Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010329.1 Corchorus capsularis cultivar CVL-1 contig10350, 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: 4866
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:2454 original size:18 final size:17
Alignment explanation
Indices: 2421--2464 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
2411 ATCCATGAAT
2421 GAAATTGATAAAATTAA
1 GAAATTGATAAAATTAA
*
2438 GAAATTAGATCAAATTAGA
1 GAAATT-GATAAAATTA-A
*
2457 CAAATTGA
1 GAAATTGA
2465 ATTTACCTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 6 0.26
18 11 0.48
19 6 0.26
ACGTcount: A:0.55, C:0.05, G:0.14, T:0.27
Consensus pattern (17 bp):
GAAATTGATAAAATTAA
Found at i:4420 original size:325 final size:318
Alignment explanation
Indices: 3738--4866 Score: 1318
Period size: 324 Copynumber: 3.5 Consensus size: 318
3728 GAGTACACTA
* * *
3738 ACACAATTTCAGCTAAAAAATGACCTGAAA-ATTTTTTTCTCAATTTTTTGCCACAATGCTCATA
1 ACACGATTTCAGCTAAAAACTGACCTGAAATTTTTTTTTCTCAATTTTTTGCCACAATGCTCATA
* * *
3802 AAAAACATATAATTCAACACCAAAAAT-ATTGAAGAGTTTTTCACGCTTCTAATATCGTTTTTCA
66 AAAAATATATAATTCAACGCCAAAAATGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCA
* *
3866 TTTTTTTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT
131 ATTTTTTCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT
* *
3931 AAATCCAATGTTGCTAAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTTTTTCTGCCAAAA
196 AAAT-CAATGTAGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAG-TTTTCTGCCAAAA
* ** **
3996 ATCATGCAAAATTGAGCCAGGACCCCC-AGAATGCGTTTTTTTAGCTAAAA--ACAATGAGGTAA
259 ATCATGCAAAACTGAGCC-GG-CCCCCGA-AACACG--TTTTTAGCTAAAATTGTAATG-GGT--
4058 AGT
316 AGT
* * ** *
4061 ACACGATTTCAGCTAAAAATTGACC--CAATTTTTTTTTCTCAATTTTTTTAGTTACAATACTCA
1 ACACGATTTCAGCTAAAAACTGACCTGAAATTTTTTTTTCTCAA-TTTTTT-GCCACAATGCTCA
* *
4124 TGAAAAATATATAATTCAACGCCAAAAAT-ATTGAAGGGTTTTTCACGCTTCTAATTTCGTTTTT
64 TAAAAAATATATAATTCAACGCCAAAAATGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTT
* * *
4188 CAATTTTTTACGAATTAATTTCTAATTAAATCGAAACAAGTTTCAGATACTCGTAAAAACAAATC
129 CAATTTTTT-CAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATC
* * * *
4253 CTTAAATCAAATGTGGTTGAGATTTGGTTCAATGAATATAGATATTTCAAGGAGTTTTCCCGCCA
193 CTTAAATC-AATGTAGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTTTT-CTGCCA
4318 AAAATCATGCAAAACTGAGCCGGCCCCCGAAACACGTTTTTAGCTATAAATTGTAATGGGTAGT
256 AAAATCATGCAAAACTGAGCCGGCCCCCGAAACACGTTTTTAGCTA-AAATTGTAATGGGTAGT
* * * *
4382 ACACGATTTCAGCTAAAAACTGACCTGAAAATTTTTTTTCCTTAATTTTTGGCCACAACGCTCAT
1 ACACGATTTCAGCTAAAAACTGACCTG-AAATTTTTTTTTCTCAATTTTTTGCCACAATGCTCAT
* ** * * *
4447 AAAGAATATATAATTCAACG-TGAAAATGATTGAAGGGTTTTTCACGCTTATAGTATTGTTTTTC
65 AAAAAATATATAATTCAACGCCAAAAATGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTC
4511 AAATTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATC
130 -AATTTTTT-CAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATC
* * * * * * *
4576 CTCATAA-CAATCTAGCCGAGATTTGGTTCGATAAATATAGATATTTCAATGAGTCTTTTTGCGA
193 CTTA-AATCAATGTAGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGT-TTTCTGCCA
* * * * * * *
4640 AAAATCATGCAAAACTGAGCC-GCTGGCCTGAAACTCATTTTTAGCTAAAAATTGTGAGGGGTTT
256 AAAATCATGCAAAACTGAGCCGGC--CCCCGAAACACGTTTTTAGCT-AAAATTGTAATGGG-TA
4704 GT
317 GT
* *
4706 ACACGATTTCAG-TCAAAAACTAACTTGAAATTTTTTTTTTCTCAATTTTTTGCCACAAT-CATC
1 ACACGATTTCAGCT-AAAAACTGACCTGAAA-TTTTTTTTTCTCAATTTTTTGCCACAATGC-TC
* ** * *
4769 ATAAAAAATATATAACTCAACGCC-AAAATGATTGAAATG-TTTTCTA-GTCTTCTAAAATCTTT
63 ATAAAAAATATATAATTCAACGCCAAAAATGATTGAAGGGTTTTTC-ACG-CTTCTAATATC-GT
4831 TTTTCAATTTTTTCTAAATTAATTTCTAATTAAATC
125 TTTTCAATTTTTTC-AAATTAATTTCTAATTAAATC
Statistics
Matches: 697, Mismatches: 80, Indels: 57
0.84 0.10 0.07
Matches are distributed among these distances:
321 46 0.07
322 138 0.20
323 153 0.22
324 228 0.33
325 132 0.19
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (318 bp):
ACACGATTTCAGCTAAAAACTGACCTGAAATTTTTTTTTCTCAATTTTTTGCCACAATGCTCATA
AAAAATATATAATTCAACGCCAAAAATGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCA
ATTTTTTCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT
AAATCAATGTAGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTTTTCTGCCAAAAAT
CATGCAAAACTGAGCCGGCCCCCGAAACACGTTTTTAGCTAAAATTGTAATGGGTAGT
Done.