Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005394.1 Corchorus capsularis cultivar CVL-1 contig05412, 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: 2061
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Found at i:1456 original size:332 final size:331
Alignment explanation
Indices: 767--2040 Score: 1298
Period size: 332 Copynumber: 3.8 Consensus size: 331
757 TTTTTACGAG
** * ** * *
767 CGATTCAATTAGGCATTAATTCGGAAAAAATAGGAAAAATGATATTAGAAGCATGAATAGTCTTT
1 CGATTCAATTAGAAATTAATTCGGAAAAAATAGAAAAAACAATATTAGAAGCATGAATAGCCCTT
* * * * * * * *
832 CAATCTTTTTGTTGTTAAATTATATACTTTCTATGAGTATTGTAGCTAAAAATTGAGGAAAATTC
66 CAATCTTTTTGGTGTTGAATTATATATTTTTTATGAATATAGTGGCCAAAAATTGAGGAAAATTC
* * * *
897 TTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGGTGTATTACCCATCACGGTTTTTTG-TT
131 TTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGGTGTACTAACCATCACGG-TTTTTGACT
* * * ** * * *
961 AAAAACACGTTCCGGGGCCTCGGCTCAGTTTTGCATTATTTTTGACGA-CAAGACTCGTTGAAAT
195 AAAAACACGTT-TGGAGCCCCGGCTCAGTTTTGCACGATTTTTGGC-ACCAAGTCTCATTGAAAT
* *
1025 ATCTATATTTATCT-AACGAAATCTCAGCCACATTGGATTTAAGTATTTGTTTTTACGAGCATCT
258 ATCTATATTTATCTAAAC-AAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCT
* *
1089 TAATCCGGTTT
322 CAAT-CTGTTT
* * *
1100 CGATTTAATTAGCAATTAATTCGGAAAAAATAGAAAAAACAATATTAGAAGCGTGACA-AGCCCT
1 CGATTCAATTAGAAATTAATTCGGAAAAAATAGAAAAAACAATATTAGAAGCATGA-ATAGCCCT
** **
1164 TCAATCTTTTTGGTGTTGAATTATATATTTTTTATGAATATAGTGGCCGGAAATTGAGTTTAAAT
65 TCAATCTTTTTGGTGTTGAATTATATATTTTTTATGAATATAGTGGCCAAAAATTGAG-GAAAAT
* * * * * *
1229 T-TCTCGGGTCGATTTTTGTAAAATTTTAGCTGAAATC-GTGTACTAACCATCACGGTTTTTTAT
129 TCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGGTGTACTAACCATCACGGTTTTTGAC
* * *
1292 TAAAGACGCGTTCTGGAGCCCCGGCTCAGTTTTGCACGATTTTTGGAACCAAGTCTCATTGAAAT
194 TAAAAACACGTT-TGGAGCCCCGGCTCAGTTTTGCACGATTTTTGGCACCAAGTCTCATTGAAAT
* * * * * *
1357 ATCTATATTCATCTAAACAAATCTTACCCATATTGGAGTTAAGGATTTGTTTTTACGAGCATATG
258 ATCTATATTTATCTAAACAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTC
1422 AATCATGTTT
323 AATC-TGTTT
* * * * * * *
1432 CGATTCAATTAAAAATTGATTCGGAAAAAATAGGAAAAACGATATCAGAAGCGTGAATAGCCTTT
1 CGATTCAATTAGAAATTAATTCGGAAAAAATAGAAAAAACAATATTAGAAGCATGAATAGCCCTT
* * *
1497 CAATATTTTTGGTGTTGAATTATATATTTTTTATGAGTATCGTGGCCAAAAATTGAGGAAAATTC
66 CAATCTTTTTGGTGTTGAATTATATATTTTTTATGAATATAGTGGCCAAAAATTGAGGAAAATTC
* * * *
1562 TTTCGGGCCAATTTTTTCAAAATTTTAGCCGAAATCGGTGTGTACTAACTATCACGGTTTTTGGC
131 TTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATC-G-GTGTACTAACCATCACGGTTTTTGAC
* * * * * *
1627 TAAAAACACATTTCGAGTCCCCGACTCAGTTTTACATGATTTTTGGCACCAAG-ATCATTGAAAT
194 TAAAAACACGTTTGGAG-CCCCGGCTCAGTTTTGCACGATTTTTGGCACCAAGTCTCATTG--A-
* * * *
1691 ATCTATATCTATATTTATCTAAAGAAAT-TTCAGTCACACTGAATTTAAGGATTTGTTTTTACGA
255 A---ATATCTATATTTATCTAAACAAATCTT-AGCCACATTGGATTTAAGGATTTGTTTTTACGA
1755 GCATCTCAATCTGGTTT
316 GCATCTCAATCT-GTTT
* * * *
1772 CG-TTTAATTAGAAATTAATTCAGAAAAAATAGAAAAAAAAAACAGTATTAGAATCATGAGA-AG
1 CGATTCAATTAGAAATTAATTCGGAAAAAATAG----AAAAAACAATATTAGAAGCATGA-ATAG
* * * **
1835 CCCTTCAATCTTTTTAGTGTTTAATTATATATTTTTTTATGAATATGGTGGCCGGAAATTGAGGA
61 CCCTTCAATCTTTTTGGTGTTGAATTATATA-TTTTTTATGAATATAGTGGCCAAAAATTGAGGA
* * * **
1900 GAAATGT-TTT-GTGTCAATTTTTACAAAATTTTAGCCGTAATC-GTGTACTAACCATCATAGTT
125 -AAAT-TCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGGTGTACTAACCATCACGGTT
* * ** * *
1962 TTTGACTAAAAACATGTTTCGGGGTTCCGGCTCTGTTTTGC-CTGATTTTTGGCGCCAAGTCTCA
188 TTTGACTAAAAACACGTTT-GGAGCCCCGGCTCAGTTTTGCAC-GATTTTTGGCACCAAGTCTCA
*
2026 TTGAAATATATATAT
251 TTGAAATATCTATAT
2041 ATATATATAT
Statistics
Matches: 778, Mismatches: 132, Indels: 59
0.80 0.14 0.06
Matches are distributed among these distances:
331 13 0.02
332 266 0.34
333 135 0.17
334 16 0.02
335 62 0.08
336 10 0.01
337 1 0.00
339 30 0.04
340 65 0.08
341 60 0.08
342 8 0.01
343 46 0.06
344 58 0.07
345 7 0.01
346 1 0.00
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (331 bp):
CGATTCAATTAGAAATTAATTCGGAAAAAATAGAAAAAACAATATTAGAAGCATGAATAGCCCTT
CAATCTTTTTGGTGTTGAATTATATATTTTTTATGAATATAGTGGCCAAAAATTGAGGAAAATTC
TTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGGTGTACTAACCATCACGGTTTTTGACTA
AAAACACGTTTGGAGCCCCGGCTCAGTTTTGCACGATTTTTGGCACCAAGTCTCATTGAAATATC
TATATTTATCTAAACAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTCAAT
CTGTTT
Found at i:2038 original size:2 final size:2
Alignment explanation
Indices: 2031--2060 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2021 TCTCATTGAA
2031 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2061 C
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.