCACATAGCTAGTGCCATCG
1 TGTACATCCCCCCACATCATGCACATAGCTAGTGCCATCG
* * *
8819537 TGTGCATGCCCCCACATCATGCACA-ATC-AGTGCCATCG
1 TGTACATCCCCCCACATCATGCACATAGCTAGTGCCATCG
8819575 TGTACATCCCCCCACATCATGCACA
1 TGTACATCCCCCCACATCATGCACA
8819600 CGGGCACTAT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
38 33 0.59
39 2 0.04
40 21 0.38
ACGTcount: A:0.24, C:0.38, G:0.16, T:0.22
Consensus pattern (40 bp):
TGTACATCCCCCCACATCATGCACATAGCTAGTGCCATCG
Found at i:8822694 original size:39 final size:39
Alignment explanation
Indices: 8822646--8822773 Score: 131
Period size: 39 Copynumber: 3.4 Consensus size: 39
8822636 TGCCGGTAGC
*
8822646 GTGCGGTGTGGGAGAGCACA-CACTGATAATATATGCCAT
1 GTGCGGTGTGGGAGAGCACATCA-TGATAATATATACCAT
* * *
8822685 GTGCAGTGTGGGAGAGCACATGATGATGATATATACCAT
1 GTGCGGTGTGGGAGAGCACATCATGATAATATATACCAT
* ** *
8822724 GTGCGGTGTGGGA-A-TACA-CATGAGGATAT-TAGCTAT
1 GTGCGGTGTGGGAGAGCACATCATGATAATATATA-CCAT
8822760 GTGCGGTGTGGGAG
1 GTGCGGTGTGGGAG
8822774 TACACATGAG
Statistics
Matches: 77, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
35 2 0.03
36 25 0.32
37 3 0.04
38 1 0.01
39 45 0.58
40 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.35, T:0.25
Consensus pattern (39 bp):
GTGCGGTGTGGGAGAGCACATCATGATAATATATACCAT
Found at i:8826520 original size:43 final size:43
Alignment explanation
Indices: 8826454--8826548 Score: 145
Period size: 43 Copynumber: 2.2 Consensus size: 43
8826444 TAGCTAGGTC
8826454 ATCATCATCGGCATATGCCCACTCCCTACTGGCACATAGCCGG
1 ATCATCATCGGCATATGCCCACTCCCTACTGGCACATAGCCGG
* * * *
8826497 ATCATCATCGGCTTATGCGCACTCCCTACTTGCACATAGCGGG
1 ATCATCATCGGCATATGCCCACTCCCTACTGGCACATAGCCGG
*
8826540 GTCATCATC
1 ATCATCATC
8826549 ACCTCATGTG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.22, C:0.35, G:0.19, T:0.24
Consensus pattern (43 bp):
ATCATCATCGGCATATGCCCACTCCCTACTGGCACATAGCCGG
Found at i:8826562 original size:43 final size:43
Alignment explanation
Indices: 8826468--8826565 Score: 124
Period size: 43 Copynumber: 2.3 Consensus size: 43
8826458 TCATCGGCAT
* ** *
8826468 ATGCCCACTCCCTACTGGCACATAGCCGGATCATCATCGGCTT
1 ATGCGCACTCCCTACTGGCACATAGCCGGATCATCATCACCTC
* * *
8826511 ATGCGCACTCCCTACTTGCACATAGCGGGGTCATCATCACCTC
1 ATGCGCACTCCCTACTGGCACATAGCCGGATCATCATCACCTC
*
8826554 ATGTGCACTCCC
1 ATGCGCACTCCC
8826566 ACACACACAT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.20, C:0.38, G:0.18, T:0.23
Consensus pattern (43 bp):
ATGCGCACTCCCTACTGGCACATAGCCGGATCATCATCACCTC
Found at i:8827993 original size:55 final size:55
Alignment explanation
Indices: 8827906--8828135 Score: 298
Period size: 55 Copynumber: 4.2 Consensus size: 55
8827896 AGGTACTACA
* * * * *
8827906 GAGCTGATGATCGGTGGATAATGATTCTAACTATGTGCGGTGTGGAAGTGCACAT
1 GAGCTGATGACCGATGGATGATGATTCCAACTATGTGCGGTGTGGGAGTGCACAT
* * *
8827961 GCGCTGATGACCGGTGGATGATGATTCCAACTATGTGCGGTGTAGGAGTGCACAT
1 GAGCTGATGACCGATGGATGATGATTCCAACTATGTGCGGTGTGGGAGTGCACAT
* * * *
8828016 GAGTTGATGACCGATGGATGATGATTCTAGCTATGTGCTGTGTGGGAGTGCACAT
1 GAGCTGATGACCGATGGATGATGATTCCAACTATGTGCGGTGTGGGAGTGCACAT
* * * * * *
8828071 GAGCTGCTGACCAATGGATGATGATTCCAGCTATTTGTGGTATGGGAGTGCACAT
1 GAGCTGATGACCGATGGATGATGATTCCAACTATGTGCGGTGTGGGAGTGCACAT
8828126 GAGCTGATGA
1 GAGCTGATGA
8828136 GCTGGTGGTT
Statistics
Matches: 153, Mismatches: 22, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
55 153 1.00
ACGTcount: A:0.23, C:0.15, G:0.33, T:0.28
Consensus pattern (55 bp):
GAGCTGATGACCGATGGATGATGATTCCAACTATGTGCGGTGTGGGAGTGCACAT
Found at i:8828214 original size:7 final size:7
Alignment explanation
Indices: 8828202--8828233 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
8828192 GTGATTGCAA
8828202 TGAATGT
1 TGAATGT
8828209 TGAATGT
1 TGAATGT
8828216 TGAATGT
1 TGAATGT
8828223 TGAATGT
1 TGAATGT
8828230 TGAA
1 TGAA
8828234 ATTGTTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.31, C:0.00, G:0.28, T:0.41
Consensus pattern (7 bp):
TGAATGT
Found at i:8844989 original size:73 final size:72
Alignment explanation
Indices: 8844901--8845098 Score: 209
Period size: 73 Copynumber: 2.7 Consensus size: 72
8844891 AAGATGGCCG
* * *** *
8844901 GTTCAGAAGCAAAGATAACTTAATCGACTAAGAAACATTGTTAGTTGGCTAAGAGCTTACTGCCA
1 GTTCAGAA-CAAAGATGACTTAATTGACTAAGAAACATTGTTAGTCAACTAAGAACTTACTGCCA
8844966 GAAACTGA
65 GAAACTGA
* ** *
8844974 GTTCAGAGACAAAGATGACTTAATTGGCTAAG-AAGTTTGGTTAGTCAACTAAGAACTTACTGCT
1 GTTCAGA-ACAAAGATGACTTAATTGACTAAGAAACATT-GTTAGTCAACTAAGAACTTACTGCC
*
8845038 AGAAACTGG
64 AGAAACTGA
* * * * *
8845047 GTTCAAAAACAGAGATGACTTAATTGACTAAGAAGCATAGTTAGTCGACTAA
1 GTTC-AGAACAAAGATGACTTAATTGACTAAGAAACATTGTTAGTCAACTAA
8845099 AAGTATTTTG
Statistics
Matches: 102, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
72 4 0.04
73 93 0.91
74 5 0.05
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (72 bp):
GTTCAGAACAAAGATGACTTAATTGACTAAGAAACATTGTTAGTCAACTAAGAACTTACTGCCAG
AAACTGA
Found at i:8846260 original size:16 final size:16
Alignment explanation
Indices: 8846239--8846270 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
8846229 AAAATGTGAC
8846239 AGGATTTTGGAAGTTA
1 AGGATTTTGGAAGTTA
*
8846255 AGGATTTTGGAGGTTA
1 AGGATTTTGGAAGTTA
8846271 TTTAATGGGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.34, T:0.38
Consensus pattern (16 bp):
AGGATTTTGGAAGTTA
Found at i:8847218 original size:121 final size:120
Alignment explanation
Indices: 8847004--8847251 Score: 478
Period size: 121 Copynumber: 2.1 Consensus size: 120
8846994 CATTTCAAAT
8847004 GCAAGTTATGCTCATAGTTTTGTCATATCAAAAAGGGAGAGCTTATTAGCTTTAAAATTATTATA
1 GCAAGTTATGCTCATAGTTTTGTCATATCAAAAAGGGAGAGCTTATTAGCTTTAAAATTATTATA
8847069 GTTTGGTTATGACAAAATGATTAAATTTGCTTGAATATTGTTTGAGGGATCTTTC
66 GTTTGGTTATGACAAAATGATTAAATTTGCTTGAATATTGTTTGAGGGATCTTTC
8847124 NGCAAGTTATGCTCATAGTTTTGTCATATCAAAAAGGGAGAGCTTATTAGCTTTAAAATTATTAT
1 -GCAAGTTATGCTCATAGTTTTGTCATATCAAAAAGGGAGAGCTTATTAGCTTTAAAATTATTAT
8847189 AGTTTGGTTATGACAAAATGATTAAATTTGCTTGAATATTGTTTGAGGGATCTTTC
65 AGTTTGGTTATGACAAAATGATTAAATTTGCTTGAATATTGTTTGAGGGATCTTTC
*
8847245 ACAAGTT
1 GCAAGTT
8847252 CTTGAAATGA
Statistics
Matches: 126, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
120 6 0.05
121 120 0.95
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (120 bp):
GCAAGTTATGCTCATAGTTTTGTCATATCAAAAAGGGAGAGCTTATTAGCTTTAAAATTATTATA
GTTTGGTTATGACAAAATGATTAAATTTGCTTGAATATTGTTTGAGGGATCTTTC
Found at i:8847621 original size:29 final size:31
Alignment explanation
Indices: 8847566--8847635 Score: 99
Period size: 29 Copynumber: 2.3 Consensus size: 31
8847556 TGCTAGTTAT
8847566 TATGGATATTCGATATATCTTGCTTAGCTAC
1 TATGGATATTCGATATATCTTGCTTAGCTAC
* *
8847597 TATGGATATT-G-TATATCTTGTTTAGCTAT
1 TATGGATATTCGATATATCTTGCTTAGCTAC
*
8847626 TGTGGATATT
1 TATGGATATT
8847636 ATAAATATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 25 0.69
30 1 0.03
31 10 0.28
ACGTcount: A:0.24, C:0.10, G:0.19, T:0.47
Consensus pattern (31 bp):
TATGGATATTCGATATATCTTGCTTAGCTAC
Found at i:8851434 original size:2 final size:2
Alignment explanation
Indices: 8851427--8851455 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
8851417 TGGTCAAGAA
8851427 AT AT 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 AT AT A
8851456 GATTGTCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8857990 original size:54 final size:54
Alignment explanation
Indices: 8857908--8858120 Score: 354
Period size: 54 Copynumber: 3.9 Consensus size: 54
8857898 TCATCGTGTG
*
8857908 CATCTCACCCAGCTCATGTGCATCCCACCACATTGTGCACATAGCCGGACATCC
1 CATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATCC
* * * *
8857962 CATCTCACCCATCTCATGTGCATCCCACCACATCATGCACATAGCTGGACTTCC
1 CATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATCC
*
8858016 CATCTCACCCAACTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATCC
1 CATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATCC
* *
8858070 CATCTCACCTAGCTCATGTACATCCCACCACATCGTGCACATAGCCGGACA
1 CATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACA
8858121 GTATCACCAT
Statistics
Matches: 147, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 147 1.00
ACGTcount: A:0.25, C:0.41, G:0.13, T:0.21
Consensus pattern (54 bp):
CATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATCC
Found at i:8868405 original size:39 final size:40
Alignment explanation
Indices: 8868324--8868417 Score: 127
Period size: 39 Copynumber: 2.4 Consensus size: 40
8868314 TGATAAAGCA
* *
8868324 TTCTCGCTGCAGCGAGATTCAAGCGGCCAAAACAAAAAGT
1 TTCTCGCTGCAGCGAAATTCAAGCCGCCAAAACAAAAAGT
* *
8868364 TTCTTGCTGCAGCGAAATTCAAGCCG-CAAAACAGAAAGT
1 TTCTCGCTGCAGCGAAATTCAAGCCGCCAAAACAAAAAGT
* *
8868403 TTCTCTCAGCAGCGA
1 TTCTCGCTGCAGCGA
8868418 GTTGCAGGTA
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 24 0.51
40 23 0.49
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.20
Consensus pattern (40 bp):
TTCTCGCTGCAGCGAAATTCAAGCCGCCAAAACAAAAAGT
Found at i:8869948 original size:18 final size:20
Alignment explanation
Indices: 8869922--8869967 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
8869912 TTGGAAATCA
*
8869922 TCATTATTTTTA-TTT-TTT
1 TCATCATTTTTACTTTATTT
8869940 TCATCA-TTTTACCTTTATTT
1 TCATCATTTTTA-CTTTATTT
8869960 TCATCATT
1 TCATCATT
8869968 CATCTATGCC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 5 0.22
18 5 0.22
19 3 0.13
20 9 0.39
21 1 0.04
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TCATCATTTTTACTTTATTT
Found at i:8874014 original size:45 final size:47
Alignment explanation
Indices: 8873945--8874063 Score: 134
Period size: 45 Copynumber: 2.6 Consensus size: 47
8873935 TTAAAGCTTG
* * *
8873945 AAGAGTTCCACAAATCCAAGAAGGAAAATCTAAAGATCAAAACCTC-
1 AAGAGTTACACATATCCAAGAAGGAAAATCTAAAGACCAAAACCTCT
* * * * *
8873991 AAGTGTT-CACATATCCAAAAAGGAAGATCTGAAGACCAAAGCCTCTT
1 AAGAGTTACACATATCCAAGAAGGAAAATCTAAAGACCAAAACCTC-T
*
8874038 TAGAGTTACACATATCCAAGAAGGAA
1 AAGAGTTACACATATCCAAGAAGGAA
8874064 CATATTATGT
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
45 32 0.53
46 6 0.10
47 5 0.08
48 17 0.28
ACGTcount: A:0.45, C:0.20, G:0.16, T:0.18
Consensus pattern (47 bp):
AAGAGTTACACATATCCAAGAAGGAAAATCTAAAGACCAAAACCTCT
Found at i:8877421 original size:40 final size:40
Alignment explanation
Indices: 8877368--8877466 Score: 137
Period size: 40 Copynumber: 2.5 Consensus size: 40
8877358 CAAGTCATAC
* *
8877368 TACTCATTCAAGATCAAG-CTGTAGACCTTTGAAGAAAGCA
1 TACTCATTCAAGATCAAGTC-GTAGACCTTTAAAGAAAACA
* *
8877408 TACTCATTTAAGATCAAGTCGTAGATCTTTAAAGAAAACA
1 TACTCATTCAAGATCAAGTCGTAGACCTTTAAAGAAAACA
*
8877448 TATTCATTCAAGATCAAGT
1 TACTCATTCAAGATCAAGT
8877467 TGCAAAACCC
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
40 51 0.98
41 1 0.02
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.29
Consensus pattern (40 bp):
TACTCATTCAAGATCAAGTCGTAGACCTTTAAAGAAAACA
Found at i:8877512 original size:32 final size:32
Alignment explanation
Indices: 8877473--8877566 Score: 107
Period size: 32 Copynumber: 2.9 Consensus size: 32
8877463 AAGTTGCAAA
* *
8877473 ACCCTTGAAACAAATTCAAGAGCCAGTTATAG
1 ACCCTTGAAACAAATTCAAGAGCAAGTCATAG
* * * * *
8877505 ACCCTTGAATCGAATTCAAAATCAAGTCGTAG
1 ACCCTTGAAACAAATTCAAGAGCAAGTCATAG
* *
8877537 ACCCTTGAAGCAAATTCAAGATCAAGTCAT
1 ACCCTTGAAACAAATTCAAGAGCAAGTCAT
8877567 TGTTGTTGAT
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.39, C:0.22, G:0.15, T:0.23
Consensus pattern (32 bp):
ACCCTTGAAACAAATTCAAGAGCAAGTCATAG
Found at i:8877742 original size:16 final size:17
Alignment explanation
Indices: 8877723--8877755 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
8877713 TTATAAACAA
8877723 TTAATT-AAAACTAAAT
1 TTAATTAAAAACTAAAT
8877739 TTAATTAGAAAACTAAA
1 TTAATTA-AAAACTAAA
8877756 CTAATTAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.33
Consensus pattern (17 bp):
TTAATTAAAAACTAAAT
Found at i:8877762 original size:17 final size:18
Alignment explanation
Indices: 8877729--8877762 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
8877719 ACAATTAATT
*
8877729 AAAACTAAATTTAATTAG
1 AAAACTAAATCTAATTAG
8877747 AAAACTAAA-CTAATTA
1 AAAACTAAATCTAATTA
8877763 ATGAAAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (18 bp):
AAAACTAAATCTAATTAG
Found at i:8881469 original size:42 final size:42
Alignment explanation
Indices: 8881412--8881545 Score: 214
Period size: 42 Copynumber: 3.2 Consensus size: 42
8881402 CGTGACAATA
8881412 ATGATGACCCAGCTATGTGCGTGTGGGAGTGCACATGAGCTG
1 ATGATGACCCAGCTATGTGCGTGTGGGAGTGCACATGAGCTG
* * *
8881454 ATGATGACCCAGCTATGTGCATATGGTAGTGCACATGAGCTG
1 ATGATGACCCAGCTATGTGCGTGTGGGAGTGCACATGAGCTG
* *
8881496 ATGATGACCCAGGTATGTGCGAGTAGGGAGTGCACATGAGCTG
1 ATGATGACCCAGCTATGTGCGTGT-GGGAGTGCACATGAGCTG
8881539 ATGATGA
1 ATGATGA
8881546 TGGGATGGTA
Statistics
Matches: 83, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
42 59 0.71
43 24 0.29
ACGTcount: A:0.25, C:0.17, G:0.34, T:0.24
Consensus pattern (42 bp):
ATGATGACCCAGCTATGTGCGTGTGGGAGTGCACATGAGCTG
Found at i:8882867 original size:43 final size:43
Alignment explanation
Indices: 8882794--8882876 Score: 114
Period size: 43 Copynumber: 1.9 Consensus size: 43
8882784 CGCACAAGGG
* *
8882794 AATATCATCATGTGCACTACTTGCACGCACATCTCAATATGGC
1 AATATCATCATGTGCACTACCTACACGCACATCTCAATATGGC
* *
8882837 AATATCATCATGTGCACT-CGCTACATGCACATTTCAATAT
1 AATATCATCATGTGCACTAC-CTACACGCACATCTCAATAT
8882877 CATCACAAGC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 1 0.03
43 34 0.97
ACGTcount: A:0.31, C:0.27, G:0.12, T:0.30
Consensus pattern (43 bp):
AATATCATCATGTGCACTACCTACACGCACATCTCAATATGGC
Found at i:8888535 original size:9 final size:9
Alignment explanation
Indices: 8888521--8888559 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
8888511 TTTCCCTTTG
8888521 TTTTCTTCC
1 TTTTCTTCC
8888530 TTTTCTTCC
1 TTTTCTTCC
* *
8888539 TTTCCTCTCT
1 TTTTCT-TCC
8888549 TTTTCTTCC
1 TTTTCTTCC
8888558 TT
1 TT
8888560 ATGGCCGGCC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
9 18 0.72
10 7 0.28
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (9 bp):
TTTTCTTCC
Found at i:8888702 original size:21 final size:22
Alignment explanation
Indices: 8888662--8888702 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
8888652 CCATTAGTCC
*
8888662 GTTTTTAAAATTTCATCCATTT
1 GTTTTCAAAATTTCATCCATTT
*
8888684 GTTTTCAAATTTTCA-CCAT
1 GTTTTCAAAATTTCATCCAT
8888703 ACACTTGTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.27, C:0.17, G:0.05, T:0.51
Consensus pattern (22 bp):
GTTTTCAAAATTTCATCCATTT
Found at i:8895796 original size:22 final size:21
Alignment explanation
Indices: 8895771--8895815 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
8895761 AATTCACCAC
8895771 ATTGATGCTAAATCACTATA-TA
1 ATTGAT-CTAAATC-CTATACTA
*
8895793 ATTGATTTAAATCCTATACTA
1 ATTGATCTAAATCCTATACTA
8895814 AT
1 AT
8895816 GCATGGTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 5 0.24
21 10 0.48
22 6 0.29
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (21 bp):
ATTGATCTAAATCCTATACTA
Found at i:8904933 original size:42 final size:42
Alignment explanation
Indices: 8904870--8905028 Score: 223
Period size: 42 Copynumber: 3.8 Consensus size: 42
8904860 GTGATAATTA
*
8904870 TGACCCAGCCATGTGCCGTGTAGGAGTGCACATGAGCTGTGC
1 TGACCCAGCCATGTGCAGTGTAGGAGTGCACATGAGCTGTGC
* *
8904912 TGACCTAGCTATGTGCAGTGTAGGAGTGCACATGAGCTGTGC
1 TGACCCAGCCATGTGCAGTGTAGGAGTGCACATGAGCTGTGC
* *
8904954 TGACCCAGCCATGTGCAATGTAGGAGTGCACATGAGCTATGC
1 TGACCCAGCCATGTGCAGTGTAGGAGTGCACATGAGCTGTGC
* *
8904996 TGACCC-GACTATGTGCGGTGT-GGTAGTGCACAT
1 TGACCCAG-CCATGTGCAGTGTAGG-AGTGCACAT
8905029 AAGTTGAGAC
Statistics
Matches: 105, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
41 3 0.03
42 102 0.97
ACGTcount: A:0.21, C:0.23, G:0.32, T:0.24
Consensus pattern (42 bp):
TGACCCAGCCATGTGCAGTGTAGGAGTGCACATGAGCTGTGC
Found at i:8910835 original size:43 final size:43
Alignment explanation
Indices: 8910765--8910922 Score: 142
Period size: 43 Copynumber: 3.7 Consensus size: 43
8910755 GTAATTATGT
* * * *
8910765 TGACACGGATATGTGCGACTAAGGAGTGCACATAAGCTGAG-GA
1 TGAC-CGGTTATGTGCGAGTAGGGAGTGCACATAAGCCGAGTGA
*
8910808 TGACTCGGTTATGTGCGAGTAGGGAGTGCACATAA-CCCAGTGA
1 TGAC-CGGTTATGTGCGAGTAGGGAGTGCACATAAGCCGAGTGA
* * * * *
8910851 TGAGCCGATTATGTGCTAGTAGGAAGTGCACAAAACCCG-GTGA
1 TGA-CCGGTTATGTGCGAGTAGGGAGTGCACATAAGCCGAGTGA
* **
8910894 TGACCCAGCCATGTGCGAGTAGGGAGTGC
1 TGA-CCGGTTATGTGCGAGTAGGGAGTGC
8910923 GCATGAGCTG
Statistics
Matches: 94, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
42 3 0.03
43 88 0.94
44 3 0.03
ACGTcount: A:0.28, C:0.19, G:0.33, T:0.20
Consensus pattern (43 bp):
TGACCGGTTATGTGCGAGTAGGGAGTGCACATAAGCCGAGTGA
Found at i:8910950 original size:20 final size:19
Alignment explanation
Indices: 8910925--8910987 Score: 81
Period size: 20 Copynumber: 3.2 Consensus size: 19
8910915 GGGAGTGCGC
8910925 ATGAGCTGGTGCTGATGATG
1 ATGAGCTGGTG-TGATGATG
8910945 ATGAGCTGGTGATGATGATG
1 ATGAGCTGGTG-TGATGATG
* * *
8910965 ATGGGTTGGTGAGATGATG
1 ATGAGCTGGTGTGATGATG
8910984 ATGA
1 ATGA
8910988 TGGGTATATA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
19 10 0.26
20 28 0.74
ACGTcount: A:0.24, C:0.05, G:0.41, T:0.30
Consensus pattern (19 bp):
ATGAGCTGGTGTGATGATG
Found at i:8911007 original size:2 final size:2
Alignment explanation
Indices: 8910992--8911032 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
8910982 TGATGATGGG
* *
8910992 TA TA TA TG TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
8911033 GTAAATGTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:8920197 original size:15 final size:15
Alignment explanation
Indices: 8920177--8920206 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
8920167 CCACTACCTT
*
8920177 GATTTTTCAATCAAA
1 GATTTTTCAAACAAA
8920192 GATTTTTCAAACAAA
1 GATTTTTCAAACAAA
8920207 TCCATTATGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (15 bp):
GATTTTTCAAACAAA
Found at i:8926633 original size:42 final size:41
Alignment explanation
Indices: 8926544--8926661 Score: 139
Period size: 42 Copynumber: 2.8 Consensus size: 41
8926534 ATTGACCCAA
* *
8926544 CTATGTGCCAGTAGGAGTGTGCATAAGCCAATGCTGACTCGG
1 CTATGTG-CAGTAGGAGTGCGCATAAGCCGATGCTGACTCGG
* * *
8926586 TTATGTGCGAGTGGGAGTGCGCATAAGTCGATGCTGAC-CTGG
1 CTATGTGC-AGTAGGAGTGCGCATAAGCCGATGCTGACTC-GG
*
8926628 CTATGTGTCAGTAAGAGTGCGCATAAGCCGATGC
1 CTATGTG-CAGTAGGAGTGCGCATAAGCCGATGC
8926662 ATATGAGCTG
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
41 2 0.03
42 61 0.95
43 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.25
Consensus pattern (41 bp):
CTATGTGCAGTAGGAGTGCGCATAAGCCGATGCTGACTCGG
Found at i:8926707 original size:2 final size:2
Alignment explanation
Indices: 8926702--8926735 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
8926692 ATGACGATTG
*
8926702 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8926736 GGTATATGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:8931335 original size:21 final size:20
Alignment explanation
Indices: 8931310--8931348 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
8931300 CGGCCACAAG
8931310 GAGAGAACAAGAAAGAAAATA
1 GAGAGAA-AAGAAAGAAAATA
* *
8931331 GAGAGGAAAGGAAGAAAA
1 GAGAGAAAAGAAAGAAAA
8931349 GAGAAAAACC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.64, C:0.03, G:0.31, T:0.03
Consensus pattern (20 bp):
GAGAGAAAAGAAAGAAAATA
Found at i:8940014 original size:2 final size:2
Alignment explanation
Indices: 8940007--8940088 Score: 132
Period size: 2 Copynumber: 42.0 Consensus size: 2
8939997 NNNNNNNNNN
8940007 TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA T- 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
* *
8940047 TA TA TA TA TA TG TA TA TA TA TA TA TA TA TG 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
8940089 ACATCCCTAA
Statistics
Matches: 74, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
1 2 0.03
2 72 0.97
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:8942011 original size:21 final size:20
Alignment explanation
Indices: 8941980--8942031 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 20
8941970 AACCAAGCTT
8941980 TTTCTTCCTTTCTCTCTTTCTC
1 TTTC-TCCTTTCTCTCTTTC-C
*
8942002 TTTCTCCTTTCTTTCTTTCC
1 TTTCTCCTTTCTCTCTTTCC
8942022 TTTCTCCTTT
1 TTTCTCCTTT
8942032 TTTCCAACTG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 11 0.38
21 14 0.48
22 4 0.14
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTCTCCTTTCTCTCTTTCC
Found at i:8942149 original size:19 final size:20
Alignment explanation
Indices: 8942125--8942165 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
8942115 TGGCAAGGTC
8942125 AAATGGC-ATGGGAGCATGG
1 AAATGGCTATGGGAGCATGG
* *
8942144 AAATGGCTTTGGGAGGATGG
1 AAATGGCTATGGGAGCATGG
8942164 AA
1 AA
8942166 GATGAGGAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.32, C:0.07, G:0.41, T:0.20
Consensus pattern (20 bp):
AAATGGCTATGGGAGCATGG
Found at i:8945275 original size:20 final size:21
Alignment explanation
Indices: 8945250--8945289 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
8945240 TCCTAGCAAG
8945250 AATGTATCGATACAT-TTGCT
1 AATGTATCGATACATCTTGCT
*
8945270 AATGTATTGATACATCTTGC
1 AATGTATCGATACATCTTGC
8945290 CCAAATTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (21 bp):
AATGTATCGATACATCTTGCT
Found at i:8949036 original size:42 final size:42
Alignment explanation
Indices: 8948963--8949081 Score: 127
Period size: 42 Copynumber: 2.8 Consensus size: 42
8948953 TGTTGATGTG
*
8948963 GACCCGGCTATGTGCGAGTAGGAGTGTACATAAG-TCGTTGCT
1 GACCCGGCTATGTACGAGTAGGAGTGTACATAAGCT-GTTGCT
*
8949005 GACCCGGCTATGTACGA-TTGAGAGT-TCACATAAGCTGTTGCT
1 GACCCGGCTATGTACGAGTAG-GAGTGT-ACATAAGCTGTTGCT
* * * **
8949047 GACCTGGCTATGTGCGAGTGGGAGTGCGCATAAGC
1 GACCCGGCTATGTACGAGTAGGAGTGTACATAAGC
8949082 CATTGCATAT
Statistics
Matches: 65, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
41 3 0.05
42 59 0.91
43 3 0.05
ACGTcount: A:0.22, C:0.20, G:0.33, T:0.25
Consensus pattern (42 bp):
GACCCGGCTATGTACGAGTAGGAGTGTACATAAGCTGTTGCT
Found at i:8956748 original size:2 final size:2
Alignment explanation
Indices: 8956741--8956780 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
8956731 ATGATGATTG
* * *
8956741 AT AT AT AT AT AT AT AT AT AT AT GT AT TT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8956781 GGTATATGGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8962105 original size:2 final size:2
Alignment explanation
Indices: 8962092--8962127 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
8962082 TCTAATCATG
* *
8962092 TA TA TA TG TA TA TA TA TA TA TA TA TA TA TC TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8962128 AATTTCATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8966308 original size:14 final size:15
Alignment explanation
Indices: 8966289--8966325 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
8966279 AATAATTTAC
8966289 TTTATTTTT-TTCTT
1 TTTATTTTTATTCTT
*
8966303 TTTATTTTTATTTTT
1 TTTATTTTTATTCTT
8966318 TTTATTTT
1 TTTATTTT
8966326 ATTATATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.11, C:0.03, G:0.00, T:0.86
Consensus pattern (15 bp):
TTTATTTTTATTCTT
Found at i:8966314 original size:20 final size:20
Alignment explanation
Indices: 8966289--8966328 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
8966279 AATAATTTAC
8966289 TTTATTTTTTTCT-TTTTATT
1 TTTATTTTTTT-TATTTTATT
8966309 TTTATTTTTTTTATTTTATT
1 TTTATTTTTTTTATTTTATT
8966329 ATATATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (20 bp):
TTTATTTTTTTTATTTTATT
Found at i:8966326 original size:14 final size:15
Alignment explanation
Indices: 8966289--8966328 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
8966279 AATAATTTAC
8966289 TTTATTTT-TTTCTT
1 TTTATTTTATTTCTT
8966303 TTTATTTTTATTT-TT
1 TTTA-TTTTATTTCTT
8966318 TTTATTTTATT
1 TTTATTTTATT
8966329 ATATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 11 0.46
15 10 0.42
16 3 0.12
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTATTTTATTTCTT
Found at i:8969309 original size:39 final size:38
Alignment explanation
Indices: 8969210--8969311 Score: 123
Period size: 38 Copynumber: 2.7 Consensus size: 38
8969200 AAAGTGCCCG
* *
8969210 TGTGCATGATGTGGGGGGATGCACACGATGGCACTAAT
1 TGTGCATGATGTGGGGGGATGCACACGATGCCACGAAT
* * * **
8969248 TCTGCATGATGTGGTGGGATGCACACGATGCCCCGGCT
1 TGTGCATGATGTGGGGGGATGCACACGATGCCACGAAT
*
8969286 ATGTGCACGATGTGGGGGGATGCACA
1 -TGTGCATGATGTGGGGGGATGCACA
8969312 TTAGCTGGGT
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
38 31 0.58
39 22 0.42
ACGTcount: A:0.21, C:0.20, G:0.37, T:0.23
Consensus pattern (38 bp):
TGTGCATGATGTGGGGGGATGCACACGATGCCACGAAT
Found at i:8969371 original size:32 final size:31
Alignment explanation
Indices: 8969330--8969392 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 31
8969320 GTGAGACGAT
8969330 GGTGATATTGG-TGTTTTTCTATGTATATATG
1 GGTGATATTGGTTGTTTTT-TATGTATATATG
8969361 NGGTGATATTGGTTGTTTTTTATGTATATATG
1 -GGTGATATTGGTTGTTTTTTATGTATATATG
8969393 TATATATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 23 0.77
33 7 0.23
ACGTcount: A:0.19, C:0.02, G:0.25, T:0.52
Consensus pattern (31 bp):
GGTGATATTGGTTGTTTTTTATGTATATATG
Found at i:8969390 original size:2 final size:2
Alignment explanation
Indices: 8969385--8969419 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
8969375 GTTTTTTATG
*
8969385 TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
8969420 CTTTATGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:8979800 original size:2 final size:2
Alignment explanation
Indices: 8979793--8979823 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
8979783 ATTGTGTTGG
8979793 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 T
8979824 GTTGTGCATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8991191 original size:49 final size:49
Alignment explanation
Indices: 8991126--8991219 Score: 161
Period size: 49 Copynumber: 1.9 Consensus size: 49
8991116 GCTACATGAG
*
8991126 AGTAGGGAGTGCGCATAAGCCGATGATGATGATGACCCGGCTATGTGCA
1 AGTACGGAGTGCGCATAAGCCGATGATGATGATGACCCGGCTATGTGCA
* *
8991175 AGTACGGAGTGTGCATAAGTCGATGATGATGATGACCCGGCTATG
1 AGTACGGAGTGCGCATAAGCCGATGATGATGATGACCCGGCTATG
8991220 ATGATGAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.27, C:0.17, G:0.34, T:0.22
Consensus pattern (49 bp):
AGTACGGAGTGCGCATAAGCCGATGATGATGATGACCCGGCTATGTGCA
Found at i:8991513 original size:21 final size:21
Alignment explanation
Indices: 8991472--8991528 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
8991462 GCCTTGTTTT
* * *
8991472 TCGCTGCAGGGAGAATGAATC
1 TCGCTGCAGCGAAAATAAATC
*
8991493 TCGTTGCAGCGAAAATAAATC
1 TCGCTGCAGCGAAAATAAATC
*
8991514 TCGCTGCAGCTAAAA
1 TCGCTGCAGCGAAAA
8991529 ACTCTCGGGC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (21 bp):
TCGCTGCAGCGAAAATAAATC
Found at i:9001638 original size:60 final size:60
Alignment explanation
Indices: 9001556--9001703 Score: 165
Period size: 60 Copynumber: 2.5 Consensus size: 60
9001546 TAGGAGACAA
* * * * * * *
9001556 AAACAGAAGGTTTTTCACTGCAGTGAGATTGAATCTCA-CTGCAGCGAAATTGTGATCC-AG
1 AAACAGAAAGTTTCTCACTGCAGTGAGATTCAATC-AAGCTACAGCAAAATTGT-AACCTAG
* *
9001616 AAACATAATGTTTCTCACTGCAGTGAGATTCAATCAAGCTACAGCAAAATTGTAACCTAG
1 AAACAGAAAGTTTCTCACTGCAGTGAGATTCAATCAAGCTACAGCAAAATTGTAACCTAG
* *
9001676 AAACAGAAAGTTTCTCGCTGCAGCGAGA
1 AAACAGAAAGTTTCTCACTGCAGTGAGA
9001704 AGCTACTATG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
59 4 0.05
60 70 0.95
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (60 bp):
AAACAGAAAGTTTCTCACTGCAGTGAGATTCAATCAAGCTACAGCAAAATTGTAACCTAG
Found at i:9002124 original size:43 final size:43
Alignment explanation
Indices: 9002065--9002180 Score: 155
Period size: 43 Copynumber: 2.7 Consensus size: 43
9002055 TCATCACCAC
* * **
9002065 CAGCTCATGTGCACTCCCTACTCGCACAT-GGCTGGGTCATCACT
1 CAGCTTATGCGCACTCCCTACTCGCACATAATC-GGGTCATC-CT
*
9002109 -AGGTTATGCGCACTCCCTACTCGCACATAATCGGGTCATCCT
1 CAGCTTATGCGCACTCCCTACTCGCACATAATCGGGTCATCCT
9002151 CAGCTTATGCGCACTCCCTACTCGCACATA
1 CAGCTTATGCGCACTCCCTACTCGCACATA
9002181 GCCGAGTCAA
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
42 2 0.03
43 61 0.95
44 1 0.02
ACGTcount: A:0.21, C:0.36, G:0.18, T:0.25
Consensus pattern (43 bp):
CAGCTTATGCGCACTCCCTACTCGCACATAATCGGGTCATCCT
Found at i:9010114 original size:20 final size:20
Alignment explanation
Indices: 9010089--9010134 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
9010079 TTTTGGCCCC
9010089 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
9010109 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
9010129 ATTTGA
1 ATTTGA
9010135 GGTTTAGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.30, C:0.04, G:0.20, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:9013677 original size:46 final size:44
Alignment explanation
Indices: 9013624--9013746 Score: 137
Period size: 43 Copynumber: 2.8 Consensus size: 44
9013614 CTTGCCACAC
*
9013624 TCAGCTCATGTGCACGCCCTACACGCACA-AT-GCAATATCATCATCA
1 TCAGCTCATGTGCACTCCC-ACACGCACACATAGC--TA-CATCATCA
* **
9013670 TCAGCTCATGTGCACTCCCACAC-CATACATAGCTAGGTCATCA
1 TCAGCTCATGTGCACTCCCACACGCACACATAGCTACATCATCA
*
9013713 TCAGCTCATGTGCACTCCCACAC-CGCACATAGCT
1 TCAGCTCATGTGCACTCCCACACGCACACATAGCT
9013747 GGGTCCACAT
Statistics
Matches: 69, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
43 38 0.55
44 5 0.07
45 6 0.09
46 20 0.29
ACGTcount: A:0.28, C:0.37, G:0.14, T:0.22
Consensus pattern (44 bp):
TCAGCTCATGTGCACTCCCACACGCACACATAGCTACATCATCA
Found at i:9013725 original size:43 final size:43
Alignment explanation
Indices: 9013664--9013751 Score: 149
Period size: 43 Copynumber: 2.0 Consensus size: 43
9013654 TGCAATATCA
*
9013664 TCATCATCAGCTCATGTGCACTCCCACACCATACATAGCTAGG
1 TCATCATCAGCTCATGTGCACTCCCACACCACACATAGCTAGG
* *
9013707 TCATCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGG
1 TCATCATCAGCTCATGTGCACTCCCACACCACACATAGCTAGG
9013750 TC
1 TC
9013752 CACATTATCA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.25, C:0.36, G:0.16, T:0.23
Consensus pattern (43 bp):
TCATCATCAGCTCATGTGCACTCCCACACCACACATAGCTAGG
Found at i:9015877 original size:36 final size:36
Alignment explanation
Indices: 9015813--9015911 Score: 144
Period size: 36 Copynumber: 2.8 Consensus size: 36
9015803 AACCGTGCAC
** *
9015813 GTGCGGTGTTAGAGTACACATGACGGTGTCGGTGGT
1 GTGCGGTGTGGGAGTGCACATGACGGTGTCGGTGGT
* *
9015849 GTGCGGTGTGGGAGTGCACGTGATGGTGTCGGTGGT
1 GTGCGGTGTGGGAGTGCACATGACGGTGTCGGTGGT
*
9015885 GTGCGGTGTGGGAGTGCACATGCCGGT
1 GTGCGGTGTGGGAGTGCACATGACGGT
9015912 AATGAAGTGG
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 55 1.00
ACGTcount: A:0.12, C:0.14, G:0.47, T:0.26
Consensus pattern (36 bp):
GTGCGGTGTGGGAGTGCACATGACGGTGTCGGTGGT
Found at i:9017409 original size:19 final size:20
Alignment explanation
Indices: 9017374--9017411 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
9017364 CTATAAATAT
*
9017374 CTCATTTCTCTAGCAGCTTC
1 CTCATTTCTCCAGCAGCTTC
9017394 CTCATTT-TCCAGCAGCTT
1 CTCATTTCTCCAGCAGCTT
9017412 TTTATTCTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.16, C:0.34, G:0.11, T:0.39
Consensus pattern (20 bp):
CTCATTTCTCCAGCAGCTTC
Found at i:9018291 original size:37 final size:37
Alignment explanation
Indices: 9018244--9018369 Score: 182
Period size: 37 Copynumber: 3.4 Consensus size: 37
9018234 ATGTTGTGTA
* *
9018244 ATGATGTTGAAGTGCGCGAGTAGGGAGTGCAGACATG
1 ATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACATG
*
9018281 ATGATGTTGAAGTGTGCGAGTAGGAAGTGCACACATG
1 ATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACATG
9018318 ATGATGTT-AGAGTGTGCGAGTAGGGAGTGCACACATG
1 ATGATGTTGA-AGTGTGCGAGTAGGGAGTGCACACATG
* *
9018355 ACGATGAATGAAGTG
1 ATGATG-TTGAAGTG
9018370 GGGTGGTGCA
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
36 1 0.01
37 73 0.91
38 5 0.06
39 1 0.01
ACGTcount: A:0.29, C:0.10, G:0.37, T:0.23
Consensus pattern (37 bp):
ATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACATG
Found at i:9023922 original size:23 final size:20
Alignment explanation
Indices: 9023873--9023922 Score: 50
Period size: 23 Copynumber: 2.4 Consensus size: 20
9023863 GGCCTAAGAC
9023873 ATAAAT-AAATGATGAAAAT
1 ATAAATAAAATGATGAAAAT
9023892 A-AAGATAAAATGATGAAGGAAAT
1 ATAA-ATAAAATGATG-A--AAAT
9023915 ATAAATAA
1 ATAAATAA
9023923 TGATGATTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
18 2 0.08
19 3 0.12
20 8 0.32
21 1 0.04
23 9 0.36
24 2 0.08
ACGTcount: A:0.64, C:0.00, G:0.14, T:0.22
Consensus pattern (20 bp):
ATAAATAAAATGATGAAAAT
Found at i:9025049 original size:37 final size:35
Alignment explanation
Indices: 9025006--9025117 Score: 170
Period size: 37 Copynumber: 3.0 Consensus size: 35
9024996 ATGTTGTGTA
9025006 ATGATGTTGAAGTGTGCATGTAGGGAGTGCACACATG
1 ATGATGTT-AAGTGTGCA-GTAGGGAGTGCACACATG
9025043 ATGATGTTAAAGTGTGCAAGTAGGGAGTGCACACATG
1 ATGATGTT-AAGTGTGC-AGTAGGGAGTGCACACATG
9025080 ATGATGTTAGAGTGTGCGAGTAGGGAGTGCACACATG
1 ATGATGTTA-AGTGTGC-AGTAGGGAGTGCACACATG
9025117 A
1 A
9025118 CAATGAATGA
Statistics
Matches: 71, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
36 1 0.01
37 69 0.97
38 1 0.01
ACGTcount: A:0.29, C:0.11, G:0.35, T:0.25
Consensus pattern (35 bp):
ATGATGTTAAGTGTGCAGTAGGGAGTGCACACATG
Found at i:9036970 original size:15 final size:15
Alignment explanation
Indices: 9036930--9036976 Score: 60
Period size: 14 Copynumber: 3.1 Consensus size: 15
9036920 ACTTCAAGAT
9036930 TTTCCATTTTCTTTTC
1 TTTCC-TTTTCTTTTC
* *
9036946 CTT-GTTTTCTTTTC
1 TTTCCTTTTCTTTTC
9036960 TTTCCTTTTCTTTTC
1 TTTCCTTTTCTTTTC
9036975 TT
1 TT
9036977 ACTCCTTCCT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 12 0.46
15 12 0.46
16 2 0.08
ACGTcount: A:0.02, C:0.23, G:0.02, T:0.72
Consensus pattern (15 bp):
TTTCCTTTTCTTTTC
Found at i:9037859 original size:52 final size:51
Alignment explanation
Indices: 9037779--9037889 Score: 150
Period size: 52 Copynumber: 2.1 Consensus size: 51
9037769 GTGGGAGTGC
* * *
9037779 CCATGATGTGTGATAGTGGTATGCTGTGTGAGTGCACACACTGATGATATATG
1 CCATG-TGCGTGATAGTGGTATGCTGTGTGAGTGCACACACT-AAGATATACG
* * *
9037832 CCATGTGCGTGATAGTGGTGTGTTGTGTGAGTGCACACACTAAGATGTACG
1 CCATGTGCGTGATAGTGGTATGCTGTGTGAGTGCACACACTAAGATATACG
9037883 CCATGTG
1 CCATGTG
9037890 GGATGTGGGA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
51 14 0.27
52 33 0.63
53 5 0.10
ACGTcount: A:0.23, C:0.15, G:0.32, T:0.31
Consensus pattern (51 bp):
CCATGTGCGTGATAGTGGTATGCTGTGTGAGTGCACACACTAAGATATACG
Found at i:9040220 original size:26 final size:31
Alignment explanation
Indices: 9040191--9040249 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 31
9040181 ATTTTCTAGT
*
9040191 TTTCCT-T-TATTTT-TCT-TTTTTC-TTCC
1 TTTCCTCTCTATTTTCTCTCTTGTTCTTTCC
9040217 TTTCCTCTCTATTTTCTCTCTTGTTCTTTCC
1 TTTCCTCTCTATTTTCTCTCTTGTTCTTTCC
9040248 TT
1 TT
9040250 ATGGCAAGCC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 6 0.22
27 1 0.04
28 6 0.22
29 3 0.11
30 5 0.19
31 6 0.22
ACGTcount: A:0.03, C:0.27, G:0.02, T:0.68
Consensus pattern (31 bp):
TTTCCTCTCTATTTTCTCTCTTGTTCTTTCC
Found at i:9056930 original size:42 final size:42
Alignment explanation
Indices: 9056872--9057004 Score: 221
Period size: 42 Copynumber: 3.1 Consensus size: 42
9056862 TTATGTGATA
*
9056872 ATGATGACCCAGCTATGTGCGTGTGGGAGTGCACATGAGCTG
1 ATGATGACCCAACTATGTGCGTGTGGGAGTGCACATGAGCTG
**
9056914 ATGATGACCCAACTATGTGCGTGTAAGAGTGCACATGAGCTG
1 ATGATGACCCAACTATGTGCGTGTGGGAGTGCACATGAGCTG
*
9056956 ATGATGACCCAACTATGTGCGAGTGGGGAGTGCACATGAGCTG
1 ATGATGACCCAACTATGTGCGTGT-GGGAGTGCACATGAGCTG
9056999 ATGATG
1 ATGATG
9057005 GTGGGATGGT
Statistics
Matches: 84, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
42 62 0.74
43 22 0.26
ACGTcount: A:0.26, C:0.18, G:0.33, T:0.23
Consensus pattern (42 bp):
ATGATGACCCAACTATGTGCGTGTGGGAGTGCACATGAGCTG
Found at i:9061126 original size:42 final size:42
Alignment explanation
Indices: 9061056--9061186 Score: 174
Period size: 42 Copynumber: 3.1 Consensus size: 42
9061046 TGTTGATATG
* *
9061056 GACCCGACTATGTGCGAGTAGGAATGCGCATACA-CCGATGAT
1 GACCCGGCTATGTGCGAGTAGGAGTGCGCATA-AGCCGATGAT
* *
9061098 GACCCGGCTATGTGCAAGTAAGAGTGCGCATAAGCCGATGAT
1 GACCCGGCTATGTGCGAGTAGGAGTGCGCATAAGCCGATGAT
* * * *
9061140 GACACGGCTATGTGTGAGTAGGAGTGCGCATAAGCCAATGCT
1 GACCCGGCTATGTGCGAGTAGGAGTGCGCATAAGCCGATGAT
9061182 GACCC
1 GACCC
9061187 AACCATATGC
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
41 1 0.01
42 76 0.99
ACGTcount: A:0.27, C:0.23, G:0.31, T:0.19
Consensus pattern (42 bp):
GACCCGGCTATGTGCGAGTAGGAGTGCGCATAAGCCGATGAT
Found at i:9061257 original size:2 final size:2
Alignment explanation
Indices: 9061250--9061293 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
9061240 ATGATGATGG
* * *
9061250 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AC AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9061292 AT
1 AT
9061294 GTGTCATGGA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:9068032 original size:2 final size:2
Alignment explanation
Indices: 9068027--9068055 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9068017 TATATATATA
9068027 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
9068056 ATGCAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:9070937 original size:61 final size:61
Alignment explanation
Indices: 9070839--9071124 Score: 335
Period size: 61 Copynumber: 4.7 Consensus size: 61
9070829 AGCTCATGTA
* * *
9070839 CATCATCACCGGCATGTGCACTGCCCACT-CTACACATGCACGACTGTAATTATCACGACAG
1 CATCATTACCGGCATGTGCACTGCCCACTCCGA-ACATGCACGATTGTAATTATCACGACAG
* * * * *
9070900 CATCATTACCAGCATGTGCACTTCCCACTCCGAACATGCACGGTTGTAATTATCATGACAT
1 CATCATTACCGGCATGTGCACTGCCCACTCCGAACATGCACGATTGTAATTATCACGACAG
* * * *
9070961 CATCATAACCGGCATGTGCACTGCCCACTCCGCACATGTACGGTTGTAATTATCACGACAG
1 CATCATTACCGGCATGTGCACTGCCCACTCCGAACATGCACGATTGTAATTATCACGACAG
** * * * **
9071022 CATCATTATTGGCATGTGCACTACCCATTTC-ACACATGCAC-AGTTGTAATTATCTTGACAG
1 CATCATTACCGGCATGTGCACTGCCCACTCCGA-ACATGCACGA-TTGTAATTATCACGACAG
* *
9071083 CATCATTATCGGCATGTGCACTGCCCACTCCGCACATGCACG
1 CATCATTACCGGCATGTGCACTGCCCACTCCGAACATGCACG
9071125 GTTGCATTTG
Statistics
Matches: 189, Mismatches: 31, Indels: 9
0.83 0.14 0.04
Matches are distributed among these distances:
61 187 0.99
62 2 0.01
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.26
Consensus pattern (61 bp):
CATCATTACCGGCATGTGCACTGCCCACTCCGAACATGCACGATTGTAATTATCACGACAG
Found at i:9071059 original size:122 final size:122
Alignment explanation
Indices: 9070839--9071128 Score: 411
Period size: 122 Copynumber: 2.4 Consensus size: 122
9070829 AGCTCATGTA
* ** **
9070839 CATCATCACCGGCATGTGCACTGCCCACTCTACACATGCACGACTGTAATTATCACGACAGCATC
1 CATCATAACCGGCATGTGCACTGCCCACTCCGCACATGCACGGTTGTAATTATCACGACAGCATC
* * *
9070904 ATTACCAGCATGTGCACTTCCCACTCCGAACATGCACGGTTGTAATTATCATGACAT
66 ATTACCAGCATGTGCACTACCCACTCCGAACATGCACAGTTGTAATTATCATGACAG
*
9070961 CATCATAACCGGCATGTGCACTGCCCACTCCGCACATGTACGGTTGTAATTATCACGACAGCATC
1 CATCATAACCGGCATGTGCACTGCCCACTCCGCACATGCACGGTTGTAATTATCACGACAGCATC
*** * * *
9071026 ATTATTGGCATGTGCACTACCCATTTC-ACACATGCACAGTTGTAATTATCTTGACAG
66 ATTACCAGCATGTGCACTACCCACTCCGA-ACATGCACAGTTGTAATTATCATGACAG
* *
9071083 CATCATTATCGGCATGTGCACTGCCCACTCCGCACATGCACGGTTG
1 CATCATAACCGGCATGTGCACTGCCCACTCCGCACATGCACGGTTG
9071129 CATTTGTCAC
Statistics
Matches: 149, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
121 1 0.01
122 148 0.99
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (122 bp):
CATCATAACCGGCATGTGCACTGCCCACTCCGCACATGCACGGTTGTAATTATCACGACAGCATC
ATTACCAGCATGTGCACTACCCACTCCGAACATGCACAGTTGTAATTATCATGACAG
Found at i:9073902 original size:14 final size:15
Alignment explanation
Indices: 9073883--9073911 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
9073873 CCATAGATTA
9073883 CATTTCCTT-GATAT
1 CATTTCCTTGGATAT
9073897 CATTTCCTTGGATAT
1 CATTTCCTTGGATAT
9073912 TTCTCCAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.21, C:0.21, G:0.10, T:0.48
Consensus pattern (15 bp):
CATTTCCTTGGATAT
Found at i:9077566 original size:2 final size:2
Alignment explanation
Indices: 9077556--9077589 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
9077546 TATAGCACAC
* *
9077556 AT AT CT AT AT AT GT 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
9077590 CCATCACCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9077688 original size:42 final size:42
Alignment explanation
Indices: 9077630--9077776 Score: 188
Period size: 42 Copynumber: 3.5 Consensus size: 42
9077620 CAACTCATAT
* * *
9077630 GCACTCCCACTAGCACATGGCTGGGTCAGCATCGGCTTATGC
1 GCACTCCTACTCGCACATAGCTGGGTCAGCATCGGCTTATGC
* *
9077672 GCACTCTTACTCGCACATAGCTGGGTCAACATCGGCTTATGC
1 GCACTCCTACTCGCACATAGCTGGGTCAGCATCGGCTTATGC
** * *
9077714 GCACTCCCCCTCGCACATAG-TCAGGTCAGCATCTGCTTATGC
1 GCACTCCTACTCGCACATAGCT-GGGTCAGCATCGGCTTATGC
*
9077756 ACACTCCTACTCGCACATAGC
1 GCACTCCTACTCGCACATAGC
9077777 CGAGTCAATA
Statistics
Matches: 89, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
41 1 0.01
42 88 0.99
ACGTcount: A:0.21, C:0.35, G:0.20, T:0.23
Consensus pattern (42 bp):
GCACTCCTACTCGCACATAGCTGGGTCAGCATCGGCTTATGC
Found at i:9077827 original size:2 final size:2
Alignment explanation
Indices: 9077822--9077848 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9077812 ACACACACAC
9077822 AT 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 AT A
9077849 AACACAGTAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9086003 original size:15 final size:15
Alignment explanation
Indices: 9085983--9086015 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
9085973 GGACAAAGCA
9085983 CATTTTATTAGACAC
1 CATTTTATTAGACAC
*
9085998 CATTTTATTAGAGAC
1 CATTTTATTAGACAC
9086013 CAT
1 CAT
9086016 GGAGTGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.33, C:0.18, G:0.09, T:0.39
Consensus pattern (15 bp):
CATTTTATTAGACAC
Found at i:9087489 original size:28 final size:28
Alignment explanation
Indices: 9087457--9087512 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
9087447 TTTCGGATTA
9087457 TAGGGGCAAAATC-GT-AATTTTTTCGCCC
1 TAGGGG-AAAATCGGTAAATTTTTT-GCCC
*
9087485 TAGGGGTAAATCGGTAAATTTTTTGCCC
1 TAGGGGAAAATCGGTAAATTTTTTGCCC
9087513 CAGCACTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 5 0.20
28 12 0.48
29 8 0.32
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (28 bp):
TAGGGGAAAATCGGTAAATTTTTTGCCC
Found at i:9088724 original size:2 final size:2
Alignment explanation
Indices: 9088717--9088742 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9088707 TATTATGATG
9088717 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
9088743 GTGTGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9089347 original size:21 final size:22
Alignment explanation
Indices: 9089313--9089353 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
9089303 TCACTGTAGC
9089313 ATCTCACTGCAGCGA-AAACGA
1 ATCTCACTGCAGCGAGAAACGA
* *
9089334 ATCTCGCTGTAGCGAGAAAC
1 ATCTCACTGCAGCGAGAAAC
9089354 TCTCGGGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.34, C:0.27, G:0.22, T:0.17
Consensus pattern (22 bp):
ATCTCACTGCAGCGAGAAACGA
Found at i:9095668 original size:28 final size:30
Alignment explanation
Indices: 9095627--9095686 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 30
9095617 GTTTATGGGC
* *
9095627 AATTTTTAAGTTTT-TGGG-GCAAAAATGT
1 AATTTTTAACTTTTACGGGAGCAAAAATGT
* *
9095655 AATTTTTCACTTTTACGGGAGCAAAAGTGT
1 AATTTTTAACTTTTACGGGAGCAAAAATGT
9095685 AA
1 AA
9095687 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
29 3 0.12
30 11 0.42
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.38
Consensus pattern (30 bp):
AATTTTTAACTTTTACGGGAGCAAAAATGT
Found at i:9095934 original size:21 final size:20
Alignment explanation
Indices: 9095909--9095947 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
9095899 CGGCCATAAG
9095909 GAGAGAACAAGAAAGAAAATA
1 GAGAGAA-AAGAAAGAAAATA
* *
9095930 GAGAGGAAAGGAAGAAAA
1 GAGAGAAAAGAAAGAAAA
9095948 GAGAAAAATC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.64, C:0.03, G:0.31, T:0.03
Consensus pattern (20 bp):
GAGAGAAAAGAAAGAAAATA
Found at i:9095966 original size:20 final size:19
Alignment explanation
Indices: 9095943--9095986 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
9095933 AGGAAAGGAA
9095943 GAAAAGAGAAAAATCAAAGG
1 GAAAAGAGAAAAATCAAA-G
** *
9095963 GAAACTAGAAAATTCAAAG
1 GAAAAGAGAAAAATCAAAG
9095982 GAAAA
1 GAAAA
9095987 ATGGCATTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.64, C:0.07, G:0.20, T:0.09
Consensus pattern (19 bp):
GAAAAGAGAAAAATCAAAG
Found at i:9101211 original size:21 final size:22
Alignment explanation
Indices: 9101185--9101225 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
9101175 TCACTGTAGC
*
9101185 ATCTCGCTGTAGCGA-AAACGA
1 ATCTCGCTGCAGCGAGAAACGA
9101206 ATCTCGCTGCAGCGAGAAAC
1 ATCTCGCTGCAGCGAGAAAC
9101226 TTTCGAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.32, C:0.27, G:0.24, T:0.17
Consensus pattern (22 bp):
ATCTCGCTGCAGCGAGAAACGA
Found at i:9103707 original size:39 final size:39
Alignment explanation
Indices: 9103663--9103748 Score: 136
Period size: 39 Copynumber: 2.2 Consensus size: 39
9103653 ACCAAGAACC
9103663 TAGGAAAAGAAAGAAAGCAGAACCAGAGGAGCATGAAAT
1 TAGGAAAAGAAAGAAAGCAGAACCAGAGGAGCATGAAAT
* * *
9103702 TAGGAAAGGAAAGAAAGCAGAACTAGGGGAGCATGAAAT
1 TAGGAAAAGAAAGAAAGCAGAACCAGAGGAGCATGAAAT
9103741 TAGAGAAA
1 TAG-GAAA
9103749 TAAGAGATAG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
39 39 0.91
40 4 0.09
ACGTcount: A:0.52, C:0.08, G:0.30, T:0.09
Consensus pattern (39 bp):
TAGGAAAAGAAAGAAAGCAGAACCAGAGGAGCATGAAAT
Found at i:9106577 original size:61 final size:61
Alignment explanation
Indices: 9106493--9106709 Score: 319
Period size: 61 Copynumber: 3.6 Consensus size: 61
9106483 TCATCACTGA
* * *
9106493 CATGTGCACTGCCCATTCTGCACATGCACGGTTGTAATTATCACAACATCATCATTACCGG
1 CATGTGCACTGCCCACTCCGCACATGCACGGTTGTAATTATCACGACATCATCATTACCGG
* *
9106554 CATGTGCACTGCCCACTCCGCACATGCACGGTTGTAATTATCATGACATCATCATTACCGA
1 CATGTGCACTGCCCACTCCGCACATGCACGGTTGTAATTATCACGACATCATCATTACCGG
* * * * *
9106615 CATGTGCACTGCCCACTCCACACATGCACGGTAGTAATTATCAGGACAGCATCATTACCAG
1 CATGTGCACTGCCCACTCCGCACATGCACGGTTGTAATTATCACGACATCATCATTACCGG
*
9106676 CATGTGCACTAG-CCACTTCGCACATGCACGGTTG
1 CATGTGCACT-GCCCACTCCGCACATGCACGGTTG
9106710 CATTTGTCAC
Statistics
Matches: 141, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
61 140 0.99
62 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (61 bp):
CATGTGCACTGCCCACTCCGCACATGCACGGTTGTAATTATCACGACATCATCATTACCGG
Found at i:9106751 original size:2 final size:2
Alignment explanation
Indices: 9106744--9106776 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
9106734 TATGACATAG
9106744 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
9106777 CATTATACAT
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:9117323 original size:35 final size:35
Alignment explanation
Indices: 9117284--9117367 Score: 132
Period size: 35 Copynumber: 2.4 Consensus size: 35
9117274 TGATGTGGGC
**
9117284 GGGAGTGCATGTGATGATATTGAAATGTGCGAGTA
1 GGGAGTGCACATGATGATATTGAAATGTGCGAGTA
*
9117319 GGGAGTGCACATGATGATATTGAAATGTGCGTGTA
1 GGGAGTGCACATGATGATATTGAAATGTGCGAGTA
*
9117354 GGGAGCGCACATGA
1 GGGAGTGCACATGA
9117368 GCTGAGTGTG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.29, C:0.10, G:0.37, T:0.25
Consensus pattern (35 bp):
GGGAGTGCACATGATGATATTGAAATGTGCGAGTA
Found at i:9124256 original size:26 final size:30
Alignment explanation
Indices: 9124200--9124258 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 30
9124190 GGCTGGCCAT
*
9124200 AAGGAAAGAACAAGAGAGAAAATAAGGAGGA
1 AAGGAAAGAACAAGAGAGAAAACAA-GAGGA
9124231 AAGG-AAGAA-AAGAGA-AAAACAA-AGGA
1 AAGGAAAGAACAAGAGAGAAAACAAGAGGA
9124257 AA
1 AA
9124259 ACTAGAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 6 0.22
28 6 0.22
29 6 0.22
30 5 0.19
31 4 0.15
ACGTcount: A:0.66, C:0.03, G:0.29, T:0.02
Consensus pattern (30 bp):
AAGGAAAGAACAAGAGAGAAAACAAGAGGA
Found at i:9136523 original size:21 final size:22
Alignment explanation
Indices: 9136498--9136538 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
9136488 CCTAGGTGGA
*
9136498 AAAATTCAAGGGAA-AAGTGTG
1 AAAATTCAAGGAAACAAGTGTG
9136519 AAAATTCAAGGAAACAAGTG
1 AAAATTCAAGGAAACAAGTG
9136539 AAAAAAAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.17
Consensus pattern (22 bp):
AAAATTCAAGGAAACAAGTGTG
Found at i:9136539 original size:20 final size:21
Alignment explanation
Indices: 9136498--9136542 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
9136488 CCTAGGTGGA
*
9136498 AAAATTCAAGGGAAAAGTGTG
1 AAAATTCAAGGGAAAAGAGTG
9136519 AAAATTCAA-GGAAACA-AGTG
1 AAAATTCAAGGGAAA-AGAGTG
9136539 AAAA
1 AAAA
9136543 AAAGGTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.56, C:0.07, G:0.22, T:0.16
Consensus pattern (21 bp):
AAAATTCAAGGGAAAAGAGTG
Found at i:9136543 original size:21 final size:20
Alignment explanation
Indices: 9136496--9136543 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
9136486 ACCCTAGGTG
*
9136496 GAAAAATTCAAGGGAAAAGT
1 GAAAAATTCAAGGAAAAAGT
*
9136516 GTGAAAATTCAAGGAAACAAGT
1 G-AAAAATTCAAGGAAA-AAGT
9136538 GAAAAA
1 GAAAAA
9136544 AAGGTAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 17 0.74
22 5 0.22
ACGTcount: A:0.56, C:0.06, G:0.23, T:0.15
Consensus pattern (20 bp):
GAAAAATTCAAGGAAAAAGT
Found at i:9140315 original size:46 final size:46
Alignment explanation
Indices: 9140247--9140338 Score: 141
Period size: 46 Copynumber: 2.0 Consensus size: 46
9140237 TTTCAAAACA
9140247 ATAATTTATTTTGTGCTTTTATGTGTTAAATATCACCAAGGTGATC
1 ATAATTTATTTTGTGCTTTTATGTGTTAAATATCACCAAGGTGATC
* * *
9140293 NATAA-TTATTTTGTGTTTTTATGTGTTTAATATCACCGAGGTGATC
1 -ATAATTTATTTTGTGCTTTTATGTGTTAAATATCACCAAGGTGATC
9140339 TATGGGTGGA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
46 38 0.90
47 4 0.10
ACGTcount: A:0.26, C:0.10, G:0.16, T:0.47
Consensus pattern (46 bp):
ATAATTTATTTTGTGCTTTTATGTGTTAAATATCACCAAGGTGATC
Found at i:9143434 original size:21 final size:20
Alignment explanation
Indices: 9143400--9143438 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
9143390 ACATGTTGAG
9143400 TAGTTTAGTTTATGTTATTT
1 TAGTTTAGTTTATGTTATTT
*
9143420 TAGTTTAATTTTATGTTAT
1 TAGTTT-AGTTTATGTTAT
9143439 ATTGCTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.23, C:0.00, G:0.13, T:0.64
Consensus pattern (20 bp):
TAGTTTAGTTTATGTTATTT
Found at i:9146240 original size:43 final size:43
Alignment explanation
Indices: 9146150--9146248 Score: 112
Period size: 43 Copynumber: 2.3 Consensus size: 43
9146140 TGACTCGGCT
* * * **
9146150 ATGTGCGAGTAGGGAGTGCGCATAAGCCGATGATGACCCGATT
1 ATGTGCGAGTAGGGAGTACGCATAAGCCGATGAGGACCAGACC
*
9146193 ATGTGCGAGTAGGGAGTACGCATAA-CTCGGTGAGGACCTAG-CC
1 ATGTGCGAGTAGGGAGTACGCATAAGC-CGATGAGGACC-AGACC
9146236 ATGTGCGAGTAGG
1 ATGTGCGAGTAGG
9146249 AAGTGAACAT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
42 1 0.02
43 46 0.96
44 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.36, T:0.20
Consensus pattern (43 bp):
ATGTGCGAGTAGGGAGTACGCATAAGCCGATGAGGACCAGACC
Found at i:9162172 original size:41 final size:41
Alignment explanation
Indices: 9162127--9162204 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
9162117 GTAATGATAT
* **
9162127 TGACCTGGCTATGTGTGAGTAGGAGTGCGCATAAGCAATGC
1 TGACCCGGCTATGTGCAAGTAGGAGTGCGCATAAGCAATGC
9162168 TGACCCGGCTATGTGCAAGTAGGAGTGCGCATAAGCA
1 TGACCCGGCTATGTGCAAGTAGGAGTGCGCATAAGCA
9162205 GTTGCATATG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.26, C:0.19, G:0.33, T:0.22
Consensus pattern (41 bp):
TGACCCGGCTATGTGCAAGTAGGAGTGCGCATAAGCAATGC
Found at i:9162257 original size:2 final size:2
Alignment explanation
Indices: 9162250--9162276 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9162240 ATGATGATTG
9162250 AT 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 AT A
9162277 CACATATGGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9169310 original size:41 final size:41
Alignment explanation
Indices: 9169265--9169342 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
9169255 GTAATGATAT
* **
9169265 TGACCTGGCTATGTGTGAGTAGGAGTGCGCATAAGCAATGC
1 TGACCCGGCTATGTGCAAGTAGGAGTGCGCATAAGCAATGC
9169306 TGACCCGGCTATGTGCAAGTAGGAGTGCGCATAAGCA
1 TGACCCGGCTATGTGCAAGTAGGAGTGCGCATAAGCA
9169343 GTTGCATATG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.26, C:0.19, G:0.33, T:0.22
Consensus pattern (41 bp):
TGACCCGGCTATGTGCAAGTAGGAGTGCGCATAAGCAATGC
Found at i:9169395 original size:2 final size:2
Alignment explanation
Indices: 9169388--9169416 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9169378 ATGATGATTG
9169388 AT AT 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 AT AT A
9169417 CACATATGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9170490 original size:94 final size:93
Alignment explanation
Indices: 9170341--9170519 Score: 286
Period size: 94 Copynumber: 1.9 Consensus size: 93
9170331 GTAAAATATT
** *
9170341 AAGATACGTGTCTTAGATGAAATATGTATATTTTAACTGTTAATGCCACCATGAGTTGAAATGTT
1 AAGATACGTGTCTTAGACAAAATATGTATATTTTAACTGTTAATGCCACCATGAGTTAAAATGTT
9170406 AACATCATTTTGGGTTTATATTAATGAA
66 AACATCATTTTGGGTTTATATTAATGAA
* * * *
9170434 ANAGATACGTGTCTTATACAAAATTTGTATATTTTAATTGTTAATGCCACTATGAGTTAAAATGT
1 A-AGATACGTGTCTTAGACAAAATATGTATATTTTAACTGTTAATGCCACCATGAGTTAAAATGT
9170499 TAACATCATTTTGGGTTTATA
65 TAACATCATTTTGGGTTTATA
9170520 ATGAAATTCT
Statistics
Matches: 78, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
93 1 0.01
94 77 0.99
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.40
Consensus pattern (93 bp):
AAGATACGTGTCTTAGACAAAATATGTATATTTTAACTGTTAATGCCACCATGAGTTAAAATGTT
AACATCATTTTGGGTTTATATTAATGAA
Found at i:9178680 original size:50 final size:50
Alignment explanation
Indices: 9178605--9178716 Score: 188
Period size: 50 Copynumber: 2.2 Consensus size: 50
9178595 TAATGAACAT
* *
9178605 GTATCGATACATCTTCATAATGTATCAATACAATTTTTTCAGAATCAAAA
1 GTATCGATACATCTTCATAATGTATCAATACAATTTTTTCAAAACCAAAA
*
9178655 GTATCGATACATCTTCATAATGTATCGATACAATTTTTTCAAAACCAAAA
1 GTATCGATACATCTTCATAATGTATCAATACAATTTTTTCAAAACCAAAA
*
9178705 GTATCTATACAT
1 GTATCGATACAT
9178717 TACCAAATGT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 58 1.00
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (50 bp):
GTATCGATACATCTTCATAATGTATCAATACAATTTTTTCAAAACCAAAA
Found at i:9178737 original size:20 final size:20
Alignment explanation
Indices: 9178698--9178757 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
9178688 TTTTTTCAAA
*
9178698 ACCAAAAGTATCT-ATACATT
1 ACCAAATGTAT-TGATACATT
*
9178718 ACCAAATGTATTGATTCATT
1 ACCAAATGTATTGATACATT
*
9178738 TCCAAATGTATTGATACATT
1 ACCAAATGTATTGATACATT
9178758 TCATCGTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 1 0.03
20 34 0.97
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (20 bp):
ACCAAATGTATTGATACATT
Found at i:9178758 original size:20 final size:20
Alignment explanation
Indices: 9178711--9178759 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
9178701 AAAAGTATCT
*
9178711 ATACATTACCAAATGTATTG
1 ATACATTTCCAAATGTATTG
*
9178731 ATTCATTTCCAAATGTATTG
1 ATACATTTCCAAATGTATTG
9178751 ATACATTTC
1 ATACATTTC
9178760 ATCGTTTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.41
Consensus pattern (20 bp):
ATACATTTCCAAATGTATTG
Found at i:9181618 original size:19 final size:19
Alignment explanation
Indices: 9181578--9181619 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
9181568 AGGCCTAACG
* *
9181578 AATAAATGAATGAGGGTAA
1 AATAAATGAATGAAGATAA
9181597 AATAAATGAA-GAAGATATA
1 AATAAATGAATGAAGATA-A
9181616 AATA
1 AATA
9181620 CTAATAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.60, C:0.00, G:0.19, T:0.21
Consensus pattern (19 bp):
AATAAATGAATGAAGATAA
Found at i:9193314 original size:2 final size:2
Alignment explanation
Indices: 9193301--9193335 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
9193291 GTTATTGTGT
*
9193301 TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9193336 TTATGCAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9195446 original size:16 final size:16
Alignment explanation
Indices: 9195425--9195456 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
9195415 AATCAACTTC
*
9195425 ACATATATGTGTATAT
1 ACATATATGTATATAT
9195441 ACATATATGTATATAT
1 ACATATATGTATATAT
9195457 CCAACCTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (16 bp):
ACATATATGTATATAT
Found at i:9198403 original size:25 final size:26
Alignment explanation
Indices: 9198374--9198425 Score: 70
Period size: 28 Copynumber: 2.0 Consensus size: 26
9198364 GTCGTAACCA
9198374 CGTATA-ACAACCTGTGGCCTTGCCG
1 CGTATACACAACCTGTGGCCTTGCCG
*
9198399 CGTATAGTCACAGCCTGTGGCCTTGCC
1 CGTATA--CACAACCTGTGGCCTTGCC
9198426 ACATATATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 6 0.26
28 17 0.74
ACGTcount: A:0.17, C:0.33, G:0.25, T:0.25
Consensus pattern (26 bp):
CGTATACACAACCTGTGGCCTTGCCG
Found at i:9203026 original size:28 final size:28
Alignment explanation
Indices: 9202990--9203044 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
9202980 TAACAACCTA
* *
9202990 TGGCTTTGCCACGTATAATCATAGCCCG
1 TGGCCTTGCCACGTATAATCACAGCCCG
* *
9203018 TGGCCTTGCCATGTATATTCACAGCCC
1 TGGCCTTGCCACGTATAATCACAGCCC
9203045 ATTGACAAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.20, C:0.31, G:0.20, T:0.29
Consensus pattern (28 bp):
TGGCCTTGCCACGTATAATCACAGCCCG
Found at i:9211284 original size:2 final size:2
Alignment explanation
Indices: 9211277--9211323 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
9211267 NNNNNNNTAG
9211277 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
*
9211319 CA TA T
1 TA TA T
9211324 GTAAATGTGT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:9211883 original size:15 final size:15
Alignment explanation
Indices: 9211865--9211894 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
9211855 ATGCCAGTAC
9211865 GAGTTGGCAATGTAT
1 GAGTTGGCAATGTAT
9211880 GAGTTGGCAATGTAT
1 GAGTTGGCAATGTAT
9211895 ATCACTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.33, T:0.33
Consensus pattern (15 bp):
GAGTTGGCAATGTAT
Found at i:9218989 original size:43 final size:43
Alignment explanation
Indices: 9218919--9219080 Score: 164
Period size: 43 Copynumber: 3.8 Consensus size: 43
9218909 GTAATTATGT
* * * *
9218919 TGACTCGGCTATGTGCGAGTAGGGAGTGTGCATAAGCCGAG-GA
1 TGACCCGGTTATGTGTGAGTAGGGAGTGTGCATAACCCG-GTGA
*
9218962 TGACCCGGTTATGTGTGAGTAAGGAGTGTGCATAACCCGGTGA
1 TGACCCGGTTATGTGTGAGTAGGGAGTGTGCATAACCCGGTGA
* * ** *
9219005 TGACCCGATTATGTGTGAGTAGGGAGTGCGCATAATGCAGTGA
1 TGACCCGGTTATGTGTGAGTAGGGAGTGTGCATAACCCGGTGA
* * ** * *
9219048 CGACCCAGCCATGTGCGAGTAGGGAGTGCGCAT
1 TGACCCGGTTATGTGTGAGTAGGGAGTGTGCAT
9219081 GAGCTGATGA
Statistics
Matches: 101, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
42 1 0.01
43 100 0.99
ACGTcount: A:0.23, C:0.18, G:0.36, T:0.22
Consensus pattern (43 bp):
TGACCCGGTTATGTGTGAGTAGGGAGTGTGCATAACCCGGTGA
Found at i:9219121 original size:20 final size:20
Alignment explanation
Indices: 9219079--9219121 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
9219069 GGGAGTGCGC
* *
9219079 ATGAGCTGATGATGATGATG
1 ATGAGCTGATGATGATAAAG
*
9219099 ATGAGCTGGTGATGATAAAG
1 ATGAGCTGATGATGATAAAG
9219119 ATG
1 ATG
9219122 GGTTGGTGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.05, G:0.35, T:0.28
Consensus pattern (20 bp):
ATGAGCTGATGATGATAAAG
Found at i:9227946 original size:66 final size:67
Alignment explanation
Indices: 9227812--9227958 Score: 174
Period size: 66 Copynumber: 2.2 Consensus size: 67
9227802 TTGTTGTAGA
* * *
9227812 TTGTGGTTGAGCCTTGGAAAAACCACTTTGGGTTTTAGTTTAGCTAGTAAAAAACTTATGTAAAA
1 TTGTGGTTGAGCCTTGGAAAAACCACTTTGGGTTTTAGTTGAGCCAGTAAAAAACATATGTAAAA
9227877 GG
66 GG
* * * *
9227879 TTGTGGTTGAGCCTT-GAAAAACCACTTTGGGTTTTGGTTGATCCCGTGAAAAACCAT-TGCT-A
1 TTGTGGTTGAGCCTTGGAAAAACCACTTTGGGTTTTAGTTGAGCCAGT-AAAAAACATATG-TAA
*
9227941 TAGG
64 AAGG
*
9227945 TTGTGGCTGAGCCT
1 TTGTGGTTGAGCCT
9227959 GCGAAAAGCC
Statistics
Matches: 69, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
66 46 0.67
67 23 0.33
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (67 bp):
TTGTGGTTGAGCCTTGGAAAAACCACTTTGGGTTTTAGTTGAGCCAGTAAAAAACATATGTAAAA
GG
Found at i:9234492 original size:19 final size:19
Alignment explanation
Indices: 9234465--9234501 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
9234455 TTTCTTATAA
9234465 ACAGAAATTTTAGAGTTAG
1 ACAGAAATTTTAGAGTTAG
*
9234484 ACAGTAATTTTAGAGTTA
1 ACAGAAATTTTAGAGTTA
9234502 TACATAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.05, G:0.19, T:0.35
Consensus pattern (19 bp):
ACAGAAATTTTAGAGTTAG
Found at i:9236118 original size:25 final size:24
Alignment explanation
Indices: 9236090--9236149 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 24
9236080 TGGACTTCTC
9236090 CCATTTCTT-TCTAATTGGACCATGT
1 CCATTT-TTCTCT-ATTGGACCATGT
9236115 CCATTTTTCCTCTATTGGACCATGT
1 CCATTTTT-CTCTATTGGACCATGT
*
9236140 CTATTTTTCT
1 CCATTTTTCT
9236150 TGCTTGTTGG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
24 4 0.12
25 25 0.78
26 3 0.09
ACGTcount: A:0.17, C:0.25, G:0.10, T:0.48
Consensus pattern (24 bp):
CCATTTTTCTCTATTGGACCATGT
Found at i:9236227 original size:4 final size:5
Alignment explanation
Indices: 9236182--9236226 Score: 69
Period size: 5 Copynumber: 9.6 Consensus size: 5
9236172 TTCCTTGTTA
9236182 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC -TTTC -TTTC -TTTC TTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTT
9236227 CCCATCGTCC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 12 0.31
5 27 0.69
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:9236612 original size:33 final size:33
Alignment explanation
Indices: 9236540--9236616 Score: 93
Period size: 34 Copynumber: 2.3 Consensus size: 33
9236530 ACACTTTTTG
* *
9236540 GCCTCCAAAATCAGCAGAAAAATGGCACTTTCCA
1 GCCTCCAAAACCAGCAGAAAAA-GACACTTTCCA
* *
9236574 ACCTCCAAAACCAGCAGAAAACA-ACTCTTTCCA
1 GCCTCCAAAACCAGCAGAAAA-AGACACTTTCCA
9236607 GCCTCCAAAA
1 GCCTCCAAAA
9236617 TTAGCCCTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
33 17 0.46
34 19 0.51
35 1 0.03
ACGTcount: A:0.40, C:0.34, G:0.10, T:0.16
Consensus pattern (33 bp):
GCCTCCAAAACCAGCAGAAAAAGACACTTTCCA
Found at i:9241352 original size:42 final size:42
Alignment explanation
Indices: 9241300--9241424 Score: 187
Period size: 42 Copynumber: 3.0 Consensus size: 42
9241290 TATCTCATAT
* * * *
9241300 GCAACGGCTTATGCGCACTCCCACTTGCACATAGTCGGGTCA
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCAGGTCA
*
9241342 GCAACAGCTTATGTGCACTCCCACTCGCACATAGCCAGGTCA
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCAGGTCA
* *
9241384 GCAACGGCTTATGTGCACTCCTACTCGCACATGGCCAGGTC
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCAGGTC
9241425 CACATCAACA
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.22, C:0.34, G:0.22, T:0.21
Consensus pattern (42 bp):
GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCAGGTCA
Done.