Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000639.1 Corchorus capsularis cultivar CVL-1 contig00639, 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: 3484
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:71 original size:23 final size:21
Alignment explanation
Indices: 45--106 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 21
35 AAAGAAAATG
*
45 AATAAATAAAATAAAAATCCATT
1 AATAAATAAAATAAAAAT--ATA
68 AATAATATAAATATAAAAATATA
1 AATAA-ATAAA-ATAAAAATATA
*
91 AATAAATTAAATAAAA
1 AATAAATAAAATAAAA
107 GTAGAAAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
21 6 0.17
22 4 0.11
23 12 0.34
24 5 0.14
25 8 0.23
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.27
Consensus pattern (21 bp):
AATAAATAAAATAAAAATATA
Found at i:742 original size:2 final size:2
Alignment explanation
Indices: 735--773 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
725 TAACAGTAAT
735 TA TA TA TA TA TA TA TA TA 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 TA TA TA T
774 CATGAATTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1620 original size:12 final size:13
Alignment explanation
Indices: 1588--1620 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1578 TGCTACATGA
*
1588 CCCTCCAATTTGT
1 CCCTCCATTTTGT
1601 CCCTCCATTTTGT
1 CCCTCCATTTTGT
1614 CCC-CCAT
1 CCCTCCAT
1621 GACGTGTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.12, C:0.45, G:0.06, T:0.36
Consensus pattern (13 bp):
CCCTCCATTTTGT
Found at i:3080 original size:323 final size:317
Alignment explanation
Indices: 2363--3472 Score: 1344
Period size: 322 Copynumber: 3.5 Consensus size: 317
2353 CTTATTATCC
* * * *
2363 TTTCGGGTCAGTTTTGAGCAGAAATCGTTTACTAATCATCACAGTTTTTGACTAAAAACGCGTTT
1 TTTCGGGTCAGTTTTAAGCAGAAATCGTGTACTAACCATCACAGTTTTTGACTAAAAACACGTTT
* *
2428 CGGGACCCCTG-CTCAGTATTACATGATTTTTTTGGCAAAAAGACTCCTTGAAATATCTACATTC
66 CGGGACCCC-GACTCAGTTTTACATGA-TTTTTTGGCAGAAAGACTCCTTGAAATATCTACATTC
* ** *
2492 TTTGAACCAAATCTCAGCCGCATTAAATTTAAGGATTTGTTTTTACGAG---T-ATC-TGATTTC
129 TTTGAACCAAATCTCAGCCACATTTGATTTGAGGATTTGTTTTTACGAGATCTAATCTTG-TTTC
* *** * * *
2552 GATACAATT-AAAATAAATTCGGAAAAAAATGGAAAAATGATATTCGAAGCATGAAAACCCTTCA
193 GATATAATTAAAAATAAATTCGG-AAAAAATGGAAAACCAATATTAGAAGCTTAAAAACCCTTCA
* * * * **
2616 ATTTTTTT-TTGCATTGAAATAACTTTTTTCTGAGTTTTGTGGCAAAAAATTGAGAAAAAAAAT
257 ATTTTTTTGTTGAATT-ATAT-A-TTTTTCCTGAGTATTGTGGTGAAAAATTGAGAAAAAAAAT
* * * * *
2679 TTTCAGGTCAATTTTTAACCA-AAATTGTGTACTAACCATCACGGTTTTTGAGCTAAAAACACGT
1 TTTCGGGTC-AGTTTTAAGCAGAAATCGTGTACTAACCATCACAGTTTTTGA-CTAAAAACACGT
* *
2743 TTC-GGAGCCCCGACTCAGTTTTAAATGATTTTTTGGCAGAAAGACTCCTTGAAATATCTATATT
64 TTCGGGA-CCCCGACTCAGTTTTACATGATTTTTTGGCAGAAAGACTCCTTGAAATATCTACATT
*
2807 -TATCT-AACCAAATCTCAGCCACATTTGATTTGAGGATTTGCTTTTACGAGCATCTAAATCTTG
128 CT-T-TGAACCAAATCTCAGCCACATTTGATTTGAGGATTTGTTTTTACGAG-ATCT-AATCTTG
* *
2870 TTTCGATATAATTAAAAATAAATTCGGAAAAAATGGGAAACCAATATTAGAAGCGTTTAAAACCC
189 TTTCGATATAATTAAAAATAAATTCGGAAAAAATGGAAAACCAATATTAGAAGC-TTAAAAACCC
* *
2935 TTCACTTTCTTTGTGTTGAATTATATATTTTTCCTGAGTATTGTGATGAAAAATTGAGAAAAAAA
253 TTCAATTT-TTT-TGTTGAATTATATATTTTTCCTGAGTATTGTGGTGAAAAATTGAG-AAAAAA
3000 AAT
315 AAT
* * *
3003 TTTCGGGTCAGTTTTAAGCAGAAATCGTGT-CTTAATCATCACAGTTTTTGGCTAAAAACAAGTT
1 TTTCGGGTCAGTTTTAAGCAGAAATCGTGTAC-TAACCATCACAGTTTTTGACTAAAAACACG-T
* * *
3067 TTGGGGA-CCCGACTCAGTTTTGCATGA-TTTTTGGCAGAAAGACTCCTTGAAATATCTATATTT
64 TTCGGGACCCCGACTCAGTTTTACATGATTTTTTGGCAGAAAGACTCCTTGAAATATCTACA-TT
** * *
3130 CACT-AACCAAATCTCAGCCACATTTGATTTGAGAATTTGTTTTTACAAGAATCTGAATCTTGTT
128 CTTTGAACCAAATCTCAGCCACATTTGATTTGAGGATTTGTTTTTACGAG-ATCT-AATCTTGTT
* *
3194 TCGATATAATTAGAAATAAATTCGGAAAAAATGGAAAACCAATATTA-AACGCATGAAAAACCCT
191 TCGATATAATTAAAAATAAATTCGGAAAAAATGGAAAACCAATATTAGAA-GC-TTAAAAACCCT
*
3258 TCAATTTTATTTTTGTTGAATTATATATTTTTGCTGAGTATTGTGGTGAAAAATTGAGAAAAAAA
254 TCAA--TT-TTTTTGTTGAATTATATATTTTTCCTGAGTATTGTGGTGAAAAATTGAGAAAAAAA
3323 AT
316 AT
* * *
3325 TTTCGGGTCAGTTTTGAGCAGAAATCGTG---T-ACCATCACGGTTTTTGACTAAAAACGCGTTT
1 TTTCGGGTCAGTTTTAAGCAGAAATCGTGTACTAACCATCACAGTTTTTGACTAAAAACACGTTT
*
3386 CGGGACCCCGGCTCAGTTTTACATGATTTTTTGGCAGAAAGACTCCTTGAAATATCTACATTCTT
66 CGGGACCCCGACTCAGTTTTACATGATTTTTTGGCAGAAAGACTCCTTGAAATATCTACATTCTT
*
3451 TGAACCAAATCTCAGCCGCATT
131 TGAACCAAATCTCAGCCACATT
3473 AAATTTAAGG
Statistics
Matches: 689, Mismatches: 73, Indels: 61
0.84 0.09 0.07
Matches are distributed among these distances:
315 1 0.00
316 113 0.16
317 47 0.07
318 45 0.07
319 52 0.08
320 1 0.00
321 2 0.00
322 222 0.32
323 139 0.20
324 53 0.08
325 8 0.01
326 6 0.01
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (317 bp):
TTTCGGGTCAGTTTTAAGCAGAAATCGTGTACTAACCATCACAGTTTTTGACTAAAAACACGTTT
CGGGACCCCGACTCAGTTTTACATGATTTTTTGGCAGAAAGACTCCTTGAAATATCTACATTCTT
TGAACCAAATCTCAGCCACATTTGATTTGAGGATTTGTTTTTACGAGATCTAATCTTGTTTCGAT
ATAATTAAAAATAAATTCGGAAAAAATGGAAAACCAATATTAGAAGCTTAAAAACCCTTCAATTT
TTTTGTTGAATTATATATTTTTCCTGAGTATTGTGGTGAAAAATTGAGAAAAAAAAT
Done.