Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015736.1 Corchorus olitorius cultivar O-4 contig15769, 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: 24629
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:1096 original size:14 final size:14
Alignment explanation
Indices: 1077--1125 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
1067 TCCATTATCC
1077 AAATAAAATTCATG
1 AAATAAAATTCATG
* *
1091 AAAT-AATTATCATCC
1 AAATAAAAT-TCAT-G
1106 AAATAAAATTCATG
1 AAATAAAATTCATG
1120 AAATAA
1 AAATAA
1126 TTATCACAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
13 3 0.11
14 14 0.50
15 8 0.29
16 3 0.11
ACGTcount: A:0.57, C:0.10, G:0.04, T:0.29
Consensus pattern (14 bp):
AAATAAAATTCATG
Found at i:1105 original size:29 final size:29
Alignment explanation
Indices: 1073--1131 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1063 CAAATCCATT
1073 ATCCAAATAAAATTCATGAAATAATTATC
1 ATCCAAATAAAATTCATGAAATAATTATC
1102 ATCCAAATAAAATTCATGAAATAATTATC
1 ATCCAAATAAAATTCATGAAATAATTATC
1131 A
1 A
1132 CAAGTTGATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.53, C:0.14, G:0.03, T:0.31
Consensus pattern (29 bp):
ATCCAAATAAAATTCATGAAATAATTATC
Found at i:1118 original size:15 final size:15
Alignment explanation
Indices: 1073--1118 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
1063 CAAATCCATT
1073 ATCCAAATAAAATTC
1 ATCCAAATAAAATTC
* *
1088 AT-GAAAT-AATTATC
1 ATCCAAATAAAAT-TC
1102 ATCCAAATAAAATTC
1 ATCCAAATAAAATTC
1117 AT
1 AT
1119 GAAATAATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 6
0.71 0.12 0.18
Matches are distributed among these distances:
13 3 0.12
14 8 0.33
15 10 0.42
16 3 0.12
ACGTcount: A:0.52, C:0.15, G:0.02, T:0.30
Consensus pattern (15 bp):
ATCCAAATAAAATTC
Found at i:1524 original size:34 final size:34
Alignment explanation
Indices: 1458--1524 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 34
1448 TCATGAATTT
* *****
1458 ATAAGACTATAATCATTCTTTTTTTTTTTGAAAA
1 ATAAGACTATAATCATTCTATTTGAACATGAAAA
1492 ATAAGACTATAATCATTCTATTTGAACATGAAA
1 ATAAGACTATAATCATTCTATTTGAACATGAAA
1525 TGCATAATAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.42
Consensus pattern (34 bp):
ATAAGACTATAATCATTCTATTTGAACATGAAAA
Found at i:3749 original size:75 final size:75
Alignment explanation
Indices: 3626--3778 Score: 234
Period size: 75 Copynumber: 2.0 Consensus size: 75
3616 AAAGTGTCGA
* * * * *
3626 CGGAGCAAGTAATGCATTCACTGATCGAGGAATGTGGTGAAAATAGTGTATATCGACATGATAAG
1 CGGAGCAAGTAACGCATTCAATGATCGAGGAATATGGTGAAAATAGTGTATAACGACATGACAAG
3691 GCAGATGCAG
66 GCAGATGCAG
* * *
3701 CGGAGCAAGTAACGCATTTAATGATTGAGGAATATGGTGAAAATAGTGTATAACGACGTGACAAG
1 CGGAGCAAGTAACGCATTCAATGATCGAGGAATATGGTGAAAATAGTGTATAACGACATGACAAG
3766 GCAGATGCAG
66 GCAGATGCAG
3776 CGG
1 CGG
3779 CAGCGCCTGT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
75 70 1.00
ACGTcount: A:0.35, C:0.13, G:0.30, T:0.22
Consensus pattern (75 bp):
CGGAGCAAGTAACGCATTCAATGATCGAGGAATATGGTGAAAATAGTGTATAACGACATGACAAG
GCAGATGCAG
Found at i:4220 original size:25 final size:25
Alignment explanation
Indices: 4183--4236 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
4173 ATCAGATTTG
*
4183 GGCCCAAGGCCAACTAGCCAAATAA
1 GGCCCAAGACCAACTAGCCAAATAA
4208 GGCCCAAGACCAACTAGCCAAATAA
1 GGCCCAAGACCAACTAGCCAAATAA
4233 GGCC
1 GGCC
4237 AAGGTTCTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.39, C:0.33, G:0.20, T:0.07
Consensus pattern (25 bp):
GGCCCAAGACCAACTAGCCAAATAA
Found at i:13612 original size:60 final size:60
Alignment explanation
Indices: 13512--13628 Score: 173
Period size: 60 Copynumber: 1.9 Consensus size: 60
13502 GGGGGGGGAG
* * *
13512 GGGGGAAATTGTTCCGATTTTGATAGTTTAAGGAGTGAAAGTTCCAAATTAAAAGTTTAA
1 GGGGAAAATTGTTCCGAGTTTGATAGTTTAAGGAGCGAAAGTTCCAAATTAAAAGTTTAA
* *
13572 GGGGAAAATTG-TCCTGAGTTTGATAGTTTAGGGAGCGAAAGTTTCAAATTAAAAGTT
1 GGGGAAAATTGTTCC-GAGTTTGATAGTTTAAGGAGCGAAAGTTCCAAATTAAAAGTT
13629 CAATAGGGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
59 3 0.06
60 48 0.94
ACGTcount: A:0.34, C:0.07, G:0.26, T:0.32
Consensus pattern (60 bp):
GGGGAAAATTGTTCCGAGTTTGATAGTTTAAGGAGCGAAAGTTCCAAATTAAAAGTTTAA
Found at i:13660 original size:60 final size:58
Alignment explanation
Indices: 13530--13666 Score: 134
Period size: 60 Copynumber: 2.3 Consensus size: 58
13520 TTGTTCCGAT
* * * * *
13530 TTTGATAGTTTAAGGAGTGAAAGTTCCAAATTAAAAGTTTAAGGGGAAAATTGTCCTGAG
1 TTTGAAAGTTTAGGGAGCGAAAGTTCCAAATTAAAAGTTCAAAGGGAAAATTGTCCT--G
* *
13590 TTTGATAGTTTAGGGAGCGAAAGTTTCAAATTAAAAGTTCAATAGGGAAAA-TGTCTCT-
1 TTTGAAAGTTTAGGGAGCGAAAGTTCCAAATTAAAAGTTCAA-AGGGAAAATTGTC-CTG
13648 TTTGTAGAAGTTTAAGGGA
1 TTTG-A-AAGTTT-AGGGA
13667 TTAAATGGGC
Statistics
Matches: 66, Mismatches: 6, Indels: 9
0.81 0.07 0.11
Matches are distributed among these distances:
58 4 0.06
59 1 0.02
60 47 0.71
61 14 0.21
ACGTcount: A:0.36, C:0.07, G:0.25, T:0.33
Consensus pattern (58 bp):
TTTGAAAGTTTAGGGAGCGAAAGTTCCAAATTAAAAGTTCAAAGGGAAAATTGTCCTG
Found at i:17276 original size:3 final size:3
Alignment explanation
Indices: 17268--17293 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
17258 TTCATTATAA
17268 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
17294 CTTTCTTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:19905 original size:2 final size:2
Alignment explanation
Indices: 19898--19933 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
19888 ACCTCCGTTT
19898 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19934 AGAAGAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20605 original size:7 final size:7
Alignment explanation
Indices: 20595--20635 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
20585 CCAAAACCCA
20595 AAAAAAG
1 AAAAAAG
20602 AAAAAAG
1 AAAAAAG
20609 AAAAAAG
1 AAAAAAG
20616 AAAAAAG
1 AAAAAAG
20623 AAAAAAG
1 AAAAAAG
20630 AAAAAA
1 AAAAAA
20636 ACCCTTTGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Done.