Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005571.1 Corchorus capsularis cultivar CVL-1 contig05589, 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, 620
Length: 1034
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34
Found at i:675 original size:333 final size:330
Alignment explanation
Indices: 1--1034 Score: 1426
Period size: 333 Copynumber: 3.1 Consensus size: 330
* * *
1 GAACGCATTTTTTGCCAAAAACTGTGATGGTTTGTACACGATTTCGGCTAAAATTTTGTAAAAAT
1 GAACGCATTTTTTGCCAAAAACTGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAAT
* *
66 TGACCCGAAAAATTTTTGCTTAATTTTTTGCCACAATAATCATAAAATATATATAATTCAACGCC
66 TGACCCGAAAAATTTTTGCTCAATTTTTTGCCACAATACTCATAAAATATATATAATTCAAC-CC
* * *
131 GAAAAGATTGAAGGGATTTTCACACTTCTAATATCGAATTTT-TATATTTGTTT-CAAATTAATT
130 -AAAATATTGAAGGGATTTTCACGCCTCTAATATCGAATTTTCT-TATTT-TTTCCAAATTAATT
* * * * * * * *
194 TTTAATTAAATCGAAAACAGTATCTGATGCTTGTAGAAACAATTCCTTAATTCTAATGTGAATGA
192 TCTAATTAAATCGAAACCGGTTTCTGATGCTTGTAGAAACAAATCCTTAAATCCAATGTGACTGA
*
259 GATTTGGCTAAATGAATACAGATATTTCAATAAGTCTTGGCATAAAAAATCATACAAACTGAGTT
257 GATTTGGCTAAATGAATACAGATATTTCAATGAGTCTTGGCATAAAAAATCATACAAACTGAGTT
*
324 GGGACCCCG
322 GAGACCCCG
* * *
333 GAACGCATTTTTTGACAAAAACTATGATGGTTAGTACATGATTTCAGCTAAAATTTTGCAAAAAT
1 GAACGCATTTTTTGCCAAAAACTGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAAT
398 TGACCCGAAAAATTTTTGCTCAATTTTTTGCCACAATACTCATAAAATATATATAATTCAACACC
66 TGACCCGAAAAATTTTTGCTCAATTTTTTGCCACAATACTCATAAAATATATATAATTCAAC-CC
* * *
463 AAAAATATTGAAGCGATTTTCACGCGTCTAATATCAAATTTTCTTACTTTTTTCCAAATTAATTT
130 -AAAATATTGAAGGGATTTTCACGCCTCTAATATCGAATTTTCTTA-TTTTTTCCAAATTAATTT
*
528 CAAATTAAATCGAAACCGGTTTCTGATGCTTGTAGAAACAAATCCTTAAATCCAATGTGACTGAG
193 CTAATTAAATCGAAACCGGTTTCTGATGCTTGTAGAAACAAATCCTTAAATCCAATGTGACTGAG
* * *
593 ATTTGGCTAAATGAATACAGATATTTCATTGAGTCTTGGCGTAAAAAATCATACAAACAGAGTTG
258 ATTTGGCTAAATGAATACAGATATTTCAATGAGTCTTGGCATAAAAAATCATACAAACTGAGTTG
*
658 CGACCCCG
323 AGACCCCG
* * **
666 GAACGCATTTTTGGCCAAAAACTGTGATGGTTATTACATC-ATTTTGGCTAAAATTTTGCAAAAA
1 GAACGCATTTTTTGCCAAAAACTGTGATGGTTAGTACA-CGATTTCAGCTAAAATTTTGCAAAAA
730 TTGACCCGAAAAATTTTTGCTCAATTTTTTGCCACAATACTCAT--AATATATATAATT-----C
65 TTGACCCGAAAAATTTTTGCTCAATTTTTTGCCACAATACTCATAAAATATATATAATTCAACCC
* * *
788 --AATATTGAAGGGATTTTCGCGCCTCTAATATCGAATTTTCTAATTTTTTTCCTAATTAATTTC
130 AAAATATTGAAGGGATTTTCACGCCTCTAATATCGAATTTTCTTA-TTTTTTCCAAATTAATTTC
* * * *
851 TAATTAAATCGAAACCGGTTTCTGAAGCTTGTAAAAACTAATCCTTAAATCCAATGTGACTGGGA
194 TAATTAAATCGAAACCGGTTTCTGATGCTTGTAGAAACAAATCCTTAAATCCAATGTGACTGAGA
* ** * * ** *
916 TTTGGCTAGATGAATACAGATAACTCAATGAGCCTTGGCACAAAAAATCATTGGAAACTGAATTG
259 TTTGGCTAAATGAATACAGATATTTCAATGAGTCTTGGCATAAAAAATCA-TACAAACTGAGTTG
*
981 AGATCCCG
323 AGACCCCG
* * *
989 GAACGCGTTTTTTGCCAAAAACTTTGATGGTTAGTATACGATTTCA
1 GAACGCATTTTTTGCCAAAAACTGTGATGGTTAGTACACGATTTCA
Statistics
Matches: 628, Mismatches: 68, Indels: 21
0.88 0.09 0.03
Matches are distributed among these distances:
322 160 0.25
323 53 0.08
325 1 0.00
331 13 0.02
332 162 0.26
333 239 0.38
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34
Consensus pattern (330 bp):
GAACGCATTTTTTGCCAAAAACTGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAAT
TGACCCGAAAAATTTTTGCTCAATTTTTTGCCACAATACTCATAAAATATATATAATTCAACCCA
AAATATTGAAGGGATTTTCACGCCTCTAATATCGAATTTTCTTATTTTTTCCAAATTAATTTCTA
ATTAAATCGAAACCGGTTTCTGATGCTTGTAGAAACAAATCCTTAAATCCAATGTGACTGAGATT
TGGCTAAATGAATACAGATATTTCAATGAGTCTTGGCATAAAAAATCATACAAACTGAGTTGAGA
CCCCG
Done.