Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006679.1 Corchorus capsularis cultivar CVL-1 contig06700, 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: 30310
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Found at i:2171 original size:36 final size:36
Alignment explanation
Indices: 2130--2198 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
2120 AAATTGAAAA
2130 GAAATAATCGAAGGAAGACAATGATGACGTTGGAAG
1 GAAATAATCGAAGGAAGACAATGATGACGTTGGAAG
**
2166 GAAATAATCGAAGGAAGATGATGATGACGTTGG
1 GAAATAATCGAAGGAAGACAATGATGACGTTGG
2199 TGAGTGAGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.42, C:0.07, G:0.32, T:0.19
Consensus pattern (36 bp):
GAAATAATCGAAGGAAGACAATGATGACGTTGGAAG
Found at i:7271 original size:13 final size:14
Alignment explanation
Indices: 7250--7282 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
7240 GAGACCAGTA
7250 TTCTTTTTTT-GTT
1 TTCTTTTTTTGGTT
7263 TT-TTTTTTTGGTT
1 TTCTTTTTTTGGTT
7276 TTCTTTT
1 TTCTTTT
7283 AACTTCCTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 7 0.39
13 7 0.39
14 4 0.22
ACGTcount: A:0.00, C:0.06, G:0.09, T:0.85
Consensus pattern (14 bp):
TTCTTTTTTTGGTT
Found at i:9194 original size:2 final size:2
Alignment explanation
Indices: 9182--9229 Score: 53
Period size: 2 Copynumber: 24.5 Consensus size: 2
9172 ATGCTGTATG
* * **
9182 TA TA AA TA TA TA TA TA AA T- TA TA CC TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9223 TA TA TA T
1 TA TA TA T
9230 GTATGTATCT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:9393 original size:3 final size:3
Alignment explanation
Indices: 9385--9424 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
9375 TTTGTATCTT
9385 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
9425 ATATGAATTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:11383 original size:32 final size:33
Alignment explanation
Indices: 11335--11415 Score: 101
Period size: 33 Copynumber: 2.5 Consensus size: 33
11325 ATTTTGGTCT
** * *
11335 AGCCGCCCCACCGGGGCAGCCT-GCCGTGGCGA
1 AGCCGCCCCAGTGGGGCAGCCTACCCATGGCGA
* *
11367 AGCCGCCCTAGTGGGGCAGCCTACCCATGGTGA
1 AGCCGCCCCAGTGGGGCAGCCTACCCATGGCGA
11400 AGCCGCCCCAGTGGGG
1 AGCCGCCCCAGTGGGG
11416 AGGCTCCGCC
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
32 19 0.46
33 22 0.54
ACGTcount: A:0.15, C:0.38, G:0.37, T:0.10
Consensus pattern (33 bp):
AGCCGCCCCAGTGGGGCAGCCTACCCATGGCGA
Found at i:11477 original size:33 final size:32
Alignment explanation
Indices: 11367--11483 Score: 101
Period size: 33 Copynumber: 3.6 Consensus size: 32
11357 GCCGTGGCGA
* * *
11367 AGCCGCCCTAGTGGGGCAGCCTAC-CCATGGTG
1 AGCCGTCCTAGTGGGG-AGGCTCCGCCATGGTG
* * *
11399 AAGCCGCCCCAGTGGGGAGGCTCCGCCGTGGTTG
1 -AGCCGTCCTAGTGGGGAGGCTCCGCCATGG-TG
* * * *
11433 AGTCTTTCTAGTAGGGAGGCTCCGCCATGGCTG
1 AGCCGTCCTAGTGGGGAGGCTCCGCCATGG-TG
11466 AGCCGTCCTAGTGGGGAG
1 AGCCGTCCTAGTGGGGAG
11484 ACTCAGTGTA
Statistics
Matches: 66, Mismatches: 16, Indels: 4
0.77 0.19 0.05
Matches are distributed among these distances:
32 5 0.08
33 59 0.89
34 2 0.03
ACGTcount: A:0.15, C:0.29, G:0.38, T:0.19
Consensus pattern (32 bp):
AGCCGTCCTAGTGGGGAGGCTCCGCCATGGTG
Found at i:13660 original size:12 final size:12
Alignment explanation
Indices: 13643--13685 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
13633 TAAATACAGG
*
13643 TATCGATGGATA
1 TATCGACGGATA
13655 TATCGAACGGATA
1 TATCG-ACGGATA
*
13668 CATCGACGGATA
1 TATCGACGGATA
13680 TATCGA
1 TATCGA
13686 GGTATCGATG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
12 17 0.63
13 10 0.37
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (12 bp):
TATCGACGGATA
Found at i:14707 original size:10 final size:10
Alignment explanation
Indices: 14692--14727 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
14682 AATTTAATAT
14692 GGATATTTAC
1 GGATATTTAC
*
14702 GGATATTTAT
1 GGATATTTAC
14712 GGATATTTAC
1 GGATATTTAC
14722 GGATAT
1 GGATAT
14728 ATCGAGGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.31, C:0.06, G:0.22, T:0.42
Consensus pattern (10 bp):
GGATATTTAC
Found at i:14714 original size:20 final size:20
Alignment explanation
Indices: 14689--14727 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
14679 TTTAATTTAA
14689 TATGGATATTTACGGATATT
1 TATGGATATTTACGGATATT
14709 TATGGATATTTACGGATAT
1 TATGGATATTTACGGATAT
14728 ATCGAGGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.44
Consensus pattern (20 bp):
TATGGATATTTACGGATATT
Found at i:15746 original size:22 final size:22
Alignment explanation
Indices: 15721--15782 Score: 61
Period size: 24 Copynumber: 2.7 Consensus size: 22
15711 GTTGTCTCTA
**
15721 GTTATCAAAATTTCATAGTTAG
1 GTTATCAAAATTTCATAGGGAG
*
15743 GTTATCTAAAAACTTCATAGGGAG
1 GTTATC--AAAATTTCATAGGGAG
* *
15767 GTTGTTAAAATTTCAT
1 GTTATCAAAATTTCAT
15783 TAAAAGAATC
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
22 15 0.47
24 17 0.53
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGGGAG
Found at i:15952 original size:22 final size:22
Alignment explanation
Indices: 15921--16007 Score: 106
Period size: 22 Copynumber: 4.0 Consensus size: 22
15911 GTTGCATCTG
*
15921 TGTGGTTATCAAAATTTCATAT
1 TGTGGTTATCAAAATTTCATAA
**
15943 TGTGACTATCAAAATTT-A-AA
1 TGTGGTTATCAAAATTTCATAA
15963 GTGTGGTTATCAAAATTTCATAA
1 -TGTGGTTATCAAAATTTCATAA
* *
15986 TGAGGTTATCAAAATTTTATAA
1 TGTGGTTATCAAAATTTCATAA
16008 AACAAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
20 1 0.02
21 16 0.29
22 36 0.65
23 2 0.04
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.40
Consensus pattern (22 bp):
TGTGGTTATCAAAATTTCATAA
Found at i:15981 original size:43 final size:43
Alignment explanation
Indices: 15920--16002 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 43
15910 TGTTGCATCT
* *
15920 GTGTGGTTATCAAAATTTCATATTGTGACTATCAAAATTTAAA
1 GTGTGGTTATCAAAATTTCATAATGAGACTATCAAAATTTAAA
**
15963 GTGTGGTTATCAAAATTTCATAATGAGGTTATCAAAATTT
1 GTGTGGTTATCAAAATTTCATAATGAGACTATCAAAATTT
16003 TATAAAACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (43 bp):
GTGTGGTTATCAAAATTTCATAATGAGACTATCAAAATTTAAA
Found at i:16015 original size:15 final size:15
Alignment explanation
Indices: 15995--16023 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
15985 ATGAGGTTAT
15995 CAAAATTTTATAAAA
1 CAAAATTTTATAAAA
16010 CAAAATTTTATAAA
1 CAAAATTTTATAAA
16024 GGAGTTATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (15 bp):
CAAAATTTTATAAAA
Found at i:16756 original size:15 final size:15
Alignment explanation
Indices: 16736--16791 Score: 85
Period size: 15 Copynumber: 3.7 Consensus size: 15
16726 TAGGTTCGGG
*
16736 CGGGTTCGGGTACTT
1 CGGGTTCGGGTATTT
*
16751 CGGGTTCAGGTATTT
1 CGGGTTCGGGTATTT
16766 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTA-TTT
16782 CGGGTTCGGG
1 CGGGTTCGGG
16792 CTCGGAAGCC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
15 24 0.65
16 13 0.35
ACGTcount: A:0.07, C:0.16, G:0.41, T:0.36
Consensus pattern (15 bp):
CGGGTTCGGGTATTT
Found at i:20608 original size:15 final size:15
Alignment explanation
Indices: 20588--20617 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
20578 AGAATAGAAA
20588 CTCAATCCCATTCAT
1 CTCAATCCCATTCAT
20603 CTCAATCCCATTCAT
1 CTCAATCCCATTCAT
20618 TGGGATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.40, G:0.00, T:0.33
Consensus pattern (15 bp):
CTCAATCCCATTCAT
Found at i:28822 original size:12 final size:12
Alignment explanation
Indices: 28805--28829 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28795 AGGGTTCGTT
28805 CATACTGTAAGA
1 CATACTGTAAGA
28817 CATACTGTAAGA
1 CATACTGTAAGA
28829 C
1 C
28830 TTATCTGATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (12 bp):
CATACTGTAAGA
Done.