Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013226.1 Corchorus capsularis cultivar CVL-1 contig13247, 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: 66387
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:8442 original size:33 final size:33
Alignment explanation
Indices: 8398--8472 Score: 114
Period size: 33 Copynumber: 2.3 Consensus size: 33
8388 AATGACCCGT
*
8398 GCCGCCCCAGGAGAGCGGCTTACCATGGCTCAA
1 GCCGCCCCAGGAGAGCGGCTTACCATGACTCAA
* * *
8431 GCCGCCTCAGGAGGGTGGCTTACCATGACTCAA
1 GCCGCCCCAGGAGAGCGGCTTACCATGACTCAA
8464 GCCGCCCCA
1 GCCGCCCCA
8473 CTAGGGCGGC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.20, C:0.37, G:0.29, T:0.13
Consensus pattern (33 bp):
GCCGCCCCAGGAGAGCGGCTTACCATGACTCAA
Found at i:9010 original size:3 final size:3
Alignment explanation
Indices: 8961--8988 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
8951 AATAATAATA
8961 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
8989 ATTAATAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:12051 original size:30 final size:28
Alignment explanation
Indices: 11978--12051 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
11968 GACTCAAACC
* * *
11978 TATAAATAGATGGACTAAATTTATTTTT
1 TATAAGTAGATGGACCAAATTGATTTTT
* *
12006 TTTAAGTAGAAGGACCAAATTGACTTTTCT
1 TATAAGTAGATGGACCAAATTGA-TTTT-T
*
12036 TATAAGTATATGGACC
1 TATAAGTAGATGGACC
12052 TGCCACGTAT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
28 18 0.50
29 4 0.11
30 14 0.39
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.39
Consensus pattern (28 bp):
TATAAGTAGATGGACCAAATTGATTTTT
Found at i:12830 original size:21 final size:21
Alignment explanation
Indices: 12806--12845 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
12796 TCCTCTCCAC
*
12806 AACCCT-TTCCTCAATTTCCGA
1 AACCCTCTTCC-CAAATTCCGA
12827 AACCCTCTTCCCAAATTCC
1 AACCCTCTTCCCAAATTCC
12846 TCAAATGCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.25, C:0.42, G:0.03, T:0.30
Consensus pattern (21 bp):
AACCCTCTTCCCAAATTCCGA
Found at i:17446 original size:32 final size:30
Alignment explanation
Indices: 17394--17457 Score: 74
Period size: 32 Copynumber: 2.1 Consensus size: 30
17384 TCAAATCACG
*
17394 ACCCATGAAATTTTAAATTTAAGATAATTT
1 ACCCATGAAATTTTAAATTTAAGACAATTT
* * *
17424 ACCCTATGAACTTTTCAGATTTAGGACAATTT
1 ACCC-ATGAAATTTT-AAATTTAAGACAATTT
17456 AC
1 AC
17458 TCATTGATGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 4 0.14
31 9 0.32
32 15 0.54
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (30 bp):
ACCCATGAAATTTTAAATTTAAGACAATTT
Found at i:18541 original size:114 final size:113
Alignment explanation
Indices: 18341--18566 Score: 335
Period size: 114 Copynumber: 2.0 Consensus size: 113
18331 ATATAACACT
* * *
18341 TTTCAATCGATTTTCAATTTTTCATATTCATTTCCGTGGCATGGGCTGTTCACAATAGCCCAACT
1 TTTCAATCGATTTTCAAATTTTCATATTCATTTCCGTGCCATGAGCTGTTCACAATAGCCCAACT
* *
18406 ATCATTATTGGGCTAGAAACCCCCATAATTTTATCCATTTGGGCCTAAC
66 ATCATTATTGGGCTA-AAAACCCCATAATTTAATCCATTTGGGCCTAAC
* * *
18455 TTTCAATCGATTTTCAAATTTTCATGTTCATTTCCGTGCCATGAGCTGTTCATAATAGCCCAATT
1 TTTCAATCGATTTTCAAATTTTCATATTCATTTCCGTGCCATGAGCTGTTCACAATAGCCCAACT
* * * *
18520 TTCATTATTGGTCTAAAAACCCCATGATTTAATCCGTTTGGGCCTAA
66 ATCATTATTGGGCTAAAAACCCCATAATTTAATCCATTTGGGCCTAA
18567 TTGGCATAAA
Statistics
Matches: 100, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
113 28 0.28
114 72 0.72
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.38
Consensus pattern (113 bp):
TTTCAATCGATTTTCAAATTTTCATATTCATTTCCGTGCCATGAGCTGTTCACAATAGCCCAACT
ATCATTATTGGGCTAAAAACCCCATAATTTAATCCATTTGGGCCTAAC
Found at i:26232 original size:17 final size:18
Alignment explanation
Indices: 26195--26232 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
26185 AGAACATGCT
* *
26195 TTTCATTTTTGTAACTTC
1 TTTCATGTTTGTAAATTC
26213 TTTCATGTTT-TAAATTC
1 TTTCATGTTTGTAAATTC
26230 TTT
1 TTT
26233 TACCACTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.18, C:0.13, G:0.05, T:0.63
Consensus pattern (18 bp):
TTTCATGTTTGTAAATTC
Found at i:27880 original size:25 final size:22
Alignment explanation
Indices: 27840--27885 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
27830 AAAGGCATAC
*
27840 ATATATATAGTGAATATACTAGA
1 ATATATATAGTCAATA-ACTAGA
27863 ATATATATAGATTCAATAACTAG
1 ATATATATAG--TCAATAACTAG
27886 TAACTATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 10 0.50
24 5 0.25
25 5 0.25
ACGTcount: A:0.48, C:0.07, G:0.11, T:0.35
Consensus pattern (22 bp):
ATATATATAGTCAATAACTAGA
Found at i:36422 original size:25 final size:25
Alignment explanation
Indices: 36366--36422 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
36356 GAAGAGAATT
*
36366 TATAACAAACAGCCACAAAACTTAA
1 TATAACAAACAACCACAAAACTTAA
* *
36391 TACAACAAACAACCACAGAACTTACA
1 TATAACAAACAACCACAAAACTTA-A
36417 T-TAACA
1 TATAACA
36423 GATAAACACT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 25 0.93
26 2 0.07
ACGTcount: A:0.54, C:0.26, G:0.04, T:0.16
Consensus pattern (25 bp):
TATAACAAACAACCACAAAACTTAA
Found at i:36949 original size:27 final size:27
Alignment explanation
Indices: 36911--36971 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
36901 TTGAGAGAGA
*
36911 GAGAGAGGGCTGTTTTTGGGTGTTTTT
1 GAGAGAGGGCTGTCTTTGGGTGTTTTT
*
36938 GAGAGAGTGCTGTCTTTGGGTGTTTTT
1 GAGAGAGGGCTGTCTTTGGGTGTTTTT
36965 GAGAGAG
1 GAGAGAG
36972 AGAGTGATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.15, C:0.05, G:0.41, T:0.39
Consensus pattern (27 bp):
GAGAGAGGGCTGTCTTTGGGTGTTTTT
Found at i:39091 original size:38 final size:37
Alignment explanation
Indices: 39004--39094 Score: 121
Period size: 38 Copynumber: 2.4 Consensus size: 37
38994 TTAATTAGTC
*
39004 GGTAAGTTTAATTGGTTAATTAGTCTTAGTCTGATTG
1 GGTATGTTTAATTGGTTAATTAGTCTTAGTCTGATTG
* * *
39041 GATCT-TTCTAATTGGTTAATTAGTCTTTAGTGTGATTG
1 GGTATGTT-TAATTGGTTAATTAGTC-TTAGTCTGATTG
39079 GGTATGTTTAATTGGT
1 GGTATGTTTAATTGGT
39095 CCGTGTCTGT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
36 2 0.04
37 19 0.42
38 22 0.49
39 2 0.04
ACGTcount: A:0.22, C:0.05, G:0.24, T:0.48
Consensus pattern (37 bp):
GGTATGTTTAATTGGTTAATTAGTCTTAGTCTGATTG
Found at i:39217 original size:49 final size:49
Alignment explanation
Indices: 39155--39254 Score: 182
Period size: 49 Copynumber: 2.0 Consensus size: 49
39145 TCCTCTTTAA
*
39155 TTAGTCTTTCGTTTTGGGTCTGTGGGTTGAGTCTGTCTCAGTAGTTAGG
1 TTAGCCTTTCGTTTTGGGTCTGTGGGTTGAGTCTGTCTCAGTAGTTAGG
*
39204 TTAGCCTTTCGTTTTGGGTCTGTGGGTTGAGTCTGTCTCAGTAGTTGGG
1 TTAGCCTTTCGTTTTGGGTCTGTGGGTTGAGTCTGTCTCAGTAGTTAGG
39253 TT
1 TT
39255 TTGGTATTGT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.09, C:0.13, G:0.33, T:0.45
Consensus pattern (49 bp):
TTAGCCTTTCGTTTTGGGTCTGTGGGTTGAGTCTGTCTCAGTAGTTAGG
Found at i:40928 original size:27 final size:27
Alignment explanation
Indices: 40890--40985 Score: 111
Period size: 27 Copynumber: 3.3 Consensus size: 27
40880 CTTCCATTTT
*
40890 TGTCTTTGGGTGTTTTTGAGATAGTGC
1 TGTCTTTGGGTGTTTTTGAGAGAGTGC
* *
40917 TGTCTTTGGGTGTTTTTGTTAGAGAGAGAGGGA
1 TGTCTTTGGGTG--TTT-TT---GAGAGAGTGC
40950 TGTCTTTGGGTGTTTTTGAGAGAGTGC
1 TGTCTTTGGGTGTTTTTGAGAGAGTGC
40977 TGTCTTTGG
1 TGTCTTTGG
40986 TGGTTGGGAA
Statistics
Matches: 58, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
27 29 0.50
29 3 0.05
30 4 0.07
31 3 0.05
33 19 0.33
ACGTcount: A:0.12, C:0.06, G:0.36, T:0.45
Consensus pattern (27 bp):
TGTCTTTGGGTGTTTTTGAGAGAGTGC
Found at i:41173 original size:2 final size:2
Alignment explanation
Indices: 41125--41153 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
41115 TTCACCCGAA
41125 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
41154 CACACACACA
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:42553 original size:21 final size:22
Alignment explanation
Indices: 42506--42568 Score: 76
Period size: 21 Copynumber: 2.9 Consensus size: 22
42496 ATTTACCTCC
*
42506 TTATGAAACTTTGATGACCATA
1 TTATGAAATTTTGATGACCATA
*
42528 TTATGAAATTTTGGT-ACCAT-
1 TTATGAAATTTTGATGACCATA
*
42548 TCTATGAAATTTTGATAACCA
1 T-TATGAAATTTTGATGACCA
42569 CACTATAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 1 0.03
21 18 0.50
22 17 0.47
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (22 bp):
TTATGAAATTTTGATGACCATA
Found at i:42574 original size:22 final size:22
Alignment explanation
Indices: 42507--42602 Score: 79
Period size: 22 Copynumber: 4.4 Consensus size: 22
42497 TTTACCTCCT
* * * *
42507 TATGAAACTTTGATGACCATAT
1 TATGAAATTTTGATAACCACAC
* **
42529 TATGAAATTTTGGT-ACCATTC
1 TATGAAATTTTGATAACCACAC
42550 TATGAAATTTTGATAACCACAC
1 TATGAAATTTTGATAACCACAC
* * *
42572 TATAAAATTGTGATAACCTCTA-
1 TATGAAATTTTGATAACCAC-AC
42594 TATGAAATT
1 TATGAAATT
42603 AATTTTGATG
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
21 18 0.30
22 42 0.69
23 1 0.02
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAC
Found at i:42692 original size:22 final size:22
Alignment explanation
Indices: 42667--42708 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
42657 GATTTGGTAC
42667 ACTATGAAATTTGGATAACCAT
1 ACTATGAAATTTGGATAACCAT
* *
42689 ACTATGAACTTTTGATAACC
1 ACTATGAAATTTGGATAACC
42709 TCCCTATGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (22 bp):
ACTATGAAATTTGGATAACCAT
Found at i:42742 original size:22 final size:22
Alignment explanation
Indices: 42700--42742 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
42690 CTATGAACTT
* *
42700 TTGATAACCTCCCTATGGAATG
1 TTGATAACCTCCATATAGAATG
*
42722 TTGATAACTTCCATATAGAAT
1 TTGATAACCTCCATATAGAAT
42743 TTCGTTAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (22 bp):
TTGATAACCTCCATATAGAATG
Found at i:42803 original size:22 final size:23
Alignment explanation
Indices: 42778--42832 Score: 87
Period size: 22 Copynumber: 2.5 Consensus size: 23
42768 GGTTACATTC
*
42778 TATGAAATTTTTG-TAACCCCAT
1 TATGAAATTTTTGATAACCACAT
42800 TATGAAA-TTTTGATAACCACAT
1 TATGAAATTTTTGATAACCACAT
42822 TATGAAATTTT
1 TATGAAATTTT
42833 GCTGGGCATA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 5 0.17
22 22 0.73
23 3 0.10
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (23 bp):
TATGAAATTTTTGATAACCACAT
Found at i:43796 original size:28 final size:28
Alignment explanation
Indices: 43765--43824 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
43755 TATTATACTA
43765 TAATATTAAGCATATGTTAGTAATTGAC
1 TAATATTAAGCATATGTTAGTAATTGAC
** *
43793 TAATATTAAGGGTATTTTAGTAATTGAC
1 TAATATTAAGCATATGTTAGTAATTGAC
43821 TAAT
1 TAAT
43825 TAAGATTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (28 bp):
TAATATTAAGCATATGTTAGTAATTGAC
Found at i:43919 original size:31 final size:31
Alignment explanation
Indices: 43884--43949 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
43874 AACTTTATGT
*
43884 TTTCCGATTGTACATTTATTTTTAAAACATA
1 TTTCCGATTGTACACTTATTTTTAAAACATA
*
43915 TTTCCGATTGTACCCTTATTTTTAAAACATA
1 TTTCCGATTGTACACTTATTTTTAAAACATA
43946 TTTC
1 TTTC
43950 TAAATTGACA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.29, C:0.17, G:0.06, T:0.48
Consensus pattern (31 bp):
TTTCCGATTGTACACTTATTTTTAAAACATA
Found at i:44135 original size:30 final size:31
Alignment explanation
Indices: 44081--44145 Score: 105
Period size: 30 Copynumber: 2.1 Consensus size: 31
44071 TCTTTTATGT
44081 TTTCCAATTGTACCCTTATTTTTAAAACATA
1 TTTCCAATTGTACCCTTATTTTTAAAACATA
* *
44112 TTTCCGATTGTACCCTT-TTTTTAAGACATA
1 TTTCCAATTGTACCCTTATTTTTAAAACATA
44142 TTTC
1 TTTC
44146 TAAATTGCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 16 0.50
31 16 0.50
ACGTcount: A:0.26, C:0.20, G:0.06, T:0.48
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTATTTTTAAAACATA
Found at i:45569 original size:14 final size:15
Alignment explanation
Indices: 45545--45574 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
45535 AAGAAAGAAG
45545 TTTGTTTTTTGTTTT
1 TTTGTTTTTTGTTTT
45560 TTTG-TTTTTGTTTT
1 TTTGTTTTTTGTTTT
45574 T
1 T
45575 GGACGGGCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (15 bp):
TTTGTTTTTTGTTTT
Found at i:46276 original size:2 final size:2
Alignment explanation
Indices: 46269--46297 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
46259 CTAAAATTAG
46269 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
46298 TACAAAATTC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52740 original size:16 final size:16
Alignment explanation
Indices: 52719--52774 Score: 66
Period size: 16 Copynumber: 3.8 Consensus size: 16
52709 AAATATAAAT
52719 ATATATATTACTAGT-
1 ATATATATTACTAGTA
52734 A-ATATA-TA-TAGTA
1 ATATATATTACTAGTA
* *
52747 ATATATTTTTCTAGTA
1 ATATATATTACTAGTA
52763 ATATATATTACT
1 ATATATATTACT
52775 GCATGGACAT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
12 4 0.12
13 3 0.09
14 9 0.27
15 2 0.06
16 15 0.45
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.48
Consensus pattern (16 bp):
ATATATATTACTAGTA
Found at i:55644 original size:22 final size:22
Alignment explanation
Indices: 55616--55660 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
55606 GCACTTATCA
55616 ATTTCAAGTTCGTATGTCTTTT
1 ATTTCAAGTTCGTATGTCTTTT
55638 ATTTCAAGTTCGTATGTCTTTT
1 ATTTCAAGTTCGTATGTCTTTT
55660 A
1 A
55661 AGTGTGTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.20, C:0.13, G:0.13, T:0.53
Consensus pattern (22 bp):
ATTTCAAGTTCGTATGTCTTTT
Found at i:56428 original size:25 final size:25
Alignment explanation
Indices: 56400--56448 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
56390 GGGATTGTGT
* *
56400 TTTTTTTTATATTTATAGGTTAACG
1 TTTTTTTTATATTTACAAGTTAACG
56425 TTTTTTTTATATTTACAAGTTAAC
1 TTTTTTTTATATTTACAAGTTAAC
56449 ATTGTTCGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.27, C:0.06, G:0.08, T:0.59
Consensus pattern (25 bp):
TTTTTTTTATATTTACAAGTTAACG
Found at i:57207 original size:2 final size:2
Alignment explanation
Indices: 57200--57230 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
57190 ATGGTCATAC
57200 AT 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 AT A
57231 AATTAATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:57381 original size:19 final size:19
Alignment explanation
Indices: 57357--57417 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
57347 CACTGTTTAG
*
57357 ATACTGTACATATGAGATT
1 ATACTGTACAGATGAGATT
* *
57376 ATACTGTACAGATCAAATT
1 ATACTGTACAGATGAGATT
*
57395 AGATACTATACAGATGAGATT
1 --ATACTGTACAGATGAGATT
57416 AT
1 AT
57418 TAGAGCAGCG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
19 18 0.53
21 16 0.47
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (19 bp):
ATACTGTACAGATGAGATT
Found at i:57416 original size:21 final size:21
Alignment explanation
Indices: 57353--57416 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
57343 TTGACACTGT
*
57353 TTAGATACTGTACATATGAGA
1 TTAGATACTGTACAGATGAGA
* *
57374 TT--ATACTGTACAGATCAAA
1 TTAGATACTGTACAGATGAGA
*
57393 TTAGATACTATACAGATGAGA
1 TTAGATACTGTACAGATGAGA
57414 TTA
1 TTA
57417 TTAGAGCAGC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 16 0.46
21 19 0.54
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.33
Consensus pattern (21 bp):
TTAGATACTGTACAGATGAGA
Found at i:65137 original size:2 final size:2
Alignment explanation
Indices: 65130--65164 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
65120 AGTTTTGATT
65130 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
65165 TGTCTACATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:66302 original size:15 final size:15
Alignment explanation
Indices: 66282--66322 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
66272 CCTTCGATTG
66282 GAGGAGGGTTGGTTA
1 GAGGAGGGTTGGTTA
* *
66297 GAGGAGGGTCGGTTG
1 GAGGAGGGTTGGTTA
66312 GAGGAGGGTTG
1 GAGGAGGGTTG
66323 TTTCATGATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.17, C:0.02, G:0.59, T:0.22
Consensus pattern (15 bp):
GAGGAGGGTTGGTTA
Done.