Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007006.1 Corchorus capsularis cultivar CVL-1 contig07027, 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: 16340
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Found at i:2351 original size:27 final size:27
Alignment explanation
Indices: 2290--2351 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
2280 CTCTCATTCC
*
2290 AAGTTAGTCAAGACAGTTCTCCATTCA
1 AAGTTAGTCAAGACAGTTCTCCAGTCA
**
2317 AAACTAGTC-AGAACAGTT-TCCCAGTCA
1 AAGTTAGTCAAG-ACAGTTCT-CCAGTCA
2344 AAGTTAGT
1 AAGTTAGT
2352 TCCCTAGGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
26 3 0.11
27 25 0.89
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.27
Consensus pattern (27 bp):
AAGTTAGTCAAGACAGTTCTCCAGTCA
Found at i:8345 original size:252 final size:252
Alignment explanation
Indices: 7895--8400 Score: 931
Period size: 252 Copynumber: 2.0 Consensus size: 252
7885 TTGAGGGGGC
* *
7895 GTGTTAAGGATCATTCAAAGTCAGACTCTCATTCCAAGTTAGTCAAGACAGTTCTCCATTCAAAG
1 GTGTGAAGGATCATTCAAAGTCAGACTCTCATTCCAACTTAGTCAAGACAGTTCTCCATTCAAAG
* * *
7960 CTAGTTAGAACAGTTTCCCAGTAAAAGTTAGTTCCCTAGGATTTATTCATTCAATGCTAGTTTGA
66 CTAGTCAGAACAGTTTCCAAGTAAAAGTTAGTTCCCTAGGATTGATTCATTCAATGCTAGTTTGA
*
8025 ATTCATATTGTAATTACTTTACAGCACAACTCTACTTGTATAAATATACTCATTGTAACACAACA
131 AATCATATTGTAATTACTTTACAGCACAACTCTACTTGTATAAATATACTCATTGTAACACAACA
*
8090 ACACTATGAATGAAAATCTCATTTCCCTCATTCATCAAACTCTCATATCTCTATATG
196 ACACTATAAATGAAAATCTCATTTCCCTCATTCATCAAACTCTCATATCTCTATATG
*
8147 GTGTGAAGGATCATTCAAAGTTAGACTCTCATTCCAACTTAGTCAAGACAGTTCTCCATTCAAAG
1 GTGTGAAGGATCATTCAAAGTCAGACTCTCATTCCAACTTAGTCAAGACAGTTCTCCATTCAAAG
*
8212 CTAGTCAGAACAGTTTCCAAGTCAAAGTTAGTTCCCTAGGATTGATTCATTCAATGCTAGTTTGA
66 CTAGTCAGAACAGTTTCCAAGTAAAAGTTAGTTCCCTAGGATTGATTCATTCAATGCTAGTTTGA
8277 AATCATATTGTAATTACTTTACAGCACAACTCTACTTGTATAAATATACTCATTGTAACACAACA
131 AATCATATTGTAATTACTTTACAGCACAACTCTACTTGTATAAATATACTCATTGTAACACAACA
8342 ACACTATAAATGAAAATCTCATTTCCCTCATTCATCAAACTCTCATATCTCTATATG
196 ACACTATAAATGAAAATCTCATTTCCCTCATTCATCAAACTCTCATATCTCTATATG
8399 GT
1 GT
8401 ATCAGACTTT
Statistics
Matches: 245, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
252 245 1.00
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.34
Consensus pattern (252 bp):
GTGTGAAGGATCATTCAAAGTCAGACTCTCATTCCAACTTAGTCAAGACAGTTCTCCATTCAAAG
CTAGTCAGAACAGTTTCCAAGTAAAAGTTAGTTCCCTAGGATTGATTCATTCAATGCTAGTTTGA
AATCATATTGTAATTACTTTACAGCACAACTCTACTTGTATAAATATACTCATTGTAACACAACA
ACACTATAAATGAAAATCTCATTTCCCTCATTCATCAAACTCTCATATCTCTATATG
Found at i:11444 original size:81 final size:81
Alignment explanation
Indices: 11291--11445 Score: 199
Period size: 81 Copynumber: 1.9 Consensus size: 81
11281 AATGAGTTCA
* * * *
11291 AAGTCTCTGTTTTTGAAAGTTGCCTTACAACATATCTTGCATAATTTCAGCACATATTCAGCTAC
1 AAGTCCCTCTTTTTGAAAGTTGCCTTACAACATATCTGGCATAATTTCAACACATATTCAGCTAC
**
11356 TTTTTTTTTTTTTTTG
66 TAATTTTTTTTTTTTG
*
11372 AAGTCCCTCTTTTTGAAAGTTGTCTTAC-A-ATATCTGGCATAATTTCATCACAACATATTCAGC
1 AAGTCCCTCTTTTTGAAAGTTGCCTTACAACATATCTGGCATAATTTCA--AC-ACATATTCAGC
11435 TAC-AATTTTTT
63 TACTAATTTTTT
11446 GTTCCGTCTT
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
79 17 0.27
80 1 0.02
81 32 0.50
82 14 0.22
ACGTcount: A:0.26, C:0.19, G:0.10, T:0.45
Consensus pattern (81 bp):
AAGTCCCTCTTTTTGAAAGTTGCCTTACAACATATCTGGCATAATTTCAACACATATTCAGCTAC
TAATTTTTTTTTTTTG
Done.