Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 129 of 135
Found at i:39296405 original size:18 final size:17
Alignment explanation
Indices: 39296370--39296415 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
39296360 AAATTTAAAA
39296370 AATATT-TATA-TT-AT
1 AATATTATATATTTAAT
39296384 AATATTATAATATTTAAT
1 AATATTAT-ATATTTAAT
39296402 AATATTATATATTT
1 AATATTATATATTT
39296416 TTTATGTAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
14 6 0.21
15 1 0.04
16 3 0.11
17 8 0.29
18 10 0.36
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AATATTATATATTTAAT
Found at i:39297569 original size:15 final size:15
Alignment explanation
Indices: 39297525--39297570 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
39297515 TCAGGTTACA
39297525 TTTTAGTCACTTATG
1 TTTTAGTCACTTATG
* *
39297540 TTTGAAAT-A-TTATG
1 TTT-TAGTCACTTATG
39297554 TTTTAGTCACTTATG
1 TTTTAGTCACTTATG
39297569 TT
1 TT
39297571 ATTATTTTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 6
0.71 0.12 0.18
Matches are distributed among these distances:
13 2 0.08
14 9 0.38
15 11 0.46
16 2 0.08
ACGTcount: A:0.24, C:0.09, G:0.13, T:0.54
Consensus pattern (15 bp):
TTTTAGTCACTTATG
Found at i:39297716 original size:14 final size:14
Alignment explanation
Indices: 39297697--39297727 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
39297687 AGAATAGATT
39297697 TTTAATTAAATAAA
1 TTTAATTAAATAAA
*
39297711 TTTAATTAATTAAA
1 TTTAATTAAATAAA
39297725 TTT
1 TTT
39297728 TTTAAATCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTAATTAAATAAA
Found at i:39300340 original size:24 final size:24
Alignment explanation
Indices: 39300313--39300388 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
39300303 TCAATTTCGA
39300313 ATGAAAGAATGGGTTGATTGAGTC
1 ATGAAAGAATGGGTTGATTGAGTC
** * ** *
39300337 ATG-AATTAT-GGTATCAATTTCG-A
1 ATGAAAGAATGGGT-T-GATTGAGTC
39300360 ATGAAAGAATGGGTTGATTGAGTC
1 ATGAAAGAATGGGTTGATTGAGTC
39300384 ATGAA
1 ATGAA
39300389 TTGAACTAAA
Statistics
Matches: 35, Mismatches: 12, Indels: 10
0.61 0.21 0.18
Matches are distributed among these distances:
22 3 0.09
23 12 0.34
24 17 0.49
25 3 0.09
ACGTcount: A:0.36, C:0.05, G:0.28, T:0.32
Consensus pattern (24 bp):
ATGAAAGAATGGGTTGATTGAGTC
Found at i:39300366 original size:47 final size:47
Alignment explanation
Indices: 39300297--39300390 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
39300287 TAAAATGATG
39300297 ATGGTATCAATTTCGAATGAAAGAATGGGTTGATTGAGTCATGAATT
1 ATGGTATCAATTTCGAATGAAAGAATGGGTTGATTGAGTCATGAATT
39300344 ATGGTATCAATTTCGAATGAAAGAATGGGTTGATTGAGTCATGAATT
1 ATGGTATCAATTTCGAATGAAAGAATGGGTTGATTGAGTCATGAATT
39300391 GAACTAAAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.34, C:0.06, G:0.26, T:0.34
Consensus pattern (47 bp):
ATGGTATCAATTTCGAATGAAAGAATGGGTTGATTGAGTCATGAATT
Found at i:39303136 original size:53 final size:50
Alignment explanation
Indices: 39303079--39303180 Score: 123
Period size: 53 Copynumber: 2.0 Consensus size: 50
39303069 TTTGTAGAAG
** * *
39303079 ATTAAATTAAAATTTTATTATTTTTAAAAAGTTTAAAATATAATTTTATTTTT
1 ATTAAATTAAAATTTTAAAAATTTTAAAAA-TTT-AAATAAAATTTT-TTTTT
* *
39303132 ATTAATTTAAATTTTTAAAAATTTTAAAAATTTAAATAAAATTTTTTTT
1 ATTAAATTAAAATTTTAAAAATTTTAAAAATTTAAATAAAATTTTTTTT
39303181 ATTTTAAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
50 4 0.09
51 11 0.26
52 3 0.07
53 25 0.58
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (50 bp):
ATTAAATTAAAATTTTAAAAATTTTAAAAATTTAAATAAAATTTTTTTTT
Found at i:39312883 original size:31 final size:31
Alignment explanation
Indices: 39312848--39312909 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
39312838 ACTCAATAAT
**
39312848 TTAAATAAAAACTTTTGAATAGTTCAATGAC
1 TTAAATAAAAACTTTAAAATAGTTCAATGAC
* *
39312879 TTAAATGAAAACTTTAAAATAGTTCAGTGAC
1 TTAAATAAAAACTTTAAAATAGTTCAATGAC
39312910 CAAATTATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.45, C:0.10, G:0.11, T:0.34
Consensus pattern (31 bp):
TTAAATAAAAACTTTAAAATAGTTCAATGAC
Found at i:39313080 original size:9 final size:9
Alignment explanation
Indices: 39313068--39313108 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
39313058 AAAAAAATAA
39313068 AAAAATTAT
1 AAAAATTAT
**
39313077 AAAAATTCC
1 AAAAATTAT
39313086 AAAAATTTAT
1 AAAAA-TTAT
39313096 AAAAATTAT
1 AAAAATTAT
39313105 AAAA
1 AAAA
39313109 GTATAATATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 20 0.74
10 7 0.26
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (9 bp):
AAAAATTAT
Found at i:39313108 original size:19 final size:19
Alignment explanation
Indices: 39313067--39313108 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
39313057 CAAAAAAATA
*
39313067 AAAAAATTATAAAAATTCC
1 AAAAAATTATAAAAATTAC
* *
39313086 AAAAATTTATAAAAATTAT
1 AAAAAATTATAAAAATTAC
39313105 AAAA
1 AAAA
39313109 GTATAATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAAAATTATAAAAATTAC
Found at i:39314569 original size:22 final size:22
Alignment explanation
Indices: 39314544--39314586 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
39314534 AATTTTCAAT
*
39314544 AAATAAAA-AATATTAAATATTA
1 AAATAAAATAA-AATAAATATTA
39314566 AAATAAAATAAAATAAATATT
1 AAATAAAATAAAATAAATATT
39314587 TTAAAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
AAATAAAATAAAATAAATATTA
Found at i:39314570 original size:26 final size:29
Alignment explanation
Indices: 39314541--39314602 Score: 76
Period size: 31 Copynumber: 2.2 Consensus size: 29
39314531 AAAAATTTTC
*
39314541 AATAAAT-AAA-AAATA-TTAAATATTAA
1 AATAAATAAAATAAATATTTAAAAATTAA
39314567 AATAAAATAAAATAAATATTTTAAAAATTAA
1 AAT-AAATAAAATAAATA-TTTAAAAATTAA
39314598 AATAA
1 AATAA
39314603 TATGAACGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
26 3 0.10
27 4 0.13
28 3 0.10
29 5 0.17
30 2 0.07
31 13 0.43
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (29 bp):
AATAAATAAAATAAATATTTAAAAATTAA
Found at i:39317799 original size:9 final size:8
Alignment explanation
Indices: 39317774--39317803 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
39317764 TTTTTGAATG
39317774 AAAATATA
1 AAAATATA
39317782 AAAATATA
1 AAAATATA
39317790 AAAATAATA
1 AAAAT-ATA
39317799 AAAAT
1 AAAAT
39317804 TCATACTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (8 bp):
AAAATATA
Found at i:39319415 original size:13 final size:13
Alignment explanation
Indices: 39319397--39319422 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39319387 AATCTTTTAA
39319397 AATATATAACTTT
1 AATATATAACTTT
39319410 AATATATAACTTT
1 AATATATAACTTT
39319423 TGTACGTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
AATATATAACTTT
Found at i:39324978 original size:26 final size:26
Alignment explanation
Indices: 39324933--39324983 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
39324923 CACTTAACCG
* *
39324933 AACTTTTCAAAAGTAGTTTTCAAAAT
1 AACTTTTCAAAAGCACTTTTCAAAAT
* *
39324959 AACTTTTCCAAAGCACTTTTTAAAA
1 AACTTTTCAAAAGCACTTTTCAAAA
39324984 GCACTTCTGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.41, C:0.16, G:0.06, T:0.37
Consensus pattern (26 bp):
AACTTTTCAAAAGCACTTTTCAAAAT
Found at i:39325973 original size:21 final size:22
Alignment explanation
Indices: 39325932--39325973 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
39325922 AAATTAAAAT
* *
39325932 AAAAAAAATAAAAAACCAGAGA
1 AAAAAAAAGAAAAAACAAGAGA
39325954 AAAAAAAAGAAAAAA-AAGAG
1 AAAAAAAAGAAAAAACAAGAG
39325974 GAGGCAATGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.81, C:0.05, G:0.12, T:0.02
Consensus pattern (22 bp):
AAAAAAAAGAAAAAACAAGAGA
Found at i:39334377 original size:168 final size:168
Alignment explanation
Indices: 39334099--39334434 Score: 591
Period size: 168 Copynumber: 2.0 Consensus size: 168
39334089 GAGACTCTCA
**
39334099 TTCACTTTCAACCTAAACCTTTTTAGTTCTTTTTCTTTTGATTCATTCTGAGAAAGTCAATGACT
1 TTCACTTTCAACCTAAACCTTTCCAGTTCTTTTTCTTTTGATTCATTCTGAGAAAGTCAATGACT
* *
39334164 TGCATGTCCTGGTTTCCAAAATCTCAACACTTTAGTTCAGCAAATTATTCTTAAAATTGTTTTTT
66 TGCATGTCCTGGTTTCCAAAATCTCAACAATTTAGTTCAGCAAATTATTCTTAAAATTGTGTTTT
*
39334229 GCCCCTTAGTAAAAAACTTAAGATTAATTTTTTCAGTT
131 GCCCCTTAGTAAAAAACTTAAGATTAATTGTTTCAGTT
* *
39334267 TTCACTTTCAACCTAAACCTTTCCAGTTCTTTTTCTTTTGATTCATTCTGGGGAAGTCAATGACT
1 TTCACTTTCAACCTAAACCTTTCCAGTTCTTTTTCTTTTGATTCATTCTGAGAAAGTCAATGACT
*
39334332 TGCATGTCCTGGTTTCCAGAATCTCAACAATTTAGTTCAGCAAATTATTCTTAAAATTGTGTTTT
66 TGCATGTCCTGGTTTCCAAAATCTCAACAATTTAGTTCAGCAAATTATTCTTAAAATTGTGTTTT
*
39334397 GCCCCTTAGTAAAAAACTTAAGATTGATTGTTTCAGTT
131 GCCCCTTAGTAAAAAACTTAAGATTAATTGTTTCAGTT
39334435 GTTGCTTAGA
Statistics
Matches: 159, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
168 159 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (168 bp):
TTCACTTTCAACCTAAACCTTTCCAGTTCTTTTTCTTTTGATTCATTCTGAGAAAGTCAATGACT
TGCATGTCCTGGTTTCCAAAATCTCAACAATTTAGTTCAGCAAATTATTCTTAAAATTGTGTTTT
GCCCCTTAGTAAAAAACTTAAGATTAATTGTTTCAGTT
Found at i:39336095 original size:35 final size:35
Alignment explanation
Indices: 39336056--39336136 Score: 90
Period size: 36 Copynumber: 2.3 Consensus size: 35
39336046 ATTAAGGCTG
* * *
39336056 AAACGAAGAAACAAACAATTCAATAATGAATGCTA
1 AAACGAAGAAAAAAACAAATCAATAATGAAAGCTA
* * *
39336091 AAACGAAGGAAAAAAATAAATCAGTGATGAAAGCTA
1 AAACGAA-GAAAAAAACAAATCAATAATGAAAGCTA
*
39336127 AAACAAAGAA
1 AAACGAAGAA
39336137 TGCTGGAAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
35 10 0.26
36 28 0.74
ACGTcount: A:0.60, C:0.11, G:0.15, T:0.14
Consensus pattern (35 bp):
AAACGAAGAAAAAAACAAATCAATAATGAAAGCTA
Found at i:39341088 original size:18 final size:18
Alignment explanation
Indices: 39341065--39341103 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
39341055 AATTGGGAAT
*
39341065 TTTTTAAT-TTTTTTTGAA
1 TTTTTAATAATTTTTT-AA
39341083 TTTTTAATAATTTTTTAA
1 TTTTTAATAATTTTTTAA
39341101 TTT
1 TTT
39341104 GACCGGTTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTTTAATAATTTTTTAA
Found at i:39344194 original size:24 final size:24
Alignment explanation
Indices: 39344167--39344215 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
39344157 TTTATAAGGA
39344167 AATAATA-AATATTTATTTTTGTAT
1 AATAATAGAATATTTATTTTT-TAT
* *
39344191 AATATTAGCATATTTATTTTTTAT
1 AATAATAGAATATTTATTTTTTAT
39344215 A
1 A
39344216 GTGTGCTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (24 bp):
AATAATAGAATATTTATTTTTTAT
Found at i:39346875 original size:29 final size:30
Alignment explanation
Indices: 39346826--39346882 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
39346816 CTATGATCCT
*
39346826 CATTTTAAATTAGTCCTTAAACT-TCAAAC
1 CATTTTAAATTAGTCCATAAACTATCAAAC
*
39346855 CATTTTATATATAG-CCATAAACTATCAA
1 CATTTTAAAT-TAGTCCATAAACTATCAA
39346883 TGTTATATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.40, C:0.19, G:0.04, T:0.37
Consensus pattern (30 bp):
CATTTTAAATTAGTCCATAAACTATCAAAC
Found at i:39352323 original size:16 final size:18
Alignment explanation
Indices: 39352304--39352340 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
39352294 CTAATAATAT
39352304 AATAT-TCATTT-TAAAA
1 AATATCTCATTTATAAAA
39352320 AATATCTCATTTATAAAA
1 AATATCTCATTTATAAAA
39352338 AAT
1 AAT
39352341 TATTTATGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.26
17 6 0.32
18 8 0.42
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (18 bp):
AATATCTCATTTATAAAA
Found at i:39354454 original size:3 final size:3
Alignment explanation
Indices: 39354441--39354488 Score: 87
Period size: 3 Copynumber: 15.7 Consensus size: 3
39354431 CTCCATGTAT
39354441 TTA TCTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
39354487 TT
1 TT
39354489 CAAATACAGT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:39354851 original size:29 final size:27
Alignment explanation
Indices: 39354785--39354851 Score: 71
Period size: 31 Copynumber: 2.3 Consensus size: 27
39354775 AAATTTCTCG
* * *
39354785 TATATAAGTACACTAAATTAAAGTTCA
1 TATATAATTACACTAAATCAAAATTCA
39354812 TATATACAATTACACATTAAATCAAAATTCA
1 TATAT--AATTACAC--TAAATCAAAATTCA
39354843 TATATAATT
1 TATATAATT
39354852 TTGATGTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 5 0.15
29 11 0.33
31 17 0.52
ACGTcount: A:0.49, C:0.12, G:0.03, T:0.36
Consensus pattern (27 bp):
TATATAATTACACTAAATCAAAATTCA
Found at i:39355537 original size:10 final size:10
Alignment explanation
Indices: 39355522--39355546 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
39355512 GTCAACGATT
39355522 AATATTTAAA
1 AATATTTAAA
39355532 AATATTTAAA
1 AATATTTAAA
39355542 AATAT
1 AATAT
39355547 AAAAAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
AATATTTAAA
Found at i:39362879 original size:20 final size:20
Alignment explanation
Indices: 39362854--39362891 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
39362844 GATTGAGATT
39362854 CTATACATCCTTAAATTACA
1 CTATACATCCTTAAATTACA
*
39362874 CTATACATTCTTAAATTA
1 CTATACATCCTTAAATTA
39362892 TAATTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (20 bp):
CTATACATCCTTAAATTACA
Found at i:39363936 original size:28 final size:28
Alignment explanation
Indices: 39363905--39363992 Score: 74
Period size: 28 Copynumber: 3.1 Consensus size: 28
39363895 TTTATATATA
*
39363905 TTTTGTATATT-TTTAGAATTTTTTAACT
1 TTTTATATATTATTTAGAA-TTTTTAACT
* * *
39363933 TTTTCTA-ATTATTTATAATTTTTAATT
1 TTTTATATATTATTTAGAATTTTTAACT
* *
39363960 TTTTATATATACATTTA-AATTTCTTAATT
1 TTTTATATAT-TATTTAGAATTT-TTAACT
39363989 TTTT
1 TTTT
39363993 TAAAAATTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
27 17 0.33
28 19 0.37
29 15 0.29
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (28 bp):
TTTTATATATTATTTAGAATTTTTAACT
Found at i:39363951 original size:10 final size:9
Alignment explanation
Indices: 39363894--39363966 Score: 53
Period size: 9 Copynumber: 8.0 Consensus size: 9
39363884 ACTTTTATGT
*
39363894 ATTTATATA
1 ATTTTTATA
39363903 TATTTTGTAT-
1 -ATTTT-TATA
*
39363913 ATTTTTAGA
1 ATTTTTATA
39363922 ATTTTT-TA
1 ATTTTTATA
*
39363930 ACTTTTTCTA
1 A-TTTTTATA
39363940 ATTATTTATA
1 ATT-TTTATA
39363950 ATTTTTA-A
1 ATTTTTATA
*
39363958 TTTTTTATA
1 ATTTTTATA
39363967 TATACATTTA
Statistics
Matches: 52, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
8 11 0.21
9 23 0.44
10 15 0.29
11 3 0.06
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (9 bp):
ATTTTTATA
Found at i:39363964 original size:17 final size:18
Alignment explanation
Indices: 39363933--39363966 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
39363923 TTTTTTAACT
39363933 TTTTCTAATTATTTATAA
1 TTTTCTAATTATTTATAA
*
39363951 TTTT-TAATTTTTTATA
1 TTTTCTAATTATTTATA
39363967 TATACATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTCTAATTATTTATAA
Found at i:39364428 original size:97 final size:93
Alignment explanation
Indices: 39364310--39364616 Score: 429
Period size: 97 Copynumber: 3.2 Consensus size: 93
39364300 AAACAAAGTT
*
39364310 AAAATTA--AATAGTTGGGTGAATAAATAGGGATCATTTTATAATTTTTTATAGTTAAGTGATCA
1 AAAATTACTAATAGTTGGGTGAATAAATAGGGATCATTTTATAATTTTTTATAATTAAGTGAT-A
39364373 TTTTGTAATTTTTTATAGTTAGACGACCAATA
65 TTTTGTAATTTTTTATA-TTAGACGA-CAA-A
* *
39364405 AAAATTACTACTAGTTGGGTGAATAAATAGGGATTATTTTATAATTTTTTATAATTAAGTGATAA
1 AAAATTACTAATAGTTGGGTGAATAAATAGGGATCATTTTATAATTTTTTATAATTAAGTGAT-A
* * *
39364470 TTTTGTAACTTTTAATATTTGAACGAACAAAA
65 TTTTGTAATTTTTTATATTAG-ACG-AC-AAA
*
39364502 AAAATTACTAATAGTTGGGTGAATAAATAAGGATCATTTTATAATTTTTTATAATTAAGTGATAT
1 AAAATTACTAATAGTTGGGTGAATAAATAGGGATCATTTTATAATTTTTTATAATTAAGTGATAT
* *
39364567 TTTGTAATTTTTTATAATTATACGATAAA
66 TTTGTAATTTTTTAT-ATTAGACGACAAA
39364596 AAAATTTACTAATAGTTGGGT
1 AAAA-TTACTAATAGTTGGGT
39364617 TGTTACTAGT
Statistics
Matches: 190, Mismatches: 15, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
94 7 0.04
95 24 0.13
96 21 0.11
97 135 0.71
98 3 0.02
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.42
Consensus pattern (93 bp):
AAAATTACTAATAGTTGGGTGAATAAATAGGGATCATTTTATAATTTTTTATAATTAAGTGATAT
TTTGTAATTTTTTATATTAGACGACAAA
Found at i:39364568 original size:28 final size:28
Alignment explanation
Indices: 39364524--39364586 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 28
39364514 AGTTGGGTGA
*
39364524 ATAAATAAGGATCATTTTATAATTTTTT
1 ATAATTAAGGATCATTTTATAATTTTTT
*
39364552 ATAATTAAGTGAT-ATTTTGTAATTTTTT
1 ATAATTAAG-GATCATTTTATAATTTTTT
39364580 ATAATTA
1 ATAATTA
39364587 TACGATAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 29 0.91
29 3 0.09
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (28 bp):
ATAATTAAGGATCATTTTATAATTTTTT
Found at i:39370592 original size:15 final size:15
Alignment explanation
Indices: 39370572--39370606 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
39370562 AACCACACGT
39370572 TATATTCAATATGAA
1 TATATTCAATATGAA
**
39370587 TATATTTTATATGAA
1 TATATTCAATATGAA
39370602 TATAT
1 TATAT
39370607 CTGGCATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (15 bp):
TATATTCAATATGAA
Found at i:39391018 original size:16 final size:16
Alignment explanation
Indices: 39390997--39391034 Score: 67
Period size: 16 Copynumber: 2.3 Consensus size: 16
39390987 GCTAAAATTC
39390997 AATATCACAATTGTAT
1 AATATCACAATTGTAT
39391013 AATATCACAATTGTAT
1 AATATCACAATTGTAT
39391029 ATATAT
1 A-ATAT
39391035 ATATTTATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.45, C:0.11, G:0.05, T:0.39
Consensus pattern (16 bp):
AATATCACAATTGTAT
Found at i:39402565 original size:75 final size:76
Alignment explanation
Indices: 39402414--39402581 Score: 194
Period size: 78 Copynumber: 2.2 Consensus size: 76
39402404 GTGCAACAAT
* * *
39402414 ACCGGAGGTTGCTTTGAAGCAGAAGAAGGTCTCGTTCTCTGATGTTAAAAGCGTTATCACGGAAG
1 ACCGGAGATTGCTTTGAACCAGAAGAAGGTCTCGTTCTCTGA--TTAAAAGCATTATCACGGAAG
* *
39402479 ATATTGCGTCAAC
64 ATACTGAGTCAAC
* * * **
39402492 ACCGGAGATTGGTTTGAACCAGAAGAAGGTTTCGTTTTCTGA-TAAAAGCATTATCATTGAAGAT
1 ACCGGAGATTGCTTTGAACCAGAAGAAGGTCTCGTTCTCTGATTAAAAGCATTATCACGGAAGAT
39402556 ACTGAGTCAAC
66 ACTGAGTCAAC
* *
39402567 CCCAGAGATTAGCTT
1 ACCGGAGATT-GCTT
39402582 AAGCCAGAAG
Statistics
Matches: 76, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
75 36 0.47
76 3 0.04
78 37 0.49
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.28
Consensus pattern (76 bp):
ACCGGAGATTGCTTTGAACCAGAAGAAGGTCTCGTTCTCTGATTAAAAGCATTATCACGGAAGAT
ACTGAGTCAAC
Found at i:39402589 original size:75 final size:76
Alignment explanation
Indices: 39402427--39402591 Score: 181
Period size: 75 Copynumber: 2.2 Consensus size: 76
39402417 GGAGGTTGCT
* * * *
39402427 TTGAAGCAGAAGAAGGTCTCGTTCTCTGATGTTAAAAGCGTTATCACGGAAGATATTGCGTCAAC
1 TTGAACCAGAAGAAGGTCTCGTTCTCTGA--TTAAAAGCATTATCACGGAAGATACTGAGTCAAC
* * *
39402492 ACCGGAGATTGGT
64 ACCAGAGATTAGC
* * ** *
39402505 TTGAACCAGAAGAAGGTTTCGTTTTCTGA-TAAAAGCATTATCATTGAAGATACTGAGTCAACCC
1 TTGAACCAGAAGAAGGTCTCGTTCTCTGATTAAAAGCATTATCACGGAAGATACTGAGTCAACAC
39402569 CAGAGATTAGC
66 CAGAGATTAGC
39402580 TT-AAGCCAGAAG
1 TTGAA-CCAGAAG
39402592 GTGCCATTCG
Statistics
Matches: 74, Mismatches: 12, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
74 2 0.03
75 46 0.62
78 26 0.35
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.27
Consensus pattern (76 bp):
TTGAACCAGAAGAAGGTCTCGTTCTCTGATTAAAAGCATTATCACGGAAGATACTGAGTCAACAC
CAGAGATTAGC
Found at i:39403669 original size:123 final size:123
Alignment explanation
Indices: 39403450--39403694 Score: 454
Period size: 123 Copynumber: 2.0 Consensus size: 123
39403440 GCACCAAAAA
* *
39403450 TTTGATCCCAGTGTAATGGAGCCTGTAAGTGTGAGAGATGCTGGAACTGAACTATTTGATAACAA
1 TTTGATCCCAGTGTAATGGAGCCTGTAAGTGAGAGAGATGCTGAAACTGAACTATTTGATAACAA
*
39403515 GCCTTACCGAGAGATTGAAGCAGATGATGCAGTAGAAGAAGATGATGATGAACAAGAG
66 GCCTTACCAAGAGATTGAAGCAGATGATGCAGTAGAAGAAGATGATGATGAACAAGAG
39403573 TTTGATCCCAGTGTAATGGAGCCTGTAAGTGAGAGAGATGCTGAAACTGAACTATTTGATAACAA
1 TTTGATCCCAGTGTAATGGAGCCTGTAAGTGAGAGAGATGCTGAAACTGAACTATTTGATAACAA
*
39403638 GCCTTACCAAGAGATTGAAGCAGATGATGCAGTAGAAGGAGATGATGATGAACAAGA
66 GCCTTACCAAGAGATTGAAGCAGATGATGCAGTAGAAGAAGATGATGATGAACAAGA
39403695 CAATCAAGAG
Statistics
Matches: 118, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
123 118 1.00
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.23
Consensus pattern (123 bp):
TTTGATCCCAGTGTAATGGAGCCTGTAAGTGAGAGAGATGCTGAAACTGAACTATTTGATAACAA
GCCTTACCAAGAGATTGAAGCAGATGATGCAGTAGAAGAAGATGATGATGAACAAGAG
Found at i:39405053 original size:126 final size:126
Alignment explanation
Indices: 39404798--39405159 Score: 638
Period size: 126 Copynumber: 2.9 Consensus size: 126
39404788 AGATTAGGAC
* * *
39404798 TTAATTGTACTGTTATTCATAGTTCTTTCCATAACTTTGAATAGCACTCTTTGCTTTCAATTCTT
1 TTAATTGTACTATTATTCATTGTTCTTTCCATAACTTTGAATAGCACTCTTAGCTTTCAATTCTT
* * *
39404863 T-TT-TTCACAGTTGCTTAGGGTCTGGTAGCTTGGTTGAGAAGTATGCATATTAACTGGAT
66 TCTTCTTCACAATTCCTTAGGGTCTGGTAGCTTGGTTGAGAAGTATGCACATTAACTGGAT
*
39404922 TTAATTGTCCTATTATTCATTGTTCTTTCCATAACTTTGAATAGCACTCTTAGCTTTCAATTCTT
1 TTAATTGTACTATTATTCATTGTTCTTTCCATAACTTTGAATAGCACTCTTAGCTTTCAATTCTT
39404987 TCTTCTTCACAATTCCTTAGGGTCTGGTAGCTTGGTTGAGAAGTATGCACATTAACTGGAT
66 TCTTCTTCACAATTCCTTAGGGTCTGGTAGCTTGGTTGAGAAGTATGCACATTAACTGGAT
*
39405048 TTAATTGTACTATTATTCATTGTTCTTTCCATAACTTTGAATAGCACTCTTAGCTTTCAATTCCT
1 TTAATTGTACTATTATTCATTGTTCTTTCCATAACTTTGAATAGCACTCTTAGCTTTCAATTCTT
39405113 TCTTCTTCACAATTCCTTAGGGTCTGGTAGCTTGGTTGAGAAGTATG
66 TCTTCTTCACAATTCCTTAGGGTCTGGTAGCTTGGTTGAGAAGTATG
39405160 AGATCAAATG
Statistics
Matches: 227, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
124 62 0.27
125 2 0.01
126 163 0.72
ACGTcount: A:0.23, C:0.18, G:0.16, T:0.44
Consensus pattern (126 bp):
TTAATTGTACTATTATTCATTGTTCTTTCCATAACTTTGAATAGCACTCTTAGCTTTCAATTCTT
TCTTCTTCACAATTCCTTAGGGTCTGGTAGCTTGGTTGAGAAGTATGCACATTAACTGGAT
Found at i:39409852 original size:4 final size:4
Alignment explanation
Indices: 39409843--39409867 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
39409833 GATATTACAG
39409843 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
39409868 TATATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:39412658 original size:3 final size:3
Alignment explanation
Indices: 39412650--39412687 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
39412640 CATAGGCGTT
39412650 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
39412688 TATCTACATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:39420397 original size:33 final size:31
Alignment explanation
Indices: 39420314--39420399 Score: 86
Period size: 33 Copynumber: 2.7 Consensus size: 31
39420304 TATAATTTTT
* * *
39420314 AAAAAATTAAATC-AAAATTTTATTATTTTA
1 AAAAAATTAAATCTAAAATTTTATAAATATA
*
39420344 AAAAAATTACTAAT-TTAAATTTTATAAAATATA
1 AAAAAATTA--AATCTAAAATTTTAT-AAATATA
39420377 AAAAAACTTAAATCTAAAATTTT
1 AAAAAA-TTAAATCTAAAATTTT
39420400 CTATTTTAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
30 9 0.20
32 15 0.33
33 18 0.40
34 3 0.07
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (31 bp):
AAAAAATTAAATCTAAAATTTTATAAATATA
Found at i:39427844 original size:21 final size:21
Alignment explanation
Indices: 39427818--39427857 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
39427808 CCAAGCTCCT
* *
39427818 ATCTTCTTCCTCTTCATCGTC
1 ATCTTCTTCATCGTCATCGTC
39427839 ATCTTCTTCATCGTCATCG
1 ATCTTCTTCATCGTCATCG
39427858 AACTCCGAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.12, C:0.35, G:0.07, T:0.45
Consensus pattern (21 bp):
ATCTTCTTCATCGTCATCGTC
Found at i:39427848 original size:15 final size:15
Alignment explanation
Indices: 39427828--39427856 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
39427818 ATCTTCTTCC
39427828 TCTTCATCGTCATCT
1 TCTTCATCGTCATCT
39427843 TCTTCATCGTCATC
1 TCTTCATCGTCATC
39427857 GAACTCCGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.34, G:0.07, T:0.45
Consensus pattern (15 bp):
TCTTCATCGTCATCT
Found at i:39428912 original size:63 final size:63
Alignment explanation
Indices: 39428813--39428937 Score: 214
Period size: 63 Copynumber: 2.0 Consensus size: 63
39428803 CCATTCTTCC
**
39428813 TCTCCAATCCTCTTCAGATACTCACATTTCGATCATCCTAATTTCCCTAGGACTCTCCGTCCA
1 TCTCCAATCCTCTTCAGATACTCACATTTCGATCATCCTAATTTCCCTAAAACTCTCCGTCCA
**
39428876 TCTCCAATCCTCTTTGGATACTCACATTTCGATCATCCTAATTTCCCTAAAACTCTCCGTCC
1 TCTCCAATCCTCTTCAGATACTCACATTTCGATCATCCTAATTTCCCTAAAACTCTCCGTCC
39428938 GTCGATCAAC
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.22, C:0.36, G:0.07, T:0.34
Consensus pattern (63 bp):
TCTCCAATCCTCTTCAGATACTCACATTTCGATCATCCTAATTTCCCTAAAACTCTCCGTCCA
Found at i:39430826 original size:14 final size:15
Alignment explanation
Indices: 39430807--39430840 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
39430797 GGAGTGACCC
39430807 TTTTATAAGTTTAT-
1 TTTTATAAGTTTATA
*
39430821 TTTTATAATTTTATA
1 TTTTATAAGTTTATA
39430836 TTTTA
1 TTTTA
39430841 GTCCTTCTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (15 bp):
TTTTATAAGTTTATA
Found at i:39440024 original size:17 final size:17
Alignment explanation
Indices: 39440002--39440036 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
39439992 GTCTTTGGGC
39440002 CTATGCGAAAAGTCCGA
1 CTATGCGAAAAGTCCGA
39440019 CTATGCGAAAAGTCCGA
1 CTATGCGAAAAGTCCGA
39440036 C
1 C
39440037 CAATGATCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.26, G:0.23, T:0.17
Consensus pattern (17 bp):
CTATGCGAAAAGTCCGA
Found at i:39440105 original size:25 final size:25
Alignment explanation
Indices: 39440077--39440129 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
39440067 TAACTTCTAA
* *
39440077 ATTTATCACATTTTCTTAAGTTGGT
1 ATTTATAACATTTTCTCAAGTTGGT
**
39440102 ATTTATAATTTTTTCTCAAGTTGGT
1 ATTTATAACATTTTCTCAAGTTGGT
39440127 ATT
1 ATT
39440130 CGAATTTTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.25, C:0.09, G:0.11, T:0.55
Consensus pattern (25 bp):
ATTTATAACATTTTCTCAAGTTGGT
Found at i:39440135 original size:24 final size:25
Alignment explanation
Indices: 39440087--39440137 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
39440077 ATTTATCACA
* *
39440087 TTTTCTTAAGTTGGTATTTATAATT
1 TTTTCTCAAGTTGGTATTTAGAATT
*
39440112 TTTTCTCAAGTTGGTA-TTCGAATT
1 TTTTCTCAAGTTGGTATTTAGAATT
39440136 TT
1 TT
39440138 CATTTCGTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 8 0.35
25 15 0.65
ACGTcount: A:0.22, C:0.08, G:0.14, T:0.57
Consensus pattern (25 bp):
TTTTCTCAAGTTGGTATTTAGAATT
Found at i:39441243 original size:30 final size:30
Alignment explanation
Indices: 39441209--39441266 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
39441199 TTATATCTGC
*
39441209 TCTTTTTGACACAATCTCTAGAATTACTGT
1 TCTTTTTGACACAATCTCTAGAACTACTGT
*
39441239 TCTTTTTGACACAATTTCTAGAACTACT
1 TCTTTTTGACACAATCTCTAGAACTACT
39441267 CATAATCTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.43
Consensus pattern (30 bp):
TCTTTTTGACACAATCTCTAGAACTACTGT
Found at i:39441695 original size:24 final size:24
Alignment explanation
Indices: 39441663--39441711 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
39441653 TCTCACTACC
39441663 AAAGCTATTATGATTTGTCTTTGA
1 AAAGCTATTATGATTTGTCTTTGA
39441687 AAAGCTATTATGATTTGTCTTTGA
1 AAAGCTATTATGATTTGTCTTTGA
39441711 A
1 A
39441712 TTTGTGTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.31, C:0.08, G:0.16, T:0.45
Consensus pattern (24 bp):
AAAGCTATTATGATTTGTCTTTGA
Found at i:39443282 original size:47 final size:47
Alignment explanation
Indices: 39443231--39443320 Score: 155
Period size: 47 Copynumber: 1.9 Consensus size: 47
39443221 TTTTTTTAAA
*
39443231 TTTTTAAATT-AAAAAGAATAATAAAAATCAGTACCATTCGTTAATTG
1 TTTTT-AATTAAAAAAGAACAATAAAAATCAGTACCATTCGTTAATTG
39443278 TTTTTAATTAAAAAAGAACAATAAAAATCAGTACCATTCGTTA
1 TTTTTAATTAAAAAAGAACAATAAAAATCAGTACCATTCGTTA
39443321 TCTCATAAGG
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
46 4 0.10
47 37 0.90
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.34
Consensus pattern (47 bp):
TTTTTAATTAAAAAAGAACAATAAAAATCAGTACCATTCGTTAATTG
Found at i:39452090 original size:10 final size:10
Alignment explanation
Indices: 39452075--39452102 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
39452065 TGTATATCTG
39452075 TCATTTTCTT
1 TCATTTTCTT
39452085 TCATTTTCTT
1 TCATTTTCTT
39452095 TCATTTTC
1 TCATTTTC
39452103 AAGCTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.11, C:0.21, G:0.00, T:0.68
Consensus pattern (10 bp):
TCATTTTCTT
Found at i:39460557 original size:92 final size:94
Alignment explanation
Indices: 39460450--39460671 Score: 315
Period size: 92 Copynumber: 2.4 Consensus size: 94
39460440 GAAAAAGTGC
* * * *
39460450 AAACCCTAATGTACAAAAATTATTAAGTTCAAACTCTAATAATATATGAAAACAATTACAAAGTT
1 AAACCCCAATATACAAAAATCATTAAGTTCAAACCCTAATAATATATGAAAACAATTACAAAGTT
*
39460515 CA-AAGACTAACTTGAAC-AAAAAAA-TTT
66 CAGAA-ACTAACTAGAACAAAAAAAATTTT
* * *
39460542 AAACTCCAATATACAAAAATCATTAAGTTCAAACCCTAATAATATGTGAAAACAATTATAAAGTT
1 AAACCCCAATATACAAAAATCATTAAGTTCAAACCCTAATAATATATGAAAACAATTACAAAGTT
*
39460607 CAGAAATTAACTAGAACAAAAAAAATTTT
66 CAGAAACTAACTAGAACAAAAAAAATTTT
* *
39460636 AAACCCCAATGTACAAAAATCATTAAATTCAAACCC
1 AAACCCCAATATACAAAAATCATTAAGTTCAAACCC
39460672 CAAATAGTGA
Statistics
Matches: 115, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
92 70 0.61
93 9 0.08
94 36 0.31
ACGTcount: A:0.52, C:0.16, G:0.06, T:0.26
Consensus pattern (94 bp):
AAACCCCAATATACAAAAATCATTAAGTTCAAACCCTAATAATATATGAAAACAATTACAAAGTT
CAGAAACTAACTAGAACAAAAAAAATTTT
Found at i:39461393 original size:3 final size:3
Alignment explanation
Indices: 39461385--39461423 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
39461375 GAAAAATATG
39461385 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
39461424 ATTTACTTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:39461609 original size:7 final size:7
Alignment explanation
Indices: 39461599--39461628 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
39461589 TTAATAAATA
39461599 ATATTAT
1 ATATTAT
39461606 ATATTAT
1 ATATTAT
39461613 ATATTAT
1 ATATTAT
39461620 ATATTAT
1 ATATTAT
39461627 AT
1 AT
39461629 GTATTAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
ATATTAT
Found at i:39463011 original size:29 final size:30
Alignment explanation
Indices: 39462943--39463022 Score: 74
Period size: 31 Copynumber: 2.6 Consensus size: 30
39462933 GTAATTGAAT
*
39462943 CAAATCAAAGTTTCATATATATATATGAACTA
1 CAAATC-AAGTTTCATGTATATATATGAAC-A
* *
39462975 CAATTCAAGTTTCATGTATATA-ATTATAC-
1 CAAATCAAGTTTCATGTATATATATGA-ACA
**
39463004 CAAATCAAACTTCATGTAT
1 CAAATCAAGTTTCATGTAT
39463023 CAAATTAAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
29 16 0.39
30 3 0.07
31 17 0.41
32 5 0.12
ACGTcount: A:0.42, C:0.15, G:0.06, T:0.36
Consensus pattern (30 bp):
CAAATCAAGTTTCATGTATATATATGAACA
Found at i:39463266 original size:30 final size:31
Alignment explanation
Indices: 39463232--39463293 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
39463222 ATTATAAACA
* **
39463232 TAAATATTAAA-ATTATACATGATGTTTGAT
1 TAAATATTAAATATCATACATGAACTTTGAT
*
39463262 TAAATGTTAAATATCATACATGAACTTTGAT
1 TAAATATTAAATATCATACATGAACTTTGAT
39463293 T
1 T
39463294 TTGTATAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 10 0.37
31 17 0.63
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (31 bp):
TAAATATTAAATATCATACATGAACTTTGAT
Found at i:39468321 original size:13 final size:13
Alignment explanation
Indices: 39468303--39468327 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39468293 AGTTTCGTTG
39468303 CCTTAGAGAATTT
1 CCTTAGAGAATTT
39468316 CCTTAGAGAATT
1 CCTTAGAGAATT
39468328 CTAACTTTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
CCTTAGAGAATTT
Found at i:39470381 original size:43 final size:43
Alignment explanation
Indices: 39470334--39470424 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 43
39470324 TCGGACAAGC
** *
39470334 CAAAGCATTTATACTGGCACATACAGTGCATCATC-AGATATAT
1 CAAAGCAACTATACTGGCACACACAGTGCATCATCGA-ATATAT
* * *
39470377 CAAAGCAACTGTATTGGCACACATAGTGCATCATCGAATATAT
1 CAAAGCAACTATACTGGCACACACAGTGCATCATCGAATATAT
39470420 CAAAG
1 CAAAG
39470425 TGATTTACAG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
43 40 0.98
44 1 0.02
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.25
Consensus pattern (43 bp):
CAAAGCAACTATACTGGCACACACAGTGCATCATCGAATATAT
Found at i:39470897 original size:2 final size:2
Alignment explanation
Indices: 39470890--39470915 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39470880 TATTAATGAA
39470890 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
39470916 TAAAGCCAAA
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:39470951 original size:2 final size:2
Alignment explanation
Indices: 39470946--39470977 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
39470936 TAAAAAAAAA
39470946 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
39470978 GTGTGTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39471086 original size:2 final size:2
Alignment explanation
Indices: 39471079--39471109 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
39471069 TTATTAACTA
39471079 AT 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 AT A
39471110 AGAAATAAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39471965 original size:41 final size:40
Alignment explanation
Indices: 39471917--39472016 Score: 107
Period size: 38 Copynumber: 2.5 Consensus size: 40
39471907 TCGACCTTGA
* *
39471917 GTCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAG
1 GTCGATGAGACACTGGGTGTCATCACTTTACTTCGGATAG
* ** *
39471957 ATTCGATGAGGTACT-GG-GT-ATCACTTTACTTCGGCTAG
1 -GTCGATGAGACACTGGGTGTCATCACTTTACTTCGGATAG
*
39471995 GCCGATGAGACACTGGGTGTCA
1 GTCGATGAGACACTGGGTGTCA
39472017 CTTTATTGCT
Statistics
Matches: 46, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
37 10 0.22
38 18 0.39
39 4 0.09
40 3 0.07
41 11 0.24
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (40 bp):
GTCGATGAGACACTGGGTGTCATCACTTTACTTCGGATAG
Found at i:39472010 original size:37 final size:38
Alignment explanation
Indices: 39471919--39472021 Score: 100
Period size: 37 Copynumber: 2.7 Consensus size: 38
39471909 GACCTTGAGT
* * **
39471919 CGATGAGACACTGGGTGTCATTATTTTACTTCGGATAGATT
1 CGATGAGACACT-GG-GT-ATCACTTTACTTCGGATAGAGC
** *
39471960 CGATGAGGTACTGGGTATCACTTTACTTCGGCTAG-GC
1 CGATGAGACACTGGGTATCACTTTACTTCGGATAGAGC
*
39471997 CGATGAGACACTGGGTGTCACTTTA
1 CGATGAGACACTGGGTATCACTTTA
39472022 TTGCTTCGAA
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
37 22 0.42
38 16 0.31
39 2 0.04
40 2 0.04
41 10 0.19
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.32
Consensus pattern (38 bp):
CGATGAGACACTGGGTATCACTTTACTTCGGATAGAGC
Found at i:39477713 original size:16 final size:17
Alignment explanation
Indices: 39477686--39477721 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
39477676 TATTAAAATT
39477686 ATTTTTTAAAATATAAA
1 ATTTTTTAAAATATAAA
39477703 ATTTTTT-AAATATAAA
1 ATTTTTTAAAATATAAA
39477719 ATT
1 ATT
39477722 ATTAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTTTTAAAATATAAA
Found at i:39477726 original size:15 final size:16
Alignment explanation
Indices: 39477694--39477729 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
39477684 TTATTTTTTA
*
39477694 AAATATAAAATTTTTT
1 AAATATAAAATTTATT
39477710 AAATATAAAA-TTATT
1 AAATATAAAATTTATT
39477725 AAATA
1 AAATA
39477730 ATTTAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATATAAAATTTATT
Found at i:39477819 original size:27 final size:29
Alignment explanation
Indices: 39477765--39477822 Score: 93
Period size: 27 Copynumber: 2.1 Consensus size: 29
39477755 TGTTTTTCCA
*
39477765 TCTAACACCACTTCTCTTCTTACCATTTT
1 TCTAACACCACTTATCTTCTTACCATTTT
39477794 TCTAACACCAC-TAT-TTCTTACCATTTT
1 TCTAACACCACTTATCTTCTTACCATTTT
39477821 TC
1 TC
39477823 CATCTAACAG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
27 15 0.54
28 2 0.07
29 11 0.39
ACGTcount: A:0.22, C:0.33, G:0.00, T:0.45
Consensus pattern (29 bp):
TCTAACACCACTTATCTTCTTACCATTTT
Found at i:39477843 original size:31 final size:32
Alignment explanation
Indices: 39477757--39477831 Score: 97
Period size: 29 Copynumber: 2.5 Consensus size: 32
39477747 TTCTTTCATG
*
39477757 TTTTTCCATCTAACACCACTTCTCTTCTTACCA
1 TTTTTCCATCTAACACCAC-TATCTTCTTACCA
39477790 -TTTT---TCTAACACCACTAT-TTCTTACCA
1 TTTTTCCATCTAACACCACTATCTTCTTACCA
39477817 TTTTTCCATCTAACA
1 TTTTTCCATCTAACA
39477832 GCGCTTCTTC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
27 9 0.24
28 6 0.16
29 11 0.30
31 7 0.19
32 4 0.11
ACGTcount: A:0.24, C:0.32, G:0.00, T:0.44
Consensus pattern (32 bp):
TTTTTCCATCTAACACCACTATCTTCTTACCA
Found at i:39478589 original size:28 final size:28
Alignment explanation
Indices: 39478548--39478603 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
39478538 TGATGATAGA
39478548 TTATAATTTT-AAAATAATTTTAATAATT
1 TTATAATTTTAAAAATAATTTTAA-AATT
39478576 TTAT-ATTTTAAAAAATAATTTTAAAATT
1 TTATAATTTT-AAAAATAATTTTAAAATT
39478604 ATTTACTGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 5 0.19
28 8 0.31
29 13 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
TTATAATTTTAAAAATAATTTTAAAATT
Found at i:39490343 original size:53 final size:53
Alignment explanation
Indices: 39490255--39490397 Score: 216
Period size: 53 Copynumber: 2.7 Consensus size: 53
39490245 ATATTCTTAT
* *
39490255 TTATATAATATATTTTAATATAATAATATATTTATTACTCCC-AATTACGACTGAA
1 TTAT-TAA-ATATTTGAATATAATAATATATTTATTAC-CCCAAATTACGACTCAA
39490310 TTATTAAATATTTGAATATAATAATATATTTATTACCCCAAATTACGACTCAA
1 TTATTAAATATTTGAATATAATAATATATTTATTACCCCAAATTACGACTCAA
* *
39490363 TTCTTAAATATTAGAATATAATAATATATTTATTA
1 TTATTAAATATTTGAATATAATAATATATTTATTA
39490398 ACCAATTCTT
Statistics
Matches: 83, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
52 3 0.04
53 73 0.88
54 3 0.04
55 4 0.05
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.43
Consensus pattern (53 bp):
TTATTAAATATTTGAATATAATAATATATTTATTACCCCAAATTACGACTCAA
Found at i:39491444 original size:38 final size:38
Alignment explanation
Indices: 39491393--39491467 Score: 150
Period size: 38 Copynumber: 2.0 Consensus size: 38
39491383 TTAAAAGGAA
39491393 AAGCAAATCAAGATATGAAAACACAATTTTTCTAATTC
1 AAGCAAATCAAGATATGAAAACACAATTTTTCTAATTC
39491431 AAGCAAATCAAGATATGAAAACACAATTTTTCTAATT
1 AAGCAAATCAAGATATGAAAACACAATTTTTCTAATT
39491468 TGAGAACACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.48, C:0.15, G:0.08, T:0.29
Consensus pattern (38 bp):
AAGCAAATCAAGATATGAAAACACAATTTTTCTAATTC
Found at i:39496358 original size:15 final size:14
Alignment explanation
Indices: 39496305--39496358 Score: 58
Period size: 15 Copynumber: 3.9 Consensus size: 14
39496295 TCCACCACCG
*
39496305 GGATATCCTCCACAA
1 GGATATCCTCC-TAA
39496320 GGATATCCT-C-AA
1 GGATATCCTCCTAA
*
39496332 GGTTATCCTCCTGAA
1 GGATATCCTCCT-AA
39496347 GGATATCCTCCT
1 GGATATCCTCCT
39496359 CCTTACGCCC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
12 10 0.29
13 1 0.03
14 1 0.03
15 22 0.65
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.28
Consensus pattern (14 bp):
GGATATCCTCCTAA
Found at i:39497065 original size:15 final size:15
Alignment explanation
Indices: 39497047--39497079 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
39497037 TCATTGAATA
39497047 AAAAAAACTTTGTGG
1 AAAAAAACTTTGTGG
39497062 AAAAAAACTTTGTGG
1 AAAAAAACTTTGTGG
39497077 AAA
1 AAA
39497080 CATTAGTCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.52, C:0.06, G:0.18, T:0.24
Consensus pattern (15 bp):
AAAAAAACTTTGTGG
Found at i:39497292 original size:29 final size:29
Alignment explanation
Indices: 39497259--39497317 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
39497249 CTGTTGTTGC
39497259 CTTCTGGATGCTTGCTTTTGAGGATCCAA
1 CTTCTGGATGCTTGCTTTTGAGGATCCAA
39497288 CTTCTGGATGCTTGCTTTTGAGGATCCAA
1 CTTCTGGATGCTTGCTTTTGAGGATCCAA
39497317 C
1 C
39497318 CATGCCGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (29 bp):
CTTCTGGATGCTTGCTTTTGAGGATCCAA
Found at i:39497909 original size:17 final size:18
Alignment explanation
Indices: 39497887--39497920 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
39497877 TAATTAAATG
*
39497887 AAAATATAAAAT-ATAAA
1 AAAATAAAAAATCATAAA
39497904 AAAATAAAAAATCATAA
1 AAAATAAAAAATCATAA
39497921 CTAATTGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (18 bp):
AAAATAAAAAATCATAAA
Found at i:39500291 original size:18 final size:17
Alignment explanation
Indices: 39500249--39500291 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
39500239 GTTTTAAGTT
*
39500249 TATAATATTTTATATTA
1 TATAATTTTTTATATTA
* *
39500266 TGTTATTTTTATATATTA
1 TATAATTTTT-TATATTA
39500284 TATAATTT
1 TATAATTT
39500292 AGAACACATT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TATAATTTTTTATATTA
Found at i:39503988 original size:15 final size:16
Alignment explanation
Indices: 39503952--39503989 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
39503942 GAGCAGTTGC
39503952 AGAAGCAGAAGCTGCA
1 AGAAGCAGAAGCTGCA
*
39503968 A-TAGCAGAAGCTG-A
1 AGAAGCAGAAGCTGCA
39503982 AGAAGCAG
1 AGAAGCAG
39503990 CAAGAGAGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
14 2 0.11
15 16 0.84
16 1 0.05
ACGTcount: A:0.45, C:0.16, G:0.32, T:0.08
Consensus pattern (16 bp):
AGAAGCAGAAGCTGCA
Found at i:39504035 original size:21 final size:21
Alignment explanation
Indices: 39504011--39504051 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
39504001 GAGGTTGCTG
*
39504011 AAGCTGATGCAGAGGCAGCAC
1 AAGCTGATGCAGAAGCAGCAC
**
39504032 AAGCTTTTGCAGAAGCAGCA
1 AAGCTGATGCAGAAGCAGCA
39504052 ATGAAAACTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.22, G:0.29, T:0.15
Consensus pattern (21 bp):
AAGCTGATGCAGAAGCAGCAC
Found at i:39504329 original size:29 final size:30
Alignment explanation
Indices: 39504286--39504376 Score: 76
Period size: 30 Copynumber: 3.1 Consensus size: 30
39504276 GTTGACGATT
** *
39504286 TTTGCAGCACACACCCAGTCATCATCCCT-
1 TTTGCAGCAGGCACCCAGTAATCATCCCTA
* ** **
39504315 TTTGCATCAGGCACCTGGTAATTGTCCCTA
1 TTTGCAGCAGGCACCCAGTAATCATCCCTA
* * *
39504345 TTTGTAGCAGGCACCCAGTGATCATCCTTA
1 TTTGCAGCAGGCACCCAGTAATCATCCCTA
39504375 TT
1 TT
39504377 ATTTGTAGCC
Statistics
Matches: 45, Mismatches: 16, Indels: 1
0.73 0.26 0.02
Matches are distributed among these distances:
29 21 0.47
30 24 0.53
ACGTcount: A:0.22, C:0.31, G:0.16, T:0.31
Consensus pattern (30 bp):
TTTGCAGCAGGCACCCAGTAATCATCCCTA
Found at i:39511983 original size:19 final size:20
Alignment explanation
Indices: 39511959--39512004 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
39511949 TTGAGGTTAC
39511959 TTGAAAGTTG-AAAGAGATA
1 TTGAAAGTTGTAAAGAGATA
**
39511978 TTGAAAG-TGTTTAGAGATA
1 TTGAAAGTTGTAAAGAGATA
39511997 TTGAAAGT
1 TTGAAAGT
39512005 GTTTGAAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 21 0.91
ACGTcount: A:0.41, C:0.00, G:0.26, T:0.33
Consensus pattern (20 bp):
TTGAAAGTTGTAAAGAGATA
Found at i:39512005 original size:19 final size:19
Alignment explanation
Indices: 39511971--39512008 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
39511961 GAAAGTTGAA
39511971 AGAGATATTGAAAGTGTTT
1 AGAGATATTGAAAGTGTTT
39511990 AGAGATATTGAAAGTGTTT
1 AGAGATATTGAAAGTGTTT
39512009 GAAGTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.26, T:0.37
Consensus pattern (19 bp):
AGAGATATTGAAAGTGTTT
Found at i:39518227 original size:11 final size:10
Alignment explanation
Indices: 39518185--39518224 Score: 55
Period size: 11 Copynumber: 3.9 Consensus size: 10
39518175 ATAATTTATC
39518185 AAATATACTTA
1 AAATATA-TTA
39518196 AAA-ATATTA
1 AAATATATTA
39518205 AAATATATTGA
1 AAATATATT-A
39518216 AAATATATT
1 AAATATATT
39518225 GAATTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 6 0.22
10 8 0.30
11 13 0.48
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (10 bp):
AAATATATTA
Found at i:39518750 original size:28 final size:28
Alignment explanation
Indices: 39518702--39518756 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
39518692 TACCCAATTT
* *
39518702 TTTTTAATCTATTCATCAT-AAATAATA
1 TTTTTAATCTATTAATAATAAAATAATA
*
39518729 TTTTTAATGTATTTAATAATAAAATAAT
1 TTTTTAATCTA-TTAATAATAAAATAAT
39518757 TTTCAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 10 0.43
28 6 0.26
29 7 0.30
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (28 bp):
TTTTTAATCTATTAATAATAAAATAATA
Found at i:39554206 original size:2 final size:2
Alignment explanation
Indices: 39554190--39554223 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
39554180 TATTAACATT
*
39554190 TA TA AA TA T- 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
39554224 TGGTAGAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39554590 original size:13 final size:13
Alignment explanation
Indices: 39554574--39554599 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39554564 GTTAATATTT
39554574 AATTAATTTTTAA
1 AATTAATTTTTAA
39554587 AATTAATTTTTAA
1 AATTAATTTTTAA
39554600 TTTTCAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AATTAATTTTTAA
Found at i:39554601 original size:20 final size:19
Alignment explanation
Indices: 39554576--39554645 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 19
39554566 TAATATTTAA
39554576 TTAATTTTTAAAATTAATTT
1 TTAATTTTTAAAA-TAATTT
*
39554596 TTAATTTTCAAAAATAATTT
1 TTAATTTT-TAAAATAATTT
* **
39554616 ATAATTTTTTGAAT--TTT
1 TTAATTTTTAAAATAATTT
39554633 TTAATTTTTAAAA
1 TTAATTTTTAAAA
39554646 ATAAAATAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
17 13 0.32
19 3 0.07
20 21 0.51
21 4 0.10
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (19 bp):
TTAATTTTTAAAATAATTT
Found at i:39556712 original size:29 final size:30
Alignment explanation
Indices: 39556637--39556714 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 30
39556627 TCAAATTGCA
* *
39556637 AAAAGTATAGAGACTAAAATTGAATAATTT
1 AAAAGTATAGAGACTAAAATTGAACAAATT
* *
39556667 GAAAAGTACA-AGTACTAAAATTGACCAAATT
1 -AAAAGTATAGAG-ACTAAAATTGAACAAATT
39556698 -AAAGTATAGAGACTAAA
1 AAAAGTATAGAGACTAAA
39556715 TTCAGAACTT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
29 13 0.32
30 4 0.10
31 23 0.57
ACGTcount: A:0.54, C:0.08, G:0.14, T:0.24
Consensus pattern (30 bp):
AAAAGTATAGAGACTAAAATTGAACAAATT
Found at i:39562747 original size:12 final size:12
Alignment explanation
Indices: 39562730--39562754 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39562720 TACGGAGTTT
39562730 TAAGCGTTTCAG
1 TAAGCGTTTCAG
39562742 TAAGCGTTTCAG
1 TAAGCGTTTCAG
39562754 T
1 T
39562755 TTTTAAATTG
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:0.16, G:0.24, T:0.36
Consensus pattern (12 bp):
TAAGCGTTTCAG
Found at i:39570326 original size:24 final size:25
Alignment explanation
Indices: 39570289--39570335 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
39570279 CTTTATACCA
*
39570289 AATAAAATTTTCAA-AAAAATGAAG
1 AATAAAATTATCAACAAAAATGAAG
* *
39570313 AATAATATTATCAACAAATATGA
1 AATAAAATTATCAACAAAAATGA
39570336 TATAATAAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.28
Consensus pattern (25 bp):
AATAAAATTATCAACAAAAATGAAG
Found at i:39571414 original size:20 final size:20
Alignment explanation
Indices: 39571368--39571414 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
39571358 TAAAAAAATT
* *
39571368 ATAAAAA-AATTAAATTTTA
1 ATAAAAATATTTAAAATTTA
39571387 ATAAAAATATTTAAAATTTA
1 ATAAAAATATTTAAAATTTA
*
39571407 TTAAAAAT
1 ATAAAAAT
39571415 TATAAAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATAAAAATATTTAAAATTTA
Found at i:39571443 original size:50 final size:48
Alignment explanation
Indices: 39571361--39571468 Score: 119
Period size: 50 Copynumber: 2.2 Consensus size: 48
39571351 CATATGGTAA
* ** *
39571361 AAAAATTATAAAAAAATTAAATTTTAATAAAAATATTTAAAATTTATT
1 AAAAATTATAAAAAAATTAAATTTTAATAAAAACATAAAAAATATATT
**
39571409 AAAAATTATAAAAACTTGTATAATTTT-ATAAAAAACATAAAAAATATATT
1 AAAAATTATAAAAAAAT-TA-AATTTTAAT-AAAAACATAAAAAATATATT
*
39571459 AAAAAATATA
1 AAAAATTATA
39571469 GAAATATAGA
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
48 15 0.30
49 4 0.08
50 31 0.62
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (48 bp):
AAAAATTATAAAAAAATTAAATTTTAATAAAAACATAAAAAATATATT
Found at i:39571756 original size:20 final size:21
Alignment explanation
Indices: 39571733--39571781 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
39571723 TTAAAAGATC
39571733 TTTTTAATACATTTTATA-AT
1 TTTTTAATACATTTTATATAT
** **
39571753 TTTTTACGATTTTTTATATAT
1 TTTTTAATACATTTTATATAT
39571774 TTTTTAAT
1 TTTTTAAT
39571782 TTTTAATGAA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (21 bp):
TTTTTAATACATTTTATATAT
Found at i:39571785 original size:20 final size:19
Alignment explanation
Indices: 39571744--39571785 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
39571734 TTTTAATACA
39571744 TTTTATAATTTTTTACGATT
1 TTTTATAATTTTTTAC-ATT
39571764 TTTTATATATTTTTTA-ATT
1 TTTTATA-ATTTTTTACATT
39571783 TTT
1 TTT
39571786 AATGAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.29
20 7 0.33
21 8 0.38
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (19 bp):
TTTTATAATTTTTTACATT
Found at i:39571796 original size:18 final size:18
Alignment explanation
Indices: 39571775--39571825 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
39571765 TTTATATATT
*
39571775 TTTTAATTTTTAATGAAA
1 TTTTAATTTTTAATAAAA
*
39571793 TTTTAACTTTTTATTAAAA
1 TTTTAA-TTTTTAATAAAA
39571812 TTTAATAATTTTTA
1 TTT--TAATTTTTA
39571826 TAACTTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 6 0.21
19 13 0.46
20 6 0.21
21 3 0.11
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (18 bp):
TTTTAATTTTTAATAAAA
Found at i:39571809 original size:29 final size:29
Alignment explanation
Indices: 39571765--39571844 Score: 69
Period size: 29 Copynumber: 2.8 Consensus size: 29
39571755 TTTACGATTT
39571765 TTTATATA-TTTT-TTAATTTTTAATGAA-A
1 TTTATA-ACTTTTATTAATTTTTAAT-AATA
** *
39571793 TTT-TAACTTTTTATTAAAATTTAATAATT
1 TTTATAAC-TTTTATTAATTTTTAATAATA
*
39571822 TTTATAACTTTTATTGATTTTTA
1 TTTATAACTTTTATTAATTTTTA
39571845 TTTTTTATAC
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
26 1 0.02
27 2 0.05
28 9 0.22
29 25 0.61
30 4 0.10
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (29 bp):
TTTATAACTTTTATTAATTTTTAATAATA
Found at i:39582813 original size:29 final size:29
Alignment explanation
Indices: 39582754--39582814 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 29
39582744 ATTAATAATT
* * *
39582754 TATGAAAATCGAATTAAATCAAAATTTTA
1 TATGAAAATCGAATAAAATCAAAAGTCTA
*
39582783 TATGTAAAATCGTATAAAATC-AAAGTCTA
1 TATG-AAAATCGAATAAAATCAAAAGTCTA
39582812 TAT
1 TAT
39582815 ATAATAATGC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 13 0.48
30 14 0.52
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.34
Consensus pattern (29 bp):
TATGAAAATCGAATAAAATCAAAAGTCTA
Found at i:39587321 original size:12 final size:12
Alignment explanation
Indices: 39587304--39587329 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
39587294 TTTTTATTTG
39587304 CACTGCTTGCAT
1 CACTGCTTGCAT
39587316 CACTGCTTGCAT
1 CACTGCTTGCAT
39587328 CA
1 CA
39587330 ATTGAAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.35, G:0.15, T:0.31
Consensus pattern (12 bp):
CACTGCTTGCAT
Found at i:39587656 original size:31 final size:31
Alignment explanation
Indices: 39587589--39587656 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
39587579 TTTAATAAAT
*
39587589 TTTTTTGAATAGTTCAGTGACTTAAATGAAA
1 TTTTTTAAATAGTTCAGTGACTTAAATGAAA
* * *
39587620 ATTTTTAAATAGTTTAGTGA-TTAAATTGTAA
1 TTTTTTAAATAGTTCAGTGACTTAAA-TGAAA
39587651 TTTTTT
1 TTTTTT
39587657 TAGTTAACTG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 5 0.16
31 26 0.84
ACGTcount: A:0.34, C:0.03, G:0.13, T:0.50
Consensus pattern (31 bp):
TTTTTTAAATAGTTCAGTGACTTAAATGAAA
Found at i:39590264 original size:20 final size:20
Alignment explanation
Indices: 39590218--39590261 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
39590208 TTTTTTAAAG
39590218 AAAA-TCAAAATAATTTTCA
1 AAAATTCAAAATAATTTTCA
39590237 AAAATTCAAAAT-ATTTAT-A
1 AAAATTCAAAATAATTT-TCA
39590256 AAAATT
1 AAAATT
39590262 TCATAATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAATTCAAAATAATTTTCA
Found at i:39591503 original size:21 final size:21
Alignment explanation
Indices: 39591479--39591518 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
39591469 TATTCTCCAC
39591479 ATATTTATTATTACTAAAAAT
1 ATATTTATTATTACTAAAAAT
39591500 ATATTTATTATTACTAAAA
1 ATATTTATTATTACTAAAA
39591519 GTAGTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (21 bp):
ATATTTATTATTACTAAAAAT
Found at i:39595208 original size:13 final size:13
Alignment explanation
Indices: 39595172--39595210 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
39595162 TTGATATATA
*
39595172 ATTTTAATTTTA-
1 ATTTTAATTTGAT
39595184 ATTTTTAATTTGAT
1 A-TTTTAATTTGAT
39595198 ATTTTAATTTGAT
1 ATTTTAATTTGAT
39595211 TTCGATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 1 0.04
13 22 0.92
14 1 0.04
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (13 bp):
ATTTTAATTTGAT
Found at i:39595221 original size:18 final size:20
Alignment explanation
Indices: 39595178--39595232 Score: 71
Period size: 18 Copynumber: 2.9 Consensus size: 20
39595168 TATAATTTTA
*
39595178 ATTTTAATTTTTAATTT-GAT
1 ATTTTAA-TTTGAATTTCGAT
39595198 ATTTTAATTTG-ATTTCGAT
1 ATTTTAATTTGAATTTCGAT
39595217 A-TTTAATTTGAATTTC
1 ATTTTAATTTGAATTTC
39595233 TAAAATTATG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
18 13 0.41
19 12 0.38
20 7 0.22
ACGTcount: A:0.29, C:0.04, G:0.07, T:0.60
Consensus pattern (20 bp):
ATTTTAATTTGAATTTCGAT
Found at i:39595771 original size:17 final size:18
Alignment explanation
Indices: 39595738--39595771 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39595728 TTATTTTTTT
*
39595738 AATATTTTATTAATTAAA
1 AATATTTTATAAATTAAA
39595756 AATATTTT-TAAATTAA
1 AATATTTTATAAATTAA
39595772 CTCTTGTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AATATTTTATAAATTAAA
Found at i:39598463 original size:38 final size:36
Alignment explanation
Indices: 39598400--39598507 Score: 109
Period size: 38 Copynumber: 3.0 Consensus size: 36
39598390 GTCAGAAATT
*
39598400 AAATTATAATTTTTAT-AATAATAAAAATATAATTTTA
1 AAATTAT-ATTTTTATAAATATTAAAAAT-TAATTTTA
* *
39598437 ATAATTATATTTTTATAAATTTTAAAAGATTAA-ATTA
1 A-AATTATATTTTTATAAATATTAAAA-ATTAATTTTA
39598474 AAATTATATTTTT-TAAA-ATT-AAAATGTAATTTTA
1 AAATTATATTTTTATAAATATTAAAAAT-TAATTTTA
39598508 TTTTTATTAA
Statistics
Matches: 61, Mismatches: 5, Indels: 13
0.77 0.06 0.16
Matches are distributed among these distances:
32 2 0.03
33 6 0.10
34 5 0.08
35 4 0.07
36 12 0.20
37 13 0.21
38 17 0.28
39 2 0.03
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (36 bp):
AAATTATATTTTTATAAATATTAAAAATTAATTTTA
Found at i:39600185 original size:12 final size:12
Alignment explanation
Indices: 39600168--39600205 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
39600158 TTAAATTAAA
39600168 TTTTATAATTCT
1 TTTTATAATTCT
39600180 TTTTATAATT-T
1 TTTTATAATTCT
*
39600191 TTTAATAATTTCT
1 TTTTATAA-TTCT
39600204 TT
1 TT
39600206 GATTTGAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 8 0.35
12 12 0.52
13 3 0.13
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTATAATTCT
Found at i:39600193 original size:11 final size:11
Alignment explanation
Indices: 39600168--39600201 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
39600158 TTAAATTAAA
39600168 TTTTATAATTCT
1 TTTTATAATT-T
39600180 TTTTATAATTT
1 TTTTATAATTT
*
39600191 TTTAATAATTT
1 TTTTATAATTT
39600202 CTTTGATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTTATAATTT
Found at i:39603645 original size:45 final size:45
Alignment explanation
Indices: 39603579--39603684 Score: 169
Period size: 45 Copynumber: 2.4 Consensus size: 45
39603569 CGGTAACCGT
* * *
39603579 CAATTCAAAGAGTTTTGTATCATACTGGTCCTGTGTTGTGA-AGAG
1 CAATTCAAAGAGTTTTCTATCATACTGGTCCTGTATTG-CATAGAG
39603624 CAATTCAAAGAGTTTTCTATCATACTGGTCCTGTATTGCATAGAG
1 CAATTCAAAGAGTTTTCTATCATACTGGTCCTGTATTGCATAGAG
39603669 CAATTCAAAGAGTTTT
1 CAATTCAAAGAGTTTT
39603685 AGTTTTCGTA
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
44 1 0.02
45 56 0.98
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (45 bp):
CAATTCAAAGAGTTTTCTATCATACTGGTCCTGTATTGCATAGAG
Found at i:39607474 original size:79 final size:82
Alignment explanation
Indices: 39607369--39607521 Score: 188
Period size: 79 Copynumber: 1.9 Consensus size: 82
39607359 GGACCCTAAT
* * * * * * *
39607369 ATGAGAAAATTTTAATTTTAATTTTTATAATTTATAAA-ATATTAA-T-TTAGTAATGATAAAAT
1 ATGAGAAAATTTTAATTTAAACTTTTAAAAATAATAAATATATAAATTATTA-AAATGATAAAAT
39607431 TAT-ATTTTAATCTCAAA
65 TATAATTTTAATCTCAAA
* *
39607448 ATGATAAAATTTTGATTTAAACTTTTAAAAATAATAAATATATAAATTATTAAAATGATAAAATT
1 ATGAGAAAATTTTAATTTAAACTTTTAAAAATAATAAATATATAAATTATTAAAATGATAAAATT
39607513 ATAATTTTA
66 ATAATTTTA
39607522 CTATGCGCGG
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
79 31 0.51
80 6 0.10
81 15 0.25
82 9 0.15
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (82 bp):
ATGAGAAAATTTTAATTTAAACTTTTAAAAATAATAAATATATAAATTATTAAAATGATAAAATT
ATAATTTTAATCTCAAA
Found at i:39609620 original size:7 final size:7
Alignment explanation
Indices: 39609608--39609658 Score: 70
Period size: 7 Copynumber: 7.3 Consensus size: 7
39609598 TTGAGTTCAT
39609608 GTTTAAG
1 GTTTAAG
39609615 GTTTAAG
1 GTTTAAG
39609622 GTTTAAG
1 GTTTAAG
39609629 GTTTAAG
1 GTTTAAG
39609636 GTTTTAA-
1 G-TTTAAG
39609643 GTTT-AG
1 GTTTAAG
39609649 GATTTAAG
1 G-TTTAAG
39609657 GT
1 GT
39609659 AAAAAAAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
5 1 0.03
6 4 0.10
7 27 0.68
8 8 0.20
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.45
Consensus pattern (7 bp):
GTTTAAG
Found at i:39613879 original size:30 final size:31
Alignment explanation
Indices: 39613832--39613923 Score: 89
Period size: 31 Copynumber: 3.0 Consensus size: 31
39613822 TCCGGATTCA
*
39613832 AAATCTTTAAAAATTTTGAAGGAACTAATTA-
1 AAAT-TTTAAAACTTTTGAAGGAACTAATTAG
* * **
39613863 AATTTTTAAATCTTTTGGAAGG-TTTAATTAG
1 AAATTTTAAAACTTTT-GAAGGAACTAATTAG
* *
39613894 AAATTTTAAAAGTTTTGAAGGACCTAATTA
1 AAATTTTAAAACTTTTGAAGGAACTAATTA
39613924 CAATAATATT
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
30 21 0.44
31 27 0.56
ACGTcount: A:0.41, C:0.05, G:0.13, T:0.40
Consensus pattern (31 bp):
AAATTTTAAAACTTTTGAAGGAACTAATTAG
Found at i:39616005 original size:16 final size:17
Alignment explanation
Indices: 39615984--39616020 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
39615974 ACAGCGTAAA
39615984 TTTAAATAA-ATTTTTT
1 TTTAAATAACATTTTTT
39616000 TTTAAATAATCATTTTTT
1 TTTAAATAA-CATTTTTT
39616018 TTT
1 TTT
39616021 TATGTTGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.47
18 10 0.53
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTAAATAACATTTTTT
Found at i:39616406 original size:20 final size:20
Alignment explanation
Indices: 39616381--39616421 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
39616371 TTTTTTCGAA
*
39616381 TCGAATAGAGTCAAAAAATT
1 TCGAATAGAGTAAAAAAATT
*
39616401 TCGAATCGAGTAAAAAAATT
1 TCGAATAGAGTAAAAAAATT
39616421 T
1 T
39616422 TAAGTTAGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.27
Consensus pattern (20 bp):
TCGAATAGAGTAAAAAAATT
Found at i:39616416 original size:103 final size:105
Alignment explanation
Indices: 39616298--39616519 Score: 358
Period size: 103 Copynumber: 2.1 Consensus size: 105
39616288 TCGAGTCGAG
* *
39616298 TCGAATCGAGTAAAAAAATTTTAAGTTAGTCAAGTTGGCGAATCTTATTTTTGCAATCGAATTCA
1 TCGAATCGAGTAAAAAAATTTTAAGTTAGTCAAGTTGGCGAATCCTATTTTTGCAATCGAACTCA
39616363 ATTTGAAATTTTTTCGAATCGAAT-A-GAGTCAAAAAATT
66 ATTTGAAATTTTTTCGAATCGAATAACGAGTCAAAAAATT
* *
39616401 TCGAATCGAGTAAAAAAATTTTAAGTTAGTCGAGTTGGCGAATCCTATTTTTGCAATTGAACTCA
1 TCGAATCGAGTAAAAAAATTTTAAGTTAGTCAAGTTGGCGAATCCTATTTTTGCAATCGAACTCA
39616466 ATTTGAAATTTTTTCGAATCGAATCGAATCGAGTCAAAAAATT
66 ATTTGAAATTTTTTCGAATCGAAT--AA-CGAGTCAAAAAATT
*
39616509 TCAAATCGAGT
1 TCGAATCGAGT
39616520 CGAGTCGAGT
Statistics
Matches: 109, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
103 85 0.78
106 1 0.01
108 23 0.21
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (105 bp):
TCGAATCGAGTAAAAAAATTTTAAGTTAGTCAAGTTGGCGAATCCTATTTTTGCAATCGAACTCA
ATTTGAAATTTTTTCGAATCGAATAACGAGTCAAAAAATT
Found at i:39627774 original size:205 final size:211
Alignment explanation
Indices: 39627383--39627862 Score: 636
Period size: 210 Copynumber: 2.3 Consensus size: 211
39627373 AATGTGACAG
* *
39627383 TAAGACTTCAGAACCATACGTTCTGTGG-GTTTAATTGAATAAACAACTTAAGCCATCATCTTAA
1 TAAGACTTCAGAACCATACGTTCTGTGGTTTTTAA-TGAATAAACAACGTAAGCCATCATCTTAA
* * *
39627447 TTCCATTTAGAGAACACATGAAATGCCAATAATCAACAAGATCATCACCTTGCAAAGACAATCAA
65 ATCCATTTAGAGAACACATAAAATGCCAATAATCAACAAGATCATCACATTGCAAAG--AATCAA
* *
39627512 TAAGCACACTTAACAATATGCAGTCACTCCATGGACCATACTAATCAAACGCCTTTAACACCATA
128 TAAGCACACTTAACAATATGCAGCCACTCCATGGACAATACTAATCAAACGCCTTTAACACCATA
*
39627577 ACACAAGAC-CA-AT-CAA
193 ACACAAGACGAATATACAA
* * * * *
39627593 TAAGACTTAAAAACTATACGTACTGTGGTTTTTAATGAATAAACTACGTAAGCCAAT-ATC-TAA
1 TAAGACTTCAGAACCATACGTTCTGTGGTTTTTAATGAATAAACAACGTAAGCC-ATCATCTTAA
* *
39627656 ATCCATTTAGAGAACACATAAAATGCCAATAATCAACAGGATCATCACATTGCATAG-A-CAATA
65 ATCCATTTAGAGAACACATAAAATGCCAATAATCAACAAGATCATCACATTGCAAAGAATCAATA
*
39627719 AGCACACTTAACAATATGCAGCCACTCCATGGACAATACTAATCAAA-GTCCTTTAACACCATAG
130 AGCACACTTAACAATATGCAGCCACTCCATGGACAATACTAATCAAACG-CCTTTAACACCATAA
* *
39627783 CCCATGACTGAATATGACAA
194 CACAAGAC-GAATAT-ACAA
* ** *
39627803 TAAGACTTCAGAACCATACATTCTGTGGTTTTTAATGAATAAACAATTTAAGCCAACATC
1 TAAGACTTCAGAACCATACGTTCTGTGGTTTTTAATGAATAAACAACGTAAGCCATCATC
39627863 GAAATGCCAA
Statistics
Matches: 234, Mismatches: 27, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
204 1 0.00
205 70 0.30
206 1 0.00
207 1 0.00
208 2 0.01
209 56 0.24
210 96 0.41
211 7 0.03
ACGTcount: A:0.41, C:0.22, G:0.11, T:0.25
Consensus pattern (211 bp):
TAAGACTTCAGAACCATACGTTCTGTGGTTTTTAATGAATAAACAACGTAAGCCATCATCTTAAA
TCCATTTAGAGAACACATAAAATGCCAATAATCAACAAGATCATCACATTGCAAAGAATCAATAA
GCACACTTAACAATATGCAGCCACTCCATGGACAATACTAATCAAACGCCTTTAACACCATAACA
CAAGACGAATATACAA
Found at i:39629638 original size:31 final size:29
Alignment explanation
Indices: 39629551--39629649 Score: 90
Period size: 29 Copynumber: 3.2 Consensus size: 29
39629541 TTAACAACCT
39629551 AAATGAAAACTGTTAAATAATTTAGTGATCA
1 AAATGAAAA-T-TTAAATAATTTAGTGATCA
* * *** *
39629582 AATTGTAAATTTTTTTAATTAAGTGATCA
1 AAATGAAAATTTAAATAATTTAGTGATCA
*
39629611 AAATGAAAATTTAACCATAATTTAGTGACTAA
1 AAATGAAAATTTAA--ATAATTTAGTGA-TCA
39629643 AAATGAA
1 AAATGAA
39629650 GTTTACCCAA
Statistics
Matches: 52, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
29 25 0.48
30 1 0.02
31 17 0.33
32 9 0.17
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.35
Consensus pattern (29 bp):
AAATGAAAATTTAAATAATTTAGTGATCA
Found at i:39633406 original size:26 final size:27
Alignment explanation
Indices: 39633349--39633407 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
39633339 AAGGTTTAAT
* *
39633349 ACAAGAATCTCTCTCAAGAATTTCAAC
1 ACAACAATCTCTCTCAAGAATTACAAC
39633376 A-AACAATCTCTCTTCAA-AA-TACAAC
1 ACAACAATCTCTC-TCAAGAATTACAAC
39633401 ACAACAA
1 ACAACAA
39633408 AAATAGTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
25 6 0.21
26 17 0.61
27 5 0.18
ACGTcount: A:0.47, C:0.27, G:0.03, T:0.22
Consensus pattern (27 bp):
ACAACAATCTCTCTCAAGAATTACAAC
Found at i:39633568 original size:22 final size:22
Alignment explanation
Indices: 39633543--39633587 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
39633533 TCAAAGAAAG
39633543 AAATGAAAACCAGAGCATGCAA
1 AAATGAAAACCAGAGCATGCAA
39633565 AAATGAAAACCAGAGCATGCAA
1 AAATGAAAACCAGAGCATGCAA
39633587 A
1 A
39633588 GATACTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.56, C:0.18, G:0.18, T:0.09
Consensus pattern (22 bp):
AAATGAAAACCAGAGCATGCAA
Found at i:39635077 original size:42 final size:38
Alignment explanation
Indices: 39635030--39635122 Score: 116
Period size: 38 Copynumber: 2.3 Consensus size: 38
39635020 ACATTAAAAA
*
39635030 TTATTTAGATTAAAAAACACTATAATAAATGTAATAAATATT
1 TTATTT-GATT-AAAAACAC-A-AATAAATATAATAAATATT
*
39635072 TTATTTTATTAAAAACACAAATAAATATAATAAATATT
1 TTATTTGATTAAAAACACAAATAAATATAATAAATATT
39635110 TTATTCT-ATTAAA
1 TTATT-TGATTAAA
39635123 TATAAATTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
38 29 0.60
39 2 0.04
40 8 0.17
41 3 0.06
42 6 0.12
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (38 bp):
TTATTTGATTAAAAACACAAATAAATATAATAAATATT
Found at i:39635103 original size:38 final size:40
Alignment explanation
Indices: 39635042--39635122 Score: 130
Period size: 38 Copynumber: 2.1 Consensus size: 40
39635032 ATTTAGATTA
* *
39635042 AAAAACACTATAATAAATGTAATAAATATTTTATTTTATT
1 AAAAACACTATAATAAATATAATAAATATTTTATTCTATT
39635082 AAAAACAC-A-AATAAATATAATAAATATTTTATTCTATT
1 AAAAACACTATAATAAATATAATAAATATTTTATTCTATT
39635120 AAA
1 AAA
39635123 TATAAATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
38 30 0.77
39 1 0.03
40 8 0.21
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.38
Consensus pattern (40 bp):
AAAAACACTATAATAAATATAATAAATATTTTATTCTATT
Found at i:39649198 original size:213 final size:213
Alignment explanation
Indices: 39648595--39649638 Score: 1539
Period size: 213 Copynumber: 4.9 Consensus size: 213
39648585 CTGTGAGCCT
* *
39648595 TGAGATAAAACCCGAAGCAGAATTAAGACACATCAGTATATATCCATTTGTATATCTCAATATAT
1 TGAGATAAAACCCGAAGCAGAATTGAGACACATCAATATATATCCATTTGTATATCTC--TATAT
* ** *
39648660 ACACATACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCGGCCACCTTATCTGTAAAAT
64 --ATATACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCATCTACCTTATCTGTAAAAT
* * * *
39648725 GTGATCAATTTGGCAAATATTCCATATTTAAGAACTTTCCTGGAATATTTTCTGAAACTATGACC
127 GTGATCATTTTAGCAAATATTCCAT-CTTAAGAACTTTCCTGGAAAATTTTCTGAAACTATGACC
*
39648790 CATCAAGGCTCTTAGCAGAATCG
191 CATCAAGACTCTTAGCAGAATCG
* *
39648813 TGAGATAAAACCTGAAGCAGAATTGAGACACATCAATATGTATCCATTTGTATATCTCAATATAT
1 TGAGATAAAACCCGAAGCAGAATTGAGACACATCAATATATATCCATTTGTATATCTC--TATAT
* * *
39648878 ATATACATACGCGTGTGTAGTTAGAATATTTGGACAAGTTGTCCTCTACCTTATCTGTAAAATGT
64 ATATACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCATCTACCTTATCTGTAAAATGT
* *
39648943 GATCATTTTAGCAAATATTCCATCTTAAGAACTTTACTGGAAAATTTTCTGATACTATGACCCAT
129 GATCATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAAATTTTCTGAAACTATGACCCAT
*
39649008 CAAGACTCTTAGCAGAATGG
194 CAAGACTCTTAGCAGAATCG
* *
39649028 TGAGATAAAACCCGAAGCAGAATTGAGACACTTCAATATATATCCAATTGTATATCTCTATATAT
1 TGAGATAAAACCCGAAGCAGAATTGAGACACATCAATATATATCCATTTGTATATCTCTATATAT
* *
39649093 ATACATACGCATGTCTAGTTAGACTATTTGGACAAGCTGTCATCTACCTTATCTGTAAAATGTGA
66 ATACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCATCTACCTTATCTGTAAAATGTGA
* *
39649158 TTATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAAATTTTCTGAAACTGTGACCCATCA
131 TCATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAAATTTTCTGAAACTATGACCCATCA
*
39649223 AGACTCTTAGCAGAGTCG
196 AGACTCTTAGCAGAATCG
* * *
39649241 TGAGATAGAATCCGAAGCAGAATTGAGACGCATCAATATATATCCATTTG------T-TATATAT
1 TGAGATAAAACCCGAAGCAGAATTGAGACACATCAATATATATCCATTTGTATATCTCTATATAT
39649299 ATACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCATCTACCTTATCTGTAAAATGTGA
66 ATACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCATCTACCTTATCTGTAAAATGTGA
*
39649364 TCATTTTGGCAAATATTCCATCTTAAGAACTTTCCTGGAAAATTTTCTGAAACTATGACCCATCA
131 TCATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAAATTTTCTGAAACTATGACCCATCA
* * *
39649429 AGGCTCTTAGTAGAGTCG
196 AGACTCTTAGCAGAATCG
*
39649447 TGAGATAAAACCCGAAGCAGAATTGAGCCACATCAATATATATATATATATATCCATTTGTATAT
1 TGAGATAAAACCCGAAGCAGAATTGAG--ACA-C-----AT-CA-ATATATATCCATTTGTATAT
* * *
39649512 CTCAATTTATATACATACGCATGTCTAG-TAGAAT-TTTGGACAAGTTGTCACCTACCTTATCTG
56 CTCTATATATATACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCATCTACCTTATCTG
39649575 TAAAATGTGATCATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAAATTTTCTGAAACT
121 TAAAATGTGATCATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAAATTTTCTGAAACT
39649639 CTTTTTCCCC
Statistics
Matches: 756, Mismatches: 53, Indels: 31
0.90 0.06 0.04
Matches are distributed among these distances:
206 173 0.23
207 1 0.00
208 2 0.00
209 1 0.00
213 189 0.25
214 2 0.00
215 111 0.15
216 95 0.13
218 61 0.08
221 91 0.12
222 7 0.01
223 23 0.03
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (213 bp):
TGAGATAAAACCCGAAGCAGAATTGAGACACATCAATATATATCCATTTGTATATCTCTATATAT
ATACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCATCTACCTTATCTGTAAAATGTGA
TCATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAAATTTTCTGAAACTATGACCCATCA
AGACTCTTAGCAGAATCG
Found at i:39649404 original size:419 final size:421
Alignment explanation
Indices: 39648595--39649638 Score: 1533
Period size: 419 Copynumber: 2.4 Consensus size: 421
39648585 CTGTGAGCCT
* * *
39648595 TGAGATAAAACCCGAAGCAGAATTAAGACACATCAGTATATATCCATTTGTATATCTCAATATAT
1 TGAGATAAAACCCGAAGCAGAATTGAGACACTTCAATATATATCCATTTGTATATCTC--TATAT
* *
39648660 ACACATACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCGGCC-ACCTTATCTGTAAAA
64 --ATATACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTC-ACCTACCTTATCTGTAAAA
* * * *
39648724 TGTGATCAATTTGGCAAATATTCCATATTTAAGAACTTTCCTGGAATATTTTCTGAAACTATGAC
126 TGTGATCATTTTAGCAAATATTCCAT-CTTAAGAACTTTCCTGGAAAATTTTCTGAAACTATGAC
* *
39648789 CCATCAAGGCTCTTAGCAGAATCGTGAGATAAAACCTGAAGCAGAATTGAGACACATCAATATGT
190 CCATCAAGACTCTTAGCAGAATCGTGAGATAAAACCTGAAGCAGAATTGAGACACATCAATATAT
* *
39648854 ATCCATTTGTATATCTCAATATATATATACATACGCGTGTGTAGTTAGAATATTTGGACAAGTTG
255 ATCCATTTG----T-T--ATATATATATACATACGCATGTCTAGTTAGAATATTTGGACAAGTTG
*
39648919 TCCTCTACCTTATCTGTAAAATGTGATCATTTTAGCAAATATTCCATCTTAAGAACTTTACTGGA
313 TCATCTACCTTATCTGTAAAATGTGATCATTTTAGCAAATATTCCATCTTAAGAACTTTACTGGA
* *
39648984 AAATTTTCTGATACTATGACCCATCAAGACTCTTAGCAGAATGG
378 AAATTTTCTGAAACTATGACCCATCAAGACTCTTAGCAGAATCG
*
39649028 TGAGATAAAACCCGAAGCAGAATTGAGACACTTCAATATATATCCAATTGTATATCTCTATATAT
1 TGAGATAAAACCCGAAGCAGAATTGAGACACTTCAATATATATCCATTTGTATATCTCTATATAT
* * *
39649093 ATACATACGCATGTCTAGTTAGACTATTTGGACAAGCTGTCATCTACCTTATCTGTAAAATGTGA
66 ATACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCACCTACCTTATCTGTAAAATGTGA
* *
39649158 TTATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAAATTTTCTGAAACTGTGACCCATCA
131 TCATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAAATTTTCTGAAACTATGACCCATCA
* * *
39649223 AGACTCTTAGCAGAGTCGTGAGATAGAATCC-GAAGCAGAATTGAGACGCATCAATATATATCCA
196 AGACTCTTAGCAGAATCGTGAGATA-AAACCTGAAGCAGAATTGAGACACATCAATATATATCCA
39649287 TTTG-T-TATATATATACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCATCTACCTTA
260 TTTGTTATATATATATACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCATCTACCTTA
* *
39649350 TCTGTAAAATGTGATCATTTTGGCAAATATTCCATCTTAAGAACTTTCCTGGAAAATTTTCTGAA
325 TCTGTAAAATGTGATCATTTTAGCAAATATTCCATCTTAAGAACTTTACTGGAAAATTTTCTGAA
* * *
39649415 ACTATGACCCATCAAGGCTCTTAGTAGAGTCG
390 ACTATGACCCATCAAGACTCTTAGCAGAATCG
*
39649447 TGAGATAAAACCCGAAGCAGAATTGAGCCACATCAATATATATATATATATATCCATTTGTATAT
1 TGAGATAAAACCCGAAGCAGAATTGAG--ACA-C----T-T-CA-ATATATATCCATTTGTATAT
* *
39649512 CTCAATTTATATACATACGCATGTCTAG-TAGAAT-TTTGGACAAGTTGTCACCTACCTTATCTG
56 CTCTATATATATACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCACCTACCTTATCTG
39649575 TAAAATGTGATCATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAAATTTTCTGAAACT
121 TAAAATGTGATCATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAAATTTTCTGAAACT
39649639 CTTTTTCCCC
Statistics
Matches: 561, Mismatches: 38, Indels: 30
0.89 0.06 0.05
Matches are distributed among these distances:
419 172 0.31
421 3 0.01
422 2 0.00
426 1 0.00
427 91 0.16
428 106 0.19
429 127 0.23
431 5 0.01
433 54 0.10
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (421 bp):
TGAGATAAAACCCGAAGCAGAATTGAGACACTTCAATATATATCCATTTGTATATCTCTATATAT
ATACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCACCTACCTTATCTGTAAAATGTGA
TCATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAAATTTTCTGAAACTATGACCCATCA
AGACTCTTAGCAGAATCGTGAGATAAAACCTGAAGCAGAATTGAGACACATCAATATATATCCAT
TTGTTATATATATATACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCATCTACCTTAT
CTGTAAAATGTGATCATTTTAGCAAATATTCCATCTTAAGAACTTTACTGGAAAATTTTCTGAAA
CTATGACCCATCAAGACTCTTAGCAGAATCG
Found at i:39670992 original size:19 final size:19
Alignment explanation
Indices: 39670968--39671007 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
39670958 GAATCTATGC
*
39670968 GTTGGTTTGATGGTAAAGA
1 GTTGGTTTGATGATAAAGA
39670987 GTTGGTTTGATGATAAAGA
1 GTTGGTTTGATGATAAAGA
39671006 GT
1 GT
39671008 GTTTATTGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.00, G:0.35, T:0.38
Consensus pattern (19 bp):
GTTGGTTTGATGATAAAGA
Done.