Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1265
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: 76017
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:816 original size:13 final size:13
Alignment explanation
Indices: 794--819 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
784 TTTTTTTTGA
794 TTTTTTTGAATTT
1 TTTTTTTGAATTT
807 TTTTTTTGAATTT
1 TTTTTTTGAATTT
820 ATTCTCTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (13 bp):
TTTTTTTGAATTT
Found at i:914 original size:10 final size:11
Alignment explanation
Indices: 899--927 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
889 CCAACTAAAT
899 TTTTTTTTGA-
1 TTTTTTTTGAC
909 TTTTTTTTGAC
1 TTTTTTTTGAC
920 TTTTTTTT
1 TTTTTTTT
928 CACATTTACG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.07, C:0.03, G:0.07, T:0.83
Consensus pattern (11 bp):
TTTTTTTTGAC
Found at i:8606 original size:23 final size:22
Alignment explanation
Indices: 8570--8630 Score: 56
Period size: 23 Copynumber: 2.9 Consensus size: 22
8560 AATGTGAAAC
**
8570 AGAAAGAATTGAAAAAGAAGTT
1 AGAAAGAAGAGAAAAAGAAGTT
*
8592 GAGAAAGAAGAGAAAATG-AGTT
1 -AGAAAGAAGAGAAAAAGAAGTT
*
8614 AGAAA-AAGA-ACAAAGAA
1 AGAAAGAAGAGAAAAAGAA
8631 AAGAAGAGGA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
19 4 0.12
20 5 0.16
21 5 0.16
22 4 0.12
23 14 0.44
ACGTcount: A:0.62, C:0.02, G:0.25, T:0.11
Consensus pattern (22 bp):
AGAAAGAAGAGAAAAAGAAGTT
Found at i:16355 original size:21 final size:22
Alignment explanation
Indices: 16305--16361 Score: 80
Period size: 21 Copynumber: 2.6 Consensus size: 22
16295 ACCTCTTTGA
*
16305 ACCATTACCATTTCGTACCAAAT
1 ACCA-TACCATTTCATACCAAAT
16328 ACCATACCATTTCATACC-AAT
1 ACCATACCATTTCATACCAAAT
*
16349 TCCATACCATTTC
1 ACCATACCATTTC
16362 GAGCCAATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 15 0.47
22 13 0.41
23 4 0.12
ACGTcount: A:0.33, C:0.33, G:0.02, T:0.32
Consensus pattern (22 bp):
ACCATACCATTTCATACCAAAT
Found at i:16368 original size:21 final size:20
Alignment explanation
Indices: 16310--16372 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 20
16300 TTTGAACCAT
*
16310 TACCATTTCGTACCAAATACCA
1 TACCATTTCG-ACC-AATTCCA
*
16332 TACCATTTCATACCAATTCCA
1 TACCATTTC-GACCAATTCCA
16353 TACCATTTCGAGCCAATTCC
1 TACCATTTCGA-CCAATTCC
16373 CAAATACCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
20 1 0.03
21 23 0.64
22 12 0.33
ACGTcount: A:0.32, C:0.33, G:0.05, T:0.30
Consensus pattern (20 bp):
TACCATTTCGACCAATTCCA
Found at i:17821 original size:22 final size:22
Alignment explanation
Indices: 17793--17836 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
17783 TTTTGAACCA
*
17793 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCATACCAAATCCC
*
17815 TTACCATTTCATACCAATTCCC
1 TTACCATTTCATACCAAATCCC
17837 AAATACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.27, C:0.36, G:0.02, T:0.34
Consensus pattern (22 bp):
TTACCATTTCATACCAAATCCC
Found at i:20686 original size:12 final size:12
Alignment explanation
Indices: 20671--20712 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
20661 AAAAAAAAAA
*
20671 AAAAAAAATTTG
1 AAAAAAAATTTC
*
20683 AAAAAAAAATTC
1 AAAAAAAATTTC
20695 AAAAAAAA--TC
1 AAAAAAAATTTC
20705 AAAAAAAA
1 AAAAAAAA
20713 AAAATTTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 10 0.36
12 18 0.64
ACGTcount: A:0.79, C:0.05, G:0.02, T:0.14
Consensus pattern (12 bp):
AAAAAAAATTTC
Found at i:20686 original size:24 final size:22
Alignment explanation
Indices: 20659--20716 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
20649 TAATTGAAAA
*
20659 AAAAAAAAAAAAAAAAAAAATTTG
1 AAAAAAAAAAAAAAAAAAAA--TC
***
20683 AAAAAAAAATTCAAAAAAAATC
1 AAAAAAAAAAAAAAAAAAAATC
20705 AAAAAAAAAAAA
1 AAAAAAAAAAAA
20717 TTTTGAAGAA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
22 10 0.37
24 17 0.63
ACGTcount: A:0.84, C:0.03, G:0.02, T:0.10
Consensus pattern (22 bp):
AAAAAAAAAAAAAAAAAAAATC
Found at i:20710 original size:39 final size:41
Alignment explanation
Indices: 20656--20732 Score: 113
Period size: 39 Copynumber: 1.9 Consensus size: 41
20646 TTGTAATTGA
20656 AAAAAAAAAAAAAAAAAAAAAAATTTGAA-AA-AAAAATTC
1 AAAAAAAAAAAAAAAAAAAAAAATTTGAAGAATAAAAATTC
** *
20695 AAAAAAAATCAAAAAAAAAAAATTTTGAAGAATAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAATTTGAAGAATAAAAA
20733 AAAAAGTGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 26 0.79
40 2 0.06
41 5 0.15
ACGTcount: A:0.79, C:0.03, G:0.04, T:0.14
Consensus pattern (41 bp):
AAAAAAAAAAAAAAAAAAAAAAATTTGAAGAATAAAAATTC
Found at i:20713 original size:11 final size:12
Alignment explanation
Indices: 20670--20713 Score: 56
Period size: 11 Copynumber: 3.8 Consensus size: 12
20660 AAAAAAAAAA
*
20670 AAAAAAAAATTTG
1 AAAAAAAAA-TTC
20683 AAAAAAAAATTC
1 AAAAAAAAATTC
20695 -AAAAAAAA-TC
1 AAAAAAAAATTC
20705 AAAAAAAAA
1 AAAAAAAAA
20714 AAATTTTGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 2 0.07
11 16 0.55
12 2 0.07
13 9 0.31
ACGTcount: A:0.80, C:0.05, G:0.02, T:0.14
Consensus pattern (12 bp):
AAAAAAAAATTC
Found at i:25350 original size:21 final size:21
Alignment explanation
Indices: 25324--25386 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
25314 TTGGTATTTG
*
25324 GGAATTGGTACAAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
25345 GGAATTGATATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
25366 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
25387 ACGGTTCAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
21 20 0.59
22 14 0.41
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:28047 original size:20 final size:20
Alignment explanation
Indices: 28022--28066 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
28012 GCGAAAATAC
*
28022 AAAAGAAAAGAAAAATGAAA
1 AAAAGAAAAGAAAAATCAAA
*
28042 AAAAG-AAAGAAAATTCAAA
1 AAAAGAAAAGAAAAATCAAA
28061 AAAAGA
1 AAAAGA
28067 GAATGAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.78, C:0.02, G:0.13, T:0.07
Consensus pattern (20 bp):
AAAAGAAAAGAAAAATCAAA
Found at i:28114 original size:14 final size:15
Alignment explanation
Indices: 28085--28114 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28075 AGAGAGCGAG
28085 AAAAGAAAAAGATGA
1 AAAAGAAAAAGATGA
28100 AAAAGAAAAAG-TGA
1 AAAAGAAAAAGATGA
28114 A
1 A
28115 TGAAAAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (15 bp):
AAAAGAAAAAGATGA
Found at i:30187 original size:30 final size:30
Alignment explanation
Indices: 30147--30219 Score: 105
Period size: 30 Copynumber: 2.5 Consensus size: 30
30137 CGAGTTTAAA
* *
30147 CTAAA-ATGAGCTAAGTTTTAGCTTGTGAG
1 CTAAATATGAGCTAAGGTTTAGCTCGTGAG
30176 CTAAAGT-TGAGCTAAGGTTTAGCTCGTGAG
1 CTAAA-TATGAGCTAAGGTTTAGCTCGTGAG
30206 CTAAATATGAGCTA
1 CTAAATATGAGCTA
30220 GGAGTGAGCT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
29 6 0.15
30 33 0.85
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.32
Consensus pattern (30 bp):
CTAAATATGAGCTAAGGTTTAGCTCGTGAG
Found at i:30230 original size:30 final size:30
Alignment explanation
Indices: 30166--30231 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
30156 GCTAAGTTTT
* * *
30166 AGCTTGTGAGCTAAAGTTGAGCTAAGGTTT
1 AGCTCGTGAGCTAAAGTTGAGCTAAGGGTG
30196 AGCTCGTGAGCTAAA-TATGAGCT-AGGAGTG
1 AGCTCGTGAGCTAAAGT-TGAGCTAAGG-GTG
30226 AGCTCG
1 AGCTCG
30232 GTTTAGCTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 4 0.13
30 27 0.87
ACGTcount: A:0.27, C:0.14, G:0.32, T:0.27
Consensus pattern (30 bp):
AGCTCGTGAGCTAAAGTTGAGCTAAGGGTG
Found at i:30798 original size:20 final size:20
Alignment explanation
Indices: 30773--30844 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
30763 TGTGGTTCAA
30773 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTTAG
* *
30793 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTTAG
* * *
30813 CTCATTCAAGCTCAATTTAA
1 CTCATTCGAGCTCAAGTTAG
30833 CTCATT-GAGCTC
1 CTCATTCGAGCTC
30845 GTTATTAGCT
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 5 0.11
20 39 0.89
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.32
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTTAG
Found at i:32584 original size:13 final size:12
Alignment explanation
Indices: 32554--32613 Score: 70
Period size: 12 Copynumber: 5.1 Consensus size: 12
32544 GTATTACGGT
*
32554 ATTGTAAAAAAA
1 ATTGAAAAAAAA
32566 A-T-AAAAAAAA
1 ATTGAAAAAAAA
*
32576 CTTGAAAAAAAA
1 ATTGAAAAAAAA
32588 ATTCGAAAAAAAA
1 ATT-GAAAAAAAA
*
32601 ATTCAAAAAAAA
1 ATTGAAAAAAAA
32613 A
1 A
32614 GTTTGTATTC
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
10 7 0.17
11 2 0.05
12 20 0.49
13 12 0.29
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.17
Consensus pattern (12 bp):
ATTGAAAAAAAA
Found at i:32703 original size:29 final size:29
Alignment explanation
Indices: 32658--32726 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 29
32648 AGTATTGAAG
* *
32658 AAAAAAAAGAAGAAAAAAAATTCGGAATTA
1 AAAAAAAAAAAGAAAAAAAATT-GAAATTA
*
32688 AAAAAAAAAAAGAAAAAAAATTGAAATTG
1 AAAAAAAAAAAGAAAAAAAATTGAAATTA
32717 AAAAAAAAAA
1 AAAAAAAAAA
32727 GAGTGATTGA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
29 15 0.42
30 21 0.58
ACGTcount: A:0.77, C:0.01, G:0.10, T:0.12
Consensus pattern (29 bp):
AAAAAAAAAAAGAAAAAAAATTGAAATTA
Found at i:33594 original size:17 final size:15
Alignment explanation
Indices: 33574--33612 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
33564 GCGAGCGAGA
33574 AAATGAACATGAAAAAG
1 AAATGAA-A-GAAAAAG
33591 AAATGAAAGAAAAAG
1 AAATGAAAGAAAAAG
33606 AAGATGA
1 AA-ATGA
33613 GTGGGAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.67, C:0.03, G:0.21, T:0.10
Consensus pattern (15 bp):
AAATGAAAGAAAAAG
Found at i:35118 original size:20 final size:20
Alignment explanation
Indices: 35093--35147 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
35083 TGTGGTTCAA
*
35093 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
35113 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
35133 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
35148 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:36957 original size:13 final size:12
Alignment explanation
Indices: 36927--36985 Score: 68
Period size: 12 Copynumber: 5.0 Consensus size: 12
36917 GTATTACGGT
*
36927 ATTGTAAAAAAA
1 ATTGAAAAAAAA
36939 A-T-AAAAAAAA
1 ATTGAAAAAAAA
*
36949 CTTGAAAAAAAA
1 ATTGAAAAAAAA
36961 ATTCGAAAAAAAA
1 ATT-GAAAAAAAA
*
36974 ATTCAAAAAAAA
1 ATTGAAAAAAAA
36986 GTTTATATTC
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
10 7 0.17
11 2 0.05
12 19 0.47
13 12 0.30
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.17
Consensus pattern (12 bp):
ATTGAAAAAAAA
Found at i:37057 original size:16 final size:13
Alignment explanation
Indices: 37026--37050 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
37016 ATTTAGTATT
37026 GAAGAAAAAAAAA
1 GAAGAAAAAAAAA
37039 GAAGAAAAAAAA
1 GAAGAAAAAAAA
37051 TTCAGAATTA
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
GAAGAAAAAAAAA
Found at i:37077 original size:26 final size:27
Alignment explanation
Indices: 37032--37094 Score: 85
Period size: 26 Copynumber: 2.3 Consensus size: 27
37022 TATTGAAGAA
37032 AAAAAAAGAAGAAAAAAAATTCAGAATT-
1 AAAAAAA-AAGAAAAAAAATTCA-AATTG
*
37060 AAAAAAAAAG-AAAAAAATTGAAATTG
1 AAAAAAAAAGAAAAAAAATTCAAATTG
37086 AAAAAAAAA
1 AAAAAAAAA
37095 AGAGTGATTG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
25 4 0.12
26 19 0.58
27 3 0.09
28 7 0.21
ACGTcount: A:0.76, C:0.02, G:0.10, T:0.13
Consensus pattern (27 bp):
AAAAAAAAAGAAAAAAAATTCAAATTG
Found at i:37095 original size:27 final size:27
Alignment explanation
Indices: 37031--37097 Score: 84
Period size: 27 Copynumber: 2.4 Consensus size: 27
37021 GTATTGAAGA
37031 AAAAAAAAGAAGAAAAAAAATTCAGAATT
1 AAAAAAAA-AAG-AAAAAAATTCAGAATT
*
37060 -AAAAAAAAAGAAAAAAATTGA-AATT
1 AAAAAAAAAAGAAAAAAATTCAGAATT
37085 GAAAAAAAAAAGA
1 -AAAAAAAAAAGA
37098 GTGATTGAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
25 4 0.11
26 10 0.29
27 14 0.40
28 7 0.20
ACGTcount: A:0.76, C:0.01, G:0.10, T:0.12
Consensus pattern (27 bp):
AAAAAAAAAAGAAAAAAATTCAGAATT
Found at i:37964 original size:17 final size:15
Alignment explanation
Indices: 37944--37982 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
37934 GCGAGCGAGA
37944 AAATGAACATGAAAAAG
1 AAATGAA-A-GAAAAAG
37961 AAATGAAAGAAAAAG
1 AAATGAAAGAAAAAG
37976 AAGATGA
1 AA-ATGA
37983 GTGGGAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.67, C:0.03, G:0.21, T:0.10
Consensus pattern (15 bp):
AAATGAAAGAAAAAG
Found at i:39487 original size:20 final size:20
Alignment explanation
Indices: 39462--39516 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
39452 TGTGGTTCAA
*
39462 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
39482 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
39502 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
39517 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:39881 original size:12 final size:12
Alignment explanation
Indices: 39864--39890 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
39854 TTTCAGCCGA
39864 ATTTATGAGCAT
1 ATTTATGAGCAT
39876 ATTTATGAGCAT
1 ATTTATGAGCAT
39888 ATT
1 ATT
39891 AAAACTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.44
Consensus pattern (12 bp):
ATTTATGAGCAT
Found at i:46085 original size:985 final size:990
Alignment explanation
Indices: 42786--47739 Score: 9423
Period size: 998 Copynumber: 5.0 Consensus size: 990
42776 ATAAGTGTTT
42786 TGATACGGGGTTACGCGCGGACCAAGATCGAGTTGCCAAGTCACGAGAAACTCCTACGAAAACCC
1 TGATACGGGGTTACGCGCGGACCAAGATCGAGTTGCCAAGTCACGAGAAACTCCTACGAAAACCC
42851 TAAACAATTAGATCTGAAACGAAACAGAAAATTAAAAGATTAGATTTTTGAATTTTCAGATCTGA
66 TAAACAATTAGATCTGAAACGAAACAGAAAATTAAAAGATTAGATTTTTGAATTTTCAGATCTGA
42916 AATAAAATCCCCAAATCAGCAAAGAATCAAATTGAGAATAGAAATAAGTGTTAGGGTTCTTGAAA
131 AATAAAATCCCCAAATCAGCAAAGAATCAAATTGAGAATAGAAATAAGTGTTAGGGTTCTTGAAA
*
42981 CCCTCAAGGAGATTGTGATTCTGTCCAATTGAACACCAAGATAGTTTTCCCCAAATTTCGACAAT
196 CCCTCAAGGAGATTGTGATTCTGCCCAATTGAACACCAAGATAGTTTTCCCCAAATTTCGACAAT
43046 CTAATTTCACCCAAAAAGAGTATGGAAAAACCCTAGAAATTGGGGATTTTTGGGCTGATTCCTTA
261 CTAATTTCACCCAAAAAGAGTATGGAAAAACCCTAGAAATTGGGGATTTTTGGGCTGATTCCTTA
*
43111 AGATAGAAAAAGGCTGAAAACACAATAAAAACAGAAAATAGATTAGATAATGATTCAGCACAAGT
326 AGATAGAAAAAGGCTGAAAACACAATAAGAACAGAAAATAGATTAGATAATGATTCAGCACAAGT
43176 AGAAATAAAGAAAGAATTGACAGTAAGAAATTAAAAGATAAGTCCTAAGAAGCCTTGAAATCTCG
391 AGAAATAAAGAAAGAATTGACAGTAAGAAATTAAAAGATAAGTCCTAAGAAGCCTTGAAATCTCG
43241 AAAGATCTCACAACTCCCTTCAAACGGCTCTAATCTCCCCTCCAAAGAATATCAATGGCAAGAAG
456 AAAGATCTCACAACTCCCTTCAAACGGCTCTAATCTCCCCTCCAAAGAATATCAATGGCAAGAAG
* *
43306 AAGGTTGAAGATGACTCCCACAATCACAAGATTGTTAAAACAACTTCTAAAGAAAACTCAAGAGA
521 AAGGTTGAAGATGGCTCCCACAATCACAAGATTGTTAAAACAACTTCTAAAGAAAACTC-AGAAA
43371 AAAATCTTGGAGAAAACTCAAAGAAAATTCTGCTCTCAACAAATCTGAAATTTTAATAATAATGA
585 AAAATCTTGGAGAAAACTCAAAGAAAATTCTGCTCTCAACAAATCTGAAATTTTAATAATAATGA
43436 TAAGTGTTTAACAAGGTGGACAGCCATGCCTTTAAATAGGCCTTATAACTAGTCCTAATCTAATT
650 TAAGTGTTTAACAAGGTGGACAGCCATGCCTTTAAATAGGCCTTATAACTAGTCCTAATCTAATT
43501 AGAAAACTAAAATAAAAAAACTCCTAATTATTTTAATATGGAAATTCGGTCAAAGGTCATTTTAT
715 AGAAAACTAAAATAAAAAAACTCCTAATTATTTTAATATGGAAATTCGGTCAAAGGTCATTTTAT
43566 CTGGGACTCTTGGACTGAATATTGACATAAAAATTTAAACTAAGTAAATAAATAAATAAATAAAT
780 CTGGGACTCTTGGACTGAATATTGACATAAAAATTTAAACTAAG----TAAATAAATAAATAAAT
43631 AAAAATAAAAATAAAACTTTACAACTTGGGCCACTTTGACAATTTGGCCTGATTTTCAACTAAGT
841 --AAATAAAAATAAAACTTTACAACTTGGGCCACTTTGACAATTTGGCCTGATTTTCAACTAAGT
43696 ATGGATGGATTTCTTGATTGGGCTGGGAATTTGCTTATTGGGCCTCGCCTTCAAGAATTTGGGCT
904 ATGGATGGATTTCTTGATTGGGC-GGGAATTTGCTTATTGGGCCTCGCCTTCAAGAATTTGGGCT
43761 TTTGTGACTCGTATCATTCTAAA
968 TTTGTGACTCGTATCATTCTAAA
*
43784 TGATACGGGGTTACGCGCGGACCAAGATCGAGTTGCCAAGTCACGAGAAACTACTACGAAAACCC
1 TGATACGGGGTTACGCGCGGACCAAGATCGAGTTGCCAAGTCACGAGAAACTCCTACGAAAACCC
43849 TAAACAATTAGATCTGAAACGAAACAGAAAATTAAAAGATTAGATTTTTGAATTTTCAGATCTGA
66 TAAACAATTAGATCTGAAACGAAACAGAAAATTAAAAGATTAGATTTTTGAATTTTCAGATCTGA
43914 AATAAAATCCCCAAATCAGCAAAGAATCAAATTGAGAATAGAAATAAGTGTTAGGGTTCTTGAAA
131 AATAAAATCCCCAAATCAGCAAAGAATCAAATTGAGAATAGAAATAAGTGTTAGGGTTCTTGAAA
43979 CCCTCAAGGAGATTGTGATTCTGCCCAATTGAACACCAAGATAGTTTTCCCCAAATTTCGACAAT
196 CCCTCAAGGAGATTGTGATTCTGCCCAATTGAACACCAAGATAGTTTTCCCCAAATTTCGACAAT
44044 CTAATTTCACCCAAAAAGAGTATGGAAAAACCCTAGAAATTGGGGATTTTTGGGCTGATTCCTTA
261 CTAATTTCACCCAAAAAGAGTATGGAAAAACCCTAGAAATTGGGGATTTTTGGGCTGATTCCTTA
44109 AGATAGAAAAAGGCTGAAAACACAATAAGAACAGAAAATAGATTAGATAATGATTCAGCACAAGT
326 AGATAGAAAAAGGCTGAAAACACAATAAGAACAGAAAATAGATTAGATAATGATTCAGCACAAGT
44174 AGAAATAAAGAAAGAATTGACAGTAAGAAATTAAAAGATAAGTCCTAAGAAGCCTTGAAATCTCG
391 AGAAATAAAGAAAGAATTGACAGTAAGAAATTAAAAGATAAGTCCTAAGAAGCCTTGAAATCTCG
44239 AAAGATCTCACAACTCCCTTCAAACGGCTCTAATCTCCCCTCCAAAGAATATCAATGGCAAGAAG
456 AAAGATCTCACAACTCCCTTCAAACGGCTCTAATCTCCCCTCCAAAGAATATCAATGGCAAGAAG
*
44304 AAGGTTGAAGATGGCTCCCACAATCACAAGATTGTTAAAACAACTTCTAAAGAAAACTCAAGAGA
521 AAGGTTGAAGATGGCTCCCACAATCACAAGATTGTTAAAACAACTTCTAAAGAAAACTC-AGAAA
44369 AAAATCTTGGAGAAAACTCAAAGAAAATTCTGCTCTCAACAAATCTGAAATTTTAATAATAATGA
585 AAAATCTTGGAGAAAACTCAAAGAAAATTCTGCTCTCAACAAATCTGAAATTTTAATAATAATGA
44434 TAAGTGTTTAACAAGGTGGACAGCCATGCCTTTAAATAGGCCTTATAACTAGTCCTAATCTAATT
650 TAAGTGTTTAACAAGGTGGACAGCCATGCCTTTAAATAGGCCTTATAACTAGTCCTAATCTAATT
*
44499 AGAAAACTAAAATAAAAAAGCTCCTAATTATTTTAATATGGAAATTCGGTCAAAGGTCATTTTAT
715 AGAAAACTAAAATAAAAAAACTCCTAATTATTTTAATATGGAAATTCGGTCAAAGGTCATTTTAT
*
44564 CTGGGACTCTTGGACTAAATATTGACATAAAAATTTAAACTAAG----TAAATAAATAAATAAAT
780 CTGGGACTCTTGGACTGAATATTGACATAAAAATTTAAACTAAGTAAATAAATAAATAAATAAAT
44625 AAAAATAAAACTTTACAACTTGGGCCACTTTGACAATTTGGCCTGATTTTCAACTAAGTATGGAT
845 AAAAATAAAACTTTACAACTTGGGCCACTTTGACAATTTGGCCTGATTTTCAACTAAGTATGGAT
44690 GGATTTCTTGATTGGGCTGGGAATTTGCTTATTGGGCCTCGCCTTCAAGAATTTGGGCTTTTGTG
910 GGATTTCTTGATTGGGC-GGGAATTTGCTTATTGGGCCTCGCCTTCAAGAATTTGGGCTTTTGTG
44755 ACTCGTATCATTCTAAA
974 ACTCGTATCATTCTAAA
44772 TGATACGGGGTTACGCGCGGACCAAGATCGAGTTGCCAAGTCACGAGAAACTCCTACGAAAACCC
1 TGATACGGGGTTACGCGCGGACCAAGATCGAGTTGCCAAGTCACGAGAAACTCCTACGAAAACCC
44837 TAAACAATTAGATCTGAAACGAAACAGAAAATTAAAAGATTAGATTTTTGAATTTTCAGATCTGA
66 TAAACAATTAGATCTGAAACGAAACAGAAAATTAAAAGATTAGATTTTTGAATTTTCAGATCTGA
44902 AATAAAATCCCCAAATCAGCAAAGAATCAAATTGAGAATAGAAATAAGTGTTAGGGTTCTTGAAA
131 AATAAAATCCCCAAATCAGCAAAGAATCAAATTGAGAATAGAAATAAGTGTTAGGGTTCTTGAAA
44967 CCCTCAAGGAGATTGTGATTCTGCCCAATTGAACACCAAGATAGTTTTCCCCAAATTTCGACAAT
196 CCCTCAAGGAGATTGTGATTCTGCCCAATTGAACACCAAGATAGTTTTCCCCAAATTTCGACAAT
* *
45032 CTAATTTCACCCAAAAAGAGTATGGAAAAACCCTAGAAATTGGGGATTTTTGGGCTCATTCTTTA
261 CTAATTTCACCCAAAAAGAGTATGGAAAAACCCTAGAAATTGGGGATTTTTGGGCTGATTCCTTA
* *
45097 AGATAGAAAAAGGCTGAAAACACAATAAAAATAGAAAATAGATTAGATAATGATTCAGCACAAGT
326 AGATAGAAAAAGGCTGAAAACACAATAAGAACAGAAAATAGATTAGATAATGATTCAGCACAAGT
45162 AGAAATAAAGAAAGAATTGACAGTAAGAAATTAAAAGATAAGTCCTAAGAAGCCTTGAAATCTCG
391 AGAAATAAAGAAAGAATTGACAGTAAGAAATTAAAAGATAAGTCCTAAGAAGCCTTGAAATCTCG
45227 AAAGATCTCACAACTCCCTTCAAACGGCTCTAATCTCCCCTCCAAAGAATATCAATGGCAAGAAG
456 AAAGATCTCACAACTCCCTTCAAACGGCTCTAATCTCCCCTCCAAAGAATATCAATGGCAAGAAG
45292 AAGGTTGAAGAT-GCTCCCACAATCACAAGATTGTTAAAACAACTTCTAAAGAAAACTCAGAAAA
521 AAGGTTGAAGATGGCTCCCACAATCACAAGATTGTTAAAACAACTTCTAAAGAAAACTCAGAAAA
45356 AAATCTTGGA-AAAACTCAAAGAAAATTCTGCTCTCAACAAATCTGAAATTTTAATAATAATGAT
586 AAATCTTGGAGAAAACTCAAAGAAAATTCTGCTCTCAACAAATCTGAAATTTTAATAATAATGAT
45420 AAGTGTTTAACAAGGTGGACAGCCATGCCTTTAAATAGG-CTTATAACTAGTCCTAATCTAATTA
651 AAGTGTTTAACAAGGTGGACAGCCATGCCTTTAAATAGGCCTTATAACTAGTCCTAATCTAATTA
45484 GAAAACTAAAATAAAAAAACTCCTAATTATTTTAATATGGAAATTC-GTCAAAGGTCATTTTATC
716 GAAAACTAAAATAAAAAAACTCCTAATTATTTTAATATGGAAATTCGGTCAAAGGTCATTTTATC
* *
45548 TAGGACTCTTGGACTAAATATTGACATAAAAATTTAAACTAAGTAAATAAATAAATAAATAAATA
781 TGGGACTCTTGGACTGAATATTGACATAAAAATTTAAACTAAGTAAATAAATAAATAAATAAATA
45613 AAAATAAAACTTTACAACTTGGGCCACTTTGACAATTTGGCCTGATTTTCAACTAAGTATGGATG
846 AAAATAAAACTTTACAACTTGGGCCACTTTGACAATTTGGCCTGATTTTCAACTAAGTATGGATG
*
45678 GATTTCTTGATTGGG-GAGAATTTGCTTATTGGGCCTCGCCTTCAAGAATTTGGGCTTTTGTGAC
911 GATTTCTTGATTGGGCGGGAATTTGCTTATTGGGCCTCGCCTTCAAGAATTTGGGCTTTTGTGAC
45742 TCGTATCATTCTAAA
976 TCGTATCATTCTAAA
* *
45757 TGATACGGGGTTACGCGCGGACCAAGATCAAGTTGCCAAGTCACGAGAAACTCCTACGAAGACCC
1 TGATACGGGGTTACGCGCGGACCAAGATCGAGTTGCCAAGTCACGAGAAACTCCTACGAAAACCC
*
45822 TAAACAATTAGATTTGAAACGAAACAGAAAATTAAAAGATTAGATTTTTGAATTTTCAGATCTGA
66 TAAACAATTAGATCTGAAACGAAACAGAAAATTAAAAGATTAGATTTTTGAATTTTCAGATCTGA
45887 AATAAAATCCCCAAATCAGCAAAGAATCAAATTGAGAATAGAAATAAGTGTTAGGGTTCTTGAAA
131 AATAAAATCCCCAAATCAGCAAAGAATCAAATTGAGAATAGAAATAAGTGTTAGGGTTCTTGAAA
45952 CCCTCAAGGAGATTGTGATTCTGCCCAATTGAACACCAAGATAGTTTTCCCCAAATTTCGACAAT
196 CCCTCAAGGAGATTGTGATTCTGCCCAATTGAACACCAAGATAGTTTTCCCCAAATTTCGACAAT
46017 CTAATTTCACCCAAAAAGAGTATGGAAAAACCCTAGAAATTGGGGATTTTTGGGCTGATTCCTTA
261 CTAATTTCACCCAAAAAGAGTATGGAAAAACCCTAGAAATTGGGGATTTTTGGGCTGATTCCTTA
46082 AGATAG-AAAAGGCTGAAAACACAATAAGAACAGAAAATAGATTAGATAATGATTCA-CACAAGT
326 AGATAGAAAAAGGCTGAAAACACAATAAGAACAGAAAATAGATTAGATAATGATTCAGCACAAGT
46145 AGAAATAAAGAAAGAATTGACAGTAAGAAATTAAAAGATAAGTCCTAAGAAGCCTTGAAATCTCG
391 AGAAATAAAGAAAGAATTGACAGTAAGAAATTAAAAGATAAGTCCTAAGAAGCCTTGAAATCTCG
46210 AAAGATCTCACAACTCCCTTCAAACGGCTCTAATCTCCCCTCCAAAGAATATCAATGGCAAGAAG
456 AAAGATCTCACAACTCCCTTCAAACGGCTCTAATCTCCCCTCCAAAGAATATCAATGGCAAGAAG
*
46275 AAGGTTGAAGATGGCTCCCACAATCACAAGATTGTTAAAACAACTTCTAAAGAAAACTCA-AGAG
521 AAGGTTGAAGATGGCTCCCACAATCACAAGATTGTTAAAACAACTTCTAAAGAAAACTCAGA-AA
46339 AAAATCTTGGAGAAAACTCAAAGAAAATTCTGCTCTCAACAAATCTGAAATTTTAATAATAATGA
585 AAAATCTTGGAGAAAACTCAAAGAAAATTCTGCTCTCAACAAATCTGAAATTTTAATAATAATGA
46404 TAAGTGTTTAACAAGGTGGACAGCCATGCCTTTAAATAGGCCTTATAACTAGTCCTAATCTAATT
650 TAAGTGTTTAACAAGGTGGACAGCCATGCCTTTAAATAGGCCTTATAACTAGTCCTAATCTAATT
46469 AGAAAACTAAAATAAAAAAAACTCCTAATTATTTTAATATGGAAATTCGGTCAAAGGTCATTTTA
715 AGAAAACTAAAAT-AAAAAAACTCCTAATTATTTTAATATGGAAATTCGGTCAAAGGTCATTTTA
46534 TCTGGGACTCTTGGACTGAATATTGACATAAAAATTTAAACTAAGTAAATAAATAAATAAATAAA
779 TCTGGGACTCTTGGACTGAATATTGACATAAAAATTTAAACTAAG----TAAATAAATAAATAAA
*
46599 TAAAAATAAAAATAAAACTTTACAACTTGGGCCACTTTGACAATTTGGCCTGATTTTCAACTATG
840 T--AAATAAAAATAAAACTTTACAACTTGGGCCACTTTGACAATTTGGCCTGATTTTCAACTAAG
46664 TATGGATGGATTTCTTGATTGGGCTGGGAATTTGCTTATTGGGCCTCGCCTTCAAGAATTTGGGC
903 TATGGATGGATTTCTTGATTGGGC-GGGAATTTGCTTATTGGGCCTCGCCTTCAAGAATTTGGGC
46729 TTTTGTGACTCGTATCATTCTAAA
967 TTTTGTGACTCGTATCATTCTAAA
46753 TGATACGGGGTTACGCGCGGACCAAGATCGAGTTGCCAAGTCACGAGAAACTCCTACGAAAACCC
1 TGATACGGGGTTACGCGCGGACCAAGATCGAGTTGCCAAGTCACGAGAAACTCCTACGAAAACCC
46818 TAAACAATTAGATCTGAAACGAAACAGAAAATTAAAAGATTAGATTTTTGAATTTTCAGATCTGA
66 TAAACAATTAGATCTGAAACGAAACAGAAAATTAAAAGATTAGATTTTTGAATTTTCAGATCTGA
46883 AATAAAATCCCCAAATCAGCAAAGAATCAAATTGAGAATAGAAATAAGTGTTAGGGTTCTTGAAA
131 AATAAAATCCCCAAATCAGCAAAGAATCAAATTGAGAATAGAAATAAGTGTTAGGGTTCTTGAAA
46948 CCCTCAAGGAGATTGTGATTCTGCCCAATTGAACACCAAGATAGTTTTCCCCAAATTTCGACAAT
196 CCCTCAAGGAGATTGTGATTCTGCCCAATTGAACACCAAGATAGTTTTCCCCAAATTTCGACAAT
47013 CTAATTTCACCCAAAAAGAGTATGGAAAAACCCTAGAAATTGGGGATTTTTGGGCTGATTCCTTA
261 CTAATTTCACCCAAAAAGAGTATGGAAAAACCCTAGAAATTGGGGATTTTTGGGCTGATTCCTTA
47078 AGATAGAAAAAGGCTGAAAACACAATAAGAACAGAAAATAGATTAGATAATGATTCAGCACAAGT
326 AGATAGAAAAAGGCTGAAAACACAATAAGAACAGAAAATAGATTAGATAATGATTCAGCACAAGT
47143 AGAAATAAAGAAAGAATTGACAGTAAGAAATTAAAAGATAAGTCCTAAGAAGCCTTGAAATCTCG
391 AGAAATAAAGAAAGAATTGACAGTAAGAAATTAAAAGATAAGTCCTAAGAAGCCTTGAAATCTCG
47208 AAAGATCTCACAACTCCCTTCAAACGGCTCTAATCTCCCCTCCAAAGAATATCAATGGCAAGAAG
456 AAAGATCTCACAACTCCCTTCAAACGGCTCTAATCTCCCCTCCAAAGAATATCAATGGCAAGAAG
*
47273 AAGGTTGAAGATGGCTCCCACAATCA-AAGATTGTTAAAACAACTTCTAAAGAAAACTCA-AGAG
521 AAGGTTGAAGATGGCTCCCACAATCACAAGATTGTTAAAACAACTTCTAAAGAAAACTCAGA-AA
47336 AAAATCTTGGAGAAAACTCAAAGAAAATTCTGCTCTCAACAAATCTGAAATTTTAATAATAATGA
585 AAAATCTTGGAGAAAACTCAAAGAAAATTCTGCTCTCAACAAATCTGAAATTTTAATAATAATGA
47401 TAAGTGTTTAACAAGGTGGACAGCCATGCCTTTAAATAGGCCTTATAACTAGTCCTAATCTAATT
650 TAAGTGTTTAACAAGGTGGACAGCCATGCCTTTAAATAGGCCTTATAACTAGTCCTAATCTAATT
47466 AGAAAACTAAAATAAAAAAAACTCCTAATTATTTTAATATGGAAATTCGGTCAAAGGTCATTTTA
715 AGAAAACTAAAAT-AAAAAAACTCCTAATTATTTTAATATGGAAATTCGGTCAAAGGTCATTTTA
47531 TCTGGGACTCTTGGACTGAATATTGACATAAAAATTTAAACTAAGTAAATAAATAAATAAATAAA
779 TCTGGGACTCTTGGACTGAATATTGACATAAAAATTTAAACTAAGTAAATAAATAAATAAATAAA
47596 TAAAAATAAAACTTTACAACTTGGGCCACTTTGACAATTTGGCCTGATTTTCAACTAAGTATGGA
844 TAAAAATAAAACTTTACAACTTGGGCCACTTTGACAATTTGGCCTGATTTTCAACTAAGTATGGA
47661 TGGATTTCTTGATTGGGCTGGGAATTTGCTTATTGGGCCTCGCCTTCAAGAATTTGGGCTTTTGT
909 TGGATTTCTTGATTGGGC-GGGAATTTGCTTATTGGGCCTCGCCTTCAAGAATTTGGGCTTTTGT
47726 GACTCGTATCATTC
973 GACTCGTATCATTC
47740 CCCCTTCCTC
Statistics
Matches: 3905, Mismatches: 31, Indels: 47
0.98 0.01 0.01
Matches are distributed among these distances:
983 210 0.05
984 177 0.05
985 575 0.15
986 52 0.01
987 178 0.05
988 737 0.19
990 13 0.00
991 146 0.04
992 17 0.00
993 17 0.00
994 84 0.02
996 391 0.10
997 327 0.08
998 981 0.25
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.27
Consensus pattern (990 bp):
TGATACGGGGTTACGCGCGGACCAAGATCGAGTTGCCAAGTCACGAGAAACTCCTACGAAAACCC
TAAACAATTAGATCTGAAACGAAACAGAAAATTAAAAGATTAGATTTTTGAATTTTCAGATCTGA
AATAAAATCCCCAAATCAGCAAAGAATCAAATTGAGAATAGAAATAAGTGTTAGGGTTCTTGAAA
CCCTCAAGGAGATTGTGATTCTGCCCAATTGAACACCAAGATAGTTTTCCCCAAATTTCGACAAT
CTAATTTCACCCAAAAAGAGTATGGAAAAACCCTAGAAATTGGGGATTTTTGGGCTGATTCCTTA
AGATAGAAAAAGGCTGAAAACACAATAAGAACAGAAAATAGATTAGATAATGATTCAGCACAAGT
AGAAATAAAGAAAGAATTGACAGTAAGAAATTAAAAGATAAGTCCTAAGAAGCCTTGAAATCTCG
AAAGATCTCACAACTCCCTTCAAACGGCTCTAATCTCCCCTCCAAAGAATATCAATGGCAAGAAG
AAGGTTGAAGATGGCTCCCACAATCACAAGATTGTTAAAACAACTTCTAAAGAAAACTCAGAAAA
AAATCTTGGAGAAAACTCAAAGAAAATTCTGCTCTCAACAAATCTGAAATTTTAATAATAATGAT
AAGTGTTTAACAAGGTGGACAGCCATGCCTTTAAATAGGCCTTATAACTAGTCCTAATCTAATTA
GAAAACTAAAATAAAAAAACTCCTAATTATTTTAATATGGAAATTCGGTCAAAGGTCATTTTATC
TGGGACTCTTGGACTGAATATTGACATAAAAATTTAAACTAAGTAAATAAATAAATAAATAAATA
AAAATAAAACTTTACAACTTGGGCCACTTTGACAATTTGGCCTGATTTTCAACTAAGTATGGATG
GATTTCTTGATTGGGCGGGAATTTGCTTATTGGGCCTCGCCTTCAAGAATTTGGGCTTTTGTGAC
TCGTATCATTCTAAA
Found at i:49002 original size:23 final size:22
Alignment explanation
Indices: 48950--49002 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
48940 TCCACGTCTT
*
48950 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
48972 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
48995 TTTCTTTT
1 TTTCTTTT
49003 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:51358 original size:4 final size:4
Alignment explanation
Indices: 51349--51376 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
51339 TTAAACTAAG
51349 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
51377 AATAAAACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:53508 original size:21 final size:21
Alignment explanation
Indices: 53459--53521 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
53449 TTTGAACCGT
* *
53459 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
* *
53481 CACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
53502 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
53522 CAAATACCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
21 24 0.69
22 11 0.31
ACGTcount: A:0.33, C:0.35, G:0.03, T:0.29
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:58557 original size:30 final size:29
Alignment explanation
Indices: 58523--58619 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 29
58513 AGCTCACTCC
*
58523 TAGCTCATAGTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTAGCTCACGAGCTAAACCT
* * * * *
58553 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTT-AGCTCACGAGCTAAACCT
* *
58583 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAAC-TTAGCTCACGAGCTAAACCT
58613 TAGCTCA
1 TAGCTCA
58620 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
29 3 0.06
30 46 0.90
31 2 0.04
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (29 bp):
TAGCTCAACTTAGCTCACGAGCTAAACCT
Found at i:59708 original size:93 final size:93
Alignment explanation
Indices: 59549--59723 Score: 341
Period size: 93 Copynumber: 1.9 Consensus size: 93
59539 GAACGTTTTT
*
59549 ATTATTGTGTGAACACCTAGATGTCGAATTTGAATGGTCATCTATGTGCCTATAAATATTTTAAT
1 ATTATTGTGTGAACACCTAGATGCCGAATTTGAATGGTCATCTATGTGCCTATAAATATTTTAAT
59614 ACATTTGTTTTCTTTCATTTGTGAAGGA
66 ACATTTGTTTTCTTTCATTTGTGAAGGA
59642 ATTATTGTGTGAACACCTAGATGCCGAATTTGAATGGTCATCTATGTGCCTATAAATATTTTAAT
1 ATTATTGTGTGAACACCTAGATGCCGAATTTGAATGGTCATCTATGTGCCTATAAATATTTTAAT
59707 ACATTTGTTTTCTTTCA
66 ACATTTGTTTTCTTTCA
59724 ATTAATCTGG
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 81 1.00
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.43
Consensus pattern (93 bp):
ATTATTGTGTGAACACCTAGATGCCGAATTTGAATGGTCATCTATGTGCCTATAAATATTTTAAT
ACATTTGTTTTCTTTCATTTGTGAAGGA
Found at i:60299 original size:23 final size:22
Alignment explanation
Indices: 60248--60299 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
60238 CCTCGTCTTT
*
60248 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
60270 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
60293 TTCTTTT
1 TTCTTTT
60300 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:61868 original size:10 final size:10
Alignment explanation
Indices: 61853--61887 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
61843 GCCCAAAATC
61853 TGATACCAAA
1 TGATACCAAA
**
61863 TGATACGGAA
1 TGATACCAAA
61873 TGATACCAAA
1 TGATACCAAA
61883 TGATA
1 TGATA
61888 GAGGGGTTGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.46, C:0.14, G:0.17, T:0.23
Consensus pattern (10 bp):
TGATACCAAA
Found at i:65158 original size:44 final size:45
Alignment explanation
Indices: 65052--65282 Score: 394
Period size: 45 Copynumber: 5.2 Consensus size: 45
65042 TCGGCCATGG
* * * *
65052 TGCTTCCTCAATTTGTTCCATAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
65097 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTC-AA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
65141 TGCTTCCTCAAATTCTTCCATGAATTATGCATGACGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
65186 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
65231 TGCTTCCTCAAATTC-TCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
65275 TGCTTCCT
1 TGCTTCCT
65283 TAATTTCATG
Statistics
Matches: 177, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
44 79 0.45
45 98 0.55
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.38
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
Found at i:65203 original size:89 final size:90
Alignment explanation
Indices: 65052--65282 Score: 394
Period size: 89 Copynumber: 2.6 Consensus size: 90
65042 TCGGCCATGG
* * * * *
65052 TGCTTCCTCAATTTGTTCCATAAATTATGCATGATGTTGGCCAAATGCTTCCTTAAATTCTTCCA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAATGCTTCCTCAAATTCTTCCA
65117 TGAATTATGCATGATGTTGGTC-AA
66 TGAATTATGCATGATGTTGGTCAAA
*
65141 TGCTTCCTCAAATTCTTCCATGAATTATGCATGACGTTGGTCAAATGCTTCCTCAAATTCTTCCA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAATGCTTCCTCAAATTCTTCCA
65206 TGAATTATGCATGATGTTGGTCAAA
66 TGAATTATGCATGATGTTGGTCAAA
65231 TGCTTCCTCAAATTC-TCCATGAATTATGCATGATGTTGGTCAAATGCTTCCT
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAATGCTTCCT
65283 TAATTTCATG
Statistics
Matches: 134, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
89 117 0.87
90 17 0.13
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.38
Consensus pattern (90 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAATGCTTCCTCAAATTCTTCCA
TGAATTATGCATGATGTTGGTCAAA
Found at i:68757 original size:20 final size:20
Alignment explanation
Indices: 68734--68780 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
68724 GGGTTAAGAT
*
68734 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
68754 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
68774 TGAGCTG
1 TGAGCTG
68781 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:71590 original size:18 final size:18
Alignment explanation
Indices: 71550--71589 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
71540 ACTCACAAGA
*
71550 CTTTTCACTTTTTTTGTT
1 CTTTTCACTTTTTTTCTT
*
71568 CTTTTTACTTTTTTTCTT
1 CTTTTCACTTTTTTTCTT
71586 -TTTT
1 CTTTT
71590 TGCTCACTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.05, C:0.15, G:0.03, T:0.78
Consensus pattern (18 bp):
CTTTTCACTTTTTTTCTT
Found at i:75330 original size:20 final size:20
Alignment explanation
Indices: 75307--75353 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
75297 GGGTTAAGAT
*
75307 TGAGCTGAATTAAGCTTGAG
1 TGAGCTGAATTAAGCTCGAG
* * *
75327 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTAAGCTCGAG
75347 TGAGCTG
1 TGAGCTG
75354 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTAAGCTCGAG
Done.