Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010639.1 Corchorus capsularis cultivar CVL-1 contig10660, 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: 29246
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:77 original size:2 final size:2
Alignment explanation
Indices: 72--108 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
62 ACACACACAC
72 AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
109 TCTTTTTGCC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2616 original size:11 final size:11
Alignment explanation
Indices: 2581--2637 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 11
2571 TTATGCACCC
2581 AAAACATTTAT
1 AAAACATTTAT
2592 CAAAACATTTTAT
1 -AAAACA-TTTAT
*
2605 AAAGCATTTATAT
1 AAAACA-TT-TAT
* *
2618 AAAACAGTAAT
1 AAAACATTTAT
2629 AAAACATTT
1 AAAACATTT
2638 CCTCAACGGG
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
11 9 0.24
12 15 0.41
13 13 0.35
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.33
Consensus pattern (11 bp):
AAAACATTTAT
Found at i:6777 original size:15 final size:15
Alignment explanation
Indices: 6757--6809 Score: 79
Period size: 15 Copynumber: 3.5 Consensus size: 15
6747 TTTAATTGTT
*
6757 ACTCTCCCTAGAATC
1 ACTCTCCTTAGAATC
* *
6772 ACTCTCATTGGAATC
1 ACTCTCCTTAGAATC
6787 ACTCTCCTTAGAATC
1 ACTCTCCTTAGAATC
6802 ACTCTCCT
1 ACTCTCCT
6810 AAGGAAAGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.25, C:0.36, G:0.08, T:0.32
Consensus pattern (15 bp):
ACTCTCCTTAGAATC
Found at i:8720 original size:65 final size:65
Alignment explanation
Indices: 8616--8743 Score: 222
Period size: 65 Copynumber: 2.0 Consensus size: 65
8606 TGCAAAATTA
*
8616 TAAAGAAACAATAATAGGATAAAGTGAAATGACAAGAAACAC-AATCCATCCCTCTCATCCCATT
1 TAAAGAAACAATAATAGGATAAAGTGAAATGACAAGAAAC-CTAATCCAACCCTCTCATCCCATT
8680 T
65 T
*
8681 TAAAGAAACAATAATAGGATGAAGTGAAATGACAAGAAACCTAATCCAACCCTCTCATCCCAT
1 TAAAGAAACAATAATAGGATAAAGTGAAATGACAAGAAACCTAATCCAACCCTCTCATCCCAT
8744 GACTTGAAGA
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
64 1 0.02
65 59 0.98
ACGTcount: A:0.46, C:0.22, G:0.12, T:0.20
Consensus pattern (65 bp):
TAAAGAAACAATAATAGGATAAAGTGAAATGACAAGAAACCTAATCCAACCCTCTCATCCCATTT
Found at i:9744 original size:429 final size:431
Alignment explanation
Indices: 8992--9990 Score: 1065
Period size: 429 Copynumber: 2.3 Consensus size: 431
8982 TTTATTTTTG
*
8992 TATTTT-TTT-TTCTATTTGTCCGATTAA-TGTGATTCAAGTGTCTATTAAAAGGTAATTTCATG
1 TATTTTCTTTGTTCTATTTGTCCAATTAAGT-TGATTC-AGTGTCTATTAAAAGGTAATTTCATG
** * ** ** *
9054 ATCTACAATTTTCAT-TTAGAACTCAAAAGTCAATTTTAATGTTTTGATTCTAAAACATGCTTCT
64 ATCTACAA-TTTCATGAAAG-ACTCAAAAG-CAATTTTTATG-TTCAATTAAAAAAAATGCTTCT
* * * * * * ** *
9118 GAAATTTTGTGGTTTTGATTGCCGGTTAATTTAATATCGTATAATTTTTTTCCACATCTCCGATT
125 GAAATTTGGTCGTTTCGAGTGCCGGTTAATTTAATACCATATAATTTTGATCCACATCTCCAATT
* * * * * *
9183 GAAGTTATTAAAGTGTCGGTTAAAAGGTTATTGCATGATTTACGATTTTCATGAAGGACCCAAAA
190 AAAGTTATTAAAGTGTCAGTTAAAAGGTTATCGCATAATTTACGACTTTCATGAAGAACCCAAAA
** * *
9248 GCTAAATTTGATATACGAGTTTTAAGAAGGGTTCAAAATGGAATTTTTATGTTTCAAGATCTCC-
255 GCTAAATTTGATATACGAGTTCCAAGAAGGATTCAAAAGGGAATTTTTATGTTTCAAGATCTCCA
* * * *
9312 ATTAACAAACATTTTCTTATTTGGATTATTTATCAAATGATCC-TAATATTTTTCTACTTTATAC
320 ATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATCA-CCTTAATACTTTTCTACTTTATAC
* * * *
9376 TACTTAGTTCTTTACATATTCTATCTTA-ATCTAAC-GTTTAAGATTT
384 TACTTAGTCCTTTACAAATTCTATCTTACATCTAACACTTCAAGATTT
*
9422 T-TTTTCTTTGTTCTATTTGTCCAATTAAGTTGATTCATGTGTCTATTAAAAGGTAATTTCATTA
1 TATTTTCTTTGTTCTATTTGTCCAATTAAGTTGATTCA-GTGTCTATTAAAAGGTAATTTCATGA
*
9486 TCTACAACTTTCGTGAAAGACTCAAAAGCAATTTTTATG-TCAATTAAAAAAAATGCTTCCT-AA
65 TCTACAA-TTTCATGAAAGACTCAAAAGCAATTTTTATGTTCAATTAAAAAAAATGCTT-CTGAA
* **
9549 ATTTGGTCGTTTCGGGTGTTGG-TATATTTAATACCATATAATTTTCGATCCACA-CGTCCAATT
128 ATTTGGTCGTTTCGAGTGCCGGTTA-ATTTAATACCATATAATTTT-GATCCACATC-TCCAATT
* * * *
9612 AAAGTTATTCAAGTGTCAGTTAAAAGGTTATCGTATAATTTACGACTTTCATTAAGAACCCGAAA
190 AAAGTTATTAAAGTGTCAGTTAAAAGGTTATCGCATAATTTACGACTTTCATGAAGAACCCAAAA
* * * ** *
9677 G-TTAATTTGGTCTACGAGTTCCCTGAAGGATTCAAAAGGGAATTTTTTATGTTTCAAGGTCTCC
255 GCTAAATTTGATATACGAGTTCCAAGAAGGATTCAAAAGGGAA-TTTTTATGTTTCAAGATCTCC
* * * *
9741 ATTAATTAACAAATATTTTCTTATTTGAATTAGTTATCAAGTCACCTTTATACTTTTCTATTTTA
319 ---AATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATCACCTTAATACTTTTCTACTTTA
* * ***
9806 TCCTACTTAGTCCTTTACAAATTCTATCTTACTCGATTTAACACTTCATTTTTT
381 TACTACTTAGTCCTTTACAAATTCTATCTTA--C-ATCTAACACTTCAAGATTT
* * * *
9860 TATTTTCTTTGTTCTATTTGTCCAATTAAGGTAATTCAG-GTATATTAAAAGGTAATTTTATGAT
1 TATTTTCTTTGTTCTATTTGTCCAATTAAGTTGATTCAGTGTCTATTAAAAGGTAATTTCATGAT
* * ** *
9924 CTACAATTTCCATGAAAGACTTAAAAGCTAATTTTTATATTTCAATTCTAAAAAATGCTTTTGAA
66 CTACAATTT-CATGAAAGACTCAAAAGC-AATTTTTAT-GTTCAATTAAAAAAAATGCTTCTGAA
9989 AT
128 AT
9991 ATTGTGATTT
Statistics
Matches: 471, Mismatches: 72, Indels: 42
0.81 0.12 0.07
Matches are distributed among these distances:
427 2 0.00
428 82 0.17
429 94 0.20
430 15 0.03
431 69 0.15
432 5 0.01
433 78 0.17
436 3 0.01
437 50 0.11
438 17 0.04
439 35 0.07
440 21 0.04
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (431 bp):
TATTTTCTTTGTTCTATTTGTCCAATTAAGTTGATTCAGTGTCTATTAAAAGGTAATTTCATGAT
CTACAATTTCATGAAAGACTCAAAAGCAATTTTTATGTTCAATTAAAAAAAATGCTTCTGAAATT
TGGTCGTTTCGAGTGCCGGTTAATTTAATACCATATAATTTTGATCCACATCTCCAATTAAAGTT
ATTAAAGTGTCAGTTAAAAGGTTATCGCATAATTTACGACTTTCATGAAGAACCCAAAAGCTAAA
TTTGATATACGAGTTCCAAGAAGGATTCAAAAGGGAATTTTTATGTTTCAAGATCTCCAATTAAC
AAACATTTTCTTATTTGAATTAGTTATCAAATCACCTTAATACTTTTCTACTTTATACTACTTAG
TCCTTTACAAATTCTATCTTACATCTAACACTTCAAGATTT
Found at i:10700 original size:22 final size:22
Alignment explanation
Indices: 10675--10728 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
10665 ATATAAATTT
*
10675 TATATAATTCAAAT-TAATATTA
1 TATATAATT-AAATAAAATATTA
*
10697 TATATATAATAAATAAAATATTA
1 TATATA-ATTAAATAAAATATTA
10720 TATACTAAT
1 TATA-TAAT
10729 ACTGGCGGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
22 10 0.38
23 14 0.54
24 2 0.08
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (22 bp):
TATATAATTAAATAAAATATTA
Found at i:11942 original size:12 final size:13
Alignment explanation
Indices: 11921--11962 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
11911 AGTAACATTT
11921 TTTCT-TTTTTTA
1 TTTCTCTTTTTTA
11933 TTTCTCTTTTTTA
1 TTTCTCTTTTTTA
*
11946 TTTGATCTTTTATTA
1 TTT-CTCTTTT-TTA
11961 TT
1 TT
11963 AATTTTATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 5 0.19
13 10 0.38
14 6 0.23
15 5 0.19
ACGTcount: A:0.12, C:0.10, G:0.02, T:0.76
Consensus pattern (13 bp):
TTTCTCTTTTTTA
Done.