Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009198.1 Corchorus capsularis cultivar CVL-1 contig09219, 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: 11494
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:630 original size:326 final size:320
Alignment explanation
Indices: 1--1120 Score: 1227
Period size: 326 Copynumber: 3.5 Consensus size: 320
*
1 AAATGTTAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAA
1 AAATGTTAGCCACATTGGATATAAAGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAA
* *
66 TTAGAAATTACTTCTG-AAAAAATGGAAAAATGATATTAGAAGCGTGAAAAGCCCGTCAATCTTT
66 TTAGAAATTAATTC-GAAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAGCCCGTTAATCTTT
*
130 TTGGCGTTGAATTATATATTTTTT-TAGTATTTTGGCAAAAAATTGAGAAA-AAAAAACTTTTCG
130 TTGGCGTTGAATTATATATTTTTTCTAGTATTGTGGCAAAAAATT-AGAAATAAAAAA---TTCG
* *
193 GGTCAGTTTTAAGCC-AAATTTGTGTACTAACCATCACGGTTTTTGGCTAAGAACGCGTTGCGGA
191 GGTCAGTTTTTAGCCGAAA-TCGTGTACTAACCATCACGGTTTTTGGCTAAGAACGCGTTGCGGA
* * * * *
257 GCTCCGGCTCAATTTTGCATGATTTTTTGCGCAAAGACTCCTTGATTTATCTATATTCATTGAAG
255 GCCCCGACTCAATTTTGCATGATTTTTTACGCAAAGACTCCTTGATTTATCTATATTCATCGAAC
322 C
320 C
* *
323 TAATGTCT-GTCACATTGGATATAAAGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTA
1 AAATGT-TAGCCACATTGGATATAAAGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTA
* * * *
387 ATTATAAATTAATTCGGAAAAAAATTGGAAAATTGATATTAGAAGCGTGAAAAGACCTTTAATCT
65 ATTAGAAATTAATTC-GAAAAAAA-TGGAAAAATGATATTAGAAGCGTGAAAAGCCCGTTAATCT
* * * *
452 TTTTGGTGTTGAATTGTATATTTTTTCTGAGTATTGCGGCAAAAAATTCAGAAATAAAAAAATCG
128 TTTTGGCGTTGAATTATATATTTTTTCT-AGTATTGTGGCAAAAAATT-AGAAATAAAAAATTCG
* *
517 GGTCAGTTTTTGGCCGAAATCGTGTACTATAACCATCACGGTTTTTGGCTTAA-AACGCGTTTCG
191 GGTCAGTTTTTAGCCGAAATCGTGTAC--TAACCATCACGGTTTTTGGC-TAAGAACGCGTTGCG
**
581 GAGCCCCGACTCAATTTTGCATGATTTTTTACGCAAAGACTTTTTGATTTATCTATATTCATCGA
253 GAGCCCCGACTCAATTTTGCATGATTTTTTACGCAAAGACTCCTTGATTTATCTATATTCATCGA
646 ACC
318 ACC
*
649 AAATGTTAGCCACATTGGATAT-AAGAATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTA
1 AAATGTTAGCCACATTGGATATAAAG-ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTA
* * *
713 ATTAGAAATTAATTCGAAAAAAATGAAAAAACGATATGAGAAGCGTGAAAAGCCCGTTAATCTTT
65 ATTAGAAATTAATTCGAAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAGCCCGTTAATCTTT
* * *
778 TTTGCGCTGAATTATATATTTTTTCTAAGTATTGTGGCAAAAAATT-G--ATAAAAACTTTCGGG
130 TTGGCGTTGAATTATATATTTTTTCT-AGTATTGTGGCAAAAAATTAGAAATAAAAA-ATTCGGG
* ** * * * * * *
840 TCAGTTTTTAGCTGAAATCGTG---T-ACCATCATAGATTTTGACTAAAAATGCCTTCCAGG-G-
193 TCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAGAACGCGTTGC-GGAGC
* ** * ** ** * ** * *
899 TCATAGCTCTATATTTTGCATGGTTTTTGGCGCTGAGACTCCTTCAAATATCTTTATT-AGTCTA
257 CCCGA-CTC-A-ATTTTGCATGATTTTTTACGCAAAGACTCCTTGATTTATCTATATTCA-TCGA
*
963 ATC
318 ACC
* * * * **
966 AAAT-TTAGGCCACATTGGATTTAAGGATTTGCTTTTACGTGCATCAAAATCTTGTTTCGATTTA
1 AAATGTTA-GCCACATTGGATATAAAGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTA
* * * * * * * *
1030 ATTAAAAATTAATTCAGAAAAAATAT-GAAAAACGATATTAAAAGCATGTAAAGTCC-TCCAACC
65 ATTAGAAATTAATTC-GAAAAAA-ATGGAAAAATGATATTAGAAGCGTGAAAAGCCCGT-TAATC
*
1093 TTTTTGGTGTTGAATTATATATATTTTT
127 TTTTTGGCGTTGAATTATATAT-TTTTT
1121 ATGATTTGTT
Statistics
Matches: 686, Mismatches: 87, Indels: 53
0.83 0.11 0.06
Matches are distributed among these distances:
314 5 0.01
315 25 0.04
316 8 0.01
317 107 0.16
318 55 0.08
319 7 0.01
320 7 0.01
321 25 0.04
322 74 0.11
323 7 0.01
324 159 0.23
325 16 0.02
326 182 0.27
327 9 0.01
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (320 bp):
AAATGTTAGCCACATTGGATATAAAGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAA
TTAGAAATTAATTCGAAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAGCCCGTTAATCTTTT
TGGCGTTGAATTATATATTTTTTCTAGTATTGTGGCAAAAAATTAGAAATAAAAAATTCGGGTCA
GTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAGAACGCGTTGCGGAGCCCCG
ACTCAATTTTGCATGATTTTTTACGCAAAGACTCCTTGATTTATCTATATTCATCGAACC
Found at i:1479 original size:2 final size:2
Alignment explanation
Indices: 1472--1501 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
1462 AAATTACTAG
1472 TA TA TA TA TA TA TA TA TA TA TA TA GTA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA T
1502 TTACAAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6099 original size:20 final size:20
Alignment explanation
Indices: 6074--6114 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
6064 CCACTCCCAG
6074 CAAGTCTACTTCAATATTCA
1 CAAGTCTACTTCAATATTCA
6094 CAAGTCTACTTCAATATTCA
1 CAAGTCTACTTCAATATTCA
6114 C
1 C
6115 TAATTTGATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.34
Consensus pattern (20 bp):
CAAGTCTACTTCAATATTCA
Done.