Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007099.1 Corchorus capsularis cultivar CVL-1 contig07120, 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: 39154
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:277 original size:10 final size:10
Alignment explanation
Indices: 264--290 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
254 AAAAATAAAA
264 AAATTAAATT
1 AAATTAAATT
274 AAATTAAATT
1 AAATTAAATT
284 AAATTAA
1 AAATTAA
291 TAAAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
AAATTAAATT
Found at i:2544 original size:29 final size:29
Alignment explanation
Indices: 2510--2566 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
2500 ACGTTTACAC
*
2510 TTTATAGTTCCAAAGTAGAAATACAAGAT
1 TTTATAGTTCCAAAGTAAAAATACAAGAT
2539 TTTATAGTTCCAAAGTAAAAATACAAGA
1 TTTATAGTTCCAAAGTAAAAATACAAGA
2567 AGTGCAGCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.30
Consensus pattern (29 bp):
TTTATAGTTCCAAAGTAAAAATACAAGAT
Found at i:4944 original size:23 final size:24
Alignment explanation
Indices: 4909--4954 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
4899 ACTAATGATT
* *
4909 AAAGCTACAC-AAAACGAAAAACA
1 AAAGCAACACAAAAAAGAAAAACA
*
4932 AAAGCAACCCAAAAAAGAAAAAC
1 AAAGCAACACAAAAAAGAAAAAC
4955 CCTTAATCCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.67, C:0.22, G:0.09, T:0.02
Consensus pattern (24 bp):
AAAGCAACACAAAAAAGAAAAACA
Found at i:8954 original size:60 final size:60
Alignment explanation
Indices: 8856--9009 Score: 211
Period size: 60 Copynumber: 2.6 Consensus size: 60
8846 TTCTCCATCT
* * * * * *
8856 TCAGACTTCTTTGTTTTGCCACATGAATTATCTATTGCAGCAAACTCTGTAT-AGTAAACC
1 TCAGATTTCTTTCTTTTGCCACACGAATTATCTATTGCAGCAAAATATGGATCA-TAAACC
* *
8916 TCAGATTTCTTTCTTTTGCCACACGAATTATCTGTTGCAGCAAAATATGGATCATAAACT
1 TCAGATTTCTTTCTTTTGCCACACGAATTATCTATTGCAGCAAAATATGGATCATAAACC
*
8976 TCAGATTTCTTTCTTTTTCCACACGAATTATCTA
1 TCAGATTTCTTTCTTTTGCCACACGAATTATCTA
9010 CTACTGCAGC
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
60 82 0.99
61 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (60 bp):
TCAGATTTCTTTCTTTTGCCACACGAATTATCTATTGCAGCAAAATATGGATCATAAACC
Found at i:11309 original size:3 final size:3
Alignment explanation
Indices: 11301--11333 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
11291 ACTCCTCTAA
11301 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
11334 ATATAATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:12119 original size:31 final size:31
Alignment explanation
Indices: 12083--12214 Score: 138
Period size: 31 Copynumber: 4.5 Consensus size: 31
12073 TCCTTTTGTG
*
12083 CACGTGGCATGCCACGTGTCACTTTTTGGTA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
* *
12114 CACGTGGCGTGACATGTGTCACTTTTTGGTA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
*
12145 CA--T---GTGGCAC--G--ACTTTTTGGTA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
* * *
12167 CATGTGGCGTGTCACATGTCACTTTTTGGTA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
12198 CACGTGGCGTGCCACGT
1 CACGTGGCGTGCCACGT
12215 CGGACACTGT
Statistics
Matches: 83, Mismatches: 9, Indels: 18
0.75 0.08 0.16
Matches are distributed among these distances:
22 13 0.16
24 2 0.02
26 5 0.06
27 6 0.07
29 2 0.02
31 55 0.66
ACGTcount: A:0.16, C:0.23, G:0.28, T:0.33
Consensus pattern (31 bp):
CACGTGGCGTGCCACGTGTCACTTTTTGGTA
Found at i:12164 original size:53 final size:53
Alignment explanation
Indices: 12103--12205 Score: 161
Period size: 53 Copynumber: 1.9 Consensus size: 53
12093 GCCACGTGTC
** *
12103 ACTTTTTGGTACACGTGGCGTGACATGTGTCACTTTTTGGTACATGTGGCACG
1 ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGCACG
* *
12156 ACTTTTTGGTACATGTGGCGTGTCACATGTCACTTTTTGGTACACGTGGC
1 ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGC
12206 GTGCCACGTC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.37
Consensus pattern (53 bp):
ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGCACG
Found at i:12855 original size:2 final size:2
Alignment explanation
Indices: 12848--12880 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
12838 AGAGTGCGTG
*
12848 TA TA TA TA TA AA 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 T
12881 TGGAGTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 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):
TA
Found at i:17564 original size:24 final size:24
Alignment explanation
Indices: 17533--17579 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
17523 TCCCTTTTTT
*
17533 AAAACTCTTTTTTAATTTTAAAAA
1 AAAACTCTTTTTTAATTTCAAAAA
17557 AAAACTCTTTTTTAATTTCAAAA
1 AAAACTCTTTTTTAATTTCAAAA
17580 CTTTAGTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.45
Consensus pattern (24 bp):
AAAACTCTTTTTTAATTTCAAAAA
Found at i:18338 original size:3 final size:3
Alignment explanation
Indices: 18332--18361 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
18322 TATATCGTCG
18332 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
18362 CCGCTTCCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:22225 original size:285 final size:285
Alignment explanation
Indices: 21713--22282 Score: 939
Period size: 285 Copynumber: 2.0 Consensus size: 285
21703 TTACAAAATC
* * *
21713 AGATAATAGCATCTCAAACATTTTTGTAATCATTGCACCTTTTTAGTAACTTTAAATAAAAAAAA
1 AGATAATAACATCTCAAACATTTTTGTAACCATTACACCTTTTTAGTAACTTTAAAT-AAAAAAA
* *
21778 AATTAGTAAGCTTCTTCATTATTGACAAAAAGTTACAAAACTTACTGAGAGTGTAAGTTTATTAA
65 AATTAGTAAGCTTCTTCATTATTGACAAAAAGTTACAAAACTTACTAAGAGTGCAAGTTTATTAA
* * *
21843 ATTAACTGATAAAATCTATGTAGAGTTTTTGCTAATCTTAGATAACAAAATTTGTTAATTACCTT
130 ATTAACTGATAAAACCTATGTAGAGTTTTTGCTAACCTCAGATAACAAAATTTGTTAATTACCTT
* * *
21908 TATTATTGACGAAAAGAAACAAAATATTGAATTTATTAATAAGAGTGTAGCATTTTCCTAATCTG
195 TAGTATTGACGAAAAGAAACAAAATATTGAATTTATTAATAAGAGTGTAGCATTTTCATAATCTC
21973 TATAGGTTTTTTAGTAATCTCATGTAA
260 TATA-GTTTTTTAGTAATCTCATGTAA
**
22000 AGATAATAACATCTCAAAC-TATTTTGTAACCATTACAGTTTTTTAGTAACTTTAAAT-AAAAAA
1 AGATAATAACATCTCAAACAT-TTTTGTAACCATTACACCTTTTTAGTAACTTTAAATAAAAAAA
22063 AATTAGTAAGCTTCTTCATTATTGACAAAAAGTTACAAAACTTACTAAGAGTGCAAGTTTATTAA
65 AATTAGTAAGCTTCTTCATTATTGACAAAAAGTTACAAAACTTACTAAGAGTGCAAGTTTATTAA
*
22128 ATTTACTGATAAAACCTATGTAGAGTTTTTGCTAACCTCAGATAACAAAAATTT-TTAATTACCT
130 ATTAACTGATAAAACCTATGTAGAGTTTTTGCTAACCTCAGATAAC-AAAATTTGTTAATTACCT
* *
22192 TTAGTATTGACGAAAGGAAACAAAATATTGAATTTATTGATAAGAGTGTAGCATTTTCATAATCT
194 TTAGTATTGACGAAAAGAAACAAAATATTGAATTTATTAATAAGAGTGTAGCATTTTCATAATCT
22257 CTATAGTTTTTTAGTAATCTCATGTA
259 CTATAGTTTTTTAGTAATCTCATGTA
22283 TGAAGATTGA
Statistics
Matches: 265, Mismatches: 16, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
284 21 0.08
285 186 0.70
286 8 0.03
287 50 0.19
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (285 bp):
AGATAATAACATCTCAAACATTTTTGTAACCATTACACCTTTTTAGTAACTTTAAATAAAAAAAA
ATTAGTAAGCTTCTTCATTATTGACAAAAAGTTACAAAACTTACTAAGAGTGCAAGTTTATTAAA
TTAACTGATAAAACCTATGTAGAGTTTTTGCTAACCTCAGATAACAAAATTTGTTAATTACCTTT
AGTATTGACGAAAAGAAACAAAATATTGAATTTATTAATAAGAGTGTAGCATTTTCATAATCTCT
ATAGTTTTTTAGTAATCTCATGTAA
Found at i:24174 original size:20 final size:21
Alignment explanation
Indices: 24129--24174 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
24119 TGATAAAAAA
24129 AAGAAAAAAAAAGAGAGAACTG
1 AAGAAAAAAAAAGAGAGAAC-G
24151 -AGAAAAAAATAAGA-AGAA-G
1 AAGAAAAAAA-AAGAGAGAACG
24170 AAGAA
1 AAGAA
24175 GAAGGAATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
19 1 0.05
20 4 0.18
21 13 0.59
22 4 0.18
ACGTcount: A:0.72, C:0.02, G:0.22, T:0.04
Consensus pattern (21 bp):
AAGAAAAAAAAAGAGAGAACG
Found at i:24784 original size:2 final size:2
Alignment explanation
Indices: 24779--24825 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
24769 GCATTTAGTA
*
24779 TG TG TG TG TG TG TG TG TG TG TG TG TG CG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
24821 TG TG T
1 TG TG T
24826 ATATATATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.02, G:0.49, T:0.49
Consensus pattern (2 bp):
TG
Found at i:24830 original size:2 final size:2
Alignment explanation
Indices: 24825--24854 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
24815 TGTGTGTGTG
24825 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
24855 GGCAAATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:26219 original size:50 final size:50
Alignment explanation
Indices: 26160--26267 Score: 141
Period size: 52 Copynumber: 2.1 Consensus size: 50
26150 TAGATTACAA
26160 AATCAAATAAT-AT-TTTCA-CAAAAAAAATCAAATAATATCTAAATATATAT
1 AATCAAATAATAATATTT-ATCAAAAAAAAT--AATAATATCTAAATATATAT
*
26210 AATCAAATAATAATCAATTTATCCAAAAAAATAATAATATCTAAATATATAT
1 AATCAAATAATAAT--ATTTATCAAAAAAAATAATAATATCTAAATATATAT
26262 AATCAA
1 AATCAA
26268 TTTAGATCTT
Statistics
Matches: 52, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
50 11 0.21
51 2 0.04
52 26 0.50
53 1 0.02
54 12 0.23
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.31
Consensus pattern (50 bp):
AATCAAATAATAATATTTATCAAAAAAAATAATAATATCTAAATATATAT
Found at i:28276 original size:16 final size:16
Alignment explanation
Indices: 28233--28281 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
28223 GGGATACAAA
28233 TTAA-ATAATTTTATT
1 TTAATATAATTTTATT
* *
28248 TTAATATATTTTTCTT
1 TTAATATAATTTTATT
28264 TTAATGA-AATTTTATT
1 TTAAT-ATAATTTTATT
28280 TT
1 TT
28282 TTTTTAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
15 4 0.14
16 23 0.82
17 1 0.04
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (16 bp):
TTAATATAATTTTATT
Found at i:34722 original size:33 final size:33
Alignment explanation
Indices: 34646--34758 Score: 131
Period size: 33 Copynumber: 3.4 Consensus size: 33
34636 TAGACAAAGG
* *
34646 GTCGCGTGGCCGGTTGTGGCCGGGCATGGCCGA-
1 GTCGCGTGGCCGGTTGTGGCCGGACATGTCC-AT
** * *
34679 GTCGTTTGGCCGGTTGTAGCCGGTCATGTCCAT
1 GTCGCGTGGCCGGTTGTGGCCGGACATGTCCAT
34712 GTCGCGTGGCCGG-TGATGGCCGGACATGTCCAT
1 GTCGCGTGGCCGGTTG-TGGCCGGACATGTCCAT
*
34745 GTCACGTGGCCGGT
1 GTCGCGTGGCCGGT
34759 CTTATGGCCG
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
32 3 0.04
33 64 0.96
ACGTcount: A:0.09, C:0.27, G:0.41, T:0.24
Consensus pattern (33 bp):
GTCGCGTGGCCGGTTGTGGCCGGACATGTCCAT
Done.