Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168270.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_5, whole genome shotgun sequence
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: 27802247
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 124000 characters in sequence are not A, C, G, or T
File 6 of 147
Found at i:1061611 original size:28 final size:29
Alignment explanation
Indices: 1061579--1061640 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
1061569 ATTAAAATTA
** *
1061579 TTATTT-ACAATTTAAATTTTATCGATAC
1 TTATTTAACAATAAAAATTTTATCAATAC
*
1061607 TTATTTAACGATAAAAATTTTATCAATAC
1 TTATTTAACAATAAAAATTTTATCAATAC
1061636 TTATT
1 TTATT
1061641 AAAAATGTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 6 0.21
29 23 0.79
ACGTcount: A:0.39, C:0.10, G:0.03, T:0.48
Consensus pattern (29 bp):
TTATTTAACAATAAAAATTTTATCAATAC
Found at i:1063472 original size:19 final size:19
Alignment explanation
Indices: 1063444--1063487 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
1063434 TATATATATA
1063444 TTCG-TTCATTCGCCTATG
1 TTCGATTCATTCGCCTATG
1063462 TTCGATTCATTCGCCTATG
1 TTCGATTCATTCGCCTATG
1063481 TTCGATT
1 TTCGATT
1063488 TATCTACGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.14, C:0.25, G:0.16, T:0.45
Consensus pattern (19 bp):
TTCGATTCATTCGCCTATG
Found at i:1064231 original size:18 final size:18
Alignment explanation
Indices: 1064210--1064252 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
1064200 TAAATATGAA
1064210 ATATATATTTTTAAATTT
1 ATATATATTTTTAAATTT
*
1064228 ATATAATTTTTTTAAATTT
1 ATAT-ATATTTTTAAATTT
1064247 -TATATA
1 ATATATA
1064253 ATACCATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 7 0.32
19 13 0.59
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATATATATTTTTAAATTT
Found at i:1064241 original size:19 final size:20
Alignment explanation
Indices: 1064217--1064254 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1064207 GAAATATATA
1064217 TTTTTAAA-TTTATATAATT
1 TTTTTAAATTTTATATAATT
1064236 TTTTTAAATTTTATATAAT
1 TTTTTAAATTTTATATAAT
1064255 ACCATTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTTAAATTTTATATAATT
Found at i:1064603 original size:15 final size:13
Alignment explanation
Indices: 1064555--1064603 Score: 64
Period size: 13 Copynumber: 3.7 Consensus size: 13
1064545 AAAGATACGA
1064555 TAAAAAT-TTTAT
1 TAAAAATATTTAT
*
1064567 TAAAAATTTTTAT
1 TAAAAATATTTAT
1064580 TAAAAATATTTAT
1 TAAAAATATTTAT
1064593 CTAAAACATAT
1 -TAAAA-ATAT
1064604 ATGAAAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
12 7 0.21
13 17 0.52
14 5 0.15
15 4 0.12
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (13 bp):
TAAAAATATTTAT
Found at i:1068303 original size:6 final size:6
Alignment explanation
Indices: 1068292--1068327 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
1068282 AATTGGGTAT
* *
1068292 ATTTTC ATTTTC ATTTTC ATTTCC ATTTCC ATTTTC
1 ATTTTC ATTTTC ATTTTC ATTTTC ATTTTC ATTTTC
1068328 TATAGTACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.17, C:0.22, G:0.00, T:0.61
Consensus pattern (6 bp):
ATTTTC
Found at i:1073999 original size:23 final size:23
Alignment explanation
Indices: 1073973--1074026 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
1073963 TTTTCTTGAC
*
1073973 ATTACATTTTCTAGTTGTATTTT
1 ATTACATTTTCTAGTTGTATTAT
* *
1073996 ATTATATTTTCTAGTTTTATTAT
1 ATTACATTTTCTAGTTGTATTAT
1074019 ACTTACAT
1 A-TTACAT
1074027 CCATGAAAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.26, C:0.09, G:0.06, T:0.59
Consensus pattern (23 bp):
ATTACATTTTCTAGTTGTATTAT
Found at i:1074853 original size:109 final size:109
Alignment explanation
Indices: 1074662--1074879 Score: 427
Period size: 109 Copynumber: 2.0 Consensus size: 109
1074652 GCAAGTAATC
1074662 ACAAAAGTAATTAACTCTACTGTAGCTGAATATGTTGAAAAGGTAAGCAGTTATCACTCTCGTGT
1 ACAAAAGTAATTAACTCTACTGTAGCTGAATATGTTGAAAAGGTAAGCAGTTATCACTCTCGTGT
1074727 TACCATACATGTTAAGCTCGTATAAGTGTTTAAATTGGTTTGAA
66 TACCATACATGTTAAGCTCGTATAAGTGTTTAAATTGGTTTGAA
*
1074771 ACAAAAGTAATTAACTCTATTGTAGCTGAATATGTTGAAAAGGTAAGCAGTTATCACTCTCGTGT
1 ACAAAAGTAATTAACTCTACTGTAGCTGAATATGTTGAAAAGGTAAGCAGTTATCACTCTCGTGT
1074836 TACCATACATGTTAAGCTCGTATAAGTGTTTAAATTGGTTTGAA
66 TACCATACATGTTAAGCTCGTATAAGTGTTTAAATTGGTTTGAA
1074880 TTTGTATGTT
Statistics
Matches: 108, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
109 108 1.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.34
Consensus pattern (109 bp):
ACAAAAGTAATTAACTCTACTGTAGCTGAATATGTTGAAAAGGTAAGCAGTTATCACTCTCGTGT
TACCATACATGTTAAGCTCGTATAAGTGTTTAAATTGGTTTGAA
Found at i:1078168 original size:2 final size:2
Alignment explanation
Indices: 1078161--1078217 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
1078151 GTCAATGCAC
1078161 TA TA 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 TA TA
1078203 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
1078218 TGATAAGGTG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1084010 original size:128 final size:127
Alignment explanation
Indices: 1083782--1084147 Score: 575
Period size: 122 Copynumber: 2.9 Consensus size: 127
1083772 CAACAAAAAG
1083782 TCTTTGCCTCAATGATGTGTTCCCATTTGGGTCTTGCCAAAAACCTTGAAATAATAGATGATTGG
1 TCTTTGCCTCAATGATGTGTTCCCATTT-GGTCTTGCCAAAAACCTTGAAATAATAGATGATTGG
1083847 TCATTGCTAGCCAATATGATCAAAGGCAAAAGAATCCTCTTAGCTTATTGTCCATGTTAAATT
65 TCATTGCTAGCCAATATGATCAAAGGCAAAAGAATCCTCTTAGCTTATTGTCCATGTTAAATT
1083910 TCTTTGCCTCAATGATGTGTTCCCATTTGGATCTTGCCAAAAACCTTGAAATAATAGATGATTGG
1 TCTTTGCCTCAATGATGTGTTCCCATTTGG-TCTTGCCAAAAACCTTGAAATAATAGATGATTGG
* * * *
1083975 TCATGGAC-AGCTAATATAATCAAAGGCAAAAGAATCCTCTTAGC------TCCATGTTAATTT
65 TCATTG-CTAGCCAATATGATCAAAGGCAAAAGAATCCTCTTAGCTTATTGTCCATGTTAAATT
*
1084032 TCTTTGCCTCAATGATGTGTTCCCATTTCGGTGTTGCCAAAAACCTTGAAATAATAGATGATTGG
1 TCTTTGCCTCAATGATGTGTTCCCATTT-GGTCTTGCCAAAAACCTTGAAATAATAGATGATTGG
* * *
1084097 TCATTGCTAGCCAATATGATCGAAGGCAAAAGAATTCTGTTAGCTTATTGT
65 TCATTGCTAGCCAATATGATCAAAGGCAAAAGAATCCTCTTAGCTTATTGT
1084148 TCATATCATG
Statistics
Matches: 217, Mismatches: 11, Indels: 20
0.88 0.04 0.08
Matches are distributed among these distances:
121 1 0.00
122 109 0.50
123 2 0.01
127 2 0.01
128 102 0.47
129 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (127 bp):
TCTTTGCCTCAATGATGTGTTCCCATTTGGTCTTGCCAAAAACCTTGAAATAATAGATGATTGGT
CATTGCTAGCCAATATGATCAAAGGCAAAAGAATCCTCTTAGCTTATTGTCCATGTTAAATT
Found at i:1084417 original size:27 final size:27
Alignment explanation
Indices: 1084387--1084439 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
1084377 AGATTTTTCA
*
1084387 GAAAAGTAAAAATAAAAATAAAAAAAG
1 GAAAAGTAAAAATAAAAAGAAAAAAAG
** *
1084414 GAAATTTAAAAATAATAAGAAAAAAA
1 GAAAAGTAAAAATAAAAAGAAAAAAA
1084440 ATCTTGTGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.75, C:0.00, G:0.09, T:0.15
Consensus pattern (27 bp):
GAAAAGTAAAAATAAAAAGAAAAAAAG
Found at i:1088716 original size:18 final size:18
Alignment explanation
Indices: 1088689--1088739 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
1088679 TGTATTTGTT
*
1088689 TTTTAATATAAATTATAA
1 TTTTATTATAAATTATAA
* *
1088707 TTTTATTATATATAAATAA
1 TTTTATTATAAAT-TATAA
*
1088726 TTTT-TTTTAAATTA
1 TTTTATTATAAATTA
1088740 AGATATTAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
17 1 0.04
18 17 0.65
19 8 0.31
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTATTATAAATTATAA
Found at i:1089138 original size:16 final size:18
Alignment explanation
Indices: 1089106--1089143 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
1089096 TATTTTTTAA
*
1089106 ATAAAATATATATAAAT-
1 ATAAAATATAAATAAATG
1089123 ATAAAA-ATAAATAAATG
1 ATAAAATATAAATAAATG
1089140 ATAA
1 ATAA
1089144 TTATATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (18 bp):
ATAAAATATAAATAAATG
Found at i:1089143 original size:23 final size:23
Alignment explanation
Indices: 1089104--1089148 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1089094 AATATTTTTT
*
1089104 AAATAAAATATATATAAATATAA
1 AAATAAAATAAATATAAATATAA
*
1089127 AAAT-AAATAAATGATAATTATA
1 AAATAAAATAAAT-ATAAATATA
1089149 TATTTTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (23 bp):
AAATAAAATAAATATAAATATAA
Found at i:1091776 original size:17 final size:18
Alignment explanation
Indices: 1091745--1091779 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1091735 ATATTCATAA
*
1091745 AAAATATTATTTTTTAAT
1 AAAATATTATGTTTTAAT
1091763 AAAA-ATTATGTTTTAAT
1 AAAATATTATGTTTTAAT
1091780 TATATACAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
AAAATATTATGTTTTAAT
Found at i:1092495 original size:2 final size:2
Alignment explanation
Indices: 1092488--1092521 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1092478 CACTGAGTAT
* *
1092488 TA TA TA TA TA TA TA TA TA TA TT TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1092522 AGTTGGCAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:1092525 original size:121 final size:122
Alignment explanation
Indices: 1092374--1092609 Score: 386
Period size: 121 Copynumber: 1.9 Consensus size: 122
1092364 CACACACAAA
*
1092374 ATATATATATATATATATATGTATGGAAGTTGGCAGAGCTGCATATTATATATCTTCTACATAAA
1 ATATATATATATATATATATGTATAGAAGTTGGCAGAGCTGCATATTATATATCTTCTACATAAA
1092439 AGAAGAAAATAAAAA-A-AAACTATAATAAATTAATAATAACACTGAGTATTATATAT
66 AGAAGAAAATAAAAATATAAA-TATAATAAATTAATAATAACACTGAGTATTATATAT
* * * * *
1092495 ATATATATATATATTTATATTTATATAAGTTGGCAGAGCTGCATGTTATATATCTTCTACATGAA
1 ATATATATATATATATATATGTATAGAAGTTGGCAGAGCTGCATATTATATATCTTCTACATAAA
*
1092560 AGAAGAAAATAAAAATATATATATAATAAATTAATAATAACACTGAGTAT
66 AGAAGAAAATAAAAATATAAATATAATAAATTAATAATAACACTGAGTAT
1092610 ACTTTCTTCT
Statistics
Matches: 106, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
121 74 0.70
122 30 0.28
123 2 0.02
ACGTcount: A:0.47, C:0.07, G:0.11, T:0.35
Consensus pattern (122 bp):
ATATATATATATATATATATGTATAGAAGTTGGCAGAGCTGCATATTATATATCTTCTACATAAA
AGAAGAAAATAAAAATATAAATATAATAAATTAATAATAACACTGAGTATTATATAT
Found at i:1104252 original size:52 final size:52
Alignment explanation
Indices: 1104174--1104276 Score: 206
Period size: 52 Copynumber: 2.0 Consensus size: 52
1104164 AGCATGGTAC
1104174 TAATAATTATAATAATAATAAAATTAAAATCAATGATAAAATATATATTTAT
1 TAATAATTATAATAATAATAAAATTAAAATCAATGATAAAATATATATTTAT
1104226 TAATAATTATAATAATAATAAAATTAAAATCAATGATAAAATATATATTTA
1 TAATAATTATAATAATAATAAAATTAAAATCAATGATAAAATATATATTTA
1104277 AATATAAACG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (52 bp):
TAATAATTATAATAATAATAAAATTAAAATCAATGATAAAATATATATTTAT
Found at i:1118736 original size:20 final size:20
Alignment explanation
Indices: 1118698--1118741 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1118688 TTAAAATAAA
*
1118698 TTATATATTTTTATTAATTT
1 TTATATATTTTTATAAATTT
*
1118718 TTATATATTTTT-TAAAATT
1 TTATATATTTTTATAAATTT
1118737 TTATA
1 TTATA
1118742 AATAAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTATATATTTTTATAAATTT
Found at i:1118806 original size:11 final size:12
Alignment explanation
Indices: 1118766--1118817 Score: 61
Period size: 12 Copynumber: 4.3 Consensus size: 12
1118756 TCTTATTTTT
1118766 AAATATATTAAA
1 AAATATATTAAA
*
1118778 AATTATATTAAA
1 AAATATATTAAA
1118790 ATAATATA-TAAA
1 A-AATATATTAAA
* *
1118802 AAATAAATTAAT
1 AAATATATTAAA
1118814 AAAT
1 AAAT
1118818 TGAACCAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
11 5 0.15
12 24 0.71
13 5 0.15
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
AAATATATTAAA
Found at i:1121536 original size:6 final size:6
Alignment explanation
Indices: 1121525--1121549 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1121515 TCAAATTAAA
1121525 TTTATT TTTATT TTTATT TTTATT T
1 TTTATT TTTATT TTTATT TTTATT T
1121550 ATTAAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTATT
Found at i:1122301 original size:16 final size:15
Alignment explanation
Indices: 1122275--1122307 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
1122265 ATCTTCTTAC
1122275 TTTTTATTTATATTA
1 TTTTTATTTATATTA
1122290 TTTTTATATTATATTA
1 TTTTTAT-TTATATTA
1122306 TT
1 TT
1122308 GTATCATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTTATTTATATTA
Found at i:1122613 original size:16 final size:15
Alignment explanation
Indices: 1122587--1122616 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1122577 AAGTATAAAG
1122587 TAAAATAAATTATTA
1 TAAAATAAATTATTA
1122602 TAAAACTAAATTATT
1 TAAAA-TAAATTATT
1122617 GGATTAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (15 bp):
TAAAATAAATTATTA
Found at i:1128200 original size:17 final size:18
Alignment explanation
Indices: 1128178--1128225 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
1128168 GTTTTGTTTG
*
1128178 AGAAAATATTGCAGA-AA
1 AGAAAATATTGAAGAGAA
1128195 AGAAAAT-TTGAAGAGAA
1 AGAAAATATTGAAGAGAA
1128212 ATG-AAATATTGAAG
1 A-GAAAATATTGAAG
1128226 CACTTTGCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 6 0.22
17 14 0.52
18 7 0.26
ACGTcount: A:0.56, C:0.02, G:0.21, T:0.21
Consensus pattern (18 bp):
AGAAAATATTGAAGAGAA
Found at i:1137654 original size:30 final size:30
Alignment explanation
Indices: 1137618--1137675 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
1137608 ACAATCAGAA
* *
1137618 AGTAGAATTAGATTGTAAACTTCTATGAAT
1 AGTAGAATTAGATCGTAAAATTCTATGAAT
*
1137648 AGTAGAATTGGATCGTAAAATTCTATGA
1 AGTAGAATTAGATCGTAAAATTCTATGA
1137676 TCCTATCAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.34
Consensus pattern (30 bp):
AGTAGAATTAGATCGTAAAATTCTATGAAT
Found at i:1142557 original size:14 final size:14
Alignment explanation
Indices: 1142529--1142570 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
1142519 CAACATTGAC
*
1142529 AAAC-AAGAGAGAA
1 AAACAAAGAAAGAA
1142542 AAACAAAG-AAGAA
1 AAACAAAGAAAGAA
*
1142555 AAACAGAGAAAGAA
1 AAACAAAGAAAGAA
1142569 AA
1 AA
1142571 GTAAAGTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 15 0.60
14 10 0.40
ACGTcount: A:0.74, C:0.07, G:0.19, T:0.00
Consensus pattern (14 bp):
AAACAAAGAAAGAA
Found at i:1142980 original size:11 final size:11
Alignment explanation
Indices: 1142949--1143117 Score: 54
Period size: 10 Copynumber: 15.9 Consensus size: 11
1142939 ATACGACTAA
**
1142949 ATTTATTTAAA
1 ATTTATTTATT
1142960 ATTTATTTATT
1 ATTTATTTATT
1142971 ATTTATTTA-T
1 ATTTATTTATT
* * *
1142981 AATAATAATATT
1 ATTTAT-TTATT
*
1142993 ATTATATTTTTT
1 ATT-TATTTATT
*
1143005 ATTT-TTAATT
1 ATTTATTTATT
* *
1143015 ATAT-TTTA-A
1 ATTTATTTATT
1143024 AGTTTATTTA-T
1 A-TTTATTTATT
* *
1143035 ATTCATTTAAT
1 ATTTATTTATT
*
1143046 ATTTATTTGTT
1 ATTTATTTATT
*
1143057 -TATATTTA-T
1 ATTTATTTATT
*
1143066 -TTTA-TTATA
1 ATTTATTTATT
* *
1143075 ATTTATTAAAT
1 ATTTATTTATT
*
1143086 ATTTATAAATATT
1 ATTTAT--TTATT
1143099 -TTTATTTA-T
1 ATTTATTTATT
*
1143108 ATATATTTAT
1 ATTTATTTAT
1143118 GAATATATTC
Statistics
Matches: 113, Mismatches: 32, Indels: 26
0.66 0.19 0.15
Matches are distributed among these distances:
8 3 0.03
9 6 0.05
10 43 0.38
11 43 0.38
12 14 0.12
13 4 0.04
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.63
Consensus pattern (11 bp):
ATTTATTTATT
Found at i:1143094 original size:10 final size:10
Alignment explanation
Indices: 1143075--1143145 Score: 51
Period size: 10 Copynumber: 7.1 Consensus size: 10
1143065 TTTTATTATA
1143075 ATTTATTAAAT
1 ATTTA-TAAAT
1143086 ATTTATAAAT
1 ATTTATAAAT
1143096 ATTT-T---T
1 ATTTATAAAT
*
1143102 ATTTATATAT
1 ATTTATAAAT
1143112 ATTTATGAATAT
1 ATTTAT-AA-AT
* *
1143124 ATTCATTTAAT
1 ATTTA-TAAAT
1143135 ATTTATAAAT
1 ATTTATAAAT
1143145 A
1 A
1143146 AATTCGTTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 15
0.71 0.07 0.22
Matches are distributed among these distances:
6 5 0.10
7 1 0.02
9 1 0.02
10 21 0.44
11 12 0.25
12 7 0.15
13 1 0.02
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (10 bp):
ATTTATAAAT
Found at i:1143106 original size:16 final size:16
Alignment explanation
Indices: 1143085--1143115 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1143075 ATTTATTAAA
1143085 TATTTATAAATATTTT
1 TATTTATAAATATTTT
*
1143101 TATTTATATATATTT
1 TATTTATAAATATTT
1143116 ATGAATATAT
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTTATAAATATTTT
Found at i:1143116 original size:14 final size:14
Alignment explanation
Indices: 1143044--1143117 Score: 52
Period size: 14 Copynumber: 5.6 Consensus size: 14
1143034 TATTCATTTA
* *
1143044 ATATTTATTTGTTT
1 ATATTTATTTATAT
1143058 ATATTTATTT-TATT
1 ATATTTATTTATA-T
1143072 ATAATTTA-TTA-A-
1 AT-ATTTATTTATAT
*
1143084 ATATTTA--TAAAT
1 ATATTTATTTATAT
*
1143096 ATTTTTATTTATAT
1 ATATTTATTTATAT
1143110 ATATTTAT
1 ATATTTAT
1143118 GAATATATTC
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
10 2 0.04
11 6 0.12
12 8 0.16
13 1 0.02
14 27 0.55
15 5 0.10
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (14 bp):
ATATTTATTTATAT
Found at i:1143968 original size:17 final size:18
Alignment explanation
Indices: 1143932--1143969 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1143922 TATATAATTT
* *
1143932 AAATAAAATTTTTAATAA
1 AAATAAAATTATTAAAAA
1143950 AAATAAAA-TATTAAAAA
1 AAATAAAATTATTAAAAA
1143967 AAA
1 AAA
1143970 CCAAATTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATAAAATTATTAAAAA
Found at i:1144063 original size:21 final size:21
Alignment explanation
Indices: 1144023--1144080 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 21
1144013 ATAATAATTT
*
1144023 TATATTAAAAT-TTATTTAAA
1 TATATTAAAATATTATATAAA
1144043 TATATTAAAATATTATAT-AA
1 TATATTAAAATATTATATAAA
1144063 -ATATTAAAA-ATTA-ATAAA
1 TATATTAAAATATTATATAAA
1144081 CTAAATCGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
17 2 0.06
18 6 0.17
19 9 0.26
20 13 0.37
21 5 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TATATTAAAATATTATATAAA
Found at i:1149522 original size:58 final size:59
Alignment explanation
Indices: 1149428--1149692 Score: 327
Period size: 58 Copynumber: 4.3 Consensus size: 59
1149418 TTTTTCTCTT
** * *
1149428 TTTGGGTTTTTTTTTTTTTTGTGTTTGGTAGTTGAGAAAATGCTAGTAAAGGAACGAAA
1 TTTGGGTGGTTTTTTTTTTTGTGTTTGGTAGCTGAGAAAATGCTAGTAAAGGAAGGAAA
*
1149487 TTTGGGTGG-ATTTTTTTTTGTGTTTGGTAGCTGAGAAAATGCTAGTAAAGGAA-GAAA
1 TTTGGGTGGTTTTTTTTTTTGTGTTTGGTAGCTGAGAAAATGCTAGTAAAGGAAGGAAA
* * *
1149544 TTTTGGGTGGGTTTCCTTTTTTTTTGTGTGTTTGGTGGCTGATAAAATGCTGGTAAAGGAAGGAA
1 -TTTGGGT-GG--T--TTTTTTTTT-TGTGTTTGGTAGCTGAGAAAATGCTAGTAAAGGAAGGAA
1149609 A
59 A
* *
1149610 CTTGGGTGGCTTTTTTTTTTTGTGTTTGGTAGCTGAGAAAATGCTGGTAAAGGAAGGAAA
1 TTTGGGTGG-TTTTTTTTTTTGTGTTTGGTAGCTGAGAAAATGCTAGTAAAGGAAGGAAA
1149670 TTTGGGTGGGCTTTTTCTTTTTT
1 TTTGGGT-GG-TTTTT-TTTTTT
1149693 TGGTGGTTTT
Statistics
Matches: 182, Mismatches: 13, Indels: 19
0.85 0.06 0.09
Matches are distributed among these distances:
57 4 0.02
58 49 0.27
59 9 0.05
60 44 0.24
61 17 0.09
62 6 0.03
63 1 0.01
64 10 0.05
65 38 0.21
66 4 0.02
ACGTcount: A:0.22, C:0.05, G:0.29, T:0.43
Consensus pattern (59 bp):
TTTGGGTGGTTTTTTTTTTTGTGTTTGGTAGCTGAGAAAATGCTAGTAAAGGAAGGAAA
Found at i:1149652 original size:60 final size:61
Alignment explanation
Indices: 1149437--1149692 Score: 342
Period size: 60 Copynumber: 4.2 Consensus size: 61
1149427 TTTTGGGTTT
* *
1149437 TTTTTTTTTTTGTGTTTGGTAGTTGAGAAAATGCTAGTAAAGGAACGAAATTTGGGT-GG-
1 TTTTTTTTTTTGTGTTTGGTAGCTGAGAAAATGCTAGTAAAGGAAGGAAATTTGGGTGGGC
*
1149496 -ATTTTTTTTTGTGTTTGGTAGCTGAGAAAATGCTAGTAAAGGAA-GAAATTTTGGGTGGGTTTC
1 TTTTTTTTTTTGTGTTTGGTAGCTGAGAAAATGCTAGTAAAGGAAGGAAA-TTTGGGTGGG----
1149559 C
61 C
* * * * *
1149560 TTTTTTTTTGTGTGTTTGGTGGCTGATAAAATGCTGGTAAAGGAAGGAAACTTGGGT-GGC
1 TTTTTTTTTTTGTGTTTGGTAGCTGAGAAAATGCTAGTAAAGGAAGGAAATTTGGGTGGGC
*
1149620 TTTTTTTTTTTGTGTTTGGTAGCTGAGAAAATGCTGGTAAAGGAAGGAAATTTGGGTGGGC
1 TTTTTTTTTTTGTGTTTGGTAGCTGAGAAAATGCTAGTAAAGGAAGGAAATTTGGGTGGGC
1149681 TTTTTCTTTTTT
1 TTTTT-TTTTTT
1149693 TGGTGGTTTT
Statistics
Matches: 174, Mismatches: 12, Indels: 19
0.85 0.06 0.09
Matches are distributed among these distances:
57 4 0.02
58 49 0.28
59 2 0.01
60 54 0.31
61 8 0.05
62 6 0.03
64 2 0.01
65 45 0.26
66 4 0.02
ACGTcount: A:0.23, C:0.05, G:0.29, T:0.43
Consensus pattern (61 bp):
TTTTTTTTTTTGTGTTTGGTAGCTGAGAAAATGCTAGTAAAGGAAGGAAATTTGGGTGGGC
Found at i:1149664 original size:125 final size:122
Alignment explanation
Indices: 1149430--1149694 Score: 374
Period size: 125 Copynumber: 2.1 Consensus size: 122
1149420 TTTCTCTTTT
* * *
1149430 TGGGTTT-TTTTTTTTTTTGTGTTTGGTAGTTGAGAAAATGCTAGTAAAGGAACGAAATTTGGGT
1 TGGGTTTCTTTTTTTTTGTGTGTTTGGTAGCTGAGAAAATGCTAGTAAAGGAACGAAACTTGGGT
1149494 GGATTTTTTTTTGTGTTTGGTAGCTGAGAAAATGCTAGTAAAGGAA-GAAATTTTGGG
66 GGATTTTTTTTTGTGTTTGGTAGCTGAGAAAATGCTAGTAAAGGAAGGAAA-TTTGGG
* * * *
1149551 TGGGTTTCCTTTTTTTTTGTGTGTTTGGTGGCTGATAAAATGCTGGTAAAGGAAGGAAACTTGGG
1 TGGGTTT-CTTTTTTTTTGTGTGTTTGGTAGCTGAGAAAATGCTAGTAAAGGAACGAAACTTGGG
* *
1149616 TGGCTTTTTTTTTTTGTGTTTGGTAGCTGAGAAAATGCTGGTAAAGGAAGGAAATTTGGG
65 TGG--ATTTTTTTTTGTGTTTGGTAGCTGAGAAAATGCTAGTAAAGGAAGGAAATTTGGG
1149676 TGGGCTTT-TTCTTTTTTTG
1 TGGG-TTTCTT-TTTTTTTG
1149695 GTGGTTTTAA
Statistics
Matches: 128, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
121 7 0.05
123 52 0.41
124 2 0.02
125 60 0.47
126 7 0.05
ACGTcount: A:0.22, C:0.05, G:0.30, T:0.43
Consensus pattern (122 bp):
TGGGTTTCTTTTTTTTTGTGTGTTTGGTAGCTGAGAAAATGCTAGTAAAGGAACGAAACTTGGGT
GGATTTTTTTTTGTGTTTGGTAGCTGAGAAAATGCTAGTAAAGGAAGGAAATTTGGG
Found at i:1156058 original size:6 final size:6
Alignment explanation
Indices: 1156047--1156077 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1156037 ATGCTCCTTG
*
1156047 CTACAA CTACAA CTACAA CTACAA ATACAA C
1 CTACAA CTACAA CTACAA CTACAA CTACAA C
1156078 CCTGTTTCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.32, G:0.00, T:0.16
Consensus pattern (6 bp):
CTACAA
Found at i:1164050 original size:16 final size:16
Alignment explanation
Indices: 1164029--1164061 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1164019 ATTTTTTTTT
1164029 ATTCAAGTTTAAT-TTG
1 ATTCAA-TTTAATCTTG
1164045 ATTCAATTTAATCTTG
1 ATTCAATTTAATCTTG
1164061 A
1 A
1164062 ATTTGTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.48
Consensus pattern (16 bp):
ATTCAATTTAATCTTG
Found at i:1166403 original size:13 final size:13
Alignment explanation
Indices: 1166381--1166419 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
1166371 TTAATTTTTA
*
1166381 ATTTTTATATATT
1 ATTTTAATATATT
**
1166394 ATTTTAATATAAA
1 ATTTTAATATATT
1166407 ATTTTAATATATT
1 ATTTTAATATATT
1166420 TAAGTAAATT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTTTAATATATT
Found at i:1166410 original size:33 final size:33
Alignment explanation
Indices: 1166373--1166453 Score: 80
Period size: 33 Copynumber: 2.5 Consensus size: 33
1166363 TTGATTTATT
*
1166373 AATTTTTAATTTTTATA-TATTATTTTAATATAA
1 AATTTTTAATTTTTATAGTA-AATTTTAATATAA
*
1166406 AA-TTTTAATATATTTA-AGTAAATTTTGATATAA
1 AATTTTTAAT-T-TTTATAGTAAATTTTAATATAA
*
1166439 AATTATT-ATTTTTAT
1 AATTTTTAATTTTTAT
1166454 TTAATAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
31 4 0.10
32 8 0.20
33 19 0.47
34 9 0.22
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (33 bp):
AATTTTTAATTTTTATAGTAAATTTTAATATAA
Found at i:1166573 original size:13 final size:13
Alignment explanation
Indices: 1166554--1166587 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1166544 AATCGATCCG
1166554 AATTTAATATATA
1 AATTTAATATATA
* *
1166567 TATTTAATATCTA
1 AATTTAATATATA
1166580 AATTTAAT
1 AATTTAAT
1166588 CTGATCAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (13 bp):
AATTTAATATATA
Found at i:1166670 original size:14 final size:15
Alignment explanation
Indices: 1166642--1166670 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1166632 TAATTTTGAA
1166642 TCAATTTTTTATTTC
1 TCAATTTTTTATTTC
1166657 TCAATTTTTT-TTTC
1 TCAATTTTTTATTTC
1166671 ATGCCTATCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.17, C:0.14, G:0.00, T:0.69
Consensus pattern (15 bp):
TCAATTTTTTATTTC
Found at i:1168522 original size:29 final size:30
Alignment explanation
Indices: 1168489--1168554 Score: 107
Period size: 29 Copynumber: 2.2 Consensus size: 30
1168479 TAGTATATCG
*
1168489 TTTAATATGATAATTGAATT-TAAAATTTT
1 TTTAATATAATAATTGAATTATAAAATTTT
*
1168518 TTTAATATAATATTTGAATTATAAAATTTT
1 TTTAATATAATAATTGAATTATAAAATTTT
1168548 TTTAATA
1 TTTAATA
1168555 AGAATTCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 18 0.53
30 16 0.47
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (30 bp):
TTTAATATAATAATTGAATTATAAAATTTT
Found at i:1169873 original size:32 final size:31
Alignment explanation
Indices: 1169792--1169873 Score: 74
Period size: 32 Copynumber: 2.5 Consensus size: 31
1169782 TGTGATTAAT
* *
1169792 TTTAAATGATAATATTTAATAAATAAATAATAT
1 TTTAAAT-ATTATA-TTAATAAATAAATAATAA
* * * * *
1169825 TTTAAGTAATAAATTAATTAATAAATTTATAA
1 TTTAAATATTATATTAATAAATAAA-TAATAA
1169857 TTTAAATATTATATTAA
1 TTTAAATATTATATTAA
1169874 AAACTTTTAT
Statistics
Matches: 38, Mismatches: 10, Indels: 3
0.75 0.20 0.06
Matches are distributed among these distances:
31 11 0.29
32 21 0.55
33 6 0.16
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (31 bp):
TTTAAATATTATATTAATAAATAAATAATAA
Found at i:1171595 original size:29 final size:29
Alignment explanation
Indices: 1171562--1171620 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
1171552 ATTCTAGAAT
* *
1171562 AATTTTGAATAA-TTAAATATCTAATTAAA
1 AATTTTGAA-AATTTAAAAATCAAATTAAA
*
1171591 AATTTTTAAAATTTAAAAATCAAATTAAA
1 AATTTTGAAAATTTAAAAATCAAATTAAA
1171620 A
1 A
1171621 TTTAAATCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 2 0.08
29 24 0.92
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (29 bp):
AATTTTGAAAATTTAAAAATCAAATTAAA
Found at i:1171627 original size:17 final size:18
Alignment explanation
Indices: 1171596--1171633 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 18
1171586 TTAAAAATTT
1171596 TTAAAATTTAAAAATCAAA
1 TTAAAATTT-AAAATCAAA
1171615 TTAAAATTT-AAATCAAA
1 TTAAAATTTAAAATCAAA
1171632 TT
1 TT
1171634 TAGAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.53
19 9 0.47
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (18 bp):
TTAAAATTTAAAATCAAA
Found at i:1177244 original size:4 final size:4
Alignment explanation
Indices: 1177237--1177263 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1177227 TATATATATA
1177237 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
1177264 ATTTGGTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:1181324 original size:19 final size:18
Alignment explanation
Indices: 1181297--1181385 Score: 83
Period size: 17 Copynumber: 4.8 Consensus size: 18
1181287 CAAAATTAAA
1181297 AAAACATTCTAAAATATTCT
1 AAAA-ATTCTAAAA-ATTCT
*
1181317 AAAAATTCTAAAAAAT-T
1 AAAAATTCTAAAAATTCT
*
1181334 AAAAATTCTATAAAAAATTCA
1 AAAAATTC--T-AAAAATTCT
*
1181355 AAAAATTC-AAAAATTTT
1 AAAAATTCTAAAAATTCT
*
1181372 AAAAATTTTAAAAA
1 AAAAATTCTAAAAA
1181386 CTAAAATTTT
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
17 23 0.40
18 7 0.12
19 10 0.17
20 10 0.17
21 8 0.14
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAAATTCTAAAAATTCT
Found at i:1181326 original size:9 final size:9
Alignment explanation
Indices: 1181297--1181385 Score: 83
Period size: 9 Copynumber: 9.6 Consensus size: 9
1181287 CAAAATTAAA
1181297 AAAACATTCT
1 AAAA-ATTCT
1181307 AAAATATTCT
1 AAAA-ATTCT
1181317 AAAAATTCT
1 AAAAATTCT
*
1181326 AAAAAAT-T
1 AAAAATTCT
1181334 AAAAATTCTAT
1 AAAAATTC--T
*
1181345 AAAAAATTCA
1 -AAAAATTCT
1181355 AAAAATTC-
1 AAAAATTCT
*
1181363 AAAAATTTT
1 AAAAATTCT
*
1181372 AAAAATTTT
1 AAAAATTCT
1181381 AAAAA
1 AAAAA
1181386 CTAAAATTTT
Statistics
Matches: 69, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
8 14 0.20
9 33 0.48
10 13 0.19
11 1 0.01
12 8 0.12
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (9 bp):
AAAAATTCT
Found at i:1181348 original size:38 final size:38
Alignment explanation
Indices: 1181306--1181385 Score: 103
Period size: 38 Copynumber: 2.2 Consensus size: 38
1181296 AAAAACATTC
* *
1181306 TAAAATATTCTAAAAATTCTAAAAA-ATTAAAAATTCTA
1 TAAAAAATTCAAAAAATTC-AAAAATATTAAAAATTCTA
*
1181344 TAAAAAATTCAAAAAATTCAAAAATTTTAAAAATT-T-
1 TAAAAAATTCAAAAAATTCAAAAATATTAAAAATTCTA
1181380 TAAAAA
1 TAAAAA
1181386 CTAAAATTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
36 6 0.16
37 6 0.16
38 26 0.68
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (38 bp):
TAAAAAATTCAAAAAATTCAAAAATATTAAAAATTCTA
Found at i:1181643 original size:18 final size:17
Alignment explanation
Indices: 1181620--1181742 Score: 104
Period size: 18 Copynumber: 6.8 Consensus size: 17
1181610 AAATTATAGG
*
1181620 TTTTTTATTTTTTTCAAA
1 TTTTTTAATTTTTT-AAA
1181638 TTTTTTAATTTTTTAGAA
1 TTTTTTAATTTTTTA-AA
* *
1181656 TGTTTCATATTTTTTAAA
1 TTTTTTA-ATTTTTTAAA
* *
1181674 TTATTTAATTTTTCAAAAA
1 TTTTTTAATTTTT--TAAA
*
1181693 TTTTATAATTTTTTATAA
1 TTTTTTAATTTTTTA-AA
*
1181711 -TTTTTAGATTTTTTAAG
1 TTTTTTA-ATTTTTTAAA
1181728 TTTTTTATATTTTTT
1 TTTTTTA-ATTTTTT
1181743 TTTAAATTTT
Statistics
Matches: 85, Mismatches: 13, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
17 14 0.16
18 49 0.58
19 22 0.26
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (17 bp):
TTTTTTAATTTTTTAAA
Found at i:1181675 original size:36 final size:33
Alignment explanation
Indices: 1181622--1181839 Score: 117
Period size: 36 Copynumber: 6.3 Consensus size: 33
1181612 ATTATAGGTT
1181622 TTTTAT-TTTTTTCAAATTTTTTAATTTTTTAGAA
1 TTTTATATTTTTT-AAATTTTTTAATTTTTTA-AA
* *
1181656 TGTTTCATATTTTTTAAATTATTTAATTTTTCAAAAA
1 T-TTT-ATATTTTTTAAATTTTTTAATTTTT--TAAA
*
1181693 TTTTATAATTTTTTATAA-TTTTTAGATTTTTTAAG
1 TTTTAT-ATTTTTTA-AATTTTTTA-ATTTTTTAAA
* * * **
1181728 TTTTTTATATTTT---TTTTTAAATTTTAAGAAA
1 TTTTATATTTTTTAAATTTTTTAATTTT-TTAAA
* * *
1181759 TTTTAT-TTTTATGAAA-ATTTTCATTTTTTGAAA
1 TTTTATATTTT-TTAAATTTTTTAATTTTTT-AAA
*
1181792 TTTTAAATTTATTATTATAATTTTTTAAATTTTTTAAA
1 TTTTATA-TT-TT-TTA-AATTTTTT-AATTTTTTAAA
*
1181830 TTTTAAATTT
1 TTTTATATTT
1181840 ATCATGTTTT
Statistics
Matches: 140, Mismatches: 23, Indels: 40
0.69 0.11 0.20
Matches are distributed among these distances:
30 8 0.06
31 13 0.09
33 16 0.11
34 7 0.05
35 14 0.10
36 39 0.28
37 21 0.15
38 15 0.11
39 7 0.05
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (33 bp):
TTTTATATTTTTTAAATTTTTTAATTTTTTAAA
Found at i:1181752 original size:9 final size:9
Alignment explanation
Indices: 1181628--1181742 Score: 83
Period size: 9 Copynumber: 12.7 Consensus size: 9
1181618 GGTTTTTTAT
1181628 TTTTTTCAAA
1 TTTTTT-AAA
1181638 TTTTTT-AA
1 TTTTTTAAA
1181646 TTTTTTAGAA
1 TTTTTTA-AA
* * *
1181656 TGTTTCATA
1 TTTTTTAAA
1181665 TTTTTTAAA
1 TTTTTTAAA
*
1181674 TTATTT-AA
1 TTTTTTAAA
*
1181682 TTTTTCAAA
1 TTTTTTAAA
**
1181691 AATTTTATAA
1 TTTTTTA-AA
1181701 TTTTTTATAA
1 TTTTTTA-AA
*
1181711 -TTTTTAGA
1 TTTTTTAAA
*
1181719 TTTTTTAAG
1 TTTTTTAAA
*
1181728 TTTTTTATA
1 TTTTTTAAA
1181737 TTTTTT
1 TTTTTT
1181743 TTTAAATTTT
Statistics
Matches: 81, Mismatches: 19, Indels: 11
0.73 0.17 0.10
Matches are distributed among these distances:
8 15 0.19
9 43 0.53
10 23 0.28
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:1181776 original size:17 final size:15
Alignment explanation
Indices: 1181755--1181796 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 15
1181745 TAAATTTTAA
1181755 GAAATTTTATTTTTAT
1 GAAATTTTATTTTT-T
1181771 GAAAATTTTCATTTTTT
1 G-AAATTTT-ATTTTTT
1181788 GAAATTTTA
1 GAAATTTTA
1181797 AATTTATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 1 0.04
16 8 0.33
17 9 0.38
18 6 0.25
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.57
Consensus pattern (15 bp):
GAAATTTTATTTTTT
Found at i:1181801 original size:17 final size:17
Alignment explanation
Indices: 1181742--1181839 Score: 69
Period size: 16 Copynumber: 5.6 Consensus size: 17
1181732 TTATATTTTT
**
1181742 TTTTAAATTTTAAGAAA
1 TTTTAAATTTTTTGAAA
1181759 TTTT--ATTTTTATGAAAA
1 TTTTAAATTTTT-TG-AAA
*
1181776 TTTT-CATTTTTTGAAA
1 TTTTAAATTTTTTGAAA
*
1181792 TTTTAAATTTATTATTATAA
1 TTTTAAATTT-TT-TGA-AA
1181812 TTTTTTAAATTTTTT-AAA
1 --TTTTAAATTTTTTGAAA
1181830 TTTTAAATTT
1 TTTTAAATTT
1181840 ATCATGTTTT
Statistics
Matches: 68, Mismatches: 4, Indels: 19
0.75 0.04 0.21
Matches are distributed among these distances:
15 5 0.07
16 18 0.26
17 17 0.25
18 10 0.15
19 3 0.04
20 3 0.04
21 2 0.03
22 10 0.15
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (17 bp):
TTTTAAATTTTTTGAAA
Found at i:1181803 original size:39 final size:38
Alignment explanation
Indices: 1181740--1181841 Score: 107
Period size: 38 Copynumber: 2.6 Consensus size: 38
1181730 TTTTATATTT
* *
1181740 TTTTTTAAATTTTAAGAAATTTTATTTTTATGAAAATTTT-CA
1 TTTTTTAAATTTT---AAA-TTTATTATTAT-AAAATTTTAAA
**
1181782 TTTTTTGAAATTTTAAATTTATTATTATAATTTTTTAAA
1 TTTTTT-AAATTTTAAATTTATTATTATAAAATTTTAAA
1181821 TTTTTTAAATTTTAAATTTAT
1 TTTTTTAAATTTTAAATTTAT
1181842 CATGTTTTAT
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
38 21 0.39
39 17 0.31
40 3 0.06
42 6 0.11
43 7 0.13
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (38 bp):
TTTTTTAAATTTTAAATTTATTATTATAAAATTTTAAA
Found at i:1185298 original size:2 final size:2
Alignment explanation
Indices: 1185291--1185315 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1185281 TGTTAGGTGA
1185291 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
1185316 ATTGTTAATA
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:1192974 original size:19 final size:19
Alignment explanation
Indices: 1192952--1192989 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1192942 TTTATAAAAT
1192952 AAATGATTTT-TTTTATTTA
1 AAATGATTTTATTTT-TTTA
*
1192971 AAATGCTTTTATTTTTTTA
1 AAATGATTTTATTTTTTTA
1192990 TTGTGAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (19 bp):
AAATGATTTTATTTTTTTA
Found at i:1193991 original size:17 final size:17
Alignment explanation
Indices: 1193943--1193995 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
1193933 TAATGAATAA
*
1193943 AAAATTTATTTTGAAAA-
1 AAAATATATTTT-AAAAT
* *
1193960 AATATATAATATTAAAAT
1 AAAATAT-ATTTTAAAAT
1193978 AAAATATATTTTAAAAT
1 AAAATATATTTTAAAAT
1193995 A
1 A
1193996 TTTTAAAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
17 19 0.66
18 10 0.34
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (17 bp):
AAAATATATTTTAAAAT
Found at i:1196069 original size:25 final size:25
Alignment explanation
Indices: 1196022--1196080 Score: 84
Period size: 26 Copynumber: 2.4 Consensus size: 25
1196012 ATAAAATATC
1196022 TCAAATTTAAATTCGAATATAAATAA
1 TCAAATTTAAATTCGAATATAAA-AA
**
1196048 TCAAATTTTTATT-GAATATAAAAA
1 TCAAATTTAAATTCGAATATAAAAA
1196072 TCAAATTTA
1 TCAAATTTA
1196081 TTTTTACATG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
24 10 0.33
25 9 0.30
26 11 0.37
ACGTcount: A:0.51, C:0.07, G:0.03, T:0.39
Consensus pattern (25 bp):
TCAAATTTAAATTCGAATATAAAAA
Found at i:1196736 original size:13 final size:13
Alignment explanation
Indices: 1196715--1196815 Score: 58
Period size: 13 Copynumber: 8.2 Consensus size: 13
1196705 GTAATTTTAG
*
1196715 ATATAATATAATA
1 ATATAATATAAAA
*
1196728 ATATGATAT-AAA
1 ATATAATATAAAA
1196740 A-ATAATATAAAAA
1 ATATAATAT-AAAA
* *
1196753 ATATAAAATTAAA
1 ATATAATATAAAA
1196766 ATA-AAT-T-AAA
1 ATATAATATAAAA
*
1196776 ATTTAATA-AAAA
1 ATATAATATAAAA
*
1196788 TATATAA-ATTTAAA
1 -ATATAATA-TAAAA
1196802 ATA-AA-ATAAAA
1 ATATAATATAAAA
1196813 ATA
1 ATA
1196816 CATTTATATT
Statistics
Matches: 69, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
10 5 0.07
11 17 0.25
12 12 0.17
13 26 0.38
14 9 0.13
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (13 bp):
ATATAATATAAAA
Found at i:1196745 original size:16 final size:18
Alignment explanation
Indices: 1196714--1196747 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1196704 CGTAATTTTA
1196714 GATATAATATAATAATAT
1 GATATAATATAATAATAT
1196732 GATATAA-A-AATAATAT
1 GATATAATATAATAATAT
1196748 AAAAAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 1 0.06
18 7 0.44
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (18 bp):
GATATAATATAATAATAT
Found at i:1196758 original size:20 final size:20
Alignment explanation
Indices: 1196733--1196770 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1196723 TAATAATATG
*
1196733 ATATAAAAATAATATAAAAA
1 ATATAAAAATAAAATAAAAA
*
1196753 ATATAAAATTAAAATAAA
1 ATATAAAAATAAAATAAA
1196771 TTAAAATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (20 bp):
ATATAAAAATAAAATAAAAA
Found at i:1196784 original size:26 final size:26
Alignment explanation
Indices: 1196750--1196815 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
1196740 AATAATATAA
1196750 AAAATATAAAATTAAAATAAA-TTAAAAT
1 AAAATA-AAAA-T-AAATAAATTTAAAAT
** *
1196778 TTAATAAAAATATATAAATTTAAAAT
1 AAAATAAAAATAAATAAATTTAAAAT
1196804 AAAATAAAAATA
1 AAAATAAAAATA
1196816 CATTTATATT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
25 6 0.19
26 18 0.56
27 4 0.12
28 4 0.12
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (26 bp):
AAAATAAAAATAAATAAATTTAAAAT
Found at i:1204886 original size:9 final size:11
Alignment explanation
Indices: 1204863--1204889 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1204853 AATTATTTAC
1204863 ATATTTAAAAT
1 ATATTTAAAAT
1204874 ATATTTAAAAT
1 ATATTTAAAAT
1204885 ATATT
1 ATATT
1204890 ATAACATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
ATATTTAAAAT
Found at i:1205513 original size:24 final size:24
Alignment explanation
Indices: 1205486--1205535 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
1205476 ATGTGCTTAA
*
1205486 TATTAATGTTGAGATGTCAATTGG
1 TATTAATGTAGAGATGTCAATTGG
1205510 TATTAATGTAGAGATGTCAATTGG
1 TATTAATGTAGAGATGTCAATTGG
1205534 TA
1 TA
1205536 AGATATGGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (24 bp):
TATTAATGTAGAGATGTCAATTGG
Found at i:1207651 original size:15 final size:15
Alignment explanation
Indices: 1207633--1207667 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
1207623 TTTTTGTATT
1207633 TTATTTTTTAAATAA
1 TTATTTTTTAAATAA
1207648 TTA-TTTTTAAATAA
1 TTATTTTTTAAATAA
1207662 TT-TTTT
1 TTATTTT
1207668 ACTTATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 16 0.84
15 3 0.16
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTATTTTTTAAATAA
Found at i:1208829 original size:27 final size:28
Alignment explanation
Indices: 1208751--1208829 Score: 67
Period size: 25 Copynumber: 2.8 Consensus size: 28
1208741 ATATATCTCT
* *
1208751 AAATTGATTTGATTTTTAATTATAATTTAA
1 AAATT-ATTTAATTTGTAATTA-AATTTAA
*
1208781 ATAATT-TTGATATTTG-AA-TAAATTT-A
1 A-AATTATTTA-ATTTGTAATTAAATTTAA
1208807 AAATTATTTAATTTGTAATTAAA
1 AAATTATTTAATTTGTAATTAAA
1208830 AGAAACTAGC
Statistics
Matches: 40, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
25 9 0.22
26 7 0.17
27 9 0.22
28 2 0.05
29 4 0.10
30 5 0.12
31 4 0.10
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (28 bp):
AAATTATTTAATTTGTAATTAAATTTAA
Found at i:1209029 original size:23 final size:23
Alignment explanation
Indices: 1208998--1209047 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
1208988 TAGTTTAAAA
* * *
1208998 TTTTGATAAAAAATAATATATAT
1 TTTTAATAAAAAATAAAAAATAT
*
1209021 TTTTAATAAAAATTAAAAAATAT
1 TTTTAATAAAAAATAAAAAATAT
1209044 TTTT
1 TTTT
1209048 TATATTTGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
TTTTAATAAAAAATAAAAAATAT
Found at i:1217668 original size:25 final size:22
Alignment explanation
Indices: 1217627--1217679 Score: 54
Period size: 22 Copynumber: 2.2 Consensus size: 22
1217617 AAATAATATC
1217627 AAAATAATATGATTTAAAATTTTAAT
1 AAAA-AATATGATTT--AA-TTTAAT
1217653 AAAAAATAT-ATATTAATTTAAT
1 AAAAAATATGAT-TTAATTTAAT
1217675 AAAAA
1 AAAAA
1217680 TAATAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
22 11 0.42
23 2 0.08
24 2 0.08
25 7 0.27
26 4 0.15
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
AAAAAATATGATTTAATTTAAT
Found at i:1229442 original size:21 final size:20
Alignment explanation
Indices: 1229406--1229446 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
1229396 AAAATAAATA
1229406 TAATATAATTT-A-AAATTT
1 TAATATAATTTAATAAATTT
1229424 TAATAATAATTTAATAAATTT
1 TAAT-ATAATTTAATAAATTT
1229445 TA
1 TA
1229447 TATTTTAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 7 0.35
20 1 0.05
21 8 0.40
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TAATATAATTTAATAAATTT
Found at i:1229480 original size:25 final size:25
Alignment explanation
Indices: 1229452--1229501 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1229442 TTTTATATTT
*
1229452 TAATGATGATATAAATTATAATATA
1 TAATGATGATATAAAATATAATATA
** *
1229477 TAATTTTTATATAAAATATAATATA
1 TAATGATGATATAAAATATAATATA
1229502 AATTTATGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (25 bp):
TAATGATGATATAAAATATAATATA
Found at i:1229487 original size:23 final size:24
Alignment explanation
Indices: 1229460--1229506 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
1229450 TTTAATGATG
*
1229460 ATATAAATTATAATATATAATTTTT
1 ATATAAAATATAATATA-AATTTTT
1229485 ATATAAAATATAATATAAATTT
1 ATATAAAATATAATATAAATTT
1229507 ATGAATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
ATATAAAATATAATATAAATTTTT
Found at i:1235965 original size:84 final size:84
Alignment explanation
Indices: 1235878--1236039 Score: 211
Period size: 83 Copynumber: 1.9 Consensus size: 84
1235868 TGAATTTTTT
* * * * * * *
1235878 TTTTTTAATTAAGTTTAAATAGTTTATCAACAGTTTGATTTTTTTGAA-TC-GAGTTCGAATAAT
1 TTTTTTAATCAAATTCAAATAATTTATCAACAGTTTGATTTTTTT-AAGTCAAAGTTCAAATAAC
1235941 TTATGAGTAATTTAATTTAA
65 TTATGAGTAATTTAATTTAA
* * *
1235961 TTTTTTAATCAAATTCAAATAATTTATGAATAGTTTGATTTTTTTAAGTCAAAGTTCAAATAGCT
1 TTTTTTAATCAAATTCAAATAATTTATCAACAGTTTGATTTTTTTAAGTCAAAGTTCAAATAACT
1236026 TATGAGTAATTTAA
66 TATGAGTAATTTAA
1236040 CTTGATTATA
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
82 2 0.03
83 41 0.61
84 24 0.36
ACGTcount: A:0.36, C:0.06, G:0.11, T:0.48
Consensus pattern (84 bp):
TTTTTTAATCAAATTCAAATAATTTATCAACAGTTTGATTTTTTTAAGTCAAAGTTCAAATAACT
TATGAGTAATTTAATTTAA
Found at i:1235982 original size:43 final size:39
Alignment explanation
Indices: 1235915--1236039 Score: 115
Period size: 43 Copynumber: 3.0 Consensus size: 39
1235905 CAACAGTTTG
* * *
1235915 ATTTTTTTGAATCGAGTTCGAATAATTTATGAGTAATTTA
1 ATTTTTTT-AATCAAATTCAAATAATTTATGAGTAATTTA
* * *
1235955 ATTTAATTTTTTAATCAAATTCAAATAATTTATGAATAGTTTG
1 A--T--TTTTTTAATCAAATTCAAATAATTTATGAGTAATTTA
**
1235998 ATTTTTTTAAGTCAAAGTTCAAATAGCTTATGAGTAATTTA
1 ATTTTTTTAA-TCAAA-TTCAAATAATTTATGAGTAATTTA
1236039 A
1 A
1236040 CTTGATTATA
Statistics
Matches: 68, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
39 8 0.12
40 6 0.09
41 21 0.31
42 1 0.01
43 26 0.38
44 6 0.09
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.46
Consensus pattern (39 bp):
ATTTTTTTAATCAAATTCAAATAATTTATGAGTAATTTA
Found at i:1241318 original size:6 final size:6
Alignment explanation
Indices: 1241306--1241368 Score: 85
Period size: 6 Copynumber: 10.8 Consensus size: 6
1241296 TGCAAACCTT
* * *
1241306 AGCTTG GGCTTG GGCTTG GGCTTG AGCTTG AGCTTG -GCTTG AGCTTG
1 AGCTTG AGCTTG AGCTTG AGCTTG AGCTTG AGCTTG AGCTTG AGCTTG
1241353 AGCTTG -GCTTG AGCTT
1 AGCTTG AGCTTG AGCTT
1241369 CACTTAGTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
5 10 0.19
6 43 0.81
ACGTcount: A:0.10, C:0.17, G:0.38, T:0.35
Consensus pattern (6 bp):
AGCTTG
Found at i:1241346 original size:17 final size:17
Alignment explanation
Indices: 1241307--1241368 Score: 97
Period size: 17 Copynumber: 3.6 Consensus size: 17
1241297 GCAAACCTTA
* *
1241307 GCTTGGGCTTGGGCTTGG
1 GCTTGAGCTTGAGCTT-G
1241325 GCTTGAGCTTGAGCTTG
1 GCTTGAGCTTGAGCTTG
1241342 GCTTGAGCTTGAGCTTG
1 GCTTGAGCTTGAGCTTG
1241359 GCTTGAGCTT
1 GCTTGAGCTT
1241369 CACTTAGTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
17 28 0.67
18 14 0.33
ACGTcount: A:0.08, C:0.18, G:0.39, T:0.35
Consensus pattern (17 bp):
GCTTGAGCTTGAGCTTG
Found at i:1244574 original size:21 final size:22
Alignment explanation
Indices: 1244536--1244587 Score: 90
Period size: 21 Copynumber: 2.5 Consensus size: 22
1244526 TCCGAAATTA
1244536 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
1244558 ATAAAATATTA-TTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
1244579 AT-AAATATT
1 ATAAAATATT
1244588 TAAAAATATC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 7 0.23
21 12 0.40
22 11 0.37
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAAATATTATTTTTTAAAAT
Found at i:1247527 original size:13 final size:14
Alignment explanation
Indices: 1247509--1247543 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
1247499 AATTAAATAT
1247509 AAATTAAAATT-AA
1 AAATTAAAATTGAA
*
1247522 AAATTAAAATTGAT
1 AAATTAAAATTGAA
1247536 AAATTAAA
1 AAATTAAA
1247544 CGGTATTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (14 bp):
AAATTAAAATTGAA
Found at i:1248681 original size:11 final size:11
Alignment explanation
Indices: 1248665--1248700 Score: 54
Period size: 11 Copynumber: 3.1 Consensus size: 11
1248655 CGGTGATACG
1248665 ATATGAAAATA
1 ATATGAAAATA
1248676 ATATGAATAAATA
1 ATATG-A-AAATA
1248689 ATATGAAAATA
1 ATATGAAAATA
1248700 A
1 A
1248701 CACGGCTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 11 0.48
12 2 0.09
13 10 0.43
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (11 bp):
ATATGAAAATA
Found at i:1248689 original size:13 final size:13
Alignment explanation
Indices: 1248671--1248695 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1248661 TACGATATGA
1248671 AAATAATATGAAT
1 AAATAATATGAAT
1248684 AAATAATATGAA
1 AAATAATATGAA
1248696 AATAACACGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (13 bp):
AAATAATATGAAT
Found at i:1252469 original size:23 final size:26
Alignment explanation
Indices: 1252437--1252485 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
1252427 AAAACATGAA
*
1252437 TTTTATTATT-TTATTTAAAT-AAAT
1 TTTTATTATTGTTATTAAAATCAAAT
1252461 TTTTA-TATTGTTATTAAAATCAAAT
1 TTTTATTATTGTTATTAAAATCAAAT
1252486 AGTTCTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 4 0.18
24 14 0.64
25 4 0.18
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (26 bp):
TTTTATTATTGTTATTAAAATCAAAT
Found at i:1257799 original size:28 final size:28
Alignment explanation
Indices: 1257742--1257809 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 28
1257732 TTACGTTTTA
*
1257742 TTAAA-TATATTTATTTATTTTTATAATT
1 TTAAATTATATTTATTTATATTTAT-ATT
*
1257770 TTAAATTATATTATTTTTATATTTAT-TT
1 TTAAATTATATT-TATTTATATTTATATT
* *
1257798 TTATATCATATT
1 TTAAATTATATT
1257810 CATATGATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
28 17 0.50
29 6 0.18
30 11 0.32
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (28 bp):
TTAAATTATATTTATTTATATTTATATT
Found at i:1258001 original size:29 final size:30
Alignment explanation
Indices: 1257960--1258028 Score: 97
Period size: 29 Copynumber: 2.3 Consensus size: 30
1257950 ATAATTTTTG
*
1257960 AATTATAATAAAAT-ATTTAATATGATATTTA
1 AATTATTA-AAAATAATTT-ATATGATATTTA
1257991 AATT-TTAAAAATAATTTATATGATATTTA
1 AATTATTAAAAATAATTTATATGATATTTA
1258020 AATTATTAA
1 AATTATTAA
1258029 TTTGTTAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
29 21 0.60
30 10 0.29
31 4 0.11
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (30 bp):
AATTATTAAAAATAATTTATATGATATTTA
Found at i:1259884 original size:18 final size:18
Alignment explanation
Indices: 1259861--1259896 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1259851 AATTTATATG
*
1259861 TAAAAATTATATTTTATA
1 TAAAAATTATATATTATA
1259879 TAAAAATTATATATTATA
1 TAAAAATTATATATTATA
1259897 ATTTATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TAAAAATTATATATTATA
Found at i:1259889 original size:31 final size:31
Alignment explanation
Indices: 1259854--1259916 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
1259844 TTTTGATAAT
* *
1259854 TTATATGTAAAAA-TTATATTTTATATAAAAA
1 TTATATATAAAAATTTATA-TTAATATAAAAA
* *
1259885 TTATATATTATAATTTATATTAATATAAAAA
1 TTATATATAAAAATTTATATTAATATAAAAA
1259916 T
1 T
1259917 ATAAAATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 22 0.81
32 5 0.19
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (31 bp):
TTATATATAAAAATTTATATTAATATAAAAA
Found at i:1259936 original size:37 final size:36
Alignment explanation
Indices: 1259876--1259956 Score: 101
Period size: 37 Copynumber: 2.2 Consensus size: 36
1259866 ATTATATTTT
1259876 ATATAAAAATTATATATTATAATTTATATTAATATAAAA
1 ATAT-AAAATTATATATTATAATTT-TATTAA-ATAAAA
* * *
1259915 ATATAAAA-TATATTTTTTAATTTTATTAAATATAA
1 ATATAAAATTATATATTATAATTTTATTAAATAAAA
1259950 ATATAAA
1 ATATAAA
1259957 TTTTTTAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
35 12 0.31
36 6 0.15
37 13 0.33
38 4 0.10
39 4 0.10
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (36 bp):
ATATAAAATTATATATTATAATTTTATTAAATAAAA
Found at i:1259984 original size:30 final size:30
Alignment explanation
Indices: 1259913--1259988 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 30
1259903 ATTAATATAA
* **
1259913 AAATATAAA-ATATATTTTTTAATTTTATT
1 AAATATAAATATAAATTTTTTAAAATTATT
1259942 AAATATAAATATAAATTTTTTAAAATT-TT
1 AAATATAAATATAAATTTTTTAAAATTATT
* *
1259971 AAAT-TATATATATATTTT
1 AAATATAAATATAAATTTT
1259989 ATATTATTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
28 12 0.29
29 15 0.37
30 14 0.34
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (30 bp):
AAATATAAATATAAATTTTTTAAAATTATT
Found at i:1265363 original size:3 final size:3
Alignment explanation
Indices: 1265348--1265390 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
1265338 ACTTCTGTCG
*
1265348 ATT ATT ATG ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1265391 CACACACACA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:1267257 original size:116 final size:116
Alignment explanation
Indices: 1267053--1267285 Score: 457
Period size: 116 Copynumber: 2.0 Consensus size: 116
1267043 CTCAGTCATC
*
1267053 TCCAACCTCAGCCAAAATCATTCTAAAAAGCACCTAACAGTAAAAGGGATTTCGGTTTCAAAGAC
1 TCCAACCTCAGCCAAAATCATTCTAAAAACCACCTAACAGTAAAAGGGATTTCGGTTTCAAAGAC
1267118 CCTTCATTTGTTAGCTTGGCCAACAAAATCGTGTTCTACCCTAATATAATT
66 CCTTCATTTGTTAGCTTGGCCAACAAAATCGTGTTCTACCCTAATATAATT
1267169 TCCAACCTCAGCCAAAATCATTCTAAAAACCACCTAACAGTAAAAGGGATTTCGGTTTCAAAGAC
1 TCCAACCTCAGCCAAAATCATTCTAAAAACCACCTAACAGTAAAAGGGATTTCGGTTTCAAAGAC
1267234 CCTTCATTTGTTAGCTTGGCCAACAAAATCGTGTTCTACCCTAATATAATT
66 CCTTCATTTGTTAGCTTGGCCAACAAAATCGTGTTCTACCCTAATATAATT
1267285 T
1 T
1267286 GAACATCTAC
Statistics
Matches: 116, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
116 116 1.00
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.29
Consensus pattern (116 bp):
TCCAACCTCAGCCAAAATCATTCTAAAAACCACCTAACAGTAAAAGGGATTTCGGTTTCAAAGAC
CCTTCATTTGTTAGCTTGGCCAACAAAATCGTGTTCTACCCTAATATAATT
Found at i:1268398 original size:22 final size:22
Alignment explanation
Indices: 1268372--1268414 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1268362 TTATGGATTT
*
1268372 AATTTGATTTATTAATTTTTAA
1 AATTTAATTTATTAATTTTTAA
* *
1268394 AATTTAATTTTTTTATTTTTA
1 AATTTAATTTATTAATTTTTA
1268415 TATATAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
AATTTAATTTATTAATTTTTAA
Found at i:1272722 original size:20 final size:21
Alignment explanation
Indices: 1272699--1272737 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1272689 TTAAAACAAT
1272699 ATATAAAAAATAAA-AAATAA
1 ATATAAAAAATAAATAAATAA
*
1272719 ATATTAAAAATAAATAAAT
1 ATATAAAAAATAAATAAAT
1272738 CGAACCGAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (21 bp):
ATATAAAAAATAAATAAATAA
Found at i:1276964 original size:29 final size:29
Alignment explanation
Indices: 1276896--1276970 Score: 71
Period size: 29 Copynumber: 2.5 Consensus size: 29
1276886 TTAATTTTTA
**
1276896 AATTATAATAAAATATTTAATATGATATTTG
1 AATTAT-A-AAAATATTTAATATGATACATG
* *
1276927 AAGTT-TAAAAATTTTTAATATGATGCATG
1 AA-TTATAAAAATATTTAATATGATACATG
*
1276956 AATTATAAATATATT
1 AATTATAAAAATATT
1276971 AATTAATATA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
28 2 0.06
29 28 0.78
30 1 0.03
31 3 0.08
32 2 0.06
ACGTcount: A:0.47, C:0.01, G:0.08, T:0.44
Consensus pattern (29 bp):
AATTATAAAAATATTTAATATGATACATG
Found at i:1277023 original size:12 final size:12
Alignment explanation
Indices: 1277006--1277081 Score: 54
Period size: 12 Copynumber: 6.4 Consensus size: 12
1276996 TAACATATAA
1277006 TAAATAATTATT
1 TAAATAATTATT
*
1277018 TAAATATCTTATT
1 TAAATA-ATTATT
*
1277031 T-AATAATAAATT
1 TAAATAAT-TATT
1277043 TATAATAA--ATT
1 TA-AATAATTATT
1277054 TAAAT-ATTATAT
1 TAAATAATTAT-T
*
1277066 TAAA-AATTTTT
1 TAAATAATTATT
1277077 TAAAT
1 TAAAT
1277082 TTAAATATTA
Statistics
Matches: 51, Mismatches: 4, Indels: 18
0.70 0.05 0.25
Matches are distributed among these distances:
9 1 0.02
10 3 0.06
11 13 0.25
12 23 0.45
13 6 0.12
14 5 0.10
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (12 bp):
TAAATAATTATT
Found at i:1277069 original size:18 final size:18
Alignment explanation
Indices: 1277015--1277069 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
1277005 ATAAATAATT
*
1277015 ATTTAAATATCT-TATTTA
1 ATTTAAATAT-TATATTAA
* *
1277033 ATAATAAAT-TTATAATAA
1 AT-TTAAATATTATATTAA
1277051 ATTTAAATATTATATTAA
1 ATTTAAATATTATATTAA
1277069 A
1 A
1277070 AATTTTTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
17 6 0.21
18 18 0.62
19 5 0.17
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTTAAATATTATATTAA
Found at i:1277080 original size:29 final size:30
Alignment explanation
Indices: 1277038--1277123 Score: 120
Period size: 29 Copynumber: 2.8 Consensus size: 30
1277028 ATTTAATAAT
1277038 AAATTTATAATAAATTTAAATATTATATTAA
1 AAATTT-TAATAAATTTAAATATTATATTAA
* *
1277069 AAATTTT-TTAAATTTAAATATTAAATTAA
1 AAATTTTAATAAATTTAAATATTATATTAA
*
1277098 AAATTTTAATATAATTTAAAAATTAT
1 AAATTTTAATA-AATTTAAATATTAT
1277124 TTATGATATT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
29 27 0.56
30 3 0.06
31 18 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (30 bp):
AAATTTTAATAAATTTAAATATTATATTAA
Found at i:1277118 original size:19 final size:20
Alignment explanation
Indices: 1277078--1277121 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
1277068 AAAATTTTTT
1277078 AAATTTAAATATTAAATTAA
1 AAATTTAAATATTAAATTAA
* *
1277098 AAATTTTAATA-TAATTTAA
1 AAATTTAAATATTAAATTAA
1277117 AAATT
1 AAATT
1277122 ATTTATGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AAATTTAAATATTAAATTAA
Found at i:1282879 original size:20 final size:20
Alignment explanation
Indices: 1282856--1282942 Score: 68
Period size: 20 Copynumber: 4.0 Consensus size: 20
1282846 GTTTTATTTT
*
1282856 TAAAAAAATTAATAAAAATT
1 TAAAAAAATTAATAAAAATA
*
1282876 TAAATTAATAAATTAATAGAATATAA
1 T-AA--AA-AAATTAATA-AAAAT-A
*
1282902 TAAAAAAATTAAT-AATATA
1 TAAAAAAATTAATAAAAATA
*
1282921 TAAAAAAATTTATTAAAAATA
1 TAAAAAAA-TTAATAAAAATA
1282942 T
1 T
1282943 CATTTATAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 15
0.74 0.05 0.20
Matches are distributed among these distances:
19 9 0.16
20 10 0.18
21 8 0.15
22 8 0.15
23 4 0.07
24 9 0.16
25 6 0.11
26 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (20 bp):
TAAAAAAATTAATAAAAATA
Found at i:1282986 original size:28 final size:28
Alignment explanation
Indices: 1282919--1282988 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
1282909 ATTAATAATA
* *
1282919 TATAAAAAAATTTATTAAAAATATCATT
1 TATAATAAAATTTAATAAAAATATCATT
* * *
1282947 TATAATTTAAATTTAATAAATAT-TTATT
1 TATAA-TAAAATTTAATAAAAATATCATT
1282975 TAATAATAAAATTT
1 T-ATAATAAAATTT
1282989 TATTAGTATT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
28 17 0.50
29 17 0.50
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (28 bp):
TATAATAAAATTTAATAAAAATATCATT
Found at i:1283079 original size:24 final size:23
Alignment explanation
Indices: 1283043--1283087 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
1283033 GCTAAAAATT
**
1283043 TAAAAAACTTTTACACTTAATTTA
1 TAAAAAAAATTTA-ACTTAATTTA
*
1283067 TAAAAAAAATTTAATTTAATT
1 TAAAAAAAATTTAACTTAATT
1283088 ATTTTTAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 7 0.39
24 11 0.61
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (23 bp):
TAAAAAAAATTTAACTTAATTTA
Found at i:1285513 original size:17 final size:17
Alignment explanation
Indices: 1285471--1285510 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
1285461 ACTTCTTGAA
1285471 ATTAT-AATTGTTTTAT
1 ATTATAAATTGTTTTAT
1285487 ATTATAAATT-TTTTAT
1 ATTATAAATTGTTTTAT
*
1285503 ATTTTAAA
1 ATTATAAA
1285511 ATTAATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (17 bp):
ATTATAAATTGTTTTAT
Found at i:1287337 original size:31 final size:31
Alignment explanation
Indices: 1287302--1287377 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
1287292 CATGAATTGT
* * *
1287302 ATATATAA-TCTATACACTGATAGTATATCAA
1 ATATA-AATTCTAAACACTGACAATATATCAA
*
1287333 ATATAAATTTTAAACACTGACAATATATCAA
1 ATATAAATTCTAAACACTGACAATATATCAA
1287364 ATATAAATTCTAAA
1 ATATAAATTCTAAA
1287378 GAGTTTATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 2 0.05
31 37 0.95
ACGTcount: A:0.50, C:0.12, G:0.04, T:0.34
Consensus pattern (31 bp):
ATATAAATTCTAAACACTGACAATATATCAA
Found at i:1287419 original size:24 final size:24
Alignment explanation
Indices: 1287392--1287451 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
1287382 TTATATTTGG
* *
1287392 TACATTATTAGTATATAGATTTTA
1 TACATTATAAGTATATAAATTTTA
*
1287416 TACACTATAAGTATATAAATTTTA
1 TACATTATAAGTATATAAATTTTA
*
1287440 TCCATTATAAGT
1 TACATTATAAGT
1287452 GAATCAGATA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.45
Consensus pattern (24 bp):
TACATTATAAGTATATAAATTTTA
Found at i:1290576 original size:17 final size:17
Alignment explanation
Indices: 1290544--1290577 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1290534 CTTTATAATA
1290544 AAATATAATAAAATATT
1 AAATATAATAAAATATT
1290561 AAAT-TAATAAATATATT
1 AAATATAATAAA-ATATT
1290578 TATGGATAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATATAATAAAATATT
Found at i:1291229 original size:30 final size:30
Alignment explanation
Indices: 1291195--1291254 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
1291185 ATATTAAGGG
* * * *
1291195 TTTATTTAGTTATAAATTAAGAGTTAAAAA
1 TTTATTTAGATACAAATAAAAAGTTAAAAA
1291225 TTTATTTAGATACAAATAAAAAGTTAAAAA
1 TTTATTTAGATACAAATAAAAAGTTAAAAA
1291255 ACAAAAATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.38
Consensus pattern (30 bp):
TTTATTTAGATACAAATAAAAAGTTAAAAA
Found at i:1292419 original size:26 final size:29
Alignment explanation
Indices: 1292388--1292455 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
1292378 TGAAAGTATT
*
1292388 ATATTA-ATTAATAAA-TTTATAA-TTAA
1 ATATTAGATTAATAAATTTTAAAATTTAA
*
1292414 ATATTAGACTAA-AAATTTTTAAAATTTAA
1 ATATTAGATTAATAAA-TTTTAAAATTTAA
*
1292443 ATATTATATTAAT
1 ATATTAGATTAAT
1292456 TTGGTTTCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
26 9 0.27
27 4 0.12
28 6 0.18
29 14 0.42
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (29 bp):
ATATTAGATTAATAAATTTTAAAATTTAA
Found at i:1292807 original size:61 final size:62
Alignment explanation
Indices: 1292732--1292855 Score: 207
Period size: 61 Copynumber: 2.0 Consensus size: 62
1292722 TTTGTAAGGG
* *
1292732 AATATTCAAAGCATTTTTT-GAGAAAAAATGCTTTGAATATTTC-AAAAAAAATGTTGAGATT
1 AATATTCAAAGCATTTTTTAG-GAAAAAACGCTTTGAATATTCCAAAAAAAAATGTTGAGATT
1292793 AATATTCAAAGCATTTTTTAGGAAAAAACGCTTTGAATATTCCAAAAAAAAATGTTGAGATT
1 AATATTCAAAGCATTTTTTAGGAAAAAACGCTTTGAATATTCCAAAAAAAAATGTTGAGATT
1292855 A
1 A
1292856 TTGAAGATGT
Statistics
Matches: 59, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
61 39 0.66
62 20 0.34
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (62 bp):
AATATTCAAAGCATTTTTTAGGAAAAAACGCTTTGAATATTCCAAAAAAAAATGTTGAGATT
Found at i:1298151 original size:20 final size:20
Alignment explanation
Indices: 1298126--1298165 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1298116 GTTTTTGGTC
1298126 AAAACACCTTGAATAATCCA
1 AAAACACCTTGAATAATCCA
*
1298146 AAAACACTTTGAATAATCCA
1 AAAACACCTTGAATAATCCA
1298166 CTCAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.50, C:0.23, G:0.05, T:0.23
Consensus pattern (20 bp):
AAAACACCTTGAATAATCCA
Found at i:1302180 original size:15 final size:15
Alignment explanation
Indices: 1302160--1302195 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1302150 GGTGTAACTC
*
1302160 TTTATCTATATTTGT
1 TTTATCGATATTTGT
*
1302175 TTTATCGATGTTTGT
1 TTTATCGATATTTGT
1302190 TTTATC
1 TTTATC
1302196 AAACTTGGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.17, C:0.08, G:0.11, T:0.64
Consensus pattern (15 bp):
TTTATCGATATTTGT
Found at i:1302730 original size:159 final size:158
Alignment explanation
Indices: 1302567--1302864 Score: 372
Period size: 159 Copynumber: 1.9 Consensus size: 158
1302557 ACCATCAATG
* * *
1302567 TAGGTAAGAAAATTAAAAAATACAAGTCTATACTAACGGATGC-TATGCATCAATATAGGTAAAA
1 TAGGTAAGAAAACTAAAAAATACAAATCTATACTAACGG--GCTTAAGCATCAATATAGGTAAAA
* * * *
1302631 AAATTACTAA-TTTATACTGA-TAGGCC-TTAATTGTCGGTATAGGTCAA-AAAAATTAAAACAT
64 AAATTA-AAAGTCTATACTGACTA--CCATTAATCGTCGGTATA-GACAAGAAAAATTAAAACAT
*
1302692 ATAGGTCTATACTACCGGGCACTAGCCATTGATA
125 ATAAGTCTATACTACCGGGCACTAGCCATTGATA
* * * * * *
1302726 TAGGTGAGAAAACTAAAACATACAAATCTATATTGATGGGCTTTAAGCATCAGTATAGGTAAAAA
1 TAGGTAAGAAAACTAAAAAATACAAATCTATACTAACGGGC-TTAAGCATCAATATAGGTAAAAA
1302791 AATTAAAAGTCTATACTGACTACCATTAATCGTCGGTATAGACAAGAAAAATTAAAACATATAAG
65 AATTAAAAGTCTATACTGACTACCATTAATCGTCGGTATAGACAAGAAAAATTAAAACATATAAG
1302856 TCTATACTA
130 TCTATACTA
1302865 ATGGGTGTTA
Statistics
Matches: 119, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
157 2 0.02
158 8 0.07
159 107 0.90
160 2 0.02
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (158 bp):
TAGGTAAGAAAACTAAAAAATACAAATCTATACTAACGGGCTTAAGCATCAATATAGGTAAAAAA
ATTAAAAGTCTATACTGACTACCATTAATCGTCGGTATAGACAAGAAAAATTAAAACATATAAGT
CTATACTACCGGGCACTAGCCATTGATA
Found at i:1304759 original size:20 final size:21
Alignment explanation
Indices: 1304736--1304782 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1304726 TTATAAACAT
* *
1304736 TATTTTTAATT-TTTTTTACA
1 TATTATTAATTCTTTATTACA
1304756 TATTATTAATTCTTTATTACA
1 TATTATTAATTCTTTATTACA
*
1304777 TTTTAT
1 TATTAT
1304783 CAATCTGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (21 bp):
TATTATTAATTCTTTATTACA
Found at i:1305791 original size:36 final size:35
Alignment explanation
Indices: 1305714--1305793 Score: 90
Period size: 36 Copynumber: 2.2 Consensus size: 35
1305704 ATCTGGACCA
* *
1305714 AAGATTTATTATATATGTTTGAGAAAAAAAAACCC
1 AAGATTTACTATATATGTGTGAGAAAAAAAAACCC
**
1305749 ATAGATTTACTATATATGTGTGA-AAAAGAAAGAACTG
1 A-AGATTTACTATATATGTGTGAGAAAA-AAA-AACCC
1305786 AAGATTTA
1 AAGATTTA
1305794 TTAGATTTGT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
35 5 0.13
36 29 0.76
37 4 0.11
ACGTcount: A:0.47, C:0.06, G:0.15, T:0.31
Consensus pattern (35 bp):
AAGATTTACTATATATGTGTGAGAAAAAAAAACCC
Found at i:1323313 original size:11 final size:11
Alignment explanation
Indices: 1323290--1323356 Score: 55
Period size: 11 Copynumber: 5.6 Consensus size: 11
1323280 TAAAGTCTAT
1323290 TTTAA-AAATAA
1 TTTAATAAA-AA
1323301 TTTAATAAAAA
1 TTTAATAAAAA
1323312 TTTAATTAAAAA
1 TTTAA-TAAAAA
1323324 TTTAAATTGATAAAA
1 TTT-AA-T-A-AAAA
*
1323339 TATAATAAAAA
1 TTTAATAAAAA
*
1323350 ATTAATA
1 TTTAATA
1323357 TTATGTAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
11 21 0.44
12 13 0.27
13 5 0.10
14 3 0.06
15 6 0.12
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (11 bp):
TTTAATAAAAA
Found at i:1323331 original size:13 final size:12
Alignment explanation
Indices: 1323299--1323352 Score: 56
Period size: 12 Copynumber: 4.3 Consensus size: 12
1323289 TTTTAAAAAT
1323299 AATTTAA-TAAA
1 AATTTAATTAAA
1323310 AATTTAATTAAA
1 AATTTAATTAAA
1323322 AATTTAAATTGATAA
1 AATTT-AATT-A-AA
* *
1323337 AATATAATAAAA
1 AATTTAATTAAA
1323349 AATT
1 AATT
1323353 AATATTATGT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
11 7 0.19
12 14 0.39
13 5 0.14
14 4 0.11
15 6 0.17
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (12 bp):
AATTTAATTAAA
Found at i:1333863 original size:20 final size:20
Alignment explanation
Indices: 1333838--1333884 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1333828 TTAAATTGAT
1333838 AAAATATA-ATAAAAATATTA
1 AAAATATATA-AAAAATATTA
* *
1333858 ATAATATGTAAAAAATATTA
1 AAAATATATAAAAAATATTA
1333878 AAAATAT
1 AAAATAT
1333885 CATTTATATT
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:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (20 bp):
AAAATATATAAAAAATATTA
Found at i:1333880 original size:9 final size:9
Alignment explanation
Indices: 1333837--1333884 Score: 51
Period size: 9 Copynumber: 5.0 Consensus size: 9
1333827 TTTAAATTGA
*
1333837 TAAAATATAA
1 TAAAA-ATAT
1333847 TAAAAATAT
1 TAAAAATAT
*
1333856 TAATAATAT
1 TAAAAATAT
1333865 GTAAAAAATAT
1 -T-AAAAATAT
1333876 TAAAAATAT
1 TAAAAATAT
1333885 CATTTATATT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
9 19 0.58
10 7 0.21
11 7 0.21
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (9 bp):
TAAAAATAT
Found at i:1333956 original size:25 final size:24
Alignment explanation
Indices: 1333927--1333986 Score: 75
Period size: 25 Copynumber: 2.5 Consensus size: 24
1333917 TATTCAATAA
* *
1333927 TAAAAATTTTATTAATATTTTTAT
1 TAAAAATTTTATTAATATATATAT
*
1333951 TAAAAATATTTTTTAATATATATAT
1 TAAAAAT-TTTATTAATATATATAT
*
1333976 TTAAAATTTTA
1 TAAAAATTTTA
1333987 CAAATTTGAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 10 0.33
25 20 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TAAAAATTTTATTAATATATATAT
Found at i:1335194 original size:7 final size:7
Alignment explanation
Indices: 1335182--1335206 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1335172 TATTTTATAA
1335182 AATTCAT
1 AATTCAT
1335189 AATTCAT
1 AATTCAT
1335196 AATTCAT
1 AATTCAT
1335203 AATT
1 AATT
1335207 TTTAATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (7 bp):
AATTCAT
Found at i:1335592 original size:30 final size:30
Alignment explanation
Indices: 1335556--1335622 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
1335546 TTTTTTATTC
* * * *
1335556 AAATAAATTTTTAATTTTTAGTTTGTATCT
1 AAATAAATTTTTAATTCTTAATTTATACCT
1335586 AAATAAATTTTTAATTCTTAATTTATACCT
1 AAATAAATTTTTAATTCTTAATTTATACCT
1335616 AAATAAA
1 AAATAAA
1335623 CCCTTAATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.49
Consensus pattern (30 bp):
AAATAAATTTTTAATTCTTAATTTATACCT
Found at i:1336058 original size:16 final size:16
Alignment explanation
Indices: 1336033--1336063 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1336023 ATTGTATTTG
1336033 TAATTGTTTTATATTA
1 TAATTGTTTTATATTA
*
1336049 TAATTTTTTTATATT
1 TAATTGTTTTATATT
1336064 TTCAAATTAA
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:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
TAATTGTTTTATATTA
Found at i:1339474 original size:24 final size:22
Alignment explanation
Indices: 1339447--1339498 Score: 52
Period size: 21 Copynumber: 2.3 Consensus size: 22
1339437 ATTAAAAATA
1339447 ATAATAAATGTGAGATTGATTATT
1 ATAATAAA--TGAGATTGATTATT
**
1339471 ATAA-CGATGAGATTGATTATT
1 ATAATAAATGAGATTGATTATT
*
1339492 GTAATAA
1 ATAATAA
1339499 TAAAAATTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 4
0.71 0.16 0.13
Matches are distributed among these distances:
21 17 0.77
23 1 0.05
24 4 0.18
ACGTcount: A:0.42, C:0.02, G:0.17, T:0.38
Consensus pattern (22 bp):
ATAATAAATGAGATTGATTATT
Done.