Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2094
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: 27631
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:695 original size:10 final size:10
Alignment explanation
Indices: 617--706 Score: 50
Period size: 10 Copynumber: 9.7 Consensus size: 10
607 TTATGTTTCA
617 ATTATAT-AT
1 ATTATATAAT
* **
626 ATTATTTTTT
1 ATTATATAAT
636 ATTAT-TAAT
1 ATTATATAAT
*
645 -TTATATTAT
1 ATTATATAAT
654 A-TA-ATAAT
1 ATTATATAAT
* *
662 ATCATATAAA
1 ATTATATAAT
* *
672 AATAAATAA-
1 ATTATATAAT
681 A-TATATAAT
1 ATTATATAAT
*
690 ATTATATTAT
1 ATTATATAAT
700 ATTATAT
1 ATTATAT
707 TTTTATATCT
Statistics
Matches: 61, Mismatches: 13, Indels: 13
0.70 0.15 0.15
Matches are distributed among these distances:
8 15 0.25
9 16 0.26
10 30 0.49
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (10 bp):
ATTATATAAT
Found at i:2829 original size:30 final size:30
Alignment explanation
Indices: 2778--2858 Score: 90
Period size: 30 Copynumber: 2.7 Consensus size: 30
2768 AGTTGGTTTC
* * *
2778 TAGTTTCACCTAAATTGTTTTCTAAATATT
1 TAGTTTCACCTAAGTTATTTTCCAAATATT
* *
2808 TAGTTTCACCTAAGTCATTTTCCAAATTTT
1 TAGTTTCACCTAAGTTATTTTCCAAATATT
* * *
2838 TGGATTCATCTAAGTTATTTT
1 TAGTTTCACCTAAGTTATTTT
2859 TCGAATTACT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.27, C:0.15, G:0.09, T:0.49
Consensus pattern (30 bp):
TAGTTTCACCTAAGTTATTTTCCAAATATT
Found at i:3641 original size:2 final size:2
Alignment explanation
Indices: 3634--3663 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3624 TTGATTAAAG
*
3634 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3664 GATAAACAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4367 original size:18 final size:17
Alignment explanation
Indices: 4331--4369 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
4321 AAAGTTAATA
*
4331 AAAGTTAAAAATCAACC
1 AAAGTTAAAAATAAACC
*
4348 AAAGTTAAATATGAAACC
1 AAAGTTAAAAAT-AAACC
4366 AAAG
1 AAAG
4370 ATTTATTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.59, C:0.13, G:0.10, T:0.18
Consensus pattern (17 bp):
AAAGTTAAAAATAAACC
Found at i:5561 original size:54 final size:54
Alignment explanation
Indices: 5468--5576 Score: 141
Period size: 54 Copynumber: 2.0 Consensus size: 54
5458 CAAGTATGTC
* *
5468 AGTGAAATTGGCCCCTAAATGAGAAAGCGCAATTCAGCTGCTAAGATTAATTCT
1 AGTGAAATTGGCCCCTAAATGAGAAAGCGCAAATCAGCTGCTAAGATTAAGTCT
* * *
5522 AGTGAAATTGGCCCCTAAATGTGAAAGC-CTAACAT-AGCTGGTAGGATTAAGTCT
1 AGTGAAATTGGCCCCTAAATGAGAAAGCGC-AA-ATCAGCTGCTAAGATTAAGTCT
5576 A
1 A
5577 ATAAAATCAG
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
53 1 0.02
54 46 0.96
55 1 0.02
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (54 bp):
AGTGAAATTGGCCCCTAAATGAGAAAGCGCAAATCAGCTGCTAAGATTAAGTCT
Found at i:5723 original size:27 final size:27
Alignment explanation
Indices: 5693--5746 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
5683 TAGTGAAATT
*
5693 AGCCTATAAAATTGTTTAAGTCCAATG
1 AGCCTATAAAAGTGTTTAAGTCCAATG
*
5720 AGCCTATAGAAGTGTTTAAGTCCAATG
1 AGCCTATAAAAGTGTTTAAGTCCAATG
5747 TAGCTAGCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (27 bp):
AGCCTATAAAAGTGTTTAAGTCCAATG
Found at i:5843 original size:57 final size:57
Alignment explanation
Indices: 5732--5877 Score: 152
Period size: 57 Copynumber: 2.6 Consensus size: 57
5722 CCTATAGAAG
* * *
5732 TGTTTAAGTCCAATGTAGCTAGCTTAAGACAAGCCTAGTCCAATTGGTACCTAGATA
1 TGTTTAAGTCCAATGTAGCTAGCTTAAGACAAGCCTAGTCAAATTGGCAACTAGATA
* * * * * *
5789 TGTTTAAGTCTATTGTAGTTGGCTTAAGACAAGCCTTGTGAAATTGGCAACTAGA-A
1 TGTTTAAGTCCAATGTAGCTAGCTTAAGACAAGCCTAGTCAAATTGGCAACTAGATA
* * *
5845 TTATTTAAGTCCAATATGGCTAG-TTCAAGACAA
1 -TGTTTAAGTCCAATGTAGCTAGCTT-AAGACAA
5878 TGTTAGTTAA
Statistics
Matches: 71, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
56 3 0.04
57 68 0.96
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (57 bp):
TGTTTAAGTCCAATGTAGCTAGCTTAAGACAAGCCTAGTCAAATTGGCAACTAGATA
Found at i:9849 original size:80 final size:79
Alignment explanation
Indices: 9628--9850 Score: 279
Period size: 79 Copynumber: 2.8 Consensus size: 79
9618 ACAACGGGGC
** **
9628 TGGAGTATCCCCGATTAT-AGAAAATCAGTGTTTT-GAAAATAAAATCAGGGTTGGAGTATCCCC
1 TGGAGTATCCCCGATTATGA-AAAATTGGTGTTTTAG-AAATAAAATTGGGGTTGGAGTATCCCC
* *
9691 TCGAAAATAACGGGGT
64 GCGAAAATAACAGGGT
* * * ***
9707 TGGAGTATCCCCGATTATGGAAAATTGATGCTTTAGAAATAAGGCTGGGGTTGGAGTATCCCCGC
1 TGGAGTATCCCCGATTATGAAAAATTGGTGTTTTAGAAATAAAATTGGGGTTGGAGTATCCCCGC
9772 GAAAATAACAGGGT
66 GAAAATAACAGGGT
* *
9786 TGGAGTATCCTCGATTGTGAAAAGATTGGTGTTTTAGAAATAAAATTGGGGTTGGAGTATCCCCG
1 TGGAGTATCCCCGATTATGAAAA-ATTGGTGTTTTAGAAATAAAATTGGGGTTGGAGTATCCCCG
9851 ATTGTGAGAA
Statistics
Matches: 121, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
79 84 0.69
80 37 0.31
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (79 bp):
TGGAGTATCCCCGATTATGAAAAATTGGTGTTTTAGAAATAAAATTGGGGTTGGAGTATCCCCGC
GAAAATAACAGGGT
Found at i:9893 original size:51 final size:52
Alignment explanation
Indices: 9782--9898 Score: 137
Period size: 51 Copynumber: 2.3 Consensus size: 52
9772 GAAAATAACA
* *** * **
9782 GGGTTGGAGTATCCTCGATTGTGAAAAGATTGGTGTTTTAGAAATAAAATTG
1 GGGTTGGAGTATCCCCGATTGTGAAAAGATCAATATTTTAGAAATAAAACCG
* **
9834 GGGTTGGAGTATCCCCGATTGTGAGAA-ATCAATATTTTAGAAATAAGGCCG
1 GGGTTGGAGTATCCCCGATTGTGAAAAGATCAATATTTTAGAAATAAAACCG
9885 GGGTTGGAGTATCC
1 GGGTTGGAGTATCC
9899 ATGAGATGAA
Statistics
Matches: 55, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
51 30 0.55
52 25 0.45
ACGTcount: A:0.29, C:0.10, G:0.30, T:0.31
Consensus pattern (52 bp):
GGGTTGGAGTATCCCCGATTGTGAAAAGATCAATATTTTAGAAATAAAACCG
Found at i:12257 original size:13 final size:13
Alignment explanation
Indices: 12236--12265 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
12226 GTAAACCCAG
12236 AATGCATCGATAC
1 AATGCATCGATAC
*
12249 AATGTATCGATAC
1 AATGCATCGATAC
12262 AATG
1 AATG
12266 AACAATGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.27
Consensus pattern (13 bp):
AATGCATCGATAC
Found at i:12964 original size:42 final size:42
Alignment explanation
Indices: 12860--13192 Score: 268
Period size: 41 Copynumber: 7.9 Consensus size: 42
12850 AAGGAAGGGG
* * *
12860 GCGTCCTGCTCTTTGAGAATTAAA-G--AAAAGGAGAATGAAAT
1 GCGTCCTGCTCTTTGAGGA-CAAAGGAAAAAAGGA-AATAAAAT
* *
12901 GGGTCCTGCTCCTTGAGGACAAAGGAAAAAAGGAAATAAAAT
1 GCGTCCTGCTCTTTGAGGACAAAGGAAAAAAGGAAATAAAAT
* * * * *
12943 GCATCATGCCCTTTGAAGACAAAGG-AAAAAGGAAATTAAAT
1 GCGTCCTGCTCTTTGAGGACAAAGGAAAAAAGGAAATAAAAT
* * * *
12984 GTGTCCTGCT-TTTCAAGGACAAAGG-AAAATGGAGAATAAAGT
1 GCGTCCTGCTCTTT-GAGGACAAAGGAAAAAAGGA-AATAAAAT
* * * * * *
13026 GCGTCCTACTCTTTGAGAACTAGAAGGGAGAAGAGGGAAATGAAGT
1 GCGTCCTGCTCTTTGAGGAC-A-AA-GGA-AAAAAGGAAATAAAAT
* *
13072 GCGTCCTACTCTTTGAGGACAAAGGAAAAAA-GAAA-AAAAG
1 GCGTCCTGCTCTTTGAGGACAAAGGAAAAAAGGAAATAAAAT
* *
13112 GCATCCTGCTCTTTGAGGACAAAAGGGAAAAGAAGGAAATGAAAT
1 GCGTCCTGCTCTTTGAGGAC-AAA-GGAAAA-AAGGAAATAAAAT
* * *
13157 GTGTCCTGCTCTTTGAGGACAAAGGAGAGAAGGAAA
1 GCGTCCTGCTCTTTGAGGACAAAGGAAAAAAGGAAA
13193 AGGCGTCCTA
Statistics
Matches: 234, Mismatches: 42, Indels: 31
0.76 0.14 0.10
Matches are distributed among these distances:
40 26 0.11
41 61 0.26
42 60 0.26
43 20 0.09
44 11 0.05
45 24 0.10
46 26 0.11
47 6 0.03
ACGTcount: A:0.41, C:0.14, G:0.26, T:0.20
Consensus pattern (42 bp):
GCGTCCTGCTCTTTGAGGACAAAGGAAAAAAGGAAATAAAAT
Found at i:12984 original size:83 final size:86
Alignment explanation
Indices: 12887--13192 Score: 322
Period size: 85 Copynumber: 3.6 Consensus size: 86
12877 AATTAAAGAA
* * *
12887 AAGGAGAATGAAATGGGTCCTGCTCCTTGAGGACAAAGGAAAAAAGGAAATAAAATGCATCATGC
1 AAGGA-AATGAAATGTGTCCTGCTCTTTGAGGACAAAGGAAAAAAGGAAATAAAATGCATCCTGC
*
12952 CCTTTGAAGAC-AAA-GGAAA-
65 TCTTTGAAGACAAAAGGGAAAG
* * * * * *
12971 AAGGAAATTAAATGTGTCCTGCT-TTTCAAGGACAAAGG-AAAATGGAGAATAAAGTGCGTCCTA
1 AAGGAAATGAAATGTGTCCTGCTCTTT-GAGGACAAAGGAAAAAAGGA-AATAAAATGCATCCTG
*
13034 CTCTTTG-AGAACTAGAAGGGAGAAG
64 CTCTTTGAAG-AC-AAAAGGGA-AAG
* * * * *
13059 AGGGAAATGAAGTGCGTCCTACTCTTTGAGGACAAAGGAAAAAA-GAAA-AAAAGGCATCCTGCT
1 AAGGAAATGAAATGTGTCCTGCTCTTTGAGGACAAAGGAAAAAAGGAAATAAAATGCATCCTGCT
*
13122 CTTTGAGGACAAAAGGGAAAAG
66 CTTTGAAGACAAAAGGG-AAAG
* *
13144 AAGGAAATGAAATGTGTCCTGCTCTTTGAGGACAAAGGAGAGAAGGAAA
1 AAGGAAATGAAATGTGTCCTGCTCTTTGAGGACAAAGGAAAAAAGGAAA
13193 AGGCGTCCTA
Statistics
Matches: 179, Mismatches: 30, Indels: 24
0.77 0.13 0.10
Matches are distributed among these distances:
82 11 0.06
83 46 0.26
84 5 0.03
85 49 0.27
86 26 0.15
87 5 0.03
88 30 0.17
89 7 0.04
ACGTcount: A:0.42, C:0.13, G:0.27, T:0.19
Consensus pattern (86 bp):
AAGGAAATGAAATGTGTCCTGCTCTTTGAGGACAAAGGAAAAAAGGAAATAAAATGCATCCTGCT
CTTTGAAGACAAAAGGGAAAG
Found at i:13143 original size:40 final size:39
Alignment explanation
Indices: 12999--13214 Score: 132
Period size: 46 Copynumber: 5.1 Consensus size: 39
12989 CTGCTTTTCA
*
12999 AGGACAAA-GGAAAATGGAGAATAAAGTGCGTCCTACTCTTTG
1 AGGACAAAGGGAAAA--GA-AAAAAAG-GCGTCCTACTCTTTG
* **
13041 AGAACTAGAAGGGAGAAGAGGGAAATGAAGTGCGTCCTACTCTTTG
1 AGGAC-A-AAGGGA-AA-A--GAAAAAAAG-GCGTCCTACTCTTTG
* * *
13087 AGGACAAAGGAAAAAAGAAAAAAAGGCATCCTGCTCTTTG
1 AGGACAAAGG-GAAAAGAAAAAAAGGCGTCCTACTCTTTG
* * *
13127 AGGACAAAAGGGAAAAGAAGGAAATGAAATGTGTCCTGCTCTTTG
1 AGGAC-AAAGGGAAAAG-A--AAA--AAAGGCGTCCTACTCTTTG
* *
13172 AGGACAAA-GG-AGAGAAGGAAAAGGCGTCCTACTCTTTG
1 AGGACAAAGGGAAAAGAA-AAAAAGGCGTCCTACTCTTTG
13210 AGGAC
1 AGGAC
13215 TAAAAAATGC
Statistics
Matches: 143, Mismatches: 18, Indels: 30
0.75 0.09 0.16
Matches are distributed among these distances:
38 21 0.15
39 1 0.01
40 24 0.17
41 14 0.10
42 7 0.05
43 7 0.05
44 11 0.08
45 26 0.18
46 28 0.20
47 4 0.03
ACGTcount: A:0.39, C:0.14, G:0.29, T:0.18
Consensus pattern (39 bp):
AGGACAAAGGGAAAAGAAAAAAAGGCGTCCTACTCTTTG
Found at i:13264 original size:61 final size:60
Alignment explanation
Indices: 13189--13962 Score: 658
Period size: 61 Copynumber: 12.9 Consensus size: 60
13179 AGGAGAGAAG
* * *
13189 GAAAAGGCGTCCTACTCTTTGAGGACTAAAAAATGCCACCAACTCGTGTGGGCTTTGAAAA
1 GAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAA
* ** * * * *
13250 GAAAAGGCGTCCTACTCTTTGAGGACTGGAAGGTGCCACCAACTTATGTGGGCTTTGCAAG
1 GAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAA
* * * * * * *
13311 GAAAAGGTGTCCTGCTCTTTGAGGACT-GAAGGTGCCACCAGCTTTTGTGGGTTTTGAAAG
1 GAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAA
* ** * *
13371 GCAAAA-GCATCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGACTTTAAAA
1 G-AAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
* * *
13431 GGAAAAGGTGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAGCTTGTGTGGGCTTTGAAAG
1 -GAAAAGGCGTCCTGCTCTTTGAGGACTA-AAAAGTGCCACCAACTTGTGTGGGCTTT-AAAA
** * ** * *
13494 GTGTAA-GCATCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGAC-TTAAAA
1 G-AAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
*
13553 GGAAAAGGTGTCCTGCTCTTTGAGGACTACAAAAGTGCCA-CAAGCTTGTGTGGGCTTT----
1 -GAAAAGGCGTCCTGCTCTTTGAGGACTA-AAAAGTGCCACCAA-CTTGTGTGGGCTTTAAAA
* **
13611 G-AAAGGCGTCCTGCTTTTTGAGGACTGGAAAAA-TGCCACCAACCGGTGTGGGCTTT----
1 GAAAAGGCGTCCTGCTCTTTGAGGACT--AAAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
** * *
13667 G-AAAGGCGTCCTGCTCTTTGAGGACTAGGAAGTGCCACCAGCTTTTGTGGGCTTTAAAAA
1 GAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAA
* * * * *
13727 GAAAAGGTGTTCTGCTCTTTGAGGACTAGAAATGTGCCACCAGCTTGTGTGGGCTTTGAAAG
1 GAAAAGGCGTCCTGCTCTTTGAGGACTA-AAAAGTGCCACCAACTTGTGTGGGCTTT-AAAA
* * ** * * *
13789 GCATAA-GCATCCTGCTCTTTGAGGACTGGAAGGTGTCACCAACTTGTGTGGACTTTAAAA
1 G-AAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
** * * *
13849 GGAAAAGGTTTCCTGCTTTTTGAGGACTAGAAAAGTGCCACCAGCTTGTGTGAGCTTT----
1 -GAAAAGGCGTCCTGCTCTTTGAGGACTA-AAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
* * *
13907 G-AAAGGCGTCCTGCTCTTTGAGGACTGGAAAAA-TGTCACAAACTAGTGTGGGCTTT
1 GAAAAGGCGTCCTGCTCTTTGAGGACT--AAAAAGTGCCACCAACTTGTGTGGGCTTT
13963 GGTGGAGTCT
Statistics
Matches: 588, Mismatches: 96, Indels: 63
0.79 0.13 0.08
Matches are distributed among these distances:
54 3 0.01
55 19 0.03
56 105 0.18
57 13 0.02
58 2 0.00
59 5 0.01
60 88 0.15
61 231 0.39
62 114 0.19
63 8 0.01
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (60 bp):
GAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
Found at i:13536 original size:123 final size:122
Alignment explanation
Indices: 13186--13963 Score: 769
Period size: 123 Copynumber: 6.5 Consensus size: 122
13176 CAAAGGAGAG
* * * * *
13186 AAGGAAAAGGCGTCCTACTCTTTGAGGACTA-AAAAATGCCACCAACTCGTGTGGGCTTTGAAAA
1 AAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAGCTTGTGTGGGCTTTGAAAG
* * * *
13250 GAAAAGGCGTCCTACTCTTTGAGGACTGGAAGGTGCCACCAACTTATGTGGGCTTTGC
66 GAAAAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGACTTT-A
* * * *
13308 AAGGAAAAGGTGTCCTGCTCTTTGAGGACT-G-AAGGTGCCACCAGCTTTTGTGGGTTTTGAAAG
1 AAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAGCTTGTGTGGGCTTTGAAAG
*
13371 GCAAAA-GCATCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGACTTTAA
66 G-AAAAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGACTTT-A
*
13429 AAGGAAAAGGTGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAGCTTGTGTGGGCTTTGAAAG
1 AAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAGCTTGTGTGGGCTTTGAAAG
** * *
13494 GTGTAA-GCATCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGACTTAA
66 G-AAAAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGACTTTA
* * *
13551 AAGGAAAAGGTGTCCTGCTCTTTGAGGACTACAAAAGTGCCACAAGCTTGTGTGGGCTTT-----
1 AAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAGCTTGTGTGGGCTTTGAAAG
* ** ** *
13611 G-AAAGGCGTCCTGCTTTTTGAGGACTGGAAAAATGCCACCAACCGGTGTGGGCTTT-
66 GAAAAGGCGTCCTGCTCTTTGAGGACTGG-AAGGTGCCACCAACTTGTGTGGACTTTA
* * * *
13667 ---G-AAAGGCGTCCTGCTCTTTGAGGACTAG-GAAGTGCCACCAGCTTTTGTGGGCTTTAAAAA
1 AAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAGCTTGTGTGGGCTTTGAAAG
* * * * * *
13727 GAAAAGGTGTTCTGCTCTTTGAGGACTAGAAATGTGCCACCAGCTTGTGTGGGCTTTGA
66 GAAAAGGCGTCCTGCTCTTTGAGGACT-GGAAGGTGCCACCAACTTGTGTGGACTTT-A
* * * * * * * *
13786 AAGGCATAA-GCATCCTGCTCTTTGAGGACT-GGAAGGTGTCACCAACTTGTGTGGACTTTAAAA
1 AAGG-AAAAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAGCTTGTGTGGGCTTTGAAA
** * * * *
13849 GGAAAAGGTTTCCTGCTTTTTGAGGACTAGAAAAGTGCCACCAGCTTGTGT-GAGCTTT-
65 GGAAAAGGCGTCCTGCTCTTTGAGGACT-GGAAGGTGCCACCAACTTGTGTGGA-CTTTA
* * * * * *
13907 ---G-AAAGGCGTCCTGCTCTTTGAGGACTGGAAAAATGTCACAAACTAGTGTGGGCTTTG
1 AAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAGCTTGTGTGGGCTTTG
13964 GTGGAGTCTT
Statistics
Matches: 562, Mismatches: 70, Indels: 52
0.82 0.10 0.08
Matches are distributed among these distances:
111 24 0.04
112 25 0.04
113 1 0.00
115 2 0.00
116 24 0.04
117 86 0.15
118 25 0.04
121 102 0.18
122 95 0.17
123 176 0.31
124 2 0.00
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (122 bp):
AAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAGCTTGTGTGGGCTTTGAAAG
GAAAAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGACTTTA
Found at i:13744 original size:295 final size:296
Alignment explanation
Indices: 13380--13963 Score: 974
Period size: 295 Copynumber: 2.0 Consensus size: 296
13370 GGCAAAAGCA
*
13380 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGACTTTAAAAGGAAAAGGTGTCCT
1 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGACTTTAAAAAGAAAAGGTGTCCT
**
13445 GCTCTTTGAGGACTAGAAAAGTGCCACCAGCTTGTGTGGGCTTTGAAAGGTGTAAGCATCCTGCT
66 GCTCTTTGAGGACTAGAAAAGTGCCACCAGCTTGTGTGGGCTTTGAAAGGCATAAGCATCCTGCT
13510 CTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGAC-TTAAAAGGAAAAGGTGTCCTGCTCTTT
131 CTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGACTTTAAAAGGAAAAGGTGTCCTGCTCTTT
* *
13574 GAGGACTACAAAAGTGCCACAAGCTTGTGTGGGCTTTGAAAGGCGTCCTGCTTTTTGAGGACTGG
196 GAGGACTACAAAAGTGCCACAAGCTTGTGTGAGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTGG
* *
13639 AAAAATGCCACCAACCGGTGTGGGCTTTGAAAGGCG
261 AAAAATGCCACAAACCAGTGTGGGCTTTGAAAGGCG
* * * *
13675 TCCTGCTCTTTGAGGACTAGGAA-GTGCCACCAGCTTTTGTGGGCTTTAAAAAGAAAAGGTGTTC
1 TCCTGCTCTTTGAGGACT-GGAAGGTGCCACCAACTTGTGTGGACTTTAAAAAGAAAAGGTGTCC
*
13739 TGCTCTTTGAGGACTAGAAATGTGCCACCAGCTTGTGTGGGCTTTGAAAGGCATAAGCATCCTGC
65 TGCTCTTTGAGGACTAGAAAAGTGCCACCAGCTTGTGTGGGCTTTGAAAGGCATAAGCATCCTGC
* * *
13804 TCTTTGAGGACTGGAAGGTGTCACCAACTTGTGTGGACTTTAAAAGGAAAAGGTTTCCTGCTTTT
130 TCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGACTTTAAAAGGAAAAGGTGTCCTGCTCTT
* *
13869 TGAGGACTAGAAAAGTGCCACCAGCTTGTGTGAGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTG
195 TGAGGACTACAAAAGTGCCACAAGCTTGTGTGAGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTG
* *
13934 GAAAAATGTCACAAACTAGTGTGGGCTTTG
260 GAAAAATGCCACAAACCAGTGTGGGCTTTG
13964 GTGGAGTCTT
Statistics
Matches: 268, Mismatches: 19, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
295 153 0.57
296 115 0.43
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.28
Consensus pattern (296 bp):
TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGACTTTAAAAAGAAAAGGTGTCCT
GCTCTTTGAGGACTAGAAAAGTGCCACCAGCTTGTGTGGGCTTTGAAAGGCATAAGCATCCTGCT
CTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGACTTTAAAAGGAAAAGGTGTCCTGCTCTTT
GAGGACTACAAAAGTGCCACAAGCTTGTGTGAGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTGG
AAAAATGCCACAAACCAGTGTGGGCTTTGAAAGGCG
Found at i:14325 original size:11 final size:11
Alignment explanation
Indices: 14306--14367 Score: 63
Period size: 11 Copynumber: 5.6 Consensus size: 11
14296 AAGCAGGTTC
* *
14306 TTTTCTTTTCT
1 TTTTTTTTTGT
14317 TTTTTTTTT-T
1 TTTTTTTTTGT
* *
14327 GTTTTTTATGT
1 TTTTTTTTTGT
*
14338 TTTTTTTATGT
1 TTTTTTTTTGT
14349 TTTTTGTTTTGT
1 TTTTT-TTTTGT
14361 TTTTTTT
1 TTTTTTT
14368 AAAAAGAAGG
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
10 8 0.18
11 26 0.59
12 10 0.23
ACGTcount: A:0.03, C:0.03, G:0.08, T:0.85
Consensus pattern (11 bp):
TTTTTTTTTGT
Found at i:19997 original size:28 final size:28
Alignment explanation
Indices: 19963--20044 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
19953 TTTTGGAGAT
*
19963 AATAACGAGGTTGGAGTGTTCCCTC-A-GA
1 AATAACGAGGTTGGAGT-ATCCC-CGATGA
* *
19991 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCCCGATGA
*
20019 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCCCGAT
20045 TGTGAAAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 1 0.02
27 5 0.11
28 40 0.87
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCCCGATGA
Found at i:20187 original size:51 final size:50
Alignment explanation
Indices: 20027--20197 Score: 171
Period size: 51 Copynumber: 3.3 Consensus size: 50
20017 GAAATAACGA
* * * *
20027 GGTTGGAGTATCCTCGATTGTGAAAAATTAGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATGA-TA-TTTTGAAAATAAAATCGG
** * * * * * *
20079 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGA-AAAATGATATTTTGAAAATAAAATCGG
*
20132 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAAT-GATATTTTGAAAATAAAATCGG
20183 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
20198 TCAGAAATAA
Statistics
Matches: 94, Mismatches: 21, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
50 4 0.04
51 35 0.37
52 16 0.17
53 32 0.34
54 3 0.03
55 4 0.04
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (50 bp):
GGTTGGAGTATCCCCGATTATGAAAAATGATATTTTGAAAATAAAATCGG
Found at i:20243 original size:27 final size:28
Alignment explanation
Indices: 20180--20255 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
20170 AAAATAAAGT
*
20180 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
20208 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
20235 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
20256 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:22739 original size:13 final size:13
Alignment explanation
Indices: 22721--22746 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
22711 ACAAAGATCC
22721 ATGTATCGATACA
1 ATGTATCGATACA
22734 ATGTATCGATACA
1 ATGTATCGATACA
22747 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:22742 original size:33 final size:33
Alignment explanation
Indices: 22700--22766 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
22690 AAAATTTCCA
***
22700 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
22733 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
22766 A
1 A
22767 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:22810 original size:19 final size:18
Alignment explanation
Indices: 22786--22853 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
22776 CAGTAGCTAA
22786 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
22805 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
22820 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
22837 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
22854 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:22826 original size:13 final size:13
Alignment explanation
Indices: 22808--22832 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22798 ACAATACTTA
22808 TGTATCGATACAT
1 TGTATCGATACAT
22821 TGTATCGATACA
1 TGTATCGATACA
22833 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:22830 original size:32 final size:32
Alignment explanation
Indices: 22789--22851 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
22779 TAGCTAATTA
*
22789 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
22821 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
22852 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:22913 original size:1 final size:1
Alignment explanation
Indices: 22907--22952 Score: 65
Period size: 1 Copynumber: 46.0 Consensus size: 1
22897 TACAGTTAAA
***
22907 TTTTTTTTTTTTTTTTTTTTCAATTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
22953 CAAACACTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.04, C:0.02, G:0.00, T:0.93
Consensus pattern (1 bp):
T
Found at i:22935 original size:23 final size:23
Alignment explanation
Indices: 22905--22949 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
22895 GATACAGTTA
22905 AATTTTTTTTTTTTTTTTTTTTC
1 AATTTTTTTTTTTTTTTTTTTTC
22928 AATTTTTTTTTTTTTTTTTTTT
1 AATTTTTTTTTTTTTTTTTTTT
22950 TTTCAAACAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.09, C:0.02, G:0.00, T:0.89
Consensus pattern (23 bp):
AATTTTTTTTTTTTTTTTTTTTC
Found at i:23632 original size:55 final size:55
Alignment explanation
Indices: 23548--24500 Score: 1459
Period size: 55 Copynumber: 17.3 Consensus size: 55
23538 ATAAATTGTA
* * * * * *
23548 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
23603 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCCACTTGTGTGGGCTTTGAAAAGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
23658 TCCTGCTCTTTGGGGAATGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
23713 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
23768 TCCTGTTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
23823 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
23878 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
23933 TCCTGCTCTTTGAGGACTGGACAA--TGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GA-AAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
23988 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
24043 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
24098 TCCTGCTCTTTGGGGAATGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
24153 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
24208 TCCTGTTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
24263 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
24318 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
24373 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
24428 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
24483 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
24501 AAAAAGCGGA
Statistics
Matches: 852, Mismatches: 31, Indels: 30
0.93 0.03 0.03
Matches are distributed among these distances:
53 2 0.00
54 18 0.02
55 814 0.96
56 16 0.02
57 2 0.00
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:24393 original size:26 final size:26
Alignment explanation
Indices: 24364--24453 Score: 83
Period size: 26 Copynumber: 3.3 Consensus size: 26
24354 GTGTGGGCTT
24364 TGAAAGGTGTCCTGCTCTTTGAGGAC
1 TGAAAGGTGTCCTGCTCTTTGAGGAC
** * * *
24390 TGAAAGGTG-CCACCAACTTGTGTGGGC
1 TGAAAGGTGTCCTGC-TCTT-TGAGGAC
*
24417 TTTAAGAGGTGTCCTGCTCTTTGAGGAC
1 -TGAA-AGGTGTCCTGCTCTTTGAGGAC
24445 TGAAAGGTG
1 TGAAAGGTG
24454 CCACCAACTT
Statistics
Matches: 47, Mismatches: 12, Indels: 10
0.68 0.17 0.14
Matches are distributed among these distances:
25 3 0.06
26 17 0.36
27 8 0.17
28 8 0.17
29 8 0.17
30 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (26 bp):
TGAAAGGTGTCCTGCTCTTTGAGGAC
Found at i:25505 original size:14 final size:13
Alignment explanation
Indices: 25482--25550 Score: 61
Period size: 13 Copynumber: 5.1 Consensus size: 13
25472 CTTTTCTCTC
*
25482 TTTTTCTTTGTTT
1 TTTTTTTTTGTTT
25495 TGTTTTTTTTGTTT
1 T-TTTTTTTTGTTT
*
25509 TTTTTTTGCT-TTT
1 TTTTTTT-TTGTTT
25522 TTTTTTTTTGCTCCTT
1 TTTTTTTTTG-T--TT
25538 TTTTTTTTT-TTT
1 TTTTTTTTTGTTT
25550 T
1 T
25551 GAAGAGAAGG
Statistics
Matches: 47, Mismatches: 3, Indels: 13
0.75 0.05 0.21
Matches are distributed among these distances:
12 4 0.09
13 17 0.36
14 15 0.32
16 11 0.23
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.86
Consensus pattern (13 bp):
TTTTTTTTTGTTT
Found at i:25513 original size:11 final size:12
Alignment explanation
Indices: 25497--25527 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
25487 CTTTGTTTTG
25497 TTTTTTTTG-TT
1 TTTTTTTTGCTT
25508 TTTTTTTTGCTT
1 TTTTTTTTGCTT
25520 TTTTTTTT
1 TTTTTTTT
25528 TTTGCTCCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.00, C:0.03, G:0.06, T:0.90
Consensus pattern (12 bp):
TTTTTTTTGCTT
Found at i:25513 original size:18 final size:17
Alignment explanation
Indices: 25482--25551 Score: 61
Period size: 17 Copynumber: 3.9 Consensus size: 17
25472 CTTTTCTCTC
* *
25482 TTTTTCTTTGTTTTGTT
1 TTTTTTTTTTTTTTGTT
25499 TTTTTTGTTTTTTTT-TT
1 TTTTTT-TTTTTTTTGTT
*
25516 GCTTTTTTTTTTTTTGCTCCT
1 -TTTTTTTTTTTTTTG-T--T
25537 TTTTTTTTTTTTTTG
1 TTTTTTTTTTTTTTG
25552 AAGAGAAGGT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
17 15 0.35
18 12 0.28
19 1 0.02
20 14 0.33
21 1 0.02
ACGTcount: A:0.00, C:0.07, G:0.09, T:0.84
Consensus pattern (17 bp):
TTTTTTTTTTTTTTGTT
Found at i:25521 original size:20 final size:19
Alignment explanation
Indices: 25482--25550 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
25472 CTTTTCTCTC
* * *
25482 TTTTTCTTTGTTTTGTTTT
1 TTTTTTTTTTTTTTGCTTT
25501 TTTTGTTTTTTTTTTGC-TT
1 TTTT-TTTTTTTTTTGCTTT
** *
25520 TTTTTTTTTTTGCTCCTTT
1 TTTTTTTTTTTTTTGCTTT
25539 TTTTTTTTTTTT
1 TTTTTTTTTTTT
25551 GAAGAGAAGG
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
18 9 0.22
19 23 0.56
20 9 0.22
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.86
Consensus pattern (19 bp):
TTTTTTTTTTTTTTGCTTT
Found at i:25530 original size:15 final size:16
Alignment explanation
Indices: 25506--25547 Score: 68
Period size: 15 Copynumber: 2.6 Consensus size: 16
25496 GTTTTTTTTG
25506 TTTTTTTTTTGCT-TT
1 TTTTTTTTTTGCTCTT
25521 TTTTTTTTTTGCTCCTT
1 TTTTTTTTTTGCT-CTT
25538 TTTTTTTTTT
1 TTTTTTTTTT
25548 TTTGAAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 13 0.52
17 12 0.48
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.86
Consensus pattern (16 bp):
TTTTTTTTTTGCTCTT
Done.