Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012517.1 Corchorus capsularis cultivar CVL-1 contig12538, 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: 16513
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:1102 original size:3 final size:3
Alignment explanation
Indices: 1094--1130 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1084 TGGCAGTTTT
1094 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 T
1131 CAAATTAACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1148 original size:21 final size:22
Alignment explanation
Indices: 1124--1182 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
1114 ATTATTATTA
1124 TTATTATCA-AATTAACTCTTT
1 TTATTATCAGAATTAACTCTTT
* *
1145 TTATTATTAGATTTAACTCTTT
1 TTATTATCAGAATTAACTCTTT
* *
1167 TTATTATTAGATTTAA
1 TTATTATCAGAATTAA
1183 AGATGGGGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
21 8 0.23
22 27 0.77
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.56
Consensus pattern (22 bp):
TTATTATCAGAATTAACTCTTT
Found at i:1163 original size:22 final size:22
Alignment explanation
Indices: 1135--1182 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
1125 TATTATCAAA
1135 TTAACTCTTTTTATTATTAGAT
1 TTAACTCTTTTTATTATTAGAT
1157 TTAACTCTTTTTATTATTAGAT
1 TTAACTCTTTTTATTATTAGAT
1179 TTAA
1 TTAA
1183 AGATGGGGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.29, C:0.08, G:0.04, T:0.58
Consensus pattern (22 bp):
TTAACTCTTTTTATTATTAGAT
Found at i:3759 original size:7 final size:7
Alignment explanation
Indices: 3747--3771 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3737 TGAAGAAAGA
3747 GAGAATT
1 GAGAATT
3754 GAGAATT
1 GAGAATT
3761 GAGAATT
1 GAGAATT
3768 GAGA
1 GAGA
3772 GAGTAGACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.32, T:0.24
Consensus pattern (7 bp):
GAGAATT
Found at i:4858 original size:20 final size:20
Alignment explanation
Indices: 4833--4874 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
4823 AGCTTTATAG
4833 TTAGATAAATATATTAAGTC
1 TTAGATAAATATATTAAGTC
4853 TTAGATAAATATATTAAGTC
1 TTAGATAAATATATTAAGTC
4873 TT
1 TT
4875 GACTAATCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.43
Consensus pattern (20 bp):
TTAGATAAATATATTAAGTC
Found at i:7326 original size:13 final size:13
Alignment explanation
Indices: 7308--7335 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
7298 ACTCTTATAC
7308 TAGCCCATTTTCT
1 TAGCCCATTTTCT
7321 TAGCCCATTTTCT
1 TAGCCCATTTTCT
7334 TA
1 TA
7336 TTACCATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.18, C:0.29, G:0.07, T:0.46
Consensus pattern (13 bp):
TAGCCCATTTTCT
Found at i:13662 original size:110 final size:110
Alignment explanation
Indices: 13529--13735 Score: 378
Period size: 110 Copynumber: 1.9 Consensus size: 110
13519 CTATATAACC
* *
13529 CATCCAAGAAAAGTAAAAGACCCAGATGAACATCCAAGAAAGCATGACTCCGTAGTAGAAGATCA
1 CATCCAAGAAAAGTAAAAGACCCAGATGAACATCCAAGAAAGCATGACTCCGCAGTAAAAGATCA
*
13594 ATAATGTGTCATATATCAAAAGAGCATCTTTACTTTTCTTTTACT
66 ATAATGTGTCATATATCAAAAAAGCATCTTTACTTTTCTTTTACT
*
13639 CATCCAAGAAAATTAAAAGACCCAGATGAACATCCAAGAAAGCATGACTCCGCAGTAAAAGATCA
1 CATCCAAGAAAAGTAAAAGACCCAGATGAACATCCAAGAAAGCATGACTCCGCAGTAAAAGATCA
13704 ATAATGTGTCATATATCAAAAAAGCATCTTTA
66 ATAATGTGTCATATATCAAAAAAGCATCTTTA
13736 GAAGCTTCAA
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
110 93 1.00
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (110 bp):
CATCCAAGAAAAGTAAAAGACCCAGATGAACATCCAAGAAAGCATGACTCCGCAGTAAAAGATCA
ATAATGTGTCATATATCAAAAAAGCATCTTTACTTTTCTTTTACT
Found at i:15632 original size:17 final size:17
Alignment explanation
Indices: 15612--15652 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
15602 GTGTTCTCCC
15612 ATTAGTGTAGTTCTTTG
1 ATTAGTGTAGTTCTTTG
15629 ATTAGTGTAGTTCTTTG
1 ATTAGTGTAGTTCTTTG
15646 ATATAGT
1 AT-TAGT
15653 AACTTTCTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.22, C:0.05, G:0.22, T:0.51
Consensus pattern (17 bp):
ATTAGTGTAGTTCTTTG
Found at i:16490 original size:2 final size:2
Alignment explanation
Indices: 16485--16513 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
16475 CAATTTGGCT
16485 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.