Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012416.1 Corchorus olitorius cultivar O-4 contig12449, 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: 35451
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:12 original size:2 final size:2
Alignment explanation
Indices: 6--78 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
1 CTTCT
6 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
48 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
79 GCCGTGCATC
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:574 original size:14 final size:16
Alignment explanation
Indices: 547--578 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
537 AGAAATTGGG
547 AAGAGAGTATAAAAGA
1 AAGAGAGTATAAAAGA
563 AAGAGAG-A-AAAAGA
1 AAGAGAGTATAAAAGA
577 AA
1 AA
579 AAGAAAAGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 1 0.06
16 7 0.44
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.06
Consensus pattern (16 bp):
AAGAGAGTATAAAAGA
Found at i:813 original size:41 final size:41
Alignment explanation
Indices: 756--838 Score: 132
Period size: 41 Copynumber: 2.0 Consensus size: 41
746 TGATAATGAA
756 ATTAGCATTAATTGAAGGAAT-AAGCTTTAATCAAACCCAGC
1 ATTAGCATTAATTGAAGGAATCAA-CTTTAATCAAACCCAGC
* *
797 ATTAGCTTTAATTGAAGGAATCAACTTTAATCAAACCTAGC
1 ATTAGCATTAATTGAAGGAATCAACTTTAATCAAACCCAGC
838 A
1 A
839 GTAATTGTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
41 37 0.95
42 2 0.05
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.29
Consensus pattern (41 bp):
ATTAGCATTAATTGAAGGAATCAACTTTAATCAAACCCAGC
Found at i:2499 original size:30 final size:30
Alignment explanation
Indices: 2463--2524 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
2453 GTTAATAAGC
2463 CATTAAAATTTGAGGGTATAAGAGGAAAGT
1 CATTAAAATTTGAGGGTATAAGAGGAAAGT
2493 CATTAAAATTTGAGGGTATAAGAGGAAAGT
1 CATTAAAATTTGAGGGTATAAGAGGAAAGT
2523 CA
1 CA
2525 AGGAAAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.44, C:0.05, G:0.26, T:0.26
Consensus pattern (30 bp):
CATTAAAATTTGAGGGTATAAGAGGAAAGT
Found at i:2634 original size:22 final size:22
Alignment explanation
Indices: 2592--2634 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2582 TTTTTTTGTT
* *
2592 TTTTGTTTTTGTTTCGCTTTTG
1 TTTTATTTTTGTTACGCTTTTG
*
2614 TTTTATTTTTGTTACGTTTTT
1 TTTTATTTTTGTTACGCTTTT
2635 TAAATTTTGA
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:0.05, C:0.07, G:0.14, T:0.74
Consensus pattern (22 bp):
TTTTATTTTTGTTACGCTTTTG
Found at i:4723 original size:13 final size:13
Alignment explanation
Indices: 4705--4731 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4695 AAACGGAAAA
4705 TCCAGAAGTGCTT
1 TCCAGAAGTGCTT
4718 TCCAGAAGTGCTT
1 TCCAGAAGTGCTT
4731 T
1 T
4732 TCAGTTGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (13 bp):
TCCAGAAGTGCTT
Found at i:14115 original size:26 final size:25
Alignment explanation
Indices: 14069--14117 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
14059 TTCAAAACAA
*
14069 ATTAATAATAATATAACTAAATACC
1 ATTAATAAAAATATAACTAAATACC
* *
14094 ATTAATTAAAAATATTATTAAATA
1 ATTAA-TAAAAATATAACTAAATA
14118 AATAATACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 5 0.25
26 15 0.75
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (25 bp):
ATTAATAAAAATATAACTAAATACC
Found at i:15300 original size:35 final size:34
Alignment explanation
Indices: 15240--15308 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
15230 CAATTTGAGC
15240 AATTAGCCCCAAAAAAATGATAAAAAAGAAACTA
1 AATTAGCCCCAAAAAAATGATAAAAAAGAAACTA
*
15274 AATTAGCCCCCAAAAAATGATAAAAAAGAAACTA
1 AATTAGCCCCAAAAAAATGATAAAAAAGAAACTA
15308 A
1 A
15309 CAAGTGATTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.61, C:0.16, G:0.09, T:0.14
Consensus pattern (34 bp):
AATTAGCCCCAAAAAAATGATAAAAAAGAAACTA
Found at i:24342 original size:15 final size:16
Alignment explanation
Indices: 24310--24340 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
24300 TTTTTAAAAA
24310 AAAAGGAAAGATTTTT
1 AAAAGGAAAGATTTTT
*
24326 AAAATGAAAGATTTT
1 AAAAGGAAAGATTTT
24341 AATTCTGAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (16 bp):
AAAAGGAAAGATTTTT
Found at i:24860 original size:9 final size:9
Alignment explanation
Indices: 24846--24939 Score: 174
Period size: 9 Copynumber: 10.7 Consensus size: 9
24836 GTTATGTTGG
24846 CCAAAGCCC
1 CCAAAGCCC
24855 CCAAAGCCC
1 CCAAAGCCC
24864 CCAAAGCCC
1 CCAAAGCCC
24873 CCAAAG-CC
1 CCAAAGCCC
24881 CCAAAG-CC
1 CCAAAGCCC
24889 CCAAAGCCC
1 CCAAAGCCC
24898 CCAAAGCCC
1 CCAAAGCCC
24907 CCAAAGCCC
1 CCAAAGCCC
24916 CCAAAGCCC
1 CCAAAGCCC
24925 CCAAAGCCC
1 CCAAAGCCC
24934 CCAAAG
1 CCAAAG
24940 GTGCTTGTGT
Statistics
Matches: 84, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
8 16 0.19
9 68 0.81
ACGTcount: A:0.35, C:0.53, G:0.12, T:0.00
Consensus pattern (9 bp):
CCAAAGCCC
Found at i:25084 original size:5 final size:5
Alignment explanation
Indices: 25074--25098 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
25064 GGTCCGATCG
25074 ATTCA ATTCA ATTCA ATTCA ATTCA
1 ATTCA ATTCA ATTCA ATTCA ATTCA
25099 CAATCACATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
ATTCA
Found at i:30937 original size:27 final size:27
Alignment explanation
Indices: 30876--30930 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
30866 TGCTGCTTCT
* * * *
30876 TCTTCTTGTTGGGGTTGTGGTGGCGCA
1 TCTTTTTGTTGAGGTTGAGGTGCCGCA
30903 TCTTTTTGTTGAGGTTGAGGTGCCGCA
1 TCTTTTTGTTGAGGTTGAGGTGCCGCA
30930 T
1 T
30931 TGTTTTGCTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.07, C:0.15, G:0.36, T:0.42
Consensus pattern (27 bp):
TCTTTTTGTTGAGGTTGAGGTGCCGCA
Found at i:31624 original size:54 final size:53
Alignment explanation
Indices: 31523--31627 Score: 156
Period size: 54 Copynumber: 2.0 Consensus size: 53
31513 CACTTGCCCT
* * *
31523 AACCTTAAAGATTGGGTAATTTCCGTATTCCTAAAATAATAATCACACACATA
1 AACCTTAAAGAATGGGTAATCTCCATATTCCTAAAATAATAATCACACACATA
* *
31576 AACCTTAAAGAATGGGTAAATCTCCATATTCCTAAAATGATAGTCACACACA
1 AACCTTAAAGAATGGGT-AATCTCCATATTCCTAAAATAATAATCACACACA
31628 AAAAAAAATA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
53 16 0.35
54 30 0.65
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (53 bp):
AACCTTAAAGAATGGGTAATCTCCATATTCCTAAAATAATAATCACACACATA
Done.