Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold452
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: 589716
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
File 1 of 5
Found at i:102 original size:24 final size:24
Alignment explanation
Indices: 74--147 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
64 AAGGAAGGCG
74 AGGCAGGGAAAGGGAACAGAGACA
1 AGGCAGGGAAAGGGAACAGAGACA
** *
98 AGGCA-AAAAAGAAGG-A-AG-G-CG
1 AGGCAGGGAAAG--GGAACAGAGACA
119 AGGCAGGGAAAGGGAACAGAGACA
1 AGGCAGGGAAAGGGAACAGAGACA
143 AGGCA
1 AGGCA
148 AAAAAAGAAG
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
20 2 0.05
21 7 0.19
22 7 0.19
23 7 0.19
24 12 0.32
25 2 0.05
ACGTcount: A:0.47, C:0.12, G:0.41, T:0.00
Consensus pattern (24 bp):
AGGCAGGGAAAGGGAACAGAGACA
Found at i:169 original size:46 final size:46
Alignment explanation
Indices: 62--207 Score: 217
Period size: 45 Copynumber: 3.2 Consensus size: 46
52 AAGCCAAAGG
62 AGAAGGAAGGCGAGGCAGGGAAAGGGAACAGAGACAAGGC-AAAAA
1 AGAAGGAAGGCGAGGCAGGGAAAGGGAACAGAGACAAGGCAAAAAA
107 AGAAGGAAGGCGAGGCAGGGAAAGGGAACAGAGACAAGGCAAAAAA
1 AGAAGGAAGGCGAGGCAGGGAAAGGGAACAGAGACAAGGCAAAAAA
** * *
153 AGAAGGAAGGCGAGGCACAGAAAGGGAAGA-AAATCAAGG-AAAAAA
1 AGAAGGAAGGCGAGGCAGGGAAAGGGAACAGAGA-CAAGGCAAAAAA
198 ACGAAGGAAG
1 A-GAAGGAAG
208 AAGAGGGAGA
Statistics
Matches: 94, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
45 49 0.52
46 45 0.48
ACGTcount: A:0.51, C:0.10, G:0.38, T:0.01
Consensus pattern (46 bp):
AGAAGGAAGGCGAGGCAGGGAAAGGGAACAGAGACAAGGCAAAAAA
Found at i:1309 original size:2 final size:2
Alignment explanation
Indices: 1304--1333 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1294 AAAGACACAC
1304 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
1334 GTATGTATTT
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:1542 original size:16 final size:17
Alignment explanation
Indices: 1521--1560 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
1511 TAGTATGAAA
*
1521 TAAATTTTTAA-TAATT
1 TAAATTTATAATTAATT
1537 TAAATTTATAATTTAATT
1 TAAATTTATAA-TTAATT
1555 TAAATT
1 TAAATT
1561 ATTATTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 10 0.48
18 11 0.52
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TAAATTTATAATTAATT
Found at i:1567 original size:17 final size:18
Alignment explanation
Indices: 1532--1569 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
1522 AAATTTTTAA
1532 TAATTTAAATTTATAATT
1 TAATTTAAATTTATAATT
*
1550 TAATTTAAA-TTATTATT
1 TAATTTAAATTTATAATT
1567 TAA
1 TAA
1570 ATAATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TAATTTAAATTTATAATT
Found at i:1629 original size:17 final size:16
Alignment explanation
Indices: 1602--1638 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
1592 TTTATTTATT
1602 TATAAAAATATATTAA
1 TATAAAAATATATTAA
*
1618 TATAATAAATATTTTAA
1 TATAA-AAATATATTAA
1635 TATA
1 TATA
1639 TTTTACATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TATAAAAATATATTAA
Found at i:2189 original size:20 final size:20
Alignment explanation
Indices: 2144--2189 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
2134 AGAATGCGAG
2144 TGTATCGATATAATTACAAT
1 TGTATCGATATAATTACAAT
*
2164 TATATCGATATAA-TACATAT
1 TGTATCGATATAATTACA-AT
2184 TGTATC
1 TGTATC
2190 TCTAGATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (20 bp):
TGTATCGATATAATTACAAT
Found at i:2878 original size:20 final size:20
Alignment explanation
Indices: 2828--2893 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 20
2818 AAAAGCTAAG
*
2828 AAAGAAAAAAAAG-AGAAAAA
1 AAAGAAAAAAAGGCA-AAAAA
* *
2848 AGAGAGGAAAAA-GCAAAAGAA
1 AAAGA-AAAAAAGGCAAAA-AA
*
2869 AAAGAAAAAAAGGGAAAAAA
1 AAAGAAAAAAAGGCAAAAAA
2889 AAAGA
1 AAAGA
2894 GGATAGCTCC
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAGAAAAAAAGGCAAAAAA
Found at i:3878 original size:58 final size:57
Alignment explanation
Indices: 3709--4070 Score: 205
Period size: 58 Copynumber: 6.2 Consensus size: 57
3699 GGTTTTTTTC
* * *
3709 ATGTCATTTCATGCATTTT-ATGTCATCTTAGTCATTTTTCATGA-CTTAAAGA-TTTG
1 ATGTCATTTCATGAATTTTGATGTCAT-TTAGTTATTTTTCATGATC-TAAGGACTTTG
** * ** * * * *
3765 TATAACATTTCATACAATTTTTTTTATCATTTTAGTCATTTTTAATGA-CTGAAGGACTTTT
1 -ATGTCATTTCAT-GAA-TTTTGATGTCA-TTTAGTTATTTTTCATGATCT-AAGGACTTTG
3826 ATGTCATTTCATGAATTTTGATGTCATTTAGGTTATTTTTCATGATCTAAGGACTTTG
1 ATGTCATTTCATGAATTTTGATGTCATTTA-GTTATTTTTCATGATCTAAGGACTTTG
* * * * * * * * *
3884 ATGTAATTTTACGAATGTTAACGTCATTCAGTTCATTTTTCATAATC-GAGAGACTTTG
1 ATGTCATTTCATGAATTTTGATGTCATTTAGTT-ATTTTTCATGATCTAAG-GACTTTG
** * * * * *
3942 ATG-CAATTTTTTGAATATTGATGTCATTAAAGTTATTTTCCATGATATAGGGACTTTG
1 ATGTC-ATTTCATGAATTTTGATGTCATT-TAGTTATTTTTCATGATCTAAGGACTTTG
** * * * ** * * * *
4000 ATGAAATTTTATCAATATTGACATCATTTAGATAATTTTTCATAATCTAGGGACTTTC
1 ATGTCATTTCATGAATTTTGATGTCATTTAG-TTATTTTTCATGATCTAAGGACTTTG
*
4058 ATGTAATTTCATG
1 ATGTCATTTCATG
4071 TGTTTTAGAG
Statistics
Matches: 237, Mismatches: 53, Indels: 29
0.74 0.17 0.09
Matches are distributed among these distances:
57 21 0.09
58 163 0.69
59 14 0.06
60 35 0.15
61 4 0.02
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.46
Consensus pattern (57 bp):
ATGTCATTTCATGAATTTTGATGTCATTTAGTTATTTTTCATGATCTAAGGACTTTG
Found at i:3939 original size:116 final size:116
Alignment explanation
Indices: 3819--4070 Score: 292
Period size: 116 Copynumber: 2.2 Consensus size: 116
3809 ATGACTGAAG
* * * * * *
3819 GACTTTTATGTCATTTCATGAATTTTGATGTCATTTAGGTTATTTTTCATGATCTAAGGACTTTG
1 GACTTTCATGTCATTTCATGAATATTGATGTCATTAAAGTTATTTTCCATGATATAAGGACTTTG
* * * * *
3884 ATGTAATTTTA-CGAATGTTAACGTCATTCAGTTCATTTTTCATAATCGAGA
66 ATGAAATTTTATC-AATATTAACATCATTCAGATAATTTTTCATAATCGAGA
* ** *
3935 GACTTTGATG-CAATTTTTTGAATATTGATGTCATTAAAGTTATTTTCCATGATATAGGGACTTT
1 GACTTTCATGTC-ATTTCATGAATATTGATGTCATTAAAGTTATTTTCCATGATATAAGGACTTT
* * * *
3999 GATGAAATTTTATCAATATTGACATCATTTAGATAATTTTTCATAATCTAGG
65 GATGAAATTTTATCAATATTAACATCATTCAGATAATTTTTCATAATCGAGA
*
4051 GACTTTCATGTAATTTCATG
1 GACTTTCATGTCATTTCATG
4071 TGTTTTAGAG
Statistics
Matches: 111, Mismatches: 22, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
115 1 0.01
116 109 0.98
117 1 0.01
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.45
Consensus pattern (116 bp):
GACTTTCATGTCATTTCATGAATATTGATGTCATTAAAGTTATTTTCCATGATATAAGGACTTTG
ATGAAATTTTATCAATATTAACATCATTCAGATAATTTTTCATAATCGAGA
Found at i:10664 original size:18 final size:19
Alignment explanation
Indices: 10630--10665 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
10620 GTAATGCTAA
10630 AAAATTTGATCGATTCATC
1 AAAATTTGATCGATTCATC
10649 AAAATTTGAT-GATTCAT
1 AAAATTTGATCGATTCAT
10666 TCAGTTTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (19 bp):
AAAATTTGATCGATTCATC
Found at i:12518 original size:28 final size:28
Alignment explanation
Indices: 12458--12525 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
12448 ATTACAATAT
* *
12458 GAATAATACGAAAACATGATTAAGACAC
1 GAATTATATGAAAACATGATTAAGACAC
* * *
12486 GAATTATATGAAACCATGTTTAGGACAC
1 GAATTATATGAAAACATGATTAAGACAC
*
12514 GAATTACATGAA
1 GAATTATATGAA
12526 TATTATCAAC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.47, C:0.13, G:0.16, T:0.24
Consensus pattern (28 bp):
GAATTATATGAAAACATGATTAAGACAC
Found at i:18970 original size:426 final size:426
Alignment explanation
Indices: 18169--19021 Score: 1483
Period size: 426 Copynumber: 2.0 Consensus size: 426
18159 GTTAGCCAAT
*
18169 TGTTAAATATAAGAGAAGAGTTAAGTGATAAAAATCAAGCAAGTGTTAGCTTCATTACCATAATC
1 TGTTAAATATAAGAGAAGAGTTAAGTGATAAAAATCAAGCAAGTGTTAGCTTCACTACCATAATC
* *
18234 TTATAGATCATTAGTAAGGTTGCTATTGATTAGCAAAAATACCATTAAGCTAAATAATGTGATCA
66 TTACAGATCATTAGTAAGGTTGCTATTGATTAGCAAAAATACCATCAAGCTAAATAATGTGATCA
* *
18299 CAGTCTTCGAAGAGAATCAGAGGATGCATAAAAAGGATCATACCAATGAAAGTGAAAGCATACTA
131 CAGTCCTCGAAGAGAATCAGAAGATGCATAAAAAGGATCATACCAATGAAAGTGAAAGCATACTA
* *
18364 GCTGTGAAGAGATATAAAAGATGAACACTTTTTGTAGTAAAATTAGAAAATGAAAAAAGTCTAGA
196 GCTGTGAAGAGATATAAAAGATGAACACTTTCTATAGTAAAATTAGAAAATGAAAAAAGTCTAGA
* *
18429 GAGAGAAACTATGGTGATATGAAGTGCTATTGTTGTGAAAAGGCTGGGCACTTTCAATCCAATGT
261 GAGAGAAACTATGGTGATATGAAGTGCTATTGTTGTGAAAAAGCTAGGCACTTTCAATCCAATGT
* *
18494 CCATAAATGTGAGAAGACTTGAAGACTCTAAAATTGTTTAAAGGGAATGTAAAGGTATTAGCTAA
326 CCATAAATGTGAGAAGACTTGAAGACTCTAAAATTGTTTAAAGAGAATGTAAAGGTATCAGCTAA
* *
18559 TGTAGGTGAAATCGATTATCAAGATTATTTGTTTTA
391 TGTAGGTGAAATCGATGATCAAGATGATTTGTTTTA
* *
18595 TGTTAAATATAAGAGAAGAGTTAAGTGATGAAAATCAAGCAATTGTTAGCTTCACTACCATAATC
1 TGTTAAATATAAGAGAAGAGTTAAGTGATAAAAATCAAGCAAGTGTTAGCTTCACTACCATAATC
*
18660 TTACAGATCATTAGTAAGGTTGCTATTGATTAGCAAAAATACCATCAAGCTAAATGATGTGATCA
66 TTACAGATCATTAGTAAGGTTGCTATTGATTAGCAAAAATACCATCAAGCTAAATAATGTGATCA
* *
18725 CAGTCCTGGAAGAGAATCAGAAGATGCATAGAAAGGATCATACCAATGAAAGTGAAAGCATACTA
131 CAGTCCTCGAAGAGAATCAGAAGATGCATAAAAAGGATCATACCAATGAAAGTGAAAGCATACTA
*
18790 GCTGTGAAGAGATATCAAAGATGAACACTTTCTATAGTAAAATTAGAAAATGAAAAAAGTCTAGA
196 GCTGTGAAGAGATATAAAAGATGAACACTTTCTATAGTAAAATTAGAAAATGAAAAAAGTCTAGA
18855 -AGGAGAAACTATGGTGATATGAAGTGCTATTGTTGTGAAAAAGCTAGGCACTTTCAATCCAATG
261 GA-GAGAAACTATGGTGATATGAAGTGCTATTGTTGTGAAAAAGCTAGGCACTTTCAATCCAATG
* *
18919 TCCATAAATGTGAGAAGACTTGAAGACTCTAAAATTGTTTAAATAGAATGTAAAGGTATCAGTTA
325 TCCATAAATGTGAGAAGACTTGAAGACTCTAAAATTGTTTAAAGAGAATGTAAAGGTATCAGCTA
* *
18984 ATGTAGGTGAAATCGATGATCATGATGATTTTTTTTA
390 ATGTAGGTGAAATCGATGATCAAGATGATTTGTTTTA
19021 T
1 T
19022 ATAAAAGGTA
Statistics
Matches: 403, Mismatches: 23, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
425 1 0.00
426 402 1.00
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (426 bp):
TGTTAAATATAAGAGAAGAGTTAAGTGATAAAAATCAAGCAAGTGTTAGCTTCACTACCATAATC
TTACAGATCATTAGTAAGGTTGCTATTGATTAGCAAAAATACCATCAAGCTAAATAATGTGATCA
CAGTCCTCGAAGAGAATCAGAAGATGCATAAAAAGGATCATACCAATGAAAGTGAAAGCATACTA
GCTGTGAAGAGATATAAAAGATGAACACTTTCTATAGTAAAATTAGAAAATGAAAAAAGTCTAGA
GAGAGAAACTATGGTGATATGAAGTGCTATTGTTGTGAAAAAGCTAGGCACTTTCAATCCAATGT
CCATAAATGTGAGAAGACTTGAAGACTCTAAAATTGTTTAAAGAGAATGTAAAGGTATCAGCTAA
TGTAGGTGAAATCGATGATCAAGATGATTTGTTTTA
Found at i:20137 original size:17 final size:18
Alignment explanation
Indices: 20115--20148 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
20105 CCTTTAGATG
20115 TTAAATAA-AAAAAATAA
1 TTAAATAATAAAAAATAA
20132 TTAAATAATAAAAAATA
1 TTAAATAATAAAAAATA
20149 TGATGTTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
TTAAATAATAAAAAATAA
Found at i:20302 original size:16 final size:18
Alignment explanation
Indices: 20264--20306 Score: 56
Period size: 16 Copynumber: 2.5 Consensus size: 18
20254 AATAAGTTAA
20264 ATTTATA-TATTTATACT
1 ATTTATATTATTTATACT
20281 ATTTTATATTATTT-TA-T
1 A-TTTATATTATTTATACT
20298 ATTTATATT
1 ATTTATATT
20307 TTATTTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 8 0.33
17 3 0.12
18 8 0.33
19 5 0.21
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTTATATTATTTATACT
Found at i:20312 original size:18 final size:17
Alignment explanation
Indices: 20265--20314 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
20255 ATAAGTTAAA
20265 TTTATA-TATTTATACTAT
1 TTTATATTATTT-TA-TAT
20283 TTTATATTATTTTATAT
1 TTTATATTATTTTATAT
*
20300 TTATATTTTATTTTA
1 TT-TATATTATTTTA
20315 AAAAATATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 5 0.17
18 19 0.66
19 5 0.17
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTATATTATTTTATAT
Found at i:20357 original size:14 final size:15
Alignment explanation
Indices: 20331--20359 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
20321 ATTTTTAAAT
20331 AAATAATAATTCAAA
1 AAATAATAATTCAAA
20346 AAATAA-AATTCAAA
1 AAATAATAATTCAAA
20360 TATTAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (15 bp):
AAATAATAATTCAAA
Found at i:20580 original size:8 final size:8
Alignment explanation
Indices: 20557--20654 Score: 59
Period size: 8 Copynumber: 12.8 Consensus size: 8
20547 AATTATACAA
20557 AATAATAT
1 AATAATAT
*
20565 AATTATAT
1 AATAATAT
*
20573 TATAATAT
1 AATAATAT
20581 AA-AATAT
1 AATAATAT
20588 AAT-ATATT
1 AATAATA-T
* *
20596 AAAAAAAT
1 AATAATAT
*
20604 AAT-ATAA
1 AATAATAT
20611 ATATAATAT
1 A-ATAATAT
20620 AA-AATAT
1 AATAATAT
20627 -AT-ATAT
1 AATAATAT
20633 AATTAAT-T
1 AA-TAATAT
20641 AA-AATAT
1 AATAATAT
20648 AAATAAT
1 -AATAAT
20655 GTAAATTATT
Statistics
Matches: 68, Mismatches: 10, Indels: 23
0.67 0.10 0.23
Matches are distributed among these distances:
6 8 0.12
7 20 0.29
8 29 0.43
9 11 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
AATAATAT
Found at i:20621 original size:44 final size:45
Alignment explanation
Indices: 20537--20644 Score: 121
Period size: 44 Copynumber: 2.4 Consensus size: 45
20527 ACTAACTTTG
* * * * *
20537 AATAGAATGTAATTATACAAAATAATATAATTATATTATAATATA-A
1 AATATAAT-TAATTA-AAAAAATAATATAAATATAATATAAAATATA
20583 AATATAA-TATATTAAAAAAATAATATAAATATAATATAAAATATA
1 AATATAATTA-ATTAAAAAAATAATATAAATATAATATAAAATATA
*
20628 TATATAATTAATTAAAA
1 AATATAATTAATTAAAA
20645 TATAAATAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
44 27 0.51
45 18 0.34
46 8 0.15
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36
Consensus pattern (45 bp):
AATATAATTAATTAAAAAAATAATATAAATATAATATAAAATATA
Found at i:20662 original size:21 final size:21
Alignment explanation
Indices: 20575--20648 Score: 77
Period size: 21 Copynumber: 3.6 Consensus size: 21
20565 AATTATATTA
20575 TAATATAAAATATA-ATAT-AT
1 TAAT-TAAAATATATATATAAT
*
20595 TAA-AAAAATA-ATATA-AAT
1 TAATTAAAATATATATATAAT
20613 ATAATATAAAATATATATATAAT
1 -TAAT-TAAAATATATATATAAT
20636 TAATTAAAATATA
1 TAATTAAAATATA
20649 AATAATGTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
17 1 0.02
18 11 0.24
19 3 0.07
20 3 0.07
21 15 0.33
22 9 0.20
23 3 0.07
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
TAATTAAAATATATATATAAT
Found at i:20690 original size:8 final size:8
Alignment explanation
Indices: 20679--20725 Score: 51
Period size: 8 Copynumber: 5.5 Consensus size: 8
20669 TTTTAAAATT
20679 TATATAAA
1 TATATAAA
20687 TATAT-AA
1 TATATAAA
20694 TATATTAAA
1 TATA-TAAA
20703 TATAAATTAAA
1 TAT--A-TAAA
20714 TATATAAA
1 TATATAAA
20722 TATA
1 TATA
20726 ATATAAATAC
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
7 6 0.17
8 14 0.40
9 6 0.17
11 9 0.26
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
TATATAAA
Found at i:20704 original size:16 final size:16
Alignment explanation
Indices: 20580--20706 Score: 50
Period size: 16 Copynumber: 8.5 Consensus size: 16
20570 TATTATAATA
20580 TAAA-ATATAATATAT
1 TAAATATATAATATAT
20595 TAAA-A-A-AATA-AT
1 TAAATATATAATATAT
* *
20607 ATAAATATA-ATATAAAA
1 -TAAATATATA-ATATAT
*
20624 TATATATATAAT-TAAT
1 TAAATATATAATAT-AT
20640 TAAA-ATATAA-ATAAT
1 TAAATATATAATAT-AT
* *
20655 GTAAAT-TATTAAAATTT
1 -TAAATATA-TAATATAT
20672 TAAA-AT-T--TATA-
1 TAAATATATAATATAT
20683 TAAATATATAATATAT
1 TAAATATATAATATAT
20699 TAAATATA
1 TAAATATA
20707 AATTAAATAT
Statistics
Matches: 86, Mismatches: 8, Indels: 35
0.67 0.06 0.27
Matches are distributed among these distances:
11 4 0.05
12 6 0.07
13 9 0.10
14 3 0.03
15 21 0.24
16 35 0.41
17 6 0.07
18 2 0.02
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (16 bp):
TAAATATATAATATAT
Found at i:20725 original size:33 final size:33
Alignment explanation
Indices: 20571--20730 Score: 93
Period size: 33 Copynumber: 4.7 Consensus size: 33
20561 ATATAATTAT
20571 ATTATAATATA-AAATATAATATATTAAA-A-AA
1 ATTA-AATATATAAATATAATATATTAAATATAA
* * * *
20602 A-TAATATAAATATAATATAAAATATATATATAATTA
1 ATTAA-ATATATA-AATATAATATAT-TAAAT-ATAA
*
20638 ATTAAA-ATATAAATAATGTAA-ATTATTAAAATTTTAAA
1 ATTAAATATATAAAT-A--TAATA-TATT-AAA-TAT-AA
*
20676 ATT-TATATA-AATATATAATATATTAAATATAA
1 ATTAAATATATAA-ATATAATATATTAAATATAA
20708 ATTAAATATATAAATATAATATA
1 ATTAAATATATAAATATAATATA
20731 AATACATCAT
Statistics
Matches: 98, Mismatches: 11, Indels: 38
0.67 0.07 0.26
Matches are distributed among these distances:
29 1 0.01
30 6 0.06
31 2 0.02
32 16 0.16
33 20 0.20
34 8 0.08
35 13 0.13
36 6 0.06
37 16 0.16
38 10 0.10
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (33 bp):
ATTAAATATATAAATATAATATATTAAATATAA
Found at i:20734 original size:11 final size:11
Alignment explanation
Indices: 20558--20734 Score: 78
Period size: 11 Copynumber: 17.1 Consensus size: 11
20548 ATTATACAAA
*
20558 ATAATATAATT
1 ATAATATAAAT
*
20569 ATATTAT-AAT
1 ATAATATAAAT
*
20579 ATAAAATATAAT
1 ATAATATA-AAT
* * *
20591 ATATTAAAAAA
1 ATAATATAAAT
20602 ATAATATAAAT
1 ATAATATAAAT
20613 ATAATATAAA-
1 ATAATATAAAT
20623 AT-ATAT--AT
1 ATAATATAAAT
*
20631 ATAAT-TAATT
1 ATAATATAAAT
*
20641 AAAATAT-AA-
1 ATAATATAAAT
*
20650 ATAATGTAAAT
1 ATAATATAAAT
*
20661 -TATTA-AAATT
1 ATAATATAAA-T
* * **
20671 TTAAAATTTAT
1 ATAATATAAAT
20682 ATAAATATATAAT
1 AT-AATATA-AAT
20695 AT-AT-TAAAT
1 ATAATATAAAT
*
20704 ATAA-ATTAA-
1 ATAATATAAAT
20713 AT-ATATAAAT
1 ATAATATAAAT
20723 ATAATATAAAT
1 ATAATATAAAT
20734 A
1 A
20735 CATCATATTT
Statistics
Matches: 119, Mismatches: 28, Indels: 38
0.64 0.15 0.21
Matches are distributed among these distances:
7 1 0.01
8 4 0.03
9 25 0.21
10 29 0.24
11 43 0.36
12 13 0.11
13 4 0.03
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.40
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:21178 original size:5 final size:5
Alignment explanation
Indices: 21164--21295 Score: 54
Period size: 5 Copynumber: 27.8 Consensus size: 5
21154 TTGTCAATGA
* * *
21164 AATA- AATAT AATAT AATAT AATAT AA-AT ATTTT AAATTTT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT -AA-TAT AATAT AATAT
* * * *
21214 AATAATT AATAT -AT-T AATATT CATAT AA-AT ATTA- AATAT -TTTT
1 AAT-A-T AATAT AATAT AATA-T AATAT AATAT AATAT AATAT AATAT
* *
21257 AA-AT AACAT --TAT AATAT AATAA AATAT -ATA- AATAT AATA
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATA
21296 GATATATAAA
Statistics
Matches: 96, Mismatches: 15, Indels: 33
0.67 0.10 0.23
Matches are distributed among these distances:
3 3 0.03
4 28 0.29
5 49 0.51
6 9 0.09
7 7 0.07
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
AATAT
Found at i:21207 original size:31 final size:31
Alignment explanation
Indices: 21166--21304 Score: 114
Period size: 31 Copynumber: 4.6 Consensus size: 31
21156 GTCAATGAAA
21166 TAAATA-TAATATAATATAATATAAATATTT
1 TAAATATTAATATAATATAATATAAATATTT
* * *
21196 TAAATTTTAATATAATATAATAATTAATATAT
1 TAAATATTAATATAATATAAT-ATAAATATTT
*
21228 T-AATATTCATATAA-AT-AT-TAAATATTTT
1 TAAATATTAATATAATATAATATAAATA-TTT
** * *
21256 TAAATAACATTATAATATAATA-AAATA-TA
1 TAAATATTAATATAATATAATATAAATATTT
*
21285 TAAATA-TAATAGATATATAA
1 TAAATATTAATATA-ATATAA
21305 ATTATTAAAT
Statistics
Matches: 86, Mismatches: 15, Indels: 17
0.73 0.13 0.14
Matches are distributed among these distances:
27 5 0.06
28 7 0.08
29 24 0.28
30 9 0.10
31 32 0.37
32 9 0.10
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (31 bp):
TAAATATTAATATAATATAATATAAATATTT
Found at i:21225 original size:12 final size:13
Alignment explanation
Indices: 21176--21301 Score: 55
Period size: 13 Copynumber: 9.6 Consensus size: 13
21166 TAAATATAAT
21176 ATAATATAATATAA
1 ATAATATAATAT-A
* * *
21190 ATATTTTAA-ATT
1 ATAATATAATATA
*
21202 TTAATATAATATA
1 ATAATATAATATA
21215 ATAAT-TAATATA
1 ATAATATAATATA
* *
21227 TTAATATTCATATAA
1 ATAATA-TAATAT-A
* *
21242 ATATTA-AATATTT
1 ATAATATAATA-TA
* * *
21255 TTAA-ATAACATT
1 ATAATATAATATA
*
21267 ATAATATAATAAA
1 ATAATATAATATA
21280 AT-ATATAAATATA
1 ATAATAT-AATATA
21293 ATAGATATA
1 ATA-ATATA
21302 TAAATTATTA
Statistics
Matches: 80, Mismatches: 22, Indels: 20
0.66 0.18 0.16
Matches are distributed among these distances:
12 27 0.34
13 30 0.38
14 14 0.17
15 9 0.11
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.43
Consensus pattern (13 bp):
ATAATATAATATA
Found at i:21247 original size:26 final size:24
Alignment explanation
Indices: 21165--21253 Score: 87
Period size: 26 Copynumber: 3.7 Consensus size: 24
21155 TGTCAATGAA
21165 ATAAATA-T-AATA-TAATATAAT
1 ATAAATATTAAATATTAATATAAT
*
21186 ATAAATATTTTAAATTTTAATATAAT
1 ATAAATA--TTAAATATTAATATAAT
*
21212 AT-AATAATTAATATATTAATATTCAT
1 ATAAAT-ATTAA-ATATTAATA-TAAT
21238 ATAAATATTAAATATT
1 ATAAATATTAAATATT
21254 TTTAAATAAC
Statistics
Matches: 56, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
21 7 0.12
24 5 0.09
25 19 0.34
26 22 0.39
27 3 0.05
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (24 bp):
ATAAATATTAAATATTAATATAAT
Found at i:21300 original size:17 final size:18
Alignment explanation
Indices: 21165--21306 Score: 63
Period size: 21 Copynumber: 7.3 Consensus size: 18
21155 TGTCAATGAA
21165 ATAAATATAATATAATATAAT
1 ATAAATATAATA-AA-AT-AT
** * *
21186 ATAAATATTTTAAATTTT
1 ATAAATATAATAAAATAT
21204 AATATAATATAATAATTAATAT
1 -ATA-AATATAATAA--AATAT
* *
21226 ATTAATATTCATATAAATAT
1 ATAAATA-TAATA-AAATAT
** * *
21246 -TAAATATTTTTAAATAAC
1 ATAAATATAATAAAAT-AT
21264 ATTATAATATAATAAAATAT
1 A-TA-AATATAATAAAATAT
*
21284 ATAAATATAAT-AGATAT
1 ATAAATATAATAAAATAT
21301 ATAAAT
1 ATAAAT
21307 TATTAAATAA
Statistics
Matches: 91, Mismatches: 20, Indels: 24
0.67 0.15 0.18
Matches are distributed among these distances:
17 15 0.16
18 12 0.13
19 11 0.12
20 23 0.25
21 26 0.29
22 4 0.04
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (18 bp):
ATAAATATAATAAAATAT
Found at i:21306 original size:25 final size:23
Alignment explanation
Indices: 21266--21315 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 23
21256 TAAATAACAT
*
21266 TATAATATAATAAAA-TATATAAA
1 TATAATAGAATAAAATTAT-TAAA
21289 TATAATAGATATATAAATTATTAAA
1 TATAATAGA-ATA-AAATTATTAAA
21314 TA
1 TA
21316 AGATAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 8 0.35
24 3 0.13
25 9 0.39
26 3 0.13
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (23 bp):
TATAATAGAATAAAATTATTAAA
Found at i:21382 original size:20 final size:22
Alignment explanation
Indices: 21359--21406 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 22
21349 ACGAATTGTT
21359 AATATATTAAAA-TT-AATATA
1 AATATATTAAAATTTAAATATA
21379 AATA-A-TAAAATTTAAATATA
1 AATATATTAAAATTTAAATATA
*
21399 ATTATATT
1 AATATATT
21407 TTAATAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
18 5 0.22
19 3 0.13
20 13 0.57
21 1 0.04
22 1 0.04
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AATATATTAAAATTTAAATATA
Found at i:21397 original size:34 final size:34
Alignment explanation
Indices: 21163--21398 Score: 102
Period size: 34 Copynumber: 6.9 Consensus size: 34
21153 CTTGTCAATG
* * * *
21163 AAATAAATATAATATAATATAATATAAATATTTTA
1 AAATTAATATAA-ATAATAAAATTTAAATATATTA
*
21198 AATTTTAATAT-AAT-ATAATAA-TT-AATATATTA
1 AA-ATTAATATAAATAATAA-AATTTAAATATATTA
* * * *
21230 ATATTCATATAAATATTAAATATTTTTAAATAACATTA
1 AAATTAATATAAATAATAAA-A--TTTAAAT-ATATTA
* * *
21268 TAATATAATA-AAAT-ATATAAATAT-AATAGATATA
1 AAAT-TAATATAAATAATA-AAATTTAAATATAT-TA
* *
21302 TAAATT-AT-TAAATAAGATAAATTTAAATAT-TTT
1 -AAATTAATATAAATAATA-AAATTTAAATATATTA
* * *
21335 AAATT--T-TATATAATACGAATTGTTAATATATTA
1 AAATTAATATAAATAATA-AAATT-TAAATATATTA
21368 AAATTAATATAAATAATAAAATTTAAATATA
1 AAATTAATATAAATAATAAAATTTAAATATA
21399 ATTATATTTT
Statistics
Matches: 149, Mismatches: 30, Indels: 45
0.67 0.13 0.20
Matches are distributed among these distances:
31 18 0.12
32 24 0.16
33 25 0.17
34 26 0.17
35 17 0.11
36 16 0.11
37 6 0.04
38 13 0.09
39 4 0.03
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (34 bp):
AAATTAATATAAATAATAAAATTTAAATATATTA
Found at i:21439 original size:138 final size:137
Alignment explanation
Indices: 21187--21448 Score: 345
Period size: 138 Copynumber: 1.9 Consensus size: 137
21177 TAATATAATA
* * * *
21187 TAAATATTTTAAATTTTAATATAATATAATAATTAATATATTAATATTCATATAAATATTAAATA
1 TAAATATTTTAAATTTTAATATAATAGAATAATTAATATATTAAAATTAATATAAATAATAAATA
21252 TTTTTAAATAACATTATAATATAATAAAATATATAAATATAATAGATATATAAATTATTAAATAA
66 -TTTTAAATAACATTATAATATAATAAAATATATAAATATAATAGATATATAAATTATTAAATAA
21317 GATAAATT
130 GATAAATT
**
21325 TAAATATTTTAAATTTT-ATATAATACGAATTGTTAATATATTAAAATTAATATAAATAATAAA-
1 TAAATATTTTAAATTTTAATATAATA-GAATAATTAATATATTAAAATTAATATAAATAATAAAT
* * * * *
21388 A-TTTAAATATA-ATTATATTTTAAT-AAATATATGAATATAATTTACATATATAAATCATTAA
65 ATTTTAAATA-ACATTATAATATAATAAAATATATAAATATAA--TAGATATATAAATTATTAA
21449 TTTCTCATAA
Statistics
Matches: 109, Mismatches: 11, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
134 15 0.14
135 19 0.17
136 18 0.17
137 9 0.08
138 48 0.44
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (137 bp):
TAAATATTTTAAATTTTAATATAATAGAATAATTAATATATTAAAATTAATATAAATAATAAATA
TTTTAAATAACATTATAATATAATAAAATATATAAATATAATAGATATATAAATTATTAAATAAG
ATAAATT
Found at i:21574 original size:29 final size:26
Alignment explanation
Indices: 21508--21574 Score: 64
Period size: 29 Copynumber: 2.4 Consensus size: 26
21498 AATATAATTT
21508 ATTTATACAATATAAATATAAATAAAA
1 ATTTATA-AATATAAATATAAATAAAA
21535 ATAATTA-AAATATATAATCATAATATAAAA
1 AT--TTATAAATATA-AAT-ATAA-ATAAAA
*
21565 GTTTATAAAT
1 ATTTATAAAT
21575 TGAGTTGAGC
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
27 8 0.24
28 7 0.21
29 11 0.33
30 7 0.21
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (26 bp):
ATTTATAAATATAAATATAAATAAAA
Found at i:22897 original size:2 final size:2
Alignment explanation
Indices: 22892--22932 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
22882 AATTGTTTAG
22892 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
22933 ATATATATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:22937 original size:2 final size:2
Alignment explanation
Indices: 22932--22977 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
22922 TCTCTCTCTC
22932 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
22974 TA TA
1 TA TA
22978 AAAGTGGTGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:26434 original size:21 final size:22
Alignment explanation
Indices: 26400--26440 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
26390 TAATATATTA
26400 TATATATAAAATTTTGATATGT
1 TATATATAAAATTTTGATATGT
26422 TATATAT-AAATTTTGATAT
1 TATATATAAAATTTTGATAT
26441 ATTAATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.51
Consensus pattern (22 bp):
TATATATAAAATTTTGATATGT
Found at i:26993 original size:28 final size:29
Alignment explanation
Indices: 26953--27008 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
26943 TTTATTTTTT
**
26953 AATTATTAAATAAAAATTATTATATTAATC
1 AATTATT-AATAAAAATTAAAATATTAATC
26983 AATTATT-ATAAAAATTAAAATATTAA
1 AATTATTAATAAAAATTAAAATATTAA
27009 ATAATAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 17 0.71
30 7 0.29
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (29 bp):
AATTATTAATAAAAATTAAAATATTAATC
Found at i:28115 original size:27 final size:27
Alignment explanation
Indices: 28062--28118 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
28052 CAAATGTGAT
28062 ATATTAAAAAATTATATATAAAAATAA
1 ATATTAAAAAATTATATATAAAAATAA
*
28089 ATATTAAAATATATT-TATAT-AATATAA
1 ATATTAAAA-A-ATTATATATAAAAATAA
28116 ATA
1 ATA
28119 ATTTATATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 18 0.67
28 6 0.22
29 3 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
ATATTAAAAAATTATATATAAAAATAA
Found at i:28124 original size:18 final size:18
Alignment explanation
Indices: 28095--28145 Score: 65
Period size: 14 Copynumber: 3.0 Consensus size: 18
28085 ATAAATATTA
28095 AAATATATTTATATAATAT
1 AAATA-ATTTATATAATAT
28114 AAATAATTTATAT-AT-T
1 AAATAATTTATATAATAT
28130 -AA-AATTTATATAATAT
1 AAATAATTTATATAATAT
28146 TTTAAATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
14 9 0.30
15 4 0.13
16 2 0.07
17 2 0.07
18 8 0.27
19 5 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AAATAATTTATATAATAT
Found at i:28164 original size:11 final size:10
Alignment explanation
Indices: 28085--28184 Score: 58
Period size: 9 Copynumber: 10.8 Consensus size: 10
28075 ATATATAAAA
28085 ATAA-ATATT
1 ATAATATATT
*
28094 AAAATATATT
1 ATAATATATT
*
28104 -T-ATATAAT
1 ATAATATATT
28112 ATAA-ATAATT
1 ATAATAT-ATT
28122 -T-ATATATT
1 ATAATATATT
* *
28130 AAAATTTA-T
1 ATAATATATT
*
28139 ATAATATTTT
1 ATAATATATT
28149 A-AATATAATT
1 ATAATAT-ATT
28159 ATAATATATT
1 ATAATATATT
*
28169 A-AAAATA-T
1 ATAATATATT
28177 ATAATATA
1 ATAATATA
28185 AATTATGAAT
Statistics
Matches: 68, Mismatches: 12, Indels: 22
0.67 0.12 0.22
Matches are distributed among these distances:
8 12 0.18
9 30 0.44
10 21 0.31
11 5 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
ATAATATATT
Found at i:28181 original size:18 final size:18
Alignment explanation
Indices: 28085--28184 Score: 71
Period size: 18 Copynumber: 5.4 Consensus size: 18
28075 ATATATAAAA
28085 ATAA-ATATT-AAAATAT
1 ATAATATATTAAAAATAT
* * *
28101 ATTTATATAATATAAATA-
1 A-TAATATATTAAAAATAT
* *
28119 ATTTATATATTAAAATTTAT
1 A-TAATATATTAAAA-ATAT
* *
28139 ATAATATTTTAAATATAATT
1 ATAATATATTAAAAAT-A-T
28159 ATAATATATTAAAAATAT
1 ATAATATATTAAAAATAT
28177 ATAATATA
1 ATAATATA
28185 AATTATGAAT
Statistics
Matches: 65, Mismatches: 12, Indels: 12
0.73 0.13 0.13
Matches are distributed among these distances:
16 1 0.02
17 2 0.03
18 27 0.42
19 19 0.29
20 16 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATAATATATTAAAAATAT
Found at i:28385 original size:20 final size:20
Alignment explanation
Indices: 28360--28398 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
28350 TATTTTAAAA
28360 TTAATA-AATATAAAATATAT
1 TTAATATAAT-TAAAATATAT
*
28380 TTAATATAATTATAATATA
1 TTAATATAATTAAAATATA
28399 ATAAATTACG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAATATAATTAAAATATAT
Found at i:28401 original size:25 final size:24
Alignment explanation
Indices: 28333--28401 Score: 56
Period size: 25 Copynumber: 2.9 Consensus size: 24
28323 CAACTTAACA
*
28333 TAATAAAATTAT-ATA-AATATTT
1 TAATATAATTATAATATAATATTT
*
28355 TAAAATTAA-TA-AATATAAAATATATT
1 TAATA-TAATTATAATAT--AATAT-TT
28381 TAATATAATTATAATATAATA
1 TAATATAATTATAATATAATA
28402 AATTACGTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 13
0.69 0.06 0.25
Matches are distributed among these distances:
22 9 0.25
23 2 0.06
25 12 0.33
26 8 0.22
27 5 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
TAATATAATTATAATATAATATTT
Found at i:28424 original size:2 final size:2
Alignment explanation
Indices: 28412--28443 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
28402 AATTACGTAA
28412 AT AT A- 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
28444 AAATTATGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:29005 original size:16 final size:15
Alignment explanation
Indices: 28960--29010 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
28950 AAGGCATGAA
28960 TTTTT-CTTGCTTTT
1 TTTTTCCTTGCTTTT
*
28974 GTTTCTCCATTG-TTTT
1 -TTTTTCC-TTGCTTTT
28990 TTTTTACCTTGCTTTT
1 TTTTT-CCTTGCTTTT
29006 TTTTT
1 TTTTT
29011 TCTCGTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
15 11 0.37
16 16 0.53
17 3 0.10
ACGTcount: A:0.04, C:0.16, G:0.08, T:0.73
Consensus pattern (15 bp):
TTTTTCCTTGCTTTT
Found at i:29379 original size:36 final size:33
Alignment explanation
Indices: 29313--29391 Score: 81
Period size: 35 Copynumber: 2.3 Consensus size: 33
29303 AATAATTAAA
* *
29313 AAATATTTTTATTTAAATTTAATTATAAAATATAT
1 AAATATTTTTATTTAAATTTAA--ATAAAAAATTT
*
29348 AAATATTTTT-TTATTAATTATAAATAAAAAATTT
1 AAATATTTTTATT-TAAATT-TAAATAAAAAATTT
29382 AAA-ATTTTTA
1 AAATATTTTTA
29392 AATAATAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
33 6 0.16
34 14 0.37
35 15 0.39
36 3 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (33 bp):
AAATATTTTTATTTAAATTTAAATAAAAAATTT
Found at i:29652 original size:2 final size:2
Alignment explanation
Indices: 29641--29672 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
29631 TCTCTTTCTC
*
29641 AT AT AC 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
29673 GGTCATATAA
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:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:32761 original size:16 final size:16
Alignment explanation
Indices: 32742--32772 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
32732 ATCATACTCA
32742 TTATATTACATATAAT
1 TTATATTACATATAAT
*
32758 TTATATTATATATAA
1 TTATATTACATATAA
32773 ATTTTGATAT
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:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (16 bp):
TTATATTACATATAAT
Found at i:34124 original size:19 final size:18
Alignment explanation
Indices: 34092--34127 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
34082 AAAATATGAT
34092 ATAATTAAATAATATAAA
1 ATAATTAAATAATATAAA
34110 ATAATTAATATAATATAA
1 ATAATTAA-ATAATATAA
34128 TATCAAATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
ATAATTAAATAATATAAA
Found at i:34177 original size:12 final size:10
Alignment explanation
Indices: 34169--34262 Score: 61
Period size: 10 Copynumber: 9.4 Consensus size: 10
34159 AAAAAAATAA
34169 ATATTAAAAT
1 ATATTAAAAT
34179 ATATTAAAAT
1 ATATTAAAAT
* *
34189 TTA-TATAAT
1 ATATTAAAAT
*
34198 ATAAATAATTAAT
1 AT-ATTAA--AAT
34211 ATATTAAAAT
1 ATATTAAAAT
* *
34221 TTA-TATAAT
1 ATATTAAAAT
*
34230 AT-TTTAAAT
1 ATATTAAAAT
*
34239 ATAATTATAAT
1 AT-ATTAAAAT
34250 ATATTAAAA-
1 ATATTAAAAT
34259 ATAT
1 ATAT
34263 AATATAAATG
Statistics
Matches: 64, Mismatches: 13, Indels: 15
0.70 0.14 0.16
Matches are distributed among these distances:
9 22 0.34
10 24 0.38
11 9 0.14
12 4 0.06
13 5 0.08
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
ATATTAAAAT
Found at i:34194 original size:14 final size:14
Alignment explanation
Indices: 34177--34227 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
34167 AAATATTAAA
34177 ATATATTAAAATTT
1 ATATATTAAAATTT
*
34191 ATATAATATAAATAATTA
1 ATAT-AT-T-AA-AATTT
34209 ATATATTAAAATTT
1 ATATATTAAAATTT
34223 ATATA
1 ATATA
34228 ATATTTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
14 13 0.42
15 4 0.13
16 2 0.06
17 4 0.13
18 8 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATATATTAAAATTT
Found at i:34250 original size:11 final size:10
Alignment explanation
Indices: 34165--34269 Score: 56
Period size: 10 Copynumber: 10.4 Consensus size: 10
34155 TATGAAAAAA
34165 ATAA-ATATT
1 ATAATATATT
*
34174 AAAATATATT
1 ATAATATATT
* *
34184 AAAATTTA-T
1 ATAATATATT
*
34193 ATAATATAAATA
1 ATAATAT--ATT
34205 ATTAATATATT
1 A-TAATATATT
* *
34216 AAAATTTA-T
1 ATAATATATT
*
34225 ATAATATTTT
1 ATAATATATT
34235 A-AATATAATT
1 ATAATAT-ATT
34245 ATAATATATT
1 ATAATATATT
* *
34255 AAAAATATAAT
1 -ATAATATATT
34266 ATAA
1 ATAA
34270 ATGTATAAAT
Statistics
Matches: 72, Mismatches: 15, Indels: 17
0.69 0.14 0.16
Matches are distributed among these distances:
9 20 0.28
10 28 0.39
11 17 0.24
12 1 0.01
13 6 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
ATAATATATT
Found at i:34253 original size:22 final size:21
Alignment explanation
Indices: 34202--34269 Score: 74
Period size: 18 Copynumber: 3.4 Consensus size: 21
34192 TATAATATAA
34202 ATAAT-TAATATATT-AAAAT
1 ATAATATAATATATTAAAAAT
* *
34221 -TTATATAATAT-TT-TAAAT
1 ATAATATAATATATTAAAAAT
34239 ATAATTATAATATATTAAAAAT
1 ATAA-TATAATATATTAAAAAT
34261 ATAATATAA
1 ATAATATAA
34270 ATGTATAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
18 9 0.22
19 8 0.20
20 8 0.20
21 7 0.17
22 8 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATAATATAATATATTAAAAAT
Found at i:34255 original size:39 final size:34
Alignment explanation
Indices: 34165--34271 Score: 118
Period size: 32 Copynumber: 3.2 Consensus size: 34
34155 TATGAAAAAA
*
34165 ATAAAT-ATTAAAATATATTAAAATTTATATAAT
1 ATAAATAATTATAATATATTAAAATTTATATAAT
34198 ATAAATAA-T-TAATATATTAAAATTTATATAAT
1 ATAAATAATTATAATATATTAAAATTTATATAAT
34230 ATTTTAAATATAATTATAATATATTAAAA---ATATAAT
1 A---T-AA-ATAATTATAATATATTAAAATTTATATAAT
34266 ATAAAT
1 ATAAAT
34272 GTATAAATTA
Statistics
Matches: 65, Mismatches: 1, Indels: 18
0.77 0.01 0.21
Matches are distributed among these distances:
31 2 0.03
32 25 0.38
33 8 0.12
34 1 0.02
35 1 0.02
36 10 0.15
37 4 0.06
38 1 0.02
39 13 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (34 bp):
ATAAATAATTATAATATATTAAAATTTATATAAT
Found at i:34268 original size:41 final size:41
Alignment explanation
Indices: 34164--34269 Score: 112
Period size: 41 Copynumber: 2.6 Consensus size: 41
34154 ATATGAAAAA
* *
34164 AATAA-ATATTAAAATATATTAAAATTTATATAATATAAAT
1 AATAATATATTAAAATATAATATAATTTATATAATATAAAT
* *
34204 AATTAATATATTAAAAT-TTATATAATATTTTA-AATAT-AAT
1 AA-TAATATATTAAAATATAATATAAT-TTATATAATATAAAT
*
34244 TATAATATATTAAAAATATAATATAA
1 AATAATATATT-AAAATATAATATAA
34270 ATGTATAAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
39 9 0.16
40 11 0.20
41 21 0.38
42 14 0.25
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (41 bp):
AATAATATATTAAAATATAATATAATTTATATAATATAAAT
Found at i:34393 original size:8 final size:8
Alignment explanation
Indices: 34379--34465 Score: 56
Period size: 8 Copynumber: 10.8 Consensus size: 8
34369 ATAATATTTT
34379 ATATATAA
1 ATATATAA
*
34387 TTATATAA
1 ATATATAA
34395 ATATAATAA
1 ATAT-ATAA
*
34404 AAATATAA
1 ATATATAA
* *
34412 TTAAATATA
1 ATATATA-A
34421 ATA-A-AA
1 ATATATAA
34427 ATATATAA
1 ATATATAA
*
34435 ATATTTTAA
1 ATA-TATAA
34444 A-ATTAATAA
1 ATA-T-ATAA
34453 ATATA-AA
1 ATATATAA
34460 ATATAT
1 ATATAT
34466 TTAATGTGAA
Statistics
Matches: 62, Mismatches: 9, Indels: 16
0.71 0.10 0.18
Matches are distributed among these distances:
6 4 0.06
7 9 0.15
8 28 0.45
9 20 0.32
10 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATATAA
Found at i:34409 original size:11 final size:11
Alignment explanation
Indices: 34393--34435 Score: 63
Period size: 11 Copynumber: 4.1 Consensus size: 11
34383 ATAATTATAT
34393 AAATATAATAA
1 AAATATAATAA
*
34404 AAATATAAT-T
1 AAATATAATAA
34414 AAATATAATAA
1 AAATATAATAA
34425 AAATAT-ATAA
1 AAATATAATAA
34435 A
1 A
34436 TATTTTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 14 0.48
11 15 0.52
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
AAATATAATAA
Found at i:34437 original size:19 final size:19
Alignment explanation
Indices: 34388--34458 Score: 90
Period size: 21 Copynumber: 3.7 Consensus size: 19
34378 TATATATAAT
34388 TATATAAATATAATAAAAA
1 TATATAAATATAATAAAAA
34407 TATAATTAAATATAATAAAAA
1 TAT-A-TAAATATAATAAAAA
** *
34428 TATATAAATATTTTAAAAT
1 TATATAAATATAATAAAAA
34447 TA-ATAAATATAA
1 TATATAAATATAA
34459 AATATATTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
18 8 0.18
19 17 0.38
20 2 0.04
21 18 0.40
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
TATATAAATATAATAAAAA
Found at i:38046 original size:2 final size:2
Alignment explanation
Indices: 38039--38077 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
38029 AGTCACTAGA
38039 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
38078 GGGGGAGAGA
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:38087 original size:2 final size:2
Alignment explanation
Indices: 38082--38112 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
38072 TATATAGGGG
38082 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
38113 GATAATGCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:41089 original size:21 final size:21
Alignment explanation
Indices: 41072--41124 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
41062 TGATATAATT
41072 ATATAATATAAAAATATAAAA
1 ATATAATATAAAAATATAAAA
**
41093 ATATAATATAAAAA-ATACGA
1 ATATAATATAAAAATATAAAA
*
41113 ACATAATATAAA
1 ATATAATATAAA
41125 TATACACTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.26
Consensus pattern (21 bp):
ATATAATATAAAAATATAAAA
Found at i:43246 original size:25 final size:24
Alignment explanation
Indices: 43201--43268 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
43191 AAAATATACA
* *
43201 TAAAATAAAT-AAATTATTAATATGT
1 TAAAATATATAAAAATA-TAATAT-T
43226 TAAAATATATAAAAATATAATATT
1 TAAAATATATAAAAATATAATATT
* * *
43250 TTAAGTATAAAAAAATATA
1 TAAAATATATAAAAATATA
43269 GATACAAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
24 17 0.46
25 15 0.41
26 5 0.14
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (24 bp):
TAAAATATATAAAAATATAATATT
Found at i:44532 original size:16 final size:15
Alignment explanation
Indices: 44511--44552 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
44501 TTTTTCTCCC
44511 ATATATAAAATAAAT
1 ATATATAAAATAAAT
*
44526 -TATATATAA-AAAT
1 ATATATAAAATAAAT
44539 ATATATAAAATAAA
1 ATATATAAAATAAA
44553 ATCAAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 4 0.17
14 16 0.70
15 3 0.13
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
ATATATAAAATAAAT
Found at i:44665 original size:19 final size:19
Alignment explanation
Indices: 44643--44683 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
44633 AATTTTTTCC
44643 TTTTT-TTTCTTTTTTGCT
1 TTTTTGTTTCTTTTTTGCT
*
44661 TTTTTGTTTCTTTTTTTCT
1 TTTTTGTTTCTTTTTTGCT
44680 TTTT
1 TTTT
44684 CACCTGAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.85
Consensus pattern (19 bp):
TTTTTGTTTCTTTTTTGCT
Found at i:46204 original size:4 final size:4
Alignment explanation
Indices: 46195--46267 Score: 71
Period size: 4 Copynumber: 19.0 Consensus size: 4
46185 ATATAATTTT
* * * *
46195 TTTC TTTC TTT- TTTT TTTC TTTT TTTC -TTC TTTC ATTC ATTC TTT-
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
* *
46240 TTTT TTTC TTAC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
46268 CCAGCCAAAC
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
3 9 0.16
4 49 0.84
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:46221 original size:23 final size:23
Alignment explanation
Indices: 46191--46267 Score: 77
Period size: 23 Copynumber: 3.3 Consensus size: 23
46181 CAACATATAA
*
46191 TTTTTTTCTTTCTTTTTTTTTTC
1 TTTTTTTCTTTCTTTTTTCTTTC
* *
46214 TTTTTTTC-TTCTTTCATTCATTC
1 TTTTTTTCTTTCTTT-TTTCTTTC
*
46237 TTTTTTT-TTTCTTACTTTCTTTC
1 TTTTTTTCTTTCTT-TTTTCTTTC
*
46260 TTTCTTTC
1 TTTTTTTC
46268 CCAGCCAAAC
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
22 6 0.14
23 37 0.86
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (23 bp):
TTTTTTTCTTTCTTTTTTCTTTC
Found at i:46325 original size:3 final size:3
Alignment explanation
Indices: 46317--46357 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
46307 TAATGTATAG
46317 ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
46358 CCTTTTTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:48408 original size:2 final size:2
Alignment explanation
Indices: 48401--48432 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
48391 ATGTCATAGA
48401 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48433 GCGTGTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55421 original size:21 final size:21
Alignment explanation
Indices: 55379--55421 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
55369 AATTTGAATA
* *
55379 TTTATAATTTTTTAATTAATT
1 TTTATAATTTTTAAATAAATT
55400 TTTATAA-TTTTAAATAATATT
1 TTTATAATTTTTAAATAA-ATT
55421 T
1 T
55422 GGATTATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTATAATTTTTAAATAAATT
Found at i:55475 original size:45 final size:43
Alignment explanation
Indices: 55388--55480 Score: 102
Period size: 45 Copynumber: 2.1 Consensus size: 43
55378 ATTTATAATT
*
55388 TTTTAATTAATTTTTATAATTTTAAATAATATTTGGATTATTATA
1 TTTTAATTAATTTTTATAATTTTAAATAATATTT-GAATATTA-A
55433 TTTTAATT-ATTATTTATAATAAATTTAAATAA-ATTT-AATATTAA
1 TTTTAATTAATT-TTTATAAT---TTTAAATAATATTTGAATATTAA
55477 TTTT
1 TTTT
55481 TAAATATTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
44 8 0.19
45 22 0.51
47 4 0.09
48 9 0.21
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (43 bp):
TTTTAATTAATTTTTATAATTTTAAATAATATTTGAATATTAA
Found at i:55499 original size:15 final size:15
Alignment explanation
Indices: 55465--55509 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
55455 ATTTAAATAA
*
55465 ATTT-AATATTAATT
1 ATTTAAATATTTATT
55479 -TTTAAATATTTATT
1 ATTTAAATATTTATT
55493 ATTTAAAT-TTATATT
1 ATTTAAATATT-TATT
55508 AT
1 AT
55510 ACTTATTGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 3 0.11
14 11 0.41
15 13 0.48
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTAAATATTTATT
Found at i:55503 original size:21 final size:21
Alignment explanation
Indices: 55444--55503 Score: 52
Period size: 21 Copynumber: 2.8 Consensus size: 21
55434 TTTAATTATT
*
55444 ATTT-ATAATAAATTTAAATAA
1 ATTTAATATTAAATTTAAAT-A
*
55465 ATTTAATATTAATTTTTAAAT-
1 ATTTAATATTAA-ATTTAAATA
*
55486 ATTTATTATTTAAATTTA
1 ATTTAATA-TTAAATTTA
55504 TATTATACTT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
21 15 0.47
22 10 0.31
23 7 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTTAATATTAAATTTAAATA
Found at i:60631 original size:16 final size:17
Alignment explanation
Indices: 60600--60652 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 17
60590 TTTAATATAC
*
60600 TTAATATTTATTTAATA
1 TTAAAATTTATTTAATA
*
60617 TTAAAATTTTTTAATAATA
1 TTAAAATTTATT--TAATA
60636 TTTAAAATATTATTTAA
1 -TTAAAAT-TTATTTAA
60653 ATGAATCGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 10 0.34
19 8 0.28
20 7 0.24
21 4 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTAAAATTTATTTAATA
Found at i:61254 original size:2 final size:2
Alignment explanation
Indices: 61249--61276 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
61239 TATCAAATAC
61249 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
61277 TTAACACTCA
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:71250 original size:3 final size:3
Alignment explanation
Indices: 71244--71271 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
71234 TTTTAAAATT
71244 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
71272 CAAAATTGCT
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):
ATA
Found at i:71592 original size:21 final size:21
Alignment explanation
Indices: 71566--71615 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
71556 ATTTATTAAA
*
71566 AAATTTAAATAATATAATTTT
1 AAATTTAAATAATAAAATTTT
*
71587 AAATTTTAATAATAAAATTTT
1 AAATTTAAATAATAAAATTTT
*
71608 TAATTTAA
1 AAATTTAA
71616 TAGTTTAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
AAATTTAAATAATAAAATTTT
Found at i:71604 original size:35 final size:37
Alignment explanation
Indices: 71531--71606 Score: 95
Period size: 35 Copynumber: 2.1 Consensus size: 37
71521 TTATTTTTAT
*
71531 ATTTAAATATATATTAAATATAAATATTTATTAAAAA
1 ATTTAAATATATATTAAATATAAATATTTAATAAAAA
* *
71568 ATTTAAATA-ATA-TAATTTTAAAT-TTTAATAATAAA
1 ATTTAAATATATATTAAATATAAATATTTAATAA-AAA
71603 ATTT
1 ATTT
71607 TTAATTTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
34 7 0.20
35 16 0.46
36 3 0.09
37 9 0.26
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (37 bp):
ATTTAAATATATATTAAATATAAATATTTAATAAAAA
Found at i:71696 original size:13 final size:14
Alignment explanation
Indices: 71678--71706 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
71668 GATCGATTTT
71678 AAATTTTT-TTAAA
1 AAATTTTTATTAAA
71691 AAATTTTTATTAAA
1 AAATTTTTATTAAA
71705 AA
1 AA
71707 TAATATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATTTTTATTAAA
Found at i:72404 original size:4 final size:4
Alignment explanation
Indices: 72395--72421 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
72385 AAGTCAACAT
72395 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
72422 TTGTTAGGAC
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:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:72864 original size:26 final size:25
Alignment explanation
Indices: 72824--72874 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 25
72814 ATAAAAATCA
72824 AATTTATTTTTATTTTAAATTAAAT
1 AATTTATTTTTATTTTAAATTAAAT
72849 AATTTAATTTTTATTTTAAATTAAAT
1 AATTT-ATTTTTATTTTAAATTAAAT
72875 TTAAATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
AATTTATTTTTATTTTAAATTAAAT
Found at i:72875 original size:18 final size:19
Alignment explanation
Indices: 72835--72900 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 19
72825 ATTTATTTTT
* * *
72835 ATTTTAAATTAAATAATTTA
1 ATTTTAATTTTAA-AATTAA
*
72855 ATTTTTATTTT-AAATTAA
1 ATTTTAATTTTAAAATTAA
* *
72873 ATTTAAATTTTAAAAATAA
1 ATTTTAATTTTAAAATTAA
72892 ATTTTAATT
1 ATTTTAATT
72901 AATCTCGAAC
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
18 14 0.38
19 15 0.41
20 8 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTTTAATTTTAAAATTAA
Found at i:73732 original size:11 final size:11
Alignment explanation
Indices: 73716--73741 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
73706 GATATAAAAA
73716 ATAATATAAAT
1 ATAATATAAAT
73727 ATAATATAAAT
1 ATAATATAAAT
73738 ATAA
1 ATAA
73742 AAATATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:73786 original size:16 final size:17
Alignment explanation
Indices: 73754--73800 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
73744 ATATTTTAAA
73754 ATTAATATAATATAAATT
1 ATTAATA-AATATAAATT
73772 ATTAATAAATA-AAATT
1 ATTAATAAATATAAATT
73788 -TTATATAAATATA
1 ATTA-ATAAATATA
73801 TAATAACTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 3 0.11
16 12 0.44
17 5 0.19
18 7 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTAATAAATATAAATT
Found at i:73861 original size:27 final size:27
Alignment explanation
Indices: 73757--74040 Score: 66
Period size: 27 Copynumber: 10.6 Consensus size: 27
73747 TTTTAAAATT
* *
73757 AATATAATATAAAT-TATTAATAAATAA
1 AATATAATATAAATATATAAATATA-AA
* * *
73784 AATTTTATATAAATATAT-AATA-ACTTA
1 AATATAATATAAATATATAAATATA--AA
**
73811 AATACGAT-TACAATATGATAAAATATAAA
1 AATATAATATA-AATAT-AT-AAATATAAA
*
73840 AATATAATATAAATATATAAAT-T-TA
1 AATATAATATAAATATATAAATATAAA
*
73865 AAT-T--TGAT-AAT-TTTAAATATAAA
1 AATATAAT-ATAAATATATAAATATAAA
* * * *
73888 TACATAATAT-AATACCGATAAA-ATAATT
1 AATATAATATAAATA--TATAAATATAA-A
* * * **
73916 TATATGATATAAATACATATCT-TAAA
1 AATATAATATAAATATATAAATATAAA
* *
73942 ATCTTATAATATAAAT-TATTAATATATTAA
1 A--ATATAATATAAATATA-TAA-ATATAAA
**
73972 AAT-TAATATAAATATA-AAATATTTTA
1 AATATAATATAAATATATAAATA-TAAA
*
73998 AATATAATA-ATAATATAATAAAATATATA
1 AATATAATATA-AATAT-AT-AAATATAAA
74027 AA-ATAATATAAATA
1 AATATAATATAAATA
74041 AACGAATTAC
Statistics
Matches: 191, Mismatches: 33, Indels: 65
0.66 0.11 0.22
Matches are distributed among these distances:
21 6 0.03
22 5 0.03
23 4 0.02
24 2 0.01
25 12 0.06
26 14 0.07
27 63 0.33
28 46 0.24
29 23 0.12
30 15 0.08
31 1 0.01
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (27 bp):
AATATAATATAAATATATAAATATAAA
Found at i:74015 original size:8 final size:8
Alignment explanation
Indices: 73998--74041 Score: 52
Period size: 8 Copynumber: 5.2 Consensus size: 8
73988 AAATATTTTA
*
73998 AATATAAT
1 AATAAAAT
*
74006 AATAATAT
1 AATAAAAT
74014 AATAAAAT
1 AATAAAAT
74022 ATATAAAAT
1 A-ATAAAAT
74031 AATATAAAT
1 AATA-AAAT
74040 AA
1 AA
74042 ACGAATTACT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
8 17 0.55
9 14 0.45
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (8 bp):
AATAAAAT
Found at i:74897 original size:27 final size:26
Alignment explanation
Indices: 74867--74924 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
74857 TCATAGTAAT
74867 TTTAT-TAGGTTATTATATTAAAATAAA
1 TTTATATA-GTTATTATA-TAAAATAAA
* * *
74894 TTTATATATTTATTATATAAATTAAG
1 TTTATATAGTTATTATATAAAATAAA
74920 TTTAT
1 TTTAT
74925 GACCAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 12 0.44
27 13 0.48
28 2 0.07
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.53
Consensus pattern (26 bp):
TTTATATAGTTATTATATAAAATAAA
Found at i:75026 original size:13 final size:13
Alignment explanation
Indices: 75008--75036 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
74998 ATGGATGGAG
75008 TTATTTATTTGGT
1 TTATTTATTTGGT
75021 TTATTTATTTGGT
1 TTATTTATTTGGT
75034 TTA
1 TTA
75037 GTATGAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.00, G:0.14, T:0.69
Consensus pattern (13 bp):
TTATTTATTTGGT
Found at i:75331 original size:20 final size:21
Alignment explanation
Indices: 75284--75323 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
75274 TATATCTATT
75284 TAAAT-TTAATTATAAAAATA
1 TAAATATTAATTATAAAAATA
75304 TAAATATTAA-TATAAAAATA
1 TAAATATTAATTATAAAAATA
75324 AATTTATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAATATTAATTATAAAAATA
Found at i:75726 original size:9 final size:11
Alignment explanation
Indices: 75701--75737 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
75691 CCAAAAAAAA
75701 TTAATTTTATG
1 TTAATTTTATG
75712 TTAATTTT-T-
1 TTAATTTTATG
75721 TTAATTTTATG
1 TTAATTTTATG
75732 TTAATT
1 TTAATT
75738 AATTTGATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 8 0.33
10 2 0.08
11 14 0.58
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (11 bp):
TTAATTTTATG
Found at i:75925 original size:23 final size:23
Alignment explanation
Indices: 75899--75945 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
75889 TGATCTTACT
* * *
75899 TTATGTATTTTCTAAATATATAA
1 TTATATATTTTATAAATAAATAA
75922 TTATATATTTTATAAATAAATAA
1 TTATATATTTTATAAATAAATAA
75945 T
1 T
75946 ATTATTAACG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
TTATATATTTTATAAATAAATAA
Found at i:76362 original size:24 final size:25
Alignment explanation
Indices: 76329--76386 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
76319 TAAATAATTC
* *
76329 ATAACAAAATAAATTAAAATTT-TTA
1 ATAATAAATTAAA-TAAAATTTATTA
* *
76354 CTAATAAATTGAATAAAATTTATTA
1 ATAATAAATTAAATAAAATTTATTA
76379 ATAATAAA
1 ATAATAAA
76387 AATATTTATA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 8 0.30
25 19 0.70
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (25 bp):
ATAATAAATTAAATAAAATTTATTA
Found at i:80737 original size:16 final size:16
Alignment explanation
Indices: 80698--80756 Score: 64
Period size: 16 Copynumber: 3.7 Consensus size: 16
80688 GTCGGGTTTG
* *
80698 AATCATTTTGATTTTG
1 AATCATTTTAATTTTA
* *
80714 AGTTATTTTAATTTTA
1 AATCATTTTAATTTTA
*
80730 AATCATTTTAAATTTA
1 AATCATTTTAATTTTA
*
80746 AATTATTTTAA
1 AATCATTTTAA
80757 GTTCGAGTTA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (16 bp):
AATCATTTTAATTTTA
Found at i:81463 original size:22 final size:22
Alignment explanation
Indices: 81435--81478 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
81425 AGAAAACTAA
*
81435 TTTTTTCTTG-ATTCAATTTTAT
1 TTTTTTCGTGAATT-AATTTTAT
81457 TTTTTTCGTGAATTAATTTTAT
1 TTTTTTCGTGAATTAATTTTAT
81479 AACGTTGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.66
Consensus pattern (22 bp):
TTTTTTCGTGAATTAATTTTAT
Found at i:82367 original size:15 final size:16
Alignment explanation
Indices: 82336--82366 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
82326 CATTGAAGGC
*
82336 TAATTTTAATTTAAAA
1 TAATTTAAATTTAAAA
82352 TAATTTAAATTTAAA
1 TAATTTAAATTTAAA
82367 TTTAATATTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TAATTTAAATTTAAAA
Found at i:82788 original size:2 final size:2
Alignment explanation
Indices: 82741--82779 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
82731 CTTTTATGGA
82741 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
82780 CTGTATATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:83659 original size:11 final size:12
Alignment explanation
Indices: 83622--83654 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
83612 ATATTATATG
83622 AATATAATATAA
1 AATATAATATAA
*
83634 AAAATAAT-TAA
1 AATATAATATAA
83645 AATATAATAT
1 AATATAATAT
83655 GAATACAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AATATAATATAA
Found at i:83664 original size:29 final size:28
Alignment explanation
Indices: 83617--83679 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
83607 TAATAATATT
*
83617 ATATGAATATAATATAAAAA-ATAATTAAA
1 ATAT-AATATAATACAAAAATAT-ATTAAA
*
83646 ATATAATATGAATACAAAAATATCTTAAA
1 ATATAATAT-AATACAAAAATATATTAAA
83675 ATATA
1 ATATA
83680 TAAAATATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 5 0.17
29 23 0.77
30 2 0.07
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (28 bp):
ATATAATATAATACAAAAATATATTAAA
Found at i:83735 original size:16 final size:15
Alignment explanation
Indices: 83671--83738 Score: 57
Period size: 16 Copynumber: 4.2 Consensus size: 15
83661 AAAAATATCT
*
83671 TAAAATATATAAAATA
1 TAAAAT-TATTAAATA
83687 T-AAATTATTAATATA
1 TAAAATTATTAA-ATA
83702 TCAAAATTTATATAAATA
1 T-AAAA-TTAT-TAAATA
*
83720 TAAAATATTTTAAATA
1 TAAAAT-TATTAAATA
83736 TAA
1 TAA
83739 TTATTATATG
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
14 5 0.11
15 8 0.18
16 11 0.25
17 9 0.20
18 8 0.18
19 3 0.07
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (15 bp):
TAAAATTATTAAATA
Found at i:83769 original size:49 final size:49
Alignment explanation
Indices: 83671--83780 Score: 118
Period size: 48 Copynumber: 2.3 Consensus size: 49
83661 AAAAATATCT
* ** *
83671 TAAAATATATAAAATATAAATTATTAATATATCAAAATTTATATAAATA
1 TAAAATATATAAAATATAAATTATTAATATATAAAAACATAAATAAATA
* *
83720 TAAAATATTTTAAATAT-AATTATT-ATATGATAAAAACATAAATATAATA
1 TAAAATATATAAAATATAAATTATTAATAT-ATAAAAACATAAATA-AATA
*
83769 T-AAATAAATAAA
1 TAAAATATATAAA
83781 TTATCAAACC
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
47 4 0.08
48 26 0.52
49 20 0.40
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.37
Consensus pattern (49 bp):
TAAAATATATAAAATATAAATTATTAATATATAAAAACATAAATAAATA
Found at i:84055 original size:6 final size:7
Alignment explanation
Indices: 84015--84061 Score: 50
Period size: 7 Copynumber: 7.4 Consensus size: 7
84005 ACATCCCATG
84015 AATTTAT
1 AATTTAT
84022 AATTTAT
1 AATTTAT
84029 AATTTAT
1 AATTTAT
84036 -ATTTA-
1 AATTTAT
*
84041 AA--TAA
1 AATTTAT
84046 AATTT-T
1 AATTTAT
84052 AATTTAT
1 AATTTAT
84059 AAT
1 AAT
84062 AAATCTTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
4 2 0.06
5 2 0.06
6 11 0.32
7 19 0.56
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (7 bp):
AATTTAT
Found at i:84065 original size:17 final size:18
Alignment explanation
Indices: 84031--84071 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
84021 TAATTTATAA
84031 TTTATATTTAAATAAAAT-
1 TTTA-ATTTAAATAAAATC
84049 TTTAATTTATAAT-AAATC
1 TTTAATTTA-AATAAAATC
84067 TTTAA
1 TTTAA
84072 AATTATCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTAATTTAAATAAAATC
Found at i:84071 original size:30 final size:31
Alignment explanation
Indices: 84015--84072 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
84005 ACATCCCATG
**
84015 AATTTATAATTTATAATTTATATTTAAATAA
1 AATTTATAATTTATAATAAATATTTAAATAA
*
84046 AATTT-TAATTTATAATAAATCTTTAAA
1 AATTTATAATTTATAATAAATATTTAAA
84073 ATTATCAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 19 0.79
31 5 0.21
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (31 bp):
AATTTATAATTTATAATAAATATTTAAATAA
Found at i:84648 original size:17 final size:16
Alignment explanation
Indices: 84628--84662 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
84618 TAATAACTTA
84628 AAATTAAAAAATAATCG
1 AAATT-AAAAATAATCG
*
84645 AAATTTAAAATAATCG
1 AAATTAAAAATAATCG
84661 AA
1 AA
84663 TCCGAATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.63, C:0.06, G:0.06, T:0.26
Consensus pattern (16 bp):
AAATTAAAAATAATCG
Found at i:84715 original size:16 final size:16
Alignment explanation
Indices: 84696--84738 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
84686 TAACTTAAAT
84696 TTAAAATGATTCGAA-A
1 TTAAAATGATTC-AAGA
*
84712 TTAAAATGATTCAAGT
1 TTAAAATGATTCAAGA
84728 TTAAAATGATT
1 TTAAAATGATT
84739 AAAATAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.37
Consensus pattern (16 bp):
TTAAAATGATTCAAGA
Found at i:85040 original size:17 final size:16
Alignment explanation
Indices: 85007--85067 Score: 50
Period size: 19 Copynumber: 3.6 Consensus size: 16
84997 TTTAATTATT
85007 TTTTAATAAAATATAA
1 TTTTAATAAAATATAA
* *
85023 TTTTAATACATATGTAA
1 TTTTAATA-AAATATAA
*
85040 TTATTTAATATAAATTTAA
1 -T-TTTAATA-AAATATAA
*
85059 TTTTTATAA
1 TTTTAATAA
85068 TTTTTAATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
16 9 0.25
17 12 0.33
18 2 0.06
19 13 0.36
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (16 bp):
TTTTAATAAAATATAA
Found at i:85066 original size:15 final size:17
Alignment explanation
Indices: 85032--85087 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
85022 ATTTTAATAC
*
85032 ATATGTAATTATTTAATA
1 ATATTTAATTATTT-ATA
*
85050 TAAATTTAATT-TTTATA
1 -ATATTTAATTATTTATA
* *
85067 ATTTTTAATTATTTATT
1 ATATTTAATTATTTATA
85084 ATAT
1 ATAT
85088 ATTTTAATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
16 8 0.27
17 11 0.37
18 3 0.10
19 8 0.27
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (17 bp):
ATATTTAATTATTTATA
Found at i:85076 original size:35 final size:35
Alignment explanation
Indices: 84985--85109 Score: 114
Period size: 35 Copynumber: 3.5 Consensus size: 35
84975 TTTATTTTTC
*
84985 AATTTTAAT-ATTTTTAATTATTTTTTAATA-AAATAT
1 AATTTTAATAATTTTTAATTA---TTTAATATAAATTT
* *
85021 AATTTTAATACATATGTAATTATTTAATATAAATTT
1 AATTTTAATA-ATTTTTAATTATTTAATATAAATTT
* * *
85057 AATTTTTATAATTTTTAATTATTTATTATATATTTT
1 AATTTTAATAATTTTTAATTATTTAATATA-AATTT
*
85093 AA-TTTAAT-ATCTTTAAT
1 AATTTTAATAATTTTTAAT
85110 GATAATTTTT
Statistics
Matches: 75, Mismatches: 10, Indels: 10
0.79 0.11 0.11
Matches are distributed among these distances:
34 8 0.11
35 29 0.39
36 29 0.39
38 9 0.12
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.58
Consensus pattern (35 bp):
AATTTTAATAATTTTTAATTATTTAATATAAATTT
Found at i:85085 original size:20 final size:19
Alignment explanation
Indices: 85058--85096 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
85048 TATAAATTTA
85058 ATTTTTATA-ATTTTTAATT
1 ATTTTTATATA-TTTTAATT
85077 ATTTATTATATATTTTAATT
1 ATTT-TTATATATTTTAATT
85097 TAATATCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 13 0.72
21 1 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
ATTTTTATATATTTTAATT
Found at i:85094 original size:36 final size:35
Alignment explanation
Indices: 84985--85109 Score: 121
Period size: 36 Copynumber: 3.5 Consensus size: 35
84975 TTTATTTTTC
* *
84985 AATTTTAAT-ATTTTTAATTATTTTTTAATAAAATAT
1 AATTTTAATAATTTTTAATTATTTATT-AT-AAATTT
* * *
85021 AATTTTAATACATATGTAATTATTTAATATAAATTT
1 AATTTTAATA-ATTTTTAATTATTTATTATAAATTT
* *
85057 AATTTTTATAATTTTTAATTATTTATTATATATTTT
1 AATTTTAATAATTTTTAATTATTTATTATA-AATTT
*
85093 AA-TTTAAT-ATCTTTAAT
1 AATTTTAATAATTTTTAAT
85110 GATAATTTTT
Statistics
Matches: 74, Mismatches: 12, Indels: 8
0.79 0.13 0.09
Matches are distributed among these distances:
34 8 0.11
35 22 0.30
36 29 0.39
37 2 0.03
38 13 0.18
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.58
Consensus pattern (35 bp):
AATTTTAATAATTTTTAATTATTTATTATAAATTT
Found at i:86495 original size:16 final size:17
Alignment explanation
Indices: 86462--86503 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
86452 ATTTAATATG
86462 AAATAATATCAATATTT
1 AAATAATATCAATATTT
86479 AAAT-ATATCAA-ATTTT
1 AAATAATATCAATA-TTT
*
86495 ATATAATAT
1 AAATAATAT
86504 TTATAATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 1 0.05
16 13 0.59
17 8 0.36
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATAATATCAATATTT
Found at i:86653 original size:19 final size:19
Alignment explanation
Indices: 86613--86662 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
86603 ATTCAAGAAT
86613 AATATAAA-A-TATAAAAA
1 AATATAAATATTATAAAAA
*
86630 AATATAAATATTATATAAA
1 AATATAAATATTATAAAAA
*
86649 TATATAAATTATTA
1 AATATAAA-TATTA
86663 AATTTATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 8 0.29
18 1 0.04
19 14 0.50
20 5 0.18
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AATATAAATATTATAAAAA
Found at i:86670 original size:16 final size:17
Alignment explanation
Indices: 86614--86670 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 17
86604 TTCAAGAATA
* * *
86614 ATATAAAATATAAAAAA
1 ATATAAATTATATAAAT
86631 ATATAAATATTATATAAAT
1 ATAT-AA-ATTATATAAAT
86650 ATATAAATTAT-TAAAT
1 ATATAAATTATATAAAT
*
86666 TTATA
1 ATATA
86671 TTTCTTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
16 9 0.26
17 9 0.26
18 4 0.12
19 12 0.35
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATATAAATTATATAAAT
Found at i:86914 original size:23 final size:23
Alignment explanation
Indices: 86831--86910 Score: 73
Period size: 24 Copynumber: 3.6 Consensus size: 23
86821 ATATATAACA
86831 TAAAT-TATTAA-A-AATATA-T
1 TAAATATATTAATATAATATATT
*
86850 TAAA-ATTTTAATATAATATATAT
1 TAAATATATTAATATAATATAT-T
*
86873 TAAATACA-TAATATTAAGTATATT
1 TAAATATATTAATA-TAA-TATATT
86897 TAAATATATTAATA
1 TAAATATATTAATA
86911 AAGTTAAATC
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
19 9 0.19
20 1 0.02
21 6 0.12
23 10 0.21
24 12 0.25
25 10 0.21
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (23 bp):
TAAATATATTAATATAATATATT
Found at i:87076 original size:19 final size:18
Alignment explanation
Indices: 87045--87082 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 18
87035 AATCAAAATT
87045 TATAATAAAATATATAAA
1 TATAATAAAATATATAAA
87063 TATAATATAAATATATAAA
1 TATAATA-AAATATATAAA
87082 T
1 T
87083 TATTATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TATAATAAAATATATAAA
Found at i:87564 original size:24 final size:24
Alignment explanation
Indices: 87537--87583 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
87527 ATAAATAAAT
87537 AAATAAAATAA-AAATAAATATTAA
1 AAAT-AAATAATAAATAAATATTAA
* *
87561 AAATATATAATAAATTAATATTA
1 AAATAAATAATAAATAAATATTA
87584 GTAATCAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (24 bp):
AAATAAATAATAAATAAATATTAA
Found at i:87574 original size:13 final size:13
Alignment explanation
Indices: 87525--87574 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
87515 ATATTTTTAG
87525 ATATA-AATAAATA
1 ATATATAATAAA-A
*
87538 A-ATAAAATAAAA
1 ATATATAATAAAA
* *
87550 ATAAATATTAAAA
1 ATATATAATAAAA
87563 ATATATAATAAA
1 ATATATAATAAA
87575 TTAATATTAG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
12 5 0.17
13 25 0.83
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
ATATATAATAAAA
Found at i:87771 original size:18 final size:17
Alignment explanation
Indices: 87731--87775 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 17
87721 TAATATCGAT
87731 ATAAAATAATATATATCA
1 ATAAAATAATATATA-CA
87749 ATAAAATAGATATATA-A
1 ATAAAATA-ATATATACA
87766 ACTAAAATAA
1 A-TAAAATAA
87776 AAAATATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 3 0.12
18 15 0.60
19 7 0.28
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.29
Consensus pattern (17 bp):
ATAAAATAATATATACA
Found at i:88183 original size:5 final size:5
Alignment explanation
Indices: 88168--88208 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
88158 AATTTTATAG
*
88168 AAATCA AAATA AAAT- -AATA AAATA AAATA AAATA GAATA AA
1 AAAT-A AAATA AAATA AAATA AAATA AAATA AAATA AAATA AA
88209 TATATTTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
3 3 0.10
5 24 0.77
6 4 0.13
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:88191 original size:13 final size:13
Alignment explanation
Indices: 88173--88197 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
88163 TATAGAAATC
88173 AAAATAAAATAAT
1 AAAATAAAATAAT
88186 AAAATAAAATAA
1 AAAATAAAATAA
88198 AATAGAATAA
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAATAAAATAAT
Done.