Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001722.1 Corchorus capsularis cultivar CVL-1 contig01722, 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: 3271
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34
Found at i:602 original size:319 final size:320
Alignment explanation
Indices: 1--691 Score: 883
Period size: 319 Copynumber: 2.1 Consensus size: 320
* * ** *
1 TTTTCGGGTCAGTTTTTAGCCAAAAGCATGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTT
1 TTTTCGGGTCAGTTTTTAGCCAAAATCGTGTA-TAACCATCACGGTTTTGGGCTAAAAACGCATT
* * * * * * *
66 CCGGAGCCCTGACTCAATTTTGCATGATTTTTTGTACAAAGACGCCTTTGAATATCTATATTTAT
65 CCGGAGCCCTAACTAAATTTTACATGATTCTTGGCACAAAGACGCCTTTGAATA-CTATATTCAT
* * *
131 CGAATCAAATGTCAACCATATTGGATATAAAGATTTGTTTTTTTGAGCATCTGAATCTTGTTTCG
129 CGAACCAAATCTCAACCATATTGGATATAAAGATTTGTTTTTTTGAGCATCTCAATCTTGTTTCG
*
196 ATTTAATTAGAAATTAATTCGGAAAAAAATGAAAAAACGATATTAGAAGCGTGAAAAGCCCGTCA
194 ATTTAATTAGAAATTAATTCGGAAAAAAATGAAAAAACGATATTAGAAGAGTGAAAAGCCCGTCA
* *
261 ATCTTTTTGTCATTGAATTATATATTTTTTCTGAGTATTATCACAAAAGATTGAGAAAAAAC
259 ATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTATCACAAAAAATTGAGAAAAAAC
* * *
323 TTTTCGGGTCAGTTTTTAGTCGAAATTGTGTATTAACCATCACGGTTTTGGGCTAAAAACGCATT
1 TTTTCGGGTCAGTTTTTAGCCAAAATCGTGTA-TAACCATCACGGTTTTGGGCTAAAAACGCATT
* **
388 CCGGAG-CCTCAACTAAATTTTACATGATTCTTGGCATAAAGATTCC-TTGAA-A-TATATTCAT
65 CCGGAGCCCT-AACTAAATTTTACATGATTCTTGGCACAAAGACGCCTTTGAATACTATATTCAT
* * * * *
449 CGAACCAAATCTCAGCCATTTTGGAT-TTAAGAATTT-TTTTTTTCGTGTATCTCAAT-TATGTT
129 CGAACCAAATCTCAACCATATTGGATATAAAG-ATTTGTTTTTTT-GAGCATCTCAATCT-TGTT
* * * *
511 TCGATTTAATTAGAAATTCATTCAGGAAAAAAATGGAAAAACGATGTTAGAAGAGTGAAAAGCCT
191 TCGATTTAATTAGAAATTAATTC-GGAAAAAAATGAAAAAACGATATTAGAAGAGTGAAAAGCCC
* *** *
576 GTCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGTAAAAAATTGAGGAAAAA
255 GTCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTATCACAAAAAATTGAGAAAAAA
641 C
320 C
* *
642 TTTTCGGGTTAGGTTTTTAGCCAAAATCGTGTACAACCATCACGGATTTT
1 TTTTCGGGTCA-GTTTTTAGCCAAAATCGTGTATAACCATCACGG-TTTT
692 TTTTTTTTAC
Statistics
Matches: 318, Mismatches: 44, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
317 12 0.04
318 69 0.22
319 117 0.37
320 23 0.07
321 8 0.03
322 89 0.28
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.36
Consensus pattern (320 bp):
TTTTCGGGTCAGTTTTTAGCCAAAATCGTGTATAACCATCACGGTTTTGGGCTAAAAACGCATTC
CGGAGCCCTAACTAAATTTTACATGATTCTTGGCACAAAGACGCCTTTGAATACTATATTCATCG
AACCAAATCTCAACCATATTGGATATAAAGATTTGTTTTTTTGAGCATCTCAATCTTGTTTCGAT
TTAATTAGAAATTAATTCGGAAAAAAATGAAAAAACGATATTAGAAGAGTGAAAAGCCCGTCAAT
CTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTATCACAAAAAATTGAGAAAAAAC
Found at i:1948 original size:95 final size:94
Alignment explanation
Indices: 1766--1948 Score: 215
Period size: 95 Copynumber: 1.9 Consensus size: 94
1756 TTCGTATAAT
* * * * * * *
1766 ACACTAAATCTGGATTATTTTGTATATTTAAGACTTTTTTGTAAATATGCGCGACATATATCGCT
1 ACACTAAATCTAGATTATTTTGGATAGTTAAGACTTATTTGTAAATATCCACGACAGATATCGCT
* *
1831 ATGCCTTGATTATAATATTTTTTTTGCAAC
66 ATCCCAT-ATTATAATATTTTTTTTGCAAC
* *
1861 ACACTAAATTTAGATTATTTTGGATAGTTAAGACTTATTTGTAAATATCCATGACAGATAATCGC
1 ACACTAAATCTAGATTATTTTGGATAGTTAAGACTTATTTGTAAATATCCACGACAGAT-ATCGC
*
1926 TCCTCCCA-ATTTATAATATTTTT
65 T-ATCCCATA-TTATAATATTTTT
1949 CCTTTACCAC
Statistics
Matches: 73, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
95 51 0.70
96 19 0.26
97 3 0.04
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (94 bp):
ACACTAAATCTAGATTATTTTGGATAGTTAAGACTTATTTGTAAATATCCACGACAGATATCGCT
ATCCCATATTATAATATTTTTTTTGCAAC
Found at i:3206 original size:2 final size:2
Alignment explanation
Indices: 3201--3271 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
3191 TTAATACTTA
3201 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3243 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Done.