Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000994.1 Corchorus capsularis cultivar CVL-1 contig00994, 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, 943
Length: 1573
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Found at i:1092 original size:48 final size:48
Alignment explanation
Indices: 1034--1220 Score: 239
Period size: 48 Copynumber: 3.8 Consensus size: 48
1024 AATAGTAACC
*
1034 AGTAAGTCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAATGAAAT
1 AGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAATGAAAT
* *
1082 AGTAAATCAGTAATTAAATAAAAAGAGATTAATCAGAGTCAATAAAAT
1 AGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAATGAAAT
* *
1130 AGTAAATCAATAATTAAGTAAAAAGAGATTAATCAGAGTCAGAGTAGTAGTGAT
1 AGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCA-A-T-G-A--AAT
* * *
1184 CAGTAAATCAGTAATCAAGTAAAAAGATAGTAATCAG
1 -AGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAG
1221 TAAATTGATA
Statistics
Matches: 121, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
48 84 0.69
49 1 0.01
50 1 0.01
52 1 0.01
54 2 0.02
55 32 0.26
ACGTcount: A:0.51, C:0.07, G:0.17, T:0.25
Consensus pattern (48 bp):
AGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAATGAAAT
Found at i:1294 original size:32 final size:31
Alignment explanation
Indices: 1229--1294 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
1219 AGTAAATTGA
*
1229 TAATTAAGAGTCAAGGTAAGAGATTAATCAG
1 TAATTAAGAGTCAAGGTAAGAAATTAATCAG
1260 TAATTAAGAGTCAAGGTAA-AAATAGTAATCAG
1 TAATTAAGAGTCAAGGTAAGAAAT--TAATCAG
1292 TAA
1 TAA
1295 ATCAGTAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 3 0.09
31 19 0.59
32 10 0.31
ACGTcount: A:0.48, C:0.06, G:0.20, T:0.26
Consensus pattern (31 bp):
TAATTAAGAGTCAAGGTAAGAAATTAATCAG
Found at i:1383 original size:7 final size:7
Alignment explanation
Indices: 1371--1473 Score: 50
Period size: 7 Copynumber: 14.6 Consensus size: 7
1361 AGGAAAAATG
1371 GTAAAGA
1 GTAAAGA
1378 GTAAAGA
1 GTAAAGA
* **
1385 ATAATCA
1 GTAAAGA
*
1392 GTAAGGA
1 GTAAAGA
**
1399 GTAATTA
1 GTAAAGA
1406 GTAAAGA
1 GTAAAGA
1413 GTAATATGA
1 GTAA-A-GA
*
1422 -TAAAAA
1 GTAAAGA
1428 GTAAAGA
1 GTAAAGA
**
1435 GTAATCA
1 GTAAAGA
1442 GTAAAAGAA
1 GT-AAAG-A
*
1451 G-AATG-
1 GTAAAGA
*
1456 GTAAAAA
1 GTAAAGA
1463 GTAAAGA
1 GTAAAGA
1470 GTAA
1 GTAA
1474 TCAGTAAAGG
Statistics
Matches: 69, Mismatches: 20, Indels: 14
0.67 0.19 0.14
Matches are distributed among these distances:
5 1 0.01
6 3 0.04
7 55 0.80
8 6 0.09
9 4 0.06
ACGTcount: A:0.55, C:0.02, G:0.22, T:0.20
Consensus pattern (7 bp):
GTAAAGA
Found at i:1460 original size:50 final size:50
Alignment explanation
Indices: 1372--1466 Score: 113
Period size: 50 Copynumber: 1.9 Consensus size: 50
1362 GGAAAAATGG
* * *
1372 TAAAGAGTAAAGAATAATCAGTAAGGAGTAATTAGTAAAGAGTAATATGA
1 TAAAAAGTAAAGAATAATCAGTAAGAAGTAATTAGTAAAAAGTAATATGA
* *
1422 TAAAAAGTAAAGAGTAATCAGTAAAAGAAG-AA-TGGTAAAAAGTAA
1 TAAAAAGTAAAGAATAATCAGT--AAGAAGTAATTAGTAAAAAGTAA
1467 AGAGTAATCA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
50 31 0.82
51 2 0.05
52 5 0.13
ACGTcount: A:0.56, C:0.02, G:0.21, T:0.21
Consensus pattern (50 bp):
TAAAAAGTAAAGAATAATCAGTAAGAAGTAATTAGTAAAAAGTAATATGA
Found at i:1468 original size:35 final size:35
Alignment explanation
Indices: 1391--1519 Score: 152
Period size: 35 Copynumber: 3.6 Consensus size: 35
1381 AAGAATAATC
* * * *
1391 AGTAAGGAGTAATTAGTAAAGAGTAA-TATGATAAAA
1 AGTAAAGAGTAATCAGTAAA-AG-AAGAATGGTAAAA
1427 AGTAAAGAGTAATCAGTAAAAGAAGAATGGTAAAA
1 AGTAAAGAGTAATCAGTAAAAGAAGAATGGTAAAA
* *
1462 AGTAAAGAGTAATCAGTAAAGGAAGAATGGTAAAG
1 AGTAAAGAGTAATCAGTAAAAGAAGAATGGTAAAA
*
1497 AGTAAAAAGGGTAATCAGTAAAA
1 AGT--AAAGAGTAATCAGTAAAA
1520 AGTAAAAAGA
Statistics
Matches: 82, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
34 2 0.02
35 46 0.56
36 18 0.22
37 16 0.20
ACGTcount: A:0.54, C:0.02, G:0.24, T:0.19
Consensus pattern (35 bp):
AGTAAAGAGTAATCAGTAAAAGAAGAATGGTAAAA
Found at i:1535 original size:23 final size:23
Alignment explanation
Indices: 1491--1541 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
1481 AGGAAGAATG
* *
1491 GTAAAGAGTAAAAAGGGTAATCA
1 GTAAAAAGTAAAAAGGATAATCA
*
1514 GTAAAAAGTAAAAA-GATAAATCG
1 GTAAAAAGTAAAAAGGAT-AATCA
1537 GTAAA
1 GTAAA
1542 GAATGAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 2 0.08
23 22 0.92
ACGTcount: A:0.57, C:0.04, G:0.22, T:0.18
Consensus pattern (23 bp):
GTAAAAAGTAAAAAGGATAATCA
Done.