Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015235.1 Corchorus capsularis cultivar CVL-1 contig15256, 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: 36192
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:4419 original size:30 final size:32
Alignment explanation
Indices: 4377--4466 Score: 93
Period size: 30 Copynumber: 3.0 Consensus size: 32
4367 TTGAGAAGTT
4377 TGGTAAGG-TTGTGAAAGTTGA-GAAAAAGAA
1 TGGTAAGGTTTGTGAAAGTTGACGAAAAAGAA
* * *
4407 TGGT-AGGTTTGTGAGAA-TTGAGGAAGATG-A
1 TGGTAAGGTTTGTGA-AAGTTGACGAAAAAGAA
*
4437 TGGTAAGGTTTG-GAAAGTTGACGAGAAAGA
1 TGGTAAGGTTTGTGAAAGTTGACGAAAAAGA
4467 TGAGGAAAAG
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
29 5 0.10
30 29 0.60
31 14 0.29
ACGTcount: A:0.37, C:0.01, G:0.37, T:0.26
Consensus pattern (32 bp):
TGGTAAGGTTTGTGAAAGTTGACGAAAAAGAA
Found at i:5788 original size:2 final size:2
Alignment explanation
Indices: 5781--5811 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
5771 TTTATGTTAT
5781 TA TA TA TA TA TA TA TA TA TA TA TA TGA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
5812 GTTTCATGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:16420 original size:22 final size:22
Alignment explanation
Indices: 16392--16436 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
16382 GAAAAACAAA
16392 AACAAAAACTAAAAAGAAAGTT
1 AACAAAAACTAAAAAGAAAGTT
16414 AACAAAAACTAAAAAGAAAGTT
1 AACAAAAACTAAAAAGAAAGTT
16436 A
1 A
16437 TAGTGTTAGT
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:0.69, C:0.09, G:0.09, T:0.13
Consensus pattern (22 bp):
AACAAAAACTAAAAAGAAAGTT
Found at i:18074 original size:17 final size:17
Alignment explanation
Indices: 18030--18074 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
18020 CGCAAACCCT
*
18030 AATTTTATTTTCGACAC
1 AATTTTTTTTTCGACAC
18047 AATTTTTTTTTCGACAC
1 AATTTTTTTTTCGACAC
18064 AATTTTTTTTT
1 AATTTTTTTTT
18075 TTTAGAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.24, C:0.13, G:0.04, T:0.58
Consensus pattern (17 bp):
AATTTTTTTTTCGACAC
Found at i:18406 original size:6 final size:6
Alignment explanation
Indices: 18390--18422 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
18380 CAAAGCAAAA
18390 TAAAT- TAAATC TAAATC TAAATC TAAATC TAAA
1 TAAATC TAAATC TAAATC TAAATC TAAATC TAAA
18423 GCAGATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (6 bp):
TAAATC
Found at i:19354 original size:10 final size:10
Alignment explanation
Indices: 19339--19363 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
19329 GAGGACTCTA
19339 GAATTTTCTG
1 GAATTTTCTG
19349 GAATTTTCTG
1 GAATTTTCTG
19359 GAATT
1 GAATT
19364 GTGCAGCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:22338 original size:12 final size:12
Alignment explanation
Indices: 22321--22345 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
22311 TTTAAAGAAA
22321 ATCTCTTTCTTT
1 ATCTCTTTCTTT
22333 ATCTCTTTCTTT
1 ATCTCTTTCTTT
22345 A
1 A
22346 ATTTCGATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.64
Consensus pattern (12 bp):
ATCTCTTTCTTT
Found at i:28215 original size:11 final size:11
Alignment explanation
Indices: 28201--28238 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
28191 ATTCATAACA
28201 AATTTATAATT
1 AATTTATAATT
28212 AATTTATAATT
1 AATTTATAATT
28223 -ATTTGATAATT
1 AATTT-ATAATT
*
28234 TATTT
1 AATTT
28239 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:30671 original size:11 final size:11
Alignment explanation
Indices: 30655--30697 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
30645 TATAATATAT
30655 CTAATTAATAG
1 CTAATTAATAG
*
30666 CTAATTAATAT
1 CTAATTAATAG
30677 CTAATTAATAG
1 CTAATTAATAG
*
30688 TTAATTAATA
1 CTAATTAATA
30698 ATGAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:30678 original size:22 final size:22
Alignment explanation
Indices: 30651--30697 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
30641 CCATTATAAT
30651 ATATCTAATTAATAGCTAATTA
1 ATATCTAATTAATAGCTAATTA
*
30673 ATATCTAATTAATAGTTAATTA
1 ATATCTAATTAATAGCTAATTA
30695 ATA
1 ATA
30698 ATGAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (22 bp):
ATATCTAATTAATAGCTAATTA
Found at i:32252 original size:17 final size:17
Alignment explanation
Indices: 32230--32264 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
32220 TGAGGACGGC
32230 AAATATTACTTACAAAA
1 AAATATTACTTACAAAA
32247 AAATATTACTTACAAAA
1 AAATATTACTTACAAAA
32264 A
1 A
32265 TTACATACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.29
Consensus pattern (17 bp):
AAATATTACTTACAAAA
Found at i:32267 original size:13 final size:13
Alignment explanation
Indices: 32246--32316 Score: 63
Period size: 13 Copynumber: 5.2 Consensus size: 13
32236 TACTTACAAA
*
32246 AAAATATTACTTAC
1 AAAA-ATTACATAC
32260 AAAAATTACATAC
1 AAAAATTACATAC
32273 AATAATAATTAACATA-
1 -A-AA-AATT-ACATAC
*
32289 AAAAATTACTTAC
1 AAAAATTACATAC
*
32302 AAAAATTGCATAC
1 AAAAATTACATAC
32315 AA
1 AA
32317 TAATAATTAC
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
12 4 0.08
13 25 0.52
14 7 0.15
15 3 0.06
16 4 0.08
17 5 0.10
ACGTcount: A:0.58, C:0.13, G:0.01, T:0.28
Consensus pattern (13 bp):
AAAAATTACATAC
Found at i:32305 original size:42 final size:43
Alignment explanation
Indices: 32245--32325 Score: 146
Period size: 42 Copynumber: 1.9 Consensus size: 43
32235 TTACTTACAA
32245 AAAAATATTACTTACAAAAATTACATACAATAATAATTAACAT
1 AAAAATATTACTTACAAAAATTACATACAATAATAATTAACAT
*
32288 AAAAA-ATTACTTACAAAAATTGCATACAATAATAATTA
1 AAAAATATTACTTACAAAAATTACATACAATAATAATTA
32326 CAAACATGTC
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
42 32 0.86
43 5 0.14
ACGTcount: A:0.58, C:0.11, G:0.01, T:0.30
Consensus pattern (43 bp):
AAAAATATTACTTACAAAAATTACATACAATAATAATTAACAT
Done.