Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008636.1 Corchorus capsularis cultivar CVL-1 contig08657, 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: 98137
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32
Found at i:10806 original size:18 final size:18
Alignment explanation
Indices: 10749--10807 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
10739 CAAAGTTTGA
* *
10749 AAGAAAATGAAAAAAAAA
1 AAGAAAATGGAAAAAAAT
10767 AAGAAAA--G-AAAAAAT
1 AAGAAAATGGAAAAAAAT
10782 GAA-AAAATGGAAAAAAAT
1 -AAGAAAATGGAAAAAAAT
*
10800 TAGAAAAT
1 AAGAAAAT
10808 TAAAAGATGA
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
15 10 0.30
16 2 0.06
17 2 0.06
18 19 0.58
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (18 bp):
AAGAAAATGGAAAAAAAT
Found at i:13688 original size:23 final size:23
Alignment explanation
Indices: 13660--13721 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
13650 AAAGAGAGAA
*
13660 GAAAAATAAGAAAAAGGAAAAAGT
1 GAAAAAAAAGAAAAA-GAAAAAGT
13684 GAAAAAAAAGAAAAAGAAAAAG-
1 GAAAAAAAAGAAAAAGAAAAAGT
*
13706 AAAAAAGAAAGAAAAA
1 GAAAAA-AAAGAAAAA
13722 TCAAGTACGA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
22 5 0.14
23 16 0.46
24 14 0.40
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (23 bp):
GAAAAAAAAGAAAAAGAAAAAGT
Found at i:13697 original size:6 final size:6
Alignment explanation
Indices: 13667--13721 Score: 60
Period size: 6 Copynumber: 9.3 Consensus size: 6
13657 GAAGAAAAAT
** *
13667 AAGAAA AAGGAAA AAGTGA AA-AAA AAGAAA AAGAAA AAGAAA AA-AGA
1 AAGAAA AA-GAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
13714 AAGAAA AA
1 AAGAAA AA
13722 TCAAGTACGA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
5 7 0.17
6 27 0.68
7 6 0.15
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (6 bp):
AAGAAA
Found at i:13721 original size:30 final size:29
Alignment explanation
Indices: 13647--13721 Score: 80
Period size: 30 Copynumber: 2.6 Consensus size: 29
13637 AAATTCCCAT
* * *
13647 AAAAAAGAGAGAAGAAAAATAAGAAAAAGG
1 AAAAAAGAAAGAAAAAAAAAAAGAAAAA-G
* *
13677 AAAAAGTGAAA-AAAAAGAAAAAGAAAAAG
1 AAAAA-AGAAAGAAAAAAAAAAAGAAAAAG
13706 AAAAAAGAAAGAAAAA
1 AAAAAAGAAAGAAAAA
13722 TCAAGTACGA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
28 4 0.11
29 11 0.30
30 19 0.51
31 3 0.08
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.03
Consensus pattern (29 bp):
AAAAAAGAAAGAAAAAAAAAAAGAAAAAG
Found at i:16295 original size:35 final size:35
Alignment explanation
Indices: 16260--16523 Score: 282
Period size: 35 Copynumber: 7.5 Consensus size: 35
16250 TCCAACGCGA
** * *
16260 TCTTTCTACAGTGAATTTCAATTAACCCAGGGCGA
1 TCTTTCTACAGTTTATTTCAGTTAACCCAGGGCGG
*
16295 TCTTTCTTA-AGTTTATTTCAGTTGACCCAGGGCGG
1 TCTTTC-TACAGTTTATTTCAGTTAACCCAGGGCGG
* * * *
16330 TCTTTCTTCAGTTTATTTCAGTTGACCCAAGGTGG
1 TCTTTCTACAGTTTATTTCAGTTAACCCAGGGCGG
* *
16365 TCTTTCGACAGTTTATTTCAGTTAACCCAGGGAGG
1 TCTTTCTACAGTTTATTTCAGTTAACCCAGGGCGG
* * *
16400 TCTTTCGT-TAGTTTATTTCAGTTGACCTAGGGCGG
1 TCTTTC-TACAGTTTATTTCAGTTAACCCAGGGCGG
** *
16435 TCTTTCTTGAGTTTATTTCAGTTGACCCAGGGCGG
1 TCTTTCTACAGTTTATTTCAGTTAACCCAGGGCGG
* * * *
16470 TCTTTCGT-TAGTTTATTTTAGTTGACCCAGGGCAG
1 TCTTTC-TACAGTTTATTTCAGTTAACCCAGGGCGG
*
16505 TCTTTCTTCAGTTTATTTC
1 TCTTTCTACAGTTTATTTC
16524 GATCTTAAGT
Statistics
Matches: 198, Mismatches: 25, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
34 3 0.02
35 192 0.97
36 3 0.02
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (35 bp):
TCTTTCTACAGTTTATTTCAGTTAACCCAGGGCGG
Found at i:16358 original size:70 final size:70
Alignment explanation
Indices: 16274--16523 Score: 335
Period size: 70 Copynumber: 3.6 Consensus size: 70
16264 TCTACAGTGA
* *
16274 ATTTCAATTAACCCAGGGCGATCTTTCTTAAGTTTATTTCAGTTGACCCAGGGCGGTCTTTC-TT
1 ATTTCAGTTGACCCAGGGCGATCTTTCTTAAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCGTT
16338 CAGTTT
66 -AGTTT
* * * * * *
16344 ATTTCAGTTGACCCAAGGTGGTCTTTC-GACAGTTTATTTCAGTTAACCCAGGGAGGTCTTTCGT
1 ATTTCAGTTGACCCAGGGCGATCTTTCTTA-AGTTTATTTCAGTTGACCCAGGGCGGTCTTTCGT
16408 TAGTTT
65 TAGTTT
* * *
16414 ATTTCAGTTGACCTAGGGCGGTCTTTCTTGAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCGTT
1 ATTTCAGTTGACCCAGGGCGATCTTTCTTAAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCGTT
16479 AGTTT
66 AGTTT
* *
16484 ATTTTAGTTGACCCAGGGC-AGTCTTTCTTCAGTTTATTTC
1 ATTTCAGTTGACCCAGGGCGA-TCTTTCTTAAGTTTATTTC
16524 GATCTTAAGT
Statistics
Matches: 157, Mismatches: 19, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
69 1 0.01
70 154 0.98
71 2 0.01
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.41
Consensus pattern (70 bp):
ATTTCAGTTGACCCAGGGCGATCTTTCTTAAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCGTT
AGTTT
Found at i:16390 original size:105 final size:104
Alignment explanation
Indices: 16246--16523 Score: 360
Period size: 105 Copynumber: 2.6 Consensus size: 104
16236 TTTCAGTAAA
* * * * ** *
16246 TTGATCCAACGCGATCTTTCTACAGTGAATTTCAATTAACCCAGGGCGATCTTTCTTAAGTTTAT
1 TTGACCCAAGGCGGTCTTTCGACAGTTTATTTCAGTTAACCCAGGGCGATCTTTCTT-AGTTTAT
16311 TTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
65 TTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* * *
16351 TTGACCCAAGGTGGTCTTTCGACAGTTTATTTCAGTTAACCCAGGGAGGTCTTTCGTTAGTTTAT
1 TTGACCCAAGGCGGTCTTTCGACAGTTTATTTCAGTTAACCCAGGGCGATCTTTC-TTAGTTTAT
* *
16416 TTCAGTTGACCTAGGGCGGTCTTTCTTGAGTTTATTTCAG
65 TTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* ** * *
16456 TTGACCCAGGGCGGTCTTTCGTTAGTTTATTTTAGTTGACCCAGGGC-AGTCTTTCTTCAGTTTA
1 TTGACCCAAGGCGGTCTTTCGACAGTTTATTTCAGTTAACCCAGGGCGA-TCTTTCTT-AGTTTA
16520 TTTC
64 TTTC
16524 GATCTTAAGT
Statistics
Matches: 150, Mismatches: 20, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
104 2 0.01
105 146 0.97
106 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.40
Consensus pattern (104 bp):
TTGACCCAAGGCGGTCTTTCGACAGTTTATTTCAGTTAACCCAGGGCGATCTTTCTTAGTTTATT
TCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
Found at i:16938 original size:12 final size:13
Alignment explanation
Indices: 16921--16951 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
16911 GCAAAGCAAT
16921 TCTAAATC-TAAA
1 TCTAAATCTTAAA
16933 TCTAAATCTTAAA
1 TCTAAATCTTAAA
16946 TCTAAA
1 TCTAAA
16952 GCAATTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.35
Consensus pattern (13 bp):
TCTAAATCTTAAA
Found at i:16947 original size:7 final size:6
Alignment explanation
Indices: 16921--16951 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
16911 GCAAAGCAAT
16921 TCTAAA TCTAAA TCTAAA TCTTAAA TCTAAA
1 TCTAAA TCTAAA TCTAAA TC-TAAA TCTAAA
16952 GCAATTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.35
Consensus pattern (6 bp):
TCTAAA
Found at i:16964 original size:13 final size:13
Alignment explanation
Indices: 16948--16981 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
16938 ATCTTAAATC
16948 TAAAGCAATTTAA
1 TAAAGCAATTTAA
16961 TAAAGCAATTTAA
1 TAAAGCAATTTAA
16974 TAAAGCAA
1 TAAAGCAA
16982 ACAATAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.56, C:0.09, G:0.09, T:0.26
Consensus pattern (13 bp):
TAAAGCAATTTAA
Found at i:17900 original size:10 final size:10
Alignment explanation
Indices: 17885--17909 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
17875 GAGGACTCTA
17885 GAATTTTCTG
1 GAATTTTCTG
17895 GAATTTTCTG
1 GAATTTTCTG
17905 GAATT
1 GAATT
17910 GAGCAGGGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:18504 original size:20 final size:20
Alignment explanation
Indices: 18481--18519 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
18471 AAAATAGGGT
18481 AAAAACACATAAAAATAGCA
1 AAAAACACATAAAAATAGCA
** *
18501 AAAAGTATATAAAAATAGC
1 AAAAACACATAAAAATAGC
18520 TATAAAAATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.67, C:0.10, G:0.08, T:0.15
Consensus pattern (20 bp):
AAAAACACATAAAAATAGCA
Found at i:19087 original size:33 final size:33
Alignment explanation
Indices: 19035--19099 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
19025 AAAGAGTGCT
* *
19035 TTAGATGTTGTTTGCGATGATACTAAATCTGTG
1 TTAGATGTTGTTTGCGATGAAACAAAATCTGTG
* *
19068 TTAGGTGTTGTTTGTGATGAAACAAAATCTGT
1 TTAGATGTTGTTTGCGATGAAACAAAATCTGT
19100 TTTTGATGCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.26, C:0.08, G:0.25, T:0.42
Consensus pattern (33 bp):
TTAGATGTTGTTTGCGATGAAACAAAATCTGTG
Found at i:19588 original size:29 final size:29
Alignment explanation
Indices: 19546--19602 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
19536 TTCAAGGGGG
*
19546 AGGGAATGATGCGCCCAAG-GCTTATCATA
1 AGGGAATGATGCG-CCAAGTACTTATCATA
19575 AGGGAATGATGCGCCAAGTACTTATCAT
1 AGGGAATGATGCGCCAAGTACTTATCAT
19603 GGACTTGAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (29 bp):
AGGGAATGATGCGCCAAGTACTTATCATA
Found at i:19672 original size:18 final size:19
Alignment explanation
Indices: 19649--19686 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
19639 GTGCATGGGC
*
19649 TGCATGGAG-GCATGGAGA
1 TGCATGGAGACCATGGAGA
19667 TGCATGGAGACCATGGAGA
1 TGCATGGAGACCATGGAGA
19686 T
1 T
19687 AACGATGGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.29, C:0.13, G:0.39, T:0.18
Consensus pattern (19 bp):
TGCATGGAGACCATGGAGA
Found at i:45555 original size:17 final size:17
Alignment explanation
Indices: 45533--45566 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
45523 TCCAAGCCTC
45533 CAGGAGAAGACGAGCAA
1 CAGGAGAAGACGAGCAA
45550 CAGGAGAAGACGAGCAA
1 CAGGAGAAGACGAGCAA
45567 ACTCAGACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.18, G:0.35, T:0.00
Consensus pattern (17 bp):
CAGGAGAAGACGAGCAA
Found at i:48964 original size:53 final size:59
Alignment explanation
Indices: 48855--48982 Score: 151
Period size: 53 Copynumber: 2.3 Consensus size: 59
48845 ATATTCCACC
* * *
48855 TTTTTTATTAACTACCATTTTCTACCTTCCTCTTTTACTAATTACTCTTTGCTTACT-T
1 TTTTTTATTGATTACCATTTTCTACCTTCCTCTTTTACTAATTACCCTTTGCTTACTCT
* *
48913 TTTTTTATTGATTACCATTTT-TA-C-T-CT-TTTTACTGATTACCCTTTTCTTACTCT
1 TTTTTTATTGATTACCATTTTCTACCTTCCTCTTTTACTAATTACCCTTTGCTTACTCT
* *
48967 GTTTTTACTGATTACC
1 TTTTTTATTGATTACC
48983 CTTTGCTTAC
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
53 22 0.35
54 17 0.27
55 1 0.02
56 1 0.02
57 2 0.03
58 19 0.31
ACGTcount: A:0.18, C:0.22, G:0.04, T:0.56
Consensus pattern (59 bp):
TTTTTTATTGATTACCATTTTCTACCTTCCTCTTTTACTAATTACCCTTTGCTTACTCT
Found at i:48971 original size:29 final size:28
Alignment explanation
Indices: 48887--49043 Score: 144
Period size: 26 Copynumber: 5.6 Consensus size: 28
48877 TACCTTCCTC
* * * *
48887 TTTTACTAATTACTCTTTGCTTACTTTT
1 TTTTACTGATTACCCTTTTCTTACTCTT
* *
48915 TTTTATTGATTA-CCATTT-TTACTC-T
1 TTTTACTGATTACCCTTTTCTTACTCTT
48940 TTTTACTGATTACCCTTTTCTTACTCTGT
1 TTTTACTGATTACCCTTTTCTTACTCT-T
* *
48969 TTTTACTGATTACCCTTTGCTTACTTTTTT
1 TTTTACTGATTACCCTTTTCTTAC--TCTT
* *
48999 CTTTTACTGAATACCATTTT-TTACTC-T
1 -TTTTACTGATTACCCTTTTCTTACTCTT
*
49026 TTTTACTGATTAACCTTT
1 TTTTACTGATTACCCTTT
49044 ACTTTTTACC
Statistics
Matches: 105, Mismatches: 17, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
25 12 0.11
26 25 0.24
27 10 0.10
28 11 0.10
29 24 0.23
30 5 0.05
31 18 0.17
ACGTcount: A:0.18, C:0.20, G:0.05, T:0.57
Consensus pattern (28 bp):
TTTTACTGATTACCCTTTTCTTACTCTT
Found at i:49046 original size:82 final size:80
Alignment explanation
Indices: 48887--49042 Score: 213
Period size: 86 Copynumber: 1.9 Consensus size: 80
48877 TACCTTCCTC
* * *
48887 TTTTACTAATTACTCTTTGCTTACTTTTTTTTATTGATTACCATTTTTACTCTTTTTACTGATTA
1 TTTTACTAATTACCCTTTGCTTACTTTTTTTTACTGAATACCATTTTTACTCTTTTTACTGATTA
*
48952 CCCTTTTCTTACTCTGT
66 ACC--TTCTTACTCTGT
*
48969 TTTTACTGATTACCCTTTGCTTACTTTTTTCTTTTACTGAATACCATTTTTTACTCTTTTTACTG
1 TTTTACTAATTACCCTTTGCTTAC--TTTT-TTTTACTGAATACCA-TTTTTACTCTTTTTACTG
49034 ATTAACCTT
62 ATTAACCTT
49043 TACTTTTTAC
Statistics
Matches: 65, Mismatches: 5, Indels: 6
0.86 0.07 0.08
Matches are distributed among these distances:
82 22 0.34
84 6 0.09
85 13 0.20
86 24 0.37
ACGTcount: A:0.18, C:0.20, G:0.05, T:0.57
Consensus pattern (80 bp):
TTTTACTAATTACCCTTTGCTTACTTTTTTTTACTGAATACCATTTTTACTCTTTTTACTGATTA
ACCTTCTTACTCTGT
Found at i:49080 original size:36 final size:36
Alignment explanation
Indices: 49017--49196 Score: 213
Period size: 36 Copynumber: 4.9 Consensus size: 36
49007 GAATACCATT
49017 TTTTACTCTTTTTACTGATTAAC-CTTTACTTTTTACCA
1 TTTTACTC--TTTACTGATT-ACTCTTTACTTTTTACCA
* * *
49055 TATAACTCTTTACTAATTACTCTTTACTTTTTACCA
1 TTTTACTCTTTACTGATTACTCTTTACTTTTTACCA
* **
49091 TTTTACTATTTACTGATTAGC-CTTTACTTTTTAGTA
1 TTTTACTCTTTACTGATTA-CTCTTTACTTTTTACCA
* *
49127 TTTTACTCCTTACTGATTACTCTTTACTCTTTACCA
1 TTTTACTCTTTACTGATTACTCTTTACTTTTTACCA
*
49163 TTTT-TTCTTTACTGATTACTCTTTTACTTTTTAC
1 TTTTACTCTTTACTGATTACTC-TTTACTTTTTAC
49197 TGATTACCAT
Statistics
Matches: 121, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
35 18 0.15
36 96 0.79
37 1 0.01
38 6 0.05
ACGTcount: A:0.21, C:0.21, G:0.03, T:0.55
Consensus pattern (36 bp):
TTTTACTCTTTACTGATTACTCTTTACTTTTTACCA
Found at i:49198 original size:22 final size:21
Alignment explanation
Indices: 49170--49555 Score: 313
Period size: 22 Copynumber: 18.0 Consensus size: 21
49160 CCATTTTTTC
49170 TTTACTGATTACTCTTTTACTT
1 TTTACTGATTAC-CTTTTACTT
49192 TTTACTGATTACCATTTTACTCT
1 TTTACTGATTACC-TTTTACT-T
* *
49215 TTT-CTAATTACTATTTTACTT
1 TTTACTGATTAC-CTTTTACTT
49236 TTTACTGATTACCTTTTTACTT
1 TTTACTGATTACC-TTTTACTT
* **
49258 TTTACTGATTACC-ATGGCTT
1 TTTACTGATTACCTTTTACTT
* *
49278 CTTACTGATTA-CTATTACTT
1 TTTACTGATTACCTTTTACTT
* * *
49298 TCTACTGATTACTTTTTTAATT
1 TTTACTGATTAC-CTTTTACTT
49320 TTTACTGATTACCATTTTACTT
1 TTTACTGATTACC-TTTTACTT
* **
49342 TTTACTAATTACCATTTTACCC
1 TTTACTGATTACC-TTTTACTT
*
49364 TTTGCTGATTACCTTTTTACTCT
1 TTTACTGATTACC-TTTTACT-T
* *
49387 TTT-TTAATTACCATTTTACTT
1 TTTACTGATTACC-TTTTACTT
*
49408 TTCACTGATTACC-TTTACTT
1 TTTACTGATTACCTTTTACTT
* *
49428 TTTACTGATTACCACTTTGCTT
1 TTTACTGATTACC-TTTTACTT
* *
49450 TTTATTGATTGCCTTTTTTACTT
1 TTTACTGATTACC--TTTTACTT
* *
49473 TTTGCTGATTACC-ATTACTT
1 TTTACTGATTACCTTTTACTT
* * * *
49493 CTTACTGGTTA-CTATTACTC
1 TTTACTGATTACCTTTTACTT
49513 TTTACTGATTACCATTTT--TT
1 TTTACTGATTACC-TTTTACTT
*
49533 CTTTACTGATTACTTTTTACTT
1 -TTTACTGATTACCTTTTACTT
49555 T
1 T
49556 ACTCTTTACT
Statistics
Matches: 292, Mismatches: 52, Indels: 41
0.76 0.14 0.11
Matches are distributed among these distances:
19 2 0.01
20 81 0.28
21 22 0.08
22 164 0.56
23 23 0.08
ACGTcount: A:0.20, C:0.19, G:0.06, T:0.55
Consensus pattern (21 bp):
TTTACTGATTACCTTTTACTT
Found at i:49232 original size:44 final size:43
Alignment explanation
Indices: 49143--49582 Score: 331
Period size: 44 Copynumber: 10.3 Consensus size: 43
49133 TCCTTACTGA
* ** * *
49143 TTACTCTTTACTCTTTACCATTTTTTC-TTTACTGATTACTC-TT
1 TTACTTTTTACTGATTACC-TTTTTACTTTTTCTGATTAC-CATT
* * *
49186 TTACTTTTTACTGATTACCATTTTACTCTTTTCTAATTACTATT
1 TTACTTTTTACTGATTACCTTTTTACT-TTTTCTGATTACCATT
49230 TTACTTTTTACTGATTACCTTTTTACTTTTTACTGATTACCA--
1 TTACTTTTTACTGATTACCTTTTTACTTTTT-CTGATTACCATT
** * * * **
49272 TGGCTTCTTACTGATTA-C-TATTACTTTCTACTGATTACTTTT
1 TTACTTTTTACTGATTACCTTTTTACTTT-TTCTGATTACCATT
* * *
49314 TTAATTTTTACTGATTACCATTTTACTTTTTACTAATTACCATT
1 TTACTTTTTACTGATTACCTTTTTACTTTTT-CTGATTACCATT
** * * *
49358 TTACCCTTTGCTGATTACCTTTTTACTCTTTTTTAATTACCATT
1 TTACTTTTTACTGATTACCTTTTTACT-TTTTCTGATTACCATT
* *
49402 TTACTTTTCACTGATTACC--TTTACTTTTTACTGATTACCACT
1 TTACTTTTTACTGATTACCTTTTTACTTTTT-CTGATTACCATT
* * *
49444 TTGCTTTTTATTGATTGCCTTTTTTACTTTTTGCTGATTACCA--
1 TTACTTTTTACTGATTACC-TTTTTACTTTTT-CTGATTACCATT
* * * *
49487 TTACTTCTTACTGGTTA-C-TATTACTCTTTACTGATTACCATT
1 TTACTTTTTACTGATTACCTTTTTACT-TTTTCTGATTACCATT
* *
49529 TT--TTCTTTACTGATTA-CTTTTTACTTTACTCT--TTACTATT
1 TTACTT-TTTACTGATTACCTTTTTACTTT-TTCTGATTACCATT
49569 TT-CTTTTTACTGAT
1 TTACTTTTTACTGAT
49583 CTCTCTTTAT
Statistics
Matches: 317, Mismatches: 58, Indels: 47
0.75 0.14 0.11
Matches are distributed among these distances:
40 52 0.16
41 23 0.07
42 73 0.23
43 34 0.11
44 111 0.35
45 24 0.08
ACGTcount: A:0.20, C:0.20, G:0.05, T:0.55
Consensus pattern (43 bp):
TTACTTTTTACTGATTACCTTTTTACTTTTTCTGATTACCATT
Found at i:49240 original size:7 final size:7
Alignment explanation
Indices: 49071--49263 Score: 61
Period size: 7 Copynumber: 26.7 Consensus size: 7
49061 TCTTTACTAA
*
49071 TTACTCT
1 TTACTTT
49078 TTACTTT
1 TTACTTT
*
49085 TTACCATT
1 TTA-CTTT
*
49093 TTACTAT
1 TTACTTT
**
49100 TTACTGA
1 TTACTTT
*
49107 TTAGC-CT
1 TTA-CTTT
49114 TTACTTT
1 TTACTTT
*
49121 TTAGTATT
1 TTACT-TT
**
49129 TTACTCC
1 TTACTTT
**
49136 TTACTGA
1 TTACTTT
*
49143 TTACTCT
1 TTACTTT
*
49150 TTACTCT
1 TTACTTT
49157 TTACCATTT
1 TTA-C-TTT
*
49166 TT--TCT
1 TTACTTT
**
49171 TTACTGA
1 TTACTTT
49178 TTACTCTT
1 TTACT-TT
49186 TTACTTT
1 TTACTTT
**
49193 TTACTGA
1 TTACTTT
*
49200 TTACCATT
1 TTA-CTTT
49208 TTACTCTT
1 TTACT-TT
**
49216 TT-CTAA
1 TTACTTT
49222 TTACTATT
1 TTACT-TT
49230 TTACTTT
1 TTACTTT
**
49237 TTACTGA
1 TTACTTT
49244 TTACCTTT
1 TTA-CTTT
49252 TTACTTT
1 TTACTTT
49259 TTACT
1 TTACT
49264 GATTACCATG
Statistics
Matches: 135, Mismatches: 37, Indels: 28
0.68 0.19 0.14
Matches are distributed among these distances:
5 4 0.03
6 3 0.02
7 87 0.64
8 37 0.27
9 4 0.03
ACGTcount: A:0.20, C:0.20, G:0.04, T:0.57
Consensus pattern (7 bp):
TTACTTT
Found at i:49564 original size:19 final size:18
Alignment explanation
Indices: 49528--49574 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
49518 TGATTACCAT
*
49528 TTTTTCTTTACTGATTAC
1 TTTTTCTTTACTCATTAC
*
49546 TTTTTACTTTACTCTTTAC
1 TTTTT-CTTTACTCATTAC
49565 TATTTTCTTT
1 T-TTTTCTTT
49575 TTACTGATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 5 0.20
19 16 0.64
20 4 0.16
ACGTcount: A:0.15, C:0.17, G:0.02, T:0.66
Consensus pattern (18 bp):
TTTTTCTTTACTCATTAC
Found at i:49597 original size:40 final size:40
Alignment explanation
Indices: 49512--49704 Score: 124
Period size: 35 Copynumber: 5.0 Consensus size: 40
49502 TACTATTACT
** * *
49512 CTTTACTGATTACCATTTTTTCTTTACTGATTACTTTTTA
1 CTTTACTCTTTACTATTTTTTCTTTACTGATTACTCTTTA
49552 CTTTACTCTTTACTATTTTCTT-TTTACTGATCT-CTCTTTA
1 CTTTACTCTTTACTATTTT-TTCTTTACTGAT-TACTCTTTA
* * ** *
49592 TTTTACTCTTTACT-CTTTACCATTTTACTAATTACTC-TT-
1 CTTTACTCTTTACTATTTTTTC--TTTACTGATTACTCTTTA
* * * *
49631 C---ATTCTTTACCATTTTTCCTTTACTAATTACTC-TT-
1 CTTTACTCTTTACTATTTTTTCTTTACTGATTACTCTTTA
* *
49666 C---ATTCTTTACTATTTTTCCTTTACTGATTACTCTTTA
1 CTTTACTCTTTACTATTTTTTCTTTACTGATTACTCTTTA
49703 CT
1 CT
49705 CTTTACCATT
Statistics
Matches: 127, Mismatches: 16, Indels: 22
0.77 0.10 0.13
Matches are distributed among these distances:
35 47 0.37
36 10 0.08
37 6 0.05
39 3 0.02
40 47 0.37
41 14 0.11
ACGTcount: A:0.19, C:0.22, G:0.02, T:0.57
Consensus pattern (40 bp):
CTTTACTCTTTACTATTTTTTCTTTACTGATTACTCTTTA
Found at i:49605 original size:7 final size:7
Alignment explanation
Indices: 49552--49710 Score: 53
Period size: 7 Copynumber: 22.9 Consensus size: 7
49542 TTACTTTTTA
49552 CTTTACT
1 CTTTACT
49559 CTTTACT
1 CTTTACT
* *
49566 ATTTTCT
1 CTTTACT
*
49573 TTTTACT
1 CTTTACT
* *
49580 GATCT-CT
1 -CTTTACT
49587 CTTTA-T
1 CTTTACT
49593 -TTTACT
1 CTTTACT
49599 CTTTACT
1 CTTTACT
49606 CTTTAC-
1 CTTTACT
49612 CATTTTACT
1 C--TTTACT
**
49621 AATTACT
1 CTTTACT
* *
49628 CTTCATT
1 CTTTACT
49635 CTTTAC-
1 CTTTACT
*
49641 CATTT-TT
1 C-TTTACT
49648 CCTTTACT
1 -CTTTACT
**
49656 AATTACT
1 CTTTACT
* *
49663 CTTCATT
1 CTTTACT
49670 CTTTACT
1 CTTTACT
* *
49677 ATTT-TT
1 CTTTACT
49683 CCTTTACT
1 -CTTTACT
**
49691 GATTACT
1 CTTTACT
49698 CTTTACT
1 CTTTACT
49705 CTTTAC
1 CTTTAC
49711 CATTTTTCTT
Statistics
Matches: 105, Mismatches: 34, Indels: 26
0.64 0.21 0.16
Matches are distributed among these distances:
5 4 0.04
6 7 0.07
7 84 0.80
8 10 0.10
ACGTcount: A:0.18, C:0.24, G:0.01, T:0.57
Consensus pattern (7 bp):
CTTTACT
Found at i:49656 original size:35 final size:35
Alignment explanation
Indices: 49615--49718 Score: 172
Period size: 35 Copynumber: 3.0 Consensus size: 35
49605 TCTTTACCAT
49615 TTTACTAATTACTCTTCATTCTTTACCATTTTTCC
1 TTTACTAATTACTCTTCATTCTTTACCATTTTTCC
*
49650 TTTACTAATTACTCTTCATTCTTTACTATTTTTCC
1 TTTACTAATTACTCTTCATTCTTTACCATTTTTCC
* * *
49685 TTTACTGATTACTCTTTACTCTTTACCATTTTTC
1 TTTACTAATTACTCTTCATTCTTTACCATTTTTC
49719 TTCGCTGATT
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 64 1.00
ACGTcount: A:0.19, C:0.24, G:0.01, T:0.56
Consensus pattern (35 bp):
TTTACTAATTACTCTTCATTCTTTACCATTTTTCC
Found at i:49785 original size:20 final size:20
Alignment explanation
Indices: 49747--49855 Score: 87
Period size: 22 Copynumber: 5.3 Consensus size: 20
49737 CTGATCACTG
49747 ATTACTATTACTC-TTACTA
1 ATTACTATTACTCTTTACTA
49766 ATTACTATTACTCTTTACTA
1 ATTACTATTACTCTTTACTA
* ** *
49786 ATTACCATTTTTCCTTTTACTG
1 ATTACTATTACT-C-TTTACTA
* * *
49808 ATCA-TCATTACTTTTTACTG
1 ATTACT-ATTACTCTTTACTA
*
49828 ATTACTATTTTACTCTTTTCTA
1 ATTACTA--TTACTCTTTACTA
49850 ATTACT
1 ATTACT
49856 CTGATTATCA
Statistics
Matches: 70, Mismatches: 13, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
19 13 0.19
20 26 0.37
21 2 0.03
22 29 0.41
ACGTcount: A:0.26, C:0.20, G:0.02, T:0.52
Consensus pattern (20 bp):
ATTACTATTACTCTTTACTA
Found at i:50896 original size:12 final size:12
Alignment explanation
Indices: 50879--50924 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
50869 AGATCGTGCA
50879 TCTCTCTCCTCT
1 TCTCTCTCCTCT
*
50891 TCTCTCTCCTCC
1 TCTCTCTCCTCT
*
50903 TCTTTCTCCTCCT
1 TCTCTCTCCT-CT
50916 TCT-TCTCCT
1 TCTCTCTCCT
50925 TCAAACCGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
12 26 0.87
13 4 0.13
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (12 bp):
TCTCTCTCCTCT
Found at i:51176 original size:18 final size:17
Alignment explanation
Indices: 51149--51182 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
51139 AAAAGTCCAT
51149 CCTTTCCCCTTCCTTTCC
1 CCTTTCCCCTT-CTTTCC
*
51167 CCTTTTCCCTTCTTTC
1 CCTTTCCCCTTCTTTC
51183 AAAACCCATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (17 bp):
CCTTTCCCCTTCTTTCC
Found at i:53534 original size:23 final size:22
Alignment explanation
Indices: 53504--53552 Score: 80
Period size: 23 Copynumber: 2.2 Consensus size: 22
53494 TTATGAACGC
*
53504 AATTTACTAAATGCCAAAGAGTG
1 AATTTACTAAATGCCAAA-AGTA
53527 AATTTACTAAATGCCAAAAGTA
1 AATTTACTAAATGCCAAAAGTA
53549 AATT
1 AATT
53553 AGAAAATGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 7 0.28
23 18 0.72
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (22 bp):
AATTTACTAAATGCCAAAAGTA
Found at i:61999 original size:177 final size:177
Alignment explanation
Indices: 61690--62016 Score: 496
Period size: 177 Copynumber: 1.8 Consensus size: 177
61680 TTTGCCTCCG
*
61690 TTCGTCTAAAATTGTTGATGTGTCCAAAAAATGCCACGTCAGCAATTCTTGGACAGAAATTATTT
1 TTCGTCTAAAATTGTTGATGTGTCCAAAAAATGCCACGTCAGCAATTCTTGAACAGAAATTATTT
** * * *
61755 TGATTTTGATAGTTTCAAGGTAAAAGTTTGAAATTAAAAATTTAAGGGGAATTTTGTCCCAATTT
66 TGATTTTGATAGTTTCAAGGTAAAAGTTCCAAATTAAAAATTTAAGAGCAATTTTATCCCAATTT
*
61820 TGATACTTAAAGGACTGAAAGTTCATTCCAAAACAAAAGTTCCTTCA
131 TGATAATTAAAGGACTGAAAGTTCATTCCAAAACAAAAGTTCCTTCA
* * * * *
61867 TTCGTCTAAAATTGTTGTTGTG-CCTAAAAAATGCCACGTTAGCATTTCTTGAAGAGAGATTATT
1 TTCGTCTAAAATTGTTGATGTGTCC-AAAAAATGCCACGTCAGCAATTCTTGAACAGAAATTATT
* *
61931 TTGATTTTGATAGTTTC-AGGTTAAAAGTTCCAAATTAAAAGTTTAAGAGCAATTTTATCCCGAT
65 TTGATTTTGATAGTTTCAAGG-TAAAAGTTCCAAATTAAAAATTTAAGAGCAATTTTATCCCAAT
61995 TTTGATAATTAAAGGACTGAAA
129 TTTGATAATTAAAGGACTGAAA
62017 ATTGCAAATC
Statistics
Matches: 134, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
176 5 0.04
177 129 0.96
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.36
Consensus pattern (177 bp):
TTCGTCTAAAATTGTTGATGTGTCCAAAAAATGCCACGTCAGCAATTCTTGAACAGAAATTATTT
TGATTTTGATAGTTTCAAGGTAAAAGTTCCAAATTAAAAATTTAAGAGCAATTTTATCCCAATTT
TGATAATTAAAGGACTGAAAGTTCATTCCAAAACAAAAGTTCCTTCA
Found at i:65828 original size:29 final size:32
Alignment explanation
Indices: 65760--65828 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 32
65750 TTAGAACATC
* * *
65760 CCTTGTACTGAATAAAATTGTTCAATTTCATT
1 CCTTGTACTGAATAAAAGTGGTCAATTTCAGT
*
65792 CC-TATACT-AA-AAAAGTGGTCAATTT-AGT
1 CCTTGTACTGAATAAAAGTGGTCAATTTCAGT
65820 CCTTGTACT
1 CCTTGTACT
65829 CATTAGATAG
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
28 4 0.13
29 18 0.58
30 2 0.06
31 5 0.16
32 2 0.06
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (32 bp):
CCTTGTACTGAATAAAAGTGGTCAATTTCAGT
Found at i:69099 original size:19 final size:20
Alignment explanation
Indices: 69056--69100 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
69046 CACGCTACAT
*
69056 ATGTACCAAAAAGTCGTGCCAC
1 ATGTACCAAAAA--CGTGACAC
69078 ATGTACCAAAAA-GTGACAC
1 ATGTACCAAAAACGTGACAC
69097 ATGT
1 ATGT
69101 CACGCCACGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 10 0.45
22 12 0.55
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (20 bp):
ATGTACCAAAAACGTGACAC
Found at i:69105 original size:55 final size:53
Alignment explanation
Indices: 69018--69122 Score: 138
Period size: 55 Copynumber: 1.9 Consensus size: 53
69008 GACGTGGCAC
* ** *
69018 GCCACGTGTACCAAAAAGTGACATGTGGCACGCTACATATGTACCAAAAAGTCGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGC--CACATGTACCAAAAAGTCGT
* *
69073 GCCACATGTACCAAAAAGTGACACATGTCACGCCACGTGTACCAAAAAGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGT
69123 GACACGTGGC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
53 15 0.34
55 29 0.66
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.18
Consensus pattern (53 bp):
GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTCGT
Found at i:69139 original size:31 final size:31
Alignment explanation
Indices: 69072--69171 Score: 128
Period size: 31 Copynumber: 3.2 Consensus size: 31
69062 CAAAAAGTCG
* *
69072 TGCCACATGTACCAAAAAGTGACACATGTCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
* *
69103 CGCCACGTGTACCAAAAAGTGACACGTGGCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
* * *
69134 TGCCACATGTTTCAAAAAAATGACACGTGGCA
1 TGCCACATG-TACCAAAAAGTGACACGTGGCA
69166 TGCCAC
1 TGCCAC
69172 GTGCACAAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
31 34 0.58
32 25 0.42
ACGTcount: A:0.35, C:0.27, G:0.20, T:0.18
Consensus pattern (31 bp):
TGCCACATGTACCAAAAAGTGACACGTGGCA
Found at i:70740 original size:75 final size:75
Alignment explanation
Indices: 70661--70839 Score: 202
Period size: 75 Copynumber: 2.4 Consensus size: 75
70651 AATGCTCAAA
*
70661 ATTTGAATTCGAATCAGAAACCTGATAAAGTGAATCAGCTACAAGATGTTG-CAAATCATCATCA
1 ATTTGAATTCGAATCAGAAACCTGATAAAGTGAATCAGCTACAAGATGTTGCCAAA-CACCATCA
*
70725 GAAAACTTAGT
65 GAAAACTCAGT
* * * * * * * *
70736 ATTTGAATTCAAAACAGGAAA-CTGATCAGGTGAATCATCTTCAAGATTTTGCCTAACACCATCA
1 ATTTGAATTCGAATCA-GAAACCTGATAAAGTGAATCAGCTACAAGATGTTGCCAAACACCATCA
*
70800 GAAAACTCATT
65 GAAAACTCAGT
* *
70811 ATTTGAATTCGAATTAGCAACCTGA-AAAG
1 ATTTGAATTCGAATCAGAAACCTGATAAAG
70840 GAGAGTCACC
Statistics
Matches: 84, Mismatches: 17, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
74 5 0.06
75 72 0.86
76 7 0.08
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.27
Consensus pattern (75 bp):
ATTTGAATTCGAATCAGAAACCTGATAAAGTGAATCAGCTACAAGATGTTGCCAAACACCATCAG
AAAACTCAGT
Found at i:74973 original size:88 final size:87
Alignment explanation
Indices: 74773--74997 Score: 382
Period size: 88 Copynumber: 2.6 Consensus size: 87
74763 AAGTTGTTAA
*
74773 AATAATAATGAGAATATTT-TCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGA
1 AATAGTAATGAGAATATTTCTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGA
*
74837 AATAAATAAATAATAAAGATTG
66 AATAAATAAACAATAAAGATTG
74859 AATAGTAATGAGAATATTTCTCTAAATCTTGCCAAATTGTGGGAGATTTACGG-GATATTTTAAG
1 AATAGTAATGAGAATATTTCTCTAAATCTTGCCAAATTGTGGGAGATTTA-GGAGATATTTTAAG
74923 AAAATAAATAAACAATAAAGATTG
65 -AAATAAATAAACAATAAAGATTG
* *
74947 AATAGTAATGAGAATATTTCTTTAAATCTTGCCAAACTGTGGGAGATTTAG
1 AATAGTAATGAGAATATTTCTCTAAATCTTGCCAAATTGTGGGAGATTTAG
74998 AAAATATAAA
Statistics
Matches: 132, Mismatches: 4, Indels: 5
0.94 0.03 0.04
Matches are distributed among these distances:
86 18 0.14
87 42 0.32
88 72 0.55
ACGTcount: A:0.42, C:0.07, G:0.17, T:0.33
Consensus pattern (87 bp):
AATAGTAATGAGAATATTTCTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGA
AATAAATAAACAATAAAGATTG
Found at i:76733 original size:21 final size:21
Alignment explanation
Indices: 76709--76749 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
76699 ATTGAGACAA
76709 TCACAAGAAGAAATGAGGCAT
1 TCACAAGAAGAAATGAGGCAT
*
76730 TCACAAGAAGAGATGAGGCA
1 TCACAAGAAGAAATGAGGCA
76750 AGAACAAGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.46, C:0.15, G:0.27, T:0.12
Consensus pattern (21 bp):
TCACAAGAAGAAATGAGGCAT
Found at i:76756 original size:21 final size:21
Alignment explanation
Indices: 76711--76757 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
76701 TGAGACAATC
***
76711 ACAAGAAGAAATGAGGCATTC
1 ACAAGAAGAAATGAGGCAAGA
*
76732 ACAAGAAGAGATGAGGCAAGA
1 ACAAGAAGAAATGAGGCAAGA
76753 ACAAG
1 ACAAG
76758 GCGTTATAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.51, C:0.13, G:0.28, T:0.09
Consensus pattern (21 bp):
ACAAGAAGAAATGAGGCAAGA
Found at i:82424 original size:30 final size:32
Alignment explanation
Indices: 82389--82451 Score: 112
Period size: 30 Copynumber: 2.0 Consensus size: 32
82379 TTGAGGTTTC
82389 AAAAAATGATGAAAAAAAA-A-AGAAAAGTTA
1 AAAAAATGATGAAAAAAAAGAGAGAAAAGTTA
82419 AAAAAATGATGAAAAAAAAGAGAGAAAAGTTA
1 AAAAAATGATGAAAAAAAAGAGAGAAAAGTTA
82451 A
1 A
82452 TGGGGGTCAC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 19 0.61
31 1 0.03
32 11 0.35
ACGTcount: A:0.71, C:0.00, G:0.16, T:0.13
Consensus pattern (32 bp):
AAAAAATGATGAAAAAAAAGAGAGAAAAGTTA
Found at i:83308 original size:35 final size:35
Alignment explanation
Indices: 83269--83768 Score: 835
Period size: 35 Copynumber: 14.3 Consensus size: 35
83259 GTGCAGTCAC
83269 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
83304 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
*
83339 TTTCAAGAAGTTTTCAAAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
* *
83374 TTTCAAGAAGTTTTCAAAGGTCAGAGTTCATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
83409 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
83444 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
* *
83479 TATCAAGAAGTTTTCAAAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
*
83514 TATCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
*
83549 TTCCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
*
83584 TTCCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
* *
83619 TATCAAGAAGTTTTCAGAGGTCAGGGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
83654 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
*
83689 TATCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
* * *
83724 TTTCAAGAAATTCTC-GATGATCAGAGTTGATC-CA
1 TTTCAAGAAGTTTTCAGA-GGTCAGAGTTGATCTCA
*
83758 GTT-AAGAAGTT
1 TTTCAAGAAGTT
83769 CACAAGCGGA
Statistics
Matches: 443, Mismatches: 21, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
33 7 0.02
34 6 0.01
35 430 0.97
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (35 bp):
TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
Found at i:86987 original size:11 final size:11
Alignment explanation
Indices: 86971--87005 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
86961 TTTTTCTATT
86971 TTTTGTTTTTG
1 TTTTGTTTTTG
*
86982 TTTTGTTTTTA
1 TTTTGTTTTTG
*
86993 CTTTGTTTTTG
1 TTTTGTTTTTG
87004 TT
1 TT
87006 GCGCTGTCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.03, C:0.03, G:0.14, T:0.80
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:92058 original size:1 final size:1
Alignment explanation
Indices: 92052--92103 Score: 50
Period size: 1 Copynumber: 52.0 Consensus size: 1
92042 TAAGAAAAGT
* * ** **
92052 AAAAAAAAAAAAAAAAGAAAAAAAGAAAAAAATGAAAAAAATGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
92104 GGTTGACATA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.88, C:0.00, G:0.08, T:0.04
Consensus pattern (1 bp):
A
Found at i:92082 original size:26 final size:26
Alignment explanation
Indices: 92037--92101 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 26
92027 GGAGAAGGCG
*
92037 AAAGATAAGAAAAGTAAAAAAAAAAAAA
1 AAAGA-AA-AAAAGAAAAAAAAAAAAAA
**
92065 AAAGAAAAAAAGAAAAAAATGAAAAA
1 AAAGAAAAAAAGAAAAAAAAAAAAAA
*
92091 AATGAAAAAAA
1 AAAGAAAAAAA
92102 AAGGTTGACA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 26 0.79
27 2 0.06
28 5 0.15
ACGTcount: A:0.83, C:0.00, G:0.11, T:0.06
Consensus pattern (26 bp):
AAAGAAAAAAAGAAAAAAAAAAAAAA
Found at i:92412 original size:31 final size:31
Alignment explanation
Indices: 92361--92432 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
92351 TTTGGTTAAT
*
92361 TAAGTCCCAAACATTACAAAATCGACTCAAA
1 TAAGTCCCTAACATTACAAAATCGACTCAAA
* * * *
92392 TCAGTCCCTAACGTTGCAAAATCGGCTCAAA
1 TAAGTCCCTAACATTACAAAATCGACTCAAA
92423 TAAGTCCCTA
1 TAAGTCCCTA
92433 GACTCAATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.39, C:0.28, G:0.11, T:0.22
Consensus pattern (31 bp):
TAAGTCCCTAACATTACAAAATCGACTCAAA
Found at i:94426 original size:364 final size:362
Alignment explanation
Indices: 93727--94444 Score: 1274
Period size: 364 Copynumber: 2.0 Consensus size: 362
93717 AAAAAGGTGT
*
93727 TGATTACAGCGAATAAAAGATAAGACGAGCGTGATTGAAGGAAATTGATTAAAGTTACACCGGAG
1 TGATTACAGCGAATAAAAGATAAGACGAGCGTGATTGAAGGAAATTGATTAAAGTCACACCGGAG
* *
93792 CATTTAATGAACAACGGTAAATAAAGTTTTTTAATAAAGCTAATGAATGAACAACAAATTGTTAT
66 CATTTAATAAACAACGGTAAATAAAGGTTTTTAATAAAGCTAATGAATGAACAACAAATTGTTAT
93857 TCGACTAAAAGTGATTGAAACTGATTACAATCAAAGGAAACAAGGTAGACAAGATTGAAAGTATT
131 TCGACTAAAAGTGATTGAAACTGATTACAATCAAAGGAAACAAGGTAGACAAGATTGAAAGTATT
*
93922 GAGAAAATTGAGAAACTCATGGTTTCAGAGAAAAATAAGTATGAAATTTGCAGAGAAAAGCACGG
196 GAGAAAATTGAGAAACTCATGGTTTCAGAGAAAAATAAGTATGAAATTTGCAGAGAAAAGCACGA
* * * * * *
93987 AGGTTGAGTTTTGCGTTGGGTAGAGTTTTTCCGGAGAAGTGTTGTGTGTCTGGAAGCAGGTGGCA
261 AGCTTGAGTTTTGCGTTGGGTAGAGTTTTCCCAGAGAAATGTTGTGTGTCTGAAAGCAGGGGGCA
*
94052 ACCTCCTTATATAGGCAATGAGAATGTAAGTCGAGTG
326 ACCTCCTTATATAGGCAACGAGAATGTAAGTCGAGTG
* *
94089 TGATTACAGCGAATAAAAGATAAGACGAGAGTGTGATTGTAGGAAATTGATTAAAGTCACACCGG
1 TGATTACAGCGAATAAAAGATAAGAC--GAGCGTGATTGAAGGAAATTGATTAAAGTCACACCGG
94154 AGCATTTAATAAACAACGGTAAATAAAGGTTTTTAATAAAGCTAATGAATGAACAACAAATTGTT
64 AGCATTTAATAAACAACGGTAAATAAAGGTTTTTAATAAAGCTAATGAATGAACAACAAATTGTT
94219 ATTCGACTAAAAGTGATTGAAACTGATTACAATCAAAGGAAACAAGGTAGACAAGATTGAAAGTA
129 ATTCGACTAAAAGTGATTGAAACTGATTACAATCAAAGGAAACAAGGTAGACAAGATTGAAAGTA
*
94284 TTGAGAAAATTGAGAAACTCATGGTTTTAGAGAAAAATAAGTATGAAATTTGCAGAGAAAAGCAC
194 TTGAGAAAATTGAGAAACTCATGGTTTCAGAGAAAAATAAGTATGAAATTTGCAGAGAAAAGCAC
*
94349 GAAGCTTGAGTTTTGTGTTGGGTAGAGTTTTCCCAGAGAAATGTTGTGTGTCTGAAAGCAGGGGG
259 GAAGCTTGAGTTTTGCGTTGGGTAGAGTTTTCCCAGAGAAATGTTGTGTGTCTGAAAGCAGGGGG
*
94414 CGACCTCCTTATATAGGCAACGAGAATGTAA
324 CAACCTCCTTATATAGGCAACGAGAATGTAA
94445 TCTCGACACC
Statistics
Matches: 338, Mismatches: 16, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
362 26 0.08
364 312 0.92
ACGTcount: A:0.39, C:0.11, G:0.24, T:0.26
Consensus pattern (362 bp):
TGATTACAGCGAATAAAAGATAAGACGAGCGTGATTGAAGGAAATTGATTAAAGTCACACCGGAG
CATTTAATAAACAACGGTAAATAAAGGTTTTTAATAAAGCTAATGAATGAACAACAAATTGTTAT
TCGACTAAAAGTGATTGAAACTGATTACAATCAAAGGAAACAAGGTAGACAAGATTGAAAGTATT
GAGAAAATTGAGAAACTCATGGTTTCAGAGAAAAATAAGTATGAAATTTGCAGAGAAAAGCACGA
AGCTTGAGTTTTGCGTTGGGTAGAGTTTTCCCAGAGAAATGTTGTGTGTCTGAAAGCAGGGGGCA
ACCTCCTTATATAGGCAACGAGAATGTAAGTCGAGTG
Found at i:95914 original size:16 final size:17
Alignment explanation
Indices: 95895--95973 Score: 58
Period size: 16 Copynumber: 4.9 Consensus size: 17
95885 GAACCCGTCC
*
95895 AAACCTGAACCC-AAAA
1 AAACCCGAACCCGAAAA
95911 AAACCCGAACCCG-AAA
1 AAACCCGAACCCGAAAA
* * *
95927 AAGCTCAAACCCG-AAA
1 AAACCCGAACCCGAAAA
* **
95943 AAATCAAAACCCG-AAA
1 AAACCCGAACCCGAAAA
*
95959 AAACCCGAAACCGAA
1 AAACCCGAACCCGAA
95974 CCTGAATTCA
Statistics
Matches: 49, Mismatches: 12, Indels: 3
0.77 0.19 0.05
Matches are distributed among these distances:
16 48 0.98
17 1 0.02
ACGTcount: A:0.54, C:0.32, G:0.10, T:0.04
Consensus pattern (17 bp):
AAACCCGAACCCGAAAA
Found at i:95943 original size:15 final size:16
Alignment explanation
Indices: 95918--95961 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
95908 AAAAAACCCG
*
95918 AACCCGAAAAAGCTC-A
1 AACCCGAAAAA-ATCAA
95934 AACCCGAAAAAATCAA
1 AACCCGAAAAAATCAA
95950 AACCCGAAAAAA
1 AACCCGAAAAAA
95962 CCCGAAACCG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 2 0.08
16 24 0.92
ACGTcount: A:0.59, C:0.27, G:0.09, T:0.05
Consensus pattern (16 bp):
AACCCGAAAAAATCAA
Found at i:96203 original size:32 final size:32
Alignment explanation
Indices: 96167--96296 Score: 174
Period size: 32 Copynumber: 4.1 Consensus size: 32
96157 TCCGAGCCCA
*
96167 AACCCGAATTAACCTGACCCAAAATTT-ACCCG
1 AACCCGAATCAACCTGACCC-AAATTTAACCCG
96199 AACCCGAATCAACCTGACCCAAATTTAACCCG
1 AACCCGAATCAACCTGACCCAAATTTAACCCG
*
96231 AATCCGAATCAA-CTCGACCCAAATTTAACCCG
1 AACCCGAATCAACCT-GACCCAAATTTAACCCG
* * * *
96263 AACCTGAATCAACCCGACCCAACTTTAACTCG
1 AACCCGAATCAACCTGACCCAAATTTAACCCG
96295 AA
1 AA
96297 AGCGACTTAA
Statistics
Matches: 88, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
31 8 0.09
32 79 0.90
33 1 0.01
ACGTcount: A:0.38, C:0.35, G:0.09, T:0.18
Consensus pattern (32 bp):
AACCCGAATCAACCTGACCCAAATTTAACCCG
Found at i:96544 original size:26 final size:25
Alignment explanation
Indices: 96495--96545 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
96485 AAATTATCAT
* *
96495 TGCACCTAATTTTTTTTTGGTAAAA
1 TGCACCTAATTTTTTTATCGTAAAA
*
96520 TGCACCTAATTTTTATTATCTTAAAA
1 TGCACCTAATTTTT-TTATCGTAAAA
96546 AATTAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (25 bp):
TGCACCTAATTTTTTTATCGTAAAA
Found at i:96771 original size:18 final size:18
Alignment explanation
Indices: 96745--96779 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
96735 AATAACGAAT
* *
96745 TTAAGAAAATAAAGGTTC
1 TTAAAAAAAAAAAGGTTC
96763 TTAAAAAAAAAAAGGTT
1 TTAAAAAAAAAAAGGTT
96780 ATAAGTACTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.03, G:0.14, T:0.26
Consensus pattern (18 bp):
TTAAAAAAAAAAAGGTTC
Done.