Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010834.1 Corchorus capsularis cultivar CVL-1 contig10855, 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: 6834
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Found at i:778 original size:333 final size:328
Alignment explanation
Indices: 1--1119 Score: 1143
Period size: 333 Copynumber: 3.4 Consensus size: 328
* * *
1 AAAAACGCGTTCCGGGACCCAC--CTCAGTTTTGTATGA-TTTTGGCGCCAACAATCCTTAGTAT
1 AAAAACGCGTTCCGGGGCCC-CGGCTCAGTTTTGTATGATTTTTGGCGCCAAGAATCCTTAGAAT
* * *
63 ATCTATATTCATCTAA-AATCTCT-GCCACATTGTATTTAAGGA-TTTTTTTTACGTGAATACGA
65 ATCTATATTCATCTAACAAACTCTAGCCACATTGGATTTAAGGATTTTTTTTTACGAGAATA-GA
* *
125 AT-CGTATTTCGATTTAATTAGAAATTAGTTCAGAATAAAATCA-GAAAAACGATATTGAATGCG
129 ATCCG-GTTTCGATTTAATTAGAAATTAATTCAGAATAAAAT-AGGAAAAACGATATTGAA-GCG
* * *
188 TGAAAAGCCCATCAATCATTTTGGCGTTGAATTATATATTTTTTATGAGTATTGTGGCCAAAAAT
191 TGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATAAGTATTGTGGCCAAAAAT
* * * * * * *
253 TGAGGAAAAATCATTC---C-ATTTTTGCAAAATATTAACTGAAACCGTGTAGGTTACCATAACG
256 TGAGGAAAAATCATTCTGTCAATTTTTGCAAAATCTTGACCGAAAACGTGT-GCTAACCATCACG
*
314 TTTTTTTTTGCT
320 --TTTTTGT-CT
* * * *
326 AAAAAAGCGTTCCGGGGCCCCGGCTTA-TTTTAGTGTGATTTTTGGCGCC-AGAAATCCTTTGAA
1 AAAAACGCGTTCCGGGGCCCCGGCTCAGTTTT-GTATGATTTTTGGCGCCAAG-AATCCTTAGAA
* * * * * *
389 TATCTATATTCATCTACCCAAA-TCTCAGCCACATAGGATTTAATGATTTGTTTTTACAAGCATC
64 TATCTATATTCATCTA-ACAAACTCT-AGCCACATTGGATTTAAGGATTTTTTTTTACGAGAAT-
* * *
453 AGAATCCGGTTTCGATTTAACTT-GAAATTAATTCGGAA-AAGCATAGGAAAAACTATATTCTGA
126 AGAATCCGGTTTCGATTTAA-TTAGAAATTAATTCAGAATAA-AATAGGAAAAACGATA-T-TGA
* * * *
516 AGCGTGGAAAA-CCCTTCAAT-TTTTTGGCGTTGATTTATATACTTTTAATAAGTATTTTGGCCA
187 AGCGT-GAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATAAGTATTGTGGCCA
* * *
579 AAAATTGAGGAAAAATTATTCTGATCAATTTTTGCAAAATCTTGACCGAAATCGTGTGCTAACAA
251 AAAATTGAGGAAAAATCATTCTG-TCAATTTTTGCAAAATCTTGACCGAAAACGTGTGCTAACCA
644 TCACAGTTTTTGTCT
315 TCAC-GTTTTTGTCT
* * * *
659 AAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGTATGATTTTTGGCGTCTAGACTTCTTAGAATA
1 AAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGTATGATTTTTGGCGCCAAGAATCCTTAGAATA
* *
724 TTTATATTCAAT-TAACAAACTCTGAGCCACATTGGATTTAA-GATTTTTTTTTTACGAGAATTT
66 TCTATATTC-ATCTAACAAACTCT-AGCCACATTGGATTTAAGGA-TTTTTTTTTACGAGAA-TA
**
787 GAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAATAAAATAGGAAAAACGATATTGAAAGCG
127 GAATCCGGTTTCGATTTAATTAGAAATTAATTCAGAATAAAATAGGAAAAACGATATTG-AAGCG
** * * *
852 TGAAAAGATCTTCAATCTTTTTTGCGTTGAATTATATATTTTTTATTATTATTGTGGCCAAAAAT
191 TGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATAAGTATTGTGGCCAAAAAT
* * * * * *
917 TGGGGATAAATCATT-TGGGTAAATTTTTGCAAAATCTTGACCCAAAAAGTGTGCAAACCATCAT
256 TGAGGAAAAATCATTCT--GTCAATTTTTGCAAAATCTTGACCGAAAACGTGTGCTAACCATCA-
* *
981 TGTTTTCGTCT
318 CGTTTTTGTCT
* * * * *
992 AAAAACGCGTTCTGAGGCCCCGACTCAGTTTTGTATGAGTTTTGGCGCCAA-AACTCCCT-GAAA
1 AAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGTATGATTTTTGGCGCCAAGAA-TCCTTAG-AA
* ** *
1055 TATCTATATTCATCTAACAAAATCTTAAACACGTTGGATTTAAGGATTTTTTTTTTTACGAGAAT
64 TATCTATATTCATCTAACAAACTC-TAGCCACATTGGATTTAAGGA--TTTTTTTTTACGAGAAT
1120 TTGAAAACTG
Statistics
Matches: 658, Mismatches: 92, Indels: 79
0.79 0.11 0.10
Matches are distributed among these distances:
324 1 0.00
325 22 0.03
326 9 0.01
327 35 0.05
328 3 0.00
329 2 0.00
330 19 0.03
331 116 0.18
332 45 0.07
333 331 0.50
334 22 0.03
335 26 0.04
336 27 0.04
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (328 bp):
AAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGTATGATTTTTGGCGCCAAGAATCCTTAGAATA
TCTATATTCATCTAACAAACTCTAGCCACATTGGATTTAAGGATTTTTTTTTACGAGAATAGAAT
CCGGTTTCGATTTAATTAGAAATTAATTCAGAATAAAATAGGAAAAACGATATTGAAGCGTGAAA
AGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATAAGTATTGTGGCCAAAAATTGAGG
AAAAATCATTCTGTCAATTTTTGCAAAATCTTGACCGAAAACGTGTGCTAACCATCACGTTTTTG
TCT
Found at i:1758 original size:9 final size:9
Alignment explanation
Indices: 1744--1777 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
1734 AAACGTTAAT
1744 AAATAAATA
1 AAATAAATA
1753 AAATAAA-A
1 AAATAAATA
1761 AGAATAAATA
1 A-AATAAATA
1771 AAATAAA
1 AAATAAA
1778 AATTACAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 2 0.09
9 19 0.83
10 2 0.09
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (9 bp):
AAATAAATA
Found at i:1766 original size:18 final size:18
Alignment explanation
Indices: 1745--1779 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1735 AACGTTAATA
1745 AATAAATAAAATAAAAAG
1 AATAAATAAAATAAAAAG
1763 AATAAATAAAATAAAAA
1 AATAAATAAAATAAAAA
1780 TTACAAGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (18 bp):
AATAAATAAAATAAAAAG
Found at i:2697 original size:15 final size:15
Alignment explanation
Indices: 2679--2724 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
2669 GTTTGAAGAT
2679 TTTTAAAATGAAGCA
1 TTTTAAAATGAAGCA
* *
2694 TTTTAAAATGTATCA
1 TTTTAAAATGAAGCA
*
2709 TTTCAAAATGACAGCA
1 TTTTAAAATGA-AGCA
2725 ATTATAATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
15 22 0.88
16 3 0.12
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.35
Consensus pattern (15 bp):
TTTTAAAATGAAGCA
Done.