Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold220
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: 3999181
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 12171 characters in sequence are not A, C, G, or T
File 5 of 19
Found at i:1057664 original size:12 final size:12
Alignment explanation
Indices: 1057643--1057677 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
1057633 TCTCCCTTTA
1057643 TTTATATATTTT
1 TTTATATATTTT
*
1057655 TTTATTTATTTT
1 TTTATATATTTT
1057667 TTGTATATATT
1 TT-TATATATT
1057678 CACAGTCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 13 0.65
13 7 0.35
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (12 bp):
TTTATATATTTT
Found at i:1069289 original size:26 final size:29
Alignment explanation
Indices: 1069260--1069314 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
1069250 AATAAAATGT
*
1069260 AAAA-AATATATATATATAAT-AATATAA
1 AAAATAATATAAATATATAATGAATATAA
*
1069287 AAAATAATATAAATATATTATGAATATA
1 AAAATAATATAAATATATAATGAATATA
1069315 TAAATATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 14 0.58
29 6 0.25
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (29 bp):
AAAATAATATAAATATATAATGAATATAA
Found at i:1069292 original size:12 final size:12
Alignment explanation
Indices: 1069259--1069299 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
1069249 GAATAAAATG
1069259 TAAAAAATATATA
1 TAAAAAATA-ATA
* *
1069272 TATATAATAATA
1 TAAAAAATAATA
1069284 TAAAAAATAATA
1 TAAAAAATAATA
1069296 TAAA
1 TAAA
1069300 TATATTATGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
12 17 0.71
13 7 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
TAAAAAATAATA
Found at i:1069304 original size:8 final size:8
Alignment explanation
Indices: 1069263--1069421 Score: 56
Period size: 8 Copynumber: 18.5 Consensus size: 8
1069253 AAAATGTAAA
1069263 AAATATAT
1 AAATATAT
*
1069271 ATATATA-
1 AAATATAT
*
1069278 ATAATATAAA
1 A-AATAT-AT
1069288 AAATAATAT
1 AAAT-ATAT
1069297 AAATATATT
1 AAATATA-T
1069306 ATGAATATAT
1 A--AATATAT
*
1069316 AAATATTT
1 AAATATAT
*
1069324 AAAAAT-T
1 AAATATAT
1069331 AATATAATAT
1 AA-AT-ATAT
1069341 AAAT-TAT
1 AAATATAT
*
1069348 TAATATATT
1 AAATATA-T
1069357 AAA-ATTAT
1 AAATA-TAT
* * *
1069365 AATTTTTT
1 AAATATAT
1069373 AATATAATTAT
1 AA-AT-A-TAT
*
1069384 AATACAGTAT
1 AA-ATA-TAT
1069394 AAATATAT
1 AAATATAT
*
1069402 ATATATAT
1 AAATATAT
*
1069410 ATATATAT
1 AAATATAT
1069418 AAAT
1 AAAT
1069422 CATGAGGTTA
Statistics
Matches: 115, Mismatches: 19, Indels: 34
0.68 0.11 0.20
Matches are distributed among these distances:
7 10 0.09
8 56 0.49
9 23 0.20
10 14 0.12
11 12 0.10
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (8 bp):
AAATATAT
Found at i:1069314 original size:39 final size:40
Alignment explanation
Indices: 1069269--1069355 Score: 113
Period size: 40 Copynumber: 2.1 Consensus size: 40
1069259 TAAAAAATAT
*
1069269 ATATATATAATAATATAAAAAATAATATAA-ATATATTATGA
1 ATATATA-AAT-ATATAAAAAATAATATAATATAAATTATGA
* * *
1069310 ATATATAAATATTTAAAAATTAATATAATATAAATTATTA
1 ATATATAAATATATAAAAAATAATATAATATAAATTATGA
1069350 ATATAT
1 ATATAT
1069356 TAAAATTATA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
39 16 0.39
40 18 0.44
41 7 0.17
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (40 bp):
ATATATAAATATATAAAAAATAATATAATATAAATTATGA
Found at i:1069319 original size:28 final size:28
Alignment explanation
Indices: 1069259--1069320 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
1069249 GAATAAAATG
* *
1069259 TAAAAAATATATATATATAATAATATAA
1 TAAATAATATAAATATATAATAATATAA
* *
1069287 AAAATAATATAAATATATTATGAATAT-A
1 TAAATAATATAAATATATAAT-AATATAA
1069315 TAAATA
1 TAAATA
1069321 TTTAAAAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
28 23 0.82
29 5 0.18
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (28 bp):
TAAATAATATAAATATATAATAATATAA
Found at i:1069359 original size:33 final size:33
Alignment explanation
Indices: 1069298--1069360 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
1069288 AAATAATATA
* *
1069298 AATATATTATGAATATATAAATATTTAAAAATT
1 AATATAATATAAATATATAAATATTTAAAAATT
*
1069331 AATATAATATAAAT-TATTAATATATTAAAA
1 AATATAATATAAATATATAAATAT-TTAAAA
1069361 TTATAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 8 0.31
33 18 0.69
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (33 bp):
AATATAATATAAATATATAAATATTTAAAAATT
Found at i:1069374 original size:16 final size:17
Alignment explanation
Indices: 1069298--1069364 Score: 59
Period size: 18 Copynumber: 3.9 Consensus size: 17
1069288 AAATAATATA
* *
1069298 AATATATTATGAATATATA
1 AATATATTA-AAAT-TATT
1069317 AATAT-TTAAAA--ATT
1 AATATATTAAAATTATT
*
1069331 AATATAATATAAATTATT
1 AATATATTA-AAATTATT
1069349 AATATATTAAAATTAT
1 AATATATTAAAATTAT
1069365 AATTTTTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
14 7 0.17
15 2 0.05
16 3 0.08
17 9 0.22
18 14 0.35
19 5 0.12
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (17 bp):
AATATATTAAAATTATT
Found at i:1075610 original size:2 final size:2
Alignment explanation
Indices: 1075603--1075640 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1075593 AGATTTTGCA
1075603 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1075641 ATATATATAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1075645 original size:2 final size:2
Alignment explanation
Indices: 1075640--1075683 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
1075630 TCTCTCTCTC
* *
1075640 TA TA TA TA TA TA TA TA TA AA AA 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
1075682 TA
1 TA
1075684 AAAGAATAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1076093 original size:22 final size:22
Alignment explanation
Indices: 1076058--1076103 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
1076048 TCATATTTAT
1076058 TTAATTATATTAA-TAAATAAAA
1 TTAATTATATTAATTAAA-AAAA
1076080 TTAATT-TATCTAATTAAAAAAA
1 TTAATTATAT-TAATTAAAAAAA
1076102 TT
1 TT
1076104 TTGTGTTAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 3 0.14
22 15 0.68
23 4 0.18
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TTAATTATATTAATTAAAAAAA
Found at i:1076805 original size:64 final size:64
Alignment explanation
Indices: 1076704--1076832 Score: 249
Period size: 64 Copynumber: 2.0 Consensus size: 64
1076694 TGTAGGTCAC
1076704 AGGAAAGTTTAACAAATAAATGTAGTTGCAGGTATTATTTATATGTGTATATATATATATATAT
1 AGGAAAGTTTAACAAATAAATGTAGTTGCAGGTATTATTTATATGTGTATATATATATATATAT
*
1076768 AGGAAAGTTTAACAAATAAATGTAGTTGCAGGTATTATTTATATGTGTGTATATATATATATAT
1 AGGAAAGTTTAACAAATAAATGTAGTTGCAGGTATTATTTATATGTGTATATATATATATATAT
1076832 A
1 A
1076833 TATGCGCGCG
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.40, C:0.03, G:0.16, T:0.40
Consensus pattern (64 bp):
AGGAAAGTTTAACAAATAAATGTAGTTGCAGGTATTATTTATATGTGTATATATATATATATAT
Found at i:1083612 original size:12 final size:12
Alignment explanation
Indices: 1083597--1083652 Score: 67
Period size: 12 Copynumber: 4.7 Consensus size: 12
1083587 ATATGCATAC
*
1083597 ATACATACATAT
1 ATACATATATAT
*
1083609 ATACATATATGT
1 ATACATATATAT
*
1083621 ATATATATATAT
1 ATACATATATAT
*
1083633 ATATATATATAT
1 ATACATATATAT
*
1083645 ATATATAT
1 ATACATAT
1083653 CTCCTAACAG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 40 1.00
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (12 bp):
ATACATATATAT
Found at i:1083618 original size:2 final size:2
Alignment explanation
Indices: 1083605--1083652 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
1083595 ACATACATAC
* *
1083605 AT AT AT AC AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1083647 AT AT AT
1 AT AT AT
1083653 CTCCTAACAG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1091433 original size:232 final size:224
Alignment explanation
Indices: 1091027--1091482 Score: 723
Period size: 232 Copynumber: 2.0 Consensus size: 224
1091017 AAATAGTAAC
*
1091027 AAAAAGCAAGGAACTAAAGTAATGATACGTACATGAATCTATTTTCTCGCAACCTCTAAAACACC
1 AAAAAGCAAGGAACTAAAGCAATGATACGTACATGAATCTATTTTCTCGCAACCTCTAAAACACC
* *
1091092 TAACGATAATAATTAAGCATTTATATATATTGTTTACATGAACTTTTCTTGGAAACCAAACAGGA
66 TAACGAAAATAATTAAGCATTTATATATATTGTTTACATGAACCTTTCTTGGAAACCAAACAGGA
*
1091157 CTCAGAAACTCGAACTCTGTATTCATCAAAACGGGGAAAATAAACTAAAATTAAGGGGGAAAAAA
131 CTCAGAAACTCGAACTCTGTATTCATCAAAACGGGAAAAATAAACTAAAATT--------AAAAA
1091222 CAAAAGGCAGCATGAAAGAAATTCTTCACAATGTTAA
188 CAAAAGGCAGCATGAAAGAAATTCTTCACAATGTTAA
* * * *
1091259 AAAAAGCAAGGAATTAAAGCAATGATACGTTCATGAATCTATTTTTTCGCAACCTCTCAAACACC
1 AAAAAGCAAGGAACTAAAGCAATGATACGTACATGAATCTATTTTCTCGCAACCTCTAAAACACC
* * * **
1091324 TAATGAAAATAATTAAGTATTTATATATATTGTTTTCATTCACCTTTCTTGGAAACCAAACAGGA
66 TAACGAAAATAATTAAGCATTTATATATATTGTTTACATGAACCTTTCTTGGAAACCAAACAGGA
1091389 CTCAGAAACTCGAACTCTGTATTCATCAAAACGGGAAAAATAAACTAAAATTAAAAACAAAAGGC
131 CTCAGAAACTCGAACTCTGTATTCATCAAAACGGGAAAAATAAACTAAAATTAAAAACAAAAGGC
1091454 AGCATGAAAGAAATTCTTCACAATGTTAA
196 AGCATGAAAGAAATTCTTCACAATGTTAA
1091483 GACTAAAAAA
Statistics
Matches: 211, Mismatches: 13, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
224 42 0.20
232 169 0.80
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.26
Consensus pattern (224 bp):
AAAAAGCAAGGAACTAAAGCAATGATACGTACATGAATCTATTTTCTCGCAACCTCTAAAACACC
TAACGAAAATAATTAAGCATTTATATATATTGTTTACATGAACCTTTCTTGGAAACCAAACAGGA
CTCAGAAACTCGAACTCTGTATTCATCAAAACGGGAAAAATAAACTAAAATTAAAAACAAAAGGC
AGCATGAAAGAAATTCTTCACAATGTTAA
Found at i:1092049 original size:26 final size:28
Alignment explanation
Indices: 1092016--1092086 Score: 92
Period size: 31 Copynumber: 2.5 Consensus size: 28
1092006 CTTTGTTAAT
1092016 AATAAATTTTTATTTT-A-TTATATTTA
1 AATAAATTTTTATTTTAATTTATATTTA
1092042 AATAAATTTTTATTTTTTAAATTTATATTTA
1 AATAAATTTTTA--TTTT-AATTTATATTTA
*
1092073 AATATATTTTTATT
1 AATAAATTTTTATT
1092087 AAAATAAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
26 12 0.31
28 4 0.10
29 2 0.05
30 1 0.03
31 20 0.51
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (28 bp):
AATAAATTTTTATTTTAATTTATATTTA
Found at i:1092055 original size:16 final size:16
Alignment explanation
Indices: 1092036--1092094 Score: 66
Period size: 16 Copynumber: 3.8 Consensus size: 16
1092026 TATTTTATTA
1092036 TATTTAAATAAATTTT
1 TATTTAAATAAATTTT
** *
1092052 TATTT-TTTAAATTTA
1 TATTTAAATAAATTTT
*
1092067 TATTTAAATATATTTT
1 TATTTAAATAAATTTT
*
1092083 TATTAAAATAAA
1 TATTTAAATAAA
1092095 AATTGATTTA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
15 12 0.36
16 21 0.64
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TATTTAAATAAATTTT
Found at i:1092065 original size:25 final size:26
Alignment explanation
Indices: 1092016--1092066 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
1092006 CTTTGTTAAT
*
1092016 AATAAATTTTTATTTTATTATATTTA
1 AATAAATTTTTATTTTATTAAATTTA
1092042 AATAAATTTTTATTTT-TTAAATTTA
1 AATAAATTTTTATTTTATTAAATTTA
1092067 TATTTAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (26 bp):
AATAAATTTTTATTTTATTAAATTTA
Found at i:1092242 original size:49 final size:47
Alignment explanation
Indices: 1092157--1092248 Score: 116
Period size: 48 Copynumber: 1.9 Consensus size: 47
1092147 AAATATAATA
* *
1092157 TTTTTTTAATTTTAATTTATACAAATTATTATTTAATAATAAAATTAT
1 TTTTTTTAAATTTAATTTATACAAATTAATATTTAAT-ATAAAATTAT
1092205 TTTTATTTAAATTTAA-TTATACAAATATAA-ATATTAATATAAAA
1 TTTT-TTTAAATTTAATTTATACAAAT-TAATAT-TTAATATAAAA
1092249 ATAAATTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
48 22 0.56
49 17 0.44
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (47 bp):
TTTTTTTAAATTTAATTTATACAAATTAATATTTAATATAAAATTAT
Found at i:1092250 original size:49 final size:50
Alignment explanation
Indices: 1092147--1092259 Score: 119
Period size: 49 Copynumber: 2.3 Consensus size: 50
1092137 GCTAAAACTT
* *
1092147 AAATATAATATTTT-TTTAATTTTAATTTATACAAATTATTATTTAATAATA
1 AAATA-AAT-TTTTATTTAAATTTAATTTATACAAATTAATATTTAATAATA
*
1092198 AAAT-TATTTTTATTTAAATTTAA-TTATACAAATATAA-ATATTAAT-ATAA
1 AAATAAATTTTTATTTAAATTTAATTTATACAAAT-TAATAT-TTAATAAT-A
1092247 AAATAAATTTTTA
1 AAATAAATTTTTA
1092260 ATAATTTATA
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
48 18 0.34
49 24 0.45
50 7 0.13
51 4 0.08
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.50
Consensus pattern (50 bp):
AAATAAATTTTTATTTAAATTTAATTTATACAAATTAATATTTAATAATA
Found at i:1092871 original size:21 final size:19
Alignment explanation
Indices: 1092846--1092894 Score: 53
Period size: 21 Copynumber: 2.5 Consensus size: 19
1092836 AAATGTAATT
*
1092846 AATTATTTTTTGATTTATTAA
1 AATTATTTTTTGAATTA--AA
* *
1092867 AATTATGTATTGAATTAAA
1 AATTATTTTTTGAATTAAA
1092886 AATTATTTT
1 AATTATTTT
1092895 AAAAGGATTA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 9 0.39
21 14 0.61
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (19 bp):
AATTATTTTTTGAATTAAA
Found at i:1099383 original size:2 final size:2
Alignment explanation
Indices: 1099376--1099403 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1099366 AAATAAATAA
1099376 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
1099404 TAATCAACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1103845 original size:18 final size:17
Alignment explanation
Indices: 1103824--1103888 Score: 53
Period size: 18 Copynumber: 3.8 Consensus size: 17
1103814 TTCATAAATA
1103824 ATAT-TAATAAAATAATTT
1 ATATATAATAAAATAA--T
* * *
1103842 ATATTTAA-AATATAAA
1 ATATATAATAAAATAAT
*
1103858 ATATATAATAAATTAAT
1 ATATATAATAAAATAAT
1103875 ATATATAATTAAAA
1 ATATATAA-TAAAA
1103889 AATTTTGTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
16 7 0.19
17 13 0.35
18 14 0.38
19 3 0.08
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATATAATAAAATAAT
Found at i:1105573 original size:3 final size:3
Alignment explanation
Indices: 1105565--1105593 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1105555 ATTTTTGCTT
1105565 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1105594 TACTGAAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1105882 original size:21 final size:21
Alignment explanation
Indices: 1105858--1105905 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
1105848 ATTTAATTAC
1105858 TATTAATTAAAATCATATACA
1 TATTAATTAAAATCATATACA
* * * * *
1105879 TATTTATTTAAATTATATTCG
1 TATTAATTAAAATCATATACA
1105900 TATTAA
1 TATTAA
1105906 CAATAATACA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (21 bp):
TATTAATTAAAATCATATACA
Found at i:1106262 original size:2 final size:2
Alignment explanation
Indices: 1106255--1106282 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1106245 TCATCTTGTT
1106255 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
1106283 AGATCTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1107285 original size:20 final size:22
Alignment explanation
Indices: 1107233--1107282 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
1107223 TTAAGTATGC
* *
1107233 AAATATGATATTTTAAATATATT
1 AAATATAAT-TTTTAAATAAATT
1107256 AAA-ATAATTTTTAAA-AAATT
1 AAATATAATTTTTAAATAAATT
1107276 AAATATA
1 AAATATA
1107283 TTTATATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 7 0.29
21 10 0.42
22 4 0.17
23 3 0.12
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
AAATATAATTTTTAAATAAATT
Found at i:1128444 original size:15 final size:15
Alignment explanation
Indices: 1128386--1128455 Score: 70
Period size: 17 Copynumber: 4.5 Consensus size: 15
1128376 TTTTAATAAT
*
1128386 TAAATTTAAATGAAA
1 TAAATTTAAATTAAA
* *
1128401 AAATATTTATTATTAAA
1 TAA-ATTTA-AATTAAA
1128418 TAATACTTTAAATTAAA
1 TAA-A-TTTAAATTAAA
1128435 TAAATTTAAATTAAA
1 TAAATTTAAATTAAA
1128450 -AAATTT
1 TAAATTT
1128456 GTTTAAAATT
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
14 6 0.13
15 13 0.28
16 6 0.13
17 18 0.38
18 4 0.09
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (15 bp):
TAAATTTAAATTAAA
Found at i:1133365 original size:19 final size:19
Alignment explanation
Indices: 1133341--1133377 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1133331 AAGATTTAAA
* *
1133341 TTTTAATATTTATAATTTT
1 TTTTAAAATTTAAAATTTT
1133360 TTTTAAAATTTAAAATTT
1 TTTTAAAATTTAAAATTT
1133378 ATATGAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTAAAATTTAAAATTTT
Found at i:1134237 original size:3 final size:3
Alignment explanation
Indices: 1134229--1134288 Score: 52
Period size: 3 Copynumber: 20.3 Consensus size: 3
1134219 TAAAATTAAA
* * * *
1134229 AAT AAT AAT AAT GAT AA- AATT AAT TAT TAT AAT AAT AAT ATT AA-
1 AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT
*
1134273 AAT AAA AAT AAT AAT A
1 AAT AAT AAT AAT AAT A
1134289 GATCAGATAT
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
2 4 0.09
3 40 0.87
4 2 0.04
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:1134634 original size:31 final size:31
Alignment explanation
Indices: 1134596--1134670 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 31
1134586 ATCTAAAAAT
*
1134596 TAATATCCGAATCCACTATTAGTGATAATTA
1 TAATATCCGAATCCACTATTAATGATAATTA
* *
1134627 TAATATCCAAATCCACTATTAATGGTAATTA
1 TAATATCCGAATCCACTATTAATGATAATTA
1134658 TAATATCCGAATC
1 TAATATCCGAATC
1134671 TAAATATTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (31 bp):
TAATATCCGAATCCACTATTAATGATAATTA
Found at i:1134935 original size:35 final size:35
Alignment explanation
Indices: 1134903--1135110 Score: 137
Period size: 35 Copynumber: 5.9 Consensus size: 35
1134893 TGTTAAAAAC
1134903 ATATTTATATGAAATAATAAAATATAAATAAAATT
1 ATATTTATATGAAATAATAAAATATAAATAAAATT
* * *
1134938 AT-TTTCATTTTGAATAATAATTAAAA-ATTATTAAAATT
1 ATATTT-A-TATG-A-AATAA-TAAAATATAAATAAAATT
* *
1134976 GTATTTATATTAAATAATAAAATATAAATAAAATT
1 ATATTTATATGAAATAATAAAATATAAATAAAATT
* * *
1135011 ATATTTATGTTGAATAATAATTAAAA-AT-TATTAAATT
1 ATATTTAT-ATG-A-AATAA-TAAAATATAAATAAAATT
* *
1135048 ATATTTATAT-AAA-AAT-AAAT-T-ATTAACATT
1 ATATTTATATGAAATAATAAAATATAAATAAAATT
* * * *
1135078 TTATTTATATTAAATAATATATATATATATAAA
1 ATATTTATATGAAATAATA-AAATATAAATAAA
1135111 TTTTAAAAAT
Statistics
Matches: 132, Mismatches: 23, Indels: 35
0.69 0.12 0.18
Matches are distributed among these distances:
30 18 0.14
31 4 0.03
32 5 0.04
33 2 0.02
34 12 0.09
35 26 0.20
36 9 0.07
37 19 0.14
38 24 0.18
39 13 0.10
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (35 bp):
ATATTTATATGAAATAATAAAATATAAATAAAATT
Found at i:1134973 original size:38 final size:38
Alignment explanation
Indices: 1134903--1135057 Score: 150
Period size: 38 Copynumber: 4.3 Consensus size: 38
1134893 TGTTAAAAAC
* *
1134903 ATATTTATA-TG-A-AATAA-TAAAATATAAATAAAATT
1 ATATTTATATTGAATAATAATTAAAA-ATTATTAAAATT
*
1134938 AT-TTTCATTTTGAATAATAATTAAAAATTATTAAAATT
1 ATATTT-ATATTGAATAATAATTAAAAATTATTAAAATT
* * *
1134976 GTATTTATATT--A-AATAA-TAAAATATAAATAAAATT
1 ATATTTATATTGAATAATAATTAAAA-ATTATTAAAATT
*
1135011 ATATTTATGTTGAATAATAATTAAAAATTATT-AAATT
1 ATATTTATATTGAATAATAATTAAAAATTATTAAAATT
1135048 ATATTTATAT
1 ATATTTATAT
1135058 AAAAATAAAT
Statistics
Matches: 97, Mismatches: 12, Indels: 20
0.75 0.09 0.16
Matches are distributed among these distances:
34 8 0.08
35 28 0.29
36 3 0.03
37 16 0.16
38 29 0.30
39 13 0.13
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (38 bp):
ATATTTATATTGAATAATAATTAAAAATTATTAAAATT
Found at i:1135085 original size:30 final size:31
Alignment explanation
Indices: 1135035--1135096 Score: 92
Period size: 30 Copynumber: 2.0 Consensus size: 31
1135025 TAATAATTAA
1135035 AAATTATTAAATTATATTTATA-TAAA-AAT
1 AAATTATTAAATTATATTTATATTAAATAAT
*
1135064 AAATTATTAACATTTTATTTATATTAAATAAT
1 AAATTATTAA-ATTATATTTATATTAAATAAT
1135096 A
1 A
1135097 TATATATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 10 0.34
30 11 0.38
31 4 0.14
32 4 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (31 bp):
AAATTATTAAATTATATTTATATTAAATAAT
Found at i:1135086 original size:73 final size:73
Alignment explanation
Indices: 1134903--1135136 Score: 268
Period size: 73 Copynumber: 3.2 Consensus size: 73
1134893 TGTTAAAAAC
* *
1134903 ATATTTATATGAAATAATAAAATATAAATAAAATTAT-TTTCATTTTGAATAATAATTAAAAATT
1 ATATTTATATTAAATAATAAAATATAAATAAAATTATATTT-ATGTTGAATAATAATTAAAAATT
1134967 ATTAAAATT
65 ATTAAAATT
*
1134976 GTATTTATATTAAATAATAAAATATAAATAAAATTATATTTATGTTGAATAATAATTAAAAATTA
1 ATATTTATATTAAATAATAAAATATAAATAAAATTATATTTATGTTGAATAATAATTAAAAATTA
1135041 TT-AAATT
66 TTAAAATT
* * * * *
1135048 ATATTTATA-TAAA-AAT-AAAT-T-ATTAACATTTTATTTATATTAAATAATATATATATATAT
1 ATATTTATATTAAATAATAAAATATAAATAAAATTATATTTATGTTGAAT-A-ATA-AT-TA-A-
*
1135108 AAATT-TTAAAAAT
60 AAATTATTAAAATT
1135121 ATATTTATATTAAATA
1 ATATTTATATTAAATA
1135137 TTATTTATGT
Statistics
Matches: 141, Mismatches: 10, Indels: 18
0.83 0.06 0.11
Matches are distributed among these distances:
67 19 0.13
68 2 0.01
69 7 0.05
70 5 0.04
71 6 0.04
72 16 0.11
73 78 0.55
74 7 0.05
75 1 0.01
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (73 bp):
ATATTTATATTAAATAATAAAATATAAATAAAATTATATTTATGTTGAATAATAATTAAAAATTA
TTAAAATT
Found at i:1135091 original size:46 final size:44
Alignment explanation
Indices: 1135039--1135165 Score: 139
Period size: 43 Copynumber: 2.8 Consensus size: 44
1135029 AATTAAAAAT
* * *
1135039 TATTAAATTATATTTATATAAAAATAAATTATTAACATTTTATTTA
1 TATTAAA-TATATTTATATAAAAATAAATT-TTAAAAATATATTTA
* * *
1135085 TATTAAATA-ATATATATATATATAAATTTTAAAAATATATTTA
1 TATTAAATATATTTATATAAAAATAAATTTTAAAAATATATTTA
* *
1135128 TATTAAATATTATTTATGTTAAAATATAATTTTAAAAA
1 TATTAAATA-TATTTATATAAAAATA-AATTTTAAAAA
1135166 ATAAAAAAAA
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
43 21 0.31
44 16 0.24
45 12 0.18
46 18 0.27
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (44 bp):
TATTAAATATATTTATATAAAAATAAATTTTAAAAATATATTTA
Found at i:1135122 original size:25 final size:25
Alignment explanation
Indices: 1135087--1135135 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1135077 TTTATTTATA
1135087 TTAAATAATATATATATATATAAATT
1 TTAAATAATATATATATAT-TAAATT
*
1135113 TTAAA-AATATATTTATATTAAAT
1 TTAAATAATATATATATATTAAAT
1135136 ATTATTTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.23
25 12 0.55
26 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
TTAAATAATATATATATATTAAATT
Found at i:1135159 original size:17 final size:16
Alignment explanation
Indices: 1135039--1135155 Score: 56
Period size: 16 Copynumber: 7.8 Consensus size: 16
1135029 AATTAAAAAT
*
1135039 TATTAAATTATATTTA
1 TATTAAAATATATTTA
**
1135055 TA-TAAAA-ATAAAT-
1 TATTAAAATATATTTA
* *
1135068 TATTAACATTTTATTTA
1 TATTAA-AATATATTTA
*
1135085 TATT-AAATA-ATATA
1 TATTAAAATATATTTA
* *
1135099 TA-TATATATAAATTT-
1 TATTA-AAATATATTTA
1135114 TA--AAAATATATTTA
1 TATTAAAATATATTTA
1135128 TATT-AAATATTATTTA
1 TATTAAAATA-TATTTA
*
1135144 TGTTAAAATATA
1 TATTAAAATATA
1135156 ATTTTAAAAA
Statistics
Matches: 74, Mismatches: 15, Indels: 24
0.65 0.13 0.21
Matches are distributed among these distances:
13 11 0.15
14 16 0.22
15 18 0.24
16 20 0.27
17 9 0.12
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (16 bp):
TATTAAAATATATTTA
Found at i:1135675 original size:21 final size:20
Alignment explanation
Indices: 1135651--1135725 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 20
1135641 TATGTATATA
1135651 ATATATTTTAATTATAATTTT
1 ATATATTTTAATTA-AATTTT
1135672 ATATATTTTTAATTAAA-TTT
1 ATATA-TTTTAATTAAATTTT
* *
1135692 ATAT-TTATATTTAATATTTT
1 ATATATTTTAATTAA-ATTTT
1135712 A-ATATATTTAATTA
1 ATATAT-TTTAATTA
1135726 TTTATATAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
18 8 0.18
19 3 0.07
20 12 0.27
21 13 0.29
22 9 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATATATTTTAATTAAATTTT
Found at i:1135684 original size:22 final size:22
Alignment explanation
Indices: 1135645--1135706 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 22
1135635 TAAAAATATG
1135645 TATATAATATATTTTAATTATAATT
1 TATAT-ATAT-TTTTAATTA-AATT
1135670 T-TATATATTTTTAATTAAATT
1 TATATATATTTTTAATTAAATT
* *
1135691 TATATTTATATTTAAT
1 TATATATATTTTTAAT
1135707 ATTTTAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 5 0.15
22 21 0.62
23 4 0.12
24 3 0.09
25 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TATATATATTTTTAATTAAATT
Found at i:1135696 original size:39 final size:37
Alignment explanation
Indices: 1135652--1135732 Score: 94
Period size: 39 Copynumber: 2.1 Consensus size: 37
1135642 ATGTATATAA
*
1135652 TATATTT-TAATT-ATAATTTTATATATTTTTAATTAAATT
1 TATATTTATAATTAAT-ATTTTA-ATATATTTAATT--ATT
*
1135691 TATATTTATATTTAATATTTTAATATATTTAATTATT
1 TATATTTATAATTAATATTTTAATATATTTAATTATT
1135728 TATAT
1 TATAT
1135733 AATTATATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
37 8 0.21
39 18 0.47
40 10 0.26
41 2 0.05
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (37 bp):
TATATTTATAATTAATATTTTAATATATTTAATTATT
Found at i:1135723 original size:9 final size:9
Alignment explanation
Indices: 1135697--1135733 Score: 53
Period size: 8 Copynumber: 4.4 Consensus size: 9
1135687 AATTTATATT
1135697 TATATTTAA
1 TATATTTAA
1135706 TAT-TTTAA
1 TATATTTAA
1135714 TATATTTAA
1 TATATTTAA
1135723 T-TATTT-A
1 TATATTTAA
1135730 TATA
1 TATA
1135734 ATTATATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
7 2 0.08
8 15 0.58
9 9 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TATATTTAA
Found at i:1136191 original size:24 final size:24
Alignment explanation
Indices: 1136130--1136197 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
1136120 AATAAAAGAG
*
1136130 AAATTCATTTATATATTAA-TATAA
1 AAATTAATTTAT-TATTAATTATAA
***
1136154 AAATTAAAAAATTATTAATTATAA
1 AAATTAATTTATTATTAATTATAA
* *
1136178 ATATTAATTTATTAATAATT
1 AAATTAATTTATTATTAATT
1136198 TATTATTTTA
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
23 6 0.18
24 28 0.82
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (24 bp):
AAATTAATTTATTATTAATTATAA
Found at i:1137959 original size:19 final size:20
Alignment explanation
Indices: 1137935--1137976 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1137925 CAAAAATTTC
1137935 CCTTTTT-TTTCCTT-CTTT
1 CCTTTTTATTTCCTTCCTTT
*
1137953 CCTTTTTATTTCTTTCCTTT
1 CCTTTTTATTTCCTTCCTTT
1137973 CCTT
1 CCTT
1137977 GCTTTCTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.33
19 6 0.29
20 8 0.38
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (20 bp):
CCTTTTTATTTCCTTCCTTT
Found at i:1144970 original size:6 final size:7
Alignment explanation
Indices: 1144954--1144978 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1144944 AAGCAGGTGC
1144954 TTTTCAT
1 TTTTCAT
1144961 TTTTCAT
1 TTTTCAT
1144968 TTTTCAT
1 TTTTCAT
1144975 TTTT
1 TTTT
1144979 TTACCCATTT
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:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTCAT
Found at i:1148039 original size:3 final size:3
Alignment explanation
Indices: 1148031--1148068 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
1148021 TGAAAGCATT
*
1148031 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1148069 TATTATTGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1148239 original size:2 final size:2
Alignment explanation
Indices: 1148232--1148257 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1148222 ATTTACATAA
1148232 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
1148258 GTATTTATTG
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:1151840 original size:2 final size:2
Alignment explanation
Indices: 1151788--1151826 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1151778 CTCCGAAGTA
1151788 AT AT 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 AT AT A
1151827 AAAGATGAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1151954 original size:23 final size:23
Alignment explanation
Indices: 1151928--1151984 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
1151918 TTTTGCTTCA
*
1151928 TATATAATATAAAAAATAGTTAT
1 TATATAATATAAAAAATAATTAT
**
1151951 TATATAACGT-AAAAATAATTAT
1 TATATAATATAAAAAATAATTAT
1151973 TATATATATATA
1 TATATA-ATATA
1151985 TGATAATTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
22 17 0.63
23 10 0.37
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (23 bp):
TATATAATATAAAAAATAATTAT
Found at i:1152074 original size:52 final size:48
Alignment explanation
Indices: 1152003--1152112 Score: 111
Period size: 52 Copynumber: 2.2 Consensus size: 48
1151993 TAAAATATGT
1152003 TATAATTA-T-ATGATA-TAAAAATAATATAAATATATTAA-ATTTTATATAA
1 TATAATTATTAAT-ATATTAAAAATAATATAAATATA-TAATA-TTT-TA-AA
* * *
1152052 TATAAATTATTAATATATTAAAATTTATATAATTATATAATATTTTAAA
1 TAT-AATTATTAATATATTAAAAATAATATAAATATATAATATTTTAAA
1152101 TATAATTATTAA
1 TATAATTATTAA
1152113 ATGATAAAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
48 9 0.17
49 8 0.15
50 7 0.13
51 10 0.19
52 19 0.36
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (48 bp):
TATAATTATTAATATATTAAAAATAATATAAATATATAATATTTTAAA
Found at i:1152712 original size:16 final size:16
Alignment explanation
Indices: 1152691--1152727 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
1152681 ATCAATTAAT
*
1152691 TTAAATTTAAATCAAA
1 TTAAATTTAAATAAAA
1152707 TTAAATTTAAATAAAA
1 TTAAATTTAAATAAAA
1152723 TTAAA
1 TTAAA
1152728 AAACAAATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
TTAAATTTAAATAAAA
Found at i:1157600 original size:14 final size:14
Alignment explanation
Indices: 1157581--1157607 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1157571 GTCCGGCCAC
1157581 CATAATTTTAATCA
1 CATAATTTTAATCA
1157595 CATAATTTTAATC
1 CATAATTTTAATC
1157608 CCTTATACAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (14 bp):
CATAATTTTAATCA
Found at i:1158644 original size:54 final size:54
Alignment explanation
Indices: 1158581--1158691 Score: 186
Period size: 54 Copynumber: 2.1 Consensus size: 54
1158571 CTGACCAAAT
*
1158581 CATCATCAAAGCATTTGGTCTTTGACTTCTTTTAACCCTTCCAACATAATTCAA
1 CATCATCAAAGCATTTGGTCTTTGACTCCTTTTAACCCTTCCAACATAATTCAA
** *
1158635 CATCATCAAAGCATTTTTTCTTTTACTCCTTTTAACCCTTCCAACATAATTCAA
1 CATCATCAAAGCATTTGGTCTTTGACTCCTTTTAACCCTTCCAACATAATTCAA
1158689 CAT
1 CAT
1158692 AATTCATTAT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.30, C:0.27, G:0.05, T:0.39
Consensus pattern (54 bp):
CATCATCAAAGCATTTGGTCTTTGACTCCTTTTAACCCTTCCAACATAATTCAA
Found at i:1160130 original size:33 final size:32
Alignment explanation
Indices: 1160085--1160158 Score: 80
Period size: 33 Copynumber: 2.2 Consensus size: 32
1160075 TTTTTAAATT
* *
1160085 TATATAATATT-AATTATAAAA-AGTTATATAAA
1 TATAAAATATTAAATTA-AAAATA-TGATATAAA
1160117 TATAAAATAATTAAATTAAAAATATGATATAAA
1 TATAAAAT-ATTAAATTAAAAATATGATATAAA
1160150 TATCAAAAT
1 TAT-AAAAT
1160159 TGATAAGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
32 7 0.19
33 18 0.50
34 11 0.31
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.36
Consensus pattern (32 bp):
TATAAAATATTAAATTAAAAATATGATATAAA
Found at i:1170904 original size:12 final size:13
Alignment explanation
Indices: 1170866--1170912 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 13
1170856 ATATATGCTC
*
1170866 ATATTATTTTTTA
1 ATATTAATTTTTA
*
1170879 AAATATATATTTTTA
1 ATAT-TA-ATTTTTA
1170894 AT-TTAATTTTTA
1 ATATTAATTTTTA
1170906 ATATTAA
1 ATATTAA
1170913 ATATATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
12 9 0.32
13 9 0.32
14 3 0.11
15 7 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
ATATTAATTTTTA
Found at i:1171148 original size:14 final size:14
Alignment explanation
Indices: 1171124--1171156 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1171114 CTGTATCATA
*
1171124 TTTTA-AATAATTT
1 TTTTATAATAATAT
1171137 TTTTATAATAATAT
1 TTTTATAATAATAT
1171151 TTTTAT
1 TTTTAT
1171157 TTAAATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTATAATAATAT
Found at i:1171183 original size:20 final size:17
Alignment explanation
Indices: 1171158--1171197 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 17
1171148 TATTTTTATT
1171158 TAAATTTTATAAATATTAAA
1 TAAATTTT-T-AATA-TAAA
1171178 TAAATTTTTAATATAAA
1 TAAATTTTTAATATAAA
1171195 TAA
1 TAA
1171198 TCAAATGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 4 0.20
19 1 0.05
20 8 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAATTTTTAATATAAA
Found at i:1176877 original size:17 final size:17
Alignment explanation
Indices: 1176855--1176901 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
1176845 AAATATTTTA
1176855 TAATTTTTATTTAAATT
1 TAATTTTTATTTAAATT
**
1176872 TAATTTAAATTTAAATT
1 TAATTTTTATTTAAATT
*
1176889 TAAAATTTTATTT
1 T-AATTTTTATTT
1176902 TTTATAAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TAATTTTTATTTAAATT
Found at i:1176879 original size:11 final size:12
Alignment explanation
Indices: 1176863--1176892 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
1176853 TATAATTTTT
1176863 ATTTAAATTT-A
1 ATTTAAATTTAA
1176874 ATTTAAATTTAA
1 ATTTAAATTTAA
1176886 ATTTAAA
1 ATTTAAA
1176893 ATTTTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATTTAAATTTAA
Found at i:1176896 original size:7 final size:6
Alignment explanation
Indices: 1176863--1176892 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1176853 TATAATTTTT
1176863 ATTTAA ATTT-A ATTTAA ATTTAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A
1176893 ATTTTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATTTAA
Found at i:1193683 original size:2 final size:2
Alignment explanation
Indices: 1193676--1193719 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1193666 CTTTTTATTT
1193676 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
1193718 TA
1 TA
1193720 CTTGTTTCAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1193852 original size:13 final size:13
Alignment explanation
Indices: 1193834--1193859 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1193824 ATTATTTTTT
1193834 TAGTAAAAAAATA
1 TAGTAAAAAAATA
1193847 TAGTAAAAAAATA
1 TAGTAAAAAAATA
1193860 AATTTATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (13 bp):
TAGTAAAAAAATA
Found at i:1193871 original size:13 final size:13
Alignment explanation
Indices: 1193855--1193897 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1193845 TATAGTAAAA
*
1193855 AAATAAATTTATT
1 AAATAAATTAATT
1193868 AAATATTAATTAATT
1 AAATA--AATTAATT
*
1193883 ATATAAATTAATT
1 AAATAAATTAATT
1193896 AA
1 AA
1193898 GTTTAATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
13 14 0.56
15 11 0.44
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAAATTAATT
Found at i:1196066 original size:2 final size:2
Alignment explanation
Indices: 1196059--1196087 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1196049 AGATATTGAA
1196059 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1196088 GATCTCTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1196577 original size:24 final size:24
Alignment explanation
Indices: 1196532--1196577 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
1196522 ATATATATCT
**
1196532 AAGCTTAAACACATTTTTTTTTTA
1 AAGCTTAAACACATTTCATTTTTA
* *
1196556 AAGCTTAAATACGTTTCATTTT
1 AAGCTTAAACACATTTCATTTT
1196578 CTGAATAGAG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.48
Consensus pattern (24 bp):
AAGCTTAAACACATTTCATTTTTA
Found at i:1201981 original size:2 final size:2
Alignment explanation
Indices: 1201976--1202005 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1201966 AGAGAGAAGA
1201976 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
1202006 TAAACTCCTA
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:1213515 original size:2 final size:2
Alignment explanation
Indices: 1213508--1213559 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1213498 TTCACTGTAA
1213508 TC TC TC TC TC TC TC 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 TC TC TC TC TC TC TC
1213550 TC TC TC TC TC
1 TC TC TC TC TC
1213560 CCGTTCATTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1213584 original size:2 final size:2
Alignment explanation
Indices: 1213577--1213606 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1213567 TTGCTAATTA
1213577 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1213607 CTTCTTCGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1213757 original size:22 final size:23
Alignment explanation
Indices: 1213731--1213779 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
1213721 TGTTAATATT
* *
1213731 AATTAAATTATAATTT-ATAATA
1 AATTAAAATATAATTTAATAACA
*
1213753 AATTAAAATATTATTTAATAACA
1 AATTAAAATATAATTTAATAACA
1213776 AATT
1 AATT
1213780 TGTTAACTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
AATTAAAATATAATTTAATAACA
Found at i:1213847 original size:16 final size:16
Alignment explanation
Indices: 1213800--1213847 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 16
1213790 TACTTCTATC
*
1213800 AAAAATTTATATTTTT
1 AAAAATATATATTTTT
**
1213816 TTAAATATAATAATTTTT
1 AAAAATAT-AT-ATTTTT
1213834 AAAAATATATATTT
1 AAAAATATATATTT
1213848 GAACACGTTG
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
16 9 0.36
17 4 0.16
18 12 0.48
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AAAAATATATATTTTT
Found at i:1213895 original size:22 final size:22
Alignment explanation
Indices: 1213867--1213910 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1213857 GGTTAACAAA
1213867 AACTTTTGTTCTATTATTTGTT
1 AACTTTTGTTCTATTATTTGTT
1213889 AACTTTTGTTCTATTATTTGTT
1 AACTTTTGTTCTATTATTTGTT
1213911 TGACATTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.09, G:0.09, T:0.64
Consensus pattern (22 bp):
AACTTTTGTTCTATTATTTGTT
Found at i:1214806 original size:12 final size:12
Alignment explanation
Indices: 1214789--1214830 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
1214779 AATTATAAAA
1214789 AATATATTTTTT
1 AATATATTTTTT
*
1214801 AATATATTTATT
1 AATATATTTTTT
*
1214813 -ATTTATTTTTT
1 AATATATTTTTT
*
1214824 AAAATAT
1 AATATAT
1214831 ATTCTATGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
AATATATTTTTT
Found at i:1215094 original size:2 final size:2
Alignment explanation
Indices: 1215081--1215112 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1215071 CGAAAACGTG
*
1215081 AT AT AA 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
1215113 TGTATGGATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1216992 original size:29 final size:28
Alignment explanation
Indices: 1216925--1217000 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 28
1216915 TTTATTTGAA
* *
1216925 TATAATAATGATATATTATTAAATTTTTT
1 TATAAAAAT-ATATATTATTAAATATTTT
*
1216954 TAAAAAAATATATAATATATT-AATATTTT
1 TATAAAAATATAT-AT-TATTAAATATTTT
*
1216983 TATAAAAATA-AAATTATT
1 TATAAAAATATATATTATT
1217001 TTATTTATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
26 4 0.10
27 2 0.05
28 5 0.12
29 25 0.62
30 4 0.10
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (28 bp):
TATAAAAATATATATTATTAAATATTTT
Found at i:1219023 original size:2 final size:2
Alignment explanation
Indices: 1219016--1219047 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1219006 CTAAATTCTG
1219016 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
1219048 ATGTAAGTAG
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:1219766 original size:23 final size:22
Alignment explanation
Indices: 1219740--1219799 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 22
1219730 AATAAAAATT
1219740 TTATTATATTTATATGTTATATA
1 TTATT-TATTTATATGTTATATA
* * * *
1219763 TTATTTTAATTATTTTTTATATT
1 TTA-TTTATTTATATGTTATATA
*
1219786 TTATTTTTTTATAT
1 TTATTTATTTATAT
1219800 AATTATATCA
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
22 8 0.28
23 19 0.66
24 2 0.07
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (22 bp):
TTATTTATTTATATGTTATATA
Found at i:1220288 original size:18 final size:18
Alignment explanation
Indices: 1220277--1220311 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1220267 TTAATTGAAT
1220277 TGATCAAATTAATCCAGA
1 TGATCAAATTAATCCAGA
1220295 TGATCAAATTAATCCAG
1 TGATCAAATTAATCCAG
1220312 CTGCGAAGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (18 bp):
TGATCAAATTAATCCAGA
Found at i:1228426 original size:13 final size:13
Alignment explanation
Indices: 1228408--1228434 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1228398 AAACTCATAT
1228408 TCGAATATAAATA
1 TCGAATATAAATA
1228421 TCGAATATAAATA
1 TCGAATATAAATA
1228434 T
1 T
1228435 ATATTTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.33
Consensus pattern (13 bp):
TCGAATATAAATA
Found at i:1228490 original size:13 final size:13
Alignment explanation
Indices: 1228472--1228519 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
1228462 ATTTAAATAT
1228472 ATATCAAATATAA
1 ATATCAAATATAA
*
1228485 ATATCAAACATAA
1 ATATCAAATATAA
* *
1228498 ATACTTAAA-ATAG
1 ATA-TCAAATATAA
1228511 ATATCAAAT
1 ATATCAAAT
1228520 CAATCTTACC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 4 0.14
13 21 0.72
14 4 0.14
ACGTcount: A:0.58, C:0.10, G:0.02, T:0.29
Consensus pattern (13 bp):
ATATCAAATATAA
Found at i:1230014 original size:7 final size:7
Alignment explanation
Indices: 1230002--1230029 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
1229992 AAATTGGCAG
1230002 GTGAAAA
1 GTGAAAA
1230009 GTGAAAA
1 GTGAAAA
1230016 GTGAAAA
1 GTGAAAA
1230023 GTGAAAA
1 GTGAAAA
1230030 CCTATTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.29, T:0.14
Consensus pattern (7 bp):
GTGAAAA
Found at i:1230736 original size:2 final size:2
Alignment explanation
Indices: 1230729--1230754 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1230719 AATAAATTTA
1230729 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
1230755 CAATTAAGCG
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:1232398 original size:2 final size:2
Alignment explanation
Indices: 1232391--1232424 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1232381 AGCAAAATTT
1232391 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
1232425 AAGATGGCAA
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):
TA
Found at i:1233010 original size:3 final size:3
Alignment explanation
Indices: 1233002--1233029 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1232992 TTAACTTATC
1233002 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1233030 TATGCACTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1233642 original size:2 final size:2
Alignment explanation
Indices: 1233632--1233666 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1233622 TAAAAAATCG
1233632 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1233667 CACGCAATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1236393 original size:45 final size:45
Alignment explanation
Indices: 1236329--1236463 Score: 189
Period size: 45 Copynumber: 3.0 Consensus size: 45
1236319 AATTGAAGGT
*
1236329 AAATTACTAACTGAATCTCTACAGTCATCTCCTATTGCTTATCAG
1 AAATTACTAACTGAATCTCTACACTCATCTCCTATTGCTTATCAG
* * *
1236374 AAATTACTAACTGAATCTCTATACTCGTCTCCTTTTGCTTATCAG
1 AAATTACTAACTGAATCTCTACACTCATCTCCTATTGCTTATCAG
** * * *
1236419 AAATTACTAACTGAATCTCTATGCACGTCTCCTTTTGCTTATCAG
1 AAATTACTAACTGAATCTCTACACTCATCTCCTATTGCTTATCAG
1236464 TTTAAGTAAA
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 84 1.00
ACGTcount: A:0.28, C:0.24, G:0.10, T:0.38
Consensus pattern (45 bp):
AAATTACTAACTGAATCTCTACACTCATCTCCTATTGCTTATCAG
Found at i:1239600 original size:162 final size:160
Alignment explanation
Indices: 1239333--1239809 Score: 824
Period size: 162 Copynumber: 3.0 Consensus size: 160
1239323 AAATACCGTT
1239333 TAGATGAGGTTCATGAAAAATGGGCCTCTTTCCCTCAGGGTAAATGTAGACTTTAAGTATTATTT
1 TAGATGAGGTTCATGAAAAATGGGCCTCTTTCCCTCAGGGTAAATGTAGACTTTAAGTATTATTT
1239398 CCATCAAATCGTAGCTCCTTAAAGTTACAGGAAAGAACATATAATTTTCAGTATTTAGTCACCAC
66 CCATC-AA-CGTAGCTCCTTAAAGTTACAGGAAAGAACATATAATTTTCAGTATTTAGTCACCAC
1239463 ATACATTGCAAAAACCACCACAAGAACTCAGA
129 ATACATTGCAAAAACCACCACAAGAACTCAGA
* *
1239495 TAGATGAGGTTCACGAAAAATGGGCCTCTTTCTCTCAGGGTAAATGTAGACTTTAAGTATTATTT
1 TAGATGAGGTTCATGAAAAATGGGCCTCTTTCCCTCAGGGTAAATGTAGACTTTAAGTATTATTT
1239560 CCATCAACGCGTAGCTCCTTAAAGTTACAGGAAAGAACATATAATTTTCAGTATTTAGTCACCAC
66 CCATCAA--CGTAGCTCCTTAAAGTTACAGGAAAGAACATATAATTTTCAGTATTTAGTCACCAC
1239625 ATACATTGCAAAAACCACCACAAGAACTCAGA
129 ATACATTGCAAAAACCACCACAAGAACTCAGA
*
1239657 TAGATGAGGTTCATGAAAAATGGACCTCTTTCCCTC-GTGGTAAATGTAGACTTTAAGTATTATT
1 TAGATGAGGTTCATGAAAAATGGGCCTCTTTCCCTCAG-GGTAAATGTAGACTTTAAGTATTATT
*
1239721 TCCATC-A---A-CT-CGTAAAGTTACAGGAAAGAACATATAATTTTCAGTATTTAGTCACCACA
65 TCCATCAACGTAGCTCCTTAAAGTTACAGGAAAGAACATATAATTTTCAGTATTTAGTCACCACA
1239780 TACATTGCAAAAACCACCACAAGAACTCAG
130 TACATTGCAAAAACCACCACAAGAACTCAG
1239810 TTTTCCAATT
Statistics
Matches: 306, Mismatches: 7, Indels: 12
0.94 0.02 0.04
Matches are distributed among these distances:
154 78 0.25
155 2 0.01
156 1 0.00
161 4 0.01
162 221 0.72
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (160 bp):
TAGATGAGGTTCATGAAAAATGGGCCTCTTTCCCTCAGGGTAAATGTAGACTTTAAGTATTATTT
CCATCAACGTAGCTCCTTAAAGTTACAGGAAAGAACATATAATTTTCAGTATTTAGTCACCACAT
ACATTGCAAAAACCACCACAAGAACTCAGA
Found at i:1242034 original size:2 final size:2
Alignment explanation
Indices: 1242027--1242056 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1242017 TTGATTAGCA
*
1242027 AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1242057 TTTGAGTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1254862 original size:24 final size:23
Alignment explanation
Indices: 1254831--1254878 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
1254821 ATGCTGCCTA
1254831 TGTTAGTTTTTCTTCTTTT-GTTT
1 TGTTAGTTTTT-TTCTTTTAGTTT
*
1254854 TGTTCAGTTTTTTTTTTTTAGTTT
1 TGTT-AGTTTTTTTCTTTTAGTTT
1254878 T
1 T
1254879 TGTCTGATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.06, C:0.06, G:0.12, T:0.75
Consensus pattern (23 bp):
TGTTAGTTTTTTTCTTTTAGTTT
Found at i:1269864 original size:144 final size:143
Alignment explanation
Indices: 1269608--1269876 Score: 322
Period size: 144 Copynumber: 1.9 Consensus size: 143
1269598 CCAAAGTTCT
* * * * *
1269608 ATTGTTTAGACCTCTAAATCTACAAGATTCAGTTCAGACGAACAACCGCAAAGATGCTAGCATGT
1 ATTGTTCAGACCTCTAAATCTACAAAATTCAGCTCACACGAACAACCGCAAAGATGCTAGAATGT
* * * * * ** **
1269673 CCTACCGATAGTCCAATACATAAACTAGTGGATTATGGGAAGGTGTTCTTTTGCTACTATTGCTA
66 CCTACCAATAGTCCAATACACAAACTAGAGCAATAACGGAACATGTTC-TTTGCTACTATTGCTA
1269738 TAATCTATCTTTCC
130 TAATCTATCTTTCC
* * * * * *
1269752 ATTGTTCAGACCTGTAAATCTATAAAATTCAGCTCACATGAACAACTGCAAAGGTTCTAGAATGT
1 ATTGTTCAGACCTCTAAATCTACAAAATTCAGCTCACACGAACAACCGCAAAGATGCTAGAATGT
* * *
1269817 CCTACCAATAGTCCAGTATACAATCTAGAGCAATAACGGAACATGTTCTTTGCTACTATT
66 CCTACCAATAGTCCAATACACAAACTAGAGCAATAACGGAACATGTTCTTTGCTACTATT
1269877 CATTCTTTAC
Statistics
Matches: 102, Mismatches: 23, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
143 12 0.12
144 90 0.88
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.31
Consensus pattern (143 bp):
ATTGTTCAGACCTCTAAATCTACAAAATTCAGCTCACACGAACAACCGCAAAGATGCTAGAATGT
CCTACCAATAGTCCAATACACAAACTAGAGCAATAACGGAACATGTTCTTTGCTACTATTGCTAT
AATCTATCTTTCC
Found at i:1273977 original size:2 final size:2
Alignment explanation
Indices: 1273970--1274002 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1273960 CAGCATTTCC
1273970 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 A
1274003 ATTGTGGTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1274804 original size:2 final size:2
Alignment explanation
Indices: 1274797--1274825 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1274787 AATTAAATGA
1274797 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1274826 AGATTTTGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1278892 original size:2 final size:2
Alignment explanation
Indices: 1278882--1278916 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1278872 GAATATATGC
*
1278882 AT AT GT 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
1278917 CCCACCATTG
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
Found at i:1281850 original size:63 final size:63
Alignment explanation
Indices: 1281743--1281863 Score: 179
Period size: 63 Copynumber: 1.9 Consensus size: 63
1281733 TACATACTCA
* * *
1281743 TGTCTAGATATGCGTTGGACATGGATATCAAATATAAATGCTTCAAGAAAAAAAATGAAGAAT
1 TGTCTAGATATGCATTGGACATAGATATCAAATATAAATACTTCAAGAAAAAAAATGAAGAAT
* * * *
1281806 TGTCTAGATATGTATTGGACATAGATATCGAATATAGATACTTCAGGAAAAAAAATGA
1 TGTCTAGATATGCATTGGACATAGATATCAAATATAAATACTTCAAGAAAAAAAATGA
1281864 TAATGGTCCA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
63 51 1.00
ACGTcount: A:0.44, C:0.09, G:0.19, T:0.28
Consensus pattern (63 bp):
TGTCTAGATATGCATTGGACATAGATATCAAATATAAATACTTCAAGAAAAAAAATGAAGAAT
Found at i:1283540 original size:39 final size:38
Alignment explanation
Indices: 1283463--1283541 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 38
1283453 AGTTAAATAA
*
1283463 AAATAATAATAAAAATTATTATTTAAAAATTAATTTTT
1 AAATAATAATAAAAATTATTATTTAAAAATTAAATTTT
*
1283501 AAATAA-AATAATAATATTATT-TTTAAAATTTAAAATTTT
1 AAATAATAATAA-AA-ATTATTATTTAAAAATT-AAATTTT
1283540 AA
1 AA
1283542 TTATTTTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
37 5 0.14
38 17 0.47
39 14 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (38 bp):
AAATAATAATAAAAATTATTATTTAAAAATTAAATTTT
Found at i:1284118 original size:22 final size:21
Alignment explanation
Indices: 1284083--1284137 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
1284073 TTTTTATTTT
*
1284083 TTTAAAAAAATTAATTAATCA
1 TTTAAAAAAATTAAATAATCA
*
1284104 TTTAATAAATATTAAATAAT--
1 TTTAA-AAAAATTAAATAATCA
1284124 TTTATAAAAAATTA
1 TTTA-AAAAAATTA
1284138 TTTATAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 11 0.38
21 6 0.21
22 12 0.41
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
TTTAAAAAAATTAAATAATCA
Found at i:1284160 original size:16 final size:16
Alignment explanation
Indices: 1284103--1284168 Score: 64
Period size: 16 Copynumber: 4.1 Consensus size: 16
1284093 TTAATTAATC
1284103 ATTTAATAAATATTAAAT
1 ATTTAATAAA-A-TAAAT
* *
1284121 AATTTTATAAAA-AATT
1 -ATTTAATAAAATAAAT
1284137 ATTT-ATAAAATAAAT
1 ATTTAATAAAATAAAT
*
1284152 ATTTAATAAATTAAAT
1 ATTTAATAAAATAAAT
1284168 A
1 A
1284169 ATTACATTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
14 6 0.15
15 11 0.27
16 14 0.34
18 1 0.02
19 9 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTTAATAAAATAAAT
Found at i:1293076 original size:21 final size:21
Alignment explanation
Indices: 1293052--1293092 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1293042 TGCAATAGCA
* * *
1293052 GCTGCTGCTGCTGTTGCCAAG
1 GCTGCAGCTGCGGCTGCCAAG
1293073 GCTGCAGCTGCGGCTGCCAA
1 GCTGCAGCTGCGGCTGCCAA
1293093 TGTTGCCTCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.12, C:0.32, G:0.34, T:0.22
Consensus pattern (21 bp):
GCTGCAGCTGCGGCTGCCAAG
Found at i:1293945 original size:19 final size:19
Alignment explanation
Indices: 1293904--1293946 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1293894 GGTTTGTGTT
*
1293904 TTTACTTGAAATATAACAT
1 TTTACTTGAAATATAACAC
*
1293923 TTTAGTTGAAATATAGA-AC
1 TTTACTTGAAATATA-ACAC
1293942 TTTAC
1 TTTAC
1293947 CACGTTCTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (19 bp):
TTTACTTGAAATATAACAC
Found at i:1298398 original size:3 final size:3
Alignment explanation
Indices: 1298390--1298423 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1298380 TCAATAAATC
1298390 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1298424 GCTGCTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1305125 original size:24 final size:22
Alignment explanation
Indices: 1305097--1305150 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 22
1305087 ATATAAAAAA
1305097 ATAAATTATTAAAATTTATAAGAT
1 ATAAATTATTAAAATTT-TAA-AT
* *
1305121 ATAAATTAATAATATTTTAAAT
1 ATAAATTATTAAAATTTTAAAT
1305143 AT-AATTAT
1 ATAAATTAT
1305151 AATATAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.19
22 4 0.15
23 3 0.11
24 15 0.56
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
ATAAATTATTAAAATTTTAAAT
Found at i:1305158 original size:17 final size:17
Alignment explanation
Indices: 1305119--1305162 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1305109 AATTTATAAG
1305119 ATATAAAT-TAATAATA
1 ATATAAATATAATAATA
* * *
1305135 TTTTAAATATAATTATA
1 ATATAAATATAATAATA
1305152 ATATAAATATA
1 ATATAAATATA
1305163 TAAATTATAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATAAATATAATAATA
Found at i:1305168 original size:20 final size:20
Alignment explanation
Indices: 1305087--1305172 Score: 59
Period size: 24 Copynumber: 4.0 Consensus size: 20
1305077 TGATATGAAT
* *
1305087 ATATAAAAAAATAAATTATTA
1 ATATTAAAATATAAATTA-TA
*
1305108 AAATTTATAAGATATAAATTAATA
1 ATA-TTA-AA-ATATAAATT-ATA
*
1305132 ATATTTTAAATAT-AATTATA
1 ATA-TTAAAATATAAATTATA
1305152 ATA-TAAATATATAAATTATA
1 ATATTAAA-ATATAAATTATA
1305172 A
1 A
1305173 AAACCATATA
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
18 3 0.06
19 4 0.08
20 14 0.26
21 6 0.11
22 6 0.11
23 4 0.08
24 15 0.28
25 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (20 bp):
ATATTAAAATATAAATTATA
Found at i:1305173 original size:15 final size:16
Alignment explanation
Indices: 1305120--1305173 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 16
1305110 ATTTATAAGA
1305120 TATAAAT-TAATAATAT
1 TATAAATATAATAA-AT
*
1305136 TTTAAATATAATTATAA-
1 TATAAATATAA-TA-AAT
1305153 TATAAATAT-ATAAAT
1 TATAAATATAATAAAT
1305168 TATAAA
1 TATAAA
1305174 AACCATATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
14 2 0.06
15 8 0.25
16 7 0.22
17 11 0.34
18 3 0.09
19 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TATAAATATAATAAAT
Found at i:1306823 original size:3 final size:3
Alignment explanation
Indices: 1306810--1306846 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
1306800 GCATTGATGG
*
1306810 TTA TATA TTA TTA TTA TTA TTA TTA TTA TTA CTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1306847 AAACATTAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1309543 original size:17 final size:16
Alignment explanation
Indices: 1309523--1309577 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 16
1309513 TATAAAAATA
1309523 ATTTGATTTAAATTAAT
1 ATTT-ATTTAAATTAAT
**
1309540 ATTTATTTAATAAAAAT
1 ATTTATTTAA-ATTAAT
1309557 ATTTTATTTAAATTAAT
1 A-TTTATTTAAATTAAT
1309574 -TTTA
1 ATTTA
1309578 AAATATATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
15 4 0.12
16 6 0.19
17 13 0.41
18 9 0.28
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
ATTTATTTAAATTAAT
Found at i:1309564 original size:18 final size:18
Alignment explanation
Indices: 1309514--1309567 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
1309504 ATATTTTAAT
*
1309514 ATAAAAATAATTTGATTTA
1 ATAAAAAT-ATTTTATTTA
**
1309533 A-ATTAATA-TTTATTTA
1 ATAAAAATATTTTATTTA
1309549 ATAAAAATATTTTATTTA
1 ATAAAAATATTTTATTTA
1309567 A
1 A
1309568 ATTAATTTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
16 8 0.29
17 6 0.21
18 13 0.46
19 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
ATAAAAATATTTTATTTA
Found at i:1309575 original size:15 final size:15
Alignment explanation
Indices: 1309521--1309577 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
1309511 AATATAAAAA
*
1309521 TAATTTGATTTAAAT
1 TAATTTTATTTAAAT
*
1309536 TAATATTTATTTAATAAA
1 TAAT-TTTATTT-A-AAT
*
1309554 AATATTTTATTTAAAT
1 TA-ATTTTATTTAAAT
1309570 TAATTTTA
1 TAATTTTA
1309578 AAATATATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 10 0.30
16 9 0.27
17 2 0.06
18 10 0.30
19 2 0.06
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TAATTTTATTTAAAT
Found at i:1309588 original size:35 final size:35
Alignment explanation
Indices: 1309512--1309593 Score: 98
Period size: 34 Copynumber: 2.4 Consensus size: 35
1309502 TTATATTTTA
**
1309512 ATATAAAAATAATTTGATTTAAATTAATATTTATTT
1 ATATAAAAAT-ATTTGATTTAAATTAATATTTAAAT
*
1309548 A-ATAAAAATATTTTATTTAAATTAAT-TTTAAA-
1 ATATAAAAATATTTGATTTAAATTAATATTTAAAT
1309580 ATATATAAAATATT
1 ATATA-AAAATATT
1309594 AATATAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
32 1 0.02
33 7 0.17
34 24 0.59
35 8 0.20
36 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (35 bp):
ATATAAAAATATTTGATTTAAATTAATATTTAAAT
Found at i:1310441 original size:18 final size:19
Alignment explanation
Indices: 1310418--1310472 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 19
1310408 AATGTTATAT
1310418 TTTATAAATTATTAAA-TA
1 TTTATAAATTATTAAATTA
1310436 TTTATAAAATTAATTCAAATTA
1 TTTAT-AAATT-ATT-AAATTA
*
1310458 TAATATAAATTATTA
1 T-TTATAAATTATTA
1310473 TTTACATTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
18 5 0.16
19 5 0.16
20 4 0.13
21 6 0.19
22 8 0.26
23 3 0.10
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
TTTATAAATTATTAAATTA
Found at i:1310589 original size:19 final size:20
Alignment explanation
Indices: 1310567--1310607 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1310557 AATAAATATT
*
1310567 TTATATATTT-ATAAATTAA
1 TTATATATTTAAAAAATTAA
*
1310586 TTATATTTTTAAAAAATTAA
1 TTATATATTTAAAAAATTAA
1310606 TT
1 TT
1310608 CAAATTATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTATATATTTAAAAAATTAA
Found at i:1319531 original size:16 final size:14
Alignment explanation
Indices: 1319495--1319609 Score: 57
Period size: 14 Copynumber: 8.4 Consensus size: 14
1319485 CTAAAAATTT
1319495 TAAATATAATTATA
1 TAAATATAATTATA
*
1319509 TAAATATAATATTTA
1 TAAATATAAT-TATA
1319524 TAAA-AT-ATTA-A
1 TAAATATAATTATA
* *
1319535 -ATATATGATGTAATA
1 TAAATATAAT-T-ATA
1319550 TAAATATATATT-TA
1 TAAATATA-ATTATA
* * *
1319564 AAAATATTATAATA
1 TAAATATAATTATA
1319578 TAAAT-T-ATTAT-
1 TAAATATAATTATA
*
1319589 TATAATAAAATTTATA
1 TA-AATATAA-TTATA
1319605 TAAAT
1 TAAAT
1319610 TTAAAATATT
Statistics
Matches: 76, Mismatches: 11, Indels: 27
0.67 0.10 0.24
Matches are distributed among these distances:
10 2 0.03
11 5 0.07
12 10 0.13
13 6 0.08
14 28 0.37
15 15 0.20
16 8 0.11
17 2 0.03
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (14 bp):
TAAATATAATTATA
Found at i:1319589 original size:28 final size:27
Alignment explanation
Indices: 1319545--1319639 Score: 77
Period size: 28 Copynumber: 3.3 Consensus size: 27
1319535 ATATATGATG
1319545 TAATATAAATATATATTTAAAAATATTA
1 TAATATAAATAT-TATTTAAAAATATTA
*
1319573 TAATATAAATTATTATTATAATAAAATTTATA
1 TAATATAAA-TATTATT-T-A-AAAATAT-TA
* *
1319605 TAAATTTAAAATATTA-TT-AAAATCTTA
1 T-AATAT-AAATATTATTTAAAAATATTA
1319632 TAATATAA
1 TAATATAA
1319640 CATAATAAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 17
0.73 0.05 0.22
Matches are distributed among these distances:
25 2 0.04
26 4 0.07
27 3 0.05
28 19 0.34
29 4 0.07
30 1 0.02
31 7 0.12
32 4 0.07
33 9 0.16
34 3 0.05
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (27 bp):
TAATATAAATATTATTTAAAAATATTA
Found at i:1319593 original size:41 final size:39
Alignment explanation
Indices: 1319488--1319579 Score: 120
Period size: 37 Copynumber: 2.4 Consensus size: 39
1319478 ATTAAATCTA
*
1319488 AAAATTTTAAATATA--ATTATATAAATATAATATTTAT
1 AAAATATTAAATATATGATTATATAAATATAATATTTAT
1319525 AAAATATTAAATATATGATGTAATATAAATAT-ATATTTA-
1 AAAATATTAAATATATGAT-T-ATATAAATATAATATTTAT
1319564 AAAATATTATAATATA
1 AAAATATTA-AATATA
1319580 AATTATTATT
Statistics
Matches: 49, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
37 14 0.29
39 11 0.22
40 14 0.29
41 10 0.20
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.42
Consensus pattern (39 bp):
AAAATATTAAATATATGATTATATAAATATAATATTTAT
Found at i:1319627 original size:18 final size:18
Alignment explanation
Indices: 1319559--1319637 Score: 53
Period size: 18 Copynumber: 4.6 Consensus size: 18
1319549 ATAAATATAT
*
1319559 ATTTAAAA-A-TATTATA
1 ATTTAAAATATTATTAAA
* * *
1319575 ATATAAATTATTATTATA
1 ATTTAAAATATTATTAAA
1319593 A--TAAAAT-TTA-TATAA
1 ATTTAAAATATTATTA-AA
1319608 ATTTAAAATATTATTAAA
1 ATTTAAAATATTATTAAA
*
1319626 ATCTTATAATAT
1 AT-TTAAAATAT
1319638 AACATAATAA
Statistics
Matches: 50, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
14 2 0.04
15 5 0.10
16 11 0.22
17 7 0.14
18 15 0.30
19 10 0.20
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTTAAAATATTATTAAA
Found at i:1319655 original size:23 final size:23
Alignment explanation
Indices: 1319590--1319673 Score: 78
Period size: 23 Copynumber: 3.4 Consensus size: 23
1319580 AATTATTATT
*
1319590 ATAATAAAATTTATATAAATTTAAA
1 ATAATAAAATTT-TAT-AATATAAA
* *
1319615 ATATTATTAAAATCTTATAATATAAC
1 ATA--A-TAAAATTTTATAATATAAA
* *
1319641 ATAATAAAATTTTATAATATGAT
1 ATAATAAAATTTTATAATATAAA
1319664 ATAATAAAAT
1 ATAATAAAAT
1319674 ATATAAAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
23 26 0.52
24 1 0.02
25 3 0.06
26 9 0.18
27 4 0.08
28 7 0.14
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.40
Consensus pattern (23 bp):
ATAATAAAATTTTATAATATAAA
Found at i:1319690 original size:17 final size:16
Alignment explanation
Indices: 1319666--1319697 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1319656 AATATGATAT
1319666 AATAAAATATATAAAA
1 AATAAAATATATAAAA
1319682 AATATAAATATATAAA
1 AATA-AAATATATAAA
1319698 TTATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
AATAAAATATATAAAA
Found at i:1320809 original size:3 final size:3
Alignment explanation
Indices: 1320801--1320836 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1320791 AATTACATGA
1320801 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1320837 TTCTAATGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1321119 original size:7 final size:7
Alignment explanation
Indices: 1321107--1321138 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
1321097 CCATCCATGT
1321107 CCATTTC
1 CCATTTC
1321114 CCATTTC
1 CCATTTC
1321121 CCATTTC
1 CCATTTC
1321128 CCATTTC
1 CCATTTC
1321135 CCAT
1 CCAT
1321139 GAACATGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.16, C:0.44, G:0.00, T:0.41
Consensus pattern (7 bp):
CCATTTC
Found at i:1322650 original size:2 final size:2
Alignment explanation
Indices: 1322645--1322670 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1322635 ATATATATAT
1322645 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
1322671 CTATTGGTAT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1324288 original size:23 final size:23
Alignment explanation
Indices: 1324257--1324348 Score: 87
Period size: 24 Copynumber: 3.9 Consensus size: 23
1324247 AAATGCTCAT
*
1324257 ATAATATAAAAAATTAAAATATA
1 ATAAGATAAAAAATTAAAATATA
1324280 ATAAGATAAAAAA-TAATAATATGA
1 ATAAGATAAAAAATTAA-AATAT-A
* *
1324304 ATAAGATATAAATATAAAAATATA
1 ATAAGATA-AAAAATTAAAATATA
* **
1324328 TATAATATAAATTATTAAAAT
1 -ATAAGATAAAAAATTAAAAT
1324349 GTTAATATTT
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
22 3 0.05
23 17 0.29
24 20 0.34
25 16 0.28
26 2 0.03
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (23 bp):
ATAAGATAAAAAATTAAAATATA
Done.