Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006208.1 Corchorus capsularis cultivar CVL-1 contig06227, 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: 16111
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:5483 original size:15 final size:17
Alignment explanation
Indices: 5452--5483 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
5442 ATAATTGGAA
5452 TTAATTAAGTGACTTAT
1 TTAATTAAGTGACTTAT
5469 TTAATT-AGT-ACTTAT
1 TTAATTAAGTGACTTAT
5484 AACTTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 3 0.20
17 6 0.40
ACGTcount: A:0.34, C:0.06, G:0.09, T:0.50
Consensus pattern (17 bp):
TTAATTAAGTGACTTAT
Found at i:6282 original size:35 final size:35
Alignment explanation
Indices: 6242--6367 Score: 105
Period size: 35 Copynumber: 3.4 Consensus size: 35
6232 CGAATATATA
*
6242 TTGTTGTTAAAATATTTTTACGCAACAATATTGAG
1 TTGTTGTTAAAATATTTTTACACAACAATATTGAG
*
6277 TTGTTGTGTAAAATACACTTCTTTTA-ACAACAATAAAATG-G
1 TTGTTGT-TAAAAT--A--T-TTTTACACAACAAT--ATTGAG
*
6318 -CGTTGTTAAAATATTTTTACACAACAATATTGAG
1 TTGTTGTTAAAATATTTTTACACAACAATATTGAG
* *
6352 TTTTTGCATAAAATAT
1 TTGTTG-TTAAAATAT
6368 AATTCTTTTA
Statistics
Matches: 72, Mismatches: 7, Indels: 23
0.71 0.07 0.23
Matches are distributed among these distances:
33 3 0.04
34 6 0.08
35 19 0.26
36 14 0.19
37 1 0.01
38 1 0.01
39 6 0.08
40 13 0.18
41 6 0.08
42 3 0.04
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.40
Consensus pattern (35 bp):
TTGTTGTTAAAATATTTTTACACAACAATATTGAG
Found at i:6325 original size:75 final size:75
Alignment explanation
Indices: 6244--6395 Score: 241
Period size: 75 Copynumber: 2.0 Consensus size: 75
6234 AATATATATT
* ** *
6244 GTTGTTAAAATATTTTTACGCAACAATATTGAGTTGTTGTGTAAAATACACTTCTTTTAACAACA
1 GTTGTTAAAATATTTTTACACAACAATATTGAGTTGTTGCATAAAATACAATTCTTTTAACAACA
6309 ATAAAATGGC
66 ATAAAATGGC
* * *
6319 GTTGTTAAAATATTTTTACACAACAATATTGAGTTTTTGCATAAAATATAATTCTTTTAGCAACA
1 GTTGTTAAAATATTTTTACACAACAATATTGAGTTGTTGCATAAAATACAATTCTTTTAACAACA
6384 ATAAAATGGC
66 ATAAAATGGC
6394 GT
1 GT
6396 AACGGAAAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 70 1.00
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.38
Consensus pattern (75 bp):
GTTGTTAAAATATTTTTACACAACAATATTGAGTTGTTGCATAAAATACAATTCTTTTAACAACA
ATAAAATGGC
Found at i:6418 original size:75 final size:75
Alignment explanation
Indices: 6250--6419 Score: 218
Period size: 75 Copynumber: 2.3 Consensus size: 75
6240 TATTGTTGTT
** *
6250 AAAATATTTTTACGCAACAATATTGAGTTGTTGTGTAAAATACACTTCTTTTAACAACAATAAAA
1 AAAATATTTTTACGCAACAATATTGAGTTGTTGCATAAAATACAATTCTTTTAACAACAATAAAA
* **
6315 TGGCGTTGTT
66 TGGCGTCGGA
* * * *
6325 AAAATATTTTTACACAACAATATTGAGTTTTTGCATAAAATATAATTCTTTTAGCAACAATAAAA
1 AAAATATTTTTACGCAACAATATTGAGTTGTTGCATAAAATACAATTCTTTTAACAACAATAAAA
6390 TGGCGTAACGGA
66 TGGCGT--CGGA
6402 AAAAT-TTTTTA-GCAACAA
1 AAAATATTTTTACGCAACAA
6420 CCACCTTAAG
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
75 70 0.85
76 6 0.07
77 6 0.07
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (75 bp):
AAAATATTTTTACGCAACAATATTGAGTTGTTGCATAAAATACAATTCTTTTAACAACAATAAAA
TGGCGTCGGA
Found at i:10589 original size:12 final size:11
Alignment explanation
Indices: 10569--10661 Score: 78
Period size: 12 Copynumber: 7.8 Consensus size: 11
10559 GGTTTAGAAT
*
10569 TTGATAATGTAG
1 TTGAAAATG-AG
10581 TTGAAAATGATG
1 TTGAAAATGA-G
*
10593 TTGAGAATGGAG
1 TTGAAAAT-GAG
*
10605 TTGAAATTGATG
1 TTGAAAATGA-G
*
10617 TTGAAAATGTTG
1 TTGAAAATG-AG
*
10629 ATGAAAATGATG
1 TTGAAAATGA-G
10641 TTGAAAATGTAG
1 TTGAAAATG-AG
10653 TTGAAAATG
1 TTGAAAATG
10662 GTGAAGAAGT
Statistics
Matches: 66, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
11 3 0.05
12 60 0.91
13 3 0.05
ACGTcount: A:0.39, C:0.00, G:0.27, T:0.34
Consensus pattern (11 bp):
TTGAAAATGAG
Found at i:10596 original size:24 final size:24
Alignment explanation
Indices: 10569--10661 Score: 132
Period size: 24 Copynumber: 3.9 Consensus size: 24
10559 GGTTTAGAAT
*
10569 TTGATAATGTAGTTGAAAATGATG
1 TTGAAAATGTAGTTGAAAATGATG
* * *
10593 TTGAGAATGGAGTTGAAATTGATG
1 TTGAAAATGTAGTTGAAAATGATG
* *
10617 TTGAAAATGTTGATGAAAATGATG
1 TTGAAAATGTAGTTGAAAATGATG
10641 TTGAAAATGTAGTTGAAAATG
1 TTGAAAATGTAGTTGAAAATG
10662 GTGAAGAAGT
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.39, C:0.00, G:0.27, T:0.34
Consensus pattern (24 bp):
TTGAAAATGTAGTTGAAAATGATG
Found at i:10620 original size:36 final size:36
Alignment explanation
Indices: 10569--10661 Score: 109
Period size: 36 Copynumber: 2.6 Consensus size: 36
10559 GGTTTAGAAT
* * *
10569 TTGATAATGTAGTTGAAAATGATGTTGAGAATGGA-G
1 TTGAAAATGTAGTTGAAAATGATGATGAAAAT-GATG
* *
10605 TTGAAATTG-ATGTTGAAAATGTTGATGAAAATGATG
1 TTGAAAATGTA-GTTGAAAATGATGATGAAAATGATG
10641 TTGAAAATGTAGTTGAAAATG
1 TTGAAAATGTAGTTGAAAATG
10662 GTGAAGAAGT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
35 3 0.06
36 44 0.92
37 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.27, T:0.34
Consensus pattern (36 bp):
TTGAAAATGTAGTTGAAAATGATGATGAAAATGATG
Found at i:10791 original size:18 final size:18
Alignment explanation
Indices: 10769--10908 Score: 93
Period size: 18 Copynumber: 7.8 Consensus size: 18
10759 AACAGTTGAG
10769 GAAGTTCCTGAAGTTGCT
1 GAAGTTCCTGAAGTTGCT
* *** *
10787 CAAGTTGAGGAAGTTCCT
1 GAAGTTCCTGAAGTTGCT
* * **
10805 GAAGTTGCTAAAGTTGAG
1 GAAGTTCCTGAAGTTGCT
10823 GAAGTTCCTGAAGTTGCT
1 GAAGTTCCTGAAGTTGCT
* *** *
10841 CAAGTTGAGGAAGTTCCT
1 GAAGTTCCTGAAGTTGCT
* * *
10859 GAAGTTGCTCAAG-TACGT
1 GAAGTTCCTGAAGTTGC-T
*
10877 GAAGTTCCTGAAGGTGCT
1 GAAGTTCCTGAAGTTGCT
*
10895 CAAGTTCCTGAAGT
1 GAAGTTCCTGAAGT
10909 CAATGATAAT
Statistics
Matches: 89, Mismatches: 31, Indels: 4
0.72 0.25 0.03
Matches are distributed among these distances:
17 2 0.02
18 85 0.96
19 2 0.02
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (18 bp):
GAAGTTCCTGAAGTTGCT
Found at i:10908 original size:27 final size:27
Alignment explanation
Indices: 10762--10900 Score: 228
Period size: 27 Copynumber: 5.1 Consensus size: 27
10752 TTGGTGAAAC
10762 AGTTGAGGAAGTTCCTGAAGTTGCTCA
1 AGTTGAGGAAGTTCCTGAAGTTGCTCA
*
10789 AGTTGAGGAAGTTCCTGAAGTTGCTAA
1 AGTTGAGGAAGTTCCTGAAGTTGCTCA
10816 AGTTGAGGAAGTTCCTGAAGTTGCTCA
1 AGTTGAGGAAGTTCCTGAAGTTGCTCA
10843 AGTTGAGGAAGTTCCTGAAGTTGCTCA
1 AGTTGAGGAAGTTCCTGAAGTTGCTCA
*
10870 AG-T-ACGTGAAGTTCCTGAAGGTGCTCA
1 AGTTGA-G-GAAGTTCCTGAAGTTGCTCA
10897 AGTT
1 AGTT
10901 CCTGAAGTCA
Statistics
Matches: 106, Mismatches: 3, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
25 1 0.01
26 2 0.02
27 102 0.96
28 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.29
Consensus pattern (27 bp):
AGTTGAGGAAGTTCCTGAAGTTGCTCA
Found at i:13429 original size:28 final size:27
Alignment explanation
Indices: 13388--13475 Score: 88
Period size: 28 Copynumber: 3.2 Consensus size: 27
13378 GCATTAGGGT
* *
13388 CATCTATGGGCATTTTGGTAATTTTCA
1 CATCTAGGGGCATTTTGGTCATTTTCA
**
13415 CATCTAGGAGGCATTTTGGTCATTTTTG
1 CATCTAGG-GGCATTTTGGTCATTTTCA
* * *
13443 CATTTAGGGGGTATTTTGGTCATTTGCA
1 CATCTA-GGGGCATTTTGGTCATTTTCA
13471 -ATCTA
1 CATCTA
13476 CTTTTGATTT
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
27 11 0.22
28 36 0.73
29 2 0.04
ACGTcount: A:0.20, C:0.14, G:0.23, T:0.43
Consensus pattern (27 bp):
CATCTAGGGGCATTTTGGTCATTTTCA
Found at i:14479 original size:16 final size:16
Alignment explanation
Indices: 14458--14501 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
14448 ACAAAGGTAT
14458 TGCAACAAGGCAACAA
1 TGCAACAAGGCAACAA
* *
14474 TGCAACAAAGCAATAA
1 TGCAACAAGGCAACAA
*
14490 TGCAGCAAGGCA
1 TGCAACAAGGCA
14502 GTGCAGGGGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.48, C:0.23, G:0.20, T:0.09
Consensus pattern (16 bp):
TGCAACAAGGCAACAA
Found at i:15259 original size:14 final size:14
Alignment explanation
Indices: 15242--15276 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
15232 CTGGAGAACC
*
15242 CTCTCACTCCCTCT
1 CTCTCACTCACTCT
*
15256 CTCTCAATCACTCT
1 CTCTCACTCACTCT
15270 CTCTCAC
1 CTCTCAC
15277 ATTTTCTAGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.14, C:0.51, G:0.00, T:0.34
Consensus pattern (14 bp):
CTCTCACTCACTCT
Done.