Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3
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: 6198200
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 200361 characters in sequence are not A, C, G, or T
File 17 of 32
Found at i:2581117 original size:15 final size:16
Alignment explanation
Indices: 2581092--2581136 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
2581082 TTATTTTATC
2581092 ATTTAATTAAATAT-AT
1 ATTT-ATTAAATATAAT
*
2581108 TTTTATTAAATATAAT
1 ATTTATTAAATATAAT
2581124 ATTTATTAAATAT
1 ATTTATTAAATAT
2581137 TTAATTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 9 0.35
16 17 0.65
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTATTAAATATAAT
Found at i:2581127 original size:18 final size:19
Alignment explanation
Indices: 2581104--2581154 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 19
2581094 TTAATTAAAT
2581104 ATATTTTTATTAAATA-TA
1 ATATTTTTATTAAATATTA
2581122 ATA--TTTATTAAATATTTA
1 ATATTTTTATTAAATA-TTA
2581140 AT-TTTTTAATTAAAT
1 ATATTTTT-ATTAAAT
2581155 CATTTAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
16 11 0.39
18 7 0.25
19 3 0.11
20 7 0.25
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATATTTTTATTAAATATTA
Found at i:2581143 original size:16 final size:16
Alignment explanation
Indices: 2581092--2581185 Score: 54
Period size: 16 Copynumber: 5.7 Consensus size: 16
2581082 TTATTTTATC
2581092 ATTTAATTAAATATATT-
1 ATTT-ATTAAATAT-TTA
*
2581109 -TTTATTAAATA-TAA
1 ATTTATTAAATATTTA
2581123 TATTTATTAAATATTTA
1 -ATTTATTAAATATTTA
2581140 ATTTTTTAATTAAATCATTTA
1 A---TTT-ATTAAAT-ATTTA
*
2581161 ATTTATT-TAT-TTTA
1 ATTTATTAAATATTTA
*
2581175 ATTGATTAAAT
1 ATTTATTAAAT
2581186 TAATTAAATT
Statistics
Matches: 62, Mismatches: 5, Indels: 22
0.70 0.06 0.25
Matches are distributed among these distances:
13 1 0.02
14 10 0.16
15 10 0.16
16 17 0.27
17 5 0.08
18 3 0.05
19 3 0.05
20 7 0.11
21 6 0.10
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (16 bp):
ATTTATTAAATATTTA
Found at i:2581161 original size:21 final size:21
Alignment explanation
Indices: 2581123--2581169 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
2581113 TTAAATATAA
2581123 TATTT-ATTAAATATTTAATT
1 TATTTAATTAAATATTTAATT
2581143 T-TTTAATTAAATCATTTAATT
1 TATTTAATTAAAT-ATTTAATT
2581164 TATTTA
1 TATTTA
2581170 TTTTAATTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.12
20 8 0.33
21 9 0.38
22 4 0.17
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTAATTAAATATTTAATT
Found at i:2589816 original size:19 final size:20
Alignment explanation
Indices: 2589776--2589822 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
2589766 ATTTATTATT
*
2589776 TATAATAACTTTATATCAAA
1 TATAATAACTTAATATCAAA
*
2589796 TATAATAA-TTAATATCTAA
1 TATAATAACTTAATATCAAA
*
2589815 TATCATAA
1 TATAATAA
2589823 ATTTCAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (20 bp):
TATAATAACTTAATATCAAA
Found at i:2589891 original size:3 final size:3
Alignment explanation
Indices: 2589883--2589907 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2589873 TAACAAAACA
2589883 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
2589908 TGTAGATACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2590160 original size:2 final size:2
Alignment explanation
Indices: 2590153--2590181 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2590143 TTTGATTTTA
2590153 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2590182 CACTAAACAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2592586 original size:24 final size:24
Alignment explanation
Indices: 2592537--2592586 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
2592527 TTGCCACATT
* * *
2592537 TAAGTGAGATGCATTTATGATTTA
1 TAAGTGAGATGCACTTATCATCTA
2592561 TAAGTTGA-ATGCACTTATCATCTA
1 TAAG-TGAGATGCACTTATCATCTA
2592585 TA
1 TA
2592587 CATGGAAGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 19 0.86
25 3 0.14
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (24 bp):
TAAGTGAGATGCACTTATCATCTA
Found at i:2593922 original size:19 final size:17
Alignment explanation
Indices: 2593873--2593939 Score: 54
Period size: 16 Copynumber: 4.1 Consensus size: 17
2593863 ATTAAAATAA
2593873 TAATAAT-AAATTT-AT
1 TAATAATAAAATTTAAT
2593888 TAATAAATAAAA-TTAACT
1 TAAT-AATAAAATTTAA-T
*
2593906 TAAATAATAAAATTTAAA
1 T-AATAATAAAATTTAAT
*
2593924 TAA-AATTAAA-TTAAT
1 TAATAATAAAATTTAAT
2593939 T
1 T
2593940 TTTAAAATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
15 9 0.21
16 11 0.26
17 6 0.14
18 10 0.23
19 7 0.16
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (17 bp):
TAATAATAAAATTTAAT
Found at i:2593945 original size:29 final size:29
Alignment explanation
Indices: 2593891--2593978 Score: 86
Period size: 29 Copynumber: 2.9 Consensus size: 29
2593881 AATTTATTAA
* * **
2593891 TAAATAAAATTAACTTAAATAATAAAATT
1 TAAATAAAATTAAATTAATTTTTAAAATT
2593920 TAAATAAAATTAAATTAATTTTTAAAATATT
1 TAAATAAAATTAAATTAATTTTT-AAA-ATT
* * *
2593951 TATATGAAATTCGAATTAATTTTTAAAA
1 TAAATAAAATT-AAATTAATTTTTAAAA
2593979 AAATTCAGTT
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
29 19 0.39
30 4 0.08
31 15 0.31
32 11 0.22
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (29 bp):
TAAATAAAATTAAATTAATTTTTAAAATT
Found at i:2593961 original size:31 final size:32
Alignment explanation
Indices: 2593917--2593978 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
2593907 AAATAATAAA
2593917 ATTTAAATAAAATT-AAATTAATTTTTAAAAT
1 ATTTAAATAAAATTCAAATTAATTTTTAAAAT
* * *
2593948 ATTTATATGAAATTCGAATTAATTTTTAAAA
1 ATTTAAATAAAATTCAAATTAATTTTTAAAA
2593979 AAATTCAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 12 0.44
32 15 0.56
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (32 bp):
ATTTAAATAAAATTCAAATTAATTTTTAAAAT
Found at i:2594551 original size:10 final size:11
Alignment explanation
Indices: 2594535--2594564 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
2594525 TAAAATAATA
2594535 ATAATTTAAAT
1 ATAATTTAAAT
2594546 -TAATTTAAAT
1 ATAATTTAAAT
2594556 ATAATTTAA
1 ATAATTTAA
2594565 TTTTTAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
ATAATTTAAAT
Found at i:2594559 original size:27 final size:26
Alignment explanation
Indices: 2594489--2594574 Score: 66
Period size: 28 Copynumber: 3.1 Consensus size: 26
2594479 TTTAAATTTT
*
2594489 ATTATTTTAAAAATATATAAATATTTAA
1 ATTAATTT-AAAATA-ATAAATATTTAA
* *
2594517 AATATATATAAAATAAT-AATAATTTAA
1 ATTA-ATTTAAAATAATAAAT-ATTTAA
* *
2594544 ATTAATTTAAATATAATTTAATTTTTAA
1 ATTAATTTAAA-ATAA-TAAATATTTAA
2594572 ATT
1 ATT
2594575 TTACCTAATG
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
26 9 0.19
27 15 0.32
28 18 0.38
29 5 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
ATTAATTTAAAATAATAAATATTTAA
Found at i:2595542 original size:18 final size:18
Alignment explanation
Indices: 2595519--2595617 Score: 73
Period size: 18 Copynumber: 5.7 Consensus size: 18
2595509 GTAATTATAT
2595519 AATATAAAATATAATTAA
1 AATATAAAATATAATTAA
* * *
2595537 AATATAATATATAAATAT
1 AATATAAAATATAATTAA
2595555 AATAT-AAATAT-A-T-A
1 AATATAAAATATAATTAA
* *
2595569 AATATAAAAAATTATTAA
1 AATATAAAATATAATTAA
* * *
2595587 TATTTTAAAT-TATATATAA
1 AATATAAAATATA-AT-TAA
2595606 AATATAAAATAT
1 AATATAAAATAT
2595618 TTTAAATATA
Statistics
Matches: 60, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
14 5 0.08
15 6 0.10
16 2 0.03
17 7 0.12
18 29 0.48
19 10 0.17
20 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AATATAAAATATAATTAA
Found at i:2595554 original size:13 final size:12
Alignment explanation
Indices: 2595515--2595577 Score: 92
Period size: 13 Copynumber: 5.1 Consensus size: 12
2595505 TCATGTAATT
2595515 ATATAATATAAA
1 ATATAATATAAA
2595527 ATATAAT-TAAA
1 ATATAATATAAA
2595538 ATATAATATATAA
1 ATATAATATA-AA
2595551 ATATAATATAAA
1 ATATAATATAAA
2595563 TATATAAATATAAA
1 -ATAT-AATATAAA
2595577 A
1 A
2595578 AATTATTAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
11 11 0.23
12 11 0.23
13 17 0.36
14 8 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
ATATAATATAAA
Found at i:2595588 original size:43 final size:43
Alignment explanation
Indices: 2595514--2595653 Score: 113
Period size: 43 Copynumber: 3.4 Consensus size: 43
2595504 ATCATGTAAT
2595514 TATAT-AATATA-AAATATAATTAAAATATAATA-TATAAA-TA
1 TATATAAATATATAAATATAA-TAAAATATAATATTATAAATTA
*
2595554 TAATATAAATATATAAATATAA-AAAATTATTAATATTTTAAATTA
1 T-ATATAAATATATAAATATAATAAAA-TA-TAATATTATAAATTA
* *
2595599 TATATAAA-ATATAAA-ATATTTTAAATAT-A-ATTAT-AA-TA
1 TATATAAATATATAAATATA-ATAAAATATAATATTATAAATTA
**
2595637 CGTATAAATATATAAAT
1 TATATAAATATATAAAT
2595654 GCAACAGACG
Statistics
Matches: 83, Mismatches: 6, Indels: 22
0.75 0.05 0.20
Matches are distributed among these distances:
38 8 0.10
39 9 0.11
40 5 0.06
41 9 0.11
42 12 0.14
43 22 0.27
44 15 0.18
45 3 0.04
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.40
Consensus pattern (43 bp):
TATATAAATATATAAATATAATAAAATATAATATTATAAATTA
Found at i:2595601 original size:28 final size:28
Alignment explanation
Indices: 2595570--2595624 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
2595560 AAATATATAA
*
2595570 ATATAAAAAAT-TATTAATATTTTAAATT
1 ATATAAAAAATATA-AAATATTTTAAATT
*
2595598 ATATATAAAATATAAAATATTTTAAAT
1 ATATAAAAAATATAAAATATTTTAAAT
2595625 ATAATTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 22 0.92
29 2 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
ATATAAAAAATATAAAATATTTTAAATT
Found at i:2595611 original size:11 final size:11
Alignment explanation
Indices: 2595515--2595611 Score: 58
Period size: 13 Copynumber: 8.5 Consensus size: 11
2595505 TCATGTAATT
2595515 ATATAATATAAA
1 ATAT-ATATAAA
2595527 ATATA-ATTAAA
1 ATATATA-TAAA
2595538 ATATAATATATAA
1 ATAT-ATATA-AA
2595551 ATATAATATAAA
1 ATAT-ATATAAA
2595563 TATATAAATATAAA
1 -ATAT--ATATAAA
* *
2595577 AAAT-TAT-TA
1 ATATATATAAA
*
2595586 ATAT-TTTAAA
1 ATATATATAAA
*
2595596 TTATATATAAA
1 ATATATATAAA
2595607 ATATA
1 ATATA
2595612 AAATATTTTA
Statistics
Matches: 69, Mismatches: 8, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
9 6 0.09
10 8 0.12
11 18 0.26
12 9 0.13
13 20 0.29
14 8 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
ATATATATAAA
Found at i:2595617 original size:16 final size:16
Alignment explanation
Indices: 2595514--2595628 Score: 65
Period size: 16 Copynumber: 6.8 Consensus size: 16
2595504 ATCATGTAAT
*
2595514 TATATAATATAAAATA
1 TATAAAATATAAAATA
2595530 TAATTAAAATAT--AATA
1 T-A-TAAAATATAAAATA
2595546 TATAAATATAATATAAATA
1 TATAAA-AT-ATA-AAATA
*
2595565 TAT-AAATATAAAAAA
1 TATAAAATATAAAATA
* *
2595580 TTATTAATATTTTAAATTATA
1 -TA-TAA-AATATAAA--ATA
2595601 TATAAAATATAAAATA
1 TATAAAATATAAAATA
* *
2595617 TTTTAAATATAA
1 TATAAAATATAA
2595629 TTATAATACG
Statistics
Matches: 77, Mismatches: 9, Indels: 26
0.69 0.08 0.23
Matches are distributed among these distances:
14 4 0.05
15 7 0.09
16 26 0.34
17 4 0.05
18 16 0.21
19 16 0.21
20 2 0.03
21 2 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TATAAAATATAAAATA
Found at i:2600498 original size:25 final size:25
Alignment explanation
Indices: 2600464--2600514 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
2600454 ATGACTGAGG
2600464 ATGATTTCACTTTTGTGTATGTTTT
1 ATGATTTCACTTTTGTGTATGTTTT
2600489 ATGATTTCACTTTTGTGTATGTTTT
1 ATGATTTCACTTTTGTGTATGTTTT
2600514 A
1 A
2600515 ACAGCTTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.18, C:0.08, G:0.16, T:0.59
Consensus pattern (25 bp):
ATGATTTCACTTTTGTGTATGTTTT
Found at i:2602623 original size:2 final size:2
Alignment explanation
Indices: 2602618--2602645 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2602608 TTCTGACAAC
2602618 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
2602646 GAAAGTAAAA
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):
AT
Found at i:2602676 original size:2 final size:2
Alignment explanation
Indices: 2602669--2602703 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2602659 ATCAACCTTG
2602669 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2602704 GAAAGTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2609107 original size:102 final size:104
Alignment explanation
Indices: 2608991--2609233 Score: 366
Period size: 102 Copynumber: 2.3 Consensus size: 104
2608981 TTTTTTTAAA
* *
2608991 AAAATAATATTTAATAATTAAAATTTAAAATTTAATATCTACCATAATTTCTTTTATTCTAACTC
1 AAAATAACATTTAATAATTAAAATTTAAAATTCAATATCTACCATAATTTCTTTTATTCTAACTC
* *
2609056 TATTTATTAAAAAA-AA-TCA-ATTTATATATATATTTTT
66 TATTTA-TAAAAAACAATTCATATATATATATATATATTT
* *
2609093 AAAATAACACTTAATAATTAAAATTTAAAATTCAATATCTACCATAATTTCTTTTATTCTAACTT
1 AAAATAACATTTAATAATTAAAATTTAAAATTCAATATCTACCATAATTTCTTTTATTCTAACTC
*
2609158 TATTTATAAAAAATCAATTTATATATATATATATATATTT
66 TATTTATAAAAAA-CAATTCATATATATATATATATATTT
* *
2609198 AAAATAACATTTAATAATTGAAATTTAAAACTCAAT
1 AAAATAACATTTAATAATTAAAATTTAAAATTCAAT
2609234 TTCTTCTCTT
Statistics
Matches: 127, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
101 7 0.06
102 67 0.53
103 2 0.02
104 2 0.02
105 49 0.39
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (104 bp):
AAAATAACATTTAATAATTAAAATTTAAAATTCAATATCTACCATAATTTCTTTTATTCTAACTC
TATTTATAAAAAACAATTCATATATATATATATATATTT
Found at i:2610388 original size:2 final size:2
Alignment explanation
Indices: 2610381--2610424 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2610371 TTTAAGGTTG
2610381 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
2610423 AT
1 AT
2610425 CAAGGCTGCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2611878 original size:14 final size:14
Alignment explanation
Indices: 2611855--2611886 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2611845 TGGGATCCTC
2611855 TTTTTCTTTTCTTT
1 TTTTTCTTTTCTTT
*
2611869 TTTTTTTTTTCTTT
1 TTTTTCTTTTCTTT
2611883 TTTT
1 TTTT
2611887 ATGGTCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (14 bp):
TTTTTCTTTTCTTT
Found at i:2613463 original size:20 final size:19
Alignment explanation
Indices: 2613425--2613463 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2613415 AAAGTGAATA
* *
2613425 ATTTTTAATATATATAATT
1 ATTTTTAAAATATAAAATT
2613444 ATTTTTAAAATATTAAAATT
1 ATTTTTAAAATA-TAAAATT
2613464 TTATTTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTTTTAAAATATAAAATT
Found at i:2613514 original size:14 final size:14
Alignment explanation
Indices: 2613505--2613542 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
2613495 ATAATTTATT
2613505 TAATTAAATTAATA
1 TAATTAAATTAATA
*
2613519 TAATTTAATTAATA
1 TAATTAAATTAATA
2613533 -ACATTAAATT
1 TA-ATTAAATT
2613543 TAATCACACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 1 0.05
14 20 0.95
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (14 bp):
TAATTAAATTAATA
Found at i:2613521 original size:23 final size:23
Alignment explanation
Indices: 2613493--2613539 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
2613483 ATCCGATTTT
*
2613493 ATATAATTTATTTAATTAA-ATTA
1 ATATAATTTAATTAA-TAACATTA
2613516 ATATAATTTAATTAATAACATTA
1 ATATAATTTAATTAATAACATTA
2613539 A
1 A
2613540 ATTTAATCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 3 0.14
23 19 0.86
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
ATATAATTTAATTAATAACATTA
Found at i:2613974 original size:19 final size:17
Alignment explanation
Indices: 2613938--2613976 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2613928 AAAATATTAA
*
2613938 AATATATTTTTAATATT
1 AATATATATTTAATATT
2613955 AATATATATTTATATAATT
1 AATATATATTTA-AT-ATT
2613974 AAT
1 AAT
2613977 TTTTTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 11 0.58
18 2 0.11
19 6 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AATATATATTTAATATT
Found at i:2617670 original size:22 final size:22
Alignment explanation
Indices: 2617644--2617687 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
2617634 TGTTAATATG
*
2617644 ATATATAATATAATTTTAAATTTT
1 ATATA-AAAATAA-TTTAAATTTT
2617668 ATATAAAAATAATTTAAATT
1 ATATAAAAATAATTTAAATT
2617688 ATAAGTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 6 0.32
24 5 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATATAAAAATAATTTAAATTTT
Found at i:2621204 original size:6 final size:6
Alignment explanation
Indices: 2621193--2621316 Score: 104
Period size: 6 Copynumber: 20.7 Consensus size: 6
2621183 ATACTAAAAC
2621193 CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT
1 CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT
* * * * * * * * * * * * *
2621241 CCCCCT CTCCCC CTCCCC CTCCCC CTCCCC CTCCCT CCCTCT CCCTCT
1 CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT
* * *
2621289 CCCTCT CCCTCT CCCTCT CTCTCT CTCT
1 CTCTCT CTCTCT CTCTCT CTCTCT CTCT
2621317 TTATATGTGT
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 110 1.00
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (6 bp):
CTCTCT
Found at i:2621206 original size:8 final size:8
Alignment explanation
Indices: 2621193--2621316 Score: 104
Period size: 8 Copynumber: 15.5 Consensus size: 8
2621183 ATACTAAAAC
2621193 CTCTCTCT
1 CTCTCTCT
2621201 CTCTCTCT
1 CTCTCTCT
2621209 CTCTCTCT
1 CTCTCTCT
2621217 CTCTCTCT
1 CTCTCTCT
2621225 CTCTCTCT
1 CTCTCTCT
2621233 CTCTCTCT
1 CTCTCTCT
* *
2621241 CCCCCTCT
1 CTCTCTCT
* * *
2621249 CCCCCTCC
1 CTCTCTCT
* * *
2621257 CCCTCCCC
1 CTCTCTCT
* *
2621265 CTCCCCCT
1 CTCTCTCT
* *
2621273 CCCTCCCT
1 CTCTCTCT
*
2621281 CTCCCTCT
1 CTCTCTCT
* *
2621289 CCCTCTCC
1 CTCTCTCT
*
2621297 CTCTCCCT
1 CTCTCTCT
2621305 CTCTCTCT
1 CTCTCTCT
2621313 CTCT
1 CTCT
2621317 TTATATGTGT
Statistics
Matches: 96, Mismatches: 20, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
8 96 1.00
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (8 bp):
CTCTCTCT
Found at i:2621327 original size:2 final size:2
Alignment explanation
Indices: 2621322--2621355 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2621312 TCTCTTTATA
2621322 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
2621356 AGCTTCATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:2624046 original size:2 final size:2
Alignment explanation
Indices: 2624041--2624065 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2624031 AGAAAAAAGA
2624041 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2624066 ATACGCAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2626809 original size:20 final size:20
Alignment explanation
Indices: 2626771--2626812 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2626761 CTTTAAAGGG
* *
2626771 TTTTTTTATGAGTATAATAA
1 TTTTTTTATAAGTAAAATAA
*
2626791 TTTTTTTATAATTAAAATAA
1 TTTTTTTATAAGTAAAATAA
2626811 TT
1 TT
2626813 ATAAGATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (20 bp):
TTTTTTTATAAGTAAAATAA
Found at i:2627272 original size:14 final size:14
Alignment explanation
Indices: 2627253--2627302 Score: 68
Period size: 14 Copynumber: 3.7 Consensus size: 14
2627243 CCCTCTATTC
2627253 CTCTATATCTTTCT
1 CTCTATATCTTTCT
*
2627267 CTCTATCTC-TT-T
1 CTCTATATCTTTCT
*
2627279 CTCTATATCTTTCC
1 CTCTATATCTTTCT
2627293 CTCTATATCT
1 CTCTATATCT
2627303 CTCTTCCTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
12 9 0.29
13 4 0.13
14 18 0.58
ACGTcount: A:0.14, C:0.32, G:0.00, T:0.54
Consensus pattern (14 bp):
CTCTATATCTTTCT
Found at i:2627551 original size:20 final size:20
Alignment explanation
Indices: 2627528--2627662 Score: 99
Period size: 20 Copynumber: 6.8 Consensus size: 20
2627518 CTCCATAAAG
* *
2627528 TTCTAGAACCTTCCACATTA
1 TTCTAGAACATTCCACAATA
* * * *
2627548 TTCTAGAACGTTCTAGAATC
1 TTCTAGAACATTCCACAATA
* * * *
2627568 TTCCAGAGCCTCCCACAATA
1 TTCTAGAACATTCCACAATA
* * *
2627588 TTCTAGAACATTCTAGAATC
1 TTCTAGAACATTCCACAATA
* * * *
2627608 TTCCAGAGCCTTCCACGATA
1 TTCTAGAACATTCCACAATA
* *
2627628 TTCTAGAACATTCCAGAACA
1 TTCTAGAACATTCCACAATA
2627648 TTCTAGAACATTCCA
1 TTCTAGAACATTCCA
2627663 AAGTGTTCTA
Statistics
Matches: 83, Mismatches: 32, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
20 83 1.00
ACGTcount: A:0.32, C:0.28, G:0.10, T:0.30
Consensus pattern (20 bp):
TTCTAGAACATTCCACAATA
Found at i:2627595 original size:40 final size:40
Alignment explanation
Indices: 2627540--2627645 Score: 167
Period size: 40 Copynumber: 2.6 Consensus size: 40
2627530 CTAGAACCTT
* *
2627540 CCACATTATTCTAGAACGTTCTAGAATCTTCCAGAGCCTC
1 CCACAATATTCTAGAACATTCTAGAATCTTCCAGAGCCTC
*
2627580 CCACAATATTCTAGAACATTCTAGAATCTTCCAGAGCCTT
1 CCACAATATTCTAGAACATTCTAGAATCTTCCAGAGCCTC
* *
2627620 CCACGATATTCTAGAACATTCCAGAA
1 CCACAATATTCTAGAACATTCTAGAA
2627646 CATTCTAGAA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 61 1.00
ACGTcount: A:0.32, C:0.28, G:0.11, T:0.28
Consensus pattern (40 bp):
CCACAATATTCTAGAACATTCTAGAATCTTCCAGAGCCTC
Found at i:2627602 original size:10 final size:10
Alignment explanation
Indices: 2627587--2627660 Score: 62
Period size: 10 Copynumber: 7.4 Consensus size: 10
2627577 CTCCCACAAT
2627587 ATTCTAGAAC
1 ATTCTAGAAC
2627597 ATTCTAGAATC
1 ATTCTAGAA-C
* *
2627608 -TTCCAGAGC
1 ATTCTAGAAC
* * *
2627617 CTTCCACG-AT
1 ATTCTA-GAAC
2627627 ATTCTAGAAC
1 ATTCTAGAAC
*
2627637 ATTCCAGAAC
1 ATTCTAGAAC
2627647 ATTCTAGAAC
1 ATTCTAGAAC
2627657 ATTC
1 ATTC
2627661 CAAAGTGTTC
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
9 2 0.04
10 47 0.92
11 2 0.04
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.30
Consensus pattern (10 bp):
ATTCTAGAAC
Found at i:2627662 original size:40 final size:39
Alignment explanation
Indices: 2627532--2627662 Score: 156
Period size: 40 Copynumber: 3.3 Consensus size: 39
2627522 ATAAAGTTCT
*
2627532 AGAACCTTCCACATTATTCTAGAACGTTCTAGAATCTTCC
1 AGAACCTTCCACA-TATTCTAGAACATTCTAGAATCTTCC
* *
2627572 AGAGCCTCCCACAATATTCTAGAACATTCTAGAATCTTCC
1 AGAACCTTCCAC-ATATTCTAGAACATTCTAGAATCTTCC
* * *
2627612 AGAGCCTTCCACGATATTCTAGAACATTCCAGAA-CATTCT
1 AGAACCTTCCAC-ATATTCTAGAACATTCTAGAATC-TTCC
*
2627652 AGAACATTCCA
1 AGAACCTTCCA
2627663 AAGTGTTCTA
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
39 1 0.01
40 78 0.98
41 1 0.01
ACGTcount: A:0.33, C:0.28, G:0.11, T:0.28
Consensus pattern (39 bp):
AGAACCTTCCACATATTCTAGAACATTCTAGAATCTTCC
Found at i:2628727 original size:19 final size:18
Alignment explanation
Indices: 2628687--2628729 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2628677 ATGATGCCTA
2628687 AAAAAGGAAATTAAGCTT
1 AAAAAGGAAATTAAGCTT
*
2628705 AAAAAGGTAA-TAGAGCTT
1 AAAAAGGAAATTA-AGCTT
*
2628723 GAAAAGG
1 AAAAAGG
2628730 TTATGGTGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.53, C:0.05, G:0.23, T:0.19
Consensus pattern (18 bp):
AAAAAGGAAATTAAGCTT
Found at i:2628730 original size:18 final size:17
Alignment explanation
Indices: 2628700--2628752 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
2628690 AAGGAAATTA
2628700 AGCTTAAAAAGGTAATAG
1 AGCTT-AAAAGGTAATAG
* *
2628718 AGCTTGAAAAGGTTATGG
1 AGCTT-AAAAGGTAATAG
*
2628736 TGTCTTAAAAGGTAATA
1 AG-CTTAAAAGGTAATA
2628753 TAATTTAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
18 25 0.89
19 3 0.11
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.28
Consensus pattern (17 bp):
AGCTTAAAAGGTAATAG
Found at i:2632097 original size:17 final size:18
Alignment explanation
Indices: 2632077--2632120 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
2632067 TTTATATTTT
*
2632077 AAAAATTATAATAAA-TA
1 AAAAATTATAAAAAATTA
*
2632094 AAAAATTTTAAAAAATTA
1 AAAAATTATAAAAAATTA
2632112 AAAAATTAT
1 AAAAATTAT
2632121 TTAATTGTTG
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAAATTATAAAAAATTA
Found at i:2632349 original size:28 final size:29
Alignment explanation
Indices: 2632317--2632379 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
2632307 TTATTTATTA
*
2632317 TAATTTTAA-AGTACAAAAATTAAAATAT
1 TAATTTTAATAATACAAAAATTAAAATAT
*
2632345 TAATTTTAATAATATAAAAATTAAAATAT
1 TAATTTTAATAATACAAAAATTAAAATAT
*
2632374 TCATTT
1 TAATTT
2632380 CATTATAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
28 9 0.29
29 22 0.71
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (29 bp):
TAATTTTAATAATACAAAAATTAAAATAT
Found at i:2640101 original size:32 final size:33
Alignment explanation
Indices: 2640024--2640104 Score: 85
Period size: 32 Copynumber: 2.4 Consensus size: 33
2640014 TGTATTGTAT
* *
2640024 TTAATATTTTATAAATTTATATAAATTTTGATACA
1 TTAATAATTTAT--ATTTATATAAATTTTGATAAA
*
2640059 TTAATAATTTATATTT-TATAAATTTTTA-AAA
1 TTAATAATTTATATTTATATAAATTTTGATAAA
*
2640090 TTTATATATTTATAT
1 TTAATA-ATTTATAT
2640105 AATATTTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
31 7 0.17
32 19 0.46
33 4 0.10
35 11 0.27
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (33 bp):
TTAATAATTTATATTTATATAAATTTTGATAAA
Found at i:2644194 original size:2 final size:2
Alignment explanation
Indices: 2644187--2644215 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2644177 TTCTTCTTCT
2644187 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2644216 TTGATATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2646590 original size:20 final size:21
Alignment explanation
Indices: 2646542--2646594 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
2646532 TATGAAAATT
*
2646542 TAAATAAAAATATTAAATTAAA
1 TAAATAAAATTATTAAA-TAAA
* *
2646564 AAAATAAAATTATTTAA-AAA
1 TAAATAAAATTATTAAATAAA
2646584 TAAATAAAATT
1 TAAATAAAATT
2646595 TTGATTTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 13 0.48
22 14 0.52
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
TAAATAAAATTATTAAATAAA
Found at i:2647152 original size:24 final size:25
Alignment explanation
Indices: 2647120--2647178 Score: 77
Period size: 26 Copynumber: 2.4 Consensus size: 25
2647110 TAATAATCTT
2647120 AAATATAATAT-A-TTAAAATTATTA
1 AAATATAATATAATTTAAAATT-TTA
2647144 AAATATAATATAATTTAAAATTTTA
1 AAATATAATATAATTTAAAATTTTA
*
2647169 TAATACTAAT
1 AAATA-TAAT
2647179 TATGACATGC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 11 0.35
25 8 0.26
26 12 0.39
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (25 bp):
AAATATAATATAATTTAAAATTTTA
Found at i:2647615 original size:27 final size:27
Alignment explanation
Indices: 2647580--2647635 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
2647570 TAAAATGTTA
* *
2647580 AATTAATATATTAAAATTTATATAAAT
1 AATTAATATATAAAAATTAATATAAAT
2647607 AATTAATATATAAAAATTAATATAAAT
1 AATTAATATATAAAAATTAATATAAAT
2647634 AA
1 AA
2647636 ATTATAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
AATTAATATATAAAAATTAATATAAAT
Found at i:2647631 original size:23 final size:25
Alignment explanation
Indices: 2647580--2647646 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 25
2647570 TAAAATGTTA
*
2647580 AATTAATATATTAAAATTTATATAAAT
1 AATTAATATA-TAAAAATTATAT-AAT
2647607 AATTAATATATAAAAATTA-AT-AT
1 AATTAATATATAAAAATTATATAAT
*
2647630 AAATAA-ATTATAAAAAT
1 AATTAATA-TATAAAAAT
2647647 ATTAAGATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
22 1 0.03
23 16 0.43
25 2 0.05
26 8 0.22
27 10 0.27
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
AATTAATATATAAAAATTATATAAT
Found at i:2647637 original size:14 final size:14
Alignment explanation
Indices: 2647578--2647639 Score: 67
Period size: 14 Copynumber: 4.5 Consensus size: 14
2647568 TATAAAATGT
*
2647578 TAAATTAATAT-AT
1 TAAATTAATATAAA
*
2647591 TAAAATTTATATAAA
1 T-AAATTAATATAAA
2647606 T-AATTAATATATAA
1 TAAATTAATATA-AA
2647620 -AAATTAATATAAA
1 TAAATTAATATAAA
2647633 TAAATTA
1 TAAATTA
2647640 TAAAAATATT
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
13 12 0.29
14 27 0.66
15 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TAAATTAATATAAA
Found at i:2648252 original size:2 final size:2
Alignment explanation
Indices: 2648245--2648275 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2648235 AGACTGACAA
2648245 AG AG AG AG AG AG AG AG AG AG AG AG AG A- AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2648276 TTGTATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2652690 original size:2 final size:2
Alignment explanation
Indices: 2652683--2652711 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2652673 TAGTGCATTC
2652683 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2652712 TCTACAGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2653001 original size:22 final size:24
Alignment explanation
Indices: 2652976--2653025 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
2652966 AAATTTTAAT
*
2652976 AATTA-TA-CTTTTTTTATCATTA
1 AATTACTATCTTTTTGTATCATTA
*
2652998 AATTACTATCTTTTTGTATGATTA
1 AATTACTATCTTTTTGTATCATTA
2653022 AATT
1 AATT
2653026 GTAAACAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 5 0.21
23 2 0.08
24 17 0.71
ACGTcount: A:0.32, C:0.08, G:0.04, T:0.56
Consensus pattern (24 bp):
AATTACTATCTTTTTGTATCATTA
Found at i:2659318 original size:22 final size:22
Alignment explanation
Indices: 2659293--2659336 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2659283 GCGAATCTTG
2659293 GTGGAAAACATTGGAGTACCAT
1 GTGGAAAACATTGGAGTACCAT
*
2659315 GTGGAGAACATTGGAGTACCAT
1 GTGGAAAACATTGGAGTACCAT
2659337 AAAGAGAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.14, G:0.30, T:0.23
Consensus pattern (22 bp):
GTGGAAAACATTGGAGTACCAT
Found at i:2659343 original size:22 final size:22
Alignment explanation
Indices: 2659299--2659344 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
2659289 CTTGGTGGAA
***
2659299 AACATTGGAGTACCATGTGGAG
1 AACATTGGAGTACCATAAAGAG
2659321 AACATTGGAGTACCATAAAGAG
1 AACATTGGAGTACCATAAAGAG
2659343 AA
1 AA
2659345 TTCTAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.41, C:0.13, G:0.26, T:0.20
Consensus pattern (22 bp):
AACATTGGAGTACCATAAAGAG
Found at i:2660100 original size:50 final size:49
Alignment explanation
Indices: 2659974--2660129 Score: 143
Period size: 50 Copynumber: 3.1 Consensus size: 49
2659964 GCAAAGTGAT
* * * * *
2659974 TTGATTATTCTTCACAAACCTTTGACAATCGAGAGAGGTG-GTCATAATTA
1 TTGACTATTCTTCACAAA-CTTTGATAATCGAGAGAGGTGACT-GTAATTG
* * *
2660024 TTGACTATTCTTTATCGACCTTTGATAATCGAGAGAGGTGACTGTAATTG
1 TTGACTATTCTTCA-CAAACTTTGATAATCGAGAGAGGTGACTGTAATTG
* ** * * *
2660074 TTGACTATTCTTCACCAACTTCTGATAATAAAAAAAGGTGACCGTAATTG
1 TTGACTATTCTTCACAAACTT-TGATAATCGAGAGAGGTGACTGTAATTG
2660124 TTGACT
1 TTGACT
2660130 CTAAACATAA
Statistics
Matches: 87, Mismatches: 16, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
49 5 0.06
50 79 0.91
51 3 0.03
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (49 bp):
TTGACTATTCTTCACAAACTTTGATAATCGAGAGAGGTGACTGTAATTG
Found at i:2660941 original size:30 final size:28
Alignment explanation
Indices: 2660898--2660954 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 28
2660888 ATTTAACTAA
2660898 AATTTTAAAAATAA-ATATATATAATTTT
1 AATTTTAAAAATAACATA-ATATAATTTT
2660926 AATTTTAATAAAATAACATAATATAATTT
1 AATTTT-A-AAAATAACATAATATAATTT
2660955 ATTAATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 6 0.23
29 1 0.04
30 16 0.62
31 3 0.12
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (28 bp):
AATTTTAAAAATAACATAATATAATTTT
Found at i:2660976 original size:26 final size:24
Alignment explanation
Indices: 2660911--2660976 Score: 57
Period size: 26 Copynumber: 2.7 Consensus size: 24
2660901 TTTAAAAATA
2660911 AATATATATAATTT-TAATTTTAAT
1 AATATATA-AATTTATAATTTTAAT
*
2660935 AA-A-ATAACATAATATAATTTATTAAT
1 AATATATAA-AT-TTATAA-TT-TTAAT
2660961 AATATATAAATTTATA
1 AATATATAAATTTATA
2660977 TATCATCAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
21 1 0.03
22 5 0.15
23 2 0.06
24 5 0.15
25 2 0.06
26 11 0.33
27 3 0.09
28 4 0.12
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
AATATATAAATTTATAATTTTAAT
Found at i:2663195 original size:50 final size:50
Alignment explanation
Indices: 2663136--2663317 Score: 231
Period size: 50 Copynumber: 3.6 Consensus size: 50
2663126 ACTTAAAGTC
* * *
2663136 AACAATTACGGTCACTTTTCTCTATTGTCAAAGGTTGGTGAAAAATAGTT
1 AACAATTACGGTCACTTCTCTCGATTATCAAAGGTTGGTGAAAAATAGTT
* * * *
2663186 AACAATTACGGTCACCTT-TTTCAATTGTCAAAAGTTGGTGAAAAATAGTT
1 AACAATTACGGTCA-CTTCTCTCGATTATCAAAGGTTGGTGAAAAATAGTT
* * * * *
2663236 AACAATTACGGTCACCTCTCTCGATTATTAAAGGTTGGTGAAGAGTAGTC
1 AACAATTACGGTCACTTCTCTCGATTATCAAAGGTTGGTGAAAAATAGTT
*
2663286 AACAATTACCGTCACTTCTCTCGATTATCAAA
1 AACAATTACGGTCACTTCTCTCGATTATCAAA
2663318 AATTAATAAA
Statistics
Matches: 115, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
49 2 0.02
50 110 0.96
51 3 0.03
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (50 bp):
AACAATTACGGTCACTTCTCTCGATTATCAAAGGTTGGTGAAAAATAGTT
Found at i:2666901 original size:12 final size:12
Alignment explanation
Indices: 2666884--2666926 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
2666874 ATTTAATTGA
2666884 AAATATTTTAAT
1 AAATATTTTAAT
2666896 AAATATTTTTTAAT
1 AAATA--TTTTAAT
2666910 -AATATTTTAAT
1 AAATATTTTAAT
*
2666921 TAATAT
1 AAATAT
2666927 AATTAATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 7 0.25
12 10 0.36
13 4 0.14
14 7 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
AAATATTTTAAT
Found at i:2666925 original size:15 final size:14
Alignment explanation
Indices: 2666875--2666936 Score: 53
Period size: 13 Copynumber: 4.6 Consensus size: 14
2666865 TATATTTTTA
2666875 TTTAATTGAAAATAT
1 TTTAATT-AAAATAT
2666890 TTTAA-T-AAATAT
1 TTTAATTAAAATAT
2666902 TTT--TTAATAATAT
1 TTTAATTAA-AATAT
*
2666915 TTTAATTAATATA-
1 TTTAATTAAAATAT
*
2666928 ATTAATTAA
1 TTTAATTAA
2666937 CATTACGTAC
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
11 1 0.03
12 10 0.25
13 16 0.40
14 4 0.10
15 9 0.22
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (14 bp):
TTTAATTAAAATAT
Found at i:2667112 original size:16 final size:16
Alignment explanation
Indices: 2667093--2667123 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2667083 AAATAGTAAA
2667093 ATAAATAAATATTTTC
1 ATAAATAAATATTTTC
*
2667109 ATAAATATATATTTT
1 ATAAATAAATATTTT
2667124 TGTTTTATTT
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:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
ATAAATAAATATTTTC
Found at i:2667690 original size:1 final size:1
Alignment explanation
Indices: 2667684--2667710 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
2667674 TTTCCCACAA
2667684 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
2667711 ACAGTTGGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:2670027 original size:6 final size:6
Alignment explanation
Indices: 2670016--2670063 Score: 69
Period size: 6 Copynumber: 8.0 Consensus size: 6
2670006 TTCAAGCCCC
* * *
2670016 GTGATG GTGATG GTGATG GTGATG GTGATG ATGATG ATGATG ATGATG
1 GTGATG GTGATG GTGATG GTGATG GTGATG GTGATG GTGATG GTGATG
2670064 ATATGCATAC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.23, C:0.00, G:0.44, T:0.33
Consensus pattern (6 bp):
GTGATG
Found at i:2670049 original size:3 final size:3
Alignment explanation
Indices: 2670017--2670065 Score: 62
Period size: 3 Copynumber: 16.3 Consensus size: 3
2670007 TCAAGCCCCG
* * * *
2670017 TGA TGG TGA TGG TGA TGG TGA TGG TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
2670065 T
1 T
2670066 ATGCATACAT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.24, C:0.00, G:0.41, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:2671050 original size:12 final size:12
Alignment explanation
Indices: 2671033--2671061 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
2671023 TTATTTTTAA
2671033 AAATTAATAAAT
1 AAATTAATAAAT
2671045 AAATTAATAAAT
1 AAATTAATAAAT
2671057 AAATT
1 AAATT
2671062 TAAAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
AAATTAATAAAT
Found at i:2674740 original size:20 final size:20
Alignment explanation
Indices: 2674708--2674746 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2674698 TATTTTTGAT
2674708 ATTTTATTTTAAAATTTATA
1 ATTTTATTTTAAAATTTATA
*
2674728 ATTTT-TTTATAAATTTTAT
1 ATTTTATTT-TAAAATTTAT
2674747 TAGATATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
ATTTTATTTTAAAATTTATA
Found at i:2675214 original size:2 final size:2
Alignment explanation
Indices: 2675207--2675236 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2675197 ATGTAAGAAG
2675207 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
2675237 TAATTCACCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2691276 original size:20 final size:24
Alignment explanation
Indices: 2691218--2691288 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 24
2691208 ATTTAAATAT
2691218 TAAATATGTAATTTTATTAATAAA
1 TAAATATGTAATTTTATTAATAAA
*
2691242 TAAATATAATAATTTT-TTAAT-AA
1 TAAATAT-GTAATTTTATTAATAAA
* *
2691265 T-AATATGT-ATTTAATTAATTAA
1 TAAATATGTAATTTTATTAATAAA
2691287 TA
1 TA
2691289 TAATTTTTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
20 4 0.10
21 6 0.15
22 8 0.20
23 3 0.08
24 12 0.30
25 7 0.17
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (24 bp):
TAAATATGTAATTTTATTAATAAA
Found at i:2691303 original size:18 final size:18
Alignment explanation
Indices: 2691250--2691305 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 18
2691240 AATAAATATA
*
2691250 ATAATTTTTTAATAATAAT
1 ATAA-TTTTTAATATTAAT
* *
2691269 AT-GTATTTAATTAATTAAT
1 ATAATTTTTAA-T-ATTAAT
2691288 ATAATTTTTAATATTAAT
1 ATAATTTTTAATATTAAT
2691306 TTAAGAAGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
17 6 0.21
18 7 0.24
19 10 0.34
20 6 0.21
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
ATAATTTTTAATATTAAT
Found at i:2691427 original size:21 final size:20
Alignment explanation
Indices: 2691374--2691427 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 20
2691364 ATTTTTACAA
2691374 TTTTT-CTAATTTTTAATAAT
1 TTTTTACTAA-TTTTAATAAT
* *
2691394 TTTTTACCAAATTTTAATTATT
1 TTTTTA-CTAATTTTAA-TAAT
2691416 TTTTTACTAATT
1 TTTTTACTAATT
2691428 CAAATGATTC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 5 0.18
21 11 0.39
22 12 0.43
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTTACTAATTTTAATAAT
Found at i:2694519 original size:3 final size:3
Alignment explanation
Indices: 2694511--2694547 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2694501 TTTTTATGTC
2694511 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2694548 GATATCAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2695861 original size:2 final size:2
Alignment explanation
Indices: 2695854--2695888 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
2695844 TGTTGCTTAC
* *
2695854 TA TA TA TA TA TA TA TA TG TA TA TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2695889 TTTAATTCAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2696093 original size:2 final size:2
Alignment explanation
Indices: 2696053--2696077 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2696043 ACTGCTATGT
2696053 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2696078 CATCAATCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2696127 original size:2 final size:2
Alignment explanation
Indices: 2696120--2696146 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2696110 CTGCCATCAA
2696120 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
2696147 TATACATCAA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2699582 original size:15 final size:16
Alignment explanation
Indices: 2699561--2699603 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
2699551 GATAAAAATT
2699561 TAAAAATTTATACAT-A
1 TAAAAATTTATA-ATGA
*
2699577 -AAAAATTTTTAATGA
1 TAAAAATTTATAATGA
2699592 TAAAAATTTATA
1 TAAAAATTTATA
2699604 TTTAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (16 bp):
TAAAAATTTATAATGA
Found at i:2699710 original size:19 final size:19
Alignment explanation
Indices: 2699680--2699724 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
2699670 TTTTAATATT
*
2699680 TTTTATTATATTTATTATTAA
1 TTTTACTAT-TTTATT-TTAA
*
2699701 TTTTACTATTTTATTTTAT
1 TTTTACTATTTTATTTTAA
2699720 TTTTA
1 TTTTA
2699725 AATAAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 8 0.36
20 6 0.27
21 8 0.36
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTACTATTTTATTTTAA
Found at i:2700726 original size:22 final size:23
Alignment explanation
Indices: 2700687--2700755 Score: 79
Period size: 23 Copynumber: 2.9 Consensus size: 23
2700677 AAAATATTAA
*
2700687 AATAAAATATTAATATTTTTTAAA-T
1 AATAAAATA--AA-ATTTTTAAAACT
2700712 AATAAAATAAAA-TTTTAAAACT
1 AATAAAATAAAATTTTTAAAACT
2700734 AATATAAATAAAATTTTTAAAA
1 AATA-AAATAAAATTTTTAAAA
2700756 ATTTAAATTA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
21 7 0.17
22 6 0.15
23 10 0.25
24 8 0.20
25 9 0.22
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (23 bp):
AATAAAATAAAATTTTTAAAACT
Found at i:2700746 original size:23 final size:22
Alignment explanation
Indices: 2700683--2700755 Score: 78
Period size: 22 Copynumber: 3.3 Consensus size: 22
2700673 ATTAAAAATA
* *
2700683 TTAAAATAA-AATATTAATATTT
1 TTAAAATAATAA-AATAAAATTT
*
2700705 TTTAAATAATAAAATAAAA-TT
1 TTAAAATAATAAAATAAAATTT
2700726 TTAAAACTAATATAAATAAAATTT
1 TTAAAA-TAATA-AAATAAAATTT
2700750 TTAAAA
1 TTAAAA
2700756 ATTTAAATTA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
21 7 0.16
22 18 0.42
23 10 0.23
24 8 0.19
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (22 bp):
TTAAAATAATAAAATAAAATTT
Found at i:2701003 original size:15 final size:15
Alignment explanation
Indices: 2700983--2701012 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2700973 CAAGTCGAAG
*
2700983 TTAAAAACACTAGGA
1 TTAAAAACACCAGGA
2700998 TTAAAAACACCAGGA
1 TTAAAAACACCAGGA
2701013 CTTGGGTTGA
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:0.53, C:0.17, G:0.13, T:0.17
Consensus pattern (15 bp):
TTAAAAACACCAGGA
Found at i:2708437 original size:16 final size:19
Alignment explanation
Indices: 2708418--2708456 Score: 57
Period size: 16 Copynumber: 2.2 Consensus size: 19
2708408 TTTTATATAC
2708418 ATTTAAA-TAA-ATTTT-T
1 ATTTAAACTAATATTTTAT
2708434 ATTTAAACTAATATTTTAT
1 ATTTAAACTAATATTTTAT
2708453 ATTT
1 ATTT
2708457 CATAAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 7 0.35
17 3 0.15
18 5 0.25
19 5 0.25
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTTAAACTAATATTTTAT
Found at i:2708501 original size:24 final size:22
Alignment explanation
Indices: 2708458--2708501 Score: 52
Period size: 24 Copynumber: 1.9 Consensus size: 22
2708448 TTTATATTTC
*
2708458 ATAAAAAATTATTTTAATATAA
1 ATAAAAAATTATTTGAATATAA
*
2708480 ATAAAAATATCTATTTGCATAT
1 ATAAAAA-AT-TATTTGAATAT
2708502 TTCAACCATC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.39
23 2 0.11
24 9 0.50
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (22 bp):
ATAAAAAATTATTTGAATATAA
Found at i:2709007 original size:2 final size:2
Alignment explanation
Indices: 2709000--2709024 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2708990 ATACTACTTA
2709000 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2709025 ATTAGCTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2709897 original size:2 final size:2
Alignment explanation
Indices: 2709886--2709915 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2709876 AAGTTTGGGA
2709886 AT AT -T 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
2709916 CACACTCATG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2716339 original size:84 final size:84
Alignment explanation
Indices: 2716198--2716447 Score: 355
Period size: 84 Copynumber: 3.0 Consensus size: 84
2716188 AAACGAGTCC
*
2716198 TTCTGGAATTGATT-GTGGTGGGAAGGATGTTGGTGTTT-GT-TCAGAAGCTGAAAAGGGTGTAG
1 TTCTGGAGTTGATTCG-GGTGGGAAGGATGTTGGT-TTTGGTAT-AGAAGCTGAAAAGGGTGTAG
2716260 AAGATGGTGGTATTTCGGCATT
63 AAGATGGTGGTATTTCGGCATT
* * *
2716282 TTCTGGAGTTGATTCGGGCGGGAAGGATGCTGGTTTTGGTATGGAAGCTGAAAAGGGTGTAGTAA
1 TTCTGGAGTTGATTCGGGTGGGAAGGATGTTGGTTTTGGTATAGAAGCTGAAAAGGGTGTAG-AA
2716347 -ATGGTGGTATTTCGGCATT
65 GATGGTGGTATTTCGGCATT
* * * * *
2716366 TGCTGGAGTTGATTCTGGTGGAAAGGATGTTGGTTTTGGTATAGAAGCTGAAAAGGATGCAGAAG
1 TTCTGGAGTTGATTCGGGTGGGAAGGATGTTGGTTTTGGTATAGAAGCTGAAAAGGGTGTAGAAG
2716431 ATGGTGGTATTTCGGCA
66 ATGGTGGTATTTCGGCA
2716448 GTATTGGATG
Statistics
Matches: 149, Mismatches: 12, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
83 5 0.03
84 140 0.94
85 4 0.03
ACGTcount: A:0.23, C:0.07, G:0.37, T:0.32
Consensus pattern (84 bp):
TTCTGGAGTTGATTCGGGTGGGAAGGATGTTGGTTTTGGTATAGAAGCTGAAAAGGGTGTAGAAG
ATGGTGGTATTTCGGCATT
Found at i:2722142 original size:2 final size:2
Alignment explanation
Indices: 2722135--2722159 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2722125 GTTGTTATAA
2722135 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
2722160 GGGGTGTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2728616 original size:3 final size:3
Alignment explanation
Indices: 2728608--2728640 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2728598 CAAATATTTT
2728608 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2728641 GATAGATAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2728850 original size:2 final size:2
Alignment explanation
Indices: 2728843--2728871 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2728833 CATTTCAAGA
2728843 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2728872 ACAACTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2730259 original size:273 final size:273
Alignment explanation
Indices: 2729772--2730319 Score: 1087
Period size: 273 Copynumber: 2.0 Consensus size: 273
2729762 GGATTTTTGA
2729772 ACGTTTGAATAGTCTGTTTGTTGCAGTTTGATATGTCAATATAAAAGAATTTTGAAATCTTGAAG
1 ACGTTTGAATAGTCTGTTTGTTGCAGTTTGATATGTCAATATAAAAGAATTTTGAAATCTTGAAG
2729837 GCTTAAATTCTTTAAGAAATAAGCGAAAAAGAACTTGGGTGGTAAGGGATTTAAATAATTCTTGA
66 GCTTAAATTCTTTAAGAAATAAGCGAAAAAGAACTTGGGTGGTAAGGGATTTAAATAATTCTTGA
2729902 ATAAAAACAGTTGCTGAATTTGAAGTAATTGGTAGATGATACAAATAGTCATAAACAATTCATGA
131 ATAAAAACAGTTGCTGAATTTGAAGTAATTGGTAGATGATACAAATAGTCATAAACAATTCATGA
2729967 ACATTTTAATCTATGCTGAAATTAGCAAGTTTTCTCCAGTCGATAAATGGAAACTTTTGTTTAAA
196 ACATTTTAATCTATGCTGAAATTAGCAAGTTTTCTCCAGTCGATAAATGGAAACTTTTGTTTAAA
2730032 GATGGTTACTCAG
261 GATGGTTACTCAG
2730045 ACGTTTGAATAGTCTGTTTGTTGCAGTTTGATATGTCAATATAAAAGAATTTTGAAATCTTGAAG
1 ACGTTTGAATAGTCTGTTTGTTGCAGTTTGATATGTCAATATAAAAGAATTTTGAAATCTTGAAG
2730110 GCTTAAATTCTTTAAGAAATAAGCGAAAAAGAACTTGGGTGGTAAGGGATTTAAATAATTCTTGA
66 GCTTAAATTCTTTAAGAAATAAGCGAAAAAGAACTTGGGTGGTAAGGGATTTAAATAATTCTTGA
2730175 ATAAAAACAGTTGCTGAATTTGAAGTAATTGGTAGATGATACAAATAGTCATAAACAATTCATGA
131 ATAAAAACAGTTGCTGAATTTGAAGTAATTGGTAGATGATACAAATAGTCATAAACAATTCATGA
*
2730240 ACATTTTAATCTATGCTGAAATTAGCAAGTTTTCTCCAGTCTATAAATGGAAACTTTTGTTTAAA
196 ACATTTTAATCTATGCTGAAATTAGCAAGTTTTCTCCAGTCGATAAATGGAAACTTTTGTTTAAA
2730305 GATGGTTACTCAG
261 GATGGTTACTCAG
2730318 AC
1 AC
2730320 AGTTATGATG
Statistics
Matches: 274, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
273 274 1.00
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.34
Consensus pattern (273 bp):
ACGTTTGAATAGTCTGTTTGTTGCAGTTTGATATGTCAATATAAAAGAATTTTGAAATCTTGAAG
GCTTAAATTCTTTAAGAAATAAGCGAAAAAGAACTTGGGTGGTAAGGGATTTAAATAATTCTTGA
ATAAAAACAGTTGCTGAATTTGAAGTAATTGGTAGATGATACAAATAGTCATAAACAATTCATGA
ACATTTTAATCTATGCTGAAATTAGCAAGTTTTCTCCAGTCGATAAATGGAAACTTTTGTTTAAA
GATGGTTACTCAG
Found at i:2734521 original size:53 final size:53
Alignment explanation
Indices: 2734463--2734563 Score: 159
Period size: 53 Copynumber: 1.9 Consensus size: 53
2734453 AGAATATTTT
* *
2734463 TATTTTTTGTTTA-TTTTTAAATAATATATTTAAAAAAATTGATCTATAAAAAA
1 TATTTTTT-TTTATTTTTTAAATAATATAATTAAAAAAATAGATCTATAAAAAA
*
2734516 TATTTTTTTTTATTTTTTAAATAATATAATTAAAATAATAGATCTATA
1 TATTTTTTTTTATTTTTTAAATAATATAATTAAAAAAATAGATCTATA
2734564 CATAATTTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
52 4 0.09
53 40 0.91
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (53 bp):
TATTTTTTTTTATTTTTTAAATAATATAATTAAAAAAATAGATCTATAAAAAA
Found at i:2735026 original size:3 final size:3
Alignment explanation
Indices: 2735011--2735054 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
2735001 ACCCATAGCG
*
2735011 TAA TAA GAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2735055 GTTGCTGCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:2736576 original size:7 final size:7
Alignment explanation
Indices: 2736564--2736589 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2736554 TTTTAATAAA
2736564 AAATTAT
1 AAATTAT
2736571 AAATTAT
1 AAATTAT
2736578 AAATTAT
1 AAATTAT
2736585 AAATT
1 AAATT
2736590 TATTAAATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
AAATTAT
Found at i:2737111 original size:2 final size:2
Alignment explanation
Indices: 2737106--2737136 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2737096 AGAGTTGGAA
2737106 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
2737137 ATCAACATCG
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:2738036 original size:2 final size:2
Alignment explanation
Indices: 2738029--2738071 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
2738019 TGTATCTATC
*
2738029 TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA T- TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2738069 TA T
1 TA T
2738072 GCATGCCTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2739074 original size:2 final size:2
Alignment explanation
Indices: 2739057--2739090 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
2739047 TAGCTAAATC
2739057 CT CT GCT CT CT C- CT CT CT CT CT CT CT CT CT CT CT
1 CT CT -CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2739091 ATCTTCCTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 27 0.90
3 2 0.07
ACGTcount: A:0.00, C:0.50, G:0.03, T:0.47
Consensus pattern (2 bp):
CT
Found at i:2740979 original size:20 final size:20
Alignment explanation
Indices: 2740940--2740979 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2740930 TTTTAATTTA
* **
2740940 ATAAAAAAAATTTATTAAAT
1 ATAAAAAAAATTAAAAAAAT
2740960 ATAAAAAAAATTAAAAAAAT
1 ATAAAAAAAATTAAAAAAAT
2740980 TAATTAATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
ATAAAAAAAATTAAAAAAAT
Found at i:2742861 original size:2 final size:2
Alignment explanation
Indices: 2742854--2742888 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2742844 GCTAAAACCT
2742854 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2742889 TTCCCTCTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2743687 original size:4 final size:4
Alignment explanation
Indices: 2743678--2743730 Score: 61
Period size: 4 Copynumber: 13.2 Consensus size: 4
2743668 ACCCTCCTTA
* * * * *
2743678 ACAC ACAC ACAC ACAC ACAC ACAC ACAC GCAC GCAC GCAC GCAA ACAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
2743726 ACAC A
1 ACAC A
2743731 AAAAATAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.45, C:0.47, G:0.08, T:0.00
Consensus pattern (4 bp):
ACAC
Found at i:2747753 original size:24 final size:24
Alignment explanation
Indices: 2747725--2747806 Score: 62
Period size: 24 Copynumber: 3.4 Consensus size: 24
2747715 ATGGTTTGCA
2747725 TATTTTTATTTTATAATATTATAT
1 TATTTTTATTTTATAATATTATAT
** * *
2747749 TATTTAAAATTTAAAATATT-TAT
1 TATTTTTATTTTATAATATTATAT
*
2747772 ATATTAATTTAATATTAT-ATATTA-AT
1 -TATT--TTT-ATTTTATAATATTATAT
2747798 TATTTTTAT
1 TATTTTTAT
2747807 ATATTATATT
Statistics
Matches: 44, Mismatches: 9, Indels: 12
0.68 0.14 0.18
Matches are distributed among these distances:
22 2 0.05
23 6 0.14
24 20 0.45
25 4 0.09
26 8 0.18
27 4 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TATTTTTATTTTATAATATTATAT
Found at i:2747754 original size:22 final size:22
Alignment explanation
Indices: 2747724--2747816 Score: 68
Period size: 22 Copynumber: 4.2 Consensus size: 22
2747714 AATGGTTTGC
2747724 ATATT-TTTATTTTATAATATT
1 ATATTATTTATTTTATAATATT
* *
2747745 ATATTATTTAAAATTTAAAATATT
1 ATATTATTT--ATTTTATAATATT
* * *
2747769 -TATATATTAATTTAATATTA-T
1 ATAT-TATTTATTTTATAATATT
*
2747790 ATATTAATTATTTT-TATATATT
1 ATATTATTTATTTTATA-ATATT
2747812 ATATT
1 ATATT
2747817 TATATAATTA
Statistics
Matches: 54, Mismatches: 11, Indels: 13
0.69 0.14 0.17
Matches are distributed among these distances:
20 2 0.04
21 15 0.28
22 19 0.35
23 3 0.06
24 15 0.28
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
ATATTATTTATTTTATAATATT
Found at i:2747810 original size:24 final size:25
Alignment explanation
Indices: 2747738--2747839 Score: 96
Period size: 22 Copynumber: 4.4 Consensus size: 25
2747728 TTTTATTTTA
*
2747738 TAATATTATATTATTTAA--A-ATT
1 TAATATTATATTATATAATTATATT
*
2747760 TAA-AATAT-TTATAT-ATTA-ATT
1 TAATATTATATTATATAATTATATT
*
2747781 TAATATTATA-TAT-TAATTATTTT
1 TAATATTATATTATATAATTATATT
2747804 TATATATTATATTTATATAATTATATT
1 TA-ATATTATA-TTATATAATTATATT
2747831 TAATATTAT
1 TAATATTAT
2747840 CAGATGAATT
Statistics
Matches: 65, Mismatches: 5, Indels: 16
0.76 0.06 0.19
Matches are distributed among these distances:
19 1 0.02
20 5 0.08
21 12 0.18
22 14 0.22
23 4 0.06
24 8 0.12
26 10 0.15
27 11 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
TAATATTATATTATATAATTATATT
Found at i:2747827 original size:8 final size:7
Alignment explanation
Indices: 2747764--2747839 Score: 58
Period size: 6 Copynumber: 11.3 Consensus size: 7
2747754 AAAATTTAAA
2747764 ATAT-TT
1 ATATATT
2747770 ATATATT
1 ATATATT
2747777 A-AT-TT
1 ATATATT
2747782 A-ATATT
1 ATATATT
2747788 ATATATT
1 ATATATT
*
2747795 AATTATTTTT
1 -A-TA-TATT
2747805 ATATATT
1 ATATATT
2747812 ATAT-TT
1 ATATATT
2747818 ATATAATT
1 ATAT-ATT
2747826 ATAT-TT
1 ATATATT
2747832 A-ATATT
1 ATATATT
2747838 AT
1 AT
2747840 CAGATGAATT
Statistics
Matches: 58, Mismatches: 2, Indels: 19
0.73 0.03 0.24
Matches are distributed among these distances:
5 7 0.12
6 21 0.36
7 15 0.26
8 9 0.16
9 3 0.05
10 3 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
ATATATT
Found at i:2754320 original size:8 final size:8
Alignment explanation
Indices: 2754307--2754343 Score: 58
Period size: 8 Copynumber: 4.8 Consensus size: 8
2754297 AAATTTAATT
2754307 ATATTAAA
1 ATATTAAA
2754315 ATATTAAA
1 ATATTAAA
2754323 ATATTAAA
1 ATATTAAA
2754331 ATA-TAAA
1 ATATTAAA
*
2754338 AAATTA
1 ATATTA
2754344 GTAATATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
ATATTAAA
Found at i:2756751 original size:2 final size:2
Alignment explanation
Indices: 2756744--2756773 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2756734 AGTTGAGACA
2756744 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
2756774 CAATAGCTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2757641 original size:21 final size:21
Alignment explanation
Indices: 2757595--2757638 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
2757585 AAATTTATTT
* *
2757595 AATT-TAATTATTTATTTTTA
1 AATTATAATTATTTATATTAA
2757615 AATTATAATTATTT-TATTAA
1 AATTATAATTATTTATATTAA
2757635 AATT
1 AATT
2757639 TATTTTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
AATTATAATTATTTATATTAA
Found at i:2757651 original size:17 final size:17
Alignment explanation
Indices: 2757585--2757658 Score: 57
Period size: 17 Copynumber: 4.5 Consensus size: 17
2757575 ATATAAATAT
*
2757585 AAATTTATTTAAT-TTA
1 AAATTTATTTTATATTA
* *
2757601 ATTATTTATTTTTAAATTA
1 A-AATTTA-TTTTATATTA
*
2757620 TAA-TTA-TTT-TATTA
1 AAATTTATTTTATATTA
2757634 AAATTTATTTTATATTA
1 AAATTTATTTTATATTA
*
2757651 ATATTTAT
1 AAATTTAT
2757659 ATATTTTATA
Statistics
Matches: 44, Mismatches: 8, Indels: 11
0.70 0.13 0.17
Matches are distributed among these distances:
14 6 0.14
15 6 0.14
16 4 0.09
17 20 0.45
18 5 0.11
19 3 0.07
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
AAATTTATTTTATATTA
Found at i:2757663 original size:21 final size:21
Alignment explanation
Indices: 2757639--2757678 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2757629 TATTAAAATT
2757639 TATTTTAT-ATTAATATTTATA
1 TATTTTATAATTAA-ATTTATA
2757660 TATTTTATAATTAAATTTA
1 TATTTTATAATTAAATTTA
2757679 AATAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTTATAATTAAATTTATA
Found at i:2758976 original size:21 final size:21
Alignment explanation
Indices: 2758927--2758997 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
2758917 TATTAGATAA
* *
2758927 ATTAAAGTTATTAAAAAATATT
1 ATTAAAATTATT-ACAAATATT
2758949 ATT-AAATTATGT-CAAATATT
1 ATTAAAATTAT-TACAAATATT
*
2758969 ATTAAAATTATTATAAATATT
1 ATTAAAATTATTACAAATATT
2758990 ATTAAAAT
1 ATTAAAAT
2758998 AAAAATATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
20 11 0.26
21 28 0.65
22 4 0.09
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (21 bp):
ATTAAAATTATTACAAATATT
Found at i:2759076 original size:17 final size:17
Alignment explanation
Indices: 2759056--2759088 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2759046 AAATGAAAAA
2759056 TTTTATAATTT-ATAAAT
1 TTTTA-AATTTAATAAAT
2759073 TTTTAAATTTAATAAA
1 TTTTAAATTTAATAAA
2759089 AATAATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTTAAATTTAATAAAT
Found at i:2759106 original size:18 final size:16
Alignment explanation
Indices: 2759078--2759120 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
2759068 TAAATTTTTA
*
2759078 AATTTAATAAAAATAAT
1 AATTAAATAAAAA-AAT
2759095 ATATTAAAT-AAAAAAT
1 A-ATTAAATAAAAAAAT
2759111 AATTAAATAA
1 AATTAAATAA
2759121 TTTTTAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 7 0.30
16 5 0.22
17 5 0.22
18 6 0.26
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATTAAATAAAAAAAT
Found at i:2759117 original size:15 final size:17
Alignment explanation
Indices: 2759087--2759120 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
2759077 AAATTTAATA
2759087 AAAATAATATATTAAAT
1 AAAATAATATATTAAAT
2759104 AAAA-AATA-ATTAAAT
1 AAAATAATATATTAAAT
2759119 AA
1 AA
2759121 TTTTTAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 4 0.24
17 4 0.24
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAATAATATATTAAAT
Found at i:2759192 original size:23 final size:21
Alignment explanation
Indices: 2759162--2759254 Score: 72
Period size: 20 Copynumber: 4.6 Consensus size: 21
2759152 TAAAATTTTT
2759162 AAAATTATTACAAAATAATATTA
1 AAAATTATTA-AAAATAATA-TA
**
2759185 AAAATTATT-AAAATTTTATA
1 AAAATTATTAAAAATAATATA
*
2759205 AAAATTATT-AAAAT--TATT
1 AAAATTATTAAAAATAATATA
* *
2759223 CAAATTATATAAAAA-AATATC
1 AAAATTAT-TAAAAATAATATA
2759244 AAAATT-TTAAA
1 AAAATTATTAAA
2759255 TTTTAAAAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
18 10 0.17
19 5 0.08
20 21 0.35
21 15 0.25
23 9 0.15
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAATTATTAAAAATAATATA
Found at i:2759206 original size:20 final size:20
Alignment explanation
Indices: 2759152--2759219 Score: 77
Period size: 20 Copynumber: 3.4 Consensus size: 20
2759142 TATTTGATAA
2759152 TAAAATTTT-T-AAAATTAT
1 TAAAATTTTATAAAAATTAT
**
2759170 TACAAAATAATATTAAAAATTAT
1 T--AAAATTTTA-TAAAAATTAT
2759193 TAAAATTTTATAAAAATTAT
1 TAAAATTTTATAAAAATTAT
2759213 TAAAATT
1 TAAAATT
2759220 ATTCAAATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
18 1 0.02
20 23 0.56
21 7 0.17
22 1 0.02
23 9 0.22
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAAATTTTATAAAAATTAT
Found at i:2759220 original size:9 final size:9
Alignment explanation
Indices: 2759152--2759236 Score: 71
Period size: 9 Copynumber: 8.6 Consensus size: 9
2759142 TATTTGATAA
*
2759152 TAAAATTTT
1 TAAAATTAT
2759161 TAAAATTAT
1 TAAAATTAT
2759170 TACAAAATAATAT
1 T--AAAAT--TAT
2759183 TAAAAATTAT
1 T-AAAATTAT
2759193 TAAAATTTTAT
1 TAAAA--TTAT
*
2759204 AAAAATTAT
1 TAAAATTAT
2759213 TAAAATTAT
1 TAAAATTAT
*
2759222 TCAAATTAT
1 TAAAATTAT
2759231 ATAAAA
1 -TAAAA
2759237 AAATATCAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
9 33 0.52
10 8 0.13
11 13 0.21
12 5 0.08
13 4 0.06
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (9 bp):
TAAAATTAT
Found at i:2764289 original size:2 final size:2
Alignment explanation
Indices: 2764282--2764310 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2764272 CATTGAAATG
2764282 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2764311 TGTGAGTGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2767626 original size:64 final size:64
Alignment explanation
Indices: 2767543--2767673 Score: 158
Period size: 64 Copynumber: 2.0 Consensus size: 64
2767533 AAAAATTTTA
* * * *
2767543 AAATAATATTAATTGTAAATTTAATG-AT-TTAAACATAATATTTTTTTAAAATTTGATGAGTAT
1 AAATAAAATTAATTATAAATTTAATGAATGTTAAACATAAT-TATTTTT-AAATTTGATAAGTAT
2767606 T
64 T
* * * *
2767607 AAATAAAATTATTTATAAATTTTATGAATGTTAAATATAATTATTTTTAAATTTGATAATTATT
1 AAATAAAATTAATTATAAATTTAATGAATGTTAAACATAATTATTTTTAAATTTGATAAGTATT
2767671 AAA
1 AAA
2767674 AAATTTCAAT
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
64 39 0.68
65 8 0.14
66 10 0.18
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.47
Consensus pattern (64 bp):
AAATAAAATTAATTATAAATTTAATGAATGTTAAACATAATTATTTTTAAATTTGATAAGTATT
Found at i:2767627 original size:32 final size:32
Alignment explanation
Indices: 2767587--2767673 Score: 106
Period size: 32 Copynumber: 2.8 Consensus size: 32
2767577 ATAATATTTT
*
2767587 TTTA-AAATTTGATGAGTATTAAATAAAATTA
1 TTTATAAATTTGATGAATATTAAATAAAATTA
* * *
2767618 TTTATAAATTTTATGAATGTTAAATATAATTA
1 TTTATAAATTTGATGAATATTAAATAAAATTA
*
2767650 TTTTTAAATTTGAT-AATTATTAAA
1 TTTATAAATTTGATGAA-TATTAAA
2767674 AAATTTCAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
31 6 0.13
32 41 0.87
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (32 bp):
TTTATAAATTTGATGAATATTAAATAAAATTA
Found at i:2770854 original size:17 final size:18
Alignment explanation
Indices: 2770829--2770862 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2770819 GTAATTATAA
2770829 TATTCGAATTT-TAATAC
1 TATTCGAATTTATAATAC
*
2770846 TATTTGAATTTATAATA
1 TATTCGAATTTATAATA
2770863 TTTAAAATGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (18 bp):
TATTCGAATTTATAATAC
Found at i:2775476 original size:2 final size:2
Alignment explanation
Indices: 2775428--2775463 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2775418 TTAATTTCAG
2775428 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
2775464 GCCCACATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.