Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015837.1 Corchorus olitorius cultivar O-4 contig15870, 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: 127048
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:73 original size:2 final size:2
Alignment explanation
Indices: 30--58 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
20 AATAAGAGGA
30 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
59 ACTTATAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:97 original size:15 final size:15
Alignment explanation
Indices: 79--112 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
69 ATATAAGAAC
*
79 AAAAACCAAAAGATA
1 AAAAACAAAAAGATA
*
94 AAAAATAAAAAGATA
1 AAAAACAAAAAGATA
109 AAAA
1 AAAA
113 GGAAAAGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.79, C:0.06, G:0.06, T:0.09
Consensus pattern (15 bp):
AAAAACAAAAAGATA
Found at i:2332 original size:17 final size:17
Alignment explanation
Indices: 2323--2374 Score: 95
Period size: 17 Copynumber: 3.0 Consensus size: 17
2313 GGAAGGAGGC
2323 TGAGAGAGGAGGATGGG
1 TGAGAGAGGAGGATGGG
2340 TGAGAGAGGAGGATGAGG
1 TGAGAGAGGAGGATG-GG
2358 TGAGAGAGGAGGATGGG
1 TGAGAGAGGAGGATGGG
2375 GAGCGGCTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
17 17 0.50
18 17 0.50
ACGTcount: A:0.31, C:0.00, G:0.58, T:0.12
Consensus pattern (17 bp):
TGAGAGAGGAGGATGGG
Found at i:2361 original size:18 final size:18
Alignment explanation
Indices: 2318--2372 Score: 94
Period size: 18 Copynumber: 3.1 Consensus size: 18
2308 TTGAAGGAAG
2318 GAGGCTGAGAGAGGAGGAT
1 GAGG-TGAGAGAGGAGGAT
2337 G-GGTGAGAGAGGAGGAT
1 GAGGTGAGAGAGGAGGAT
2354 GAGGTGAGAGAGGAGGAT
1 GAGGTGAGAGAGGAGGAT
2372 G
1 G
2373 GGGAGCGGCT
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
17 15 0.43
18 19 0.54
19 1 0.03
ACGTcount: A:0.31, C:0.02, G:0.56, T:0.11
Consensus pattern (18 bp):
GAGGTGAGAGAGGAGGAT
Found at i:3714 original size:5 final size:5
Alignment explanation
Indices: 3692--3742 Score: 79
Period size: 5 Copynumber: 10.6 Consensus size: 5
3682 TTTAATAACT
*
3692 TAAAA T-AAA T-AAA TAAAA CAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
3740 TAA
1 TAA
3743 GCAGTCCATG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
4 8 0.19
5 35 0.81
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:13693 original size:42 final size:42
Alignment explanation
Indices: 13632--13716 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
13622 GCCAATGTAT
* *
13632 TAGCACATTCTCTAGCTAAGATTGAGTCGGATAATCGTGTGG
1 TAGCACATTCTCTAACTAAGATTGAGCCGGATAATCGTGTGG
13674 TAGCACATTCTCTAACTAAGATTGAGCCGGATAATCGTGTGG
1 TAGCACATTCTCTAACTAAGATTGAGCCGGATAATCGTGTGG
13716 T
1 T
13717 GCGGGACTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.31
Consensus pattern (42 bp):
TAGCACATTCTCTAACTAAGATTGAGCCGGATAATCGTGTGG
Found at i:13789 original size:21 final size:20
Alignment explanation
Indices: 13749--13791 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
13739 TTGTAATCTC
*
13749 TGATTATTGATTAATGAAAA
1 TGATTATTGATTAATAAAAA
*
13769 TGATTATTTGATCTAAAAAAAA
1 TGATTA-TTGAT-TAATAAAAA
13791 T
1 T
13792 TATGTTCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.32
21 5 0.26
22 8 0.42
ACGTcount: A:0.47, C:0.02, G:0.12, T:0.40
Consensus pattern (20 bp):
TGATTATTGATTAATAAAAA
Found at i:13852 original size:65 final size:65
Alignment explanation
Indices: 13743--13876 Score: 252
Period size: 65 Copynumber: 2.1 Consensus size: 65
13733 TGGTATTTGT
13743 AATCTCTGATTATTGATTAATGAAAATGATTATTTGATCTAAAAAAAATTATGTTCTAACAACGA
1 AATCTCTGATTATTGATTAATGAAAATGATTATTTGATCTAAAAAAAATTATGTTCTAACAACGA
*
13808 AATCTCTGATTATTGATTAATGAAAGTGATTATTTGAT-TAAAAAAAATTATGTTCTAACAACGA
1 AATCTCTGATTATTGATTAATGAAAATGATTATTTGATCTAAAAAAAATTATGTTCTAACAACGA
13872 AATCT
1 AATCT
13877 AATCTCTGGA
Statistics
Matches: 68, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
64 31 0.46
65 37 0.54
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (65 bp):
AATCTCTGATTATTGATTAATGAAAATGATTATTTGATCTAAAAAAAATTATGTTCTAACAACGA
Found at i:20919 original size:13 final size:13
Alignment explanation
Indices: 20901--20931 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
20891 TCAAAAACAA
20901 CTGAAAAGTACTT
1 CTGAAAAGTACTT
*
20914 CTGAAAGGTACTT
1 CTGAAAAGTACTT
20927 CTGAA
1 CTGAA
20932 TTTTCCGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (13 bp):
CTGAAAAGTACTT
Found at i:26582 original size:42 final size:42
Alignment explanation
Indices: 26536--26633 Score: 124
Period size: 42 Copynumber: 2.3 Consensus size: 42
26526 TGATGGTCTC
*
26536 TCTTCTGGCTGCTCCTCTCTCCTCCTTGGACTCCATTCTTCT
1 TCTTCTCGCTGCTCCTCTCTCCTCCTTGGACTCCATTCTTCT
* ** * * *
26578 TCTTCCCGAGGCTGCTCTCTTCTTCTTGGACTCCATTCTTCT
1 TCTTCTCGCTGCTCCTCTCTCCTCCTTGGACTCCATTCTTCT
*
26620 TCCTCTCGCTGCTC
1 TCTTCTCGCTGCTC
26634 TTGTTCTTCC
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.05, C:0.40, G:0.13, T:0.42
Consensus pattern (42 bp):
TCTTCTCGCTGCTCCTCTCTCCTCCTTGGACTCCATTCTTCT
Found at i:28629 original size:30 final size:31
Alignment explanation
Indices: 28590--28652 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 31
28580 TTTATCTTGA
28590 TTTTCCTCTTATACCCTCAAATTTTAATGAC
1 TTTTCCTCTTATACCCTCAAATTTTAATGAC
28621 TTTT-CTCTTATACCCTCAAATTTTAATGAC
1 TTTTCCTCTTATACCCTCAAATTTTAATGAC
28651 TT
1 TT
28653 ATTAACCATT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 28 0.88
31 4 0.12
ACGTcount: A:0.25, C:0.24, G:0.03, T:0.48
Consensus pattern (31 bp):
TTTTCCTCTTATACCCTCAAATTTTAATGAC
Found at i:43218 original size:2 final size:2
Alignment explanation
Indices: 43211--43235 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
43201 GATAACATTC
43211 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
43236 AGGGAATGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:46562 original size:20 final size:20
Alignment explanation
Indices: 46537--46575 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
46527 TTTTAAAAAT
46537 TTGGAACGGATTTAGGAACA
1 TTGGAACGGATTTAGGAACA
*
46557 TTGGAATGGATTTAGGAAC
1 TTGGAACGGATTTAGGAAC
46576 GACTCCCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.08, G:0.31, T:0.28
Consensus pattern (20 bp):
TTGGAACGGATTTAGGAACA
Found at i:55185 original size:36 final size:36
Alignment explanation
Indices: 55138--55207 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
55128 GAGATTTTGG
* *
55138 AGAAATATGATAATCAAAATTACAAAATATGTAATA
1 AGAAATATGATAACCAAAATTACAAAAAATGTAATA
55174 AGAAATATGATAACCAAAATTACAAAAAATGTAA
1 AGAAATATGATAACCAAAATTACAAAAAATGTAA
55208 GGTTATTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.60, C:0.07, G:0.09, T:0.24
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATTACAAAAAATGTAATA
Found at i:55961 original size:180 final size:180
Alignment explanation
Indices: 55659--56006 Score: 606
Period size: 180 Copynumber: 1.9 Consensus size: 180
55649 TTACTAATGT
*
55659 TATTAAGAATGTAAGGATTGGTAAATACAATTTAAAAAACTTTTATAGCTTTTTTAGTAGATTAC
1 TATTAAGAATGTAAGGATTGGTAAATACAATTTAAAAAACTTTTATAGCTTTTATAGTAGATTAC
*
55724 TCAAGTAATTAAATTGGTAACTTTCATTATTAATCATAAAAAGTTACTAAAATTAATAAGGATGT
66 TCAAGTAATTAAATTGGCAACTTTCATTATTAATCATAAAAAGTTACTAAAATTAATAAGGATGT
55789 AAGATTACTTGAATCTAGATAGTACTATAATGTTTTTCGGCAAAAAAAAA
131 AAGATTACTTGAATCTAGATAGTACTATAATGTTTTTCGGCAAAAAAAAA
* * *
55839 TATTAAGAATGTAAGGATTGGTAAATACAATTTTAATAACTTTTTTAGCTTTTATAGTAGATTAC
1 TATTAAGAATGTAAGGATTGGTAAATACAATTTAAAAAACTTTTATAGCTTTTATAGTAGATTAC
* * * *
55904 TTAAGTAATTAAATTGGCAGCTTTCATTATTGATCATACAAAGTTACTAAAATTAATAAGGATGT
66 TCAAGTAATTAAATTGGCAACTTTCATTATTAATCATAAAAAGTTACTAAAATTAATAAGGATGT
*
55969 AAGATTATTTGAATCTAGATAGTACTATAATGTTTTTC
131 AAGATTACTTGAATCTAGATAGTACTATAATGTTTTTC
56007 ATAACTTTTT
Statistics
Matches: 158, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
180 158 1.00
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (180 bp):
TATTAAGAATGTAAGGATTGGTAAATACAATTTAAAAAACTTTTATAGCTTTTATAGTAGATTAC
TCAAGTAATTAAATTGGCAACTTTCATTATTAATCATAAAAAGTTACTAAAATTAATAAGGATGT
AAGATTACTTGAATCTAGATAGTACTATAATGTTTTTCGGCAAAAAAAAA
Found at i:57741 original size:95 final size:95
Alignment explanation
Indices: 57627--57808 Score: 319
Period size: 95 Copynumber: 1.9 Consensus size: 95
57617 AAATTGATAA
*
57627 TCTTATTGCATCAGAGATCGATAACCTTCTTAATTGATTAATATTTAACTTCGTTCTTAGTAACC
1 TCTTATTGCATCAGAGATCGATAACCTTCTTAATTGATTAATATTTAACTTCGTTCTTAATAACC
57692 CTGTAGTTCTTTTAGTAAATTCTTTCTTCT
66 CTGTAGTTCTTTTAGTAAATTCTTTCTTCT
* * *
57722 TCTTCTTGCATCAGAGATCGATAACCTTCTTAATTGATTAATGTTTAACTTCGTTCTTAATAGCC
1 TCTTATTGCATCAGAGATCGATAACCTTCTTAATTGATTAATATTTAACTTCGTTCTTAATAACC
*
57787 CTGTAGTTTTTTTAGTAAATTC
66 CTGTAGTTCTTTTAGTAAATTC
57809 AAATAAGAAA
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
95 82 1.00
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.46
Consensus pattern (95 bp):
TCTTATTGCATCAGAGATCGATAACCTTCTTAATTGATTAATATTTAACTTCGTTCTTAATAACC
CTGTAGTTCTTTTAGTAAATTCTTTCTTCT
Found at i:60656 original size:21 final size:21
Alignment explanation
Indices: 60614--60658 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
60604 CGCAGCCAAC
*
60614 TCCTCCTCCGCCTCCTCCCCT
1 TCCTCCTCCGCCACCTCCCCT
* * *
60635 TCCTCCTCCTCCACTTCTCCT
1 TCCTCCTCCGCCACCTCCCCT
60656 TCC
1 TCC
60659 ACTCTCAGCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.02, C:0.62, G:0.02, T:0.33
Consensus pattern (21 bp):
TCCTCCTCCGCCACCTCCCCT
Found at i:82258 original size:21 final size:21
Alignment explanation
Indices: 82217--82259 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
82207 ACTTAATTAA
*
82217 AAATAAAGAAAATAAATAAAT
1 AAATAAAGAAAATAAAAAAAT
*
82238 AAATAAATAAAA-ACAAAAAAT
1 AAATAAAGAAAATA-AAAAAAT
82259 A
1 A
82260 TGTACCCAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.16
Consensus pattern (21 bp):
AAATAAAGAAAATAAAAAAAT
Found at i:84202 original size:13 final size:13
Alignment explanation
Indices: 84184--84211 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
84174 CTATAGTGTA
84184 GACTGGTAATTGG
1 GACTGGTAATTGG
84197 GACTGGTAATTGG
1 GACTGGTAATTGG
84210 GA
1 GA
84212 AGAAGAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.07, G:0.39, T:0.29
Consensus pattern (13 bp):
GACTGGTAATTGG
Found at i:84590 original size:1 final size:1
Alignment explanation
Indices: 84584--84615 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
84574 TTAGTCTGGG
84584 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
84616 AACTTTTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:92648 original size:23 final size:21
Alignment explanation
Indices: 92616--92657 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
92606 AAGCGGAGAA
92616 AACAGGGAAGGAAAAAAGAAAAG
1 AACAGGGAA-G-AAAAAGAAAAG
*
92639 AACAGTGAAGAAAAAGAAA
1 AACAGGGAAGAAAAAGAAA
92658 GAAGAGGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 1 0.06
23 8 0.44
ACGTcount: A:0.67, C:0.05, G:0.26, T:0.02
Consensus pattern (21 bp):
AACAGGGAAGAAAAAGAAAAG
Found at i:92708 original size:5 final size:5
Alignment explanation
Indices: 92698--92741 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
92688 CTTATCATGC
* *
92698 CTTTT CTTTT CCCTTT CTTTT CTTTT CTTTT CCTTTT TTTTT CT
1 CTTTT CTTTT -CTTTT CTTTT CTTTT CTTTT -CTTTT CTTTT CT
92742 GAAAATTACG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
5 24 0.73
6 9 0.27
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (5 bp):
CTTTT
Found at i:92716 original size:11 final size:11
Alignment explanation
Indices: 92697--92740 Score: 63
Period size: 11 Copynumber: 4.1 Consensus size: 11
92687 GCTTATCATG
92697 CCTTTTCTTTT
1 CCTTTTCTTTT
*
92708 CCCTTTCTTTT
1 CCTTTTCTTTT
92719 -CTTTTCTTTT
1 CCTTTTCTTTT
*
92729 CCTTTTTTTTT
1 CCTTTTCTTTT
92740 C
1 C
92741 TGAAAATTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 9 0.31
11 20 0.69
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (11 bp):
CCTTTTCTTTT
Found at i:92724 original size:21 final size:21
Alignment explanation
Indices: 92698--92741 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
92688 CTTATCATGC
92698 CTTTTCTTTTCCCTTTCTTTT
1 CTTTTCTTTTCCCTTTCTTTT
* *
92719 CTTTTCTTTTCCTTTTTTTTT
1 CTTTTCTTTTCCCTTTCTTTT
92740 CT
1 CT
92742 GAAAATTACG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (21 bp):
CTTTTCTTTTCCCTTTCTTTT
Found at i:92733 original size:16 final size:16
Alignment explanation
Indices: 92697--92741 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
92687 GCTTATCATG
*
92697 CCTTTTCTTTTCCCTTT
1 CCTTTTCTTTT-CTTTT
92714 -CTTTTCTTTTCTTTT
1 CCTTTTCTTTTCTTTT
*
92729 CCTTTTTTTTTCT
1 CCTTTTCTTTTCT
92742 GAAAATTACG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 4 0.16
16 21 0.84
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (16 bp):
CCTTTTCTTTTCTTTT
Found at i:93469 original size:53 final size:53
Alignment explanation
Indices: 93389--93521 Score: 187
Period size: 53 Copynumber: 2.5 Consensus size: 53
93379 GACCAGAGCC
* *
93389 TTCATAGGCATAGCTACTTTTATCTCACTGAA-CAACATTCTAATCTTACTAGT
1 TTCATAGACATAGCTACTTTTATCTCACT-AAGCAACATCCTAATCTTACTAGT
* * *
93442 TTCATAGACATAGCTACTTTTATCTCACTAAGTAATATCCTAATTTTACTAGT
1 TTCATAGACATAGCTACTTTTATCTCACTAAGCAACATCCTAATCTTACTAGT
* *
93495 TTCATAGACATAGCTGCTTTGATCTCA
1 TTCATAGACATAGCTACTTTTATCTCA
93522 TCGAAGACCG
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
52 2 0.03
53 70 0.97
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (53 bp):
TTCATAGACATAGCTACTTTTATCTCACTAAGCAACATCCTAATCTTACTAGT
Found at i:97092 original size:17 final size:18
Alignment explanation
Indices: 97070--97104 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
97060 AAAAATGTAG
97070 GCCAT-AAACAGAAACAT
1 GCCATAAAACAGAAACAT
97087 GCCATAAAACAGAAACAT
1 GCCATAAAACAGAAACAT
97105 ACTTGATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.54, C:0.23, G:0.11, T:0.11
Consensus pattern (18 bp):
GCCATAAAACAGAAACAT
Found at i:102937 original size:11 final size:11
Alignment explanation
Indices: 102921--102945 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
102911 AACCATTGCA
102921 TTTTTATATAC
1 TTTTTATATAC
102932 TTTTTATATAC
1 TTTTTATATAC
102943 TTT
1 TTT
102946 GGGGATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTTTATATAC
Done.