Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008325.1 Corchorus capsularis cultivar CVL-1 contig08346, 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: 2130
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Found at i:558 original size:6 final size:6
Alignment explanation
Indices: 543--578 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
533 GAACTGACGG
*
543 AAGGAA AAGGAG AAGG-A AAGGAA AAGGAA AAGGAA A
1 AAGGAA AAGGAA AAGGAA AAGGAA AAGGAA AAGGAA A
579 CAAATGATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (6 bp):
AAGGAA
Found at i:565 original size:17 final size:17
Alignment explanation
Indices: 543--578 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
533 GAACTGACGG
*
543 AAGGAAAAGGAGAAGGA
1 AAGGAAAAGGAAAAGGA
560 AAGGAAAAGGAAAAGGA
1 AAGGAAAAGGAAAAGGA
577 AA
1 AA
579 CAAATGATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (17 bp):
AAGGAAAAGGAAAAGGA
Found at i:651 original size:28 final size:25
Alignment explanation
Indices: 598--682 Score: 106
Period size: 21 Copynumber: 3.4 Consensus size: 25
588 ACTTACTCTT
598 GAGGAGAAGGGCGCGAATCGAAGGA
1 GAGGAGAAGGGCGCGAATCGAAGGA
*
623 GAGGAGAAGGCCGCTGCGAATCGATGGA
1 GAGGAGAAGG--GC-GCGAATCGAAGGA
651 GA-G-GAA-GG-GCGAATCGAAGGA
1 GAGGAGAAGGGCGCGAATCGAAGGA
672 GAGGAGAAGGG
1 GAGGAGAAGGG
683 AGAACTGACG
Statistics
Matches: 52, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
21 14 0.27
22 1 0.02
23 4 0.08
24 2 0.04
25 11 0.21
26 3 0.06
27 3 0.06
28 14 0.27
ACGTcount: A:0.34, C:0.12, G:0.48, T:0.06
Consensus pattern (25 bp):
GAGGAGAAGGGCGCGAATCGAAGGA
Found at i:773 original size:134 final size:134
Alignment explanation
Indices: 560--823 Score: 528
Period size: 134 Copynumber: 2.0 Consensus size: 134
550 AGGAGAAGGA
560 AAGGAAAAGGAAAAGGAAACAAATGATGACTTACTCTTGAGGAGAAGGGCGCGAATCGAAGGAGA
1 AAGGAAAAGGAAAAGGAAACAAATGATGACTTACTCTTGAGGAGAAGGGCGCGAATCGAAGGAGA
625 GGAGAAGGCCGCTGCGAATCGATGGAGAGGAAGGGCGAATCGAAGGAGAGGAGAAGGGAGAACTG
66 GGAGAAGGCCGCTGCGAATCGATGGAGAGGAAGGGCGAATCGAAGGAGAGGAGAAGGGAGAACTG
690 ACGG
131 ACGG
694 AAGGAAAAGGAAAAGGAAACAAATGATGACTTACTCTTGAGGAGAAGGGCGCGAATCGAAGGAGA
1 AAGGAAAAGGAAAAGGAAACAAATGATGACTTACTCTTGAGGAGAAGGGCGCGAATCGAAGGAGA
759 GGAGAAGGCCGCTGCGAATCGATGGAGAGGAAGGGCGAATCGAAGGAGAGGAGAAGGGAGAACTG
66 GGAGAAGGCCGCTGCGAATCGATGGAGAGGAAGGGCGAATCGAAGGAGAGGAGAAGGGAGAACTG
824 TGGAGAAAAA
Statistics
Matches: 130, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
134 130 1.00
ACGTcount: A:0.39, C:0.12, G:0.39, T:0.10
Consensus pattern (134 bp):
AAGGAAAAGGAAAAGGAAACAAATGATGACTTACTCTTGAGGAGAAGGGCGCGAATCGAAGGAGA
GGAGAAGGCCGCTGCGAATCGATGGAGAGGAAGGGCGAATCGAAGGAGAGGAGAAGGGAGAACTG
ACGG
Found at i:785 original size:28 final size:25
Alignment explanation
Indices: 732--816 Score: 106
Period size: 21 Copynumber: 3.4 Consensus size: 25
722 ACTTACTCTT
732 GAGGAGAAGGGCGCGAATCGAAGGA
1 GAGGAGAAGGGCGCGAATCGAAGGA
*
757 GAGGAGAAGGCCGCTGCGAATCGATGGA
1 GAGGAGAAGG--GC-GCGAATCGAAGGA
785 GA-G-GAA-GG-GCGAATCGAAGGA
1 GAGGAGAAGGGCGCGAATCGAAGGA
806 GAGGAGAAGGG
1 GAGGAGAAGGG
817 AGAACTGTGG
Statistics
Matches: 52, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
21 14 0.27
22 1 0.02
23 4 0.08
24 2 0.04
25 11 0.21
26 3 0.06
27 3 0.06
28 14 0.27
ACGTcount: A:0.34, C:0.12, G:0.48, T:0.06
Consensus pattern (25 bp):
GAGGAGAAGGGCGCGAATCGAAGGA
Found at i:1357 original size:220 final size:218
Alignment explanation
Indices: 968--1459 Score: 736
Period size: 220 Copynumber: 2.2 Consensus size: 218
958 CGGCGTCGTA
* * *
968 TTACCTAAGACGCTGCTAAATAGTGGCGTTTAACAACTCAGATGCCGCCATCTATGAGGAAATAA
1 TTACCTAAGACGCCGCTAAATAGTGGCGTTTAAC-ACTCAGACGCCGCCATTTATGAGGAAATAA
*
1033 ATTAGATAAGAAAAGAGACCTGGGGGCCCGGTTGGGGGCGAAGTCGGCTCCCAGTCAGGACAGTG
65 ATTAGACAAGAAAAGAGACCTGGGGGCCCGGTTGGGGGCGAAGTCGGCTCCCAGTCAGGACAGTG
* *
1098 ACTTCGCCCCAAATTGAAGGGTCCAACCGGGCACCCAATTGGGTGGTAACTGGGATCCCAGATGG
130 ACTTCGCCCCAAATTGAAGGGCCCAACCGGGCACCCAATT-GGTGGTAACTGGGAGCCCAGATGG
**
1163 ACTCCACCCAAATAGCGGCATCTTG
194 ACTCCACCCAAATAGCGGCATCTAC
*
1188 TTACCTAAGACGCCGCTAAATAGTGGGGTTTAACACTTCAGACGCCGCCATTTATGAGGAAATAA
1 TTACCTAAGACGCCGCTAAATAGTGGCGTTTAACAC-TCAGACGCCGCCATTTATGAGGAAATAA
* * * *
1253 ATTGGACAAGAAATGAGACCTGGGGGCCCGGTTGGGTGCGAAGTCGGCTCCCATTCAGGACAGTG
65 ATTAGACAAGAAAAGAGACCTGGGGGCCCGGTTGGGGGCGAAGTCGGCTCCCAGTCAGGACAGTG
* *
1318 ACTTCTCCCCAAATTGAAGGGCCCAACCGGGCTCCCAATTGGTGGTAACTGGGAGCCCAGATGGA
130 ACTTCGCCCCAAATTGAAGGGCCCAACCGGGCACCCAATTGGTGGTAACTGGGAGCCCAGATGGA
*
1383 CTCCACCCAAATAGCGGCGTCTAC
195 CTCCACCCAAATAGCGGCATCTAC
** * *
1407 TTAGTTTAGACGCCGCTAAATAAG-GGCGTTTAAGTCA-TCAGACGCCGCTATTT
1 TTACCTAAGACGCCGCTAAAT-AGTGGCGTTTAA--CACTCAGACGCCGCCATTT
1460 GGGAAATTAA
Statistics
Matches: 247, Mismatches: 21, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
219 88 0.36
220 157 0.64
221 2 0.01
ACGTcount: A:0.27, C:0.25, G:0.27, T:0.21
Consensus pattern (218 bp):
TTACCTAAGACGCCGCTAAATAGTGGCGTTTAACACTCAGACGCCGCCATTTATGAGGAAATAAA
TTAGACAAGAAAAGAGACCTGGGGGCCCGGTTGGGGGCGAAGTCGGCTCCCAGTCAGGACAGTGA
CTTCGCCCCAAATTGAAGGGCCCAACCGGGCACCCAATTGGTGGTAACTGGGAGCCCAGATGGAC
TCCACCCAAATAGCGGCATCTAC
Found at i:1921 original size:33 final size:32
Alignment explanation
Indices: 1850--1924 Score: 107
Period size: 32 Copynumber: 2.3 Consensus size: 32
1840 TGTTTCGTTG
1850 GACGCCGCTAAATAGTGGCGTTGGATTCATTA
1 GACGCCGCTAAATAGTGGCGTTGGATTCATTA
**
1882 -AGCGCCGCTAAATAGTGGCGTTTTATTTCATTA
1 GA-CGCCGCTAAATAGTGGCGTTGGA-TTCATTA
1915 GACGCCGCTA
1 GACGCCGCTA
1925 TTGTGCAGCA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
31 1 0.03
32 21 0.55
33 15 0.39
34 1 0.03
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.29
Consensus pattern (32 bp):
GACGCCGCTAAATAGTGGCGTTGGATTCATTA
Done.