Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015711.1 Corchorus capsularis cultivar CVL-1 contig15732, 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, 789
Length: 1316
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.38
Found at i:41 original size:22 final size:21
Alignment explanation
Indices: 15--95 Score: 83
Period size: 22 Copynumber: 3.8 Consensus size: 21
5 GATCTACATA
*
15 CTATGAAATTTTGATAACCCT
1 CTATGAAATTTTGATAACCAT
* *
36 CTTATGAAATTTTGA-AACTAAA
1 C-TATGAAATTTTGATAAC-CAT
* *
58 CTATGAAAATTTGATAACCTT
1 CTATGAAATTTTGATAACCAT
79 CATATGAAATTTTGATA
1 C-TATGAAATTTTGATA
96 TCATCACTGA
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
21 17 0.35
22 31 0.65
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (21 bp):
CTATGAAATTTTGATAACCAT
Found at i:110 original size:19 final size:19
Alignment explanation
Indices: 86--153 Score: 91
Period size: 20 Copynumber: 3.5 Consensus size: 19
76 CTTCATATGA
* *
86 AATTTTGATATCATCACTG
1 AATTTTGATATCCTCCCTG
105 AATTTTCGATATCCTCCCTG
1 AATTTT-GATATCCTCCCTG
*
125 AATTTTGGTATCCTCCCTG
1 AATTTTGATATCCTCCCTG
144 AAATTTTGAT
1 -AATTTTGAT
154 TACTCCATCA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
19 18 0.42
20 25 0.58
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.43
Consensus pattern (19 bp):
AATTTTGATATCCTCCCTG
Found at i:284 original size:22 final size:22
Alignment explanation
Indices: 259--450 Score: 76
Period size: 22 Copynumber: 8.6 Consensus size: 22
249 AATCACATTT
259 TGAAAATTTGATAAGC-TCTTTA
1 TGAAAATTTGATAA-CATCTTTA
*
281 TGAAATTTTGATAACATCTTTA
1 TGAAAATTTGATAACATCTTTA
* * ** *
303 T-AAAATTTTGTTGACCCCTCTA
1 TGAAAA-TTTGATAACATCTTTA
* *
325 TGAAATTTTGATAATCA-CATTA
1 TGAAAATTTGATAA-CATCTTTA
* * * *
347 TGTAATTTTGATAACCTCGCTT-
1 TGAAAATTTGATAACATC-TTTA
* * **
369 TGAAATTTTGATAACAACACTA
1 TGAAAATTTGATAACATCTTTA
*
391 TGAAATTTTGAT-A-ATCTTCATA
1 TGAAAATTTGATAACATCTT--TA
*
413 T-AAATTTTGATAATCCTATCTTTA
1 TGAAAATTTGATAA--C-ATCTTTA
437 TG-AAATTTCGATAA
1 TGAAAATTT-GATAA
451 TCATTCTATG
Statistics
Matches: 129, Mismatches: 25, Indels: 29
0.70 0.14 0.16
Matches are distributed among these distances:
20 2 0.02
21 17 0.13
22 86 0.67
23 6 0.05
24 8 0.06
25 5 0.04
26 5 0.04
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.42
Consensus pattern (22 bp):
TGAAAATTTGATAACATCTTTA
Found at i:327 original size:44 final size:43
Alignment explanation
Indices: 234--404 Score: 139
Period size: 44 Copynumber: 3.9 Consensus size: 43
224 AAAAATAACA
* * * *
234 CTATGAAATTTTTG-TAATCACATTTTGAAAA-TTTGATAAGCTCT
1 CTATGAAA-TTTTGATAA-CACATTAT-AAAATTTTGATAACCCCG
* * * * *
278 TTATGAAATTTTGATAACATCTTTATAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAACA-CATTATAAAATTTTGATAACCCCG
** *
322 CTATGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAA-CACATTATAAAATTTTGATAACCCCG
* * *
366 CTTTGAAATTTTGATAACAACACTATGAAATTTTGATAA
1 CTATGAAATTTTGATAAC-ACATTATAAAATTTTGATAA
405 TCTTCATATA
Statistics
Matches: 104, Mismatches: 18, Indels: 10
0.79 0.14 0.08
Matches are distributed among these distances:
43 12 0.12
44 90 0.87
45 2 0.02
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (43 bp):
CTATGAAATTTTGATAACACATTATAAAATTTTGATAACCCCG
Found at i:335 original size:66 final size:65
Alignment explanation
Indices: 259--450 Score: 174
Period size: 66 Copynumber: 2.9 Consensus size: 65
249 AATCACATTT
* * * * ** *
259 TGAAAATTTGATAAGCTCTTTATGAAATTTTGATAACATCTTTATAAAATTTTGTTGACCCCTCT
1 TGAAATTTTGATAA-CTCTTTATGAAATTTTGATAACATCTTTATGAAATTTTGATAACAACACT
324 A
65 A
* * * * *
325 TGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACAACAC
1 TGAAATTTTGATAA-CTCTTTATGAAATTTTGATAACATC-TTTATGAAATTTTGATAACAACAC
389 TA
64 TA
*
391 TGAAATTTTGATAA-TCTTCATAT-AAATTTTGATAATCCTATCTTTATGAAATTTCGATAA
1 TGAAATTTTGATAACTCTT--TATGAAATTTTGATAA--C-ATCTTTATGAAATTTTGATAA
451 TCATTCTATG
Statistics
Matches: 100, Mismatches: 19, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
64 2 0.02
65 11 0.11
66 67 0.67
67 5 0.05
68 15 0.15
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.42
Consensus pattern (65 bp):
TGAAATTTTGATAACTCTTTATGAAATTTTGATAACATCTTTATGAAATTTTGATAACAACACTA
Found at i:397 original size:88 final size:88
Alignment explanation
Indices: 234--400 Score: 221
Period size: 88 Copynumber: 1.9 Consensus size: 88
224 AAAAATAACA
* * * *
234 CTATGAAATTTTTGTAATCACATTTTGAAAATTTGATAAGCTCTTTATGAAATTTTGATAACATC
1 CTATGAAATTTTTGTAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
**
299 TTTATAAAATTTTGTTGACCCCT
66 ACTATAAAATTTTGTTGACCCCT
* *
322 CTATGAAA-TTTTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACA
1 CTATGAAATTTTTG-TAATCACATTATGAAAATTTGATAACCTC-CTTATGAAATTTTGATAACA
*
385 ACACTATGAAATTTTG
64 ACACTATAAAATTTTG
401 ATAATCTTCA
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
87 5 0.07
88 61 0.90
89 2 0.03
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.43
Consensus pattern (88 bp):
CTATGAAATTTTTGTAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
ACTATAAAATTTTGTTGACCCCT
Found at i:540 original size:22 final size:22
Alignment explanation
Indices: 279--599 Score: 114
Period size: 22 Copynumber: 14.4 Consensus size: 22
269 ATAAGCTCTT
279 TATGAAATTTTGATAACATCTT--
1 TATGAAATTTTGATAAC--CTTCA
* * * *
301 TATAAAATTTTGTTGACCCCTC-
1 TATGAAATTTTGAT-AACCTTCA
* *
323 TATGAAATTTTGATAATC-ACA
1 TATGAAATTTTGATAACCTTCA
* *
344 TTATGTAATTTTGATAACC-TCGC
1 -TATGAAATTTTGATAACCTTC-A
* **
367 TTTGAAATTTTGATAA-CAACA
1 TATGAAATTTTGATAACCTTCA
*
388 CTATGAAATTTTGATAATCTTCA
1 -TATGAAATTTTGATAACCTTCA
*
411 TAT-AAATTTTGATAATCCTATCTT
1 TATGAAATTTTGATAA-CCT-TC-A
* *
435 TATGAAATTTCGATAATCATTC-
1 TATGAAATTTTGATAA-CCTTCA
* *
457 TATGAGA-TTTAATAACCTTC-
1 TATGAAATTTTGATAACCTTCA
* * *
477 TATCAAATTTTGGTACTCCTT-A
1 TATGAAATTTTGATA-ACCTTCA
*
499 TGAAATTGAGACTTTT-ATAACCTTCA
1 T---A-TGA-AATTTTGATAACCTTCA
* *
525 TATGAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCA
* * *
547 GATGAAGTATT-AGTAACCTTC-
1 TATGAAATTTTGA-TAACCTTCA
* *
568 TAATGAAATTTTGTTAA-CTACA
1 T-ATGAAATTTTGATAACCTTCA
590 CTATGAAATT
1 -TATGAAATT
600 CGTATAATCT
Statistics
Matches: 223, Mismatches: 49, Indels: 54
0.68 0.15 0.17
Matches are distributed among these distances:
20 10 0.04
21 37 0.17
22 132 0.59
23 9 0.04
24 5 0.02
25 19 0.09
26 6 0.03
27 5 0.02
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCA
Found at i:725 original size:24 final size:22
Alignment explanation
Indices: 670--868 Score: 77
Period size: 22 Copynumber: 9.0 Consensus size: 22
660 AATTAACTAC
*
670 CCTATGAAATTTCAATAACCAA
1 CCTATGAAATTTTAATAACCAA
*
692 CCTATGAAATTTTAATAACCTGAT
1 CCTATGAAATTTTAATAACC--AA
* ** *
716 TCTATGAAATTTTGGTAGCC-A
1 CCTATGAAATTTTAATAACCAA
** *
737 CTCTATGAAATTTTGGTAA-CTA
1 C-CTATGAAATTTTAATAACCAA
**
759 CACTATGAAATTTTGGTAACC-A
1 C-CTATGAAATTTTAATAACCAA
* **
781 CACTATAAAATTTTGGTAACCATA
1 C-CTATGAAATTTTAATAACCA-A
* *
805 -CTATTG-AATTTTGATAACC-T
1 CCTA-TGAAATTTTAATAACCAA
* * * * *
825 CCTCATGGAATTATAAAAATCAT
1 CCT-ATGAAATTTTAATAACCAA
* *
848 CTTATGAAATTTTGATAACCA
1 CCTATGAAATTTTAATAACCA
869 CATAGAGACA
Statistics
Matches: 141, Mismatches: 24, Indels: 24
0.75 0.13 0.13
Matches are distributed among these distances:
21 5 0.04
22 113 0.80
23 5 0.04
24 18 0.13
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.36
Consensus pattern (22 bp):
CCTATGAAATTTTAATAACCAA
Found at i:743 original size:46 final size:44
Alignment explanation
Indices: 663--794 Score: 131
Period size: 44 Copynumber: 3.0 Consensus size: 44
653 TTGTGATAAT
* ***
663 TAACTACCCTATGAAATTTCAATAACCA-ACCTATGAAATTTTAA
1 TAACTACACTATGAAATTTTGGTAACCACA-CTATGAAATTTTAA
** * * **
707 TAACCTGATTCTATGAAATTTTGGTAGCCACTCTATGAAATTTTGG
1 TAA-CT-ACACTATGAAATTTTGGTAACCACACTATGAAATTTTAA
*
753 TAACTACACTATGAAATTTTGGTAACCACACTATAAAATTTT
1 TAACTACACTATGAAATTTTGGTAACCACACTATGAAATTTT
795 GGTAACCATA
Statistics
Matches: 71, Mismatches: 14, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
44 35 0.49
45 4 0.06
46 32 0.45
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (44 bp):
TAACTACACTATGAAATTTTGGTAACCACACTATGAAATTTTAA
Found at i:744 original size:22 final size:22
Alignment explanation
Indices: 717--823 Score: 144
Period size: 22 Copynumber: 4.9 Consensus size: 22
707 TAACCTGATT
* *
717 CTATGAAATTTTGGTAGCCACT
1 CTATGAAATTTTGGTAACCACA
*
739 CTATGAAATTTTGGTAACTACA
1 CTATGAAATTTTGGTAACCACA
761 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGGTAACCACA
* *
783 CTATAAAATTTTGGTAACCATA
1 CTATGAAATTTTGGTAACCACA
*
805 CTATTG-AATTTTGATAACC
1 CTA-TGAAATTTTGGTAACC
824 TCCTCATGGA
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
22 75 0.99
23 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (22 bp):
CTATGAAATTTTGGTAACCACA
Found at i:1180 original size:29 final size:30
Alignment explanation
Indices: 1139--1201 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 30
1129 TGACAATTTA
* *
1139 GAAATATGTTTTTTAAA-AAAGGTACAATTG
1 GAAATATG-ATTTTAAATAAAGGTACAATAG
*
1169 GAAATAT-ATTTTAAATAAGGGTACAATAG
1 GAAATATGATTTTAAATAAAGGTACAATAG
1198 GAAA
1 GAAA
1202 ACATAAATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 7 0.24
29 15 0.52
30 7 0.24
ACGTcount: A:0.48, C:0.03, G:0.17, T:0.32
Consensus pattern (30 bp):
GAAATATGATTTTAAATAAAGGTACAATAG
Found at i:1237 original size:2 final size:2
Alignment explanation
Indices: 1230--1308 Score: 94
Period size: 2 Copynumber: 40.5 Consensus size: 2
1220 ATTCGTACTT
*
1230 TA TA TA TA GTA TA GA TA TA TA TA TA TA TA TA TA TA T- TA CTA -A
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
*
1272 GA -A TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1309 CTTTTTAA
Statistics
Matches: 69, Mismatches: 2, Indels: 12
0.83 0.02 0.14
Matches are distributed among these distances:
1 4 0.06
2 61 0.88
3 4 0.06
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Done.