Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010119.1 Kokia drynarioides strain JFW-HI SEQ_124908, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 140055
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 135 characters in sequence are not A, C, G, or T
Found at i:674 original size:29 final size:29
Alignment explanation
Indices: 632--1112 Score: 364
Period size: 29 Copynumber: 16.4 Consensus size: 29
622 CTAAACTGTT
* *
632 CAAAAATTACATTTTTACCCTCGAGCTTC
1 CAAAAATTCCATTTTTACCCTCGAACTTC
* * *
661 CAAAAATCCCATTTTGACCC-CAAACTTC
1 CAAAAATTCCATTTTTACCCTCGAACTTC
**
689 CAAAAATTCCATTTTTACCCTTAAACTTC
1 CAAAAATTCCATTTTTACCCTCGAACTTC
**
718 CAAAAACCCCATTTTTAGCCC-CGAAACTTC
1 CAAAAATTCCATTTTTA-CCCTCG-AACTTC
748 CAAAAATTCCATTTTTACCCTCGAACTTC
1 CAAAAATTCCATTTTTACCCTCGAACTTC
* * *
777 CAAAAATTCCATTCTTAACCTTGAAACTTC
1 CAAAAATTCCATTTTTACCCTCG-AACTTC
* * *
807 CAAAAATTCTA-TTTTACCC-CTAAACTTT
1 CAAAAATTCCATTTTTACCCTC-GAACTTC
*
835 CAAAAATTCCATTCTTGA-CCTCGAAACTTC
1 CAAAAATTCCATT-TTTACCCTCG-AACTTC
*
865 TAAAAATT-CATTTTTACCCTCGAACTTC
1 CAAAAATTCCATTTTTACCCTCGAACTTC
* *
893 CAAAAATTCCATTTTCGACCC-CAAAACTTC
1 CAAAAATTCCATTTT-TACCCTC-GAACTTC
* * *
923 CAAAAAATCCATTTTTACCCTTGAACCTC
1 CAAAAATTCCATTTTTACCCTCGAACTTC
* * *
952 CAAAATTTCCATTTTTGA-CCTTGAAACTTT
1 CAAAAATTCCATTTTT-ACCCTCG-AACTTC
*
982 CAAAAATTACCA-TTTTACCCTCG-AGTGTC
1 CAAAAATT-CCATTTTTACCCTCGAACT-TC
* *
1011 CATAAACTCCATTTTCTA-CCTCGAAAC-TC
1 CAAAAATTCCATTTT-TACCCTCG-AACTTC
* * *
1040 TC-GAAATTACC-CTTTTACCCCCGAA-TGTC
1 -CAAAAATT-CCATTTTTACCCTCGAACT-TC
* *
1069 TAAAAATTCCATTTTTAACCC-CGAATTTTC
1 CAAAAATTCCATTTTT-ACCCTCGAA-CTTC
*
1099 CCAAAATTACCATT
1 CAAAAATT-CCATT
1113 CCCCTCGGGA
Statistics
Matches: 360, Mismatches: 57, Indels: 68
0.74 0.12 0.14
Matches are distributed among these distances:
28 66 0.18
29 165 0.46
30 119 0.33
31 10 0.03
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (29 bp):
CAAAAATTCCATTTTTACCCTCGAACTTC
Found at i:766 original size:59 final size:60
Alignment explanation
Indices: 632--1112 Score: 426
Period size: 59 Copynumber: 8.2 Consensus size: 60
622 CTAAACTGTT
* * *
632 CAAAAATTACATTTTTACCCTCGAGCTTCCAAAAATCCCA-TTTT-GACCCC-AAACTTC
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAGACCCCGAAACTTC
** **
689 CAAAAATTCCATTTTTACCCTTAAACTTCCAAAAACCCCATTTTTAG-CCCCGAAACTTC
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAGACCCCGAAACTTC
* **
748 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTCTTA-ACCTTGAAACTTC
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAGACCCCGAAACTTC
* * * * *
807 CAAAAATTCTA-TTTTACCC-CTAAACTTTCAAAAATTCCATTCTT-GACCTCGAAACTTC
1 CAAAAATTCCATTTTTACCCTC-GAACTTCCAAAAATTCCATTTTTAGACCCCGAAACTTC
* * *
865 TAAAAATT-CATTTTTACCCTCGAACTTCCAAAAATTCCA-TTTTCGACCCCAAAACTTC
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAGACCCCGAAACTTC
* * * * ** *
923 CAAAAAATCCATTTTTACCCTTGAACCTCCAAAATTTCCATTTTT-GACCTTGAAACTTT
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAGACCCCGAAACTTC
* * * *
982 CAAAAATTACCA-TTTTACCCTCG-AGTGTCCATAAACTCCATTTTCT--ACCTCGAAAC-TC
1 CAAAAATT-CCATTTTTACCCTCGAACT-TCCAAAAATTCCATTTT-TAGACCCCGAAACTTC
* * * * **
1040 TC-GAAATTACC-CTTTTACCCCCGAA-TGTCTAAAAATTCCATTTTTA-ACCCCGAATTTTC
1 -CAAAAATT-CCATTTTTACCCTCGAACT-TCCAAAAATTCCATTTTTAGACCCCGAAACTTC
*
1099 CCAAAATTACCATT
1 CAAAAATT-CCATT
1113 CCCCTCGGGA
Statistics
Matches: 352, Mismatches: 51, Indels: 39
0.80 0.12 0.09
Matches are distributed among these distances:
57 41 0.12
58 142 0.40
59 160 0.45
60 9 0.03
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (60 bp):
CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAGACCCCGAAACTTC
Found at i:3843 original size:16 final size:16
Alignment explanation
Indices: 3815--3847 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3805 TTTTACAAAT
3815 TTAATATAAAAAATAA
1 TTAATATAAAAAATAA
3831 TTAAT-TAACAAAATAA
1 TTAATATAA-AAAATAA
3847 T
1 T
3848 ACCTCCATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.19
16 13 0.81
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (16 bp):
TTAATATAAAAAATAA
Found at i:4233 original size:29 final size:29
Alignment explanation
Indices: 4201--4297 Score: 106
Period size: 35 Copynumber: 3.2 Consensus size: 29
4191 TTTATTAATT
*
4201 TAATACAAAAAAATATTTATTTACTAAAA
1 TAATATAAAAAAATATTTATTTACTAAAA
4230 TAATATAAAAAATTATTTATTTTATTTGACTAAAA
1 TAATATAAAAAA--A--TA-TTTATTT-ACTAAAA
* *
4265 TAATATTAAAAAATATTTATTTAATAAAA
1 TAATATAAAAAAATATTTATTTACTAAAA
4294 -AATA
1 TAATA
4298 AAATTAAATA
Statistics
Matches: 59, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
28 4 0.07
29 17 0.29
30 7 0.12
31 3 0.05
33 3 0.05
34 7 0.12
35 18 0.31
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (29 bp):
TAATATAAAAAAATATTTATTTACTAAAA
Found at i:4254 original size:34 final size:35
Alignment explanation
Indices: 4216--4286 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 35
4206 CAAAAAAATA
4216 TTTATTT-ACTAAAATAATA-TAAAAAATTATTTAT
1 TTTATTTGACTAAAATAATATTAAAAAA-TATTTAT
4250 TTTATTTGACTAAAATAATATTAAAAAATATTTAT
1 TTTATTTGACTAAAATAATATTAAAAAATATTTAT
4285 TT
1 TT
4287 AATAAAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
34 7 0.20
35 21 0.60
36 7 0.20
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (35 bp):
TTTATTTGACTAAAATAATATTAAAAAATATTTAT
Found at i:4426 original size:3 final size:3
Alignment explanation
Indices: 4420--4447 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
4410 AATATTATTA
4420 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
4448 GTGGTGCCAA
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:7469 original size:15 final size:15
Alignment explanation
Indices: 7451--7576 Score: 84
Period size: 14 Copynumber: 8.7 Consensus size: 15
7441 GGTTTAAGGG
*
7451 TTTAGTGTTTTGAAT
1 TTTAGGGTTTTGAAT
*
7466 TTTAGGGTTTT-AAA
1 TTTAGGGTTTTGAAT
*
7480 TTTAAGGTTTTGAA-
1 TTTAGGGTTTTGAAT
*
7494 TTAAGGGTTTTGAAT
1 TTTAGGGTTTTGAAT
* * *
7509 TTTAAGGTTTAGGA-
1 TTTAGGGTTTTGAAT
*
7523 TTTATGGTTTT-AA-
1 TTTAGGGTTTTGAAT
* *
7536 TTTAGAGTTTTAAATT
1 TTTAGGGTTTTGAA-T
* *
7552 TTTAGGGATTT-AGAG
1 TTTAGGGTTTTGA-AT
7567 TTTAGGGTTT
1 TTTAGGGTTT
7577 CAAAATTAAA
Statistics
Matches: 87, Mismatches: 18, Indels: 12
0.74 0.15 0.10
Matches are distributed among these distances:
13 10 0.11
14 35 0.40
15 32 0.37
16 10 0.11
ACGTcount: A:0.25, C:0.00, G:0.23, T:0.52
Consensus pattern (15 bp):
TTTAGGGTTTTGAAT
Found at i:7489 original size:29 final size:28
Alignment explanation
Indices: 7457--7552 Score: 97
Period size: 29 Copynumber: 3.4 Consensus size: 28
7447 AGGGTTTAGT
7457 GTTTTGAATTTTAGGGTTTTAAATTTAAG
1 GTTTTGAA-TTTAGGGTTTTAAATTTAAG
* *
7486 GTTTTGAATTAAGGGTTTTGAATTTTAAG
1 GTTTTGAATTTAGGGTTTT-AAATTTAAG
* * *
7515 GTTTAGGATTTATGGTTTT-AATTT-AG
1 GTTTTGAATTTAGGGTTTTAAATTTAAG
*
7541 AGTTTTAAATTT
1 -GTTTTGAATTT
7553 TTAGGGATTT
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
26 2 0.04
27 12 0.22
28 10 0.18
29 31 0.56
ACGTcount: A:0.27, C:0.00, G:0.21, T:0.52
Consensus pattern (28 bp):
GTTTTGAATTTAGGGTTTTAAATTTAAG
Found at i:7504 original size:43 final size:42
Alignment explanation
Indices: 7457--7576 Score: 125
Period size: 43 Copynumber: 2.8 Consensus size: 42
7447 AGGGTTTAGT
*
7457 GTTTTGAATTTTAGGGTTTTA-AATTTAAGGTTTTGAATTAAGG
1 GTTTTGAATTTTAGGG-TTTAGAATTTAAGGTTTT-AATTAAGA
* * * *
7500 GTTTTGAATTTTAAGGTTTAGGATTTATGGTTTTAATTTAGA
1 GTTTTGAATTTTAGGGTTTAGAATTTAAGGTTTTAATTAAGA
* * *
7542 GTTTTAAATTTTTAGGGATTTAGAGTTTAGGGTTT
1 GTTTTGAA-TTTTAGGG-TTTAGAATTTAAGGTTT
7577 CAAAATTAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
42 17 0.27
43 33 0.52
44 14 0.22
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (42 bp):
GTTTTGAATTTTAGGGTTTAGAATTTAAGGTTTTAATTAAGA
Found at i:7608 original size:15 final size:15
Alignment explanation
Indices: 7588--7642 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
7578 AAAATTAAAG
7588 TTTAGAGTTTAGGAT
1 TTTAGAGTTTAGGAT
*
7603 TTTAGAGTTTATGAT
1 TTTAGAGTTTAGGAT
* *
7618 TTAAG-GTTTAGGGT
1 TTTAGAGTTTAGGAT
*
7632 TTTGGAGTTTA
1 TTTAGAGTTTA
7643 TAATTTAGGG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
14 10 0.30
15 23 0.70
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (15 bp):
TTTAGAGTTTAGGAT
Found at i:7634 original size:29 final size:29
Alignment explanation
Indices: 7594--7654 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
7584 AAAGTTTAGA
*
7594 GTTTAGGATTTTAGAGTTTATGATTTAAG
1 GTTTAGGATTTTAGAGTTTATAATTTAAG
* * *
7623 GTTTAGGGTTTTGGAGTTTATAATTTAGG
1 GTTTAGGATTTTAGAGTTTATAATTTAAG
7652 GTT
1 GTT
7655 AAAGAGTATG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (29 bp):
GTTTAGGATTTTAGAGTTTATAATTTAAG
Found at i:7916 original size:21 final size:21
Alignment explanation
Indices: 7883--7926 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
7873 TAGGGTCCAT
*
7883 TTGCCCCGAAGGAGTAGATTA
1 TTGCCCCGAAGGAGTAGAGTA
* *
7904 TTGCCTCGGAGGAGTAGAGTA
1 TTGCCCCGAAGGAGTAGAGTA
7925 TT
1 TT
7927 ACGGTGGCTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.25, C:0.16, G:0.32, T:0.27
Consensus pattern (21 bp):
TTGCCCCGAAGGAGTAGAGTA
Found at i:8038 original size:6 final size:6
Alignment explanation
Indices: 8029--8064 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
8019 TCATCCAATG
*
8029 CCTCTT CCTCTT CTTCTT CCTCTT CCTCTT CCTCTT
1 CCTCTT CCTCTT CCTCTT CCTCTT CCTCTT CCTCTT
8065 GCTTTGGCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (6 bp):
CCTCTT
Found at i:10449 original size:29 final size:32
Alignment explanation
Indices: 10415--10478 Score: 89
Period size: 29 Copynumber: 2.1 Consensus size: 32
10405 AACATTAAAT
*
10415 AACAAATAA-TTAAAA-ATTAAAT-TAAACAA
1 AACAAATAACTTAAAATAATAAATATAAACAA
10444 AACAAATAACTTAAAATAATAAATACTAAACAA
1 AACAAATAACTTAAAATAATAAATA-TAAACAA
10477 AA
1 AA
10479 TATAACTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 9 0.30
30 6 0.20
31 6 0.20
33 9 0.30
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.22
Consensus pattern (32 bp):
AACAAATAACTTAAAATAATAAATATAAACAA
Found at i:10694 original size:4 final size:4
Alignment explanation
Indices: 10687--10729 Score: 54
Period size: 4 Copynumber: 11.0 Consensus size: 4
10677 ACCTTCTTCC
*
10687 TTCT TTCT TTCT TTCT CTTC- TTC- TTCC TTCT TTCT TTCT TTCT
1 TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTCT TTCT TTCT
10730 ACTCTGGTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
3 6 0.17
4 27 0.75
5 3 0.08
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (4 bp):
TTCT
Found at i:12844 original size:78 final size:78
Alignment explanation
Indices: 12705--12936 Score: 324
Period size: 78 Copynumber: 3.0 Consensus size: 78
12695 GATAATGTGC
* * * * * * *
12705 TTCAGGGCACCCATGTCCTCTTGCATTGACAATAATGCTAATGCCAATCGACCTAAGACTCAATC
1 TTCAGCGCACCCATATCCTCTTGCACTGACAACAATGCTCATGCCAATAGAGCTAAGACTCAATC
*
12770 GGTTCATCATTTA
66 GGTTGATCATTTA
* *
12783 TTCAGCGCACCCATATCCTCTTGCACTGACAACAATGCTCATGCCAATAGAGCTAAAACTCAATT
1 TTCAGCGCACCCATATCCTCTTGCACTGACAACAATGCTCATGCCAATAGAGCTAAGACTCAATC
12848 GGTTGATCATTTA
66 GGTTGATCATTTA
* * * *
12861 TTCAGCACA-CCATATCCTCTTGCACTGACATCAATGCTCATGCCAATAAAGTTAAGACTCAATC
1 TTCAGCGCACCCATATCCTCTTGCACTGACAACAATGCTCATGCCAATAGAGCTAAGACTCAATC
12925 GGTTGAT-ATTTA
66 GGTTGATCATTTA
12937 CACTTTAATT
Statistics
Matches: 138, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
76 5 0.04
77 57 0.41
78 76 0.55
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.29
Consensus pattern (78 bp):
TTCAGCGCACCCATATCCTCTTGCACTGACAACAATGCTCATGCCAATAGAGCTAAGACTCAATC
GGTTGATCATTTA
Found at i:13868 original size:158 final size:158
Alignment explanation
Indices: 13597--13899 Score: 446
Period size: 158 Copynumber: 1.9 Consensus size: 158
13587 TCACACGAGC
* *
13597 TGTGAAATGGGTCTACTCACACGAGCTATGGGTCGAGATGTTAGGCTACAAGATGCTGCTCACAC
1 TGTGAAATGGGCCTACTCACACGAGCTATGGGTCGAGATGTTAGGCTACAAGATGCTACTCACAC
* * * * ***
13662 GAGCTTTGGAGAATCCGCAACAAATGCTGGATCTCAGCTATCGATAGGACATCTAAGACCTGTAC
66 GAGCTGTGGAGAATCCGCAACAAATGCTGAATCTCAACCATCGATAGGACATCTAAGACCAACAC
13727 CCATATAACATGTAATGATCAAATGAGG
131 CCATATAACATGTAATGATCAAATGAGG
* * *
13755 TGTGAAGTGGGCCTACTCACACGAGCTGTGGGTCGAGATGTTAGGCTACACGATGCTACTCACAC
1 TGTGAAATGGGCCTACTCACACGAGCTATGGGTCGAGATGTTAGGCTACAAGATGCTACTCACAC
* * *
13820 GAGCTGTGGAGAATCCGCAACAAATG-TCGAATCTCAACCATCGGTAGGACATTTAATACCAACA
66 GAGCTGTGGAGAATCCGCAACAAATGCT-GAATCTCAACCATCGATAGGACATCTAAGACCAACA
*
13884 CCCATATAACCTGTAA
130 CCCATATAACATGTAA
13900 ATCCCGAAAT
Statistics
Matches: 128, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
157 1 0.01
158 127 0.99
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (158 bp):
TGTGAAATGGGCCTACTCACACGAGCTATGGGTCGAGATGTTAGGCTACAAGATGCTACTCACAC
GAGCTGTGGAGAATCCGCAACAAATGCTGAATCTCAACCATCGATAGGACATCTAAGACCAACAC
CCATATAACATGTAATGATCAAATGAGG
Found at i:15561 original size:18 final size:18
Alignment explanation
Indices: 15538--15584 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
15528 AGTTTAAATT
* * *
15538 ATTTTAGATTTATTTTTA
1 ATTTTAAATTTACTTTAA
15556 ATTTTAAATTTACTTTAA
1 ATTTTAAATTTACTTTAA
15574 A-TTTAAATTTA
1 ATTTTAAATTTA
15585 AATTCATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 10 0.38
18 16 0.62
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (18 bp):
ATTTTAAATTTACTTTAA
Found at i:15582 original size:24 final size:25
Alignment explanation
Indices: 15555--15605 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
15545 ATTTATTTTT
*
15555 AATTTTAAATTTA-CTTTAAATTTA
1 AATTTTAAATTCATCTTTAAATTTA
*
15579 AA-TTTAAATTCATTTTTAAATTTA
1 AATTTTAAATTCATCTTTAAATTTA
15603 AAT
1 AAT
15606 ATGTTTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (25 bp):
AATTTTAAATTCATCTTTAAATTTA
Found at i:15594 original size:41 final size:41
Alignment explanation
Indices: 15540--15625 Score: 109
Period size: 41 Copynumber: 2.1 Consensus size: 41
15530 TTTAAATTAT
* * * *
15540 TTTAGATTTATTTTTAATTTTAAATTTACTTTAAATTTAAA
1 TTTAAATTCATTTTTAAATTTAAATATACTTTAAATTTAAA
** *
15581 TTTAAATTCATTTTTAAATTTAAATATGTTTTAAATTTCAA
1 TTTAAATTCATTTTTAAATTTAAATATACTTTAAATTTAAA
15622 TTTA
1 TTTA
15626 GTTTAAATTT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.57
Consensus pattern (41 bp):
TTTAAATTCATTTTTAAATTTAAATATACTTTAAATTTAAA
Found at i:15596 original size:18 final size:18
Alignment explanation
Indices: 15575--15640 Score: 68
Period size: 17 Copynumber: 3.7 Consensus size: 18
15565 TTACTTTAAA
15575 TTTAAATTTAAATTCAT-T
1 TTTAAATTTAAATT-ATGT
15593 TTTAAATTTAAA-TATGT
1 TTTAAATTTAAATTATGT
*
15610 TTTAAATTTCAATT-TAG-
1 TTTAAATTTAAATTAT-GT
15627 TTTAAATTTGAAAT
1 TTTAAATTT-AAAT
15641 AATTTTAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
16 2 0.05
17 23 0.55
18 17 0.40
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (18 bp):
TTTAAATTTAAATTATGT
Found at i:15602 original size:6 final size:6
Alignment explanation
Indices: 15552--15671 Score: 61
Period size: 6 Copynumber: 20.3 Consensus size: 6
15542 TAGATTTATT
* * * **
15552 TTTAAT TTTAAA TTT-AC TTTAAA TTTAAA TTTAAA TTCATT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* ** * * *
15599 TTTAAA TAT-GT TTTAAA TTTCAA TTT-AG TTTAAA TTTGAAA --TAAT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
* *
15644 TTTAAAA CTTAAA CTTTAAA ATTAAA TT
1 TTT-AAA TTTAAA -TTTAAA TTTAAA TT
15672 CAAAGTCCAT
Statistics
Matches: 82, Mismatches: 24, Indels: 16
0.67 0.20 0.13
Matches are distributed among these distances:
4 2 0.02
5 11 0.13
6 57 0.70
7 12 0.15
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:15614 original size:35 final size:34
Alignment explanation
Indices: 15575--15649 Score: 89
Period size: 35 Copynumber: 2.2 Consensus size: 34
15565 TTACTTTAAA
* *
15575 TTTAAATTTAAATTCATTTTTAAATTT-AAATATGT
1 TTTAAATTTAAATTCA-GTTTAAATTTGAAATA-AT
* *
15610 TTTAAATTTCAATTTAGTTTAAATTTGAAATAAT
1 TTTAAATTTAAATTCAGTTTAAATTTGAAATAAT
15644 TTTAAA
1 TTTAAA
15650 ACTTAAACTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
34 16 0.46
35 19 0.54
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.52
Consensus pattern (34 bp):
TTTAAATTTAAATTCAGTTTAAATTTGAAATAAT
Found at i:15647 original size:17 final size:16
Alignment explanation
Indices: 15554--15649 Score: 66
Period size: 17 Copynumber: 5.6 Consensus size: 16
15544 GATTTATTTT
**
15554 TAATTTTAAATTTACTT
1 TAATTTTAAATTTA-AA
*
15571 TAAATTTAAATTTAAA
1 TAATTTTAAATTTAAA
*
15587 TTCATTTTTAAATTTAAA
1 -T-AATTTTAAATTTAAA
* *
15605 TATGTTTTAAATTTCAAT
1 TA-ATTTTAAATTT-AAA
* *
15623 TTAGTTTAAATTTGAAA
1 TAATTTTAAATTT-AAA
15640 TAATTTTAAA
1 TAATTTTAAA
15650 ACTTAAACTT
Statistics
Matches: 61, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
16 1 0.02
17 44 0.72
18 16 0.26
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (16 bp):
TAATTTTAAATTTAAA
Found at i:16467 original size:49 final size:47
Alignment explanation
Indices: 16383--16476 Score: 136
Period size: 49 Copynumber: 2.0 Consensus size: 47
16373 ATAAATGCAT
*
16383 ATATTAAATATTTTAATAGCATTAATAATAATAATAAT-ATAATAATA
1 ATATTAAATATATTAATAGCATTAATAATAATAAT-ATCATAATAATA
*
16430 ATATTAAATGATATTAATAGGCATTAATATTAATAATATCATAATAA
1 ATATTAAAT-ATATTAATA-GCATTAATAATAATAATATCATAATAA
16477 AAAGGGGAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
47 9 0.21
48 10 0.24
49 23 0.55
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.39
Consensus pattern (47 bp):
ATATTAAATATATTAATAGCATTAATAATAATAATATCATAATAATA
Found at i:17436 original size:29 final size:29
Alignment explanation
Indices: 17404--17555 Score: 127
Period size: 29 Copynumber: 5.3 Consensus size: 29
17394 CCCTCGACTT
*
17404 TTCCAAAATTCCATTTTTGAACCCGAAAC
1 TTCCAAAATTCCATTTTTGAACCCAAAAC
** * *
17433 TTCCAAAAATTATATTTTT-ACCCCTAAAC
1 TTCC-AAAATTCCATTTTTGAACCCAAAAC
*
17462 TTTCAAAAATTCCA-TTTTG-ACCCTAAAAC
1 -TTCCAAAATTCCATTTTTGAACCC-AAAAC
* * *
17491 TTCCAAAATTAC-TATTTT-ATCCCTAAAC
1 TTCCAAAATTCCAT-TTTTGAACCCAAAAC
17519 TTCCAAAATTCCATTTTTG-ACCCAAAAAC
1 TTCCAAAATTCCATTTTTGAACCC-AAAAC
*
17548 TTTCAAAA
1 TTCCAAAA
17556 ATTACCTTTT
Statistics
Matches: 96, Mismatches: 17, Indels: 20
0.72 0.13 0.15
Matches are distributed among these distances:
28 39 0.41
29 42 0.44
30 15 0.16
ACGTcount: A:0.38, C:0.25, G:0.03, T:0.35
Consensus pattern (29 bp):
TTCCAAAATTCCATTTTTGAACCCAAAAC
Found at i:17479 original size:28 final size:28
Alignment explanation
Indices: 17365--17570 Score: 121
Period size: 29 Copynumber: 7.1 Consensus size: 28
17355 CACTTATAAA
* ** *
17365 CCCTAAACTATCCAAAAATTATATTTTAA
1 CCCTAAACT-TTCAAAAATTCCATTTTAC
** * *
17394 CCCTCGACTTTTCCAAAATTCCATTTTTGAA
1 CCCTAAAC-TTTCAAAAATTCCA-TTTT-AC
* * **
17425 CCCGAAACTTCCAAAAATTATATTTTTAC
1 CCCTAAACTTTCAAAAATTCCA-TTTTAC
17454 CCCTAAACTTTCAAAAATTCCATTTTGA-
1 CCCTAAACTTTCAAAAATTCCATTTT-AC
* * *
17482 CCCTAAAAC-TTCCAAAATTACTATTTTAT
1 CCCT-AAACTTTCAAAAATT-CCATTTTAC
*
17511 CCCTAAAC-TTCCAAAATTCCATTTTTGAC
1 CCCTAAACTTTCAAAAATTCCA-TTTT-AC
** *
17540 CCAAAAACTTTCAAAAATTACCTTTTTAC
1 CCCTAAACTTTCAAAAATT-CCATTTTAC
17569 CC
1 CC
17571 TCGGATGTCA
Statistics
Matches: 140, Mismatches: 26, Indels: 22
0.74 0.14 0.12
Matches are distributed among these distances:
27 2 0.01
28 36 0.26
29 60 0.43
30 33 0.24
31 9 0.06
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.35
Consensus pattern (28 bp):
CCCTAAACTTTCAAAAATTCCATTTTAC
Found at i:17526 original size:57 final size:57
Alignment explanation
Indices: 17364--17559 Score: 229
Period size: 57 Copynumber: 3.4 Consensus size: 57
17354 TCACTTATAA
**
17364 ACCCT-AAACTATCCAAAAATTATATTTTAACCCTCGACTTTTCCAAAATTCCATTTTTG
1 ACCCTAAAACT-TCCAAAAATTATATTTTAACCCTAAAC--TTCCAAAATTCCATTTTTG
* * *
17423 AACCC-GAAACTTCCAAAAATTATATTTTTACCCCTAAACTTTCAAAAATTCCA-TTTTG
1 -ACCCTAAAACTTCCAAAAATTATA-TTTTAACCCTAAAC-TTCCAAAATTCCATTTTTG
*
17481 ACCCTAAAACTTCC-AAAATTACTATTTTATCCCTAAACTTCCAAAATTCCATTTTTG
1 ACCCTAAAACTTCCAAAAATTA-TATTTTAACCCTAAACTTCCAAAATTCCATTTTTG
* *
17538 ACCCAAAAACTTTCAAAAATTA
1 ACCCTAAAACTTCCAAAAATTA
17560 CCTTTTTACC
Statistics
Matches: 121, Mismatches: 9, Indels: 14
0.84 0.06 0.10
Matches are distributed among these distances:
56 12 0.10
57 41 0.34
58 22 0.18
59 26 0.21
60 20 0.17
ACGTcount: A:0.38, C:0.25, G:0.03, T:0.35
Consensus pattern (57 bp):
ACCCTAAAACTTCCAAAAATTATATTTTAACCCTAAACTTCCAAAATTCCATTTTTG
Found at i:17565 original size:29 final size:28
Alignment explanation
Indices: 17424--17570 Score: 106
Period size: 28 Copynumber: 5.1 Consensus size: 28
17414 CCATTTTTGA
* * **
17424 ACCCGAAACTTCCAAAAATTATATTTTT
1 ACCCAAAACTTTCAAAAATTACCTTTTT
* *
17452 ACCCCTAAACTTTCAAAAATT-CCATTTTG
1 A-CCCAAAACTTTCAAAAATTACC-TTTTT
*
17481 ACCCTAAAAC-TTCCAAAATTA-CTATTTT
1 ACCC-AAAACTTTCAAAAATTACCT-TTTT
* *
17509 ATCCCTAAAC-TTCCAAAATT-CCATTTTT
1 A-CCCAAAACTTTCAAAAATTACC-TTTTT
17537 GACCCAAAAACTTTCAAAAATTACCTTTTT
1 -ACCC-AAAACTTTCAAAAATTACCTTTTT
17567 ACCC
1 ACCC
17571 TCGGATGTCA
Statistics
Matches: 96, Mismatches: 11, Indels: 23
0.74 0.08 0.18
Matches are distributed among these distances:
27 1 0.01
28 40 0.42
29 39 0.41
30 14 0.15
31 2 0.02
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.35
Consensus pattern (28 bp):
ACCCAAAACTTTCAAAAATTACCTTTTT
Found at i:17665 original size:62 final size:61
Alignment explanation
Indices: 17548--17691 Score: 143
Period size: 62 Copynumber: 2.4 Consensus size: 61
17538 ACCCAAAAAC
* * *
17548 TTTCAAAAATTACCTTTTTACCCTCGGATGTCAAAAAATTTCGTTTTTGATCCTGATTTTT
1 TTTCAAAAATTACCGTTTTACCCTCGGATGTCAAAAAATTTCGTTTTTAACCCTGATTTTT
* * * * **
17609 TTTCTAAAAGTTACCGTTTTACTCTCGGATGTC--TAAAGTTCTGTTTTTAAACCCTGA--ACT
1 TTTC-AAAAATTACCGTTTTACCCTCGGATGTCAAAAAATTTC-GTTTTT-AACCCTGATTTTT
*
17669 TTCCAAAAATTACCGTTTTACCC
1 TTTCAAAAATTACCGTTTTACCC
17692 CCCGAGAGTC
Statistics
Matches: 68, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
59 17 0.25
60 10 0.15
61 10 0.15
62 31 0.46
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.42
Consensus pattern (61 bp):
TTTCAAAAATTACCGTTTTACCCTCGGATGTCAAAAAATTTCGTTTTTAACCCTGATTTTT
Found at i:24671 original size:100 final size:100
Alignment explanation
Indices: 24484--24719 Score: 332
Period size: 100 Copynumber: 2.4 Consensus size: 100
24474 GCATCATGAA
*
24484 ACATGACGGGAAAGATCTAAGACCGTAATGGCGGATCCAGTACCGTAAAGATACAAAAGGGAAGG
1 ACATGACGGGAAAGATCTAAGACCGCAATGGCGGATCCAGTACCGTAAAGATACAAAAGGGAAGG
* *
24549 GTTTAAATCGTAACGGCAAACCTTATACCTTAGAG
66 GTTTAAATCGCAACGGCAAACCTTATACCTCAGAG
* * *
24584 ACATGACGGGAAA-ATTTTAAGACCGCAATGGCGGATCCAGTACCGTAAATATACGAAAGGGAAG
1 ACATGACGGGAAAGA-TCTAAGACCGCAATGGCGGATCCAGTACCGTAAAGATACAAAAGGGAAG
* * * *
24648 GGTTTAAGTCGCAATGGCGAACCTTGTACCTCAGAG
65 GGTTTAAATCGCAACGGCAAACCTTATACCTCAGAG
* * *
24684 ACATGACGAGAAAGATCTAAG-CTGCAACGGCGGATC
1 ACATGACGGGAAAGATCTAAGACCGCAATGGCGGATC
24720 TAGTGCCGCG
Statistics
Matches: 120, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
99 14 0.12
100 105 0.88
101 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.19
Consensus pattern (100 bp):
ACATGACGGGAAAGATCTAAGACCGCAATGGCGGATCCAGTACCGTAAAGATACAAAAGGGAAGG
GTTTAAATCGCAACGGCAAACCTTATACCTCAGAG
Found at i:24973 original size:100 final size:98
Alignment explanation
Indices: 24786--25008 Score: 222
Period size: 100 Copynumber: 2.2 Consensus size: 98
24776 ACGAAGACAC
* * *
24786 AAGGGAAAAGTTTAAGTCACAATGGCGGACCTAGTACCTCAGAGACATAAAGGGAAAGATCTAGA
1 AAGGGAAAGGTTTAAGTCGCAATGGCGGA-CTAGTACCTCAGAGACAAAAAGGGAAAGATCTAGA
* * *
24851 CCGTAACGGCAGATCCAATACCAC-AA-ATATACA
65 CCGCAACGGAAAATCCAATACCACGAAGAT-TACA
* * * *
24884 TAAGGGAAAGGTTTACGTCGCAATGGCGGA-TTGTGAACCTTAGAAGACAAAAAGGGAAAGATTT
1 -AAGGGAAAGGTTTAAGTCGCAATGGCGGACTAGT--ACCTCAG-AGACAAAAAGGGAAAGATCT
**
24948 A-AGCCGCAACGGAAAAT-CAAGTACCACGAAGATTTGA
62 AGA-CCGCAACGGAAAATCCAA-TACCACGAAGATTACA
*
24985 AGGGGAAAGGTTTAAGTCGCAATG
1 AAGGGAAAGGTTTAAGTCGCAATG
25009 ACAAACCCGA
Statistics
Matches: 103, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
97 3 0.03
99 36 0.35
100 58 0.56
101 4 0.04
102 2 0.02
ACGTcount: A:0.40, C:0.17, G:0.26, T:0.18
Consensus pattern (98 bp):
AAGGGAAAGGTTTAAGTCGCAATGGCGGACTAGTACCTCAGAGACAAAAAGGGAAAGATCTAGAC
CGCAACGGAAAATCCAATACCACGAAGATTACA
Found at i:25271 original size:101 final size:101
Alignment explanation
Indices: 25101--25302 Score: 307
Period size: 101 Copynumber: 2.0 Consensus size: 101
25091 GATCAAAACT
* *
25101 ACAATAGCAAGTCTTTATCTCTCTGAAGTTGAAGCAAGAGCAAGATGAAGCTTTAACATCAATTC
1 ACAATAGCAAGTCTTTATCTCTCTGAAGTTGAAGCAAGAGCAAGATGAAGCTTCAACATAAATTC
* *
25166 CTATCCTCTTGAAGTTACAGTAAAGTCGGATTAAAA
66 CTATCCTCTTGAAGTTACAGCAAAGTCGGAGTAAAA
** *
25202 ACAATAGCAAGTCTTTATCTCTCTGAAGTTGTGGTAAGAGCAAGATGAAGCTTCAACATTAAATT
1 ACAATAGCAAGTCTTTATCTCTCTGAAGTTGAAGCAAGAGCAAGATGAAGCTTCAACA-TAAATT
* *
25267 -CTATCTTCTTGAAGTTACAGCAAAGTTGGAGTAAAA
65 CCTATCCTCTTGAAGTTACAGCAAAGTCGGAGTAAAA
25303 CTACAGCAAT
Statistics
Matches: 91, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
101 86 0.95
102 5 0.05
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (101 bp):
ACAATAGCAAGTCTTTATCTCTCTGAAGTTGAAGCAAGAGCAAGATGAAGCTTCAACATAAATTC
CTATCCTCTTGAAGTTACAGCAAAGTCGGAGTAAAA
Found at i:25429 original size:39 final size:39
Alignment explanation
Indices: 25364--25573 Score: 133
Period size: 39 Copynumber: 5.4 Consensus size: 39
25354 CTACATCGTT
* *
25364 AACCAATCACTTA-CCTCGAGCCTGGGGCAGATCATCATC
1 AACCAATCTCTTACCCT-GAGCTTGGGGCAGATCATCATC
*
25403 AACCAATCTCTTACCCTGAGCTTGGGGCAGAT--TGAAGTC
1 AACCAATCTCTTACCCTGAGCTTGGGGCAGATCAT-CA-TC
**** * * *
25442 ATTTGATCTTTTACCCCGAGCCTGGGGCAGATCATCATC
1 AACCAATCTCTTACCCTGAGCTTGGGGCAGATCATCATC
* * * *
25481 AACCAATCTCTTA-CCTCGAGCTAGAGGAAGATTA-CAGTC
1 AACCAATCTCTTACCCT-GAGCTTGGGGCAGATCATCA-TC
** * * * * *
25520 ATTCGATCTCTTACCCCGAGCTTGGAGCAAATCATCGTC
1 AACCAATCTCTTACCCTGAGCTTGGGGCAGATCATCATC
* *
25559 AACCAAACTCCTACC
1 AACCAATCTCTTACC
25574 TCGATCACAG
Statistics
Matches: 124, Mismatches: 38, Indels: 18
0.69 0.21 0.10
Matches are distributed among these distances:
37 1 0.01
38 5 0.04
39 110 0.89
40 7 0.06
41 1 0.01
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (39 bp):
AACCAATCTCTTACCCTGAGCTTGGGGCAGATCATCATC
Found at i:25513 original size:78 final size:78
Alignment explanation
Indices: 25373--25577 Score: 270
Period size: 78 Copynumber: 2.6 Consensus size: 78
25363 TAACCAATCA
* * * *
25373 CTTACCTCGAGCCTGGGGCAGATCATCATCAACCAATCTCTTACC-CTGAGCTTGGGGCAGATTG
1 CTTACCCCGAGCCTGGGGCAGATCATCATCAACCAATCTCTTACCTC-GAGCTAGAGGAAGATT-
*
25437 A-AGTCATTTGATCT
64 ACAGTCATTCGATCT
*
25451 TTTACCCCGAGCCTGGGGCAGATCATCATCAACCAATCTCTTACCTCGAGCTAGAGGAAGATTAC
1 CTTACCCCGAGCCTGGGGCAGATCATCATCAACCAATCTCTTACCTCGAGCTAGAGGAAGATTAC
25516 AGTCATTCGATCT
66 AGTCATTCGATCT
* * * * * *
25529 CTTACCCCGAGCTTGGAGCAAATCATCGTCAACCAAACTCCTACCTCGA
1 CTTACCCCGAGCCTGGGGCAGATCATCATCAACCAATCTCTTACCTCGA
25578 TCACAGGGCA
Statistics
Matches: 112, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
77 1 0.01
78 110 0.98
79 1 0.01
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.25
Consensus pattern (78 bp):
CTTACCCCGAGCCTGGGGCAGATCATCATCAACCAATCTCTTACCTCGAGCTAGAGGAAGATTAC
AGTCATTCGATCT
Found at i:26028 original size:206 final size:206
Alignment explanation
Indices: 25661--27088 Score: 2068
Period size: 206 Copynumber: 6.9 Consensus size: 206
25651 AACTCAAAGG
* * *
25661 TGAGCAAATCTTCGAATCCCAGCTTCCTAATGAGATACTGAGAAGC-GAGTCGAAGCAATAAAAT
1 TGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAG-GTCGAAGTAATAAAAT
* *
25725 GGTTAACTTCCTGATTAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAA
65 GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAA
* * *
25790 GTGGATTGAAACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAAC
130 GCGGATTGAAACAAACGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAAC
* *
25855 TCACGCTCAATG
195 TCACGCTCGATA
* * * * *
25867 TGAGCAAATCTTCGAATCACAGCTTCTTGATGAGATATTGAGAAGCAGGTCGAAGCAATAAAATG
1 TGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAATG
* * * * *
25932 GTTAGCTTCTTGATGAGACACTGGGAAGTGAACCAAATTCGTCTTCTTGATGAGATACAGAGAAG
66 GTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAG
* * * *
25997 CGGATTGTAACAAACGATGCGGTCGTCTTCCTGATGAGATATTGAGAAGAAGACCAAATTAAACT
131 CGGATTGAAACAAACGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACT
*
26062 CACACTCGATA
196 CACGCTCGATA
*
26073 TGAGCAAATCTTCGAACCCCAGCTTCTTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAATG
1 TGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAATG
* * * *
26138 GTTAACTTCTTGATGAGACACCGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAG
66 GTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAG
* *
26203 CGGATTGAAACAAACGACGCGGTCATCTTCCTGAAGAGATACTGAGAAGAAGACCAAATCAAACT
131 CGGATTGAAACAAACGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACT
*
26268 CACACTCGATA
196 CACGCTCGATA
* * * ** * * *
26279 TGAGCAAACCTTCGAACCTCAACTTTTTGATGAGATACTGAGAAACAGGTCTAAGCAATAAAATG
1 TGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAATG
*
26344 GTTAGCTTCCTGATAAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAG
66 GTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAG
* *
26409 CGGATTGAAACAAACGATGCGGTCGTCTTCCTGATGAGATACTAAGAAGAAGACCAAATCAAACT
131 CGGATTGAAACAAACGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACT
26474 CACGCTCGATA
196 CACGCTCGATA
26485 TGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAATG
1 TGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAATG
* * *
26550 GTTAGCTTCCTGATGAGATACCGAGAAGTGGACCAAATTCATCTTCCTAATGAGATACAGAGAAG
66 GTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAG
*
26615 CGGATTGAAACAAACGATGCGGTCATCTTCCTGATAAGATACTGAGAAGAAGACCAAATCAAACT
131 CGGATTGAAACAAACGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACT
26680 CACGCTCGATA
196 CACGCTCGATA
* *
26691 TAAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAACAGGTCGAAGTAATAAAATG
1 TGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAATG
* * *
26756 GTTAACTTCCTGATGAGATATTGAGAAGTGGACCAAATTTGTCTTCCT-AGTGAGATACAGAGAA
66 GTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGA-TGAGATACAGAGAA
* *
26820 GCGGATTGAAACAAACGATGCAGTCATCTTCCTGATGAGATACTGAGAATAAGACCAAATCAAAC
130 GCGGATTGAAACAAACGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAAC
*
26885 CCACGCTCGATA
195 TCACGCTCGATA
* * * * * *
26897 TGAACAAATCTTCAAACCTCAGCTTCCTGATGAGATACTGAGAAGTAGATCGAAGTAATAAAGTG
1 TGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAATG
* * * ** * * * * * *
26962 GTTAGTTTCCTAATGAGATACGGAGAACCGAACCTAATCCGTCTTCCTGATGAAACACGGAGAAG
66 GTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAG
** ** ** * * * * *
27027 TAGATCAAAACAAGTGATGTGGTCATCTTCTTGATAAGATACTAAGAAGAAGACCAAGTCAA
131 CGGATTGAAACAAACGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAA
27089 TGAAACCAGA
Statistics
Matches: 1105, Mismatches: 114, Indels: 6
0.90 0.09 0.00
Matches are distributed among these distances:
205 1 0.00
206 1102 1.00
207 2 0.00
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (206 bp):
TGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAATG
GTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAG
CGGATTGAAACAAACGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACT
CACGCTCGATA
Found at i:27470 original size:6 final size:6
Alignment explanation
Indices: 27461--27578 Score: 75
Period size: 6 Copynumber: 20.0 Consensus size: 6
27451 TATTTCTAAG
* * **
27461 TTTAAA TTT-AC TTTAAA TTTAAA TTTAAA TTCATT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
** * * *
27508 TTT-GT TTTAAA TTTCAA TTT-AG TTTAAA TTTGAAA --TAAT TTTAAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTT-AAA
* *
27554 CTTAAA CTTTAAA ATTAAA TTTAAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA
27579 GTCCATTTAC
Statistics
Matches: 83, Mismatches: 21, Indels: 16
0.69 0.17 0.13
Matches are distributed among these distances:
4 2 0.02
5 12 0.14
6 57 0.69
7 12 0.14
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:27483 original size:17 final size:17
Alignment explanation
Indices: 27426--27552 Score: 82
Period size: 17 Copynumber: 7.4 Consensus size: 17
27416 AAATTTTTAC
*
27426 TTTTGAATTTAAA-TTA
1 TTTTAAATTTAAATTTA
* *
27442 TTTTAGATTT-ATTTCTAA
1 TTTTAAATTTAAATT-T-A
* *
27460 GTTTAAATTT-ACTTTAA
1 TTTTAAATTTAAATTT-A
* *
27477 ATTTAAATTTAAATTCA
1 TTTTAAATTTAAATTTA
*
27494 TTTTTAAATTTAAATTTG
1 -TTTTAAATTTAAATTTA
*
27512 TTTTAAATTTCAATTTA
1 TTTTAAATTTAAATTTA
* *
27529 GTTTAAATTTGAAA-TAA
1 TTTTAAATTT-AAATTTA
27546 TTTTAAA
1 TTTTAAA
27553 ACTTAAACTT
Statistics
Matches: 87, Mismatches: 18, Indels: 11
0.75 0.16 0.09
Matches are distributed among these distances:
15 1 0.01
16 9 0.10
17 46 0.53
18 31 0.36
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:27517 original size:41 final size:41
Alignment explanation
Indices: 27443--27528 Score: 109
Period size: 41 Copynumber: 2.1 Consensus size: 41
27433 TTTAAATTAT
* * *
27443 TTTAGATTTATTTCTAAGTTTAAATTTACTTTAAATTTAAA
1 TTTAAATTCATTTCTAAATTTAAATTTACTTTAAATTTAAA
* ** *
27484 TTTAAATTCATTTTTAAATTTAAATTTGTTTTAAATTTCAA
1 TTTAAATTCATTTCTAAATTTAAATTTACTTTAAATTTAAA
27525 TTTA
1 TTTA
27529 GTTTAAATTT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (41 bp):
TTTAAATTCATTTCTAAATTTAAATTTACTTTAAATTTAAA
Found at i:28369 original size:49 final size:45
Alignment explanation
Indices: 28275--28381 Score: 130
Period size: 46 Copynumber: 2.3 Consensus size: 45
28265 TCAAAAAAAT
*
28275 GTAATA-AATACAT-ATATTAAATATTTTAATAGCATTAATAATAATA
1 GTAATATAATA-ATAATATTAAATATATTAATAGCATTAATAAT-A-A
*
28321 GTAATATAATAATAATATTAAATGATATTAATAGGCATTAATATTAA
1 GTAATATAATAATAATATTAAAT-ATATTAATA-GCATTAATAATAA
28368 -TAATATAATAATAA
1 GTAATATAATAATAA
28382 AAAAGGGAAG
Statistics
Matches: 55, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
46 22 0.40
47 14 0.25
48 9 0.16
49 10 0.18
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.38
Consensus pattern (45 bp):
GTAATATAATAATAATATTAAATATATTAATAGCATTAATAATAA
Found at i:29545 original size:29 final size:29
Alignment explanation
Indices: 29483--29677 Score: 136
Period size: 29 Copynumber: 6.7 Consensus size: 29
29473 CCCTGGAGGC
* *
29483 CCCTAAACTATCTAAAAATTATA-TTTTGA
1 CCCTAAACTTTC-CAAAATTATATTTTTGA
*
29512 CCCCT-GACTTCTCCAAAATTATATTTTTGA
1 -CCCTAAACTT-TCCAAAATTATATTTTTGA
** * *
29542 CCCTAAACAGTCC-AAATTTTA-TATTGA
1 CCCTAAACTTTCCAAAATTATATTTTTGA
*
29569 CCCTCAAA-TTCTCCAAAATTACATTTTT-A
1 CCCT-AAACTT-TCCAAAATTATATTTTTGA
29598 CCCTAAACTTTCCAAAAATT-TCATTTTT-A
1 CCCTAAACTTTCC-AAAATTAT-ATTTTTGA
** *
29627 CACCCGAACTTTCCAAAATTCTATTTTTGA
1 C-CCTAAACTTTCCAAAATTATATTTTTGA
* *
29657 CCCAAAAACTTTCAAAAATTA
1 CCC-TAAACTTTCCAAAATTA
29678 CCCTTTTACC
Statistics
Matches: 131, Mismatches: 20, Indels: 28
0.73 0.11 0.16
Matches are distributed among these distances:
27 9 0.07
28 19 0.15
29 60 0.46
30 43 0.33
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.36
Consensus pattern (29 bp):
CCCTAAACTTTCCAAAATTATATTTTTGA
Found at i:29639 original size:30 final size:29
Alignment explanation
Indices: 29583--29689 Score: 103
Period size: 29 Copynumber: 3.7 Consensus size: 29
29573 CAAATTCTCC
*
29583 AAAATTACATTTTTACCCTAAACTTTCCA
1 AAAATTACATTTTTACCCCAAACTTTCCA
* *
29612 AAAATTTCATTTTTACACCCGAACTTTCC-
1 AAAATTACATTTTTAC-CCCAAACTTTCCA
*
29641 AAAATT-CTATTTTTGACCCAAAAACTTT-CA
1 AAAATTAC-ATTTTT-ACCC-CAAACTTTCCA
**
29671 AAAATTACCCTTTTACCCC
1 AAAATTACATTTTTACCCC
29690 CGGTTGTCCA
Statistics
Matches: 64, Mismatches: 8, Indels: 13
0.75 0.09 0.15
Matches are distributed among these distances:
28 1 0.02
29 34 0.53
30 28 0.44
31 1 0.02
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.36
Consensus pattern (29 bp):
AAAATTACATTTTTACCCCAAACTTTCCA
Found at i:29851 original size:29 final size:29
Alignment explanation
Indices: 29790--29851 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
29780 AAACTTTCCC
* *
29790 AAAATTACCGTTTTACCCCTCGAGAGTCC
1 AAAATTACCATTTTACCCCTCGAGAGTCA
*
29819 AAAATTACCATTTTACCCC-CGAGTATTCA
1 AAAATTACCATTTTACCCCTCGAG-AGTCA
29848 AAAA
1 AAAA
29852 GTCTCATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 4 0.14
29 25 0.86
ACGTcount: A:0.35, C:0.27, G:0.10, T:0.27
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCTCGAGAGTCA
Found at i:29928 original size:23 final size:23
Alignment explanation
Indices: 29897--29940 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
29887 TTCTCTTCAA
*
29897 TATTTGTATTTAT-TTTTTTAAT
1 TATTTGTATTCATATTTTTTAAT
29919 TATTATGTATTCATATTTTTTA
1 TATT-TGTATTCATATTTTTTA
29941 TTTTTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 8 0.42
24 7 0.37
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (23 bp):
TATTTGTATTCATATTTTTTAAT
Found at i:35558 original size:73 final size:73
Alignment explanation
Indices: 35467--35612 Score: 292
Period size: 73 Copynumber: 2.0 Consensus size: 73
35457 GAACAACAAA
35467 GATCCATCTAAGAAAACAAAAAACAACTTGTTAGAATAATATAATTAATAAAATATGTCAAATAA
1 GATCCATCTAAGAAAACAAAAAACAACTTGTTAGAATAATATAATTAATAAAATATGTCAAATAA
35532 TTGAAATT
66 TTGAAATT
35540 GATCCATCTAAGAAAACAAAAAACAACTTGTTAGAATAATATAATTAATAAAATATGTCAAATAA
1 GATCCATCTAAGAAAACAAAAAACAACTTGTTAGAATAATATAATTAATAAAATATGTCAAATAA
35605 TTGAAATT
66 TTGAAATT
35613 TTGGGTATAT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.29
Consensus pattern (73 bp):
GATCCATCTAAGAAAACAAAAAACAACTTGTTAGAATAATATAATTAATAAAATATGTCAAATAA
TTGAAATT
Found at i:36719 original size:16 final size:16
Alignment explanation
Indices: 36698--36746 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
36688 GGATGAAGAT
36698 ATTATTTTGGTAATTA
1 ATTATTTTGGTAATTA
36714 ATTATTTT--TATATT-
1 ATTATTTTGGTA-ATTA
36728 A-TATTTTGGTAATTA
1 ATTATTTTGGTAATTA
36743 ATTA
1 ATTA
36747 ACTAGGTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
13 6 0.21
14 6 0.21
15 6 0.21
16 10 0.36
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (16 bp):
ATTATTTTGGTAATTA
Found at i:44068 original size:93 final size:93
Alignment explanation
Indices: 43904--44078 Score: 305
Period size: 93 Copynumber: 1.9 Consensus size: 93
43894 TTATACTTTT
*
43904 TTAATCCTTTAACAACGCACACACACTTTACATATACAAGCGCTCGAACTCGAGACCCTTAAAAT
1 TTAACCCTTTAACAACGCACACACACTTTACATATACAAGCGCTCGAACTCGAGACCCTTAAAAT
* *
43969 GAACAACATTCTCTTTTCCACCGATTTC
66 AAACAACATCCTCTTTTCCACCGATTTC
* *
43997 TTAACCCTTTAACAACGCACACACACTTTACATATACAAGTGCTCGAACTCGAGACCCTTAAGAT
1 TTAACCCTTTAACAACGCACACACACTTTACATATACAAGCGCTCGAACTCGAGACCCTTAAAAT
44062 AAACAACATCCTCTTTT
66 AAACAACATCCTCTTTT
44079 TCACTGAAGC
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 77 1.00
ACGTcount: A:0.34, C:0.30, G:0.09, T:0.27
Consensus pattern (93 bp):
TTAACCCTTTAACAACGCACACACACTTTACATATACAAGCGCTCGAACTCGAGACCCTTAAAAT
AAACAACATCCTCTTTTCCACCGATTTC
Found at i:45828 original size:30 final size:30
Alignment explanation
Indices: 45794--46005 Score: 186
Period size: 30 Copynumber: 7.1 Consensus size: 30
45784 AAATAAGAAT
*
45794 TTTTTGGAAATTTTAGGGGTCAAAACTTAA
1 TTTTTGGAAAGTTTAGGGGTCAAAACTTAA
* *
45824 TTTTTGGAAATTTTAGGGGTTAAAACTTAA
1 TTTTTGGAAAGTTTAGGGGTCAAAACTTAA
*
45854 TTTTTGGAAAGTTTAAGGGTCAAAA-TATAA
1 TTTTTGGAAAGTTTAGGGGTCAAAACT-TAA
* ** * *
45884 TTTTTGG-AAGTTCAAAGGCCAAATC-TAA
1 TTTTTGGAAAGTTTAGGGGTCAAAACTTAA
* *
45912 TTTTTTGGAAAG-TTCGAGGGTCAAATC-TAA
1 -TTTTTGGAAAGTTTAG-GGGTCAAAACTTAA
* *
45942 TTTTTTGAACAGTTT-GAAGGTCAAAA-TATAA
1 TTTTTGGAA-AGTTTAG-GGGTCAAAACT-TAA
* *
45973 TTTTTGGATAGTTTAGGGGTCAAAACATAA
1 TTTTTGGAAAGTTTAGGGGTCAAAACTTAA
46003 TTT
1 TTT
46006 CTAAGTAAAA
Statistics
Matches: 151, Mismatches: 20, Indels: 22
0.78 0.10 0.11
Matches are distributed among these distances:
28 3 0.02
29 30 0.20
30 105 0.70
31 13 0.09
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.39
Consensus pattern (30 bp):
TTTTTGGAAAGTTTAGGGGTCAAAACTTAA
Found at i:45893 original size:119 final size:118
Alignment explanation
Indices: 45734--46005 Score: 263
Period size: 119 Copynumber: 2.3 Consensus size: 118
45724 TCAAAAATGG
* * * *
45734 AATTTTT-GAAAGTTT-AGGGACTAAAT-TCAAATTTTTGGAAGCTT-AGGGTCAAATAAGAATT
1 AATTTTTGGAAAGTTTAAGGGTCAAAATAT--AATTTTTGGAAG-TTAAAGGCCAAAT-AGAATT
* * * *
45795 TTTTGGAAATTTTAG-GGGTCAAAACTTAATTTTTGGAA-A-TTTTAGGGGTTAAAACT-T
62 TTTTGGAAA-GTTAGAGGGTCAAAAC-TAATTTTTGGAACAGTTTGA-AGGTCAAAA-TAT
**
45852 AATTTTTGGAAAGTTTAAGGGTCAAAATATAATTTTTGGAAGTTCAAAGGCCAAATCTAATTTTT
1 AATTTTTGGAAAGTTTAAGGGTCAAAATATAATTTTTGGAAGTT-AAAGGCCAAATAGAATTTTT
* * *
45917 TGGAAAGTTCGAGGGTCAAATCTAATTTTTTGAACAGTTTGAAGGTCAAAATAT
65 TGGAAAGTTAGAGGGTCAAAACTAATTTTTGGAACAGTTTGAAGGTCAAAATAT
* * *
45971 AATTTTTGGATAGTTTAGGGGTCAAAACATAATTT
1 AATTTTTGGAAAGTTTAAGGGTCAAAATATAATTT
46006 CTAAGTAAAA
Statistics
Matches: 129, Mismatches: 16, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
118 24 0.19
119 83 0.64
120 21 0.16
121 1 0.01
ACGTcount: A:0.35, C:0.07, G:0.20, T:0.38
Consensus pattern (118 bp):
AATTTTTGGAAAGTTTAAGGGTCAAAATATAATTTTTGGAAGTTAAAGGCCAAATAGAATTTTTT
GGAAAGTTAGAGGGTCAAAACTAATTTTTGGAACAGTTTGAAGGTCAAAATAT
Found at i:48711 original size:19 final size:19
Alignment explanation
Indices: 48689--48725 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
48679 ATTTAAACTT
*
48689 AACAACATAATTAAAATTA
1 AACAAAATAATTAAAATTA
*
48708 AACAAAATAGTTAAAATT
1 AACAAAATAATTAAAATT
48726 TTTAATGATC
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:0.62, C:0.08, G:0.03, T:0.27
Consensus pattern (19 bp):
AACAAAATAATTAAAATTA
Found at i:49394 original size:27 final size:28
Alignment explanation
Indices: 49328--49413 Score: 86
Period size: 27 Copynumber: 3.0 Consensus size: 28
49318 TTGAAGAGCA
49328 CTAACCCAAAAT-CTCCAAAATCAAAACCT
1 CTAACCCAAAATCCT-C-AAATCAAAACCT
* *
49357 CTAAACAAAAATCCTCAAATCAAAA-CT
1 CTAACCCAAAATCCTCAAATCAAAACCT
* *
49384 CTTACCCAAAATCCCCAAATTCAACAACCT
1 CTAACCCAAAATCCTCAAA-TCAA-AACCT
49414 AAAATCTCCA
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
27 17 0.36
28 13 0.28
29 13 0.28
30 4 0.09
ACGTcount: A:0.48, C:0.34, G:0.00, T:0.19
Consensus pattern (28 bp):
CTAACCCAAAATCCTCAAATCAAAACCT
Found at i:49935 original size:18 final size:18
Alignment explanation
Indices: 49894--49935 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
49884 GTTTTAAAGG
*
49894 TTTTTTTAATTTTAATTA
1 TTTTTTTAAGTTTAATTA
* *
49912 TGTTTTTAAGTTTAAGT-
1 TTTTTTTAAGTTTAATTA
49929 TTTTTTT
1 TTTTTTT
49936 GTCGACGTGG
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.71
Consensus pattern (18 bp):
TTTTTTTAAGTTTAATTA
Found at i:52416 original size:33 final size:33
Alignment explanation
Indices: 52360--52424 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
52350 ATTTCACACT
*
52360 TTTTCAATTCACTCACAACTCTCTCTCAATTCA
1 TTTTCAATCCACTCACAACTCTCTCTCAATTCA
* * * *
52393 TTTTCAATCCTCTCTCAATTCTCTCTTAATTC
1 TTTTCAATCCACTCACAACTCTCTCTCAATTC
52425 TCACTCGATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.23, C:0.32, G:0.00, T:0.45
Consensus pattern (33 bp):
TTTTCAATCCACTCACAACTCTCTCTCAATTCA
Found at i:52423 original size:11 final size:11
Alignment explanation
Indices: 52363--52438 Score: 64
Period size: 11 Copynumber: 6.9 Consensus size: 11
52353 TCACACTTTT
*
52363 TCAATTCACTC
1 TCAATTCTCTC
* *
52374 ACAACTCTCTC
1 TCAATTCTCTC
*
52385 TCAATTCAT-TT
1 TCAATTC-TCTC
*
52396 TCAATCCTCTC
1 TCAATTCTCTC
52407 TCAATTCTCTC
1 TCAATTCTCTC
* *
52418 TTAATTCTCAC
1 TCAATTCTCTC
*
52429 TCGATTCTCT
1 TCAATTCTCT
52439 TAGTCCACTC
Statistics
Matches: 49, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
10 1 0.02
11 47 0.96
12 1 0.02
ACGTcount: A:0.22, C:0.34, G:0.01, T:0.42
Consensus pattern (11 bp):
TCAATTCTCTC
Found at i:54810 original size:28 final size:28
Alignment explanation
Indices: 54756--54810 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
54746 AAATTTTAAT
* *
54756 TTTTTTAACTGTTAATTGAATTAAAATA
1 TTTTTAAACTGTTAATTGAAATAAAATA
*
54784 TTTTTAAACTTGTTAATT-AAATCAAAT
1 TTTTTAAAC-TGTTAATTGAAATAAAAT
54811 TAATTTCGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.49
Consensus pattern (28 bp):
TTTTTAAACTGTTAATTGAAATAAAATA
Found at i:57827 original size:45 final size:45
Alignment explanation
Indices: 57776--57866 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
57766 TTTAGGTCTC
57776 TTGGATATTGACTTATAAGGTTGTTTATTGGTAAGGGATGTAATT
1 TTGGATATTGACTTATAAGGTTGTTTATTGGTAAGGGATGTAATT
57821 TTGGATATTGACTTATAAGGTTGTTTATTGGTAAGGGATGTAATT
1 TTGGATATTGACTTATAAGGTTGTTTATTGGTAAGGGATGTAATT
57866 T
1 T
57867 CAAACAAATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.26, C:0.02, G:0.26, T:0.45
Consensus pattern (45 bp):
TTGGATATTGACTTATAAGGTTGTTTATTGGTAAGGGATGTAATT
Found at i:59328 original size:22 final size:21
Alignment explanation
Indices: 59303--59373 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 21
59293 TTAATTGCTG
*
59303 TTTTGATGTTATTTTTTTACTA
1 TTTTGATGCTATTTTTTTA-TA
* * *
59325 TTTTGGTGCTATTATTATTATT
1 TTTTGATGCTATT-TTTTTATA
*
59347 TTTTGTTGCTATTTTTTCTATTA
1 TTTTGATGCTATTTTTT-TA-TA
59370 TTTT
1 TTTT
59374 TGTTGCTGTT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
21 3 0.08
22 26 0.67
23 10 0.26
ACGTcount: A:0.15, C:0.06, G:0.10, T:0.69
Consensus pattern (21 bp):
TTTTGATGCTATTTTTTTATA
Found at i:64118 original size:24 final size:24
Alignment explanation
Indices: 64071--64118 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
64061 TGATATAAAG
*
64071 TATTATAAATTTTAATATTGTTAA
1 TATTATAAATTTTAATATTATTAA
* *
64095 TATTATAATTTTTAATTTTATTAA
1 TATTATAAATTTTAATATTATTAA
64119 ACATACATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (24 bp):
TATTATAAATTTTAATATTATTAA
Found at i:64331 original size:22 final size:23
Alignment explanation
Indices: 64305--64356 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
64295 TTTAATAATA
*
64305 AATA-TTTATATTATA-CACTATG
1 AATATTTTA-ATTATATCAATATG
*
64327 AATATTTTAATTATATGAATATG
1 AATATTTTAATTATATCAATATG
64350 AATATTT
1 AATATTT
64357 GTTTAAATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (23 bp):
AATATTTTAATTATATCAATATG
Found at i:67189 original size:43 final size:43
Alignment explanation
Indices: 67128--67323 Score: 187
Period size: 43 Copynumber: 4.5 Consensus size: 43
67118 TTATGAAGGA
* * * *
67128 AAACGCCGCTATAGAACATGGTATTTAGTGGTGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGTGGCGCTTTACCCAC
* * *
67171 AAACGCCGCTAAAGAACATGGTCTTTAACT-GCGTTTTACACAC
1 AAACGCCGCTAAAGAACATGGTCTTT-AGTGGCGCTTTACCCAC
* ***** *
67214 AAACGCCGTTAAAGAACATGGTCTNNNNNNNNNGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGGTCT----TTAGTGGCGCTTTACCCAC
* * *
67261 AAACGCTGCTAAAGAACATGGTCTTTAGCGGCGCTTTAACCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGTGGCGCTTTACCCAC
67304 AAACGCCGCTAAAGAACATG
1 AAACGCCGCTAAAGAACATG
67324 ATATTTTTTA
Statistics
Matches: 121, Mismatches: 26, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
43 87 0.72
44 2 0.02
47 32 0.26
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGGTCTTTAGTGGCGCTTTACCCAC
Found at i:67341 original size:35 final size:35
Alignment explanation
Indices: 67295--67393 Score: 171
Period size: 35 Copynumber: 2.8 Consensus size: 35
67285 TTAGCGGCGC
*
67295 TTTAACCACAAACGCCGCTAAAGAACATGATATTT
1 TTTAATCACAAACGCCGCTAAAGAACATGATATTT
* *
67330 TTTAATCACAAACACCGCTAAAGAACATGATCTTT
1 TTTAATCACAAACGCCGCTAAAGAACATGATATTT
67365 TTTAATCACAAACGCCGCTAAAGAACATG
1 TTTAATCACAAACGCCGCTAAAGAACATG
67394 GTCACAAACG
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 60 1.00
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.25
Consensus pattern (35 bp):
TTTAATCACAAACGCCGCTAAAGAACATGATATTT
Found at i:67457 original size:43 final size:43
Alignment explanation
Indices: 67396--67497 Score: 150
Period size: 43 Copynumber: 2.4 Consensus size: 43
67386 AGAACATGGT
* * *
67396 CACAAACGCCGCTAAAGAATATGTTCTTTAGCAGCGCTTTTCC
1 CACAAACGCTGCTAAAGAACATGGTCTTTAGCAGCGCTTTTCC
** *
67439 CACAAACGCTGCTAAAGAACATGGTCTTTAGTGGCGCTTTTCT
1 CACAAACGCTGCTAAAGAACATGGTCTTTAGCAGCGCTTTTCC
67482 CACAAACGCTGCTAAA
1 CACAAACGCTGCTAAA
67498 ATTAACAGAT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 53 1.00
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.26
Consensus pattern (43 bp):
CACAAACGCTGCTAAAGAACATGGTCTTTAGCAGCGCTTTTCC
Found at i:68983 original size:18 final size:18
Alignment explanation
Indices: 68960--69007 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
68950 GTTGGTGGAA
*
68960 ATTAGGGATTTAGAAATG
1 ATTAGGAATTTAGAAATG
68978 ATTAGGAATTTAGAAATG
1 ATTAGGAATTTAGAAATG
*
68996 AATGAGGAATTT
1 -ATTAGGAATTT
69008 TCGAATCAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 17 0.63
19 10 0.37
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
ATTAGGAATTTAGAAATG
Found at i:69142 original size:18 final size:18
Alignment explanation
Indices: 69119--69166 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
69109 GTTGGTGGAA
*
69119 ATTAGGGATTTAGAAATG
1 ATTAGGAATTTAGAAATG
69137 ATTAGGAATTTAGAAATG
1 ATTAGGAATTTAGAAATG
*
69155 AATGAGGAATTT
1 -ATTAGGAATTT
69167 TTTTGATAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 17 0.63
19 10 0.37
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
ATTAGGAATTTAGAAATG
Found at i:69190 original size:159 final size:159
Alignment explanation
Indices: 68879--69167 Score: 436
Period size: 159 Copynumber: 1.8 Consensus size: 159
68869 TTGAGATGAT
** **
68879 GGTGGTGGTCGGTCGATGGGTGTTGGTGTAGATTGGAGTGAAGAATGAAACGGAGGAGACAAATG
1 GGTGGTGGTCGACCGACAGGTGTTGGTGTAGATTGGAGTGAAGAATGAAACGGAGGAGACAAATG
68944 ATAGGTGTTGGTGGAAATTAGGGATTTAGAAATGATTAGGAATTTAGAAATGAATGAGGAATTTT
66 ATAGGTGTTGGTGGAAATTAGGGATTTAGAAATGATTAGGAATTTAGAAATGAATGAGGAATTTT
* *** *
69009 CGAATCAGCTTTTGGAGAAGGAAAAGGCA
131 CGAATAAGCGAATGAAGAAGGAAAAGGCA
* * * *
69038 GGTGGTGGTCGACCGACAGGTGTTTGTGTAGATTGGAGTGGAGAATGAAATGGAGGAGGCAAACT
1 GGTGGTGGTCGACCGACAGGTGTTGGTGTAGATTGGAGTGAAGAATGAAACGGAGGAGACAAA-T
*
69103 -ATGGGTGTTGGTGGAAATTAGGGATTTAGAAATGATTAGGAATTTAGAAATGAATGAGGAATTT
65 GATAGGTGTTGGTGGAAATTAGGGATTTAGAAATGATTAGGAATTTAGAAATGAATGAGGAATTT
69167 T
130 T
69168 TTTGATAAGG
Statistics
Matches: 120, Mismatches: 9, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
159 119 0.99
160 1 0.01
ACGTcount: A:0.32, C:0.05, G:0.36, T:0.27
Consensus pattern (159 bp):
GGTGGTGGTCGACCGACAGGTGTTGGTGTAGATTGGAGTGAAGAATGAAACGGAGGAGACAAATG
ATAGGTGTTGGTGGAAATTAGGGATTTAGAAATGATTAGGAATTTAGAAATGAATGAGGAATTTT
CGAATAAGCGAATGAAGAAGGAAAAGGCA
Found at i:69370 original size:42 final size:43
Alignment explanation
Indices: 69324--69434 Score: 125
Period size: 43 Copynumber: 2.6 Consensus size: 43
69314 ATGCTCTGGC
*** *
69324 CCTTTTGCGGCGTTTTTGGGA-AAACGCCACTAATGTTCTATA
1 CCTTTTGCGGCGTTTTTCAAATAAACGCCACTAATGCTCTATA
** ** *
69366 CCTTTTGCAACGTTTTTCAAATAAACGCTGCTATTGCTCTATA
1 CCTTTTGCGGCGTTTTTCAAATAAACGCCACTAATGCTCTATA
*
69409 CCTTTTGCGGCGATTTTCAAATAAAC
1 CCTTTTGCGGCGTTTTTCAAATAAAC
69435 ACTGCTATTG
Statistics
Matches: 56, Mismatches: 12, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
42 16 0.29
43 40 0.71
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.37
Consensus pattern (43 bp):
CCTTTTGCGGCGTTTTTCAAATAAACGCCACTAATGCTCTATA
Found at i:69407 original size:43 final size:43
Alignment explanation
Indices: 69360--69455 Score: 142
Period size: 43 Copynumber: 2.3 Consensus size: 43
69350 CCACTAATGT
* *
69360 TCTATACCTTTTGCAACGTTTTTCAAATAAACGCTGCTATTGC
1 TCTATACCTTTTGCAACGATTTTCAAATAAACACTGCTATTGC
**
69403 TCTATACCTTTTGCGGCGATTTTCAAATAAACACTGCTATTGC
1 TCTATACCTTTTGCAACGATTTTCAAATAAACACTGCTATTGC
69446 T-T-TACCTTTT
1 TCTATACCTTTT
69456 ACAGTGTTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
41 8 0.16
42 1 0.02
43 40 0.82
ACGTcount: A:0.24, C:0.23, G:0.11, T:0.42
Consensus pattern (43 bp):
TCTATACCTTTTGCAACGATTTTCAAATAAACACTGCTATTGC
Found at i:69956 original size:24 final size:24
Alignment explanation
Indices: 69928--69990 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
69918 AGAAATAATC
69928 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAGTTAAACTCTGTTTAATTG
* *
69952 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTAATTG
* *
69976 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
69991 TATTAGTCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.25, C:0.14, G:0.11, T:0.49
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTTAATTG
Found at i:70600 original size:24 final size:24
Alignment explanation
Indices: 70572--70634 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
70562 AGAAATAATC
70572 TTTCAGTTAAATTCTATTTAATTG
1 TTTCAGTTAAATTCTATTTAATTG
* * * *
70596 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAGTTAAATTCTATTTAATTG
* *
70620 TTTTAGTAAAATTCT
1 TTTCAGTTAAATTCT
70635 TATTAGTCTA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.29, C:0.10, G:0.08, T:0.54
Consensus pattern (24 bp):
TTTCAGTTAAATTCTATTTAATTG
Found at i:72317 original size:42 final size:41
Alignment explanation
Indices: 72270--72411 Score: 162
Period size: 41 Copynumber: 3.4 Consensus size: 41
72260 CGTTTACTTA
* * *
72270 ACCTTTAGCGGTGTTTTTCCTATAAACGTCGTTAATGCTCTG
1 ACCTTTAGCGGCGTTTTT-CTATAAACGCCGCTAATGCTCTG
*
72312 ACCTTTAGCTGCG-TTTTCTAATAAACGCCGCTAATGCTCTG
1 ACCTTTAGCGGCGTTTTTCT-ATAAACGCCGCTAATGCTCTG
* * *
72353 ATCTTTAGCGGCGTTTTAT-AATAAATGCCGCTAATGCTCTG
1 ACCTTTAGCGGCGTTTT-TCTATAAACGCCGCTAATGCTCTG
* *
72394 ACCTTTAGTGGTGTTTTT
1 ACCTTTAGCGGCGTTTTT
72412 TCGTAAACGC
Statistics
Matches: 86, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
40 3 0.03
41 68 0.79
42 14 0.16
43 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.39
Consensus pattern (41 bp):
ACCTTTAGCGGCGTTTTTCTATAAACGCCGCTAATGCTCTG
Found at i:72347 original size:41 final size:41
Alignment explanation
Indices: 72291--72410 Score: 168
Period size: 41 Copynumber: 2.9 Consensus size: 41
72281 TGTTTTTCCT
* * * *
72291 ATAAACGTCGTTAATGCTCTGACCTTTAGCTGCGTTTTCTA
1 ATAAACGCCGCTAATGCTCTGACCTTTAGCGGCGTTTTATA
*
72332 ATAAACGCCGCTAATGCTCTGATCTTTAGCGGCGTTTTATA
1 ATAAACGCCGCTAATGCTCTGACCTTTAGCGGCGTTTTATA
* * *
72373 ATAAATGCCGCTAATGCTCTGACCTTTAGTGGTGTTTT
1 ATAAACGCCGCTAATGCTCTGACCTTTAGCGGCGTTTT
72411 TTCGTAAACG
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 70 1.00
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.38
Consensus pattern (41 bp):
ATAAACGCCGCTAATGCTCTGACCTTTAGCGGCGTTTTATA
Found at i:72604 original size:40 final size:40
Alignment explanation
Indices: 72522--72626 Score: 122
Period size: 40 Copynumber: 2.6 Consensus size: 40
72512 TAAACACTGT
* * ***
72522 TATTGCTTTACATTTTGCGGCATTTATGTAAAAACGTTGC
1 TATTGCTTTACATTTTGCGGCGTTTATGGAAAAACCCAGC
*
72562 TATTGCTTTACCTTTTGCGGCGTTTATGGAAAAACCCAGC
1 TATTGCTTTACATTTTGCGGCGTTTATGGAAAAACCCAGC
* *
72602 TATTGATTTACTTTTTAG-GGCGTTT
1 TATTGCTTTACATTTT-GCGGCGTTT
72627 TCTGTCTAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
40 55 0.98
41 1 0.02
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.43
Consensus pattern (40 bp):
TATTGCTTTACATTTTGCGGCGTTTATGGAAAAACCCAGC
Found at i:82410 original size:15 final size:15
Alignment explanation
Indices: 82390--82439 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
82380 GAAGCCAGAT
82390 CACCATGACCACGAG
1 CACCATGACCACGAG
**
82405 CACCATGATGA--AG
1 CACCATGACCACGAG
*
82418 -ACCATGACCACGAA
1 CACCATGACCACGAG
82432 CACCATGA
1 CACCATGA
82440 TGAAGACCTT
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
12 8 0.30
13 2 0.07
14 1 0.04
15 16 0.59
ACGTcount: A:0.38, C:0.34, G:0.18, T:0.10
Consensus pattern (15 bp):
CACCATGACCACGAG
Found at i:82513 original size:27 final size:27
Alignment explanation
Indices: 82391--82515 Score: 182
Period size: 27 Copynumber: 4.6 Consensus size: 27
82381 AAGCCAGATC
82391 ACCATGACCAC-GAGCACCATGATGAAG
1 ACCATGACCACGGA-CACCATGATGAAG
*
82418 ACCATGACCACGAACACCATGATGAAG
1 ACCATGACCACGGACACCATGATGAAG
* *
82445 ACCTTGACAAC-GACCACCATGATGAAG
1 ACCATGACCACGGA-CACCATGATGAAG
*
82472 ACCATGACCATGGACACCATGATGAAG
1 ACCATGACCACGGACACCATGATGAAG
82499 ACCATGACCACGGACAC
1 ACCATGACCACGGACAC
82516 GGACACGGAC
Statistics
Matches: 87, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
26 1 0.01
27 83 0.95
28 3 0.03
ACGTcount: A:0.38, C:0.30, G:0.20, T:0.12
Consensus pattern (27 bp):
ACCATGACCACGGACACCATGATGAAG
Found at i:82590 original size:3 final size:3
Alignment explanation
Indices: 82582--82619 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
82572 TGAGGAAGAG
82582 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
82620 TCATCACCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.66, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:85058 original size:6 final size:6
Alignment explanation
Indices: 85049--85077 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
85039 TAATGAAATT
85049 GAAAAG GAAAAG GAAAAG GAAAAG GAAAA
1 GAAAAG GAAAAG GAAAAG GAAAAG GAAAA
85078 CAATAATGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (6 bp):
GAAAAG
Found at i:87510 original size:164 final size:164
Alignment explanation
Indices: 87239--87556 Score: 627
Period size: 164 Copynumber: 1.9 Consensus size: 164
87229 TAATGCAACC
87239 AAAACCCAAATCTTTAAAAAAGTGAACAAAGAAAAAAGAAAAGGAAAGAAAAGCAAGAACAGCAG
1 AAAACCCAAATCTTTAAAAAAGTGAACAAAGAAAAAAGAAAAGGAAAGAAAAGCAAGAACAGCAG
87304 TCATATAGAAGAATCACTCTTTGCAATTATTATTATAAATTATACTAGTTCATAATTAAAACCCA
66 TCATATAGAAGAATCACTCTTTGCAATTATTATTATAAATTATACTAGTTCATAATTAAAACCCA
87369 GATTACAGCTTTCATTACCATTTTGCAATTATAT
131 GATTACAGCTTTCATTACCATTTTGCAATTATAT
*
87403 AAAACCCAAATCTTTAAAAAAGTGAACAAAGAATAAAGAAAAGGAAAGAAAAGCAAGAACAGCAG
1 AAAACCCAAATCTTTAAAAAAGTGAACAAAGAAAAAAGAAAAGGAAAGAAAAGCAAGAACAGCAG
87468 TCATATAGAAGAATCACTCTTTGCAATTATTATTATAAATTATACTAGTTCATAATTAAAACCCA
66 TCATATAGAAGAATCACTCTTTGCAATTATTATTATAAATTATACTAGTTCATAATTAAAACCCA
87533 GATTACAGCTTTCATTACCATTTT
131 GATTACAGCTTTCATTACCATTTT
87557 AGAAGCAAAG
Statistics
Matches: 153, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
164 153 1.00
ACGTcount: A:0.47, C:0.15, G:0.11, T:0.27
Consensus pattern (164 bp):
AAAACCCAAATCTTTAAAAAAGTGAACAAAGAAAAAAGAAAAGGAAAGAAAAGCAAGAACAGCAG
TCATATAGAAGAATCACTCTTTGCAATTATTATTATAAATTATACTAGTTCATAATTAAAACCCA
GATTACAGCTTTCATTACCATTTTGCAATTATAT
Found at i:92367 original size:30 final size:30
Alignment explanation
Indices: 92316--92659 Score: 244
Period size: 30 Copynumber: 11.4 Consensus size: 30
92306 GGTAAAATGG
* * * **
92316 TTTTGG-ATTTTCGGGGGCAAAAATAAAAT
1 TTTTGGAAGTTTCGAGGTCAAAAATGGAAT
92345 TTTTGGAAGTTTCGAGGTCAAAAATGGAAT
1 TTTTGGAAGTTTCGAGGTCAAAAATGGAAT
* *
92375 TTTTGGAAGTTTAGGGGT-AAAATGGATTTTTTGGAAT
1 TTTTGGAAGTTTCGAGGTCAAAA---A-----TGGAAT
* * *
92412 TTTTGAAAGTTTCGGGGTCGAAAATGGAAT
1 TTTTGGAAGTTTCGAGGTCAAAAATGGAAT
* *
92442 TTTTTGAAG-TTCGGGGGT-AAAAATGGAAT
1 TTTTGGAAGTTTC-GAGGTCAAAAATGGAAT
92471 TTTT-GAAG-TTC-AGGGTCAAAAATGGAAT
1 TTTTGGAAGTTTCGA-GGTCAAAAATGGAAT
* * * *
92499 TTTTGGAAGTTGTAG-GGTTACAAATGAAAT
1 TTTTGGAAGTT-TCGAGGTCAAAAATGGAAT
* *
92529 TTTTGGAAGTTTAGGGGT-AAAAATGGAAT
1 TTTTGGAAGTTTCGAGGTCAAAAATGGAAT
* * *
92558 TTTTGAAAGTTT-TAGGGTCAAAAATAGAAT
1 TTTTGGAAGTTTCGA-GGTCAAAAATGGAAT
* *
92588 TTTTTGAAG-TTCGAGGGT-AAAATTGGAAT
1 TTTTGGAAGTTTCGA-GGTCAAAAATGGAAT
** *
92617 TTTCAGAAGTTTTGAGGTCAAAAATGGAAT
1 TTTTGGAAGTTTCGAGGTCAAAAATGGAAT
92647 TTTTGGACAGTTT
1 TTTTGGA-AGTTT
92660 AGGGACCTCC
Statistics
Matches: 256, Mismatches: 35, Indels: 46
0.76 0.10 0.14
Matches are distributed among these distances:
27 3 0.01
28 22 0.09
29 78 0.30
30 120 0.47
31 6 0.02
32 1 0.00
35 1 0.00
37 22 0.09
38 3 0.01
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.36
Consensus pattern (30 bp):
TTTTGGAAGTTTCGAGGTCAAAAATGGAAT
Found at i:92422 original size:37 final size:39
Alignment explanation
Indices: 92369--92447 Score: 117
Period size: 37 Copynumber: 2.1 Consensus size: 39
92359 AGGTCAAAAA
*
92369 TGGAATTTTTGGAAGTTTAGGGGT-AAAATGG-ATTTTT
1 TGGAATTTTTGAAAGTTTAGGGGTCAAAATGGAATTTTT
*
92406 TGGAATTTTTGAAAGTTTCGGGGTCGAAAATGGAATTTTT
1 TGGAATTTTTGAAAGTTTAGGGGTC-AAAATGGAATTTTT
92446 TG
1 TG
92448 AAGTTCGGGG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
37 22 0.59
39 7 0.19
40 8 0.22
ACGTcount: A:0.27, C:0.03, G:0.29, T:0.42
Consensus pattern (39 bp):
TGGAATTTTTGAAAGTTTAGGGGTCAAAATGGAATTTTT
Found at i:92451 original size:67 final size:68
Alignment explanation
Indices: 92342--92475 Score: 198
Period size: 67 Copynumber: 2.0 Consensus size: 68
92332 GCAAAAATAA
* * *
92342 AATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTTAGGGGT-AAAATGGATTTTT
1 AATTTTTGAAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCAGGGGTAAAAATGGAATTTT
92406 TGG
66 TGG
* * * *
92409 AATTTTTGAAAGTTTCGGGGTCGAAAATGGAATTTTTTGAAGTTCGGGGGTAAAAATGGAATTTT
1 AATTTTTGAAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCAGGGGTAAAAATGGAATTTT
92474 TG
66 TG
92476 AAGTTCAGGG
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
67 45 0.76
68 14 0.24
ACGTcount: A:0.30, C:0.04, G:0.28, T:0.38
Consensus pattern (68 bp):
AATTTTTGAAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCAGGGGTAAAAATGGAATTTT
TGG
Found at i:92559 original size:59 final size:60
Alignment explanation
Indices: 92409--92663 Score: 240
Period size: 59 Copynumber: 4.3 Consensus size: 60
92399 GATTTTTTGG
* * * * * *
92409 AATTTTTGAAAGTTTCGGGGTCGAAAATGGAATTTTTTGAAGTTCG-GGGGT-AAAAATGG
1 AATTTTTGGAAGTTTAGGGGTCAAAAATGGAATTTTTGGAAGTT-GTAGGGTCAAAAATGA
* * *
92468 AATTTTT-GAAGTTCA-GGGTCAAAAATGGAATTTTTGGAAGTTGTAGGGTTACAAATGA
1 AATTTTTGGAAGTTTAGGGGTCAAAAATGGAATTTTTGGAAGTTGTAGGGTCAAAAATGA
* *
92526 AATTTTTGGAAGTTTAGGGGT-AAAAATGGAATTTTTGAAAGTTTTAGGGTCAAAAAT-A
1 AATTTTTGGAAGTTTAGGGGTCAAAAATGGAATTTTTGGAAGTTGTAGGGTCAAAAATGA
* * * ** * *
92584 GAATTTTTTGAAG-TTCGAGGGT-AAAATTGGAATTTTCAGAAGTT-TTGAGGTCAAAAATGG
1 -AATTTTTGGAAGTTTAG-GGGTCAAAAATGGAATTTTTGGAAGTTGTAG-GGTCAAAAATGA
92644 AATTTTTGGACAGTTTAGGG
1 AATTTTTGGA-AGTTTAGGG
92664 ACCTCCTGGC
Statistics
Matches: 163, Mismatches: 23, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
56 1 0.01
57 29 0.18
58 24 0.15
59 98 0.60
60 8 0.05
61 3 0.02
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.35
Consensus pattern (60 bp):
AATTTTTGGAAGTTTAGGGGTCAAAAATGGAATTTTTGGAAGTTGTAGGGTCAAAAATGA
Found at i:93742 original size:3 final size:3
Alignment explanation
Indices: 93734--93825 Score: 67
Period size: 3 Copynumber: 29.7 Consensus size: 3
93724 TCAGCTCTTT
* * *
93734 TTA TTA TTA TTAA TTA TTA ATA TTA TTA TTAA TTA CTA ATA GTTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TT-A TTA TTA TTA -TTA TTA
* * * * ** *
93782 TCA TTA TTA TTA ATA ATA ATA TTA TTA TTA AAA TAA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
93826 GCCATTAATA
Statistics
Matches: 73, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
3 65 0.89
4 8 0.11
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.54
Consensus pattern (3 bp):
TTA
Found at i:93763 original size:12 final size:12
Alignment explanation
Indices: 93735--93823 Score: 61
Period size: 13 Copynumber: 6.9 Consensus size: 12
93725 CAGCTCTTTT
93735 TATTATTATTAA
1 TATTATTATTAA
* *
93747 TTATTAATATTAT
1 -TATTATTATTAA
*
93760 TATTAATTACTAA
1 TATT-ATTATTAA
* *
93773 TAGTTATTATCAT
1 TA-TTATTATTAA
93786 TATTATTAATAATAA
1 TATTATT-AT--TAA
93801 TATTATTATTAA
1 TATTATTATTAA
* *
93813 AATAATTATTA
1 TATTATTATTA
93824 TTGCCATTAA
Statistics
Matches: 59, Mismatches: 12, Indels: 11
0.72 0.15 0.13
Matches are distributed among these distances:
12 21 0.36
13 26 0.44
14 4 0.07
15 8 0.14
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (12 bp):
TATTATTATTAA
Found at i:93779 original size:29 final size:28
Alignment explanation
Indices: 93746--93808 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 28
93736 ATTATTATTA
*
93746 ATTATTAAT-ATTATTATTAATTACTAAT
1 ATTATTAATCATTATTATTAA-TAATAAT
93774 AGTTATT-ATCATTATTATTAATAATAAT
1 A-TTATTAATCATTATTATTAATAATAAT
93802 ATTATTA
1 ATTATTA
93809 TTAAAATAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
27 5 0.16
28 10 0.32
29 16 0.52
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (28 bp):
ATTATTAATCATTATTATTAATAATAAT
Found at i:94527 original size:17 final size:17
Alignment explanation
Indices: 94505--94564 Score: 84
Period size: 17 Copynumber: 3.5 Consensus size: 17
94495 ATTGTTTAAT
94505 TTTAAATTTATAATAAA
1 TTTAAATTTATAATAAA
*
94522 TTTAAATTTCTAATAAA
1 TTTAAATTTATAATAAA
* * *
94539 CTTAATTTTAAAATAAA
1 TTTAAATTTATAATAAA
94556 TTTAAATTT
1 TTTAAATTT
94565 TGTTGGGCCC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTAAATTTATAATAAA
Found at i:98153 original size:17 final size:18
Alignment explanation
Indices: 98128--98161 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
98118 GAAAATTTTG
98128 TTAAATTAAATT-TAAAA
1 TTAAATTAAATTCTAAAA
*
98145 TTAAGTTAAATTCTAAA
1 TTAAATTAAATTCTAAA
98162 TGTCCTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (18 bp):
TTAAATTAAATTCTAAAA
Found at i:99992 original size:15 final size:14
Alignment explanation
Indices: 99964--99990 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
99954 AAAATTGTTT
99964 TTTTTTAATATTTA
1 TTTTTTAATATTTA
99978 TTTTTTAATATTT
1 TTTTTTAATATTT
99991 TACTATACTC
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:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTTTAATATTTA
Found at i:104916 original size:2 final size:2
Alignment explanation
Indices: 104909--104948 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
104899 TTACTAACTA
104909 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
104949 AAAGAATAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:115763 original size:23 final size:23
Alignment explanation
Indices: 115710--115763 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
115700 TTTTAAGGTC
* * *
115710 AAATTTAAATTATAATTTTTATA
1 AAATTAAAAATATAATTTTTAAA
* *
115733 ATAGTAAAAATATAATTTTTAAA
1 AAATTAAAAATATAATTTTTAAA
115756 AAATTAAA
1 AAATTAAA
115764 TCAAAAATTT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
AAATTAAAAATATAATTTTTAAA
Found at i:116742 original size:30 final size:29
Alignment explanation
Indices: 116708--116780 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 29
116698 GCAAATGATT
*
116708 TTAAAATATTTTTTTAAGAATATAAAATTA
1 TTAAAATATTTTTTTAA-AATAAAAAATTA
* *
116738 TTAAAATTATTTATTTGAAATAAAAAATTA
1 TTAAAA-TATTTTTTTAAAATAAAAAATTA
*
116768 TT-AAATAATTTTT
1 TTAAAATATTTTTT
116781 ATTTTTAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 6 0.16
29 3 0.08
30 19 0.51
31 9 0.24
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (29 bp):
TTAAAATATTTTTTTAAAATAAAAAATTA
Found at i:117482 original size:18 final size:18
Alignment explanation
Indices: 117438--117483 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
117428 GTGTTTTGTT
*
117438 TTTTTTTTTTAATTTTAA
1 TTTTTTTTTTAACTTTAA
* * *
117456 TTATGTTTTTCACTTTAA
1 TTTTTTTTTTAACTTTAA
117474 TTTTTTTTTT
1 TTTTTTTTTT
117484 TGCTAATGTC
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.76
Consensus pattern (18 bp):
TTTTTTTTTTAACTTTAA
Found at i:124409 original size:2 final size:2
Alignment explanation
Indices: 124404--124428 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
124394 TACAAAAAAT
124404 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
124429 TACCAACTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:135395 original size:21 final size:21
Alignment explanation
Indices: 135353--135395 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
135343 ATTCCAACAC
* * *
135353 AACAATCGATTTAAACATATA
1 AACAATCGATTAAAAAAAATA
135374 AACAATCGATTAAAAAAAATA
1 AACAATCGATTAAAAAAAATA
135395 A
1 A
135396 TATTCCAACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.60, C:0.12, G:0.05, T:0.23
Consensus pattern (21 bp):
AACAATCGATTAAAAAAAATA
Found at i:135415 original size:54 final size:52
Alignment explanation
Indices: 135319--135489 Score: 184
Period size: 51 Copynumber: 3.2 Consensus size: 52
135309 CATGCTACAT
* * *
135319 AACAATCGATTCAAAAGAAGCATCATTCCAACACAACAATCGATTTAAACATATA
1 AACAATCGATTAAAAATAAG--T-ATTCCAACATAACAATCGATTTAAACATATA
* **
135374 AACAATCGATTAAAAAAAATAA-TATTCCAACATTATTATCGATTTAAACATAT-
1 AACAATCGATT---AAAAATAAGTATTCCAACATAACAATCGATTTAAACATATA
* * *
135427 AACAATCGATTCAAAATAAGTATTCCACCATAACAATCGGTTTAAACATATA
1 AACAATCGATTAAAAATAAGTATTCCAACATAACAATCGATTTAAACATATA
*
135479 AACAATTGATT
1 AACAATCGATT
135490 TTTGGGTGGG
Statistics
Matches: 98, Mismatches: 13, Indels: 13
0.79 0.10 0.10
Matches are distributed among these distances:
50 7 0.07
51 26 0.27
52 10 0.10
53 11 0.11
54 26 0.27
55 12 0.12
58 6 0.06
ACGTcount: A:0.49, C:0.18, G:0.06, T:0.27
Consensus pattern (52 bp):
AACAATCGATTAAAAATAAGTATTCCAACATAACAATCGATTTAAACATATA
Found at i:139137 original size:10 final size:10
Alignment explanation
Indices: 139122--139245 Score: 57
Period size: 10 Copynumber: 12.8 Consensus size: 10
139112 TGGTCCGAAA
139122 TATAAAAATT
1 TATAAAAATT
139132 TAT-AAAATT
1 TATAAAAATT
*
139141 AATAAAACA-T
1 TATAAAA-ATT
* *
139151 AATTAAAATAT
1 TATAAAAAT-T
*
139162 T-TAAAAGTT
1 TATAAAAATT
**
139171 TATAAAAACA
1 TATAAAAATT
*
139181 TATTAAAATT
1 TATAAAAATT
*
139191 CTATAAATA-T
1 -TATAAAAATT
*
139201 CATAAAAAGTT
1 TATAAAAA-TT
139212 T-T-AAAA-T
1 TATAAAAATT
* *
139219 TATATAAACT
1 TATAAAAATT
139229 TATAAAAA-T
1 TATAAAAATT
139238 TATAAAAA
1 TATAAAAA
139246 CTTGAACGGG
Statistics
Matches: 85, Mismatches: 18, Indels: 23
0.67 0.14 0.18
Matches are distributed among these distances:
7 2 0.02
8 1 0.01
9 33 0.39
10 40 0.47
11 9 0.11
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (10 bp):
TATAAAAATT
Found at i:139147 original size:19 final size:18
Alignment explanation
Indices: 139122--139245 Score: 74
Period size: 19 Copynumber: 6.4 Consensus size: 18
139112 TGGTCCGAAA
139122 TATAAAAATTTATAAAAT
1 TATAAAAATTTATAAAAT
139140 TAATAAAACATAATTA-AAATAT
1 T-ATAAAA-AT--TTATAAA-AT
* *
139162 T-TAAAAGTTTATAAAAACA
1 TATAAAAATTTAT-AAAA-T
*
139181 TATTAAAATTCTATAAATAT
1 TATAAAAATT-TATAAA-AT
*
139201 CATAAAAAGTTT-TAAAAT
1 TATAAAAA-TTTATAAAAT
* *
139219 TATATAAACTTATAAAAAT
1 TATAAAAATTTAT-AAAAT
139238 TATAAAAA
1 TATAAAAA
139246 CTTGAACGGG
Statistics
Matches: 81, Mismatches: 11, Indels: 27
0.68 0.09 0.23
Matches are distributed among these distances:
17 5 0.06
18 11 0.14
19 27 0.33
20 23 0.28
21 9 0.11
22 6 0.07
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (18 bp):
TATAAAAATTTATAAAAT
Found at i:139164 original size:31 final size:31
Alignment explanation
Indices: 139124--139197 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 31
139114 GTCCGAAATA
139124 TAAAA-ATTTATAAAATTAAT-AAAACATAAT
1 TAAAATATTTATAAAATTAATAAAAACAT-AT
* *
139154 TAAAATATTTA-AAAGTTTATAAAAACATAT
1 TAAAATATTTATAAAATTAATAAAAACATAT
*
139184 TAAAAT-TCTATAAA
1 TAAAATATTTATAAA
139198 TATCATAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
29 3 0.08
30 23 0.61
31 12 0.32
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.35
Consensus pattern (31 bp):
TAAAATATTTATAAAATTAATAAAAACATAT
Found at i:139188 original size:21 final size:21
Alignment explanation
Indices: 139162--139217 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
139152 ATTAAAATAT
139162 TTAAAAGTTTATAAAAACATA
1 TTAAAAGTTTATAAAAACATA
*
139183 TTAAAA-TTCTATAAATATCATA
1 TTAAAAGTT-TATAAA-AACATA
139205 --AAAAGTTT-TAAAA
1 TTAAAAGTTTATAAAA
139218 TTATATAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
18 1 0.03
19 4 0.13
20 7 0.23
21 14 0.45
22 5 0.16
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.36
Consensus pattern (21 bp):
TTAAAAGTTTATAAAAACATA
Found at i:139236 original size:29 final size:28
Alignment explanation
Indices: 139121--139236 Score: 78
Period size: 29 Copynumber: 4.0 Consensus size: 28
139111 ATGGTCCGAA
*
139121 ATATAAAAATT-TATAAAATTA-ATAAAAC
1 ATATTAAAATTATAT-AAATTATA-AAAAC
*
139149 ATAATTAAAA-TATTTAAAAGTTTATAAAAAC
1 AT-ATTAAAATTATAT-AAA--TTATAAAAAC
*
139180 ATATTAAAATTCTATAAATATCATAAAAA-
1 ATATTAAAATTATATAAAT-T-ATAAAAAC
* *
139209 GTTTTAAAATTATATAAACTTATAAAAA
1 ATATTAAAATTATATAAA-TTATAAAAA
139237 TTATAAAAAC
Statistics
Matches: 72, Mismatches: 7, Indels: 18
0.74 0.07 0.19
Matches are distributed among these distances:
28 11 0.15
29 29 0.40
30 18 0.25
31 13 0.18
32 1 0.01
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (28 bp):
ATATTAAAATTATATAAATTATAAAAAC
Found at i:139245 original size:9 final size:9
Alignment explanation
Indices: 139122--139245 Score: 56
Period size: 9 Copynumber: 12.9 Consensus size: 9
139112 TGGTCCGAAA
139122 TATAAAAAT
1 TATAAAAAT
139131 T-TATAAAAT
1 TATA-AAAAT
139140 TAATAAAACAT
1 T-ATAAAA-AT
*
139151 AATTAAAATAT
1 TA-TAAAA-AT
*
139162 T-TAAAAGTT
1 TATAAAA-AT
*
139171 TATAAAAACA
1 TATAAAAA-T
*
139181 TATTAAAATT
1 TA-TAAAAAT
*
139191 CTATAAATAT
1 -TATAAAAAT
*
139201 CATAAAAAGT
1 TATAAAAA-T
*
139211 T-TTAAAAT
1 TATAAAAAT
*
139219 TATATAAACT
1 TATA-AAAAT
139229 TATAAAAAT
1 TATAAAAAT
139238 TATAAAAA
1 TATAAAAA
139246 CTTGAACGGG
Statistics
Matches: 85, Mismatches: 18, Indels: 24
0.67 0.14 0.19
Matches are distributed among these distances:
8 4 0.05
9 38 0.45
10 25 0.29
11 18 0.21
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (9 bp):
TATAAAAAT
Found at i:139821 original size:19 final size:19
Alignment explanation
Indices: 139764--139823 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 19
139754 TTTAAATAAG
139764 TTATTA-ATTTTATAAT-T
1 TTATTATATTTTATAATAT
*
139781 TGT-TTATAATTTACTAGA-AT
1 T-TATTATATTTTA-TA-ATAT
139801 TTATTATATTTTATAATAT
1 TTATTATATTTTATAATAT
139820 TTAT
1 TTAT
139824 AATTTAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
17 4 0.12
18 7 0.21
19 11 0.32
20 12 0.35
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (19 bp):
TTATTATATTTTATAATAT
Found at i:139898 original size:19 final size:20
Alignment explanation
Indices: 139869--139908 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
139859 AATTTCTCCA
*
139869 ATTTTTATAATGTTTGTATG
1 ATTTTTATAATATTTGTATG
*
139889 ATTTTT-TAATATTTTTATG
1 ATTTTTATAATATTTGTATG
139908 A
1 A
139909 AAAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (20 bp):
ATTTTTATAATATTTGTATG
Done.