Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01003803.1 Corchorus capsularis cultivar CVL-1 contig03811, 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: 1923
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:295 original size:22 final size:22
Alignment explanation
Indices: 212--296 Score: 57
Period size: 22 Copynumber: 3.8 Consensus size: 22
202 ATAACCCTCT
* * *
212 TATGAAATTTTGAAAACTAAAC
1 TATGAAATTTTGATAACCATAC
* *
234 TATGAAATTTTGATATCCTTAATC
1 TATGAAATTTTGATAACCAT-A-C
** *
258 T-TCCTAA-TTTGGTAACCATAC
1 TAT-GAAATTTTGATAACCATAC
279 TATGAAATTTTGATAACC
1 TATGAAATTTTGATAACC
297 TCCCTAGAAA
Statistics
Matches: 45, Mismatches: 13, Indels: 10
0.66 0.19 0.15
Matches are distributed among these distances:
21 4 0.09
22 26 0.58
23 11 0.24
24 4 0.09
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCATAC
Found at i:362 original size:22 final size:22
Alignment explanation
Indices: 337--461 Score: 103
Period size: 22 Copynumber: 5.7 Consensus size: 22
327 AATCACATTT
337 TGAAAATTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTTTA
*
359 TGAAATTTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTTTA
* * * *
381 T-AAAATTTTGTTGACCCCTCTA
1 TGAAAA-TTTGATAACCTCTTTA
* * *
403 TG-AAATTCTGATAATCACATTA
1 TGAAAATT-TGATAACCTCTTTA
* *
425 TGTAATTTTGATAACCTCTCTT-
1 TGAAAATTTGATAACCTCT-TTA
*
447 TGAAATTTTGATAAC
1 TGAAAATTTGATAAC
462 AATACTATGA
Statistics
Matches: 81, Mismatches: 17, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
21 5 0.06
22 70 0.86
23 6 0.07
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (22 bp):
TGAAAATTTGATAACCTCTTTA
Found at i:363 original size:44 final size:44
Alignment explanation
Indices: 313--505 Score: 143
Period size: 44 Copynumber: 4.4 Consensus size: 44
303 GAAATACCAC
313 TATGAAATTTTTG-TAATCACATTTTGAAAATTTGATAACCTCTT
1 TATGAAA-TTTTGATAATCACATTTTGAAAATTTGATAACCTCTT
* * * * * *
357 TATGAAATTTTGATAACCTC-TTTAT-AAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAATCACATTT-TGAAAA-TTTGATAACCTCTT
* * * *
401 TATGAAATTCTGATAATCACATTATGTAATTTTGATAACCTCTCT
1 TATGAAATTTTGATAATCACATTTTGAAAATTTGATAACCTCT-T
* *
446 T-TGAAATTTTGATAA-CA-ATACTATGAAATTTTGATAA--TCTT
1 TATGAAATTTTGATAATCACAT--TTTGAAAATTTGATAACCTCTT
487 ACTAT-AAATTTTGATAATC
1 --TATGAAATTTTGATAATC
506 TGATCTCTAT
Statistics
Matches: 119, Mismatches: 18, Indels: 24
0.74 0.11 0.15
Matches are distributed among these distances:
41 1 0.01
42 5 0.04
43 27 0.23
44 81 0.68
45 5 0.04
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.44
Consensus pattern (44 bp):
TATGAAATTTTGATAATCACATTTTGAAAATTTGATAACCTCTT
Found at i:470 original size:66 final size:66
Alignment explanation
Indices: 356--503 Score: 167
Period size: 66 Copynumber: 2.3 Consensus size: 66
346 GATAACCTCT
* * **
356 TTATGAAATTTTGATAACCTCTTTATAAAATTTTGTTGACCCCTCTATGAAATTCTGATAATCAC
1 TTATGAAATTTTGATAACCTCTTTATAAAATTTTGATGAACAATCTATGAAATTCTGATAATCAC
421 A
66 A
* * *
422 TTATGTAATTTTGATAACCTCTCTT-TGAAATTTTGAT-AACAATACTATGAAATTTTGATAATC
1 TTATGAAATTTTGATAACCTCT-TTATAAAATTTTGATGAACAAT-CTATGAAATTCTGATAATC
**
485 TTA
64 ACA
*
488 CTAT-AAATTTTGATAA
1 TTATGAAATTTTGATAA
504 TCTGATCTCT
Statistics
Matches: 69, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
65 14 0.20
66 53 0.77
67 2 0.03
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (66 bp):
TTATGAAATTTTGATAACCTCTTTATAAAATTTTGATGAACAATCTATGAAATTCTGATAATCAC
A
Found at i:472 original size:22 final size:22
Alignment explanation
Indices: 400--533 Score: 114
Period size: 22 Copynumber: 6.0 Consensus size: 22
390 GTTGACCCCT
* *
400 CTATGAAATTCTGATAATCACA
1 CTATGAAATTTTGATAATCATA
* *
422 TTATGTAATTTTGATAACCTC-T-
1 CTATGAAATTTTGATAA--TCATA
*
444 CTTTGAAATTTTGATAA-CAATA
1 CTATGAAATTTTGATAATC-ATA
*
466 CTATGAAATTTTGATAATCTTA
1 CTATGAAATTTTGATAATCATA
*
488 CTAT-AAATTTTGATAATCTGATCT
1 CTATGAAATTTTGATAATC--AT-A
*
512 CTATGAAATTTCGATAATCATA
1 CTATGAAATTTTGATAATCATA
534 ATCACTAGCC
Statistics
Matches: 89, Mismatches: 13, Indels: 20
0.73 0.11 0.16
Matches are distributed among these distances:
19 1 0.01
21 15 0.17
22 50 0.56
23 4 0.04
24 6 0.07
25 13 0.15
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.42
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCATA
Found at i:1166 original size:4 final size:4
Alignment explanation
Indices: 1157--1256 Score: 72
Period size: 4 Copynumber: 25.5 Consensus size: 4
1147 GGAGTGGCCT
* *
1157 TTTA TTTA TTTA TTTA -TTA TTTA TATT- TATA TTTA TTGA -TTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA
1203 --TA TTTA TCGTATA TTTA TTATA TTTA TTTA -TTA TTTA --TA TTTA
1 TTTA TTTA T--T-TA TTTA TT-TA TTTA TTTA TTTA TTTA TTTA TTTA
1246 TTTTA TTTA TT
1 -TTTA TTTA TT
1257 ACTTATATTT
Statistics
Matches: 78, Mismatches: 4, Indels: 28
0.71 0.04 0.25
Matches are distributed among these distances:
2 4 0.05
3 9 0.12
4 50 0.64
5 11 0.14
6 1 0.01
7 3 0.04
ACGTcount: A:0.28, C:0.01, G:0.02, T:0.69
Consensus pattern (4 bp):
TTTA
Found at i:1185 original size:13 final size:13
Alignment explanation
Indices: 1167--1268 Score: 89
Period size: 13 Copynumber: 8.5 Consensus size: 13
1157 TTTATTTATT
1167 TATTTATTATTTA
1 TATTTATTATTTA
1180 TATTTA-TA-TT-
1 TATTTATTATTTA
*
1190 TATTGATTATTTA
1 TATTTATTATTTA
**
1203 TATTTA-T-CGTA
1 TATTTATTATTTA
1214 TATTTATTATATT-
1 TATTTATTAT-TTA
1227 TATTTATTATTTA
1 TATTTATTATTTA
1240 TA--T-TTATTT-
1 TATTTATTATTTA
*
1249 TATTTATTACTTA
1 TATTTATTATTTA
1262 TATTTAT
1 TATTTAT
1269 CGTATATTTA
Statistics
Matches: 71, Mismatches: 7, Indels: 22
0.71 0.07 0.22
Matches are distributed among these distances:
9 2 0.03
10 11 0.15
11 14 0.20
12 13 0.18
13 30 0.42
14 1 0.01
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (13 bp):
TATTTATTATTTA
Found at i:1265 original size:59 final size:59
Alignment explanation
Indices: 1157--1278 Score: 210
Period size: 59 Copynumber: 2.1 Consensus size: 59
1147 GGAGTGGCCT
*
1157 TTTATTTATTTATTTATTATTTATATTTATATTTATTGATTATTTATATTTATCGTATA
1 TTTATTTATTTATTTATTATTTATATTTATATTTATTGATTACTTATATTTATCGTATA
*
1216 TTTATTATATTTATTTATTATTTATATTTAT-TTTATTTATTACTTATATTTATCGTATA
1 TTTATT-TATTTATTTATTATTTATATTTATATTTATTGATTACTTATATTTATCGTATA
1275 TTTA
1 TTTA
1279 CTTTTATATA
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
59 36 0.60
60 24 0.40
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (59 bp):
TTTATTTATTTATTTATTATTTATATTTATATTTATTGATTACTTATATTTATCGTATA
Found at i:1267 original size:17 final size:17
Alignment explanation
Indices: 1157--1248 Score: 98
Period size: 17 Copynumber: 5.2 Consensus size: 17
1147 GGAGTGGCCT
*
1157 TTTATTTATTTATTTATTA
1 TTTA-TTATTTATAT-TTA
1176 TTTA-TATTTATATTTA
1 TTTATTATTTATATTTA
*
1192 TTGATTATTTATATTTA
1 TTTATTATTTATATTTA
1209 TCGTATATT-TATTATATTTA
1 T--T-TATTAT-TTATATTTA
1229 TTTATTATTTATATTTA
1 TTTATTATTTATATTTA
1246 TTT
1 TTT
1249 TATTTATTAC
Statistics
Matches: 64, Mismatches: 3, Indels: 14
0.79 0.04 0.17
Matches are distributed among these distances:
16 6 0.09
17 37 0.58
18 2 0.03
19 6 0.09
20 13 0.20
ACGTcount: A:0.28, C:0.01, G:0.02, T:0.68
Consensus pattern (17 bp):
TTTATTATTTATATTTA
Found at i:1294 original size:21 final size:21
Alignment explanation
Indices: 1255--1294 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1245 ATTTTATTTA
* *
1255 TTACTTATATTTATCGTATAT
1 TTACTTATATATATAGTATAT
*
1276 TTACTTTTATATATAGTAT
1 TTACTTATATATATAGTAT
1295 TCCCGGCCAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.57
Consensus pattern (21 bp):
TTACTTATATATATAGTATAT
Done.