Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 125 of 126
Found at i:37443377 original size:16 final size:15
Alignment explanation
Indices: 37443356--37443386 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
37443346 AGTTTTAAAA
37443356 TTTTTGGATTTAGGTT
1 TTTTTGGATTT-GGTT
37443372 TTTTTGGATTTGGTT
1 TTTTTGGATTTGGTT
37443387 AATTTCAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.10, C:0.00, G:0.26, T:0.65
Consensus pattern (15 bp):
TTTTTGGATTTGGTT
Found at i:37449203 original size:114 final size:118
Alignment explanation
Indices: 37449007--37449236 Score: 299
Period size: 114 Copynumber: 2.0 Consensus size: 118
37448997 CGTCGTTAAA
* * * **
37449007 GATGATGATGAAGATGAAAGGACCAGCTCATTGGAGTTTCAAGACGACAACGAGAAGAAGATGGT
1 GATGAAGATGAAGACGAAAGGA-CAGCTCATTGGAGTTTCAAGACGACAAC-AGAAGAAGAAGAA
* * * *
37449072 GATGATGATATCATTGGGGGAATTGAAGGCAAATGATGATGATGGTGATGGTGAT
64 GAAGATGATATCATTGGGAGAACTGAAGGCAAATGATGATGATGATGATGGTGAT
37449127 GATGAAGATGAAGACGAAAGGA-A-CTCATTGGAGTTTCAAGAC-A-AGA-AGAAGAAGAAGAAG
1 GATGAAGATGAAGACGAAAGGACAGCTCATTGGAGTTTCAAGACGACA-ACAGAAGAAGAAGAAG
* *
37449187 AAGATTATATCATTGGGAGAACTGAAGGCAAATGATGGTGATGATGATGG
65 AAGATGATATCATTGGGAGAACTGAAGGCAAATGATGATGATGATGATGG
37449237 GTTTAAGACT
Statistics
Matches: 98, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
114 55 0.56
115 1 0.01
116 2 0.02
117 19 0.19
118 1 0.01
120 20 0.20
ACGTcount: A:0.39, C:0.08, G:0.32, T:0.21
Consensus pattern (118 bp):
GATGAAGATGAAGACGAAAGGACAGCTCATTGGAGTTTCAAGACGACAACAGAAGAAGAAGAAGA
AGATGATATCATTGGGAGAACTGAAGGCAAATGATGATGATGATGATGGTGAT
Found at i:37451426 original size:28 final size:28
Alignment explanation
Indices: 37451358--37451428 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 28
37451348 CCCTATGTTA
* *
37451358 TTTAGTTTTAAAATTTAGTCCCTTTGCT
1 TTTAATTTTAAAATCTAGTCCCTTTGCT
*
37451386 TTTAATTTCTAAAGTCTAGT-CCTTTGCT
1 TTTAATTT-TAAAATCTAGTCCCTTTGCT
37451414 TGTCTAA-TTTAAAAT
1 T-T-TAATTTTAAAAT
37451429 ATTAAAGTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
28 21 0.58
29 12 0.33
30 3 0.08
ACGTcount: A:0.25, C:0.14, G:0.10, T:0.51
Consensus pattern (28 bp):
TTTAATTTTAAAATCTAGTCCCTTTGCT
Found at i:37452531 original size:33 final size:33
Alignment explanation
Indices: 37452444--37452531 Score: 149
Period size: 33 Copynumber: 2.7 Consensus size: 33
37452434 GCGACAGCGG
*
37452444 CACCACCAATCGTGGCACCAAAATCACCAGTGA
1 CACCACCAATCGTGGCACCAATATCACCAGTGA
* *
37452477 CACCACCAATCGTGGCACCAATGTCGCCAGTGA
1 CACCACCAATCGTGGCACCAATATCACCAGTGA
37452510 CACCACCAATCGTGGCACCAAT
1 CACCACCAATCGTGGCACCAAT
37452532 TTTGCCTAAC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.32, C:0.38, G:0.17, T:0.14
Consensus pattern (33 bp):
CACCACCAATCGTGGCACCAATATCACCAGTGA
Found at i:37460675 original size:15 final size:15
Alignment explanation
Indices: 37460655--37460701 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
37460645 ACAAAACGAT
37460655 AATATAAATAATTAA
1 AATATAAATAATTAA
*
37460670 AATATAACAT--TTTA
1 AATATAA-ATAATTAA
*
37460684 AACATAAATAATTAA
1 AATATAAATAATTAA
37460699 AAT
1 AAT
37460702 GTACCTTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
13 2 0.08
14 9 0.36
15 12 0.48
16 2 0.08
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (15 bp):
AATATAAATAATTAA
Found at i:37460990 original size:25 final size:26
Alignment explanation
Indices: 37460952--37461001 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
37460942 GTGTACTCTA
* *
37460952 ATAAAAAATATAAGTATTGAATTAAC
1 ATAAAAAATATAAGAATTAAATTAAC
37460978 ATAAAAAAT-TAAGAATTAAATTAA
1 ATAAAAAATATAAGAATTAAATTAA
37461002 ATATTGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (26 bp):
ATAAAAAATATAAGAATTAAATTAAC
Found at i:37462560 original size:12 final size:12
Alignment explanation
Indices: 37462525--37462560 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 12
37462515 TTTCTGTTTC
37462525 CTCTGTTTTCTT
1 CTCTGTTTTCTT
*
37462537 CTTCTATTTTCTT
1 C-TCTGTTTTCTT
37462550 CTCTGTTTTCT
1 CTCTGTTTTCT
37462561 CTTTAATGGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.03, C:0.25, G:0.06, T:0.67
Consensus pattern (12 bp):
CTCTGTTTTCTT
Found at i:37466480 original size:24 final size:24
Alignment explanation
Indices: 37466441--37466499 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
37466431 TCTCTTCCAC
*
37466441 TTTTTTATTTTCATTTTC-CTCTG
1 TTTTTTCTTTTCATTTTCTCTCTG
37466464 TTTTTTCTTTTCTATTTTCTTCTCTG
1 TTTTTTCTTTTC-ATTTTC-TCTCTG
*
37466490 TTTTCTCTTT
1 TTTTTTCTTT
37466500 AATGGCCACA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
23 11 0.35
24 6 0.19
26 14 0.45
ACGTcount: A:0.05, C:0.19, G:0.03, T:0.73
Consensus pattern (24 bp):
TTTTTTCTTTTCATTTTCTCTCTG
Found at i:37470073 original size:12 final size:13
Alignment explanation
Indices: 37470056--37470084 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
37470046 ATTTTTAAAA
37470056 TTTT-AAAAATAT
1 TTTTAAAAAATAT
37470068 TTTTAAAAAATAT
1 TTTTAAAAAATAT
37470081 TTTT
1 TTTT
37470085 TATATTTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.25
13 12 0.75
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TTTTAAAAAATAT
Found at i:37470303 original size:30 final size:30
Alignment explanation
Indices: 37470253--37470309 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
37470243 GGATGATTTA
* *
37470253 ATAAAAAAATAATTTTAAAGGTTAAAAAGG
1 ATAAAAAAATAATTTAAAAGGCTAAAAAGG
37470283 ATAAAAAAATTAA-TTAAAAGGCTAAAA
1 ATAAAAAAA-TAATTTAAAAGGCTAAAA
37470310 TAATATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 21 0.88
31 3 0.12
ACGTcount: A:0.63, C:0.02, G:0.11, T:0.25
Consensus pattern (30 bp):
ATAAAAAAATAATTTAAAAGGCTAAAAAGG
Found at i:37470477 original size:2 final size:2
Alignment explanation
Indices: 37470470--37470497 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
37470460 GTCCACATTC
37470470 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
37470498 GGTGAATTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:37473093 original size:18 final size:18
Alignment explanation
Indices: 37473053--37473096 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
37473043 TATGTATAAT
*
37473053 TTTAATATTTTTTTATGTG
1 TTTAAT-TTTTTTTATGTC
37473072 TTTAATTTTTTTTAT-TAC
1 TTTAATTTTTTTTATGT-C
37473090 TTTAATT
1 TTTAATT
37473097 AAAATAGTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 1 0.04
18 16 0.70
19 6 0.26
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (18 bp):
TTTAATTTTTTTTATGTC
Found at i:37474195 original size:21 final size:20
Alignment explanation
Indices: 37474156--37474196 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
37474146 GTTATTGATA
*
37474156 TTATAATGCTATTGCTATAT
1 TTATAATGCTATTGATATAT
*
37474176 TTATAATTGCTATTTATATAT
1 TTATAA-TGCTATTGATATAT
37474197 GCTGTAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.32, C:0.07, G:0.07, T:0.54
Consensus pattern (20 bp):
TTATAATGCTATTGATATAT
Found at i:37477704 original size:148 final size:148
Alignment explanation
Indices: 37477417--37478007 Score: 798
Period size: 148 Copynumber: 4.0 Consensus size: 148
37477407 AGCCAAAGTT
* * *
37477417 TAATTCAACATATAGCTATCAGTTCACCTAAAGATTCAAGAAA-CAGTACGATTCAGCTTCGAAC
1 TAATTCATCAAATAGCTA-CAGTTCACATAAAGATTCAA-AAACCAGTACGATTCAGCTTCGAAC
* *
37477481 TAGGATCTAAAAACAAGCTAAAGTTGTTCTTCCTACGTAAATCTTAGCAAACTTAGCTCGTAAAC
64 TAGAATCTAAAAACAAGCTAAAGTTGTTCTTCCTACGTAAATCTTAGCAAACTTAGCTAGTAAAC
37477546 TTCAGATCTGTATTTTTTTG
129 TTCAGATCTGTATTTTTTTG
37477566 TAATTCATCAAATAGCTACAGTTCACATAAAGATTCAAAAACCAGTACGATTCAGCTTCGAACTA
1 TAATTCATCAAATAGCTACAGTTCACATAAAGATTCAAAAACCAGTACGATTCAGCTTCGAACTA
* * *
37477631 GGATCTAAAAACAAGCTAAAGTTTTTCTCCCTACGTAAATCTTAGCAAACTTAGCTAGTAAACTT
66 GAATCTAAAAACAAGCTAAAGTTGTTCTTCCTACGTAAATCTTAGCAAACTTAGCTAGTAAACTT
37477696 CAGATCTGTA-TTTTTTG
131 CAGATCTGTATTTTTTTG
* * *
37477713 CAATCCATCAAATAGCTACAGTTCACATAAAGATTCAGAAACCAGTACGATTCAGCTTCGAACTA
1 TAATTCATCAAATAGCTACAGTTCACATAAAGATTCAAAAACCAGTACGATTCAGCTTCGAACTA
* * * * * * * *
37477778 TAATCCAAAAACAAGCTAAAGCTGTTCTTCTTACGCT-AGTCATAG-GAACTTAGCTTGTAAACT
66 GAATCTAAAAACAAGCTAAAGTTGTTCTTCCTACG-TAAATCTTAGCAAACTTAGCTAGTAAACT
* *
37477841 TCAGTTCTGTATTTTTTTTA
130 TCAGATCTGTA-TTTTTTTG
* * * *
37477861 TAACTCATCAAATAGCTAACAGTTCACATAAAGATTCAAAAAGCGGAACCG-TTCAAGCTTCGAA
1 TAATTCATCAAATAGCT-ACAGTTCACATAAAGATTCAAAAACCAGTA-CGATTC-AGCTTCGAA
* * * *
37477925 CTAGAATCTAAAAACAAGTTAAA-TCTGTTCTTCCTACGTAAATCTTTGCAATCTTAGCTAATAA
63 CTAGAATCTAAAAACAAGCTAAAGT-TGTTCTTCCTACGTAAATCTTAGCAAACTTAGCTAGTAA
*
37477989 ACTTCAGATCCGTATTTTT
127 ACTTCAGATCTGTATTTTT
37478008 AAGCAAAACA
Statistics
Matches: 389, Mismatches: 43, Indels: 19
0.86 0.10 0.04
Matches are distributed among these distances:
146 26 0.07
147 106 0.27
148 135 0.35
149 46 0.12
150 53 0.14
151 23 0.06
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (148 bp):
TAATTCATCAAATAGCTACAGTTCACATAAAGATTCAAAAACCAGTACGATTCAGCTTCGAACTA
GAATCTAAAAACAAGCTAAAGTTGTTCTTCCTACGTAAATCTTAGCAAACTTAGCTAGTAAACTT
CAGATCTGTATTTTTTTG
Found at i:37484672 original size:31 final size:29
Alignment explanation
Indices: 37484626--37484689 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 29
37484616 TTCTTTAAAT
37484626 ATGTATAATTGAATCA-AAATCAAAGTTTC
1 ATGTATAATTGAATCACAAATC-AAGTTTC
*
37484655 ATGTATATATATGAATCACAATTCAAGTTTC
1 ATGTATA-AT-TGAATCACAAATCAAGTTTC
37484686 ATGT
1 ATGT
37484690 GTACAATTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 7 0.23
30 2 0.06
31 18 0.58
32 4 0.13
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.38
Consensus pattern (29 bp):
ATGTATAATTGAATCACAAATCAAGTTTC
Found at i:37488559 original size:39 final size:42
Alignment explanation
Indices: 37488505--37488589 Score: 149
Period size: 39 Copynumber: 2.1 Consensus size: 42
37488495 TCTTCCCAGG
37488505 CTTGCATACCACCATGTGTGTCTTTG-T-T-CTATAAAGCCT
1 CTTGCATACCACCATGTGTGTCTTTGTTCTCCTATAAAGCCT
37488544 CTTGCATACCACCATGTGTGTCTTTGTTCTCCTATAAAGCCT
1 CTTGCATACCACCATGTGTGTCTTTGTTCTCCTATAAAGCCT
37488586 CTTG
1 CTTG
37488590 TCAACCGATC
Statistics
Matches: 43, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
39 26 0.60
40 1 0.02
41 1 0.02
42 15 0.35
ACGTcount: A:0.19, C:0.27, G:0.15, T:0.39
Consensus pattern (42 bp):
CTTGCATACCACCATGTGTGTCTTTGTTCTCCTATAAAGCCT
Found at i:37495054 original size:142 final size:142
Alignment explanation
Indices: 37494865--37495211 Score: 678
Period size: 141 Copynumber: 2.5 Consensus size: 142
37494855 TGGTTCCTGG
*
37494865 GGGATTCGAGCCCAGGTCTCCACGGCCACGACGTGGAATTCTTACCACTAAACTACAGCCACAAT
1 GGGATTCGAGCCCAGGTCTCCACGGCCACAACGTGGAATTCTTACCACTAAACTACAGCCACAAT
37494930 GTACCCAAAGGAACAAAATAAACTACTTAATAGCTATAATTAACATATTAAAGTAAAAAATGTTC
66 GTACCCAAAGGAACAAAATAAACTACTTAATAGCTATAATTAACATATTAAAGTAAAAAATGTTC
37494995 AATGTGGCTGCT
131 AATGTGGCTGCT
37495007 GGGATTCGAGCCCAGGTCTCCACGGCCACAACGTGGAATTCTTACCACTAAACTACAGCCAC-AT
1 GGGATTCGAGCCCAGGTCTCCACGGCCACAACGTGGAATTCTTACCACTAAACTACAGCCACAAT
37495071 GTACCCAAAGGAACAAAATAAACTACTTAATAGCTATAATTAACATATTAAAGTAAAAAATGTTC
66 GTACCCAAAGGAACAAAATAAACTACTTAATAGCTATAATTAACATATTAAAGTAAAAAATGTTC
37495136 AATGTGGCTGCT
131 AATGTGGCTGCT
37495148 GGGATTCGAGCCCAGGTCTCCACGGCCACAACGTGGAATTCTTACCACTAAACTACAGCCACAA
1 GGGATTCGAGCCCAGGTCTCCACGGCCACAACGTGGAATTCTTACCACTAAACTACAGCCACAA
37495212 CTTGACATGA
Statistics
Matches: 203, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
141 141 0.69
142 62 0.31
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.22
Consensus pattern (142 bp):
GGGATTCGAGCCCAGGTCTCCACGGCCACAACGTGGAATTCTTACCACTAAACTACAGCCACAAT
GTACCCAAAGGAACAAAATAAACTACTTAATAGCTATAATTAACATATTAAAGTAAAAAATGTTC
AATGTGGCTGCT
Found at i:37504472 original size:23 final size:23
Alignment explanation
Indices: 37504423--37504472 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
37504413 GTTTTCTTTT
**
37504423 ATGGGATTTTGAAAACAAGTGTG
1 ATGGGATTTTGAAAACAAGTGAA
*
37504446 ATGGGATTTT-AAAGAGAAGTGAA
1 ATGGGATTTTGAAA-ACAAGTGAA
37504469 ATGG
1 ATGG
37504473 AATCTCCTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 3 0.13
23 20 0.87
ACGTcount: A:0.38, C:0.02, G:0.32, T:0.28
Consensus pattern (23 bp):
ATGGGATTTTGAAAACAAGTGAA
Found at i:37504962 original size:27 final size:26
Alignment explanation
Indices: 37504919--37504975 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
37504909 ATATTTATAT
*
37504919 TATATTATTTTAATATTTAATAATTTA
1 TATATTATTTTAATA-TTAAAAATTTA
* *
37504946 TATATT-TTTTATTTATTAAAAATTTT
1 TATATTATTTTA-ATATTAAAAATTTA
37504972 TATA
1 TATA
37504976 GGCATCTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 18 0.69
27 8 0.31
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (26 bp):
TATATTATTTTAATATTAAAAATTTA
Found at i:37506142 original size:16 final size:16
Alignment explanation
Indices: 37506116--37506153 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
37506106 GTTACGTTAG
37506116 TTTTT-AATTTA-ATA
1 TTTTTAAATTTATATA
37506130 TTTATTAAATTTATATA
1 TTT-TTAAATTTATATA
37506147 TTTTTAA
1 TTTTTAA
37506154 TAAAATTCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 3 0.14
15 2 0.10
16 10 0.48
17 6 0.29
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTTTAAATTTATATA
Found at i:37508088 original size:115 final size:115
Alignment explanation
Indices: 37507884--37508105 Score: 372
Period size: 115 Copynumber: 1.9 Consensus size: 115
37507874 TTCTGGTCTA
*
37507884 TTTGGTACTGAAATCTAGCATTTGAATTAGGGTTTAAGGTGTTACTTTTATGTTGTTTCTCGAAA
1 TTTGGTACTGAAATCTAGCATTTGAATTAGGGTTTAAGGTGTTACTTTTATGCTGTTTCTCGAAA
* * *
37507949 GAATTTTGGGTCATTCGAGATTGTTTAGTGTGTGTTTATGTGCCTTTTGT
66 GAATTTCGGGTCATTCAAGATTGTTTAGGGTGTGTTTATGTGCCTTTTGT
* * *
37507999 TTTGGTATTGAAATGTAGCATTTGAATTAGGGTTTAAGGTGTTATTTTTATGCTGTTTCTCGAAA
1 TTTGGTACTGAAATCTAGCATTTGAATTAGGGTTTAAGGTGTTACTTTTATGCTGTTTCTCGAAA
*
37508064 GAATTTCGGGTCATTCAAGTTTGTTTAGGGTGTGTTTATGTG
66 GAATTTCGGGTCATTCAAGATTGTTTAGGGTGTGTTTATGTG
37508106 TTACAAAGTT
Statistics
Matches: 99, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
115 99 1.00
ACGTcount: A:0.21, C:0.08, G:0.25, T:0.46
Consensus pattern (115 bp):
TTTGGTACTGAAATCTAGCATTTGAATTAGGGTTTAAGGTGTTACTTTTATGCTGTTTCTCGAAA
GAATTTCGGGTCATTCAAGATTGTTTAGGGTGTGTTTATGTGCCTTTTGT
Found at i:37519111 original size:87 final size:87
Alignment explanation
Indices: 37518965--37519139 Score: 341
Period size: 87 Copynumber: 2.0 Consensus size: 87
37518955 ATAATACTGA
37518965 GTTCAAGACTGTCTATATGACTCCATATTGAAACATTAGACACCATTGTATGCAAAAACAGAGAA
1 GTTCAAGACTGTCTATATGACTCCATATTGAAACATTAGACACCATTGTATGCAAAAACAGAGAA
37519030 ACATGAAATGGGGTTCAGGTGG
66 ACATGAAATGGGGTTCAGGTGG
*
37519052 GTTCAAGACTGTCTATATGACTCCATATTGAAACATTAGACACCATTGTATGCAAAAACAGAGCA
1 GTTCAAGACTGTCTATATGACTCCATATTGAAACATTAGACACCATTGTATGCAAAAACAGAGAA
37519117 ACATGAAATGGGGTTCAGGTGG
66 ACATGAAATGGGGTTCAGGTGG
37519139 G
1 G
37519140 GTTGAAGCAC
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 87 1.00
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25
Consensus pattern (87 bp):
GTTCAAGACTGTCTATATGACTCCATATTGAAACATTAGACACCATTGTATGCAAAAACAGAGAA
ACATGAAATGGGGTTCAGGTGG
Found at i:37521334 original size:16 final size:18
Alignment explanation
Indices: 37521308--37521343 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
37521298 TAGAATTGAG
37521308 TTGACAAAATT-ATTTAA
1 TTGACAAAATTAATTTAA
37521325 TTGA-AAAATTAATTTAA
1 TTGACAAAATTAATTTAA
37521342 TT
1 TT
37521344 AATTAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (18 bp):
TTGACAAAATTAATTTAA
Found at i:37539318 original size:21 final size:21
Alignment explanation
Indices: 37539293--37539340 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
37539283 ACCTATAATA
*
37539293 AAATTATAAA-AAATAATATTT
1 AAATT-TAAATAAATAAAATTT
*
37539314 TAATTTAAATAAATAAAATTT
1 AAATTTAAATAAATAAAATTT
37539335 AAATTT
1 AAATTT
37539341 TACACTTACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AAATTTAAATAAATAAAATTT
Found at i:37543013 original size:37 final size:40
Alignment explanation
Indices: 37542964--37543049 Score: 133
Period size: 37 Copynumber: 2.2 Consensus size: 40
37542954 AATAATTATA
* *
37542964 TTTAATACAATAAAATATTTATTATA-TTAT-TTA-TGTT
1 TTTAATATAATAAAATATTTATTATATTTATGATAGTGTT
37543001 TTTAATATAATAAAATATTTATTATATTTATGATAGTGTT
1 TTTAATATAATAAAATATTTATTATATTTATGATAGTGTT
37543041 TTTAATATA
1 TTTAATATA
37543050 TTAGAAAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
37 25 0.57
38 4 0.09
39 2 0.05
40 13 0.30
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.53
Consensus pattern (40 bp):
TTTAATATAATAAAATATTTATTATATTTATGATAGTGTT
Found at i:37549181 original size:29 final size:30
Alignment explanation
Indices: 37549139--37549201 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 30
37549129 ATTTTAAATT
37549139 AATAAAAGTAAAATTAAAATTTAATC-TTTAA
1 AATAAAAG-AAAATT-AAATTTAATCATTTAA
**
37549170 AATAAAA-AAAATTTGATTTAATCATTTAA
1 AATAAAAGAAAATTAAATTTAATCATTTAA
37549199 AAT
1 AAT
37549202 TTATAAAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 8 0.28
29 14 0.48
31 7 0.24
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (30 bp):
AATAAAAGAAAATTAAATTTAATCATTTAA
Found at i:37566760 original size:30 final size:30
Alignment explanation
Indices: 37566724--37566783 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
37566714 ATCCAATTAT
37566724 CCAGCTTTACTTGAGCTCACACACAAAGAA
1 CCAGCTTTACTTGAGCTCACACACAAAGAA
*
37566754 CCAGCTTTACTTGAGCTCACACCCAAAGAA
1 CCAGCTTTACTTGAGCTCACACACAAAGAA
37566784 AATAACTTGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.35, C:0.32, G:0.13, T:0.20
Consensus pattern (30 bp):
CCAGCTTTACTTGAGCTCACACACAAAGAA
Found at i:37574141 original size:16 final size:16
Alignment explanation
Indices: 37574117--37574164 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
37574107 CAAGCTTACA
*
37574117 AGTTTAAATCATTTTG
1 AGTTCAAATCATTTTG
* *
37574133 AGTTCAAATTATTTAG
1 AGTTCAAATCATTTTG
* *
37574149 AATCCAAATCATTTTG
1 AGTTCAAATCATTTTG
37574165 GGTGTAGATT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.44
Consensus pattern (16 bp):
AGTTCAAATCATTTTG
Found at i:37576256 original size:24 final size:24
Alignment explanation
Indices: 37576229--37576277 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
37576219 ATTGAGTGGC
*
37576229 AAAAAATA-CAAAATTAAATAATT
1 AAAAAAAACCAAAATTAAATAATT
* *
37576252 AAAAAAAACCATAATTAGATAATT
1 AAAAAAAACCAAAATTAAATAATT
37576276 AA
1 AA
37576278 TTTATAAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.67, C:0.06, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAAAAAACCAAAATTAAATAATT
Found at i:37584174 original size:376 final size:373
Alignment explanation
Indices: 37583471--37584459 Score: 1507
Period size: 376 Copynumber: 2.6 Consensus size: 373
37583461 AACCAACCTA
* * *
37583471 AACTCAAAATGACCCCAACTCGTAATTTCCTAACCCCAAAAAACTAAGCTTCAAACCTAAATGTG
1 AACTCGAAATGACCCCAACTCGTAATGTCCTAA-CCCAAAAAACTAAGCTTCAAACCTGAATG-G
* *
37583536 CTCAACTCAAAACAACCAGAGTTCAAACCCATAAGTTGAAGTAAAAATGACCCAAACCCAAAATT
64 CTCAACTCAAAACAACCAGAATTCAAACCCATAAGTTGAAGTAAAAATGA-CCAAACCCGAAATT
*
37583601 AATCCAAAAATAACCCACTCAATTGACAGGCTAATTGTACTGCAATGAATTCACCATGCAAACAA
128 AATCCAAAAATAATCCACTCAATTGACAGGCTAATTGTACTGCAATGAATTCACCATGCAAACAA
* *
37583666 ATCAAATTAAAAGCTACCCTACAAAGAAACAAAGTTAAAGAATCTTCAACAAACATCATCCTAAT
193 ATCAAATTAAAAGCTACCCTATAAAGAAACAAAGTTGAAGAATCTTCAACAAACATCATCCTAAT
* *
37583731 GGAAGATGGTCAATGTCAACCAACATCATCCACAGTTACCAAGTACCATCCTTAACCATCGGCTT
258 GGAAGATGATCAATGTCAACCAACATCATCCACAGTTACCAAGTACCATCCTCAACCATCGGCTT
37583796 CTTCCACCCGAATTGGCTCAAACCAAAAGCAACCCGAACCCAAGATACCAT
323 CTTCCACCCGAATTGGCTCAAACCAAAAGCAACCCGAACCCAAGATACCAT
* *
37583847 AACTCGAAACGACCCCAACTCGTAATGTCCTAACCCAAAAAACTAATCTTCAAACCTGAATGAGC
1 AACTCGAAATGACCCCAACTCGTAATGTCCTAACCCAAAAAACTAAGCTTCAAACCTGAATG-GC
*
37583912 TCAACTCAAAACAACCCGAATTCAAACCCATAAGTTGAAGTAAAAATGACCTAAACCCGAAATTA
65 TCAACTCAAAACAACCAGAATTCAAACCCATAAGTTGAAGTAAAAATGACC-AAACCCGAAATTA
* *
37583977 ATCCAAAAATAATCCACTCAATTGACAGGCCTAATTGTACTGCAATGAATTTACCATTCAAACAA
129 ATCCAAAAATAATCCACTCAATTGACAGG-CTAATTGTACTGCAATGAATTCACCATGCAAACAA
* * *
37584042 ATCAAGTTAACAGCTACCCTATAGAGAAACAAAGTTGAAGAATCTTCAACAAACATCATCCTAAT
193 ATCAAATTAAAAGCTACCCTATAAAGAAACAAAGTTGAAGAATCTTCAACAAACATCATCCTAAT
*
37584107 GGATGATGATCAATGTCAACCAACATCATCCACAGTTACCAAGTACCATCCTCAACCATCGGCTT
258 GGAAGATGATCAATGTCAACCAACATCATCCACAGTTACCAAGTACCATCCTCAACCATCGGCTT
* *
37584172 CTTCCACTCGAATTGGCTCAAGCCAAAAGCAACCCGAACCCAAGATACCAT
323 CTTCCACCCGAATTGGCTCAAACCAAAAGCAACCCGAACCCAAGATACCAT
*
37584223 AACTCGAAATGATCCCAACTCGTAATGTCCTAACCCAAAAAACTAAGCTTCAAACCTGAAT-G-T
1 AACTCGAAATGACCCCAACTCGTAATGTCCTAACCCAAAAAACTAAGCTTCAAACCTGAATGGCT
* * * * **
37584286 CAACTCGAAACAACCTGAATTCGAACCCATAACAAGTTAAAGCCAAAATGACACAAACCCGAAAT
66 CAACTCAAAACAACCAGAATTCAAACCCAT---AAGTTGAAGTAAAAATGAC-CAAACCCGAAAT
* * * *
37584351 TAGTTCAACTGAAAAAATCCACTCAATTGACAGGTCTAATTGTACTGCAAT-ACATTCACCAAGC
127 TAATCCAA---AAATAATCCACTCAATTGACAGG-CTAATTGTACTGCAATGA-ATTCACCATGC
* * *
37584415 AAACAAATCAAATTAAAAGCTACTCTATATAGAAACAAAGATGAA
187 AAACAAATCAAATTAAAAGCTACCCTATAAAGAAACAAAGTTGAA
37584460 ATGTTACCAG
Statistics
Matches: 560, Mismatches: 43, Indels: 17
0.90 0.07 0.03
Matches are distributed among these distances:
373 28 0.05
374 3 0.01
375 116 0.21
376 325 0.58
377 1 0.00
378 1 0.00
379 86 0.15
ACGTcount: A:0.42, C:0.27, G:0.11, T:0.21
Consensus pattern (373 bp):
AACTCGAAATGACCCCAACTCGTAATGTCCTAACCCAAAAAACTAAGCTTCAAACCTGAATGGCT
CAACTCAAAACAACCAGAATTCAAACCCATAAGTTGAAGTAAAAATGACCAAACCCGAAATTAAT
CCAAAAATAATCCACTCAATTGACAGGCTAATTGTACTGCAATGAATTCACCATGCAAACAAATC
AAATTAAAAGCTACCCTATAAAGAAACAAAGTTGAAGAATCTTCAACAAACATCATCCTAATGGA
AGATGATCAATGTCAACCAACATCATCCACAGTTACCAAGTACCATCCTCAACCATCGGCTTCTT
CCACCCGAATTGGCTCAAACCAAAAGCAACCCGAACCCAAGATACCAT
Found at i:37586129 original size:94 final size:97
Alignment explanation
Indices: 37585798--37586161 Score: 470
Period size: 94 Copynumber: 3.7 Consensus size: 97
37585788 TAGAATTTTG
* * *
37585798 CTTTTAATTTGATGAATTTATTTTACTCTGAGTGAGCTCGCTGTTGTATTTGTGATGATATATTG
1 CTTTTAATTTGATGAATTTA-TTTACTCGGAGTGAGCTAGCTGTTGTATTTGTGATGATATAGTG
* * *
37585863 TTAATTGATTAGAGTTTAGTAATTGTTATGATTTTGA
65 TTAATT-A-TAGAGTTTAGTTA-TGTT-TAATTTTAA
*
37585900 -TTTTAATTTAATGAATTTATTTACTCGGAGTGAGCTAGCTGTTGTATTTGTGATGATATAGTGT
1 CTTTTAATTTGATGAATTTATTTACTCGGAGTGAGCTAGCTGTTGTATTTGTGATGATATAGTGT
* *
37585964 TAATTTATTAGAGTTTAG-TATTTGTTAGTTTTAA
66 TAA-TTA-TAGAGTTTAGTTATGT-TTAATTTTAA
* * * *
37585998 CTTTTAATTTGACGAATTTTTTTAATCGTAGTGAGCTAGCTGTTGTATTTGTGATGATATAGTGT
1 CTTTTAATTTGATGAATTTATTTACTCGGAGTGAGCTAGCTGTTGTATTTGTGATGATATAGTGT
*
37586063 T-ATTA-ATA-TTT-GTTATGATTTAATTTTAA
66 TAATTATAGAGTTTAGTTATG-TTTAATTTTAA
*
37586092 CTTTTACTTTGATGAATTTATTTACTCGGAGTGAGCTAGCTGTTGTATTTGTGATGATATAGTGT
1 CTTTTAATTTGATGAATTTATTTACTCGGAGTGAGCTAGCTGTTGTATTTGTGATGATATAGTGT
37586157 TAATT
66 TAATT
37586162 GATTACAGAT
Statistics
Matches: 234, Mismatches: 22, Indels: 19
0.85 0.08 0.07
Matches are distributed among these distances:
93 1 0.00
94 76 0.32
95 6 0.03
97 3 0.01
98 9 0.04
99 62 0.26
100 57 0.24
101 20 0.09
ACGTcount: A:0.25, C:0.06, G:0.19, T:0.50
Consensus pattern (97 bp):
CTTTTAATTTGATGAATTTATTTACTCGGAGTGAGCTAGCTGTTGTATTTGTGATGATATAGTGT
TAATTATAGAGTTTAGTTATGTTTAATTTTAA
Found at i:37586134 original size:193 final size:199
Alignment explanation
Indices: 37585798--37586183 Score: 556
Period size: 193 Copynumber: 2.0 Consensus size: 199
37585788 TAGAATTTTG
* * * *
37585798 CTTTTAATTTGATGAATTTATTTTACTCTGAGTGAGCTCGCTGTTGTATTTGTGATGATATATTG
1 CTTTTAATTTGACGAATTTATTTTAATCTGAGTGAGCTAGCTGTTGTATTTGTGATGATATAGTG
* *
37585863 TTAATTGATTAGAGTTTAGTAATTGTTATGATTTTGATTTTAATTTAATGAATTTATTTACTCGG
66 TTAATTGA-TAGAGTTTAGTAATTGTTATAATTTTAATTTTAATTTAATGAATTTATTTACTCGG
* * *
37585928 AGTGAGCTAGCTGTTGTATTTGTGATGATATAGTGTTAATTTATTAGAGTTTAGTATTTGTTAGT
130 AGTGAGCTAGCTGTTGTATTTGTGATGATATAGTGTTAATTGATTACAGATTAGTATTTGTTAGT
37585993 TTTAA
195 TTTAA
37585998 CTTTTAATTTGACGAATTT-TTTTAATC-GTAGTGAGCTAGCTGTTGTATTTGTGATGATATAGT
1 CTTTTAATTTGACGAATTTATTTTAATCTG-AGTGAGCTAGCTGTTGTATTTGTGATGATATAGT
* * * *
37586061 GTT-ATT-A-ATA-TTT-GTTA-TGATT-TAATTTTAACTTTTACTTTGATGAATTTATTTACTC
65 GTTAATTGATAGAGTTTAGTAATTG-TTATAATTTTAA-TTTTAATTTAATGAATTTATTTACTC
37586119 GGAGTGAGCTAGCTGTTGTATTTGTGATGATATAGTGTTAATTGATTACAGATTAGTATTTGTTA
128 GGAGTGAGCTAGCTGTTGTATTTGTGATGATATAGTGTTAATTGATTACAGATTAGTATTTGTTA
37586184 TGATTTAGTA
Statistics
Matches: 170, Mismatches: 13, Indels: 13
0.87 0.07 0.07
Matches are distributed among these distances:
192 9 0.05
193 91 0.54
194 3 0.02
195 2 0.01
197 1 0.01
198 4 0.02
199 42 0.25
200 18 0.11
ACGTcount: A:0.26, C:0.06, G:0.19, T:0.49
Consensus pattern (199 bp):
CTTTTAATTTGACGAATTTATTTTAATCTGAGTGAGCTAGCTGTTGTATTTGTGATGATATAGTG
TTAATTGATAGAGTTTAGTAATTGTTATAATTTTAATTTTAATTTAATGAATTTATTTACTCGGA
GTGAGCTAGCTGTTGTATTTGTGATGATATAGTGTTAATTGATTACAGATTAGTATTTGTTAGTT
TTAA
Found at i:37597291 original size:6 final size:6
Alignment explanation
Indices: 37597280--37597305 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
37597270 GAAAGTTTCG
37597280 GAGTTC GAGTTC GAGTTC GAGTTC GA
1 GAGTTC GAGTTC GAGTTC GAGTTC GA
37597306 ATCGACAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.15, G:0.35, T:0.31
Consensus pattern (6 bp):
GAGTTC
Found at i:37597610 original size:21 final size:21
Alignment explanation
Indices: 37597586--37597633 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
37597576 CCACGAAGCT
37597586 CTTGGTTCATCAAATGAAAAC
1 CTTGGTTCATCAAATGAAAAC
** *
37597607 CTTGAATCGTCAAATGAAAAC
1 CTTGGTTCATCAAATGAAAAC
37597628 CTTGGT
1 CTTGGT
37597634 GGAGCTATAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (21 bp):
CTTGGTTCATCAAATGAAAAC
Found at i:37614470 original size:16 final size:17
Alignment explanation
Indices: 37614443--37614474 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
37614433 TAAATTGTTT
37614443 TAAAAAATTTATAAAAA
1 TAAAAAATTTATAAAAA
37614460 TAAAAAA-TTATAAAA
1 TAAAAAATTTATAAAA
37614475 CTTCTTTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
TAAAAAATTTATAAAAA
Found at i:37629293 original size:16 final size:17
Alignment explanation
Indices: 37629264--37629297 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
37629254 TAAATTTGAT
*
37629264 TAAAAATATACCAAAAA
1 TAAAAACATACCAAAAA
37629281 TAAAAACAT-CCAAAAA
1 TAAAAACATACCAAAAA
37629297 T
1 T
37629298 CCAATATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.68, C:0.15, G:0.00, T:0.18
Consensus pattern (17 bp):
TAAAAACATACCAAAAA
Found at i:37629544 original size:21 final size:21
Alignment explanation
Indices: 37629520--37629563 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
37629510 ATAATAAATA
37629520 AAATCCAAATTCAAATAATTG
1 AAATCCAAATTCAAATAATTG
* * **
37629541 AAATTCATATTCTCATAATTG
1 AAATCCAAATTCAAATAATTG
37629562 AA
1 AA
37629564 TAACTTAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.34
Consensus pattern (21 bp):
AAATCCAAATTCAAATAATTG
Found at i:37631433 original size:47 final size:47
Alignment explanation
Indices: 37631364--37631460 Score: 124
Period size: 47 Copynumber: 2.1 Consensus size: 47
37631354 AACAAATTCT
* * * * *
37631364 TTTTTGGTCACTTAACTATGAAAATTTATAAAATGGTTAT-TCAACTA
1 TTTTTAGTCACTCAACTATGAAAAGTTACAAAATAGTTATCT-AACTA
*
37631411 TTTTTAGTCACTCAATTATGAAAAGTTACAAAATAGTTATCTAACTA
1 TTTTTAGTCACTCAACTATGAAAAGTTACAAAATAGTTATCTAACTA
37631458 TTT
1 TTT
37631461 AATTTTGTCT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
47 42 0.98
48 1 0.02
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.42
Consensus pattern (47 bp):
TTTTTAGTCACTCAACTATGAAAAGTTACAAAATAGTTATCTAACTA
Found at i:37636358 original size:29 final size:28
Alignment explanation
Indices: 37636326--37636380 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
37636316 GACATAAAAT
*
37636326 TTATATATTAATTTATCTGAGTATTAATG
1 TTATATATTAATTTATATGA-TATTAATG
*
37636355 TTATGTATTAATTTATATGATATTAA
1 TTATATATTAATTTATATGATATTAA
37636381 CATGAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.53
Consensus pattern (28 bp):
TTATATATTAATTTATATGATATTAATG
Found at i:37648276 original size:28 final size:26
Alignment explanation
Indices: 37648245--37648304 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 26
37648235 AAAACGAGGT
37648245 TTTTGGA-TGCCCGAGGGCAAAATGGTAA
1 TTTTGGACT-CCCGAGGG--AAATGGTAA
* *
37648273 TTTTGAACTCTCGAGGGAAATGGTAA
1 TTTTGGACTCCCGAGGGAAATGGTAA
37648299 TTTTGG
1 TTTTGG
37648305 GAAAATTTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
26 14 0.50
28 13 0.46
29 1 0.04
ACGTcount: A:0.27, C:0.12, G:0.30, T:0.32
Consensus pattern (26 bp):
TTTTGGACTCCCGAGGGAAATGGTAA
Found at i:37648357 original size:144 final size:144
Alignment explanation
Indices: 37648100--37648361 Score: 359
Period size: 144 Copynumber: 1.8 Consensus size: 144
37648090 AAACGGGACC
* *
37648100 TTTGGATACCCGGGGGCAAAATGGTAATTTTAGACTTTCGGGGACAAAATGGTAATTTTGGAAAA
1 TTTGGATACCCGAGGGCAAAATGGTAATTTTAGACTCTCGGGG--AAAATGGTAATTTTGGAAAA
* * ** *
37648165 ATTTCGGGTTAAAAATGACATTTTAGACATTTTGGGATAATATAGTAATTTTTAAAAAAAATCGA
64 ATTTAGGGCTAAAAATGACATTTTAGACATTAAGGGATAAAATAGTAATTTTTAAAAAAAATCGA
37648230 TATCAAAAACGAGGTT
129 TATCAAAAACGAGGTT
* *
37648246 TTTGGATGCCCGAGGGCAAAATGGTAATTTT-GAACTCTCGAGGG-AAATGGTAATTTTGGGAAA
1 TTTGGATACCCGAGGGCAAAATGGTAATTTTAG-ACTCTCG-GGGAAAATGGTAATTTTGGAAAA
* *
37648309 ATTTAGGGCTAAAAATGATATTTTAGACACTTAAGGG-TAAAATGGTAATTTTT
64 ATTTAGGGCTAAAAATGACATTTTAGACA-TTAAGGGATAAAATAGTAATTTTT
37648362 GGAAGAATAG
Statistics
Matches: 102, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
144 58 0.57
145 6 0.06
146 35 0.34
147 3 0.03
ACGTcount: A:0.36, C:0.09, G:0.23, T:0.32
Consensus pattern (144 bp):
TTTGGATACCCGAGGGCAAAATGGTAATTTTAGACTCTCGGGGAAAATGGTAATTTTGGAAAAAT
TTAGGGCTAAAAATGACATTTTAGACATTAAGGGATAAAATAGTAATTTTTAAAAAAAATCGATA
TCAAAAACGAGGTT
Found at i:37648450 original size:30 final size:29
Alignment explanation
Indices: 37648416--37648539 Score: 85
Period size: 28 Copynumber: 4.2 Consensus size: 29
37648406 AAAATAGTAA
37648416 TTTTGAGAGTTTTGAAGTCAAAAATGGAAT
1 TTTTGAGAG-TTTGAAGTCAAAAATGGAAT
* *
37648446 TTTTG-GAAG-TCGAGGTCAAAAATGGAAT
1 TTTTGAG-AGTTTGAAGTCAAAAATGGAAT
* * * *
37648474 TTTTGAAAGTTTGGAGGCAAAAAAATGTAATT
1 TTTTGAGAGTTTGAAGTC--AAAAATGGAA-T
* *
37648506 TTTTGA-AGTTTTG-AGAACAAAAATAGAAT
1 TTTTGAGAG-TTTGAAG-TCAAAAATGGAAT
37648535 TTTTG
1 TTTTG
37648540 GACAGTTTAG
Statistics
Matches: 75, Mismatches: 11, Indels: 17
0.73 0.11 0.17
Matches are distributed among these distances:
28 24 0.32
29 11 0.15
30 15 0.20
31 13 0.17
32 12 0.16
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.35
Consensus pattern (29 bp):
TTTTGAGAGTTTGAAGTCAAAAATGGAAT
Found at i:37648528 original size:31 final size:31
Alignment explanation
Indices: 37648463--37648539 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
37648453 AGTCGAGGTC
*
37648463 AAAAATGGAATTTTTGAAAGTTTGGAGGCAA
1 AAAAATGGAATTTTTGAAAGTTTGGAGACAA
* * *
37648494 AAAAATGTAATTTTTTG-AAGTTTTGAGA-AC
1 AAAAATGGAA-TTTTTGAAAGTTTGGAGACAA
*
37648524 AAAAATAGAATTTTTG
1 AAAAATGGAATTTTTG
37648540 GACAGTTTAG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 6 0.15
30 9 0.23
31 18 0.46
32 6 0.15
ACGTcount: A:0.43, C:0.03, G:0.19, T:0.35
Consensus pattern (31 bp):
AAAAATGGAATTTTTGAAAGTTTGGAGACAA
Found at i:37661369 original size:61 final size:63
Alignment explanation
Indices: 37661235--37661374 Score: 212
Period size: 63 Copynumber: 2.3 Consensus size: 63
37661225 ACATACATTG
* *
37661235 TTTGCCTGCAATTCAATAAATTCAATCAAAGAAGAGGGAACTTTAGGACATATTTACCCAACA
1 TTTGCCTTCAATTCAATAAATTCAAGCAAAGAAGAGGGAACTTTAGGACATATTTACCCAACA
* * *
37661298 TTTGCCTTCAATTCCATAAATTCAAGCAAA-AAGAGGGAGCTTTAGGTCA-ATTTACCCAACA
1 TTTGCCTTCAATTCAATAAATTCAAGCAAAGAAGAGGGAACTTTAGGACATATTTACCCAACA
*
37661359 TTTGCTTTCAATTCAA
1 TTTGCCTTCAATTCAA
37661375 AACCCGACAT
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
61 26 0.37
62 17 0.24
63 27 0.39
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (63 bp):
TTTGCCTTCAATTCAATAAATTCAAGCAAAGAAGAGGGAACTTTAGGACATATTTACCCAACA
Found at i:37671626 original size:18 final size:18
Alignment explanation
Indices: 37671603--37671640 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
37671593 TGAAAAGCCT
37671603 AAAAA-TTATAATTATATA
1 AAAAATTTA-AATTATATA
*
37671621 AAAAATTTAAATTTTATA
1 AAAAATTTAAATTATATA
37671639 AA
1 AA
37671641 GTTCTAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AAAAATTTAAATTATATA
Found at i:37672449 original size:23 final size:23
Alignment explanation
Indices: 37672419--37672464 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
37672409 ATTGATTGGG
*
37672419 TCAAATTACGGTTTTGTTCTTAT
1 TCAAATTACGATTTTGTTCTTAT
* *
37672442 TCAAATTATGATTTTGTTGTTAT
1 TCAAATTACGATTTTGTTCTTAT
37672465 ACTACATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.09, G:0.13, T:0.54
Consensus pattern (23 bp):
TCAAATTACGATTTTGTTCTTAT
Found at i:37683510 original size:30 final size:32
Alignment explanation
Indices: 37683468--37683526 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
37683458 GGTTAAAACT
*
37683468 TTTTTAATAATTTTAG-ATTTTAAAAAAATAC
1 TTTTTAATAATTTTAGAAATTTAAAAAAATAC
*
37683499 TTTTT-ATAATTTTTGAAATTTAAAAAAA
1 TTTTTAATAATTTTAGAAATTTAAAAAAA
37683527 AATTAGTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 9 0.36
31 16 0.64
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (32 bp):
TTTTTAATAATTTTAGAAATTTAAAAAAATAC
Found at i:37685676 original size:108 final size:107
Alignment explanation
Indices: 37685481--37685768 Score: 423
Period size: 108 Copynumber: 2.7 Consensus size: 107
37685471 CAATTGAAAC
* * * * *
37685481 CCTTTTATCAGGGTTAATAGTATCAAATTATATCAAATCAAAATATAAAGATTAAGCATATACCG
1 CCTTTTATCAGGGTCAATAGTACCAAATTATATCAAATTAAAATATAGAGATTAAGCATATACCA
* * * *
37685546 TATATAGTCGACTGATTGCCAACAAATCAACAAATTAACAAA
66 TATATAGACGACTAAATCCCAACAAATCAACAAATTAACAAA
*
37685588 CCTTTTTATCAGGGTCAATAGTACCAAATTATATCAAATTAAAATATAGAGATTAAGTATATACC
1 CC-TTTTATCAGGGTCAATAGTACCAAATTATATCAAATTAAAATATAGAGATTAAGCATATACC
* * *
37685653 ATACATAGACGATTAAATCCCAACAAATCAACAAATTAGCAGAA
65 ATATATAGACGACTAAATCCCAACAAATCAACAAATTAACA-AA
* *
37685697 ACTTTTATCAGGGTCAATAGTACCAAATTATATCAAATTAAAATATAGAGATTAAGGATATACCA
1 CCTTTTATCAGGGTCAATAGTACCAAATTATATCAAATTAAAATATAGAGATTAAGCATATACCA
37685762 TATATAG
66 TATATAG
37685769 TTCATGCAAT
Statistics
Matches: 163, Mismatches: 16, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
107 2 0.01
108 158 0.97
109 3 0.02
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.29
Consensus pattern (107 bp):
CCTTTTATCAGGGTCAATAGTACCAAATTATATCAAATTAAAATATAGAGATTAAGCATATACCA
TATATAGACGACTAAATCCCAACAAATCAACAAATTAACAAA
Found at i:37709417 original size:24 final size:24
Alignment explanation
Indices: 37709384--37709456 Score: 85
Period size: 24 Copynumber: 3.1 Consensus size: 24
37709374 ATTTGAGAAA
* *
37709384 TAATT-TTTCAGTTAAACTCTGTT
1 TAATTGTTTCAATTAAACTCTATT
* *
37709407 TAATTGTTTCAATTAAATTTTATT
1 TAATTGTTTCAATTAAACTCTATT
* *
37709431 TATTTGTTTCAACTAAACTCTATT
1 TAATTGTTTCAATTAAACTCTATT
37709455 TA
1 TA
37709457 TTTATTTAAG
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 5 0.12
24 36 0.88
ACGTcount: A:0.30, C:0.11, G:0.05, T:0.53
Consensus pattern (24 bp):
TAATTGTTTCAATTAAACTCTATT
Found at i:37709473 original size:24 final size:24
Alignment explanation
Indices: 37709396--37709463 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
37709386 ATTTTTCAGT
* * * *
37709396 TAAACTCTGTTTAATTGTTTCAAT
1 TAAACTCTATTTATTTATTTCAAC
* * *
37709420 TAAATTTTATTTATTTGTTTCAAC
1 TAAACTCTATTTATTTATTTCAAC
37709444 TAAACTCTATTTATTTATTT
1 TAAACTCTATTTATTTATTT
37709464 AAGTCAAACT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.29, C:0.10, G:0.04, T:0.56
Consensus pattern (24 bp):
TAAACTCTATTTATTTATTTCAAC
Found at i:37711216 original size:24 final size:24
Alignment explanation
Indices: 37711183--37711257 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
37711173 AGAAATAATC
* *
37711183 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAATTAAACTCTGTTTATTTG
* *
37711207 TTTCAATTAAACTTTGTTTATTTA
1 TTTCAATTAAACTCTGTTTATTTG
* *
37711231 TTTTAATTAAACTCTATTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
37711255 TTT
1 TTT
37711258 GAGTCAAACT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.27, C:0.09, G:0.07, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:37712823 original size:26 final size:26
Alignment explanation
Indices: 37712793--37712842 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
37712783 CAATAAAAGA
* *
37712793 ATATTTAAGTGTCAAAATAAAAAAAT
1 ATATTTAAATATCAAAATAAAAAAAT
*
37712819 ATATTTAAATATTAAAATAAAAAA
1 ATATTTAAATATCAAAATAAAAAA
37712843 TAAATATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (26 bp):
ATATTTAAATATCAAAATAAAAAAAT
Found at i:37712840 original size:24 final size:23
Alignment explanation
Indices: 37712773--37712844 Score: 63
Period size: 26 Copynumber: 3.0 Consensus size: 23
37712763 ATTTTTTGGA
* *
37712773 TTAAAAATTACAATAAAAGAATAT
1 TTAAATATTAAAATAAAA-AATAT
* * *
37712797 TTAAGTGTCAAAATAAAAAAATATAT
1 TTAAATATTAAAAT--AAAAA-ATAT
37712823 TTAAATATTAAAATAAAAAATA
1 TTAAATATTAAAATAAAAAATA
37712845 AATATAATTT
Statistics
Matches: 37, Mismatches: 8, Indels: 7
0.71 0.15 0.13
Matches are distributed among these distances:
23 3 0.08
24 14 0.38
25 1 0.03
26 19 0.51
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.31
Consensus pattern (23 bp):
TTAAATATTAAAATAAAAAATAT
Found at i:37717230 original size:16 final size:16
Alignment explanation
Indices: 37717186--37717236 Score: 57
Period size: 18 Copynumber: 3.0 Consensus size: 16
37717176 TGGGACATGA
* *
37717186 ATTGATTAAATTCAAA
1 ATTGATTAAATTTAAT
37717202 ATCTGAGTTAAATTTAAT
1 AT-TGA-TTAAATTTAAT
37717220 ATTGATTAAATTATAAT
1 ATTGATTAAATT-TAAT
37717237 TGAGTTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
16 9 0.30
17 10 0.33
18 11 0.37
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (16 bp):
ATTGATTAAATTTAAT
Found at i:37717244 original size:16 final size:15
Alignment explanation
Indices: 37717185--37717248 Score: 58
Period size: 16 Copynumber: 3.9 Consensus size: 15
37717175 TTGGGACATG
*
37717185 AATTGATTAAATTCAA
1 AATTGATTAAATT-AT
37717201 AATCTGAGTTAAATT-T
1 AAT-TGA-TTAAATTAT
37717217 AATATTGATTAAATTAT
1 -A-ATTGATTAAATTAT
37717234 AATTGAGTTAAATTA
1 AATTGA-TTAAATTA
37717249 CATGTTTTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
15 5 0.12
16 19 0.46
17 8 0.20
18 9 0.22
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.42
Consensus pattern (15 bp):
AATTGATTAAATTAT
Found at i:37718202 original size:4 final size:4
Alignment explanation
Indices: 37718193--37718220 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
37718183 GAGAAAGGGC
37718193 TGAG TGAG TGAG TGAG TGAG TGAG TGAG
1 TGAG TGAG TGAG TGAG TGAG TGAG TGAG
37718221 GTGAAGAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.50, T:0.25
Consensus pattern (4 bp):
TGAG
Found at i:37728384 original size:26 final size:27
Alignment explanation
Indices: 37728352--37728447 Score: 158
Period size: 27 Copynumber: 3.6 Consensus size: 27
37728342 TAAATCTAAC
* *
37728352 TTAAAAAAATATAATATAAATATTTTT
1 TTAAAATAATATAATTTAAATATTTTT
*
37728379 TTAAAAGAATATAATTTAAATA-TTTT
1 TTAAAATAATATAATTTAAATATTTTT
37728405 TTAAAATAATATAATTTAAATATTTTT
1 TTAAAATAATATAATTTAAATATTTTT
37728432 TTAAAATAATATAATT
1 TTAAAATAATATAATT
37728448 AGACTTAAAA
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
26 25 0.38
27 40 0.62
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (27 bp):
TTAAAATAATATAATTTAAATATTTTT
Found at i:37735760 original size:197 final size:195
Alignment explanation
Indices: 37735239--37735819 Score: 862
Period size: 198 Copynumber: 3.0 Consensus size: 195
37735229 CCACTTCAAG
*
37735239 GTAAGTTTTAAAGAAAATTTAGGTCCCTTGGGCAATTGGAAATAAAAGAAAATGTTTATATCCTA
1 GTAAGTTTTAAAGAAAATTTAGGTCCCTTGGGCAATTGGAAATAAAAGAAAATGTTTATATCCTT
* * * *
37735304 AATTGCCAAGCATGACCAGACATGATATTGGCAACAAGGAAAAGAGGAGATCAAAAAGAAATTAA
66 AAGTGCCTAGCATGACCAGACATGATATTGGCAACAGGGAAAAGAGGAGATCAAAAAGATATTAA
* * *
37735369 CCACCTCGGCAAAGCTGCCCAGCCTTCAAATTCTATTCTACACCTTTCAAAGATACAACCACTTT
131 CCACCTCGGCAAAGTTGCCCAGCCTTCAAATTCTATTCTACACCTTACAAAG-T--GACCACTTT
37735434 ATA
193 ATA
* * *
37735437 GTAATTTTTAAATAAAATTTAGGTCCCTTAGGCAATTGGAAATAAAAGAAAATGTTTATATCCTT
1 GTAAGTTTTAAAGAAAATTTAGGTCCCTTGGGCAATTGGAAATAAAAGAAAATGTTTATATCCTT
37735502 AAGTGCCTAGCATGACCAGACAAT-ATATTGGCAACAGGGAAAAGAGGAGATCAAAAAGATATTA
66 AAGTGCCTAGCATGACCAGAC-ATGATATTGGCAACAGGGAAAAGAGGAGATCAAAAAGATATTA
37735566 ACCACCTCGGCAAAGTTGCCCAGCCTTCAAATTCTATTCTACACCTTACAAAGTGACCACTTTAT
130 ACCACCTCGGCAAAGTTGCCCAGCCTTCAAATTCTATTCTACACCTTACAAAGTGACCACTTTAT
37735631 A
195 A
* *
37735632 GTAA-TTTTAAAGAAAATTTAGGTCCCTTGGGCAATTAGAATAAAACAAGAAAATGTTTATATCC
1 GTAAGTTTTAAAGAAAATTTAGGTCCCTTGGGCAATTGGAA-ATAA-AAGAAAATGTTTATATCC
* * * *
37735696 TTAAGGAGCCTAGCAAGACCAGACATGATATTGGCAACAGGGAAAAGAGGAGATCGATAAGATA-
64 TTAA-GTGCCTAGCATGACCAGACATGATATTGGCAACAGGGAAAAGAGGAGATCAAAAAGATAT
* * * * * *
37735760 TAGACGACCTCGGCAAAGTTGCCCATCCTTCAAATTCCAGTCTACATCTTACAGAGTGAC
128 TA-ACCACCTCGGCAAAGTTGCCCAGCCTTCAAATTCTATTCTACACCTTACAAAGTGAC
37735820 AAACATTTAT
Statistics
Matches: 352, Mismatches: 25, Indels: 13
0.90 0.06 0.03
Matches are distributed among these distances:
194 33 0.09
195 18 0.05
196 26 0.07
197 104 0.30
198 169 0.48
199 2 0.01
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (195 bp):
GTAAGTTTTAAAGAAAATTTAGGTCCCTTGGGCAATTGGAAATAAAAGAAAATGTTTATATCCTT
AAGTGCCTAGCATGACCAGACATGATATTGGCAACAGGGAAAAGAGGAGATCAAAAAGATATTAA
CCACCTCGGCAAAGTTGCCCAGCCTTCAAATTCTATTCTACACCTTACAAAGTGACCACTTTATA
Found at i:37739967 original size:8 final size:8
Alignment explanation
Indices: 37739954--37739979 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
37739944 ACGACATTGA
37739954 AGCGAGAG
1 AGCGAGAG
37739962 AGCGAGAG
1 AGCGAGAG
37739970 AGCGAGAG
1 AGCGAGAG
37739978 AG
1 AG
37739980 AATTTTTACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.50, T:0.00
Consensus pattern (8 bp):
AGCGAGAG
Found at i:37742379 original size:1 final size:1
Alignment explanation
Indices: 37742373--37742401 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
37742363 TTTCAGACTC
37742373 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
37742402 ACCTTTAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:37742929 original size:37 final size:36
Alignment explanation
Indices: 37742858--37742930 Score: 85
Period size: 37 Copynumber: 2.0 Consensus size: 36
37742848 CGAACTATTA
* *
37742858 TTAATCGAATTAATCGATTTTTTTAAATATTTAACCG
1 TTAATCGAATTAATC-ATTTTTTTAAAAAATTAACCG
*
37742895 TTAATCGAATTAAAT-TTTTTTTTAAAAAAATTAACC
1 TTAATCGAATT-AATCATTTTTTT-AAAAAATTAACC
37742931 AAACCGAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
36 7 0.23
37 21 0.68
38 3 0.10
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (36 bp):
TTAATCGAATTAATCATTTTTTTAAAAAATTAACCG
Found at i:37743544 original size:16 final size:16
Alignment explanation
Indices: 37743525--37743555 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
37743515 CGTGCTGCTG
37743525 CCACCACCAGCTCCAT
1 CCACCACCAGCTCCAT
*
37743541 CCACCACCTGCTCCA
1 CCACCACCAGCTCCA
37743556 CCATGCCCTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.58, G:0.06, T:0.13
Consensus pattern (16 bp):
CCACCACCAGCTCCAT
Found at i:37745156 original size:30 final size:30
Alignment explanation
Indices: 37745118--37745294 Score: 196
Period size: 30 Copynumber: 5.9 Consensus size: 30
37745108 TAAATTGTCC
*
37745118 AAAAATTACATTTTGACCCCAAAACCTTCT
1 AAAAATTACATTTTGACCCCAAAACTTTCT
*
37745148 AGAAATTACATTTTGACCCCAAAACTTTCT
1 AAAAATTACATTTTGACCCCAAAACTTTCT
*
37745178 AAAAATTACATTTTGACCCTAAAACTTT-T
1 AAAAATTACATTTTGACCCCAAAACTTTCT
* * ** * *
37745207 CCAAAATTATATTTTGACCATAAAAGTTTCA
1 -AAAAATTACATTTTGACCCCAAAACTTTCT
* * *
37745238 AAAAATTGCATTTTTACCCCGAAACTTTC-
1 AAAAATTACATTTTGACCCCAAAACTTTCT
* *
37745267 AAAAATTACCATTTTTACCCCCAAACTT
1 AAAAATTA-CATTTTGACCCCAAAACTT
37745295 CCCTAAATCC
Statistics
Matches: 125, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
29 8 0.06
30 117 0.94
ACGTcount: A:0.39, C:0.23, G:0.05, T:0.34
Consensus pattern (30 bp):
AAAAATTACATTTTGACCCCAAAACTTTCT
Found at i:37745339 original size:30 final size:30
Alignment explanation
Indices: 37745304--37745400 Score: 78
Period size: 28 Copynumber: 3.3 Consensus size: 30
37745294 TCCCTAAATC
37745304 CCATTTTAAACCCTAATTTCACTAAAATTA
1 CCATTTTAAACCCTAATTTCACTAAAATTA
*
37745334 CCATTTT--ACCCTCAAACTTTC-CT-AAA-TC
1 CCATTTTAAACCCT--AA-TTTCACTAAAATTA
* ** *
37745362 CCATTTTTAACCCCGATTTCACCAAAATTTA
1 CCATTTTAAACCCTAATTTCACTAAAA-TTA
37745393 CCATTTTA
1 CCATTTTA
37745401 CCCTCGGGTA
Statistics
Matches: 52, Mismatches: 6, Indels: 17
0.69 0.08 0.23
Matches are distributed among these distances:
27 4 0.08
28 15 0.29
29 6 0.12
30 15 0.29
31 12 0.23
ACGTcount: A:0.33, C:0.29, G:0.01, T:0.37
Consensus pattern (30 bp):
CCATTTTAAACCCTAATTTCACTAAAATTA
Found at i:37745404 original size:59 final size:58
Alignment explanation
Indices: 37745268--37745405 Score: 204
Period size: 58 Copynumber: 2.3 Consensus size: 58
37745258 GAAACTTTCA
* * *
37745268 AAAATTACCATTTTTACCCCCAAACTTCCCTAAATCCCATTTTAAACCCTAATTTCACT
1 AAAATTACCA-TTTTACCCTCAAACTTCCCTAAATCCCATTTTAAACCCCAATTTCACC
* * *
37745327 AAAATTACCATTTTACCCTCAAACTTTCCTAAATCCCATTTTTAACCCCGATTTCACC
1 AAAATTACCATTTTACCCTCAAACTTCCCTAAATCCCATTTTAAACCCCAATTTCACC
37745385 AAAATTTACCATTTTACCCTC
1 AAAA-TTACCATTTTACCCTC
37745406 GGGTATCCTA
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
58 46 0.64
59 26 0.36
ACGTcount: A:0.33, C:0.32, G:0.01, T:0.35
Consensus pattern (58 bp):
AAAATTACCATTTTACCCTCAAACTTCCCTAAATCCCATTTTAAACCCCAATTTCACC
Found at i:37748956 original size:73 final size:73
Alignment explanation
Indices: 37748863--37749040 Score: 311
Period size: 73 Copynumber: 2.4 Consensus size: 73
37748853 GTCCGAAGCT
*
37748863 ATTTTAACTCAAGCCTGCCTACCACATAGCTACAGGCACGAGAAGGTCCAAGTCCTAAGCTAAAA
1 ATTTTAACGCAAGCCTGCCTACCACATAGCTACAGGCACGAGAAGGTCCAAGTCCTAAGCTAAAA
*
37748928 TCTATGAG
66 TCCATGAG
*
37748936 ATTTTAACGCAAGCCTGCCTACCACATAGCTACAGGCACGAGAAGGTCCAAGTCCTAAGCTAAAC
1 ATTTTAACGCAAGCCTGCCTACCACATAGCTACAGGCACGAGAAGGTCCAAGTCCTAAGCTAAAA
37749001 TCCATGAG
66 TCCATGAG
**
37749009 ATTTTAACGCAAGCCTGCCTACTGCATAGCTA
1 ATTTTAACGCAAGCCTGCCTACCACATAGCTA
37749041 TATGCATAGG
Statistics
Matches: 100, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 100 1.00
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.22
Consensus pattern (73 bp):
ATTTTAACGCAAGCCTGCCTACCACATAGCTACAGGCACGAGAAGGTCCAAGTCCTAAGCTAAAA
TCCATGAG
Found at i:37752226 original size:18 final size:18
Alignment explanation
Indices: 37752205--37752242 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
37752195 GTTATTATTA
37752205 TTTA-TATATTGTATAATT
1 TTTATTATATTGT-TAATT
*
37752223 TTTATTTTATTGTTAATT
1 TTTATTATATTGTTAATT
37752241 TT
1 TT
37752243 GTTAATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.68
Consensus pattern (18 bp):
TTTATTATATTGTTAATT
Found at i:37759715 original size:15 final size:15
Alignment explanation
Indices: 37759695--37759724 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
37759685 ACTTTTATTG
*
37759695 AAAAAATAAATCAAT
1 AAAAAACAAATCAAT
37759710 AAAAAACAAATCAAT
1 AAAAAACAAATCAAT
37759725 TAACATAACT
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:0.73, C:0.10, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAAAACAAATCAAT
Found at i:37782056 original size:18 final size:18
Alignment explanation
Indices: 37782033--37782068 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
37782023 AAACGGAGAA
37782033 AAAATCATCTTCCGCATG
1 AAAATCATCTTCCGCATG
37782051 AAAATCATCTTCCGCATG
1 AAAATCATCTTCCGCATG
37782069 CTACCTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.28, G:0.11, T:0.28
Consensus pattern (18 bp):
AAAATCATCTTCCGCATG
Found at i:37782618 original size:31 final size:30
Alignment explanation
Indices: 37782550--37782631 Score: 87
Period size: 31 Copynumber: 2.7 Consensus size: 30
37782540 TTTTAATAAC
* * *
37782550 ATATATCTTTA-TAATTTTAAATAATTAAA
1 ATATATTTTTATTATTTTTAAAAAATTAAA
* *
37782579 TTAAATTTTTATTATTTTTAAAGAAATTAAA
1 ATATATTTTTATTATTTTTAAA-AAATTAAA
37782610 ATATATTTTTATT-TTTATTAAA
1 ATATATTTTTATTATTT-TTAAA
37782632 TTTAAAATTT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
29 8 0.19
30 12 0.28
31 23 0.53
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (30 bp):
ATATATTTTTATTATTTTTAAAAAATTAAA
Found at i:37791483 original size:26 final size:26
Alignment explanation
Indices: 37791447--37791498 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
37791437 AAAGAAAAGA
37791447 AAGTTCCTCGTCTTCCCTACTTGTGG
1 AAGTTCCTCGTCTTCCCTACTTGTGG
37791473 AAGTTCCTCGTCTTCCCTACTTGTGG
1 AAGTTCCTCGTCTTCCCTACTTGTGG
37791499 TGGTGGTCGT
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:0.12, C:0.31, G:0.19, T:0.38
Consensus pattern (26 bp):
AAGTTCCTCGTCTTCCCTACTTGTGG
Found at i:37792520 original size:16 final size:16
Alignment explanation
Indices: 37792499--37792529 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
37792489 AGCTAATCCT
37792499 ATACATATATATATAC
1 ATACATATATATATAC
37792515 ATACATATATATATA
1 ATACATATATATATA
37792530 TATCTTCCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.39
Consensus pattern (16 bp):
ATACATATATATATAC
Found at i:37795863 original size:27 final size:27
Alignment explanation
Indices: 37795812--37795863 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
37795802 ATTGTCTCTT
* *
37795812 GATATTTTACCTTCTGCAAGGTTGGGA
1 GATATTTTACATTCTGCAAGATTGGGA
* *
37795839 GATATTTTACATTTTGTAAGATTGG
1 GATATTTTACATTCTGCAAGATTGG
37795864 AGGTAAAAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.25, C:0.10, G:0.23, T:0.42
Consensus pattern (27 bp):
GATATTTTACATTCTGCAAGATTGGGA
Found at i:37813692 original size:21 final size:22
Alignment explanation
Indices: 37813668--37813708 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
37813658 AAAGATTGTA
37813668 AAATAATTA-TTAAATTATTTG
1 AAATAATTATTTAAATTATTTG
**
37813689 AAATTTTTATTTAAATTATT
1 AAATAATTATTTAAATTATT
37813709 AAATTATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (22 bp):
AAATAATTATTTAAATTATTTG
Found at i:37815488 original size:287 final size:288
Alignment explanation
Indices: 37814937--37815827 Score: 1407
Period size: 287 Copynumber: 3.1 Consensus size: 288
37814927 ACTTTCGAAA
* * *
37814937 CAAATGAATACGGA-AACGTAGCATCAAACTAC-AGTTATACTTACCATATACCATAATCGAAAA
1 CAAAAGAATAC-GACAACATAGCATCAAACTACAAGCTATACTTACCATATACCATAATCGAAAA
* * * *
37815000 GATGCCGTCCTAATCATCATCAAACTATGTTGAAAATAGGAAATTATGAATGTTTATACGATACC
65 GGTGCCGTCCAAATCATCATCAAACTATGTTGAAAATAGGAAATCACGAATGTTTATACGATACC
*
37815065 AAAAGAACAGGAAAGTCGTGCTCTTAAACCACTTGAAAGCATAATCAATGACTTCACATTTTTAA
130 AAAAGAACAGGAAAGTCGTGTTCTTAAACCACTTGAAAGCATAATCAATGACTTCACATTTTTAA
* *
37815130 GTT-AAAAAATGTAGTAATATCACTTCCGAAGCACGTCATTATATTGGCTTTCCACTACCAATCA
195 GTTCAAAAAATGTAGTAATATCACTTCCGAAGCACGTAATTATATTGGCTTTTCACTACCAATCA
37815194 CTACTTCCGAACAACTTCAAAGTTAAAAG
260 CTACTTCCGAACAACTTCAAAGTTAAAAG
* *
37815223 CAAAAGAATACGACAACATAGCATCAAACCACAAGCTATACTTACCAGATACCATAATCGAAAAG
1 CAAAAGAATACGACAACATAGCATCAAACTACAAGCTATACTTACCATATACCATAATCGAAAAG
37815288 GTGCCGTCCAAATCATCATCAAACTATGTTGAAAATAGGAAATCACGAATGTTTATACGATACCA
66 GTGCCGTCCAAATCATCATCAAACTATGTTGAAAATAGGAAATCACGAATGTTTATACGATACCA
*
37815353 TAAGAACAGGAAAGTCGTGTTCTTAAACCACTTGAAAGCATAATCAATGACTTCACATTTTTAAG
131 AAAGAACAGGAAAGTCGTGTTCTTAAACCACTTGAAAGCATAATCAATGACTTCACATTTTTAAG
*
37815418 TTCAAAAAAT-TAGTAATATCACTTCCGAAGCACGTAATTATATTGGTTTTTCACTACCAATCAC
196 TTCAAAAAATGTAGTAATATCACTTCCGAAGCACGTAATTATATTGGCTTTTCACTACCAATCAC
37815482 TACTTCCGAACAACTTCAAAGTTAAAAG
261 TACTTCCGAACAACTTCAAAGTTAAAAG
*
37815510 CAAAAGAATAGGACAACATAGCATCAAACTACAAGCTATACTTACCATATACCATAATCGAAAAG
1 CAAAAGAATACGACAACATAGCATCAAACTACAAGCTATACTTACCATATACCATAATCGAAAAG
* * * *
37815575 GTGCCGTCCAAATTATCATCAAACTATGTTGAAAATAGGAAATCACAAATGCTGATACGATACCA
66 GTGCCGTCCAAATCATCATCAAACTATGTTGAAAATAGGAAATCACGAATGTTTATACGATACCA
* * * *
37815640 AAAGAACAGGAAAGTCGTGTCCTTCAACCACTTGAAAGCACAATCAATGACTTCAGATTTTTAAG
131 AAAGAACAGGAAAGTCGTGTTCTTAAACCACTTGAAAGCATAATCAATGACTTCACATTTTTAAG
* * * **
37815705 TTC-AAAAATGTACTAATATCACTTCCGAAGCACGTTATCATATCCGCTTTTCACTACCAA-CGA
196 TTCAAAAAATGTAGTAATATCACTTCCGAAGCACGTAATTATATTGGCTTTTCACTACCAATC-A
* * *
37815768 CTACTTCCAAACAACTTCAAAGATAAAAA
260 CTACTTCCGAACAACTTCAAAGTTAAAAG
* * *
37815797 CAAAAGAATAGGACAAATATAGCATAAAACT
1 CAAAAGAATACGAC-AACATAGCATCAAACT
37815828 GCAACTAATA
Statistics
Matches: 562, Mismatches: 37, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
285 2 0.00
286 33 0.06
287 506 0.90
288 21 0.04
ACGTcount: A:0.41, C:0.21, G:0.13, T:0.25
Consensus pattern (288 bp):
CAAAAGAATACGACAACATAGCATCAAACTACAAGCTATACTTACCATATACCATAATCGAAAAG
GTGCCGTCCAAATCATCATCAAACTATGTTGAAAATAGGAAATCACGAATGTTTATACGATACCA
AAAGAACAGGAAAGTCGTGTTCTTAAACCACTTGAAAGCATAATCAATGACTTCACATTTTTAAG
TTCAAAAAATGTAGTAATATCACTTCCGAAGCACGTAATTATATTGGCTTTTCACTACCAATCAC
TACTTCCGAACAACTTCAAAGTTAAAAG
Found at i:37821495 original size:31 final size:31
Alignment explanation
Indices: 37821457--37821521 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
37821447 AGCATTGCTT
37821457 TAATGATTAAAGTAGCCCGCCCCTCTCTTAG
1 TAATGATTAAAGTAGCCCGCCCCTCTCTTAG
37821488 TAATGATTAAAGTAGCCCGCCCCTCTCTTAG
1 TAATGATTAAAGTAGCCCGCCCCTCTCTTAG
37821519 TAA
1 TAA
37821522 GTTAATAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (31 bp):
TAATGATTAAAGTAGCCCGCCCCTCTCTTAG
Found at i:37826096 original size:14 final size:14
Alignment explanation
Indices: 37826077--37826106 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
37826067 TTGACATCTT
37826077 TTTAAAAATTTTAA
1 TTTAAAAATTTTAA
37826091 TTTAAAAATTTTAA
1 TTTAAAAATTTTAA
37826105 TT
1 TT
37826107 ATATAAACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTTAAAAATTTTAA
Found at i:37826920 original size:15 final size:15
Alignment explanation
Indices: 37826900--37826929 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
37826890 ATTTTTATTT
37826900 CCACCCCACCCCATC
1 CCACCCCACCCCATC
37826915 CCACCCCACCCCATC
1 CCACCCCACCCCATC
37826930 TATCTCAAAT
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:0.20, C:0.73, G:0.00, T:0.07
Consensus pattern (15 bp):
CCACCCCACCCCATC
Found at i:37830443 original size:37 final size:38
Alignment explanation
Indices: 37830374--37830458 Score: 95
Period size: 37 Copynumber: 2.2 Consensus size: 38
37830364 TTAAGTAAAT
*
37830374 AAATAATAAAATTTTAATTTAATCCTTCTAAAAACTATA-A
1 AAATAATAAAATTTTAATTTAA--CTTATAAAAA-TATATA
37830414 AAATAATAAAA-TTTAATTTTAA-TTATAAAAATATATA
1 AAATAATAAAATTTTAA-TTTAACTTATAAAAATATATA
*
37830451 AAACAATA
1 AAATAATA
37830459 TCTACCACCC
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
36 4 0.10
37 16 0.39
39 5 0.12
40 16 0.39
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (38 bp):
AAATAATAAAATTTTAATTTAACTTATAAAAATATATA
Found at i:37832809 original size:22 final size:23
Alignment explanation
Indices: 37832784--37832834 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
37832774 TAAAATTTTG
*
37832784 ATTTAATAATT-TAAAAATTAAA
1 ATTTAATAATTGCAAAAATTAAA
* * *
37832806 ATTTTATTATTGCAAAAATTATA
1 ATTTAATAATTGCAAAAATTAAA
37832829 ATTTAA
1 ATTTAA
37832835 CTTCGGCCCT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTTAATAATTGCAAAAATTAAA
Found at i:37848358 original size:17 final size:17
Alignment explanation
Indices: 37848336--37848447 Score: 117
Period size: 17 Copynumber: 6.8 Consensus size: 17
37848326 AAACTTTGAT
* *
37848336 TTTTAAGTTTAAATTAA
1 TTTTAAATTTAAATTTA
37848353 TTTTAAATTTTAAATTT-
1 TTTTAAA-TTTAAATTTA
*
37848370 TATTTAGATTTAAATTTA
1 T-TTTAAATTTAAATTTA
*
37848388 TCTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
37848405 -TTT--ATTTAAATTTA
1 TTTTAAATTTAAATTTA
*
37848419 CTTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
*
37848436 -ATTAAATTTAAA
1 TTTTAAATTTAAA
37848448 AATAATATTA
Statistics
Matches: 82, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
14 11 0.13
15 3 0.04
16 13 0.16
17 41 0.50
18 14 0.17
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:37848386 original size:6 final size:6
Alignment explanation
Indices: 37848337--37848447 Score: 83
Period size: 6 Copynumber: 19.0 Consensus size: 6
37848327 AACTTTGATT
* * * *
37848337 TTTAAG TTTAAA -TTAAT TTTAAA TTTTAAA TTT-TA TTTAGA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA
* *
37848384 TTT--A TCTTAAA TTTAAA TTTATTTA TTTAAA TTT-AC TTTAAA TTTAAA
1 TTTAAA T-TTAAA TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA TTTAAA
37848432 TTT-AA -TTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA
37848448 AATAATATTA
Statistics
Matches: 84, Mismatches: 10, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
4 4 0.05
5 18 0.21
6 49 0.58
7 8 0.10
8 5 0.06
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:37848438 original size:11 final size:11
Alignment explanation
Indices: 37848337--37848447 Score: 74
Period size: 11 Copynumber: 10.0 Consensus size: 11
37848327 AACTTTGATT
37848337 TTTAAGTTTAAA
1 TTTAA-TTTAAA
37848349 -TTAATTTTAAA
1 TTTAA-TTTAAA
*
37848360 TTTTAAATTT-TA
1 -TTT-AATTTAAA
37848372 TTTAGATTTAAA
1 TTTA-ATTTAAA
37848384 TTT-ATCTTAAA
1 TTTAAT-TTAAA
37848395 TTTAAATTT--A
1 TTT-AATTTAAA
37848405 TTT-ATTTAAA
1 TTTAATTTAAA
*
37848415 TTTACTTTAAA
1 TTTAATTTAAA
37848426 TTTAAATTT-AA
1 TTT-AATTTAAA
*
37848437 TTAAATTTAAA
1 TTTAATTTAAA
37848448 AATAATATTA
Statistics
Matches: 80, Mismatches: 6, Indels: 27
0.71 0.05 0.24
Matches are distributed among these distances:
8 4 0.05
10 16 0.20
11 40 0.50
12 11 0.14
13 7 0.09
14 2 0.03
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:37850458 original size:30 final size:29
Alignment explanation
Indices: 37850422--37850726 Score: 224
Period size: 30 Copynumber: 10.2 Consensus size: 29
37850412 CTTTGTAAGT
37850422 CCCTAAATTATTCAAAAATTACATTTTGAC
1 CCCTAAATT-TTCAAAAATTACATTTTGAC
*
37850452 CCCTAAACTTTCTAAAAATTACATTTTGAC
1 CCCTAAATTTTC-AAAAATTACATTTTGAC
* * *
37850482 CCCAAAACTTTTCCAAAATTATATTTTGA-
1 CCCTAAA-TTTTCAAAAATTACATTTTGAC
* * *
37850511 CCCTAAAACTTTTCCAAAATTATATTTAGA-
1 CCCT-AAA-TTTTCAAAAATTACATTTTGAC
* * *
37850541 CCTTAAAACTTTCTAGAAATTACATTTTGAC
1 CCCT-AAATTTTC-AAAAATTACATTTTGAC
* * *
37850572 CCCCAAATTTTTCCAAAGTTACATTTTGAC
1 CCCTAAA-TTTTCAAAAATTACATTTTGAC
* * *
37850602 CCCAAAACTTTTCCAAAATTACATTTTAAC
1 CCCTAAA-TTTTCAAAAATTACATTTTGAC
* * * *
37850632 CCCAAAACTTTTCCAAAATCATATTTTGAC
1 CCCTAAA-TTTTCAAAAATTACATTTTGAC
* * * *
37850662 CCC-AAATTTCCAAAAAAATGCATTTTTA-
1 CCCTAAATTTTC-AAAAATTACATTTTGAC
*
37850690 CCCTAAAACTTTCAAAAATTACCATTTT-AC
1 CCCT-AAATTTTCAAAAATTA-CATTTTGAC
*
37850720 CTCTAAA
1 CCCTAAA
37850727 CTTCCCTAAA
Statistics
Matches: 226, Mismatches: 38, Indels: 23
0.79 0.13 0.08
Matches are distributed among these distances:
28 7 0.03
29 33 0.15
30 176 0.78
31 10 0.04
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.35
Consensus pattern (29 bp):
CCCTAAATTTTCAAAAATTACATTTTGAC
Found at i:37850530 original size:60 final size:59
Alignment explanation
Indices: 37850436--37850717 Score: 286
Period size: 60 Copynumber: 4.7 Consensus size: 59
37850426 AAATTATTCA
*
37850436 AAAATTACATTTTGACCCCT-AAAC-TTTCTAAAAATTACATTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTGA-CCCTAAAACTTTTC-CAAAATTACATTTTGACCCCAAAAC-TTTCC
* * * ** *
37850496 AAAATTATATTTTGACCCTAAAACTTTTCCAAAATTATATTTAGACCTTAAAACTTTCT
1 AAAATTACATTTTGACCCTAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTCC
** * *
37850555 AGAAATTACATTTTGACCCCCAAATTTTTCCAAAGTTACATTTTGACCCCAAAACTTTTCC
1 A-AAATTACATTTTGACCCTAAAACTTTTCCAAAATTACATTTTGACCCCAAAAC-TTTCC
* * * *
37850616 AAAATTACATTTTAACCCCAAAACTTTTCCAAAATCATATTTTGACCCC-AAA-TTTCC
1 AAAATTACATTTTGACCCTAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTCC
* * * *
37850673 AAAAAAATGCATTTTTACCCTAAAAC-TTTCAAAAATTACCATTTT
1 --AAAATTACATTTTGACCCTAAAACTTTTCCAAAATTA-CATTTT
37850718 ACCTCTAAAC
Statistics
Matches: 185, Mismatches: 30, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
57 5 0.03
58 10 0.05
59 37 0.20
60 124 0.67
61 9 0.05
ACGTcount: A:0.38, C:0.23, G:0.04, T:0.36
Consensus pattern (59 bp):
AAAATTACATTTTGACCCTAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTCC
Found at i:37850588 original size:90 final size:88
Alignment explanation
Indices: 37850436--37850718 Score: 313
Period size: 90 Copynumber: 3.2 Consensus size: 88
37850426 AAATTATTCA
* * *
37850436 AAAATTACATTTTGACCCCTAAACTTTCTAAAAATTACATTTTGACCCCAAAACTTTTCCAAAAT
1 AAAATTACATTTTAACCCCAAAACTTTCT-AAAATTACATTTTGACCCCCAAA-TTTTCCAAAAT
37850501 TATATTTTGACCCTAAAACTTTTCC
64 TATATTTTGACCCTAAAACTTTTCC
* ** *
37850526 AAAATTATA-TTTAGACCTTAAAACTTTCTAGAAATTACATTTTGACCCCCAAATTTTTCCAAAG
1 AAAATTACATTTTA-ACCCCAAAACTTTCTA-AAATTACATTTTGACCCCCAAA-TTTTCCAAAA
* *
37850590 TTACATTTTGACCCCAAAACTTTTCC
63 TTATATTTTGACCCTAAAACTTTTCC
* * * **
37850616 AAAATTACATTTTAACCCCAAAACTTTTCCAAAATCATATTTTGA-CCCCAAA-TTTCCAAAAAA
1 AAAATTACATTTTAACCCCAAAAC-TTTCTAAAATTACATTTTGACCCCCAAATTTTCCAAAATT
* *
37850679 ATGCATTTTTACCCTAAAAC-TTTCA
65 AT--ATTTTGACCCTAAAACTTTTCC
37850704 AAAATTACCATTTTA
1 AAAATTA-CATTTTA
37850719 CCTCTAAACT
Statistics
Matches: 163, Mismatches: 23, Indels: 15
0.81 0.11 0.07
Matches are distributed among these distances:
87 9 0.06
88 11 0.07
89 32 0.20
90 102 0.63
91 9 0.06
ACGTcount: A:0.38, C:0.23, G:0.04, T:0.36
Consensus pattern (88 bp):
AAAATTACATTTTAACCCCAAAACTTTCTAAAATTACATTTTGACCCCCAAATTTTCCAAAATTA
TATTTTGACCCTAAAACTTTTCC
Found at i:37850766 original size:58 final size:56
Alignment explanation
Indices: 37850704--37850892 Score: 261
Period size: 58 Copynumber: 3.2 Consensus size: 56
37850694 AAAACTTTCA
*
37850704 AAAATTACCATTTTACCTCTAAACTTCCCTAAATCCCATTTAAAACCTCGATTTCACT
1 AAAATTACCATTTTACC-CTAAACTTCCCTAAATCCCATTTTAAACC-CGATTTCACT
* *
37850762 AAAATTACCATTTTACCCCCAAACTTCCCTAAATCCTATTTTAAACCCCGATTTCACT
1 AAAATTACCATTTTA-CCCTAAACTTCCCTAAATCCCATTTTAAA-CCCGATTTCACT
* * *
37850820 AAAATTACCATTTTACCCTCAAACTTCCCTAAATCTCATTTTTAACCCTGATTTCACC
1 AAAATTACCATTTTACCCT-AAACTTCCCTAAATCCCATTTTAAACCC-GATTTCACT
37850878 AAAATCTACCATTTT
1 AAAAT-TACCATTTT
37850893 GCCCCCGGGT
Statistics
Matches: 118, Mismatches: 8, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
57 6 0.05
58 99 0.84
59 13 0.11
ACGTcount: A:0.33, C:0.30, G:0.02, T:0.35
Consensus pattern (56 bp):
AAAATTACCATTTTACCCTAAACTTCCCTAAATCCCATTTTAAACCCGATTTCACT
Found at i:37850794 original size:30 final size:30
Alignment explanation
Indices: 37850704--37850852 Score: 96
Period size: 30 Copynumber: 5.1 Consensus size: 30
37850694 AAAACTTTCA
* *
37850704 AAAATTACCATTTTACCTCTAAACTTCCCT
1 AAAATTACCATTTTACCCCCAAACTTCCCT
* * * * * * *
37850734 -AAA-TCCCATTTAAAACCTC-GATTTCACT
1 AAAATTACCATTT-TACCCCCAAACTTCCCT
37850762 AAAATTACCATTTTACCCCCAAACTTCCCT
1 AAAATTACCATTTTACCCCCAAACTTCCCT
* * * *
37850792 -AAA-T-CCTATTTTAAACCCC-GATTTCACT
1 AAAATTACC-ATTTT-ACCCCCAAACTTCCCT
*
37850820 AAAATTACCATTTTACCCTCAAACTTCCCT
1 AAAATTACCATTTTACCCCCAAACTTCCCT
37850850 AAA
1 AAA
37850853 TCTCATTTTT
Statistics
Matches: 84, Mismatches: 25, Indels: 20
0.65 0.19 0.16
Matches are distributed among these distances:
27 2 0.02
28 25 0.30
29 27 0.32
30 28 0.33
31 2 0.02
ACGTcount: A:0.35, C:0.31, G:0.01, T:0.33
Consensus pattern (30 bp):
AAAATTACCATTTTACCCCCAAACTTCCCT
Found at i:37850804 original size:28 final size:27
Alignment explanation
Indices: 37850769--37850861 Score: 80
Period size: 28 Copynumber: 3.3 Consensus size: 27
37850759 ACTAAAATTA
37850769 CCATTTTACCCCCAAACTTCCCTAAAT
1 CCATTTTACCCCCAAACTTCCCTAAAT
* * * *
37850796 CCTATTTTAAACCCC-GATTTCACTAAAATT
1 CC-ATTTT-ACCCCCAAACTTCCCT-AAA-T
*
37850826 ACCATTTTACCCTCAAACTTCCCTAAAT
1 -CCATTTTACCCCCAAACTTCCCTAAAT
37850854 CTCATTTT
1 C-CATTTT
37850862 TAACCCTGAT
Statistics
Matches: 50, Mismatches: 9, Indels: 13
0.69 0.12 0.18
Matches are distributed among these distances:
27 3 0.06
28 18 0.36
29 15 0.30
30 12 0.24
31 2 0.04
ACGTcount: A:0.30, C:0.33, G:0.01, T:0.35
Consensus pattern (27 bp):
CCATTTTACCCCCAAACTTCCCTAAAT
Found at i:37860531 original size:19 final size:20
Alignment explanation
Indices: 37860494--37860532 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
37860484 TTCAACAATC
*
37860494 AAAATTTTTTATGTTGATTTT
1 AAAATTTTTTA-GTCGATTTT
37860515 AAAATTTTTTA-TCGATTT
1 AAAATTTTTTAGTCGATTT
37860533 CAAACAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
21 11 0.65
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.59
Consensus pattern (20 bp):
AAAATTTTTTAGTCGATTTT
Found at i:37863267 original size:8 final size:8
Alignment explanation
Indices: 37863254--37863313 Score: 75
Period size: 8 Copynumber: 7.4 Consensus size: 8
37863244 TGATTGCGTA
37863254 TGTATGTG
1 TGTATGTG
37863262 TGTATGTG
1 TGTATGTG
37863270 TGTATGTG
1 TGTATGTG
*
37863278 TGTATGTA
1 TGTATGTG
**
37863286 TGTGCGTG
1 TGTATGTG
*
37863294 TGTATATG
1 TGTATGTG
37863302 TGTTATGTG
1 TG-TATGTG
37863311 TGT
1 TGT
37863314 GAGAGGAGGT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
8 36 0.84
9 7 0.16
ACGTcount: A:0.13, C:0.02, G:0.35, T:0.50
Consensus pattern (8 bp):
TGTATGTG
Found at i:37870326 original size:2 final size:2
Alignment explanation
Indices: 37870321--37870363 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
37870311 AAAAATACAA
* *
37870321 AG AG AG AG GG A- AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
37870362 AG
1 AG
37870364 TAATGAAGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:37886537 original size:16 final size:16
Alignment explanation
Indices: 37886516--37886550 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
37886506 CAGTTGAACC
37886516 AATTTTATTTAATTTT
1 AATTTTATTTAATTTT
* *
37886532 AATTTTTTTTATTTTT
1 AATTTTATTTAATTTT
37886548 AAT
1 AAT
37886551 AATTTATTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
AATTTTATTTAATTTT
Found at i:37893371 original size:19 final size:19
Alignment explanation
Indices: 37893331--37893372 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
37893321 TTAATTATTG
* *
37893331 AAAATTTAAAAATTCGAGC
1 AAAATTTAAAAATACGACC
37893350 AAAATTT-AAAATACGATCC
1 AAAATTTAAAAATACGA-CC
37893369 AAAA
1 AAAA
37893373 ATACACGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.57, C:0.12, G:0.07, T:0.24
Consensus pattern (19 bp):
AAAATTTAAAAATACGACC
Found at i:37904825 original size:17 final size:19
Alignment explanation
Indices: 37904798--37904832 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
37904788 TAAAACGTTT
37904798 ATTGTTAATATAT-TTATA
1 ATTGTTAATATATATTATA
37904816 ATTG-TAATATATATTAT
1 ATTGTTAATATATATTAT
37904833 TAAAATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (19 bp):
ATTGTTAATATATATTATA
Found at i:37904899 original size:36 final size:34
Alignment explanation
Indices: 37904813--37904901 Score: 83
Period size: 36 Copynumber: 2.5 Consensus size: 34
37904803 TAATATATTT
* *
37904813 ATAATTGTAATAT-ATATTATTAAAATATTAATATA
1 ATAATT-TATTATAATA-TATTAAAATATAAATATA
*
37904848 AGTAATTT-TCAATAATATATTAAAATTATAAATTATA
1 A-TAATTTAT-TATAATATATTAAAA-TATAAA-TATA
37904885 ATAATTTATTATAATAT
1 ATAATTTATTATAATAT
37904902 TAAATAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
35 12 0.27
36 26 0.59
37 6 0.14
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (34 bp):
ATAATTTATTATAATATATTAAAATATAAATATA
Found at i:37907258 original size:10 final size:10
Alignment explanation
Indices: 37907232--37907263 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
37907222 GCCCCAAACC
37907232 TTTTCTTTC-
1 TTTTCTTTCT
37907241 TTTT-TTTCT
1 TTTTCTTTCT
37907250 TTTTCTTTCT
1 TTTTCTTTCT
37907260 TTTT
1 TTTT
37907264 TCCTTGTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 4 0.19
9 8 0.38
10 9 0.43
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTCTTTCT
Found at i:37907273 original size:17 final size:18
Alignment explanation
Indices: 37907230--37907273 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
37907220 GTGCCCCAAA
37907230 CCTTTTCTTTCTTTTTTT
1 CCTTTTCTTTCTTTTTTT
*
37907248 CTTTTTCTTTC-TTTTTT
1 CCTTTTCTTTCTTTTTTT
*
37907265 CCTTGTCTT
1 CCTTTTCTT
37907274 ACATATCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.00, C:0.23, G:0.02, T:0.75
Consensus pattern (18 bp):
CCTTTTCTTTCTTTTTTT
Found at i:37907759 original size:21 final size:22
Alignment explanation
Indices: 37907726--37907819 Score: 111
Period size: 21 Copynumber: 4.1 Consensus size: 22
37907716 TCTTTAAAAA
37907726 CCAAATTCTATTTAAACCAAAC
1 CCAAATTCTATTTAAACCAAAC
37907748 CCAAATTC-ATTTAAACCTCCATTAAGC
1 CCAAATTCTATTTAAA---CCA--AA-C
*
37907775 CCAAATCCTATTTAAACCAAAC
1 CCAAATTCTATTTAAACCAAAC
37907797 CCAAATTC-ATTTAAACCAAAC
1 CCAAATTCTATTTAAACCAAAC
37907818 CC
1 CC
37907820 TTTTGAACCA
Statistics
Matches: 63, Mismatches: 2, Indels: 15
0.79 0.03 0.19
Matches are distributed among these distances:
21 22 0.35
22 16 0.25
23 2 0.03
24 3 0.05
25 3 0.05
26 2 0.03
27 8 0.13
28 7 0.11
ACGTcount: A:0.43, C:0.31, G:0.01, T:0.26
Consensus pattern (22 bp):
CCAAATTCTATTTAAACCAAAC
Found at i:37907922 original size:13 final size:13
Alignment explanation
Indices: 37907918--37907965 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
37907908 ACCGTTGACT
*
37907918 TTGACTGTTGATCG
1 TTGACT-TTGACCG
*
37907932 ATGACTTTGACCG
1 TTGACTTTGACCG
37907945 TTGACTTTGACCG
1 TTGACTTTGACCG
*
37907958 TTGCCTTT
1 TTGACTTT
37907966 TTTTCAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
13 25 0.83
14 5 0.17
ACGTcount: A:0.15, C:0.21, G:0.23, T:0.42
Consensus pattern (13 bp):
TTGACTTTGACCG
Found at i:37909025 original size:3 final size:3
Alignment explanation
Indices: 37909013--37909045 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
37909003 TATTCTATTC
*
37909013 TAT T-T TAT TAT TAT TAT TAT TAT CAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
37909046 TTGGGATGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:37921422 original size:2 final size:2
Alignment explanation
Indices: 37921415--37921441 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
37921405 TTTAATTTTC
37921415 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
37921442 GTGCGTGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:37922647 original size:19 final size:19
Alignment explanation
Indices: 37922625--37922667 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
37922615 AATAATTAAA
* *
37922625 TAATTATTTTATAAAATTT
1 TAATTATTTAATAAAATTG
* *
37922644 TAATAATTTAATAACATTG
1 TAATTATTTAATAAAATTG
37922663 TAATT
1 TAATT
37922668 TACTCATAAA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (19 bp):
TAATTATTTAATAAAATTG
Found at i:37927845 original size:22 final size:21
Alignment explanation
Indices: 37927801--37927847 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
37927791 CGATCTAAGG
*
37927801 AAAAATAAAAGAAACAGATTT
1 AAAAATAAAAGAAACAGAATT
* *
37927822 AAAAATTAAAGAAAATAGAATT
1 AAAAATAAAAG-AAACAGAATT
37927844 AAAA
1 AAAA
37927848 GAAATAGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.70, C:0.02, G:0.09, T:0.19
Consensus pattern (21 bp):
AAAAATAAAAGAAACAGAATT
Found at i:37929186 original size:14 final size:14
Alignment explanation
Indices: 37929167--37929194 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
37929157 ATTTTAATAG
37929167 TCATTGAATCATTA
1 TCATTGAATCATTA
37929181 TCATTGAATCATTA
1 TCATTGAATCATTA
37929195 AAATTGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (14 bp):
TCATTGAATCATTA
Found at i:37929997 original size:2 final size:2
Alignment explanation
Indices: 37929992--37930052 Score: 104
Period size: 2 Copynumber: 30.5 Consensus size: 2
37929982 CATATATACA
37929992 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* *
37930034 TG CG TG TG TG TG CG TG TG T
1 TG TG TG TG TG TG TG TG TG T
37930053 TGCAAATCTA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.00, C:0.03, G:0.49, T:0.48
Consensus pattern (2 bp):
TG
Found at i:37965375 original size:33 final size:34
Alignment explanation
Indices: 37965327--37965393 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 34
37965317 ACACACTCTC
37965327 TCTCAAAGCTGTAGTCCCTT-TC-CCCAAATCTTG
1 TCTCAAAGCTGTAGT-CCTTCTCACCCAAATCTTG
* *
37965360 TCTCAGAGCTTTAGTCCTTCTCACCCAAATCTTG
1 TCTCAAAGCTGTAGTCCTTCTCACCCAAATCTTG
37965394 GCAAAAGATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
32 4 0.13
33 15 0.50
34 11 0.37
ACGTcount: A:0.21, C:0.33, G:0.12, T:0.34
Consensus pattern (34 bp):
TCTCAAAGCTGTAGTCCTTCTCACCCAAATCTTG
Found at i:37973331 original size:17 final size:17
Alignment explanation
Indices: 37973309--37973342 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
37973299 AATATTTGAA
37973309 TTATTTTGAGTTTAGAT
1 TTATTTTGAGTTTAGAT
*
37973326 TTATTTTGTGTTTAGAT
1 TTATTTTGAGTTTAGAT
37973343 AATATTAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.18, T:0.62
Consensus pattern (17 bp):
TTATTTTGAGTTTAGAT
Found at i:37974355 original size:32 final size:32
Alignment explanation
Indices: 37974317--37974381 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
37974307 CGCAAATTTC
37974317 TGATAACAAAATATAAAATTTTGAGTGAAATA
1 TGATAACAAAATATAAAATTTTGAGTGAAATA
37974349 TGATAACAAAATATAAAATTTTGAGTGAAATA
1 TGATAACAAAATATAAAATTTTGAGTGAAATA
37974381 T
1 T
37974382 CATTTAGTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.52, C:0.03, G:0.12, T:0.32
Consensus pattern (32 bp):
TGATAACAAAATATAAAATTTTGAGTGAAATA
Found at i:37984243 original size:28 final size:29
Alignment explanation
Indices: 37984180--37984234 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
37984170 TGGTTTAATA
*
37984180 TACAATTTTATACAAGAATTTTGATTTTG
1 TACAATTTTATACAAGAAATTTGATTTTG
*
37984209 TACAATTTTATA-ATGAAATTTGATTT
1 TACAATTTTATACAAGAAATTTGATTT
37984235 GATCCAATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 12 0.50
29 12 0.50
ACGTcount: A:0.36, C:0.05, G:0.09, T:0.49
Consensus pattern (29 bp):
TACAATTTTATACAAGAAATTTGATTTTG
Found at i:37986932 original size:12 final size:12
Alignment explanation
Indices: 37986915--37986939 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
37986905 GCAATCAACT
37986915 TAGAGGTGTTTA
1 TAGAGGTGTTTA
37986927 TAGAGGTGTTTA
1 TAGAGGTGTTTA
37986939 T
1 T
37986940 GGATTAAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (12 bp):
TAGAGGTGTTTA
Found at i:37989519 original size:11 final size:11
Alignment explanation
Indices: 37989503--37989533 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
37989493 TGTCTTACCC
37989503 TTTGTTTTTTT
1 TTTGTTTTTTT
37989514 TTTGTTTTTTT
1 TTTGTTTTTTT
*
37989525 TTGGTTTTT
1 TTTGTTTTT
37989534 AAGCATTGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (11 bp):
TTTGTTTTTTT
Found at i:37992403 original size:25 final size:25
Alignment explanation
Indices: 37992375--37992426 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
37992365 CATCATGATC
37992375 ATGGGTCATCCAACATAAATCTTAA
1 ATGGGTCATCCAACATAAATCTTAA
37992400 ATGGGTCATCCAACATAAATCTTAA
1 ATGGGTCATCCAACATAAATCTTAA
37992425 AT
1 AT
37992427 ATATTCCTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (25 bp):
ATGGGTCATCCAACATAAATCTTAA
Found at i:38006811 original size:2 final size:2
Alignment explanation
Indices: 38006804--38006863 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
38006794 GGATAAATAC
38006804 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38006846 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
38006864 TTATTTATCC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38017799 original size:7 final size:7
Alignment explanation
Indices: 38017786--38017820 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
38017776 TTCCGTGATG
38017786 CCATGAA
1 CCATGAA
*
38017793 TCATGAA
1 CCATGAA
*
38017800 CCAAGAA
1 CCATGAA
38017807 CCATGAA
1 CCATGAA
38017814 CCATGAA
1 CCATGAA
38017821 ACTCATTCTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.46, C:0.26, G:0.14, T:0.14
Consensus pattern (7 bp):
CCATGAA
Found at i:38033933 original size:6 final size:6
Alignment explanation
Indices: 38033922--38033952 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
38033912 ATGCTTTCAT
38033922 AATGGG AATGGG AATGGG AATGGG AATGGG A
1 AATGGG AATGGG AATGGG AATGGG AATGGG A
38033953 TTCCATTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.00, G:0.48, T:0.16
Consensus pattern (6 bp):
AATGGG
Found at i:38035050 original size:5 final size:5
Alignment explanation
Indices: 38035040--38035068 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
38035030 ATACAAAAGC
38035040 CACTA CACTA CACTA CACTA CACTA CACT
1 CACTA CACTA CACTA CACTA CACTA CACT
38035069 GATGAATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.38, C:0.41, G:0.00, T:0.21
Consensus pattern (5 bp):
CACTA
Found at i:38042699 original size:2 final size:2
Alignment explanation
Indices: 38042692--38042754 Score: 83
Period size: 2 Copynumber: 31.5 Consensus size: 2
38042682 AAATAAATAA
* * *
38042692 AT AT AT AT AT AT AT AT AT AT A- ACT GT AA AT AA AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
38042734 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
38042755 ACTGTAAATT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:38049182 original size:18 final size:18
Alignment explanation
Indices: 38049137--38049185 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
38049127 CTCTCTTAAC
*
38049137 AAAAATTATAGAAAAATTA
1 AAAAATT-TATAAAAATTA
*
38049156 AAAATATTTATAAAAATTC
1 AAAA-ATTTATAAAAATTA
*
38049175 CAAAATTTATA
1 AAAAATTTATA
38049186 TTTTTAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 7 0.27
19 16 0.62
20 3 0.12
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (18 bp):
AAAAATTTATAAAAATTA
Found at i:38049798 original size:6 final size:6
Alignment explanation
Indices: 38049787--38049813 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
38049777 GGGTTGAGAT
38049787 TGGTGA TGGTGA TGGTGA TGGTGA TGG
1 TGGTGA TGGTGA TGGTGA TGGTGA TGG
38049814 GTTTTAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.52, T:0.33
Consensus pattern (6 bp):
TGGTGA
Done.