Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold8
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: 6381039
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 22487 characters in sequence are not A, C, G, or T
File 15 of 33
Found at i:2083251 original size:31 final size:31
Alignment explanation
Indices: 2083213--2083282 Score: 90
Period size: 34 Copynumber: 2.2 Consensus size: 31
2083203 TACTTAAAAA
2083213 AATTAAAAAGT-AAA-TATTTAAATAATATAT
1 AATTAAAAAGTAAAATTATTTAAATAATA-AT
*
2083243 AATCTAAAAATTAAAATTTATTTAAATAATAAT
1 AAT-TAAAAAGTAAAA-TTATTTAAATAATAAT
2083276 AATTAAA
1 AATTAAA
2083283 TTAAACAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
30 3 0.09
31 7 0.20
32 7 0.20
33 5 0.14
34 13 0.37
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (31 bp):
AATTAAAAAGTAAAATTATTTAAATAATAAT
Found at i:2083422 original size:29 final size:30
Alignment explanation
Indices: 2083359--2083427 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
2083349 TAAATTTATC
2083359 AAAATTTAAATCATTTGTATTATAAATCAT
1 AAAATTTAAATCATTTGTATTATAAATCAT
* *
2083389 AAAATTTAACATCAATT-T-TTATATAATTAT
1 AAAATTTAA-ATCATTTGTATTATA-AATCAT
*
2083419 AAATTTTAA
1 AAAATTTAA
2083428 TTTAATCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 5 0.15
30 23 0.68
31 6 0.18
ACGTcount: A:0.48, C:0.06, G:0.01, T:0.45
Consensus pattern (30 bp):
AAAATTTAAATCATTTGTATTATAAATCAT
Found at i:2083442 original size:31 final size:30
Alignment explanation
Indices: 2083407--2083469 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 30
2083397 ACATCAATTT
2083407 TTATATAATTATAAATTTTAAT-TTAATCAAA
1 TTATATAATTA-AAATTTTAATATTAAT-AAA
* * *
2083438 TTATATTATTAAATTTTTATTATTAATAAA
1 TTATATAATTAAAATTTTAATATTAATAAA
2083468 TT
1 TT
2083470 TAACTATGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 13 0.46
31 15 0.54
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (30 bp):
TTATATAATTAAAATTTTAATATTAATAAA
Found at i:2083711 original size:6 final size:7
Alignment explanation
Indices: 2083694--2083740 Score: 76
Period size: 7 Copynumber: 6.7 Consensus size: 7
2083684 TAACTGATAA
*
2083694 AAAAAGT
1 AAAAATT
2083701 AAAAATT
1 AAAAATT
2083708 AAAAATT
1 AAAAATT
2083715 AAAAATT
1 AAAAATT
*
2083722 AAAAATA
1 AAAAATT
2083729 AAAAATT
1 AAAAATT
2083736 AAAAA
1 AAAAA
2083741 ATTAGTAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (7 bp):
AAAAATT
Found at i:2084622 original size:30 final size:27
Alignment explanation
Indices: 2084599--2084682 Score: 77
Period size: 23 Copynumber: 3.2 Consensus size: 27
2084589 TTTTGTATTA
2084599 TTATAATAATATTTAAAATATTTTATAT
1 TTATAATAAT-TTTAAAATATTTTATAT
* * * *
2084627 TTATATTAATTTTAATATA-TTAATAA
1 TTATAATAATTTTAAAATATTTTATAT
*
2084653 TT-T-AT-ATTATAAAATATTTATATAT
1 TTATAATAATTTTAAAATATTT-TATAT
2084678 TTATA
1 TTATA
2084683 TTATATTATA
Statistics
Matches: 43, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
23 9 0.21
24 3 0.07
25 6 0.14
26 8 0.19
27 8 0.19
28 9 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
TTATAATAATTTTAAAATATTTTATAT
Found at i:2084627 original size:27 final size:27
Alignment explanation
Indices: 2084597--2084687 Score: 73
Period size: 24 Copynumber: 3.3 Consensus size: 27
2084587 TATTTTGTAT
2084597 TATTATAATAATATTTAAAATATTTTA
1 TATTATAATAATATTTAAAATATTTTA
*
2084624 TATTTATATTAAT-TTTAATATATTAATAATTTA
1 TA-TTATAATAATATTTAA-A-A-T-AT--TTTA
*
2084657 TATTATAA-AATATTT-ATATA-TTTA
1 TATTATAATAATATTTAAAATATTTTA
2084681 TATTATA
1 TATTATA
2084688 TTATATTATA
Statistics
Matches: 53, Mismatches: 3, Indels: 19
0.71 0.04 0.25
Matches are distributed among these distances:
24 11 0.21
27 8 0.15
28 11 0.21
29 2 0.04
30 1 0.02
31 6 0.11
32 8 0.15
33 6 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
TATTATAATAATATTTAAAATATTTTA
Found at i:2084628 original size:16 final size:16
Alignment explanation
Indices: 2084607--2084694 Score: 63
Period size: 17 Copynumber: 5.3 Consensus size: 16
2084597 TATTATAATA
2084607 ATATTTAAAATATTTT
1 ATATTTAAAATATTTT
* *
2084623 ATATTTATATTAATTTT
1 ATATTTAAAAT-ATTTT
*
2084640 AATATATT--AATAATTT
1 -ATAT-TTAAAATATTTT
2084656 ATATTATAAAATATTTAT
1 ATATT-TAAAATATTT-T
* * *
2084674 ATATTTATATTATATT
1 ATATTTAAAATATTTT
2084690 ATATT
1 ATATT
2084695 ATAATTATTT
Statistics
Matches: 57, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
14 1 0.02
15 5 0.09
16 19 0.33
17 20 0.35
18 10 0.18
19 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATATTTAAAATATTTT
Found at i:2084701 original size:16 final size:16
Alignment explanation
Indices: 2084621--2084720 Score: 61
Period size: 15 Copynumber: 6.4 Consensus size: 16
2084611 TTAAAATATT
2084621 TTATATT-TA-TATTAA
1 TTATATTATATTA-TAA
* *
2084636 TTTTAATATATTAATAA
1 TTATATTATATT-ATAA
** *
2084653 TTTATATTATAAAATAT
1 -TTATATTATATTATAA
2084670 TTATA-TAT-TTAT-A
1 TTATATTATATTATAA
2084683 TTATATTATATTATAA
1 TTATATTATATTATAA
*
2084699 TTAT-TTATA-AATAA
1 TTATATTATATTATAA
2084713 TATATATT
1 T-TATATT
2084721 TTTAAATATA
Statistics
Matches: 65, Mismatches: 11, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
13 5 0.08
14 10 0.15
15 20 0.31
16 14 0.22
17 7 0.11
18 9 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTATATTATATTATAA
Found at i:2084702 original size:29 final size:29
Alignment explanation
Indices: 2084616--2084702 Score: 74
Period size: 29 Copynumber: 3.1 Consensus size: 29
2084606 AATATTTAAA
*
2084616 ATAT-TTTATATTTATATTA-ATTTTAA-T
1 ATATATTTATA-TTATATTATATTATAATT
* * ** *
2084643 ATATTAATAAT-TTATATTATAAAATATTT
1 ATA-TATTTATATTATATTATATTATAATT
2084672 ATATATTTATATTATATTATATTATAATT
1 ATATATTTATATTATATTATATTATAATT
2084701 AT
1 AT
2084703 TTATAAATAA
Statistics
Matches: 44, Mismatches: 11, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
27 11 0.25
28 9 0.20
29 24 0.55
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (29 bp):
ATATATTTATATTATATTATATTATAATT
Found at i:2084708 original size:10 final size:10
Alignment explanation
Indices: 2084624--2084708 Score: 50
Period size: 10 Copynumber: 7.9 Consensus size: 10
2084614 AAATATTTTA
2084624 TATTTAT-AT
1 TATTTATAAT
2084633 TAATTT-TAAT
1 T-ATTTATAAT
*
2084643 ATATTAATAATT
1 -TATTTATAA-T
*
2084655 TATATTATAAAA
1 TAT-TTAT-AAT
2084667 TATTTATATATT
1 TATTTATA-A-T
2084679 TATATTAT-AT
1 TAT-TTATAAT
2084689 TATATTATAAT
1 TAT-TTATAAT
2084700 TATTTATAA
1 TATTTATAA
2084709 ATAATATATA
Statistics
Matches: 61, Mismatches: 4, Indels: 21
0.71 0.05 0.24
Matches are distributed among these distances:
9 2 0.03
10 25 0.41
11 18 0.30
12 10 0.16
13 6 0.10
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TATTTATAAT
Found at i:2084712 original size:60 final size:59
Alignment explanation
Indices: 2084597--2084729 Score: 146
Period size: 60 Copynumber: 2.2 Consensus size: 59
2084587 TATTTTGTAT
* * *
2084597 TATTATAATAATATTTAAAATATTTTATATTTATATTAATTTTAATATATTAATAATTTA
1 TATTATAA-AATATTTAAAATATTTTATATTTATATTAATTATAATATATAAATAATATA
*
2084657 TATTATAAAATATTT-ATATA-TTTATA-TTATATTATATTATAATTATTTATAAATAATATA
1 TATTATAAAATATTTAAAATATTTTATATTTATATTA-ATTATAA-TA--TATAAATAATATA
* *
2084717 TATTTTTAAATAT
1 TATTATAAAATAT
2084730 AATTAATATT
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
56 8 0.13
57 12 0.19
58 6 0.10
59 7 0.11
60 30 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (59 bp):
TATTATAAAATATTTAAAATATTTTATATTTATATTAATTATAATATATAAATAATATA
Found at i:2084716 original size:24 final size:24
Alignment explanation
Indices: 2084639--2084717 Score: 69
Period size: 25 Copynumber: 3.3 Consensus size: 24
2084629 ATATTAATTT
2084639 TAATATATTAATAATTTATATTAT-AA
1 TAATATATT-ATAA-TTAT-TTATAAA
*
2084665 -AATAT-TTAT-A-TATTTATATTA
1 TAATATATTATAATTATTTATA-AA
*
2084686 TATTATATTATAATTATTTATAAA
1 TAATATATTATAATTATTTATAAA
2084710 TAATATAT
1 TAATATAT
2084718 ATTTTTAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
19 4 0.09
20 3 0.07
21 1 0.02
22 5 0.12
23 6 0.14
24 11 0.26
25 13 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TAATATATTATAATTATTTATAAA
Found at i:2086274 original size:21 final size:19
Alignment explanation
Indices: 2086242--2086280 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
2086232 CAATAGTTTC
*
2086242 TTTTTTCATTTGAATGTACG
1 TTTTTACATTTGAA-GTACG
2086262 TTTTTACATTTTGAAGTAC
1 TTTTTACA-TTTGAAGTAC
2086281 TGAGCTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.23, C:0.10, G:0.13, T:0.54
Consensus pattern (19 bp):
TTTTTACATTTGAAGTACG
Found at i:2091731 original size:2 final size:2
Alignment explanation
Indices: 2091724--2091751 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2091714 GCACGTTATG
2091724 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
2091752 TATTTATGTG
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:2094273 original size:13 final size:13
Alignment explanation
Indices: 2094236--2094277 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
2094226 CACAATATGA
* *
2094236 AAAAAAAAAAAAA
1 AAAAAAACAAAAC
2094249 AAAAAAAC-AAAC
1 AAAAAAACAAAAC
*
2094261 AAAAATACAAAAC
1 AAAAAAACAAAAC
2094274 AAAA
1 AAAA
2094278 GAGTTCAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.88, C:0.10, G:0.00, T:0.02
Consensus pattern (13 bp):
AAAAAAACAAAAC
Found at i:2094924 original size:25 final size:25
Alignment explanation
Indices: 2094905--2094953 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
2094895 AATCCTCTGT
2094905 GATTCAACACAAACTTATCCCAGAG
1 GATTCAACACAAACTTATCCCAGAG
2094930 GATTCAACACAAACTTATCCCAGA
1 GATTCAACACAAACTTATCCCAGA
2094954 TTCCCACTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.41, C:0.29, G:0.10, T:0.20
Consensus pattern (25 bp):
GATTCAACACAAACTTATCCCAGAG
Found at i:2098942 original size:2 final size:2
Alignment explanation
Indices: 2098937--2098964 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2098927 CTCTCTCTCT
2098937 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
2098965 TATATATATA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2101222 original size:22 final size:21
Alignment explanation
Indices: 2101196--2101241 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 21
2101186 AAATAAATTA
2101196 AAAAATTATTATTTATTATTTTT
1 AAAAATTA-TATTT-TTATTTTT
2101219 AAAAAATTATATTTTTATTTTT
1 -AAAAATTATATTTTTATTTTT
2101241 A
1 A
2101242 TGTCAATCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 1 0.05
22 8 0.36
23 5 0.23
24 8 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
AAAAATTATATTTTTATTTTT
Found at i:2101225 original size:24 final size:22
Alignment explanation
Indices: 2101193--2101241 Score: 80
Period size: 24 Copynumber: 2.1 Consensus size: 22
2101183 TATAAATAAA
2101193 TTAAAAAATTATTATTTATTATTT
1 TTAAAAAATTA-TATTT-TTATTT
2101217 TTAAAAAATTATATTTTTATTT
1 TTAAAAAATTATATTTTTATTT
2101239 TTA
1 TTA
2101242 TGTCAATCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 9 0.36
23 5 0.20
24 11 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TTAAAAAATTATATTTTTATTT
Found at i:2102583 original size:31 final size:31
Alignment explanation
Indices: 2102540--2102618 Score: 96
Period size: 29 Copynumber: 2.7 Consensus size: 31
2102530 AAAATACACG
2102540 AATATA-ATATAAATATATAAATGTA-TAAA
1 AATATATATATAAATATATAAATGTATTAAA
* *
2102569 AATATATATAATAAAT-TATTAATTTATTAAA
1 AATATATAT-ATAAATATATAAATGTATTAAA
2102600 AAT-T-TATATAAATATATAA
1 AATATATATATAAATATATAA
2102619 TATTTTAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
28 6 0.14
29 13 0.30
30 11 0.26
31 13 0.30
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (31 bp):
AATATATATATAAATATATAAATGTATTAAA
Found at i:2102665 original size:2 final size:2
Alignment explanation
Indices: 2102658--2102685 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2102648 TAACAACTGA
2102658 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
2102686 GTATCTATAG
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:2103186 original size:2 final size:2
Alignment explanation
Indices: 2103179--2103208 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2103169 TCTGATACCA
2103179 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
2103209 CTGTTCAGAC
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:2111170 original size:33 final size:33
Alignment explanation
Indices: 2111113--2111178 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2111103 AAAGTAACAA
* *
2111113 TTGAATAATGTTTTAGTCATCTTTTATGAATAT
1 TTGAATAATGTTTTAATCAACTTTTATGAATAT
2111146 TTGAATAAT-TTTTAAATCAACTTTTATGAATAT
1 TTGAATAATGTTTT-AATCAACTTTTATGAATAT
2111179 GGTAATGATG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 4 0.13
33 26 0.87
ACGTcount: A:0.35, C:0.06, G:0.09, T:0.50
Consensus pattern (33 bp):
TTGAATAATGTTTTAATCAACTTTTATGAATAT
Found at i:2113605 original size:3 final size:3
Alignment explanation
Indices: 2113597--2113628 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2113587 TCGGTTCACA
2113597 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2113629 ATAAATAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2114067 original size:17 final size:16
Alignment explanation
Indices: 2114038--2114070 Score: 57
Period size: 16 Copynumber: 2.0 Consensus size: 16
2114028 TTTTATTTGT
2114038 TTTTTAAATTATTTTA
1 TTTTTAAATTATTTTA
2114054 TTTTTAAATATATTTTA
1 TTTTTAAAT-TATTTTA
2114071 AAAAATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTTAAATTATTTTA
Found at i:2114513 original size:20 final size:20
Alignment explanation
Indices: 2114488--2114530 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
2114478 TATATATGTA
2114488 TATTATATATACTA-AAAAAT
1 TATTATATAT-CTATAAAAAT
*
2114508 TATTATATATCTATTAAAAT
1 TATTATATATCTATAAAAAT
2114528 TAT
1 TAT
2114531 ATTCATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (20 bp):
TATTATATATCTATAAAAAT
Found at i:2114541 original size:15 final size:17
Alignment explanation
Indices: 2114489--2114548 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
2114479 ATATATGTAT
*
2114489 ATTATATATACTAAAAAA
1 ATTATATAT-CTATAAAA
*
2114507 TTATTATATATCTATTAAA
1 --ATTATATATCTATAAAA
*
2114526 ATTATAT-TCATAAAAAA
1 ATTATATATC-TATAAAA
2114543 ATTATA
1 ATTATA
2114549 ACATTTTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
16 2 0.06
17 18 0.51
19 6 0.17
20 9 0.26
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTATATATCTATAAAA
Found at i:2118914 original size:25 final size:26
Alignment explanation
Indices: 2118886--2118937 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
2118876 TGAAAACTTG
*
2118886 AGAA-AAAAATGGGTTTTGAGAGTAA
1 AGAAGAAAAATGGGTTTTGAGAATAA
**
2118911 AGAAGAATGATGGGTTTTGAGAATAA
1 AGAAGAAAAATGGGTTTTGAGAATAA
2118937 A
1 A
2118938 TTTGAGTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.46, C:0.00, G:0.29, T:0.25
Consensus pattern (26 bp):
AGAAGAAAAATGGGTTTTGAGAATAA
Found at i:2119392 original size:21 final size:22
Alignment explanation
Indices: 2119358--2119402 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
2119348 AGCAGTTTCT
* *
2119358 AATAAAATT-TTTTTAGATAAA
1 AATAAAATTATTTTAACATAAA
*
2119379 AATAATATTATTTTAACATAAA
1 AATAAAATTATTTTAACATAAA
2119401 AA
1 AA
2119403 AGTATTTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (22 bp):
AATAAAATTATTTTAACATAAA
Found at i:2119960 original size:30 final size:28
Alignment explanation
Indices: 2119890--2119960 Score: 72
Period size: 30 Copynumber: 2.5 Consensus size: 28
2119880 TTTATAAATG
* *
2119890 AAATAAT-TATTTTATATATCAATAACA
1 AAATAATATATTTTATAAATAAATAACA
* * *
2119917 AAATAAAAAATTTTATAAATAAAATTAATA
1 AAATAATATATTTTATAAAT-AAA-TAACA
2119947 AAATAATATATTTT
1 AAATAATATATTTT
2119961 TTATTTATTT
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
27 6 0.18
28 10 0.29
29 2 0.06
30 16 0.47
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (28 bp):
AAATAATATATTTTATAAATAAATAACA
Found at i:2124702 original size:30 final size:30
Alignment explanation
Indices: 2124666--2124726 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
2124656 TTTAAAAGTA
2124666 ACAATCTGAAGTAAGAAAAGAATATCAATT
1 ACAATCTGAAGTAAGAAAAGAATATCAATT
*
2124696 ACAATCTGGAGTAAGAAAAGAATATCAATT
1 ACAATCTGAAGTAAGAAAAGAATATCAATT
2124726 A
1 A
2124727 TCACAACAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.52, C:0.10, G:0.15, T:0.23
Consensus pattern (30 bp):
ACAATCTGAAGTAAGAAAAGAATATCAATT
Found at i:2130316 original size:15 final size:15
Alignment explanation
Indices: 2130292--2130322 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2130282 TCCATATTCA
*
2130292 TGTCTGAATATATGT
1 TGTCTAAATATATGT
2130307 TGTCTAAATATATGT
1 TGTCTAAATATATGT
2130322 T
1 T
2130323 AGATACAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.16, T:0.48
Consensus pattern (15 bp):
TGTCTAAATATATGT
Found at i:2132350 original size:2 final size:2
Alignment explanation
Indices: 2132339--2132374 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2132329 TATGCCATTT
2132339 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2132375 TGTAATTCCC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2133348 original size:1 final size:1
Alignment explanation
Indices: 2133342--2133370 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
2133332 CCTTTGAGGG
2133342 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2133371 CCTCTATAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2136029 original size:2 final size:2
Alignment explanation
Indices: 2136024--2136052 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2136014 TTTATTTGTA
2136024 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
2136053 AAAGAGAGAT
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:2138472 original size:25 final size:25
Alignment explanation
Indices: 2138444--2138527 Score: 66
Period size: 25 Copynumber: 3.3 Consensus size: 25
2138434 ATGATTTAAA
2138444 ATTTTTAAATTATTTTTTATTTATT
1 ATTTTTAAATTATTTTTTATTTATT
* *
2138469 A-TTTTATAATTATTTTATAATTA-T
1 ATTTTTA-AATTATTTTTTATTTATT
* * *
2138493 ATTTAAATAAAAATATTATTT-TTTATT
1 ATTT---TTAAATTATTTTTTATTTATT
2138520 ATTTTTAA
1 ATTTTTAA
2138528 TAATTTAAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 13
0.68 0.12 0.20
Matches are distributed among these distances:
24 10 0.22
25 17 0.38
26 3 0.07
27 13 0.29
28 2 0.04
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
ATTTTTAAATTATTTTTTATTTATT
Found at i:2138481 original size:14 final size:13
Alignment explanation
Indices: 2138445--2138492 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 13
2138435 TGATTTAAAA
2138445 TTTTTA-AATTAT
1 TTTTTATAATTAT
2138457 TTTTTAT--TTAT
1 TTTTTATAATTAT
2138468 TATTTTATAATTA-
1 T-TTTTATAATTAT
2138481 -TTTTATAATTAT
1 TTTTTATAATTAT
2138493 ATTTAAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
11 16 0.52
12 12 0.39
14 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTTATAATTAT
Found at i:2139278 original size:17 final size:16
Alignment explanation
Indices: 2139258--2139295 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
2139248 TTACAATTAA
*
2139258 AATTAATTTTTATTATT
1 AATTAATGTTTATT-TT
2139275 AATTAATGTTTATTTT
1 AATTAATGTTTATTTT
2139291 AATTA
1 AATTA
2139296 CTTATATGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
AATTAATGTTTATTTT
Found at i:2142876 original size:29 final size:29
Alignment explanation
Indices: 2142807--2142877 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 29
2142797 CTCAAAATTT
*
2142807 TAAAATTTTGAGAGATATATTTTATATAA
1 TAAATTTTTGAGAGATATATTTTATATAA
2142836 TAAAATATATTTTTGAGAGATATATTTTATATAA
1 T---A-A-ATTTTTGAGAGATATATTTTATATAA
2142870 TAAATTTT
1 TAAATTTT
2142878 AAAAAAATTG
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
29 6 0.17
30 1 0.03
31 1 0.03
32 1 0.03
33 1 0.03
34 26 0.72
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (29 bp):
TAAATTTTTGAGAGATATATTTTATATAA
Found at i:2143060 original size:28 final size:28
Alignment explanation
Indices: 2143004--2143061 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
2142994 AATTAATATT
* * *
2143004 ATTTAATTAATAAAAATATTATATTTAA
1 ATTTAATTAATAAAAATATAAAATATAA
2143032 ATTTAATT-ATAAAATATATAAAATATAA
1 ATTTAATTAATAAAA-ATATAAAATATAA
2143060 AT
1 AT
2143062 ATAAAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 6 0.23
28 20 0.77
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (28 bp):
ATTTAATTAATAAAAATATAAAATATAA
Found at i:2143554 original size:20 final size:20
Alignment explanation
Indices: 2143529--2143575 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2143519 AATTTGTAAG
2143529 TTTAATTTA-ATTTTTTAATT
1 TTTAATTTAGA-TTTTTAATT
*
2143549 TTTAATATAGATTTTTAATT
1 TTTAATTTAGATTTTTAATT
*
2143569 TGTAATT
1 TTTAATT
2143576 ATTATTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (20 bp):
TTTAATTTAGATTTTTAATT
Found at i:2144323 original size:17 final size:18
Alignment explanation
Indices: 2144301--2144346 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
2144291 AATATATATT
2144301 TATAAAAT-TTATAAAATA
1 TATAAAATATTA-AAAATA
2144319 T-TAAAATATTAAAAATA
1 TATAAAATATTAAAAATA
2144336 TATAAATATAT
1 TATAAA-ATAT
2144347 ATTTTTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 13 0.52
18 8 0.32
19 4 0.16
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TATAAAATATTAAAAATA
Found at i:2152291 original size:10 final size:11
Alignment explanation
Indices: 2152256--2152295 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
2152246 TCGTACTGTG
2152256 TTTATATTATT
1 TTTATATTATT
*
2152267 TTTATAATATAT
1 TTTATATTAT-T
2152279 TTTA-ATTATT
1 TTTATATTATT
2152289 TTTATAT
1 TTTATAT
2152296 AAAATAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 5 0.20
11 15 0.60
12 5 0.20
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTATATTATT
Found at i:2152753 original size:12 final size:11
Alignment explanation
Indices: 2152736--2152833 Score: 56
Period size: 11 Copynumber: 8.4 Consensus size: 11
2152726 ACGTGTAATT
2152736 TTATATGTTAAA
1 TTATAT-TTAAA
2152748 TTATATTTAAAGTA
1 TTATATTT-AA--A
*
2152762 TTATAATTTATA
1 TTAT-ATTTAAA
*
2152774 -TAAATTTTAAA
1 TTATA-TTTAAA
*
2152785 ATAT-TTTAATA
1 TTATATTTAA-A
*
2152796 TTTATATTTATA
1 -TTATATTTAAA
*
2152808 TTATATTTTAA
1 TTATATTTAAA
*
2152819 TTATTTTTAAA
1 TTATATTTAAA
2152830 TTAT
1 TTAT
2152834 TTAATAATTA
Statistics
Matches: 67, Mismatches: 10, Indels: 19
0.70 0.10 0.20
Matches are distributed among these distances:
10 6 0.09
11 32 0.48
12 15 0.22
13 4 0.06
14 6 0.09
15 4 0.06
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (11 bp):
TTATATTTAAA
Found at i:2152801 original size:26 final size:26
Alignment explanation
Indices: 2152753--2152831 Score: 65
Period size: 26 Copynumber: 3.0 Consensus size: 26
2152743 TTAAATTATA
* *
2152753 TTTAAAGTATTATAAT-TTATATAAAT
1 TTTAAAATATTTTAATATT-TATAAAT
2152779 TTTAAAATATTTTAATATTTAT--AT
1 TTTAAAATATTTTAATATTTATAAAT
** *
2152803 TTATATTATATTTTAATTATTTTTAAAT
1 TT-TAAAATATTTTAA-TATTTATAAAT
2152831 T
1 T
2152832 ATTTAATAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
24 4 0.09
25 11 0.26
26 23 0.53
27 2 0.05
28 3 0.07
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (26 bp):
TTTAAAATATTTTAATATTTATAAAT
Found at i:2152841 original size:22 final size:22
Alignment explanation
Indices: 2152778--2152845 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
2152768 TTTATATAAA
* *
2152778 TTTTAAAATATTTTAATATTTAT
1 TTTTAAATTA-TTTAATAATTAT
* * *
2152801 ATTTATATTATATT-TTAATTAT
1 TTTTAAATTAT-TTAATAATTAT
2152823 TTTTAAATTATTTAATAATTAT
1 TTTTAAATTATTTAATAATTAT
2152845 T
1 T
2152846 ATTTTAAAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
21 2 0.06
22 24 0.69
23 9 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTTAAATTATTTAATAATTAT
Found at i:2152857 original size:15 final size:15
Alignment explanation
Indices: 2152829--2152866 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
2152819 TTATTTTTAA
*
2152829 ATTA-TTTAATAATT
1 ATTATTTTAAAAATT
2152843 ATTATTTTAAAAATT
1 ATTATTTTAAAAATT
2152858 ATTAATTTT
1 ATT-ATTTT
2152867 GACCTGTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 4 0.19
15 12 0.57
16 5 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTATTTTAAAAATT
Found at i:2154040 original size:11 final size:12
Alignment explanation
Indices: 2154025--2154053 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
2154015 ATAATTAATT
2154025 TAATATTAAATA
1 TAATATTAAATA
2154037 -AATATTAAATA
1 TAATATTAAATA
2154048 TAATAT
1 TAATAT
2154054 ATAATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TAATATTAAATA
Found at i:2154354 original size:18 final size:18
Alignment explanation
Indices: 2154311--2154365 Score: 78
Period size: 16 Copynumber: 3.1 Consensus size: 18
2154301 TATTATATAA
2154311 ATAATATATATAAAAAATT
1 ATAATATA-ATAAAAAATT
2154330 A-AA-ATAATAAAAAATT
1 ATAATATAATAAAAAATT
2154346 ATAATATAATATAAAAATT
1 ATAATATAATA-AAAAATT
2154365 A
1 A
2154366 ATACGAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
16 11 0.33
17 5 0.15
18 8 0.24
19 9 0.27
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
ATAATATAATAAAAAATT
Found at i:2154374 original size:23 final size:23
Alignment explanation
Indices: 2154348--2154391 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2154338 AAAAAATTAT
*
2154348 AATATAATATAAAAATTAATACG
1 AATATAATATAAAAATGAATACG
*
2154371 AATATAATATATAAATGAATA
1 AATATAATATAAAAATGAATA
2154392 TATCAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (23 bp):
AATATAATATAAAAATGAATACG
Found at i:2154509 original size:40 final size:41
Alignment explanation
Indices: 2154465--2154563 Score: 104
Period size: 39 Copynumber: 2.5 Consensus size: 41
2154455 AAATATTATT
2154465 ATTATATATAAAAATATTTAAATGAAA-T-ATAAATACATAA
1 ATTATATATAAAAATATTTAAATGAAATTAATAAATA-ATAA
* **
2154505 ATTAT-TATTAATTTATATT-AATGAAATTAATAAATAATAA
1 ATTATATATAAAAATAT-TTAAATGAAATTAATAAATAATAA
2154545 A-TA-ATATAAAAAT-TTTAAA
1 ATTATATATAAAAATATTTAAA
2154564 ACAGAGAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
37 2 0.04
38 3 0.06
39 23 0.48
40 13 0.27
41 7 0.15
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (41 bp):
ATTATATATAAAAATATTTAAATGAAATTAATAAATAATAA
Found at i:2154559 original size:41 final size:40
Alignment explanation
Indices: 2154470--2154559 Score: 91
Period size: 41 Copynumber: 2.3 Consensus size: 40
2154460 TTATTATTAT
*
2154470 ATATAAAAA--TATTTAAATGAAATATAAATACATAAATT
1 ATATAAAAATTTATTTAAATGAAATATAAATACATAAATA
**
2154508 AT-TATTAATTTATATT-AATGAAATTAATAAATA-ATAAATA
1 ATATAAAAATTTAT-TTAAATGAAA-T-ATAAATACATAAATA
2154548 ATATAAAAATTT
1 ATATAAAAATTT
2154560 TAAAACAGAG
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
37 4 0.10
38 2 0.05
39 10 0.24
40 11 0.27
41 14 0.34
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (40 bp):
ATATAAAAATTTATTTAAATGAAATATAAATACATAAATA
Found at i:2157710 original size:122 final size:121
Alignment explanation
Indices: 2157494--2157712 Score: 325
Period size: 122 Copynumber: 1.8 Consensus size: 121
2157484 CCTTTTTTCT
* * * * *
2157494 TCCTTCCAGGTCCTTAACTACTAGTCTTCTGTTGCAAATCCTTAACTGTTTTTATCTATGTTGCT
1 TCCTTCCAAGTCCTTAACTACTAGTCTTCTGTTACAAATCCTAAAATGATTTTATCTATGTTGCT
2157559 CCGACTCTTCATTTTTCTTGGAATACCCTTGTTAAAAATGCATATTAAGACATGGG
66 CCGACTCTTCATTTTTCTTGGAATACCCTTGTTAAAAATGCATATTAAGACATGGG
* *
2157615 TCCTTCCAAGTCCTTAACTACTTGTCTTCTGTTATACAAATTC-AAAATGATTTTATCTATGTTG
1 TCCTTCCAAGTCCTTAACTACTAGTCTTCTG-T-TACAAATCCTAAAATGATTTTATCTATGTTG
*
2157679 -TCCAGACTCTTCATTTTTCTTGGAGTACCCTTGT
64 CTCC-GACTCTTCATTTTTCTTGGAATACCCTTGT
2157713 CCAGCATATA
Statistics
Matches: 87, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
121 32 0.37
122 48 0.55
123 7 0.08
ACGTcount: A:0.23, C:0.22, G:0.13, T:0.42
Consensus pattern (121 bp):
TCCTTCCAAGTCCTTAACTACTAGTCTTCTGTTACAAATCCTAAAATGATTTTATCTATGTTGCT
CCGACTCTTCATTTTTCTTGGAATACCCTTGTTAAAAATGCATATTAAGACATGGG
Found at i:2159790 original size:60 final size:61
Alignment explanation
Indices: 2159691--2159814 Score: 187
Period size: 60 Copynumber: 2.0 Consensus size: 61
2159681 ACCGTCCGAC
* * *
2159691 ATCCGAAATATCCTCCTATCCTTCTCACTAAAATCTTTAGATCGCCCTGATGTTGTAGTTG
1 ATCCAAAATATCCTCCTATCCTTATCACTAAAAGCTTTAGATCGCCCTGATGTTGTAGTTG
* * *
2159752 ATCCAAAATATCC-CCTATTCTTATCGCTAAAAGCTTTAGATTGCCCTGATGTTGTAGTTG
1 ATCCAAAATATCCTCCTATCCTTATCACTAAAAGCTTTAGATCGCCCTGATGTTGTAGTTG
2159812 ATC
1 ATC
2159815 TTTGTTAAGG
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
60 45 0.79
61 12 0.21
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (61 bp):
ATCCAAAATATCCTCCTATCCTTATCACTAAAAGCTTTAGATCGCCCTGATGTTGTAGTTG
Found at i:2166013 original size:28 final size:28
Alignment explanation
Indices: 2165961--2166039 Score: 83
Period size: 28 Copynumber: 2.8 Consensus size: 28
2165951 TAAAATTATT
*
2165961 ATAA-ATAATATTT-TTAATTAGTATTTCAA
1 ATAATATAATATTTATTAATTA-T-TATC-A
*
2165990 ATAATATAA-ATTTTATTAATTATTATCT
1 ATAATATAATA-TTTATTAATTATTATCA
2166018 ATAATATAATATTTATTAATTA
1 ATAATATAATATTTATTAATTA
2166040 ATATATATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
28 20 0.45
29 9 0.20
30 8 0.18
31 7 0.16
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.51
Consensus pattern (28 bp):
ATAATATAATATTTATTAATTATTATCA
Found at i:2166144 original size:19 final size:19
Alignment explanation
Indices: 2166122--2166171 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
2166112 ATATTAATTT
*
2166122 AATTAAAAGAT-TAAATTAA
1 AATTAAAA-ATATAAAATAA
*
2166141 AATTATAAATATAAAATAA
1 AATTAAAAATATAAAATAA
2166160 AATTAAAAATAT
1 AATTAAAAATAT
2166172 TTAAATCTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 2 0.07
19 25 0.93
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (19 bp):
AATTAAAAATATAAAATAA
Found at i:2167278 original size:26 final size:26
Alignment explanation
Indices: 2167242--2167293 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
2167232 GCAGGCATGG
2167242 GCTGTCATTCCCCATCCTAATCTTCA
1 GCTGTCATTCCCCATCCTAATCTTCA
* *
2167268 GCTGTCATTCCCCTTCCTATTCTTCA
1 GCTGTCATTCCCCATCCTAATCTTCA
2167294 CTACTTCCGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.15, C:0.38, G:0.08, T:0.38
Consensus pattern (26 bp):
GCTGTCATTCCCCATCCTAATCTTCA
Found at i:2167445 original size:13 final size:14
Alignment explanation
Indices: 2167427--2167460 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
2167417 AATTTTAATT
2167427 TTATTAAA-TTATA
1 TTATTAAATTTATA
*
2167440 TTATTAAATTTTTA
1 TTATTAAATTTATA
2167454 TTATTAA
1 TTATTAA
2167461 TAAATTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATTAAATTTATA
Found at i:2167453 original size:30 final size:29
Alignment explanation
Indices: 2167353--2167493 Score: 105
Period size: 29 Copynumber: 4.9 Consensus size: 29
2167343 ATCTTTGTAT
* *
2167353 AATTATTTAAGTTTAATTTATATT---TTA
1 AATTATTAAATTTTAATTT-TATTAAATTA
* * *
2167380 AGTTATTAAATTTAATAAATTT-TT-AAGTA
1 AATTATTAAATTT--TAATTTTATTAAATTA
*
2167409 AATTATAAAATTTTAATTTTATTAAATTA
1 AATTATTAAATTTTAATTTTATTAAATTA
* * *
2167438 TATTATTAAATTTTTATTATTAATAAATTA
1 AATTATTAAATTTTAATT-TTATTAAATTA
* *
2167468 AATTATT-TATATTAATTTTATTAAAT
1 AATTATTAAATTTTAATTTTATTAAAT
2167494 AATTTTAATA
Statistics
Matches: 89, Mismatches: 18, Indels: 13
0.74 0.15 0.11
Matches are distributed among these distances:
27 18 0.20
28 11 0.12
29 44 0.49
30 16 0.18
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (29 bp):
AATTATTAAATTTTAATTTTATTAAATTA
Found at i:2167459 original size:22 final size:22
Alignment explanation
Indices: 2167425--2167493 Score: 61
Period size: 22 Copynumber: 3.0 Consensus size: 22
2167415 AAAATTTTAA
2167425 TTTTATTAAATTATATTATTAAAT
1 TTTTATT--ATTATATTATTAAAT
*
2167449 TTTTATTATTA-ATAAATTAAAT
1 TTTTATTATTATAT-TATTAAAT
*
2167471 TATTTA-TATTAATTTTATTAAAT
1 T-TTTATTATT-ATATTATTAAAT
2167494 AATTTTAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
21 2 0.05
22 16 0.42
23 12 0.32
24 8 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTTATTATTATATTATTAAAT
Found at i:2167909 original size:20 final size:20
Alignment explanation
Indices: 2167873--2167926 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
2167863 TTTTTTAAAA
*
2167873 ATTTAATTATAAAA-ATATAT
1 ATTTAAATATAAAATA-ATAT
2167893 AATATT-AATATAAAATAATAT
1 -AT-TTAAATATAAAATAATAT
2167914 ATTTAAATATAAA
1 ATTTAAATATAAA
2167927 TTTTTCAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
19 2 0.07
20 10 0.34
21 14 0.48
22 3 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATTTAAATATAAAATAATAT
Found at i:2168100 original size:2 final size:2
Alignment explanation
Indices: 2168093--2168125 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2168083 AAATCTAATA
*
2168093 AT AT AT AT AT AT AT AT AT AT -T AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2168126 TTTTTATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:2168122 original size:17 final size:17
Alignment explanation
Indices: 2168096--2168140 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
2168086 TCTAATAATA
*
2168096 TATATATATATATATAT
1 TATATTTATATATATAT
* *
2168113 TATATTTATATATTTTT
1 TATATTTATATATATAT
*
2168130 TATAATTATAT
1 TATATTTATAT
2168141 TTAAAATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATATTTATATATATAT
Found at i:2168370 original size:2 final size:2
Alignment explanation
Indices: 2168325--2168359 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2168315 TAATATAAAC
2168325 AT AT 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 AT AT A
2168360 AGTACATATA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2171167 original size:19 final size:20
Alignment explanation
Indices: 2171140--2171181 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
2171130 AATTTAAAAT
*
2171140 AATAAATATATTTATA-TTA
1 AATAAATATACTTATATTTA
*
2171159 AATACATATACTTATATTTA
1 AATAAATATACTTATATTTA
2171179 AAT
1 AAT
2171182 TAAAAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (20 bp):
AATAAATATACTTATATTTA
Found at i:2171248 original size:18 final size:18
Alignment explanation
Indices: 2171225--2171280 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
2171215 AATCCTAAGA
2171225 ATATAGGTTTAGGTATGG
1 ATATAGGTTTAGGTATGG
* *
2171243 ATATA-GTCCTA---AT-A
1 ATATAGGT-TTAGGTATGG
2171257 ATATAGGTTTAGGTATGG
1 ATATAGGTTTAGGTATGG
2171275 ATATAG
1 ATATAG
2171281 AACAAAGCGT
Statistics
Matches: 28, Mismatches: 4, Indels: 12
0.64 0.09 0.27
Matches are distributed among these distances:
14 7 0.25
15 4 0.14
17 4 0.14
18 13 0.46
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.38
Consensus pattern (18 bp):
ATATAGGTTTAGGTATGG
Found at i:2171254 original size:32 final size:32
Alignment explanation
Indices: 2171217--2171280 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
2171207 TGCATCCAAA
2171217 TCCTAAGAATATAGGTTTAGGTATGGATATAG
1 TCCTAAGAATATAGGTTTAGGTATGGATATAG
*
2171249 TCCTAATAATATAGGTTTAGGTATGGATATAG
1 TCCTAAGAATATAGGTTTAGGTATGGATATAG
2171281 AACAAAGCGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.34, C:0.06, G:0.23, T:0.36
Consensus pattern (32 bp):
TCCTAAGAATATAGGTTTAGGTATGGATATAG
Found at i:2174409 original size:16 final size:15
Alignment explanation
Indices: 2174390--2174457 Score: 57
Period size: 17 Copynumber: 4.2 Consensus size: 15
2174380 ATATATATTT
2174390 TAAAATTTTTATAATA
1 TAAAATTTTTA-AATA
*
2174406 T-AAATTATTAATATAA
1 TAAAATTTTTAA-AT-A
2174422 TAAAATTTATATAAATA
1 TAAAATTT-T-TAAATA
*
2174439 TAAAATAATTTAAATA
1 TAAAAT-TTTTAAATA
2174455 TAA
1 TAA
2174458 TCATAAAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
14 1 0.02
15 10 0.23
16 12 0.28
17 13 0.30
18 4 0.09
19 3 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TAAAATTTTTAAATA
Found at i:2174440 original size:20 final size:18
Alignment explanation
Indices: 2174399--2174458 Score: 56
Period size: 20 Copynumber: 3.3 Consensus size: 18
2174389 TTAAAATTTT
2174399 TATAATATAAA-TTATTAA
1 TATAATA-AAATTTATTAA
2174417 TATAATAAAATTTATATAAA
1 TATAATAAAATTTAT-T-AA
2174437 TATAA-AATAATTTA--AA
1 TATAATAA-AATTTATTAA
2174453 TATAAT
1 TATAAT
2174459 CATAAAATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
16 7 0.19
17 3 0.08
18 11 0.30
19 3 0.08
20 13 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TATAATAAAATTTATTAA
Found at i:2174470 original size:16 final size:16
Alignment explanation
Indices: 2174400--2174483 Score: 54
Period size: 16 Copynumber: 5.2 Consensus size: 16
2174390 TAAAATTTTT
2174400 ATAATATAAAT-TATTAA
1 ATAATA-AAATATA-TAA
2174417 TATAATAAAATTTATATAA
1 -ATAATAAAA--TATATAA
*
2174436 AT-ATAAAATAATTTAA
1 ATAATAAAAT-ATATAA
2174452 AT-AT--AATCATA-AA
1 ATAATAAAAT-ATATAA
2174465 ATAATAAAATATATAA
1 ATAATAAAATATATAA
2174481 ATA
1 ATA
2174484 TGATATGAAT
Statistics
Matches: 55, Mismatches: 3, Indels: 18
0.72 0.04 0.24
Matches are distributed among these distances:
13 4 0.07
14 7 0.13
15 4 0.07
16 17 0.31
17 9 0.16
18 8 0.15
19 4 0.07
20 2 0.04
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (16 bp):
ATAATAAAATATATAA
Found at i:2175399 original size:11 final size:10
Alignment explanation
Indices: 2175377--2175425 Score: 55
Period size: 11 Copynumber: 4.7 Consensus size: 10
2175367 AAATTTAAAA
2175377 ATATTTTA-T
1 ATATTTTATT
2175386 ATATTTATATT
1 ATATTT-TATT
2175397 ATATTTTAATT
1 ATATTTT-ATT
*
2175408 ATTTTTATATT
1 ATATTT-TATT
2175419 ATATTTT
1 ATATTTT
2175426 TTACATAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
9 6 0.18
10 4 0.12
11 23 0.68
12 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
ATATTTTATT
Found at i:2175402 original size:20 final size:22
Alignment explanation
Indices: 2175377--2175425 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
2175367 AAATTTAAAA
2175377 ATATTTT-A-TATATTTATATT
1 ATATTTTAATTATATTTATATT
*
2175397 ATATTTTAATTATTTTTATATT
1 ATATTTTAATTATATTTATATT
2175419 ATATTTT
1 ATATTTT
2175426 TTACATAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 7 0.27
21 1 0.04
22 18 0.69
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
ATATTTTAATTATATTTATATT
Found at i:2175648 original size:29 final size:27
Alignment explanation
Indices: 2175574--2175657 Score: 80
Period size: 31 Copynumber: 2.9 Consensus size: 27
2175564 TATATTTATA
*
2175574 TTTAAAAA-ATATTATAATTTATATAAT
1 TTTAAAAATATATT-TATTTTATATAAT
2175601 TTTAATAAATTAATAATTTATTTTATATAAAT
1 TTTAA-AAA-T-AT-ATTTATTTTATAT-AAT
*
2175633 TTTAAAATATATATTTATATTATAT
1 TTTAAAA-ATATATTTATTTTATAT
2175658 TTTATATTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
27 5 0.10
28 3 0.06
29 12 0.25
30 2 0.04
31 14 0.29
32 12 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
TTTAAAAATATATTTATTTTATATAAT
Found at i:2175662 original size:36 final size:31
Alignment explanation
Indices: 2175581--2175664 Score: 89
Period size: 36 Copynumber: 2.5 Consensus size: 31
2175571 ATATTTAAAA
*
2175581 AATATTATAATTTATATAATTTTAATAAATT
1 AATATTATATTTTATATAATTTTAATAAATT
2175612 AATAATT-TATTTTATATAAATTTTAAAATATATATT
1 AAT-ATTATATTTTATAT-AATTTT--AATA-A-ATT
*
2175648 TATATTATATTTTATAT
1 AATATTATATTTTATAT
2175665 TTAATACTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
31 12 0.27
32 9 0.20
34 4 0.09
35 4 0.09
36 15 0.34
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (31 bp):
AATATTATATTTTATATAATTTTAATAAATT
Found at i:2175663 original size:12 final size:12
Alignment explanation
Indices: 2175619--2175665 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
2175609 ATTAATAATT
2175619 TATTTTATA-TA
1 TATTTTATATTA
* * *
2175630 AATTTTAAAATA
1 TATTTTATATTA
2175642 TATATTTATATTA
1 TAT-TTTATATTA
2175655 TATTTTATATT
1 TATTTTATATT
2175666 TAATACTTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
11 7 0.24
12 12 0.41
13 10 0.34
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TATTTTATATTA
Found at i:2175954 original size:31 final size:33
Alignment explanation
Indices: 2175911--2175986 Score: 93
Period size: 31 Copynumber: 2.3 Consensus size: 33
2175901 AAATAATAAG
* *
2175911 AATTATATTTAAATTTGATTGATTT-ATT-AATA
1 AATT-TATTTAAATTCGATTCATTTAATTAAATA
2175943 AATTTATTTAAATTCGATTCATTTAAATTAAATA
1 AATTTATTTAAATTCGATTCATTT-AATTAAATA
*
2175977 ATTTTATTTA
1 AATTTATTTA
2175987 TTAATATATT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 18 0.47
32 4 0.11
33 3 0.08
34 13 0.34
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.53
Consensus pattern (33 bp):
AATTTATTTAAATTCGATTCATTTAATTAAATA
Found at i:2176323 original size:16 final size:16
Alignment explanation
Indices: 2176304--2176380 Score: 52
Period size: 16 Copynumber: 4.8 Consensus size: 16
2176294 TTAAAATTTA
2176304 TATAATATAAATTATT
1 TATAATATAAATTATT
*
2176320 TAT-ATATCAAAATTA-A
1 TATAATAT--AAATTATT
* *
2176336 TATAAATATAAAATACT
1 TAT-AATATAAATTATT
* *
2176353 TAAAATAT-AATTATGG
1 TATAATATAAATTAT-T
2176369 TATAATATAAAT
1 TATAATATAAAT
2176381 ATAAAAATTA
Statistics
Matches: 46, Mismatches: 8, Indels: 13
0.69 0.12 0.19
Matches are distributed among these distances:
15 8 0.17
16 23 0.50
17 11 0.24
18 4 0.09
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (16 bp):
TATAATATAAATTATT
Found at i:2176788 original size:18 final size:18
Alignment explanation
Indices: 2176765--2176802 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2176755 AACATTTTTA
*
2176765 AAATATT-TAATATTAAAT
1 AAATATTGT-ATAATAAAT
2176783 AAATATTGTATAATAAAT
1 AAATATTGTATAATAAAT
2176801 AA
1 AA
2176803 TTAATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (18 bp):
AAATATTGTATAATAAAT
Found at i:2177368 original size:21 final size:22
Alignment explanation
Indices: 2177325--2177374 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
2177315 TAGTTTTATA
*
2177325 TAATT-TTATATTTATTTAATT
1 TAATTATTATATTTATATAATT
*
2177346 TAATTATTATATTT-TATACTT
1 TAATTATTATATTTATATAATT
*
2177367 TATTTATT
1 TAATTATT
2177375 TAGATCATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (22 bp):
TAATTATTATATTTATATAATT
Found at i:2177385 original size:29 final size:28
Alignment explanation
Indices: 2177322--2177396 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 28
2177312 ATTTAGTTTT
*
2177322 ATATAATTTTATATTTATTTAATTTAATT
1 ATAT-ATTTTATATTTATTTAATTTAATC
2177351 ATTATATTTTATACTTTATTT-ATTTAGATC
1 A-TATATTTTATA-TTTATTTAATTTA-ATC
* *
2177381 ATATATATTAAATTTA
1 ATATATTTTATATTTA
2177397 AATAAATTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
28 4 0.10
29 23 0.57
30 13 0.32
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (28 bp):
ATATATTTTATATTTATTTAATTTAATC
Found at i:2177461 original size:18 final size:17
Alignment explanation
Indices: 2177429--2177462 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2177419 ATTTATTTGA
2177429 TTAAAAAATTAAATAAG
1 TTAAAAAATTAAATAAG
*
2177446 TTAAAAATATTTAATAA
1 TTAAAAA-ATTAAATAA
2177463 TTTACTCAAT
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:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (17 bp):
TTAAAAAATTAAATAAG
Found at i:2177479 original size:43 final size:43
Alignment explanation
Indices: 2177394--2177480 Score: 104
Period size: 43 Copynumber: 2.0 Consensus size: 43
2177384 TATATTAAAT
* * **
2177394 TTAAATAAATTTAAAATATTTAACTATTTATTTGATTAAAAAA
1 TTAAATAAATTAAAAATATTTAACTATTTACTCAATTAAAAAA
*
2177437 TTAAATAAGTTAAAAATATTTAA-TAATTTACTCAATTTAAAAAA
1 TTAAATAAATTAAAAATATTTAACT-ATTTACTCAA-TTAAAAAA
2177481 ATAATTGTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
42 1 0.03
43 28 0.76
44 8 0.22
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.41
Consensus pattern (43 bp):
TTAAATAAATTAAAAATATTTAACTATTTACTCAATTAAAAAA
Found at i:2177601 original size:21 final size:23
Alignment explanation
Indices: 2177571--2177620 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 23
2177561 AACAAATGCA
2177571 ATTAAATTATTAAA-T-CTAATT
1 ATTAAATTATTAAAGTACTAATT
* *
2177592 ATTAACTTATTAAAGTATTAATT
1 ATTAAATTATTAAAGTACTAATT
2177615 ATTAAA
1 ATTAAA
2177621 AAAATATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 13 0.54
22 1 0.04
23 10 0.42
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (23 bp):
ATTAAATTATTAAAGTACTAATT
Found at i:2177618 original size:15 final size:16
Alignment explanation
Indices: 2177591--2177620 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2177581 TAAATCTAAT
2177591 TATTAACTTATTAAAG
1 TATTAACTTATTAAAG
2177607 TATTAA-TTATTAAA
1 TATTAACTTATTAAA
2177621 AAAATATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (16 bp):
TATTAACTTATTAAAG
Found at i:2178624 original size:20 final size:18
Alignment explanation
Indices: 2178591--2178636 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
2178581 TATATTAAAT
2178591 TAAAAATTAATTAAATTAG
1 TAAAAATTAATT-AATTAG
* *
2178610 TAAAAATCTATTTAATTGG
1 TAAAAAT-TAATTAATTAG
2178629 TAAAAATT
1 TAAAAATT
2178637 GATAAAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 1 0.04
19 19 0.79
20 4 0.17
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (18 bp):
TAAAAATTAATTAATTAG
Found at i:2178788 original size:12 final size:12
Alignment explanation
Indices: 2178771--2178795 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2178761 TTAATTATAT
2178771 TTAATATTTAAA
1 TTAATATTTAAA
2178783 TTAATATTTAAA
1 TTAATATTTAAA
2178795 T
1 T
2178796 ATTAAAAGAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAATATTTAAA
Found at i:2186141 original size:16 final size:17
Alignment explanation
Indices: 2186117--2186149 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2186107 AATAAATAAT
*
2186117 TTTTTAGAAAGA-AAAA
1 TTTTAAGAAAGATAAAA
2186133 TTTTAAGAAAGATAAAA
1 TTTTAAGAAAGATAAAA
2186150 GGAGAGTGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.58, C:0.00, G:0.12, T:0.30
Consensus pattern (17 bp):
TTTTAAGAAAGATAAAA
Found at i:2186254 original size:22 final size:21
Alignment explanation
Indices: 2186202--2186254 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
2186192 AAATAAATAG
*
2186202 ATATTTTTTAAAAAATATTTT
1 ATATTTATTAAAAAATATTTT
**
2186223 ATAAAATATTAAAAAATATATTT
1 AT-ATTTATTAAAAAATAT-TTT
2186246 ATATTTATT
1 ATATTTATT
2186255 TAATTTATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 2 0.08
22 18 0.72
23 5 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATATTTATTAAAAAATATTTT
Found at i:2186262 original size:9 final size:9
Alignment explanation
Indices: 2186241--2186273 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
2186231 TTAAAAAATA
2186241 TATTTATATT
1 TATTTA-ATT
2186251 TATTTAATT
1 TATTTAATT
2186260 TATTTAATT
1 TATTTAATT
2186269 T-TTTA
1 TATTTA
2186274 TTAATTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 4 0.17
9 13 0.57
10 6 0.26
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (9 bp):
TATTTAATT
Found at i:2186505 original size:19 final size:18
Alignment explanation
Indices: 2186469--2186523 Score: 56
Period size: 19 Copynumber: 3.0 Consensus size: 18
2186459 TTATTTATAA
*
2186469 AATATTTAAAATATTTTT
1 AATATTTAAAATAATTTT
*
2186487 AATATTTTAATATAATTTT
1 AATA-TTTAAAATAATTTT
* * *
2186506 AATAATGAAATTAATTTT
1 AATATTTAAAATAATTTT
2186524 TTAAATTTGA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
18 14 0.47
19 16 0.53
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
AATATTTAAAATAATTTT
Found at i:2187753 original size:2 final size:2
Alignment explanation
Indices: 2187746--2187779 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
2187736 AAATTTTGTT
2187746 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
2187780 GGTAGTAAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2189924 original size:18 final size:17
Alignment explanation
Indices: 2189890--2189984 Score: 90
Period size: 18 Copynumber: 5.7 Consensus size: 17
2189880 ATAAATATGC
**
2189890 ATATATTATATGCATTA
1 ATATATTATATTAATTA
*
2189907 AGTATATTATGTTAATT-
1 A-TATATTATATTAATTA
*
2189924 AT-TATTATATTATTTAA
1 ATATATTATATTAATT-A
2189941 ATATATTATATTAATTA
1 ATATATTATATTAATTA
*
2189958 A-AT-TTATATTAATTT
1 ATATATTATATTAATTA
*
2189973 TTATATTATATT
1 ATATATTATATT
2189985 TAAAATTATC
Statistics
Matches: 64, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
15 22 0.34
16 5 0.08
17 13 0.20
18 24 0.38
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (17 bp):
ATATATTATATTAATTA
Found at i:2189931 original size:33 final size:33
Alignment explanation
Indices: 2189893--2189957 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
2189883 AATATGCATA
* *
2189893 TATTATATGCA-TTAAGTATATTATGTTAATTAT
1 TATTATAT-CATTTAAATATATTATATTAATTAT
*
2189926 TATTATATTATTTAAATATATTATATTAATTA
1 TATTATATCATTTAAATATATTATATTAATTA
2189958 AATTTATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 1 0.04
33 27 0.96
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.54
Consensus pattern (33 bp):
TATTATATCATTTAAATATATTATATTAATTAT
Found at i:2189965 original size:33 final size:34
Alignment explanation
Indices: 2189904--2189984 Score: 89
Period size: 33 Copynumber: 2.5 Consensus size: 34
2189894 ATTATATGCA
* * *
2189904 TTAAGTATATTATGTTAATTATTATTATATT-AT
1 TTAAATATATTATATTAATTAATATTATATTAAT
2189937 TTAAATATATTATATTAATTAA-ATTTATATTAAT
1 TTAAATATATTATATTAATTAATA-TTATATTAAT
*
2189971 TT--TTATATTATATT
1 TTAAATATATTATATT
2189985 TAAAATTATC
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
32 12 0.29
33 26 0.62
34 4 0.10
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (34 bp):
TTAAATATATTATATTAATTAATATTATATTAAT
Found at i:2190567 original size:9 final size:9
Alignment explanation
Indices: 2190555--2190582 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
2190545 TTTGCTTTTA
2190555 ATAAGGTTG
1 ATAAGGTTG
2190564 ATAAGGTTG
1 ATAAGGTTG
2190573 ATAAGGTTG
1 ATAAGGTTG
2190582 A
1 A
2190583 ATTTAGTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (9 bp):
ATAAGGTTG
Found at i:2190821 original size:2 final size:2
Alignment explanation
Indices: 2190809--2190837 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2190799 AATGAATAGA
2190809 AT AT A- 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
2190838 TCTATATGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2192018 original size:10 final size:10
Alignment explanation
Indices: 2191998--2192027 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
2191988 TTATATGATA
2191998 TAAATAATAAT
1 TAAA-AATAAT
2192009 TAAAAATAAT
1 TAAAAATAAT
2192019 TAAAAATAA
1 TAAAAATAA
2192028 ATATTATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.79
11 4 0.21
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
TAAAAATAAT
Found at i:2192051 original size:15 final size:15
Alignment explanation
Indices: 2192024--2192061 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
2192014 ATAATTAAAA
2192024 ATAAATATTATAT-AT
1 ATAAAT-TTATATAAT
2192039 ATTAAATTTATATAAT
1 A-TAAATTTATATAAT
2192055 ATAAATT
1 ATAAATT
2192062 ATTAAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATAAATTTATATAAT
Found at i:2194085 original size:2 final size:2
Alignment explanation
Indices: 2194078--2194119 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
2194068 GGGATGCAGA
* *
2194078 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AA AC AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2194120 TCAAATGTGT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.52, C:0.02, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2195577 original size:10 final size:10
Alignment explanation
Indices: 2195562--2195604 Score: 59
Period size: 10 Copynumber: 4.3 Consensus size: 10
2195552 ACTTACATAC
*
2195562 ATACATACAT
1 ATACATATAT
2195572 ATACATATAT
1 ATACATATAT
*
2195582 ATATATATAT
1 ATACATATAT
*
2195592 ATATATATAT
1 ATACATATAT
2195602 ATA
1 ATA
2195605 TTATAGTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (10 bp):
ATACATATAT
Found at i:2195621 original size:2 final size:2
Alignment explanation
Indices: 2195570--2195609 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
2195560 ACATACATAC
*
2195570 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2195610 GTTTTATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2198750 original size:2 final size:2
Alignment explanation
Indices: 2198743--2198768 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2198733 CTATCTCTAC
2198743 CT CT 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
2198769 GCCATGTGTT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2200134 original size:18 final size:18
Alignment explanation
Indices: 2200111--2200153 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2200101 AAATTAATAT
2200111 AAAAT-ATTTAATAATTAA
1 AAAATAATTTAA-AATTAA
*
2200129 AAAATAATTTTAAATTAA
1 AAAATAATTTAAAATTAA
*
2200147 AAGATAA
1 AAAATAA
2200154 CATTGATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (18 bp):
AAAATAATTTAAAATTAA
Found at i:2207516 original size:10 final size:10
Alignment explanation
Indices: 2207501--2207567 Score: 62
Period size: 10 Copynumber: 6.5 Consensus size: 10
2207491 CTATGATGGA
2207501 ATATACATAT
1 ATATACATAT
*
2207511 ATATACACAT
1 ATATACATAT
* *
2207521 TTATTCATAATT
1 ATATACAT-A-T
*
2207533 ATATATATAT
1 ATATACATAT
*
2207543 ATATATATAT
1 ATATACATAT
*
2207553 ATATATATAT
1 ATATACATAT
2207563 ATATA
1 ATATA
2207568 TACACACACA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
10 40 0.83
11 2 0.04
12 6 0.12
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (10 bp):
ATATACATAT
Found at i:2207539 original size:2 final size:2
Alignment explanation
Indices: 2207532--2207569 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2207522 TATTCATAAT
2207532 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2207570 CACACACATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2209367 original size:73 final size:66
Alignment explanation
Indices: 2209269--2209408 Score: 151
Period size: 73 Copynumber: 2.0 Consensus size: 66
2209259 CACTAAATAT
*
2209269 TAAATTTAATAATTTAGATATTTATATAATATTTATAAGTTATAATTATATTTAAAATATTATAT
1 TAAATTTAATAATTTAGATATTTATAT--TA--TATAAATTATAA-TATATTTAAAATA-TAT-T
2209334 AT-TTATA
59 ATCTTATA
*
2209341 TAAATTTTAAT-ATATTA-ATATTTTATATTATATAAATTATAATATATTTAAATTATATTATCT
1 TAAA-TTTAATAAT-TTAGATA-TTTATATTATATAAATTATAATATATTTAAAATATATTATCT
2209404 TATA
63 TATA
2209408 T
1 T
2209409 CATATTTTTA
Statistics
Matches: 62, Mismatches: 2, Indels: 13
0.81 0.03 0.17
Matches are distributed among these distances:
66 3 0.05
67 9 0.15
68 12 0.19
69 11 0.18
71 2 0.03
72 9 0.15
73 16 0.26
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (66 bp):
TAAATTTAATAATTTAGATATTTATATTATATAAATTATAATATATTTAAAATATATTATCTTAT
A
Found at i:2209373 original size:5 final size:5
Alignment explanation
Indices: 2209325--2209433 Score: 54
Period size: 5 Copynumber: 23.0 Consensus size: 5
2209315 TATATTTAAA
* * * *
2209325 ATATT ATA-T AT-TT ATA-T AAATT TTAAT ATATT A-A-T ATTTT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
* * * * *
2209370 ATA-T AAATT ATAAT ATATTT AAATT ATATT ATCTT ATATC ATATT -T-TT
1 ATATT ATATT ATATT ATA-TT ATATT ATATT ATATT ATATT ATATT ATATT
*
2209418 ATTTTT ATATT ATATT
1 A-TATT ATATT ATATT
2209434 TAAAATAATT
Statistics
Matches: 75, Mismatches: 19, Indels: 20
0.66 0.17 0.18
Matches are distributed among these distances:
3 4 0.05
4 14 0.19
5 51 0.68
6 6 0.08
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (5 bp):
ATATT
Found at i:2209377 original size:32 final size:33
Alignment explanation
Indices: 2209324--2209408 Score: 111
Period size: 32 Copynumber: 2.5 Consensus size: 33
2209314 TTATATTTAA
*
2209324 AATATTATATATTTATATAAATTTTAATATATT
1 AATATTATATATTTATATAAATTATAATATATT
*
2209357 AATATTTTATA-TTATATAAATTATAATATATTT
1 AATATTATATATTTATATAAATTATAATATA-TT
2209390 AA-ATTATATTATCTTATAT
1 AATATTATA-TAT-TTATAT
2209409 CATATTTTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
32 23 0.51
33 16 0.36
35 6 0.13
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (33 bp):
AATATTATATATTTATATAAATTATAATATATT
Found at i:2209394 original size:16 final size:16
Alignment explanation
Indices: 2209293--2209397 Score: 63
Period size: 16 Copynumber: 6.2 Consensus size: 16
2209283 TAGATATTTA
*
2209293 TATAATAT-TTATAAGT
1 TATAATATATT-TAAAT
2209309 TATAATTATATTTAAAATAT
1 TATAA-TATATTT--AA-AT
* *
2209329 TATATATTTATATAAAT
1 TATA-ATATATTTAAAT
*
2209346 TTTAATATA-TTAATAT
1 TATAATATATTTAA-AT
* *
2209362 T-TTATATTATATAAAT
1 TATAATA-TATTTAAAT
2209378 TATAATATATTTAAAT
1 TATAATATATTTAAAT
2209394 TATA
1 TATA
2209398 TTATCTTATA
Statistics
Matches: 69, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
15 7 0.10
16 29 0.42
17 16 0.23
18 4 0.06
19 2 0.03
20 10 0.14
21 1 0.01
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (16 bp):
TATAATATATTTAAAT
Found at i:2212142 original size:15 final size:14
Alignment explanation
Indices: 2212124--2212243 Score: 52
Period size: 15 Copynumber: 8.1 Consensus size: 14
2212114 TAAATTCGAT
2212124 TATTAAAAATAATTA
1 TATTAAAAATAA-TA
2212139 TATTAAAATATAATA
1 TATTAAAA-ATAATA
*
2212154 TA--ATAAATAATA
1 TATTAAAAATAATA
2212166 TGA-TAAAATTATTAATA
1 T-ATTAAAA--A-TAATA
*
2212183 TATT-AAAATATTA
1 TATTAAAAATAATA
*
2212196 TA-TAAATATGTAATA
1 TATTAAA-A-ATAATA
* *
2212211 TTTTAAATATAATTA
1 TATTAAAAATAA-TA
*
2212226 TAATATAAAAATTATA
1 T-AT-TAAAAATAATA
2212242 TA
1 TA
2212244 AATATAAAAT
Statistics
Matches: 80, Mismatches: 11, Indels: 28
0.67 0.09 0.24
Matches are distributed among these distances:
12 8 0.10
13 12 0.15
14 8 0.10
15 21 0.26
16 17 0.21
17 14 0.17
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (14 bp):
TATTAAAAATAATA
Found at i:2212216 original size:28 final size:27
Alignment explanation
Indices: 2212162--2212228 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 27
2212152 TATAATAAAT
*
2212162 AATATGATAAAATTATTAATATATTAA
1 AATATTATAAAATTATTAATATATTAA
*
2212189 AATATTATATAAA-TATGTAATATTTTAA
1 AATATTATA-AAATTAT-TAATATATTAA
2212217 ATATAATTATAA
1 A-AT-ATTATAA
2212229 TATAAAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 11 0.32
28 14 0.41
29 3 0.09
30 6 0.18
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (27 bp):
AATATTATAAAATTATTAATATATTAA
Found at i:2213241 original size:2 final size:2
Alignment explanation
Indices: 2213234--2213261 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2213224 CTTTTTAATT
2213234 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2213262 GTCATATCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2214391 original size:2 final size:2
Alignment explanation
Indices: 2214384--2214408 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2214374 ATTGGACGGG
2214384 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
2214409 ATTGTATGAT
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:2214498 original size:21 final size:22
Alignment explanation
Indices: 2214446--2214489 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
2214436 GAGTAATTAA
2214446 AATAT-AATTT-ATTATAAAAAT
1 AATATAAATTTGA-TATAAAAAT
2214467 AATATAAATTTGATATAAAAAT
1 AATATAAATTTGATATAAAAAT
2214489 A
1 A
2214490 TTAATATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.24
22 15 0.71
23 1 0.05
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
AATATAAATTTGATATAAAAAT
Found at i:2214503 original size:21 final size:22
Alignment explanation
Indices: 2214446--2214503 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 22
2214436 GAGTAATTAA
2214446 AATAT-AA-TTTATTATAAAAAT
1 AATATAAATTTTA-TATAAAAAT
*
2214467 AATATAAATTTGATATAAAAAT
1 AATATAAATTTTATATAAAAAT
2214489 -AT-TAATATTTTATAT
1 AATATAA-ATTTTATAT
2214504 TTTATATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 3 0.09
21 15 0.47
22 11 0.34
23 3 0.09
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
AATATAAATTTTATATAAAAAT
Found at i:2214589 original size:28 final size:27
Alignment explanation
Indices: 2214507--2214604 Score: 85
Period size: 27 Copynumber: 3.6 Consensus size: 27
2214497 TTTATATTTT
* * *
2214507 ATATAATATGAAT-TATTAATATATCAGA
1 ATATAATATGAATATA-AAAAATATTA-A
* * *
2214535 ATAT-ATATAAATATAAAATATCTTAA
1 ATATAATATGAATATAAAAAATATTAA
2214561 ATATAATAAT-AATATAAAAAATATATAA
1 ATATAAT-ATGAATATAAAAAATAT-TAA
2214589 ATATAATATGAATATA
1 ATATAATATGAATATA
2214605 TAAATCGTCG
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
26 5 0.08
27 30 0.51
28 24 0.41
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (27 bp):
ATATAATATGAATATAAAAAATATTAA
Found at i:2215425 original size:7 final size:7
Alignment explanation
Indices: 2215415--2215456 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
2215405 TTAATAACAT
2215415 ATAATTA
1 ATAATTA
2215422 ATAATTA
1 ATAATTA
2215429 ATAATT-
1 ATAATTA
2215435 AT-ATTA
1 ATAATTA
*
2215441 ATTATTA
1 ATAATTA
*
2215448 ATTATTA
1 ATAATTA
2215455 AT
1 AT
2215457 TAGACTTTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 3 0.09
6 4 0.12
7 26 0.79
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (7 bp):
ATAATTA
Found at i:2215449 original size:23 final size:22
Alignment explanation
Indices: 2215404--2215458 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
2215394 GTAATATGTG
*
2215404 ATTAATAA-CATATAATTAATA
1 ATTAATAATTATATAATTAATA
*
2215425 ATTAATAATTATATTAATTATTA
1 ATTAATAATTATA-TAATTAATA
*
2215448 ATTATTAATTA
1 ATTAATAATTA
2215459 GACTTTCAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 8 0.28
22 3 0.10
23 18 0.62
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
ATTAATAATTATATAATTAATA
Found at i:2220027 original size:17 final size:17
Alignment explanation
Indices: 2220007--2220040 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2219997 GAAAATACCC
*
2220007 AGAAAAAAAAAATAAAG
1 AGAAAAAAAAAAGAAAG
*
2220024 AGAAAAGAAAAAGAAAG
1 AGAAAAAAAAAAGAAAG
2220041 GTGACCTAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (17 bp):
AGAAAAAAAAAAGAAAG
Found at i:2224274 original size:34 final size:33
Alignment explanation
Indices: 2224226--2224292 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 33
2224216 ATCATTTTAA
*
2224226 TTATATATTATATATAATAGAAATAAAATATAT
1 TTATATAGTATATATAATAGAAATAAAATATAT
* ** *
2224259 TTATATAAGTATATATCATTTAATTAAAATATAT
1 TTATAT-AGTATATATAATAGAAATAAAATATAT
2224293 ATAACTTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 6 0.21
34 22 0.79
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (33 bp):
TTATATAGTATATATAATAGAAATAAAATATAT
Done.