Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold25
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: 9553305
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 6276 characters in sequence are not A, C, G, or T
File 5 of 56
Found at i:821601 original size:33 final size:36
Alignment explanation
Indices: 821555--821632 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 36
821545 ATAATTATGA
*
821555 TTAAACTATTATATATTATAT-AAAATTTT-ATAT-T
1 TTAAA-TAATATATATTATATAAAAATTTTAATATAT
821589 TTAAATAATATATATTATATAAAAATTTTAATATAT
1 TTAAATAATATATATTATATAAAAATTTTAATATAT
821625 TTATAATA
1 TTA-AATA
821633 TTTATTTATA
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
33 14 0.36
34 13 0.33
35 4 0.10
36 4 0.10
37 4 0.10
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (36 bp):
TTAAATAATATATATTATATAAAAATTTTAATATAT
Found at i:821678 original size:28 final size:29
Alignment explanation
Indices: 821620--821679 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
821610 AAAATTTTAA
*
821620 TATATTTATAATATTTATTTATATTACAT
1 TATATTTATAATATTTATTTATATTAAAT
821649 TATATTT-TAATTATTT-TTTACT-TTAAAT
1 TATATTTATAA-TATTTATTTA-TATTAAAT
821677 TAT
1 TAT
821680 CATGTCTCTC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
28 15 0.54
29 13 0.46
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (29 bp):
TATATTTATAATATTTATTTATATTAAAT
Found at i:831564 original size:16 final size:16
Alignment explanation
Indices: 831514--831566 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
831504 TTTAAATTAT
831514 TTTATATT-TATATAAA
1 TTTATATTATATA-AAA
*
831530 TTT-TAATATATTAATAA
1 TTTATATTATA-TAA-AA
831547 TTTATATTATATAAAA
1 TTTATATTATATAAAA
831563 TTTA
1 TTTA
831567 AAATATTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
15 3 0.10
16 12 0.39
17 10 0.32
18 6 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTATATTATATAAAA
Found at i:831608 original size:12 final size:12
Alignment explanation
Indices: 831591--831654 Score: 59
Period size: 12 Copynumber: 5.8 Consensus size: 12
831581 TTATGTTATG
*
831591 TTTATATTATTT
1 TTTATATTATAT
831603 TTTATATTATAT
1 TTTATATTATAT
831615 TTTAT-TTATA-
1 TTTATATTATAT
831625 ---ATATTAT-T
1 TTTATATTATAT
831633 TTTATATTATAT
1 TTTATATTATAT
* *
831645 CTAATATTAT
1 TTTATATTAT
831655 CAAATTCAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
7 2 0.05
8 4 0.09
11 12 0.28
12 25 0.58
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (12 bp):
TTTATATTATAT
Found at i:831612 original size:28 final size:30
Alignment explanation
Indices: 831547--831644 Score: 87
Period size: 28 Copynumber: 3.4 Consensus size: 30
831537 ATATTAATAA
* * * *
831547 TTTATATTATATAAAATTTAAAATATT-TA
1 TTTATATTATATTATATTTATAATATTATT
* * * *
831576 TGTAT-TTATGTTATGTTTATATTA-T-TT
1 TTTATATTATATTATATTTATAATATTATT
*
831603 TTTATATTATATTTTATTTATAATATTATT
1 TTTATATTATATTATATTTATAATATTATT
831633 TTTATATTATAT
1 TTTATATTATAT
831645 CTAATATTAT
Statistics
Matches: 53, Mismatches: 13, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
27 6 0.11
28 28 0.53
29 5 0.09
30 14 0.26
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (30 bp):
TTTATATTATATTATATTTATAATATTATT
Found at i:831617 original size:14 final size:14
Alignment explanation
Indices: 831598--831644 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
831588 ATGTTTATAT
831598 TATTTTTTATATTA
1 TATTTTTTATATTA
*
831612 TATTTTATT-TATAA
1 TATTTT-TTATATTA
831626 TATTATTTTTATATTA
1 TA-T-TTTTTATATTA
831642 TAT
1 TAT
831645 CTAATATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
14 12 0.44
15 6 0.22
16 9 0.33
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTTTTTATATTA
Found at i:831621 original size:19 final size:18
Alignment explanation
Indices: 831606--831643 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 18
831596 ATTATTTTTT
831606 ATATTATATTTTATTTATA
1 ATATTAT-TTTTATTTATA
831625 ATATTATTTTTATATTATA
1 ATATTATTTTTAT-TTATA
831644 TCTAATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
ATATTATTTTTATTTATA
Found at i:832145 original size:28 final size:29
Alignment explanation
Indices: 832096--832152 Score: 107
Period size: 28 Copynumber: 2.0 Consensus size: 29
832086 ACAAATGTTC
832096 ATAATACCTTTTTTTAGTTAGTTAATATA
1 ATAATACCTTTTTTTAGTTAGTTAATATA
832125 ATAATACC-TTTTTTAGTTAGTTAATATA
1 ATAATACCTTTTTTTAGTTAGTTAATATA
832153 TTATCTATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 20 0.71
29 8 0.29
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.51
Consensus pattern (29 bp):
ATAATACCTTTTTTTAGTTAGTTAATATA
Found at i:832187 original size:26 final size:27
Alignment explanation
Indices: 832146--832205 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
832136 TTTAGTTAGT
832146 TAATA-TATTATCTATAAT-AATAATAA
1 TAATATTATTATCTATAATAAAT-ATAA
*
832172 TAATATTATTAT-TATATTAAATATAA
1 TAATATTATTATCTATAATAAATATAA
832198 TAAT-TTAT
1 TAATATTAT
832206 AATTTTATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
25 4 0.13
26 18 0.58
27 9 0.29
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (27 bp):
TAATATTATTATCTATAATAAATATAA
Found at i:832683 original size:22 final size:21
Alignment explanation
Indices: 832654--832695 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
832644 TAATATTTAA
832654 AATTTTAATTAAAAATAATTT
1 AATTTTAATTAAAAATAATTT
**
832675 AATTATTAATTTTAAATAATT
1 AATT-TTAATTAAAAATAATT
832696 ACATATCTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AATTTTAATTAAAAATAATTT
Found at i:833087 original size:3 final size:3
Alignment explanation
Indices: 833079--833121 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
833069 GAATAAACTT
833079 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
833122 GTCCCAAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:836700 original size:10 final size:10
Alignment explanation
Indices: 836685--836714 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
836675 AAAAGGAGGT
836685 TAGTGGGGTG
1 TAGTGGGGTG
836695 TAGTGGGGTG
1 TAGTGGGGTG
*
836705 GAGTGGGGTG
1 TAGTGGGGTG
836715 AGGAGAGGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.10, C:0.00, G:0.63, T:0.27
Consensus pattern (10 bp):
TAGTGGGGTG
Found at i:836889 original size:94 final size:98
Alignment explanation
Indices: 836710--836897 Score: 249
Period size: 94 Copynumber: 1.9 Consensus size: 98
836700 GGGTGGAGTG
* * *
836710 GGGTGAGGAGAGGAGAGATCCGACATCATTGGACATGCAAGAAAAACCAAGTGAAACACAACAGC
1 GGGTGAGGAGAGGAGAGATCCAACATCATTAGACATGCAAG--AAA-CAAGTGAAACACAACAAC
* *
836775 TGAAGGAGTGGATGAGGGAAGAGAAAACATTGGGCA
63 TGAAAGAGTGAATGAGGGAAGAGAAAACATTGGGCA
* * *
836811 GGGTGAGG-GAGGAGAGATCCAACATTATTAGACATGCAAG-AA-AA-TGAAACGCACCAACTGA
1 GGGTGAGGAGAGGAGAGATCCAACATCATTAGACATGCAAGAAACAAGTGAAACACAACAACTGA
836872 AAGAGTGAATGAGGGAAGAGAAAACA
66 AAGAGTGAATGAGGGAAGAGAAAACA
836898 ACATCTGTTC
Statistics
Matches: 79, Mismatches: 8, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
94 38 0.48
95 2 0.03
97 2 0.03
100 29 0.37
101 8 0.10
ACGTcount: A:0.43, C:0.13, G:0.32, T:0.12
Consensus pattern (98 bp):
GGGTGAGGAGAGGAGAGATCCAACATCATTAGACATGCAAGAAACAAGTGAAACACAACAACTGA
AAGAGTGAATGAGGGAAGAGAAAACATTGGGCA
Found at i:839181 original size:19 final size:20
Alignment explanation
Indices: 839154--839191 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
839144 TCCCTTTTCC
839154 TTTACATTTTTATTTTTATT
1 TTTACATTTTTATTTTTATT
*
839174 TTTA-ATTTTTTTTTTTAT
1 TTTACATTTTTATTTTTAT
839192 GGGTAATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTACATTTTTATTTTTATT
Found at i:840254 original size:2 final size:2
Alignment explanation
Indices: 840247--840278 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
840237 AATGCTCACC
840247 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
840279 ATTCCAAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:840661 original size:44 final size:44
Alignment explanation
Indices: 840561--840669 Score: 111
Period size: 43 Copynumber: 2.5 Consensus size: 44
840551 TGGTTGAGTG
*
840561 TAAAAATAAATTTTTAA-TA-ATTTTAAAAATATAAATATAAATA
1 TAAAAATAAA-TTTAAATTATATTTTAAAAATATAAATATAAATA
* *
840604 TAAAAATAAATTTATATTTATATTTTAAATAATA-AAATA-AAATT
1 TAAAAATAAATTTA-AATTATATTTTAAA-AATATAAATATAAATA
*
840648 TAAAAA-ATTATTTAAATTATAT
1 TAAAAATA-AATTTAAATTATAT
840670 CAAACTTAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
42 3 0.05
43 19 0.34
44 17 0.30
45 13 0.23
46 4 0.07
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (44 bp):
TAAAAATAAATTTAAATTATATTTTAAAAATATAAATATAAATA
Found at i:846124 original size:24 final size:21
Alignment explanation
Indices: 846097--846143 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
846087 TTAATGTACT
846097 AATTCTATTTCTTTTAAGTATTGA
1 AATTC-ATTTCTTTT-AG-ATTGA
*
846121 AATTCCTTTCTTTTAGATTGA
1 AATTCATTTCTTTTAGATTGA
846142 AA
1 AA
846144 ATTATCCTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 7 0.32
22 2 0.09
23 8 0.36
24 5 0.23
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.51
Consensus pattern (21 bp):
AATTCATTTCTTTTAGATTGA
Found at i:846727 original size:25 final size:26
Alignment explanation
Indices: 846673--846728 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
846663 GTCATAACAT
* * *
846673 TATTAAAAATTATTTTTATATTTATA
1 TATTAAAAATTAATTATATATTTAAA
846699 -ATTAAAAATTAATTAT-TATTTAAA
1 TATTAAAAATTAATTATATATTTAAA
846723 TATTAA
1 TATTAA
846729 TTTGAATGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 7 0.27
25 19 0.73
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
TATTAAAAATTAATTATATATTTAAA
Found at i:847415 original size:28 final size:27
Alignment explanation
Indices: 847358--847411 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
847348 GACTTAAATG
* *
847358 TAAAAGAAAAAAATTGTAAATTGATTA
1 TAAAAGAAAAAAAATGTAAATTGATAA
*
847385 TAAAATAAAAAAAATGT-AATCTGATAA
1 TAAAAGAAAAAAAATGTAAAT-TGATAA
847412 ATAACAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 3 0.13
27 20 0.87
ACGTcount: A:0.61, C:0.02, G:0.09, T:0.28
Consensus pattern (27 bp):
TAAAAGAAAAAAAATGTAAATTGATAA
Found at i:847659 original size:3 final size:3
Alignment explanation
Indices: 847646--847678 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
847636 TAATCTTTAT
*
847646 TTA TAA TTA TTA TTA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
847679 GAATAACAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:848912 original size:15 final size:16
Alignment explanation
Indices: 848894--849015 Score: 55
Period size: 17 Copynumber: 7.9 Consensus size: 16
848884 TTTTAGTATC
848894 TATATTAAA-TATATA
1 TATATTAAATTATATA
* *
848909 TATAATAAAATTATTTA
1 TAT-ATTAAATTATATA
*
848926 TATATTAATATTTTATA
1 TATATTAA-ATTATATA
* *
848943 TGTATT--ATTTTA-A
1 TATATTAAATTATATA
848956 TATA-T-AA-TA-ATA
1 TATATTAAATTATATA
* * *
848968 TATATTAAAATCATGTT
1 TATATT-AAATTATATA
*
848985 TATGAATAAATTATA-A
1 TAT-ATTAAATTATATA
849001 TAATATTAAATTATA
1 T-ATATTAAATTATA
849016 AATAATTGAT
Statistics
Matches: 79, Mismatches: 16, Indels: 23
0.67 0.14 0.19
Matches are distributed among these distances:
11 1 0.01
12 7 0.09
13 6 0.08
14 6 0.08
15 5 0.06
16 21 0.27
17 31 0.39
18 2 0.03
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.48
Consensus pattern (16 bp):
TATATTAAATTATATA
Found at i:849027 original size:27 final size:27
Alignment explanation
Indices: 848984--849036 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
848974 AAAATCATGT
* * *
848984 TTATGAATAAATTATAATAATATTAAA
1 TTATAAATAAATTATAAAAAAATTAAA
849011 TTATAAAT-AATTGATAAAAAAATTAA
1 TTATAAATAAATT-ATAAAAAAATTAA
849037 TTGAAAAGGC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (27 bp):
TTATAAATAAATTATAAAAAAATTAAA
Found at i:850036 original size:3 final size:3
Alignment explanation
Indices: 850028--850072 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
850018 CATATTTTAA
*
850028 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
850073 TTATATAGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:851444 original size:2 final size:2
Alignment explanation
Indices: 851437--851461 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
851427 ATTTATCCTT
851437 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
851462 AATAGCTGTC
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:855013 original size:70 final size:70
Alignment explanation
Indices: 854935--855315 Score: 221
Period size: 70 Copynumber: 5.4 Consensus size: 70
854925 TGTATCATCC
* * * *
854935 ATATATTCCATAGATAAGGTAGTTA-CCTTTTCTTTGACTAGATAAATGGCTAC-TCGGTTGAAA
1 ATATATTCCATTGATAAGGTAGTTATCC-TTTCTTTGACTAGATAAATGGATACGT-AGCTGAAA
854998 TATCTCA
64 TATCTCA
* ** * * * * * * *
855005 GTATATTCCATTGATGTGGTAGTTATGCTTTCTTTGCCTTGCTAAGTGGATACGTAGCTGATATT
1 ATATATTCCATTGATAAGGTAGTTATCCTTTCTTTGACTAGATAAATGGATACGTAGCTGAAATA
855070 TCTCA
66 TCTCA
** * * * * * * *
855075 ATATATTCCATTGATAAGGTAGTTATGGTTTCCTTGATTTGATAAGTGGATTCTTAGCTGATATA
1 ATATATTCCATTGATAAGGTAGTTATCCTTTCTTTGACTAGATAAATGGATACGTAGCTGAAATA
* *
855140 CCTCT
66 TCTCA
* * * * * * * ** * *
855145 GTATATTCCATTGATATGGTAGTTACCCTTGAC-TTGACTTGGTAAGTGCTTACTTAGCTGATAT
1 ATATATTCCATTGATAAGGTAGTTATCCTT-TCTTTGACTAGATAAATGGATACGTAGCTGAAAT
* *
855209 ACCTCT
65 ATCTCA
* * * * * * * ** * *
855215 GTATATTCCATTGATATGGTAGTTACCCTTGAC-TTGACTTGGTAAGTGCTTACTTAGCTGATAT
1 ATATATTCCATTGATAAGGTAGTTATCCTT-TCTTTGACTAGATAAATGGATACGTAGCTGAAAT
*
855279 ATCTCT
65 ATCTCA
* * *
855285 GTATATTCCATTGATGAGGTAGTTACCCTTT
1 ATATATTCCATTGATAAGGTAGTTATCCTTT
855316 TTTTAATGTA
Statistics
Matches: 266, Mismatches: 42, Indels: 7
0.84 0.13 0.02
Matches are distributed among these distances:
70 263 0.99
71 3 0.01
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.41
Consensus pattern (70 bp):
ATATATTCCATTGATAAGGTAGTTATCCTTTCTTTGACTAGATAAATGGATACGTAGCTGAAATA
TCTCA
Found at i:855191 original size:140 final size:140
Alignment explanation
Indices: 854935--855314 Score: 372
Period size: 140 Copynumber: 2.7 Consensus size: 140
854925 TGTATCATCC
* ** * * ** ** * *
854935 ATATATTCCATAGATAAGGTAGTTA-CCTTTTCTTTGACTAGATAAATGGCTACTCGGTTGAAAT
1 ATATATTCCATTGATAAGGTAGTTACCCTTGAC-TTGACTTGATAAGTGATTACTTAGCTGATAT
* * * ** * * *
854999 ATCTCAGTATATTCCATTGATGTGGTAGTTATGCTTTCTTTGCCTTGCTAAGTGGATACGTAGCT
65 ACCTCTGTATATTCCATTGATATGGTAGTTACCCTTACTTTGACTTGCTAAGTGCATACGTAGCT
**
855064 GATATTTCTCA
130 GATATACCTCA
*** ** *
855075 ATATATTCCATTGATAAGGTAGTTATGGTTTCCTTGATTTGATAAGTGGATT-CTTAGCTGATAT
1 ATATATTCCATTGATAAGGTAGTTACCCTTGACTTGACTTGATAAGT-GATTACTTAGCTGATAT
* * *
855139 ACCTCTGTATATTCCATTGATATGGTAGTTACCCTTGAC-TTGACTTGGTAAGTGCTTACTTAGC
65 ACCTCTGTATATTCCATTGATATGGTAGTTACCCTT-ACTTTGACTTGCTAAGTGCATACGTAGC
*
855203 TGATATACCTCT
129 TGATATACCTCA
* * * *
855215 GTATATTCCATTGATATGGTAGTTACCCTTGACTTGACTTGGTAAGTGCTTACTTAGCTGATATA
1 ATATATTCCATTGATAAGGTAGTTACCCTTGACTTGACTTGATAAGTGATTACTTAGCTGATATA
*
855280 TCTCTGTATATTCCATTGATGA-GGTAGTTACCCTT
66 CCTCTGTATATTCCATTGAT-ATGGTAGTTACCCTT
855315 TTTTTAATGT
Statistics
Matches: 197, Mismatches: 38, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
139 3 0.02
140 186 0.94
141 8 0.04
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.41
Consensus pattern (140 bp):
ATATATTCCATTGATAAGGTAGTTACCCTTGACTTGACTTGATAAGTGATTACTTAGCTGATATA
CCTCTGTATATTCCATTGATATGGTAGTTACCCTTACTTTGACTTGCTAAGTGCATACGTAGCTG
ATATACCTCA
Found at i:855620 original size:3 final size:3
Alignment explanation
Indices: 855614--855640 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
855604 TATTATTAAC
855614 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
855641 TGCGACTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:855778 original size:13 final size:13
Alignment explanation
Indices: 855760--855806 Score: 58
Period size: 13 Copynumber: 3.4 Consensus size: 13
855750 AAAATAATAA
855760 TATTTTGATAATT
1 TATTTTGATAATT
*
855773 TATTTTAAATTAATAT
1 TATTTT-GA-TAAT-T
855789 TATTTTGATAATT
1 TATTTTGATAATT
855802 TATTT
1 TATTT
855807 AAAAATTAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
13 12 0.41
14 5 0.17
15 5 0.17
16 7 0.24
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (13 bp):
TATTTTGATAATT
Found at i:855823 original size:30 final size:30
Alignment explanation
Indices: 855748--855831 Score: 118
Period size: 29 Copynumber: 2.8 Consensus size: 30
855738 TTTTTATGAA
855748 TAAAAA-TAATAATATTTTGATAATTTATT
1 TAAAAATTAATAATATTTTGATAATTTATT
* *
855777 T-TAAATTAATATTATTTTGATAATTTATT
1 TAAAAATTAATAATATTTTGATAATTTATT
*
855806 TAAAAATTAGTAATATTTTGAATAAT
1 TAAAAATTAATAATATTTTG-ATAAT
855832 ATGTTATGTA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
28 3 0.06
29 24 0.51
30 15 0.32
31 5 0.11
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (30 bp):
TAAAAATTAATAATATTTTGATAATTTATT
Found at i:856257 original size:67 final size:67
Alignment explanation
Indices: 856149--856283 Score: 261
Period size: 67 Copynumber: 2.0 Consensus size: 67
856139 GACTAACTCA
856149 CTCACTGCGTATGAATTGACGAAGATGGAATGGCAACTAAACAACGAGGAAAAATGCCACCGTCC
1 CTCACTGCGTATGAATTGACGAAGATGGAATGGCAACTAAACAACGAGGAAAAATGCCACCGTCC
856214 AG
66 AG
*
856216 CTCACTGCGTATGAATTGACGAAGATGGAATGGCAAGTAAACAACGAGGAAAAATGCCACCGTCC
1 CTCACTGCGTATGAATTGACGAAGATGGAATGGCAACTAAACAACGAGGAAAAATGCCACCGTCC
856281 AG
66 AG
856283 C
1 C
856284 CAATGGGTCA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.16
Consensus pattern (67 bp):
CTCACTGCGTATGAATTGACGAAGATGGAATGGCAACTAAACAACGAGGAAAAATGCCACCGTCC
AG
Found at i:857076 original size:15 final size:14
Alignment explanation
Indices: 857061--857096 Score: 63
Period size: 15 Copynumber: 2.5 Consensus size: 14
857051 ATTAAATTTA
857061 AATTTAATTTAATT
1 AATTTAATTTAATT
857075 AATTTATATTTAATT
1 AATTTA-ATTTAATT
857090 AATTTAA
1 AATTTAA
857097 AATTATTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
AATTTAATTTAATT
Found at i:857085 original size:6 final size:5
Alignment explanation
Indices: 857055--857096 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
857045 ATTTTTATTA
857055 AATTT AAATTT AATTT AA-TT AATTT ATATTT AA-TT AATTT AA
1 AATTT -AATTT AATTT AATTT AATTT A-ATTT AATTT AATTT AA
857097 AATTATTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
4 8 0.24
5 15 0.45
6 10 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (5 bp):
AATTT
Found at i:857096 original size:20 final size:20
Alignment explanation
Indices: 857055--857093 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
857045 ATTTTTATTA
857055 AATTTAAATTTAATTTAATT
1 AATTTAAATTTAATTTAATT
*
857075 AATTTATATTTAA-TTAATT
1 AATTTAAATTTAATTTAATT
857094 TAAAATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
AATTTAAATTTAATTTAATT
Found at i:857430 original size:2 final size:2
Alignment explanation
Indices: 857425--857457 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
857415 GCTCCACCAC
857425 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
857458 TTTTGCAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:858000 original size:31 final size:32
Alignment explanation
Indices: 857964--858037 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
857954 ATATTTATAT
857964 TTAATATATATTT-AAATATAAATAT-AAAAA
1 TTAATATATATTTAAAATATAAATATAAAAAA
*
857994 TATAATATAT-TTTAAAAATATATATATAAAAAA
1 T-TAATATATATTT-AAAATATAAATATAAAAAA
858027 TTAA-ATATATT
1 TTAATATATATT
858038 CAAACTAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
30 4 0.11
31 12 0.32
32 16 0.42
33 6 0.16
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (32 bp):
TTAATATATATTTAAAATATAAATATAAAAAA
Found at i:859657 original size:22 final size:24
Alignment explanation
Indices: 859612--859668 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 24
859602 ATAAATTTTT
859612 TATTTTTTAAATTATATCATGTGA
1 TATTTTTTAAATTATATCATGTGA
859636 TATTTTTT-AATT-TCATCA-GTGA
1 TATTTTTTAAATTAT-ATCATGTGA
*
859658 -AATTTTTAAAT
1 TATTTTTTAAAT
859669 CTAACATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
21 6 0.20
22 8 0.27
23 8 0.27
24 8 0.27
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.54
Consensus pattern (24 bp):
TATTTTTTAAATTATATCATGTGA
Found at i:866935 original size:20 final size:20
Alignment explanation
Indices: 866902--866940 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
866892 TTTTAAAAAA
** *
866902 TTAAATTTTTATATTTATAT
1 TTAAATTTAAATATATATAT
866922 TTAAATTTAAATATATATA
1 TTAAATTTAAATATATATA
866941 GAATATGAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTAAATTTAAATATATATAT
Found at i:873723 original size:19 final size:16
Alignment explanation
Indices: 873687--873717 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
873677 GAAATAACAG
873687 AAAAAAAAAAAACTAA
1 AAAAAAAAAAAACTAA
*
873703 AAAAAGAAAAAACTA
1 AAAAAAAAAAAACTA
873718 CTAAAACAAT
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:0.84, C:0.06, G:0.03, T:0.06
Consensus pattern (16 bp):
AAAAAAAAAAAACTAA
Found at i:875300 original size:109 final size:112
Alignment explanation
Indices: 875109--875309 Score: 302
Period size: 109 Copynumber: 1.8 Consensus size: 112
875099 ATTTGTTACT
*
875109 ATGAATATTTAAGAAATGAATATATATATACTTAATTTTGTTAATTAAATAGGCTTTTATTTATA
1 ATGAATATTTAAGAAATGAATATATATATACTTAATTTTGTTAATT-AAGAGGCTTTTATTTATA
* *
875174 GTAATTTTAAAAAGTATAAAATGTAAAAAAAATGTATAATTTATTATG
65 GTAATTCTAAAAAGTATAAAAAGTAAAAAAAATGTATAATTTATTATG
* *
875222 ATGAATATTTAAG-AATGAATA-A-ATATATTTAATTTTGTTAATT-AGAGGAGTTTTATTTATA
1 ATGAATATTTAAGAAATGAATATATATATACTTAATTTTGTTAATTAAGAGG-CTTTTATTTATA
*
875283 GTAATTCTAAAATGTATAAAAAGTAAA
65 GTAATTCTAAAAAGTATAAAAAGTAAA
875310 TTAGAATGTA
Statistics
Matches: 81, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
108 4 0.05
109 35 0.43
110 20 0.25
111 1 0.01
112 8 0.10
113 13 0.16
ACGTcount: A:0.46, C:0.01, G:0.11, T:0.42
Consensus pattern (112 bp):
ATGAATATTTAAGAAATGAATATATATATACTTAATTTTGTTAATTAAGAGGCTTTTATTTATAG
TAATTCTAAAAAGTATAAAAAGTAAAAAAAATGTATAATTTATTATG
Found at i:875673 original size:30 final size:31
Alignment explanation
Indices: 875620--875680 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
875610 TCAAATAAGT
* *
875620 TTTTAATATTTAATTTATATTTAAGATAAAA
1 TTTTAACATTTAATTTATATTTAAAATAAAA
*
875651 TTTTAACATTT-ATTTTTATTTAAAATAAAA
1 TTTTAACATTTAATTTATATTTAAAATAAAA
875681 AATTATTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 17 0.63
31 10 0.37
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (31 bp):
TTTTAACATTTAATTTATATTTAAAATAAAA
Found at i:875723 original size:29 final size:28
Alignment explanation
Indices: 875670--875736 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
875660 TTATTTTTAT
875670 TTAAAATA-AAAAATTATTTAAATATGAA
1 TTAAAATATAAAAATTATTTAAATAT-AA
**
875698 TTAAAATATAAAAATTATTTTGATATAA
1 TTAAAATATAAAAATTATTTAAATATAA
*
875726 TAAAAATATAA
1 TTAAAATATAA
875737 CAGTTTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
28 20 0.57
29 15 0.43
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (28 bp):
TTAAAATATAAAAATTATTTAAATATAA
Found at i:879815 original size:14 final size:13
Alignment explanation
Indices: 879796--879834 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
879786 TCAGTTTTTT
879796 TTTTAAATTATAAA
1 TTTTAAATT-TAAA
879810 TTTTAATATTTAAA
1 TTTTAA-ATTTAAA
*
879824 ATTTAAATTTA
1 TTTTAAATTTA
879835 TTAAATATAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 5 0.22
14 15 0.65
15 3 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TTTTAAATTTAAA
Found at i:885958 original size:25 final size:25
Alignment explanation
Indices: 885903--885958 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
885893 ATTTATTAAA
*
885903 AAAAATTTAAATTAATTAATCTTCT
1 AAAAATTTAAATTAATTAATCATCT
* * *
885928 ATAAATTATAATTTAATTCATCAT-T
1 AAAAATT-TAAATTAATTAATCATCT
885953 AAAAAT
1 AAAAAT
885959 ACTTCAAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
25 12 0.48
26 13 0.52
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (25 bp):
AAAAATTTAAATTAATTAATCATCT
Found at i:908710 original size:3 final size:3
Alignment explanation
Indices: 908702--908758 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
908692 AAGAGGAAAT
* * * * *
908702 AGA AGA AGA AGT AGA AGT AGA AGA GGA AGT TGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
*
908750 TGA AGA AGA
1 AGA AGA AGA
908759 GGAGGATAAC
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.56, C:0.00, G:0.35, T:0.09
Consensus pattern (3 bp):
AGA
Found at i:908716 original size:12 final size:12
Alignment explanation
Indices: 908683--908758 Score: 57
Period size: 12 Copynumber: 6.3 Consensus size: 12
908673 CAGCAACTAC
*
908683 AAGAAGTGGAAG
1 AAGAAGTAGAAG
* *
908695 AGGAAATAGAAG
1 AAGAAGTAGAAG
908707 AAGAAGTAGAAG
1 AAGAAGTAGAAG
*
908719 TAGAAG-AGGAAG
1 AAGAAGTA-GAAG
** *
908731 TTGAAGAAGAAG
1 AAGAAGTAGAAG
908743 AAGAAG-ATGAAG
1 AAGAAGTA-GAAG
908755 AAGA
1 AAGA
908759 GGAGGATAAC
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
11 2 0.04
12 49 0.94
13 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.36, T:0.09
Consensus pattern (12 bp):
AAGAAGTAGAAG
Found at i:911915 original size:2 final size:2
Alignment explanation
Indices: 911908--911939 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
911898 AAGGTCCTAG
911908 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
911940 TTGGCATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:921741 original size:3 final size:3
Alignment explanation
Indices: 921733--921786 Score: 81
Period size: 3 Copynumber: 18.0 Consensus size: 3
921723 TTGCGCTTGG
* * *
921733 TAA TAA TAA TAA TGA TGA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
921781 TAA TAA
1 TAA TAA
921787 CAATGTAATG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:924078 original size:3 final size:3
Alignment explanation
Indices: 924070--924101 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
924060 AATGAAGCAA
924070 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
924102 CAGCTTTTTA
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:924776 original size:14 final size:15
Alignment explanation
Indices: 924746--924779 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
924736 ACAGCCTACC
924746 ATTTGGACGGATTTG
1 ATTTGGACGGATTTG
*
924761 ATTTGG-CGGCTTTG
1 ATTTGGACGGATTTG
924775 ATTTG
1 ATTTG
924780 ATTATTACCG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.15, C:0.09, G:0.32, T:0.44
Consensus pattern (15 bp):
ATTTGGACGGATTTG
Found at i:926911 original size:20 final size:20
Alignment explanation
Indices: 926886--926925 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
926876 TACGATAATT
926886 TAAAAATAATATAAA-TATAA
1 TAAAAAT-ATATAAATTATAA
926906 TAAAAATATATAAATTATAA
1 TAAAAATATATAAATTATAA
926926 ATTTTAATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
TAAAAATATATAAATTATAA
Found at i:926925 original size:17 final size:18
Alignment explanation
Indices: 926882--926926 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 18
926872 TTAGTACGAT
926882 AATT-TAAAAATAATATA
1 AATTATAAAAATAATATA
926899 AATATAATAAAAAT-ATATA
1 AAT-T-ATAAAAATAATATA
926918 AATTATAAA
1 AATTATAAA
926927 TTTTAATCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 8 0.32
18 2 0.08
19 8 0.32
20 7 0.28
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AATTATAAAAATAATATA
Found at i:928561 original size:17 final size:17
Alignment explanation
Indices: 928535--928568 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
928525 TTACACATGA
928535 AATCTCAAAATTTTTAT
1 AATCTCAAAATTTTTAT
*
928552 AATCTTAAAATTTTTAT
1 AATCTCAAAATTTTTAT
928569 CATATTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (17 bp):
AATCTCAAAATTTTTAT
Found at i:928576 original size:17 final size:17
Alignment explanation
Indices: 928541--928576 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
928531 ATGAAATCTC
*
928541 AAAATTTTTATAATCTT
1 AAAATTTTTATAATATT
*
928558 AAAATTTTTATCATATT
1 AAAATTTTTATAATATT
928575 AA
1 AA
928577 TATAATAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
AAAATTTTTATAATATT
Found at i:928641 original size:14 final size:14
Alignment explanation
Indices: 928605--928641 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
928595 CTCACAATAT
928605 AATTTAATTATTAA
1 AATTTAATTATTAA
* *
928619 TATTAAATTATTAA
1 AATTTAATTATTAA
928633 AATTTAATT
1 AATTTAATT
928642 TTTACTTAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
AATTTAATTATTAA
Found at i:928935 original size:17 final size:16
Alignment explanation
Indices: 928896--928935 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
928886 TAATTATAAT
*
928896 TATAAATAAATAAAAA
1 TATAAATAAAAAAAAA
928912 TATTAAATAATAAAAAAA
1 TA-TAAATAA-AAAAAAA
928930 TATAAA
1 TATAAA
928936 GTTTGAAGCG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 2 0.10
17 11 0.52
18 8 0.38
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
TATAAATAAAAAAAAA
Found at i:929483 original size:2 final size:2
Alignment explanation
Indices: 929476--929506 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
929466 TATGCCAACT
929476 TC 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 TC T
929507 TTTTGTTGTT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:935258 original size:12 final size:14
Alignment explanation
Indices: 935211--935260 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
935201 CATTTTCTTT
*
935211 TATATGATATATATA
1 TATAT-ATATATAAA
*
935226 TATATATATATATA
1 TATATATATATAAA
935240 TATATATATTATAAA
1 TATATATA-TATAAA
935255 -ATATAT
1 TATATAT
935261 GCCGTATGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
14 23 0.70
15 10 0.30
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (14 bp):
TATATATATATAAA
Found at i:935260 original size:2 final size:2
Alignment explanation
Indices: 935211--935252 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
935201 CATTTTCTTT
935211 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
935253 AAATATATGC
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 35 0.92
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:935898 original size:2 final size:2
Alignment explanation
Indices: 935891--935916 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
935881 AATAGTGTCA
935891 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
935917 GTATGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:938934 original size:707 final size:706
Alignment explanation
Indices: 937579--938964 Score: 2070
Period size: 707 Copynumber: 2.0 Consensus size: 706
937569 TCCCTGACCC
937579 CAAAAAAAAAAATTAGAGGAAAGTTACATAGAAAATGAGCATCCTCATAATTGAAGAACTGATTT
1 CAAAAAAAAAAATTAGAGGAAAGTTACATAGAAAATGAGCATCCTCATAATTGAAGAACTGATTT
937644 TAATTATTAATAATTCAAGTTGTAGTTGTAACAATTAATCATACCAATGTAAATTAATTTATAAA
66 TAATTATTAATAATTCAAGTTGTAGTTGTAACAATTAATCATACCAATGTAAATTAATTTATAAA
* *
937709 TTTTATAGCAAGTGTCTTAAAAAATATATTTTTTAAATTATTAGATATAATGTTATTAAAACATT
131 TTTTATAACAAGTGTCTTAAAAAATATATTTTTTAAATTATTAGATATAATGTAATTAAAACATT
* ** *
937774 ACATTAATAATATATTATTTATAAATAATAAATTAATAAATTTTTTTAAAAATATTAAAGACACT
196 ACATTAATAATATATTATTTATAAATAATAAATTAATAAATCTTTAAAAAAATACTAAAGACACT
* * * * *
937839 TGTTAACTAACCCCTTAATTTATGTTATATCTCAATTATCATTACCAATTGATCTTCAAAAAAAT
261 TGTTAACTAACCCCTTAATTTATGTGATATCTCAATCAACATTACCAACTGATCATCAAAAAAAT
** * *
937904 ACTTACCTCCAAATCATATTCGTCAAGTGGACTGTTGTACATTTTTCAAAGTCTGACAAATAATC
326 ACTTACCTCCAAATCATATTCGTCAAGTAAACTATTGTACATTTTTCAAAATCTGACAAATAATC
* * * * * *
937969 AAACCTTAATAGACATTTAAAAGTCGTAAGTATATTAAAAAAATATATGATCTGACAATAAATAA
391 AAACCTTAACAAACATTTAAAAATCATAAGTATATCAAAAAAATATATAATCTGACAATAAATAA
* * * *
938034 TTTACACAATCATATAATAAAAGAAATCTGACAATTTCAATAATACTTCATATCAACAAAAAATT
456 CTTACACAATCATATAATAAAAGAAATCTAACAATTTCAACAATACTTCACATCAACAAAAAATT
* *
938099 CATACAATCCTTTTCAATTATAAAATAATAAGCATCAAAAAAATAAATTTAAAAACTCAAATTAC
521 CATACAATCCTTTTCAATTATAAAATAATAAACATAAAAAAAATAAATTTAAAAACTCAAATTAC
* *
938164 TGCTCACCATCTTCATTATCATATTCTTTTTATATTTAATTTAAGTATCAAAATATACATTAAAA
586 TACTCACCATCTTCATTATCATATTCTCTTTATATTTAATTTAAGTATCAAAATATACATTAAAA
938229 TTCAAACTTCAATATCCCTCTCACAGTTGGAAACATTTAACATCCTCATATAGTAT
651 TTCAAACTTCAATATCCCTCTCACAGTTGGAAACATTTAACATCCTCATATAGTAT
* *
938285 CAAAAAAAAAAA-TAGAGTAAAGTTATATAGAAAATGAGCATCCTCATAATTGAAGAACTGATTT
1 CAAAAAAAAAAATTAGAGGAAAGTTACATAGAAAATGAGCATCCTCATAATTGAAGAACTGATTT
*
938349 TAATTATTAATAATTCAAGTTGTAGTTGTAACAATTAATCATATCAATGTAAATTAATTTATAAA
66 TAATTATTAATAATTCAAGTTGTAGTTGTAACAATTAATCATACCAATGTAAATTAATTTATAAA
* *
938414 TTTTATAACAAGTGTCTTAAAAATTATATATTTTTTAAATTATTAGATATAGTGTAATTAGAACA
131 TTTTATAACAAGTGTCTTAAAAA--ATATATTTTTTAAATTATTAGATATAATGTAATTAAAACA
*
938479 TTACATTTAATACTATATTATTTATAAATAATAAATTAATAAATCTTTAAAAAGAATACTAAAGA
194 TTACA-TTAATAATATATTATTTATAAATAATAAATTAATAAATCTTTAAAAA-AATACTAAAGA
* ** *
938544 CACTTGTTAACTAATCTTTTAATTTATGTGATATCTCAATCAACATTATCAACTGATCATC-AAA
257 CACTTGTTAACTAACCCCTTAATTTATGTGATATCTCAATCAACATTACCAACTGATCATCAAAA
* * * * * * *
938608 AAATATTTA-CTCTCAAATCATGTTTGTCAAAG-AAATTATTGTGCATTTTTTAAAATCTGATAA
322 AAATACTTACCTC-CAAATCATATTCGTC-AAGTAAACTATTGTACATTTTTCAAAATCTGACAA
* * * *
938671 ATAATTAAATCTTAACAAATATTTAAAAATCATGAGTATATCAAAAAAATATATAATCTGAC-AT
385 ATAATCAAACCTTAACAAACATTTAAAAATCATAAGTATATCAAAAAAATATATAATCTGACAAT
* * *
938735 AAATAACTTACACGA-CGATATAATAAAA-AAATCTAACAA-TTCTAACAATTCTTCACGTCAAC
450 AAATAACTTACACAATC-ATATAATAAAAGAAATCTAACAATTTC-AACAATACTTCACATCAAC
* * *
938797 AAAAAAATTCATATAAT-CTCTTTCAATTATAAAATGATAAACGTAAAAAAAATAAATTTAAAAA
513 -AAAAAATTCATACAATCCT-TTTCAATTATAAAATAATAAACATAAAAAAAATAAATTTAAAAA
* * *
938861 CTCAAATTACTATTCATCATCTTCATTATCATATTCTCTTTATATTTAATTTAAGTATCAATATA
576 CTCAAATTACTACTCACCATCTTCATTATCATATTCTCTTTATATTTAATTTAAGTATCAAAATA
* *
938926 TACATTAAACTTCAAACTTCAATATCGCTCTCACAGTTG
641 TACATTAAAATTCAAACTTCAATATCCCTCTCACAGTTG
938965 TTCTCCTTGC
Statistics
Matches: 609, Mismatches: 61, Indels: 19
0.88 0.09 0.03
Matches are distributed among these distances:
705 139 0.23
706 40 0.07
707 223 0.37
708 142 0.23
709 65 0.11
ACGTcount: A:0.45, C:0.13, G:0.07, T:0.36
Consensus pattern (706 bp):
CAAAAAAAAAAATTAGAGGAAAGTTACATAGAAAATGAGCATCCTCATAATTGAAGAACTGATTT
TAATTATTAATAATTCAAGTTGTAGTTGTAACAATTAATCATACCAATGTAAATTAATTTATAAA
TTTTATAACAAGTGTCTTAAAAAATATATTTTTTAAATTATTAGATATAATGTAATTAAAACATT
ACATTAATAATATATTATTTATAAATAATAAATTAATAAATCTTTAAAAAAATACTAAAGACACT
TGTTAACTAACCCCTTAATTTATGTGATATCTCAATCAACATTACCAACTGATCATCAAAAAAAT
ACTTACCTCCAAATCATATTCGTCAAGTAAACTATTGTACATTTTTCAAAATCTGACAAATAATC
AAACCTTAACAAACATTTAAAAATCATAAGTATATCAAAAAAATATATAATCTGACAATAAATAA
CTTACACAATCATATAATAAAAGAAATCTAACAATTTCAACAATACTTCACATCAACAAAAAATT
CATACAATCCTTTTCAATTATAAAATAATAAACATAAAAAAAATAAATTTAAAAACTCAAATTAC
TACTCACCATCTTCATTATCATATTCTCTTTATATTTAATTTAAGTATCAAAATATACATTAAAA
TTCAAACTTCAATATCCCTCTCACAGTTGGAAACATTTAACATCCTCATATAGTAT
Found at i:939547 original size:2 final size:2
Alignment explanation
Indices: 939540--939567 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
939530 TAATATCCCT
939540 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
939568 CATTCATTTC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:943543 original size:18 final size:18
Alignment explanation
Indices: 943520--943555 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
943510 TTTTTTTTAT
943520 GTATCTTTAAGCTTTAAC
1 GTATCTTTAAGCTTTAAC
943538 GTATCTTTAAGCTTTAAC
1 GTATCTTTAAGCTTTAAC
943556 ATAAAGTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.44
Consensus pattern (18 bp):
GTATCTTTAAGCTTTAAC
Found at i:944027 original size:3 final size:3
Alignment explanation
Indices: 944019--944044 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
944009 ACAAAATCAA
944019 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
944045 CTTTCGTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:944229 original size:22 final size:21
Alignment explanation
Indices: 944201--944274 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 21
944191 ATATAAAAAT
*
944201 AATATAAATTTATAATATTTTA
1 AATATAAA-TTATAATATTTAA
944223 AATAT-AATTATAATATTTAA
1 AATATAAATTATAATATTTAA
*
944243 AATATATAAATATAATA--TAA
1 AATATA-AATTATAATATTTAA
944263 ATATATAAATTA
1 A-ATATAAATTA
944275 ATAAAATAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
20 25 0.54
21 7 0.15
22 14 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AATATAAATTATAATATTTAA
Found at i:944235 original size:28 final size:26
Alignment explanation
Indices: 944170--944270 Score: 100
Period size: 28 Copynumber: 3.8 Consensus size: 26
944160 TGGTAATTTT
* *
944170 TAAATATAAAAT-AATTATGTAATATA
1 TAAATATAATATAAATT-TATAATATA
*
944196 -AAA-ATAATATAAATTTATAATATTT
1 TAAATATAATATAAATTTATAATA-TA
*
944221 TAAATATAATTATAATATTTAAAATATA
1 TAAATATAA-TATAA-ATTTATAATATA
*
944249 TAAATATAATATAAATATATAA
1 TAAATATAATATAAATTTATAA
944271 ATTAATAAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
24 12 0.19
25 8 0.13
26 9 0.15
27 9 0.15
28 15 0.24
29 9 0.15
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (26 bp):
TAAATATAATATAAATTTATAATATA
Found at i:944260 original size:11 final size:11
Alignment explanation
Indices: 944170--944267 Score: 60
Period size: 11 Copynumber: 8.7 Consensus size: 11
944160 TGGTAATTTT
*
944170 TAAATATAAAA
1 TAAATATAATA
*
944181 TAATTATGTAATA
1 TAA--ATATAATA
*
944194 TAAAAATAATA
1 TAAATATAATA
944205 TAAATTTATAATA
1 TAAA--TATAATA
**
944218 T-TTTA-AATA
1 TAAATATAATA
*
944227 TAATTATAATA
1 TAAATATAATA
944238 TTTAAA-AT-ATA
1 --TAAATATAATA
944249 TAAATATAATA
1 TAAATATAATA
944260 TAAATATA
1 TAAATATA
944268 TAAATTAATA
Statistics
Matches: 68, Mismatches: 9, Indels: 20
0.70 0.09 0.21
Matches are distributed among these distances:
9 9 0.13
10 7 0.10
11 31 0.46
12 2 0.03
13 19 0.28
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (11 bp):
TAAATATAATA
Found at i:944271 original size:28 final size:28
Alignment explanation
Indices: 944191--944285 Score: 99
Period size: 27 Copynumber: 3.5 Consensus size: 28
944181 TAATTATGTA
* * *
944191 ATATAAAAATAATATAAATTTATAATAT
1 ATATAAATATAATATAAATATATAAAAT
* *
944219 -TTTAAATATAAT-TATAATATTTAAAAT
1 ATATAAATATAATATA-AATATATAAAAT
*
944246 ATATAAATATAATATAAATATATAAATT
1 ATATAAATATAATATAAATATATAAAAT
944274 A-ATAAA-ATAATA
1 ATATAAATATAATA
944286 ATTTATTGAT
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
26 8 0.14
27 24 0.43
28 22 0.39
29 2 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (28 bp):
ATATAAATATAATATAAATATATAAAAT
Found at i:950845 original size:2 final size:2
Alignment explanation
Indices: 950838--950867 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
950828 TCAAAAGATC
950838 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
950868 GAAAAATTGA
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:951090 original size:27 final size:28
Alignment explanation
Indices: 951056--951125 Score: 76
Period size: 27 Copynumber: 2.6 Consensus size: 28
951046 GTATTATTTT
951056 TATA-TTATAATATATTTTA-AATATTA
1 TATATTTATAATATATTTTATAATATTA
* *
951082 TATATTTATAA-AAATTTTATTATATTA
1 TATATTTATAATATATTTTATAATATTA
951109 -ATAATTTATAATTATAT
1 TAT-ATTTATAA-TATAT
951126 AAATTTTAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
26 13 0.36
27 20 0.56
29 3 0.08
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
TATATTTATAATATATTTTATAATATTA
Found at i:951096 original size:19 final size:20
Alignment explanation
Indices: 951074--951112 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
951064 AATATATTTT
*
951074 AAATATTA-TATATTTATAA
1 AAATATTATTATATTAATAA
*
951093 AAATTTTATTATATTAATAA
1 AAATATTATTATATTAATAA
951113 TTTATAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AAATATTATTATATTAATAA
Found at i:951130 original size:33 final size:33
Alignment explanation
Indices: 951082--951192 Score: 100
Period size: 33 Copynumber: 3.3 Consensus size: 33
951072 TTAAATATTA
* *
951082 TATATTTATAAAAATTTTATTATATTAATAATT
1 TATAATTATATAAATTTTATTATATTAATAATT
** **
951115 TATAATTATATAAATTTTAAGATATTAATTTTT
1 TATAATTATATAAATTTTATTATATTAATAATT
* * *
951148 TATAA-TAT-TATATTTTAGTTTTTATATAATAATA
1 TATAATTATATAAATTTTA--TTATAT-TAATAATT
951182 TATAATTATAT
1 TATAATTATAT
951193 TACGATTAAA
Statistics
Matches: 60, Mismatches: 13, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
31 8 0.13
32 3 0.05
33 35 0.58
34 10 0.17
35 3 0.05
36 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (33 bp):
TATAATTATATAAATTTTATTATATTAATAATT
Found at i:960717 original size:2 final size:2
Alignment explanation
Indices: 960710--960735 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
960700 ACCTCCCCCA
960710 AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC
960736 GGAAGGAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:961694 original size:35 final size:35
Alignment explanation
Indices: 961655--961752 Score: 114
Period size: 35 Copynumber: 2.9 Consensus size: 35
961645 ATAATTTTAA
*
961655 TAAAAATATAATATTTTTATTTAATTTTTAATAAT-
1 TAAAAATTTAATATTTTTATTTAATTTTTAA-AATG
* *
961690 TAAAATTTTAAT-TTTTTA-TTAAATTTTAAAATG
1 TAAAAATTTAATATTTTTATTTAATTTTTAAAATG
*
961723 TAAATAATTTAATATATTT-TTTAATTTTTA
1 TAAA-AATTTAATATTTTTATTTAATTTTTA
961753 TATTATATAT
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
32 3 0.06
33 14 0.26
34 13 0.25
35 23 0.43
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (35 bp):
TAAAAATTTAATATTTTTATTTAATTTTTAAAATG
Found at i:961695 original size:34 final size:34
Alignment explanation
Indices: 961652--961752 Score: 102
Period size: 34 Copynumber: 3.0 Consensus size: 34
961642 AAAATAATTT
* *
961652 TAATAAAAATATAATATTTTTATTTAATTTTTAA
1 TAATTAAAATTTAATATTTTTATTTAATTTTTAA
*
961686 TAATTAAAATTTTAAT-TTTTTA-TTAAATTTTAA
1 TAATTAAAA-TTTAATATTTTTATTTAATTTTTAA
*
961719 -AATGTAAATAATTTAATATATTT-TTTAATTTTTA
1 TAAT-T-AA-AATTTAATATTTTTATTTAATTTTTA
961753 TATTATATAT
Statistics
Matches: 56, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
32 3 0.05
33 11 0.20
34 22 0.39
35 20 0.36
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (34 bp):
TAATTAAAATTTAATATTTTTATTTAATTTTTAA
Found at i:968660 original size:20 final size:19
Alignment explanation
Indices: 968635--968677 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
968625 TGAACATTAG
*
968635 AAATGTTAAT-TTAATATTT
1 AAATG-TAATATTAAAATTT
968654 CAAATGTAATATTAAAATTT
1 -AAATGTAATATTAAAATTT
968674 AAAT
1 AAAT
968678 TCCGTAACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATGTAATATTAAAATTT
Found at i:970861 original size:2 final size:2
Alignment explanation
Indices: 970854--970878 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
970844 CAGACGTAAA
970854 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
970879 ATTTTTTTTA
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:982825 original size:12 final size:12
Alignment explanation
Indices: 982808--982840 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
982798 TAATTAATTT
982808 AAAATTACAATA
1 AAAATTACAATA
982820 AAAATTACAATA
1 AAAATTACAATA
982832 AAAATTACA
1 AAAATTACA
982841 TATTTTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAATTACAATA
Found at i:983074 original size:27 final size:27
Alignment explanation
Indices: 983009--983063 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
982999 TAATAAAATA
983009 AAAAATATATAATTTTTAAAAAAATCT
1 AAAAATATATAATTTTTAAAAAAATCT
*
983036 AAAAATATATAATTTTTTAAAAAATCT
1 AAAAATATATAATTTTTAAAAAAATCT
983063 A
1 A
983064 CTTACTTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (27 bp):
AAAAATATATAATTTTTAAAAAAATCT
Found at i:988836 original size:16 final size:16
Alignment explanation
Indices: 988815--988850 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
988805 TTTACAATTG
988815 ATCTATCTGAATGAGT
1 ATCTATCTGAATGAGT
988831 ATCTATCTGAATGAGT
1 ATCTATCTGAATGAGT
988847 ATCT
1 ATCT
988851 CCTTTAGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.39
Consensus pattern (16 bp):
ATCTATCTGAATGAGT
Found at i:994554 original size:25 final size:27
Alignment explanation
Indices: 994526--994581 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
994516 ATTTATGTAA
994526 TTTATTTAAA-TTAA-AATAAAAATAT
1 TTTATTTAAATTTAATAATAAAAATAT
* *
994551 TTTATTTAAATTTAATTATAAAACTAT
1 TTTATTTAAATTTAATAATAAAAATAT
994578 TTTA
1 TTTA
994582 AATATTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 10 0.37
26 4 0.15
27 13 0.48
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (27 bp):
TTTATTTAAATTTAATAATAAAAATAT
Found at i:999873 original size:21 final size:20
Alignment explanation
Indices: 999812--999877 Score: 53
Period size: 20 Copynumber: 3.1 Consensus size: 20
999802 ATTTCGTAAA
*
999812 TTATTTTATTATATATTTATAT
1 TTATTTTA--ATATATTAATAT
**
999834 AAATTTTAATATATTAATAAT
1 TTATTTTAATATATTAAT-AT
*
999855 TTATTTTTATAT-TTAAATAT
1 TTATTTTAATATATT-AATAT
999875 TTA
1 TTA
999878 AATATTTATA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
20 16 0.44
21 14 0.39
22 6 0.17
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTATTTTAATATATTAATAT
Found at i:999878 original size:28 final size:29
Alignment explanation
Indices: 999818--999896 Score: 76
Period size: 28 Copynumber: 2.8 Consensus size: 29
999808 TAAATTATTT
* * *
999818 TATTATATATTTAT-A-TAAATTTTAATA
1 TATTAAATATTTATAATTATATTTAAATA
**
999845 TATT-AATAATTTATTTTTATATTTAAATA
1 TATTAAAT-ATTTATAATTATATTTAAATA
999874 T-TTAAATATTTATAATTATATTT
1 TATTAAATATTTATAATTATATTT
999897 TATATTATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
26 2 0.05
27 10 0.24
28 16 0.38
29 14 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (29 bp):
TATTAAATATTTATAATTATATTTAAATA
Found at i:999883 original size:35 final size:35
Alignment explanation
Indices: 999819--999943 Score: 109
Period size: 35 Copynumber: 3.6 Consensus size: 35
999809 AAATTATTTT
999819 ATTATATATTTATA--TAAATTTTAATATATTAATA
1 ATTATAT-TTTATATTTAAATTTTAATATATTAATA
*
999853 ATT-TATTTTTATATTTAAATATTTAA-ATATTTATA
1 ATTATA-TTTTATATTTAAAT-TTTAATATATTAATA
** *
999888 ATTATATTTTATA-TTATTTTTTTATATAGTT-ATA
1 ATTATATTTTATATTTAAATTTTAATATA-TTAATA
* *
999922 ATTATATATTATAATTATAATT
1 ATTATATTTTATATTTA-AATT
999944 ATATATTATC
Statistics
Matches: 75, Mismatches: 7, Indels: 16
0.77 0.07 0.16
Matches are distributed among these distances:
33 12 0.16
34 26 0.35
35 28 0.37
36 9 0.12
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (35 bp):
ATTATATTTTATATTTAAATTTTAATATATTAATA
Found at i:999900 original size:13 final size:13
Alignment explanation
Indices: 999882--999940 Score: 56
Period size: 13 Copynumber: 4.9 Consensus size: 13
999872 TATTTAAATA
999882 TTTATAATTATAT
1 TTTATAATTATAT
999895 TTTAT-ATTAT-T
1 TTTATAATTATAT
*
999906 TTT-TTA-TATA-
1 TTTATAATTATAT
*
999916 GTTATAATTATAT
1 TTTATAATTATAT
*
999929 ATTATAATTATA
1 TTTATAATTATA
999941 ATTATATATT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
10 6 0.16
11 7 0.18
12 9 0.24
13 16 0.42
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (13 bp):
TTTATAATTATAT
Found at i:999925 original size:34 final size:35
Alignment explanation
Indices: 999874--999939 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 35
999864 TATTTAAATA
* *
999874 TTTAAATATTTATAATTATATTTTAT-ATTATTTT
1 TTTAAATAGTTATAATTATATATTATAATTATTTT
*
999908 TTTATATAGTTATAATTATATATTATAATTAT
1 TTTAAATAGTTATAATTATATATTATAATTAT
999940 AATTATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 23 0.82
35 5 0.18
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (35 bp):
TTTAAATAGTTATAATTATATATTATAATTATTTT
Found at i:999939 original size:19 final size:19
Alignment explanation
Indices: 999883--999952 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
999873 ATTTAAATAT
*
999883 TTATAATTATATTTTAT-A
1 TTATAATTATATATTATAA
* * *
999901 TTAT--TTTTTTA-TATAG
1 TTATAATTATATATTATAA
999917 TTATAATTATATATTATAA
1 TTATAATTATATATTATAA
999936 TTATAATTATATATTAT
1 TTATAATTATATATTAT
999953 CCAAAATTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
15 3 0.07
16 8 0.20
18 9 0.22
19 21 0.51
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (19 bp):
TTATAATTATATATTATAA
Found at i:1000285 original size:15 final size:14
Alignment explanation
Indices: 1000261--1000291 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
1000251 TATATCAAAT
1000261 AAAATTATATATTA
1 AAAATTATATATTA
1000275 AAAATTCATATATTA
1 AAAATT-ATATATTA
1000290 AA
1 AA
1000292 TAATAACGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (14 bp):
AAAATTATATATTA
Found at i:1000808 original size:22 final size:23
Alignment explanation
Indices: 1000766--1000812 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1000756 TAGAATGTAA
*
1000766 ATAAAAAGATTATATATATTTGT
1 ATAAAAACATTATATATATTTGT
*
1000789 ATAAAAACATTATTTA-ATTTGT
1 ATAAAAACATTATATATATTTGT
1000811 AT
1 AT
1000813 TATATAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (23 bp):
ATAAAAACATTATATATATTTGT
Found at i:1001032 original size:14 final size:15
Alignment explanation
Indices: 1001015--1001052 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
1001005 TATAAAAATA
1001015 TTAATATAAT-TATT
1 TTAATATAATATATT
1001029 TTAATATTAATATATT
1 TTAATA-TAATATATT
1001045 TTAA-ATAA
1 TTAATATAA
1001053 AGAAATAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 9 0.41
15 5 0.23
16 8 0.36
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTAATATAATATATT
Found at i:1005891 original size:17 final size:18
Alignment explanation
Indices: 1005860--1005893 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1005850 TGGGTCTAAG
1005860 ATAATTTTCCTTAATAAA
1 ATAATTTTCCTTAATAAA
1005878 ATAATTTT-CTTAATAA
1 ATAATTTTCCTTAATAA
1005894 GATATTCACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (18 bp):
ATAATTTTCCTTAATAAA
Found at i:1005990 original size:20 final size:21
Alignment explanation
Indices: 1005954--1005993 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1005944 TAAATTTAAA
*
1005954 TTTAAAAATTTATTTTATTAT
1 TTTAAAAATATATTTTATTAT
1005975 TTTAAAAATATA-TTTATTA
1 TTTAAAAATATATTTTATTA
1005994 AATATATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTAAAAATATATTTTATTAT
Found at i:1012677 original size:19 final size:19
Alignment explanation
Indices: 1012626--1012677 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
1012616 CTGCAAATAC
* *
1012626 AAAAATAAAAAATAATAAA
1 AAAAAGAAAAAAAAATAAA
* * *
1012645 AAAAAGCAATAAAAATAGA
1 AAAAAGAAAAAAAAATAAA
*
1012664 AACAAGAAAAAAAA
1 AAAAAGAAAAAAAA
1012678 CACTAAATTT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.81, C:0.04, G:0.06, T:0.10
Consensus pattern (19 bp):
AAAAAGAAAAAAAAATAAA
Found at i:1020572 original size:16 final size:18
Alignment explanation
Indices: 1020536--1020572 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1020526 TGTTTAATTT
*
1020536 ATTTTATATTTATATAAA
1 ATTTTATATATATATAAA
1020554 ATTTTATATAT-TA-AAA
1 ATTTTATATATATATAAA
1020570 ATT
1 ATT
1020573 CATATTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 6 0.33
17 2 0.11
18 10 0.56
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTTATATATATATAAA
Found at i:1021115 original size:14 final size:14
Alignment explanation
Indices: 1021096--1021132 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1021086 GTAAAAAATT
*
1021096 TTTAAAATTTATGA
1 TTTAAAATTTATAA
1021110 TTTAAAATTT-TAA
1 TTTAAAATTTATAA
1021123 TTT-AAATTTA
1 TTTAAAATTTA
1021133 ATCAAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
12 6 0.29
13 5 0.24
14 10 0.48
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (14 bp):
TTTAAAATTTATAA
Found at i:1021127 original size:13 final size:13
Alignment explanation
Indices: 1021096--1021144 Score: 50
Period size: 14 Copynumber: 3.9 Consensus size: 13
1021086 GTAAAAAATT
*
1021096 TTTAAAATTTATGA
1 TTTAAAATTT-TAA
1021110 TTTAAAATTTTAA
1 TTTAAAATTTTAA
1021123 TTT-AAA-TTTAA
1 TTTAAAATTTTAA
*
1021134 -TCAAAATTTTA
1 TTTAAAATTTTA
1021145 TCTCAAGTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
10 1 0.03
11 8 0.26
12 7 0.23
13 5 0.16
14 10 0.32
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (13 bp):
TTTAAAATTTTAA
Found at i:1034102 original size:2 final size:2
Alignment explanation
Indices: 1034097--1034134 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1034087 AAGGTGTGTG
1034097 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
1034135 ATCCTCTTTA
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:1034592 original size:2 final size:2
Alignment explanation
Indices: 1034585--1034619 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1034575 CTTTGTAATT
1034585 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
1034620 TTCATTGCCT
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:1041924 original size:29 final size:28
Alignment explanation
Indices: 1041882--1041988 Score: 108
Period size: 29 Copynumber: 3.7 Consensus size: 28
1041872 GCCCATAAAG
* *
1041882 TTTAATTAGCACCCAGATAAGTCTTTACC
1 TTTAATTTGTACCCA-ATAAGTCTTTACC
1041911 TTTAATTTGTACCCAACTAAGTCTTTACC
1 TTTAATTTGTACCCAA-TAAGTCTTTACC
* *
1041940 TTTAACTTT-TACCCAAATAAGCCCTTAACC
1 TTTAA-TTTGTACCC-AATAAG-TCTTTACC
* *
1041970 TTTAATTTTTACCAAATAA
1 TTTAATTTGTACCCAATAA
1041989 ACCCTTAACA
Statistics
Matches: 68, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
28 1 0.01
29 47 0.69
30 20 0.29
ACGTcount: A:0.33, C:0.23, G:0.06, T:0.38
Consensus pattern (28 bp):
TTTAATTTGTACCCAATAAGTCTTTACC
Found at i:1041973 original size:30 final size:29
Alignment explanation
Indices: 1041862--1041997 Score: 107
Period size: 29 Copynumber: 4.7 Consensus size: 29
1041852 CCCTTACTGC
* ** **
1041862 ACCCAAATAAGCCCATAAAGTTTAATTAGC
1 ACCCAAATAAGCCCTTAACCTTTAATT-TT
* * *
1041892 ACCCAGATAAG-TCTTTACCTTTAATTTGT
1 ACCCAAATAAGCCCTTAACCTTTAATTT-T
* * *
1041921 ACCCAACTAAG-TCTTTACCTTTAACTTTT
1 ACCCAAATAAGCCCTTAACCTTTAA-TTTT
1041950 ACCCAAATAAGCCCTTAACCTTTAATTTTT
1 ACCCAAATAAGCCCTTAACCTTTAA-TTTT
*
1041980 A-CCAAATAAACCCTTAAC
1 ACCCAAATAAGCCCTTAAC
1041998 ATTAATAAAT
Statistics
Matches: 88, Mismatches: 15, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
29 59 0.67
30 29 0.33
ACGTcount: A:0.35, C:0.26, G:0.06, T:0.33
Consensus pattern (29 bp):
ACCCAAATAAGCCCTTAACCTTTAATTTT
Found at i:1042781 original size:60 final size:60
Alignment explanation
Indices: 1042688--1042804 Score: 198
Period size: 60 Copynumber: 1.9 Consensus size: 60
1042678 AAGAATCCTC
1042688 ACATCCTAGAAGAAAATGTTATTCCTTGCATCTTCAGCTATTATTTCAAAATTTAGCGAT
1 ACATCCTAGAAGAAAATGTTATTCCTTGCATCTTCAGCTATTATTTCAAAATTTAGCGAT
** * *
1042748 ACATCCTAGAAGATGATGTTATTCTTTGCATCTTCATCTATTATTTCAAAATTTAGC
1 ACATCCTAGAAGAAAATGTTATTCCTTGCATCTTCAGCTATTATTTCAAAATTTAGC
1042805 AACTCAATTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (60 bp):
ACATCCTAGAAGAAAATGTTATTCCTTGCATCTTCAGCTATTATTTCAAAATTTAGCGAT
Found at i:1058210 original size:2 final size:2
Alignment explanation
Indices: 1058203--1058237 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1058193 CTGGGGTAGC
1058203 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
1058238 CACATATGTA
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:1058936 original size:28 final size:28
Alignment explanation
Indices: 1058905--1058959 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
1058895 CTACATATTT
1058905 ATTAA-CTAAATATTTATTTCATAAAATA
1 ATTAATCTAAA-ATTTATTTCATAAAATA
* * *
1058933 ATTAATTTTAAATTTATTTTATAAAAT
1 ATTAATCTAAAATTTATTTCATAAAAT
1058960 TTTAGAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 20 0.87
29 3 0.13
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (28 bp):
ATTAATCTAAAATTTATTTCATAAAATA
Found at i:1059038 original size:5 final size:5
Alignment explanation
Indices: 1059028--1059105 Score: 50
Period size: 5 Copynumber: 15.2 Consensus size: 5
1059018 AATTTTAAAA
* * * * * *
1059028 TATTT TATTT TATTA AATTA AATTAT TATTA TAATT -ATTT TATTT TATTT
1 TATTT TATTT TATTT TATTT TATT-T TATTT TATTT TATTT TATTT TATTT
* *
1059078 TATAAT TATTT TATTAT AATTT TATTT T
1 TAT-TT TATTT TATT-T TATTT TATTT T
1059106 CCCCTAATTT
Statistics
Matches: 57, Mismatches: 12, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
4 3 0.05
5 43 0.75
6 11 0.19
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (5 bp):
TATTT
Found at i:1059067 original size:35 final size:32
Alignment explanation
Indices: 1059019--1059105 Score: 97
Period size: 32 Copynumber: 2.7 Consensus size: 32
1059009 AAAAATTTAA
*
1059019 ATTTTA-AAATATTTTATTTTATTAAATTA-AATT
1 ATTTTATAATTATTTTATTTTATT---TTATAATT
1059052 ATTATTATAATTATTTTATTTTATTTTATAATT
1 ATT-TTATAATTATTTTATTTTATTTTATAATT
* *
1059085 ATTTTATTATAATTTTATTTT
1 ATTTTATAATTATTTTATTTT
1059106 CCCCTAATTT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
32 19 0.40
33 10 0.21
34 3 0.06
35 16 0.33
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (32 bp):
ATTTTATAATTATTTTATTTTATTTTATAATT
Found at i:1059082 original size:21 final size:22
Alignment explanation
Indices: 1059049--1059102 Score: 83
Period size: 21 Copynumber: 2.5 Consensus size: 22
1059039 ATTAAATTAA
1059049 ATTATTATTATAATTATTTTATT
1 ATTATT-TTATAATTATTTTATT
1059072 -TTATTTTATAATTATTTTATT
1 ATTATTTTATAATTATTTTATT
*
1059093 ATAATTTTAT
1 ATTATTTTAT
1059103 TTTCCCCTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 16 0.55
22 13 0.45
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
ATTATTTTATAATTATTTTATT
Found at i:1059103 original size:11 final size:11
Alignment explanation
Indices: 1059049--1059103 Score: 67
Period size: 11 Copynumber: 5.0 Consensus size: 11
1059039 ATTAAATTAA
*
1059049 ATTATTATTATA
1 ATTATT-TTATT
1059061 ATTATTTTATT
1 ATTATTTTATT
*
1059072 -TTATTTTATA
1 ATTATTTTATT
1059082 ATTATTTTATT
1 ATTATTTTATT
*
1059093 ATAATTTTATT
1 ATTATTTTATT
1059104 TTCCCCTAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
10 9 0.24
11 23 0.61
12 6 0.16
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
ATTATTTTATT
Found at i:1060776 original size:20 final size:20
Alignment explanation
Indices: 1060751--1060788 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1060741 AAAATTATCG
*
1060751 ATTATTATATTTAATATAAC
1 ATTATTATAATTAATATAAC
1060771 ATTATTATAATTAATATA
1 ATTATTATAATTAATATA
1060789 TTATTTACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTATTATAATTAATATAAC
Found at i:1063469 original size:21 final size:22
Alignment explanation
Indices: 1063445--1063488 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1063435 TTTTTAGTTT
* *
1063445 TATATATAAAATAATA-AATTA
1 TATAAATAAAATAAAATAATTA
1063466 TATAAATAAAATAAAATAATTA
1 TATAAATAAAATAAAATAATTA
1063488 T
1 T
1063489 TAAGTTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
TATAAATAAAATAAAATAATTA
Found at i:1063981 original size:20 final size:21
Alignment explanation
Indices: 1063956--1064006 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1063946 ATTTAAATAT
*
1063956 TTATAAT-TTTTTATTTTAAA
1 TTATAATATTTTTATATTAAA
1063976 TTATAATATTTTTATATTAAA
1 TTATAATATTTTTATATTAAA
*
1063997 -AATAATATTT
1 TTATAATATTT
1064007 AAAATTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTATAATATTTTTATATTAAA
Found at i:1063999 original size:23 final size:20
Alignment explanation
Indices: 1063946--1063997 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 20
1063936 TAAATTTTAA
1063946 ATTTAAATATTTATAATTTTTT
1 ATTTAAA-A-TTATAATTTTTT
*
1063968 ATTTTAAATTATAATATTTTT
1 ATTTAAAATTATAAT-TTTTT
1063989 ATATTAAAA
1 AT-TTAAAA
1063998 ATAATATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 7 0.27
21 8 0.31
22 11 0.42
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTTAAAATTATAATTTTTT
Found at i:1064996 original size:35 final size:37
Alignment explanation
Indices: 1064933--1065027 Score: 101
Period size: 33 Copynumber: 2.6 Consensus size: 37
1064923 ATTATATAAA
*
1064933 TTTTAAAATATTTATATATTA-A-TCTTATATCAT-T
1 TTTTAAAATATTTATATATTATATTCTTATAACATAT
*
1064967 TTTTAAAAT-TTTATATATTATATTTTTATAACATAT
1 TTTTAAAATATTTATATATTATATTCTTATAACATAT
* *
1065003 TTTCAAATCATGTTTA-ATATTATAT
1 TTTTAAA--ATATTTATATATTATAT
1065028 CTAGTTGTAA
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
33 11 0.21
34 10 0.19
35 9 0.17
36 7 0.13
38 11 0.21
39 4 0.08
ACGTcount: A:0.38, C:0.05, G:0.01, T:0.56
Consensus pattern (37 bp):
TTTTAAAATATTTATATATTATATTCTTATAACATAT
Found at i:1066787 original size:3 final size:3
Alignment explanation
Indices: 1066779--1066813 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1066769 CCTGTGAATG
1066779 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1066814 ATGGCTAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1067109 original size:22 final size:19
Alignment explanation
Indices: 1067057--1067095 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1067047 AATATACTAC
1067057 TCTTAAAAATTATTCATTT
1 TCTTAAAAATTATTCATTT
1067076 TCTTAAAAATTATTCATTT
1 TCTTAAAAATTATTCATTT
1067095 T
1 T
1067096 TTGTTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.54
Consensus pattern (19 bp):
TCTTAAAAATTATTCATTT
Found at i:1067542 original size:2 final size:2
Alignment explanation
Indices: 1067491--1067524 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1067481 GGCTATTTAC
1067491 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
1067525 GAGTAGATAT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1068004 original size:3 final size:3
Alignment explanation
Indices: 1067996--1068028 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
1067986 TATAGATGTA
*
1067996 TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1068029 CAAGATATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1068961 original size:15 final size:15
Alignment explanation
Indices: 1068937--1069003 Score: 66
Period size: 15 Copynumber: 4.5 Consensus size: 15
1068927 TTCTATTTGA
1068937 TAATATTAAATATAAT
1 TAATA-TAAATATAAT
*
1068953 TTATATAAATATAAT
1 TAATATAAATATAAT
*
1068968 AAATATAAA-ATAAT
1 TAATATAAATATAAT
* *
1068982 TAAAATATAATATTAT
1 TAATATA-AATATAAT
1068998 T-ATATA
1 TAATATA
1069004 TTTTAAAATT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
14 10 0.24
15 23 0.55
16 9 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TAATATAAATATAAT
Found at i:1069021 original size:40 final size:37
Alignment explanation
Indices: 1068976--1069070 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 37
1068966 ATAAATATAA
1068976 AATAATTAAAATATAATATTATTATATATTTTAAAATTTAT
1 AATAATTAAAATATAATATTA--ATATA--TTAAAATTTAT
1069017 -ATAA-TAAAA-AT--TATTAATATATTAAAATTTAT
1 AATAATTAAAATATAATATTAATATATTAAAATTTAT
1069049 AAATAAATATAAAATATAATAT
1 -AAT-AAT-TAAAATATAATAT
1069071 AGTATTTGGA
Statistics
Matches: 46, Mismatches: 0, Indels: 17
0.73 0.00 0.27
Matches are distributed among these distances:
32 11 0.24
34 7 0.15
35 2 0.04
36 5 0.11
37 5 0.11
38 4 0.09
39 5 0.11
40 7 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (37 bp):
AATAATTAAAATATAATATTAATATATTAAAATTTAT
Found at i:1069036 original size:18 final size:18
Alignment explanation
Indices: 1069015--1069071 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
1069005 TTTAAAATTT
1069015 ATATAATAAAAATTATTA
1 ATATAATAAAAATTATTA
* * *
1069033 ATATATTAAAATTTATAA
1 ATATAATAAAAATTATTA
1069051 ATA-AATATAAAA-TA-TA
1 ATATAATA-AAAATTATTA
1069067 ATATA
1 ATATA
1069072 GTATTTGGAG
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
16 4 0.13
17 6 0.19
18 21 0.68
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATAATAAAAATTATTA
Found at i:1069047 original size:32 final size:32
Alignment explanation
Indices: 1068984--1069055 Score: 101
Period size: 32 Copynumber: 2.2 Consensus size: 32
1068974 AAAATAATTA
* *
1068984 AAATATAATATTATTATATATTTTAAAATTTAT
1 AAATA-AAAATTATTATATATATTAAAATTTAT
1069017 ATAATAAAAATTATTA-ATATATTAAAATTTAT
1 A-AATAAAAATTATTATATATATTAAAATTTAT
1069049 AAATAAA
1 AAATAAA
1069056 TATAAAATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
31 6 0.17
32 16 0.44
33 10 0.28
34 4 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (32 bp):
AAATAAAAATTATTATATATATTAAAATTTAT
Found at i:1070070 original size:2 final size:2
Alignment explanation
Indices: 1070063--1070097 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1070053 AAAAGGAGTG
*
1070063 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1070098 ACATTTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Done.