Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014431.1 Corchorus capsularis cultivar CVL-1 contig14452, 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: 46717
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:9 original size:2 final size:2
Alignment explanation
Indices: 3--46 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1 TC
3 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
45 CT
1 CT
47 TTCACACATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:9124 original size:24 final size:24
Alignment explanation
Indices: 9092--9146 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
9082 TCCTCCAGGC
* * * *
9092 AGAAAAAACCGGCCGTTCCGAAGG
1 AGAAGAAACCGGCAGCTCCAAAGG
*
9116 AGAAGAAACCGGTAGCTCCAAAGG
1 AGAAGAAACCGGCAGCTCCAAAGG
9140 AGAAGAA
1 AGAAGAA
9147 GCCCAAGCAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.44, C:0.20, G:0.29, T:0.07
Consensus pattern (24 bp):
AGAAGAAACCGGCAGCTCCAAAGG
Found at i:11334 original size:29 final size:29
Alignment explanation
Indices: 11294--11353 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
11284 GTAGCGTTTA
*
11294 GACATTTTGCCCCCCAAACTTCAATCTTG
1 GACATTTTGCCCCACAAACTTCAATCTTG
* *
11323 GACATTTTGCCCCATAAACTTCAATTTTG
1 GACATTTTGCCCCACAAACTTCAATCTTG
11352 GA
1 GA
11354 ACGTTTTACC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.27, C:0.28, G:0.12, T:0.33
Consensus pattern (29 bp):
GACATTTTGCCCCACAAACTTCAATCTTG
Found at i:11598 original size:29 final size:30
Alignment explanation
Indices: 11553--11620 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 30
11543 GTTAAGTTGA
*
11553 GGGGTAAAATGTCCCAAAATTGAAGTTCAG-
1 GGGGCAAAATGTCCCAAAATTGAAGTTC-GT
*
11583 GGGGCAAAATGT-CCAAGATTGAAGTTCGT
1 GGGGCAAAATGTCCCAAAATTGAAGTTCGT
11612 GGGGCAAAA
1 GGGGCAAAA
11621 CGTGTAAACG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
28 1 0.03
29 23 0.66
30 11 0.31
ACGTcount: A:0.35, C:0.13, G:0.31, T:0.21
Consensus pattern (30 bp):
GGGGCAAAATGTCCCAAAATTGAAGTTCGT
Found at i:12044 original size:21 final size:21
Alignment explanation
Indices: 12012--12075 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 21
12002 GCCTTATAAG
12012 AAACAATA-ATATATAATGAA
1 AAACAATAGATATATAATGAA
* * * * *
12032 AAACTATAGATATCTTATCAT
1 AAACAATAGATATATAATGAA
12053 AAACAATAG-TATATAATGAA
1 AAACAATAGATATATAATGAA
12073 AAA
1 AAA
12076 TTACCATAGA
Statistics
Matches: 33, Mismatches: 10, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
20 17 0.52
21 16 0.48
ACGTcount: A:0.58, C:0.08, G:0.06, T:0.28
Consensus pattern (21 bp):
AAACAATAGATATATAATGAA
Found at i:18645 original size:13 final size:16
Alignment explanation
Indices: 18627--18666 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
18617 TTGCACCACT
18627 TATAATAT-TT-A-AA
1 TATAATATATTAATAA
18640 TATAATATATTAATAA
1 TATAATATATTAATAA
18656 TATAATATATT
1 TATAATATATT
18667 TTAATCCTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.33
14 2 0.08
15 1 0.04
16 13 0.54
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAATATATTAATAA
Found at i:22030 original size:7 final size:7
Alignment explanation
Indices: 22020--22045 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
22010 ATATAAAATA
22020 TTCAATT
1 TTCAATT
22027 TTCAATT
1 TTCAATT
22034 TTCAATT
1 TTCAATT
22041 TTCAA
1 TTCAA
22046 ATTAAAGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (7 bp):
TTCAATT
Found at i:23662 original size:31 final size:31
Alignment explanation
Indices: 23582--23722 Score: 182
Period size: 31 Copynumber: 4.7 Consensus size: 31
23572 AAAAATGACA
* *
23582 CGTGGCACGTGT--CCTTTT-GTGCACGTGG
1 CGTGCCACGTGTCACCTTTTGGTACACGTGG
* *
23610 CATGTCACGTGTCA-CTTTTGGTACACGTGG
1 CGTGCCACGTGTCACCTTTTGGTACACGTGG
*
23640 CGTGCCACGTGTCACCTTTTGGTACACATGG
1 CGTGCCACGTGTCACCTTTTGGTACACGTGG
* *
23671 CGTGCAATGTGTCACCTTTTGGTACACGTGG
1 CGTGCCACGTGTCACCTTTTGGTACACGTGG
*
23702 CGTGTCACGTGTCACCTTTTG
1 CGTGCCACGTGTCACCTTTTG
23723 TTATATGTGC
Statistics
Matches: 97, Mismatches: 12, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
28 10 0.10
29 5 0.05
30 21 0.22
31 61 0.63
ACGTcount: A:0.13, C:0.26, G:0.28, T:0.33
Consensus pattern (31 bp):
CGTGCCACGTGTCACCTTTTGGTACACGTGG
Found at i:28204 original size:30 final size:30
Alignment explanation
Indices: 28140--28204 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
28130 CTTTTAGATT
** ***
28140 TTCTTACCTGAACTCATCATTTCTTTTTTT
1 TTCTTACCTGAACTCATCATTTCTAATGAG
28170 TTCTTACCTGAACTCATCATTTCTAATGAG
1 TTCTTACCTGAACTCATCATTTCTAATGAG
28200 TTCTT
1 TTCTT
28205 GATTTGTAGG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.20, C:0.23, G:0.06, T:0.51
Consensus pattern (30 bp):
TTCTTACCTGAACTCATCATTTCTAATGAG
Found at i:31296 original size:31 final size:31
Alignment explanation
Indices: 31258--31319 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
31248 GCTTCTTGCA
*
31258 GGCTTATCAAGGGCAGTTAAGAGTGTAGCAT
1 GGCTTATCAAGGGCAGTTAAAAGTGTAGCAT
*
31289 GGCTTATCAATGGCAGTTAAAAGTGTAGCAT
1 GGCTTATCAAGGGCAGTTAAAAGTGTAGCAT
31320 TCGGCAGTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.31, C:0.13, G:0.29, T:0.27
Consensus pattern (31 bp):
GGCTTATCAAGGGCAGTTAAAAGTGTAGCAT
Found at i:34957 original size:21 final size:21
Alignment explanation
Indices: 34933--35000 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 21
34923 CCAATTAAGC
34933 AGCTAAAGGTGGAGCTAATGG
1 AGCTAAAGGTGGAGCTAATGG
* *
34954 AGCTAACGGTGGACCTAATGTAG
1 AGCTAAAGGTGGAGCTAATG--G
* *
34977 TAGCTAATGGTGAAGCTAATGG
1 -AGCTAAAGGTGGAGCTAATGG
34999 AG
1 AG
35001 TTGGTAATCA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
21 20 0.51
22 1 0.03
23 1 0.03
24 17 0.44
ACGTcount: A:0.32, C:0.12, G:0.34, T:0.22
Consensus pattern (21 bp):
AGCTAAAGGTGGAGCTAATGG
Found at i:35802 original size:21 final size:22
Alignment explanation
Indices: 35778--35827 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 22
35768 GTATTCTCCC
*
35778 TTATT-ATATTTGTACAAGGTG
1 TTATTCATATTTGTACAAAGTG
*
35799 TTATTCTCTTATTTGTACAAAGTG
1 TTA-T-TCATATTTGTACAAAGTG
35823 TTATT
1 TTATT
35828 TTTTAGTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
21 3 0.12
22 2 0.08
23 2 0.08
24 17 0.71
ACGTcount: A:0.26, C:0.08, G:0.14, T:0.52
Consensus pattern (22 bp):
TTATTCATATTTGTACAAAGTG
Found at i:36305 original size:12 final size:12
Alignment explanation
Indices: 36288--36313 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
36278 GAAACATGAA
36288 TGATATTTGTTT
1 TGATATTTGTTT
36300 TGATATTTGTTT
1 TGATATTTGTTT
36312 TG
1 TG
36314 CTTAATGTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.19, T:0.65
Consensus pattern (12 bp):
TGATATTTGTTT
Found at i:45620 original size:2 final size:2
Alignment explanation
Indices: 45613--45649 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
45603 TTAACTTGAA
45613 AT AT AT 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 AT AT AT A
45650 ATAAACAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.