Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017084.1 Corchorus olitorius cultivar O-4 contig17117, 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: 13719
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:153 original size:7 final size:7
Alignment explanation
Indices: 141--207 Score: 50
Period size: 7 Copynumber: 9.6 Consensus size: 7
131 TTTTTTAATT
141 ATTATTA
1 ATTATTA
148 ATTATTA
1 ATTATTA
155 ATTATT-
1 ATTATTA
161 ATTAATTTAA
1 ATT-A-TT-A
*
171 ATTGTT-
1 ATTATTA
177 ATTATTA
1 ATTATTA
184 ATTA-TA
1 ATTATTA
* *
190 ATAAATA
1 ATTATTA
*
197 ATTAATA
1 ATTATTA
204 ATTA
1 ATTA
208 AAAAACAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
6 13 0.26
7 30 0.60
8 4 0.08
10 3 0.06
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (7 bp):
ATTATTA
Found at i:157 original size:17 final size:16
Alignment explanation
Indices: 133--180 Score: 69
Period size: 17 Copynumber: 2.9 Consensus size: 16
123 AGATTATTTT
133 TTTTAATTATTATTAA
1 TTTTAATTATTATTAA
149 TTATTAATTATTATTAA
1 TT-TTAATTATTATTAA
* *
166 TTTAAATTGTTATTA
1 TTTTAATTATTATTA
181 TTAATTATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 13 0.45
17 16 0.55
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
TTTTAATTATTATTAA
Found at i:368 original size:29 final size:28
Alignment explanation
Indices: 329--384 Score: 94
Period size: 29 Copynumber: 2.0 Consensus size: 28
319 GTTATTCCAC
*
329 GTTCTTTAGCGTTCTTGAAGATTAGAAAT
1 GTTCTTGAGCGTTCTTGAA-ATTAGAAAT
358 GTTCTTGAGCGTTCTTGAAATTAGAAA
1 GTTCTTGAGCGTTCTTGAAATTAGAAA
385 GTTTGAAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (28 bp):
GTTCTTGAGCGTTCTTGAAATTAGAAAT
Found at i:862 original size:30 final size:30
Alignment explanation
Indices: 826--897 Score: 126
Period size: 30 Copynumber: 2.4 Consensus size: 30
816 TAAGTTTTAA
826 AGTTTTGTTTTAATGCTCACTGAAATTTTT
1 AGTTTTGTTTTAATGCTCACTGAAATTTTT
* *
856 ATTTTTGTTTTAATGCTCATTGAAATTTTT
1 AGTTTTGTTTTAATGCTCACTGAAATTTTT
886 AGTTTTGTTTTA
1 AGTTTTGTTTTA
898 GGTACATGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.22, C:0.07, G:0.12, T:0.58
Consensus pattern (30 bp):
AGTTTTGTTTTAATGCTCACTGAAATTTTT
Found at i:1208 original size:61 final size:61
Alignment explanation
Indices: 1113--1236 Score: 221
Period size: 61 Copynumber: 2.0 Consensus size: 61
1103 ATAATCAAAA
1113 GGGAATTCAGTTTAGAGATCTCATTCGCAGTTACAATTCACTCTTTCAGTTTACTTCAATG
1 GGGAATTCAGTTTAGAGATCTCATTCGCAGTTACAATTCACTCTTTCAGTTTACTTCAATG
** *
1174 GGGAATTTGGTTTAGAGATCTCATTCGCAGTTACAATTCGCTCTTTCAGTTTACTTCAATG
1 GGGAATTCAGTTTAGAGATCTCATTCGCAGTTACAATTCACTCTTTCAGTTTACTTCAATG
1235 GG
1 GG
1237 TTCTAAGGTG
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (61 bp):
GGGAATTCAGTTTAGAGATCTCATTCGCAGTTACAATTCACTCTTTCAGTTTACTTCAATG
Found at i:4544 original size:21 final size:22
Alignment explanation
Indices: 4501--4544 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
4491 AACAATTATC
*
4501 AAGTGAGAAAACAACAGTCAAG
1 AAGTGAGAAAACAACAATCAAG
* *
4523 AAGTGAGAATA-AACAATGAAG
1 AAGTGAGAAAACAACAATCAAG
4544 A
1 A
4545 GAAAGATAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.57, C:0.09, G:0.23, T:0.11
Consensus pattern (22 bp):
AAGTGAGAAAACAACAATCAAG
Found at i:5276 original size:12 final size:13
Alignment explanation
Indices: 5248--5302 Score: 62
Period size: 13 Copynumber: 4.4 Consensus size: 13
5238 TCATGCACCC
5248 AAAATCATTTAAT
1 AAAATCATTTAAT
5261 AAAATCATTT-AT
1 AAAATCATTTAAT
*
5273 AAAAACAATTTAAT
1 AAAATC-ATTTAAT
*
5287 AAAA-CA-GTAAT
1 AAAATCATTTAAT
5298 AAAAT
1 AAAAT
5303 AGTTCCTCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
11 8 0.22
12 8 0.22
13 15 0.41
14 6 0.16
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.31
Consensus pattern (13 bp):
AAAATCATTTAAT
Found at i:6322 original size:2 final size:2
Alignment explanation
Indices: 6315--6346 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
6305 TCTCAGTAAC
6315 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6347 CATTCTCAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7966 original size:41 final size:41
Alignment explanation
Indices: 7921--8184 Score: 138
Period size: 41 Copynumber: 6.2 Consensus size: 41
7911 CATATATTAA
* *
7921 GCAACGACTAACAAAATTCGTTGCGAAAAGTTTAAGATTTC
1 GCAACGACTAACAAAAGTCGCTGCGAAAAGTTTAAGATTTC
* *
7962 GCAACGACTAACAAAAGTCGCTGTGGAAAGTTTAAGATTTC
1 GCAACGACTAACAAAAGTCGCTGCGAAAAGTTTAAGATTTC
* * *** * * * * * *
8003 GGAACGACTTA-ATTTGTCGTTTC-AAAAGTAATCATGTTTTTT
1 GCAACGACTAACAAAAGTCGCTGCGAAAAGT--TTAAG-ATTTC
* * *** * * * *
8045 GTAGCGACT-TTTAAGGTCGCTGCGAAAATCAATTAGTAACATATATTAA
1 GCAACGACTAACAAAAGTCGCTGCG-AAA--AGTT--T-A-AGAT-TT-C
8094 GCAACGACTAACAAAAGTCGCTGCGAAAAGTTTAAGATTTC
1 GCAACGACTAACAAAAGTCGCTGCGAAAAGTTTAAGATTTC
* * ***
8135 GCAATGACTAACAAAAGTCGCTGCGGAAAGTTTGTTATTTC
1 GCAACGACTAACAAAAGTCGCTGCGAAAAGTTTAAGATTTC
8176 GCAACGACT
1 GCAACGACT
8185 TAATCTGTCG
Statistics
Matches: 161, Mismatches: 47, Indels: 30
0.68 0.20 0.13
Matches are distributed among these distances:
39 5 0.03
40 6 0.04
41 93 0.58
42 18 0.11
43 3 0.02
44 5 0.03
45 1 0.01
46 2 0.01
47 5 0.03
48 2 0.01
49 10 0.06
50 11 0.07
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (41 bp):
GCAACGACTAACAAAAGTCGCTGCGAAAAGTTTAAGATTTC
Found at i:8184 original size:173 final size:173
Alignment explanation
Indices: 7887--8327 Score: 729
Period size: 173 Copynumber: 2.5 Consensus size: 173
7877 AAAGCTGAAA
* *
7887 GTCGCTGCGAAAATCATTTAGTAACATATATTAAGCAACGACTAACAAAATTCGTTGCGAAAAGT
1 GTCGCTGCGAAAATCAATTAGTAACATATATTAAGCAACGACTAACAAAAGTCGTTGCGAAAAGT
* * *
7952 TTAAGATTTCGCAACGACTAACAAAAGTCGCTGTGGAAAGTTTAAGATTTCGGAACGACTTAATT
66 TTAAGATTTCGCAACGACTAACAAAAGTCGCTGCGGAAAGTTTAAGATTTCGCAACGACTTAATC
* *
8017 TGTCGTTTCAAAAGTAATCATGTTTTTTGTAGCGACTTTTAAG
131 TGTCGTTTCAAAAATAATCATGTTTTTTGTAGCGACTTTCAAG
*
8060 GTCGCTGCGAAAATCAATTAGTAACATATATTAAGCAACGACTAACAAAAGTCGCTGCGAAAAGT
1 GTCGCTGCGAAAATCAATTAGTAACATATATTAAGCAACGACTAACAAAAGTCGTTGCGAAAAGT
* ***
8125 TTAAGATTTCGCAATGACTAACAAAAGTCGCTGCGGAAAGTTTGTTATTTCGCAACGACTTAATC
66 TTAAGATTTCGCAACGACTAACAAAAGTCGCTGCGGAAAGTTTAAGATTTCGCAACGACTTAATC
8190 TGTCGTTTCAAAAATAATCATGTTTTTTGTAGCGACTTTCAAG
131 TGTCGTTTCAAAAATAATCATGTTTTTTGTAGCGACTTTCAAG
* *
8233 GTCGTTGCGAAAATCAATTAGTAACATATATTAAGCAACGACTAACAAAAGTCGTTGCGAAAAGA
1 GTCGCTGCGAAAATCAATTAGTAACATATATTAAGCAACGACTAACAAAAGTCGTTGCGAAAAGT
* * *
8298 CTATGATTTCGCAACGACTAATAAAAGTCG
66 TTAAGATTTCGCAACGACTAACAAAAGTCG
8328 TTGTAAAACT
Statistics
Matches: 249, Mismatches: 19, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
173 249 1.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.29
Consensus pattern (173 bp):
GTCGCTGCGAAAATCAATTAGTAACATATATTAAGCAACGACTAACAAAAGTCGTTGCGAAAAGT
TTAAGATTTCGCAACGACTAACAAAAGTCGCTGCGGAAAGTTTAAGATTTCGCAACGACTTAATC
TGTCGTTTCAAAAATAATCATGTTTTTTGTAGCGACTTTCAAG
Found at i:9490 original size:5 final size:5
Alignment explanation
Indices: 9480--9523 Score: 65
Period size: 5 Copynumber: 9.2 Consensus size: 5
9470 TATATGATTG
*
9480 GTTTT GTTTT GTTTT GTTTT GTTTT ATTTT -TTTT GTTTT -TTTT G
1 GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT G
9524 CACTCATGAC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
4 8 0.22
5 28 0.78
ACGTcount: A:0.02, C:0.00, G:0.16, T:0.82
Consensus pattern (5 bp):
GTTTT
Found at i:10806 original size:74 final size:74
Alignment explanation
Indices: 10685--10832 Score: 269
Period size: 74 Copynumber: 2.0 Consensus size: 74
10675 TTACCTATTG
*
10685 AAGAATGCTACAATAGCCTTATCAAACATTGATTTTCCTGCTGCTCTCCTTGTAACAATCCTAAC
1 AAGAATGCCACAATAGCCTTATCAAACATTGATTTTCCTGCTGCTCTCCTTGTAACAATCCTAAC
10750 ACTCAATTC
66 ACTCAATTC
*
10759 AAGAATGCCACAATAGCCTTATCAAACGTTGATTTTCCTGCTGCTCTCCTTGTAACAATCCTAAC
1 AAGAATGCCACAATAGCCTTATCAAACATTGATTTTCCTGCTGCTCTCCTTGTAACAATCCTAAC
*
10824 GCTCAATTC
66 ACTCAATTC
10833 TTTCCCTTTG
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 71 1.00
ACGTcount: A:0.30, C:0.28, G:0.11, T:0.32
Consensus pattern (74 bp):
AAGAATGCCACAATAGCCTTATCAAACATTGATTTTCCTGCTGCTCTCCTTGTAACAATCCTAAC
ACTCAATTC
Found at i:12267 original size:5 final size:5
Alignment explanation
Indices: 12257--12290 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
12247 TTCCTAGTTC
*
12257 TTTTG TTTTG TTTTG TTTTA TTTTG TTTTG TTTT
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
12291 AAAATGGTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.03, C:0.00, G:0.15, T:0.82
Consensus pattern (5 bp):
TTTTG
Found at i:13555 original size:74 final size:74
Alignment explanation
Indices: 13434--13581 Score: 278
Period size: 74 Copynumber: 2.0 Consensus size: 74
13424 TTACCTATTG
* *
13434 AAGAATGCTACAATAGCCTTATCAAACGTTGATTTTCCTGCTGCTCTCCTTGTAACAATCCTAAC
1 AAGAATGCCACAATAGCCTTATCAAACGTTGATTTTCCTACTGCTCTCCTTGTAACAATCCTAAC
13499 GCTCAATTC
66 GCTCAATTC
13508 AAGAATGCCACAATAGCCTTATCAAACGTTGATTTTCCTACTGCTCTCCTTGTAACAATCCTAAC
1 AAGAATGCCACAATAGCCTTATCAAACGTTGATTTTCCTACTGCTCTCCTTGTAACAATCCTAAC
13573 GCTCAATTC
66 GCTCAATTC
13582 TTTCCCTTTG
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 72 1.00
ACGTcount: A:0.29, C:0.28, G:0.11, T:0.32
Consensus pattern (74 bp):
AAGAATGCCACAATAGCCTTATCAAACGTTGATTTTCCTACTGCTCTCCTTGTAACAATCCTAAC
GCTCAATTC
Done.