Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015549.1 Corchorus olitorius cultivar O-4 contig15582, 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: 44703
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:3382 original size:6 final size:6
Alignment explanation
Indices: 3364--3400 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
3354 CTGATGTTTT
3364 TGCTTC TTG-TTC TGCTTC TGCTTC TGCTTC TGCTTC T
1 TGCTTC -TGCTTC TGCTTC TGCTTC TGCTTC TGCTTC T
3401 TCTTTTCCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 2 0.07
6 25 0.86
7 2 0.07
ACGTcount: A:0.00, C:0.30, G:0.16, T:0.54
Consensus pattern (6 bp):
TGCTTC
Found at i:4110 original size:15 final size:15
Alignment explanation
Indices: 4090--4118 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4080 TAGTAGTATC
4090 TATACTATGATTATA
1 TATACTATGATTATA
4105 TATACTATGATTAT
1 TATACTATGATTAT
4119 TCATCAATAT
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:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (15 bp):
TATACTATGATTATA
Found at i:8190 original size:66 final size:62
Alignment explanation
Indices: 8113--8318 Score: 256
Period size: 60 Copynumber: 3.3 Consensus size: 62
8103 AATATTAGCC
* * *
8113 GGATTGAATAGAACGATGAGGTGGATCAATTGATAATTCGGGTACAATATACAATCCGATCAAGC
1 GGATTTAATAGAACGATGA-GTGGATCAATTGATAATTTGGGTACAATATTCAATCC--T-AAGC
8178 T
62 T
* * * * *
8179 GGATTTAATAGAATGATAATGTGGATCAATTGATAATTTTGGTATAATATTCAATCCT-AGCC
1 GGATTTAATAGAACGATGA-GTGGATCAATTGATAATTTGGGTACAATATTCAATCCTAAGCT
*
8241 GGATTTAATAGAATGAT-AGTGGATCAATTGATAATTTGGGTACAATATTCAATCCTAA-CT
1 GGATTTAATAGAACGATGAGTGGATCAATTGATAATTTGGGTACAATATTCAATCCTAAGCT
*
8301 GGATTTTATAGAACGATG
1 GGATTTAATAGAACGATG
8319 TATATACCAT
Statistics
Matches: 124, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
60 52 0.42
61 2 0.02
62 20 0.16
64 1 0.01
66 49 0.40
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.33
Consensus pattern (62 bp):
GGATTTAATAGAACGATGAGTGGATCAATTGATAATTTGGGTACAATATTCAATCCTAAGCT
Found at i:8276 original size:60 final size:62
Alignment explanation
Indices: 8108--8313 Score: 254
Period size: 66 Copynumber: 3.3 Consensus size: 62
8098 GGTACAATAT
* * * * *
8108 TAGCCGGATTGAATAGAACGATGAGGTGGATCAATTGATAATTCGGGTACAATATACAATCC
1 TAGCCGGATTTAATAGAATGATAAGGTGGATCAATTGATAATTTGGGTACAATATTCAATCC
* * * *
8170 GATCAAGCTGGATTTAATAGAATGATAATGTGGATCAATTGATAATTTTGGTATAATATTCAATC
1 --T--AGCCGGATTTAATAGAATGATAAGGTGGATCAATTGATAATTTGGGTACAATATTCAATC
8235 C
62 C
8236 TAGCCGGATTTAATAGAATGAT-A-GTGGATCAATTGATAATTTGGGTACAATATTCAATCC
1 TAGCCGGATTTAATAGAATGATAAGGTGGATCAATTGATAATTTGGGTACAATATTCAATCC
* * *
8296 TAACTGGATTTTATAGAA
1 TAGCCGGATTTAATAGAA
8314 CGATGTATAT
Statistics
Matches: 125, Mismatches: 15, Indels: 8
0.84 0.10 0.05
Matches are distributed among these distances:
60 50 0.40
61 1 0.01
62 20 0.16
64 2 0.02
66 52 0.42
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (62 bp):
TAGCCGGATTTAATAGAATGATAAGGTGGATCAATTGATAATTTGGGTACAATATTCAATCC
Found at i:9296 original size:80 final size:80
Alignment explanation
Indices: 9205--9357 Score: 261
Period size: 80 Copynumber: 1.9 Consensus size: 80
9195 TAATGATCAG
* * *
9205 GAGGCGGAAGAAGTCATGTAAAGATATGAAATTAGGAGAAGCATTTGATTATATAAACCTATGAT
1 GAGGCGGAAGAAGTCATGTAAAGATATGAAATTAGGAGAAACATTTGATTATATAAACATACGAT
*
9270 TGTAAAAACTTTCGA
66 GGTAAAAACTTTCGA
*
9285 GAGGCGGAAGAAGTCATGTAAAGATATGAAATTAGGAGAAACATTTGATTATGTAAACATACGAT
1 GAGGCGGAAGAAGTCATGTAAAGATATGAAATTAGGAGAAACATTTGATTATATAAACATACGAT
9350 GGTAAAAA
66 GGTAAAAA
9358 TTTTTCTAAT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
80 68 1.00
ACGTcount: A:0.43, C:0.08, G:0.24, T:0.25
Consensus pattern (80 bp):
GAGGCGGAAGAAGTCATGTAAAGATATGAAATTAGGAGAAACATTTGATTATATAAACATACGAT
GGTAAAAACTTTCGA
Found at i:10454 original size:163 final size:159
Alignment explanation
Indices: 10203--10514 Score: 463
Period size: 158 Copynumber: 2.0 Consensus size: 159
10193 TTCTTTTTTC
*
10203 TATTTTTAATAACTCCCCTAATTATTTGTTTATTGACAAATCTTTCTGTATGTGTTTTAGTTACT
1 TATTTTTAATAACTCCCCGAATTATTTGTTTATTGACAAATCTTTCTGTATGTGTTTTAGTTA-T
*
10268 ATTAAGGTCCATTAGATTTTCTTTTCTTTTTTATTAG-ATACAGTATATAATCCTTCAATTAAAA
65 AGTAAGGTCCATTAGATTTTC-TTTCTTTTTTATTAGCA-ACAGTATATAATCCTTCAATT-AAA
*
10332 TATATATGCCAAATTAGTGTTATTCAAGAATTAT
127 -ATATATGCCAAATTAGTATTATTCAAGAATTAT
* * *
10366 TATTTTTAATAACTCTCCGAATTATTTGTTTATTGAC-AATCTTTGTGTCTGTGTTTTAG-T-TA
1 TATTTTTAATAACTCCCCGAATTATTTGTTTATTGACAAATCTTTCTGTATGTGTTTTAGTTATA
* *
10428 GTAAGG-CCAATTAGATTTTCTTTCTTTTTTATTAGCAACAGTATATATTCCTTCAATTAAAATC
66 GTAAGGTCC-ATTAGATTTTCTTTCTTTTTTATTAGCAACAGTATATAATCCTTCAATTAAAATA
10492 TATGCCAAATTAGTATTATTCAA
130 TATGCCAAATTAGTATTATTCAA
10515 TATAATCATA
Statistics
Matches: 139, Mismatches: 8, Indels: 11
0.88 0.05 0.07
Matches are distributed among these distances:
156 24 0.17
157 3 0.02
158 37 0.27
159 19 0.14
161 1 0.01
162 20 0.14
163 35 0.25
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.47
Consensus pattern (159 bp):
TATTTTTAATAACTCCCCGAATTATTTGTTTATTGACAAATCTTTCTGTATGTGTTTTAGTTATA
GTAAGGTCCATTAGATTTTCTTTCTTTTTTATTAGCAACAGTATATAATCCTTCAATTAAAATAT
ATGCCAAATTAGTATTATTCAAGAATTAT
Found at i:12240 original size:12 final size:12
Alignment explanation
Indices: 12223--12253 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
12213 TCTTCCCTGA
12223 TGGTTGTTGTTG
1 TGGTTGTTGTTG
12235 TGGTTGTTGTTG
1 TGGTTGTTGTTG
12247 TGGTTGT
1 TGGTTGT
12254 GCTGGCACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.42, T:0.58
Consensus pattern (12 bp):
TGGTTGTTGTTG
Found at i:15582 original size:442 final size:432
Alignment explanation
Indices: 14735--15594 Score: 1028
Period size: 442 Copynumber: 2.0 Consensus size: 432
14725 CGCGTTCGCT
* * *
14735 TTTATTTTTATATTTTTTTTACTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAAGTAA
1 TTTATTTTTATATTTTTTTTACTATTTGTCCAATGAAGGTAATTCAAGTGTCTATTAAAAAGTAA
* * ** * ** * *
14800 TTTCATAATCTACAATTTTCATTTAGAACTCAAAAGTCAATTTTAATATTTTTATTCTAAAAATT
66 TTTCATAATCTACAACTTCCATGAAGAACTCAAAAGTCAATTTT-ATATGTCAATTCAAAAAAAT
* * * * * * *
14865 ACTTCTGAAATTTTGTGGTTTTGATTGCCGATGAATTTAATATCGTATAATTTTTTGTCTACATC
130 ACTTCTGAAATTTGGTGGTTTCGATTGACGATCAATTTAATACCATATAATTTTTTGTCCACATC
** * * * * *
14930 TCTGATTGAAGTTATTGAAGTGTCGGTTAAAAGGTTATTGCATGATTTACGACTTTCATGAACCG
195 TCCAATTAAAGTTATTCAAGTGTCGGTTAAAAGATTATTGCATAATCTACGACTTTCATGAACCG
* * * * *
14995 AAAGCTAAATTTGATCTACGAGTTTCGTTAAGGGTTCAAAAGTGAATTTTATGTTTCAAGATCTC
260 AAAGCTAAATTTAATCTACGAGTTTCATGAAGGATTCAAAAGGGAATTTTATGTTTCAAGATCTC
* **
15060 CATTAACAAACATCTTCTTATTTGAATTATTTATCAAATGGCCCTCATACTTTTCTACTTTATAC
325 CATTAACAAACATCTTCTTATTTGAATTAGTTATCAAATCACCCTCATACTTTTCTACTTTATAC
*
15125 TACTTAATTCTTTACAAATTCTATCTTAATCTAATGTTTAAAC
390 TACTTAATCCTTTACAAATTCTATCTTAATCTAATGTTTAAAC
* * * *
15168 TTTATTTTTTTAATTCTTTTTT-CTATTTGTCCAATGAAGTTAATTCATGTGTCTATTAAAAGGT
1 TTTATTTTTAT-ATT-TTTTTTACTATTTGTCCAATGAAGGTAATTCAAGTGTCTATTAAAAAGT
*
15232 AATTTCATGATCTACAACTTCCATGAAGAACTCAAAAG-CAAATTTT-TATGTCAATTCAAAAAA
64 AATTTCATAATCTACAACTTCCATGAAGAACTCAAAAGTC-AATTTTATATGTCAATTCAAAAAA
* * * * *
15295 ATGCTTCCT-AAATTTGGTTGTTTCGATTGATGGTCTATTTAATACCATATAATTTTTTGATCCA
128 ATACTT-CTGAAATTTGGTGGTTTCGATTGACGATCAATTTAATACCATATAATTTTTTG-TCCA
* *
15359 CATGTCCAATTAAAGTTATTCAAGTGTCGGTTAAAAGATTATTGTATAATCTACGACTTTCATGA
191 CATCTCCAATTAAAGTTATTCAAGTGTCGGTTAAAAGATTATTGCATAATCTACGACTTTCAT--
* *
15424 AGAACCCGAAAG-TTAATTTAATCTACGAGTTTCATGAATGATTCAAAAGGGAATTTTTTATGTT
254 -GAA-CCGAAAGCTAAATTTAATCTACGAGTTTCATGAAGGATTCAAAAGGGAA--TTTTATGTT
* * * *
15488 TCAAGATCTCCATTAATTAACAAATATTTTCTTATTTGAATTAGTTATCAAATCACCTTTATACT
315 TCAAGATCTCC----ATTAACAAACATCTTCTTATTTGAATTAGTTATCAAATCACCCTCATACT
* * * *
15553 TTTTTATTTTATGCTACTTAGTCCTTTACAAATTCTATCTTA
376 TTTCTACTTTATACTACTTAATCCTTTACAAATTCTATCTTA
15595 CTCGATTTAA
Statistics
Matches: 355, Mismatches: 57, Indels: 21
0.82 0.13 0.05
Matches are distributed among these distances:
432 57 0.16
433 70 0.20
434 78 0.22
435 6 0.02
436 37 0.10
437 7 0.02
438 20 0.06
442 80 0.23
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (432 bp):
TTTATTTTTATATTTTTTTTACTATTTGTCCAATGAAGGTAATTCAAGTGTCTATTAAAAAGTAA
TTTCATAATCTACAACTTCCATGAAGAACTCAAAAGTCAATTTTATATGTCAATTCAAAAAAATA
CTTCTGAAATTTGGTGGTTTCGATTGACGATCAATTTAATACCATATAATTTTTTGTCCACATCT
CCAATTAAAGTTATTCAAGTGTCGGTTAAAAGATTATTGCATAATCTACGACTTTCATGAACCGA
AAGCTAAATTTAATCTACGAGTTTCATGAAGGATTCAAAAGGGAATTTTATGTTTCAAGATCTCC
ATTAACAAACATCTTCTTATTTGAATTAGTTATCAAATCACCCTCATACTTTTCTACTTTATACT
ACTTAATCCTTTACAAATTCTATCTTAATCTAATGTTTAAAC
Found at i:16700 original size:30 final size:30
Alignment explanation
Indices: 16659--16719 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
16649 AGTAAACGGA
16659 GAAAGCAAGGAAGAAGTATCCAAGATAAAT
1 GAAAGCAAGGAAGAAGTATCCAAGATAAAT
* * *
16689 GAAATCAAGGAAGAAGTGTCCAAGGTAAAT
1 GAAAGCAAGGAAGAAGTATCCAAGATAAAT
16719 G
1 G
16720 GAGTATCCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.49, C:0.10, G:0.26, T:0.15
Consensus pattern (30 bp):
GAAAGCAAGGAAGAAGTATCCAAGATAAAT
Found at i:24504 original size:3 final size:3
Alignment explanation
Indices: 24496--24530 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
24486 TACACCTACA
24496 ATT ATT ATT A-T ATT ATT A-T ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
24531 CGAGGGTTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.13
3 26 0.87
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:24511 original size:8 final size:8
Alignment explanation
Indices: 24498--24530 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
24488 CACCTACAAT
24498 TATTATTA
1 TATTATTA
24506 TATTATTA
1 TATTATTA
24514 TATTATTA
1 TATTATTA
24522 TTATTATTA
1 -TATTATTA
24531 CGAGGGTTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 16 0.67
9 8 0.33
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TATTATTA
Found at i:24512 original size:11 final size:11
Alignment explanation
Indices: 24496--24528 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
24486 TACACCTACA
24496 ATTATTATTAT
1 ATTATTATTAT
24507 ATTATTA-TATT
1 ATTATTATTA-T
24518 ATTATTATTAT
1 ATTATTATTAT
24529 TACGAGGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 2 0.10
11 16 0.80
12 2 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
ATTATTATTAT
Found at i:25275 original size:42 final size:42
Alignment explanation
Indices: 25216--25344 Score: 258
Period size: 42 Copynumber: 3.1 Consensus size: 42
25206 ACTATATATC
25216 ACACCAGTTGTGTGCCTGAGGTCAAATGAGGACTCCATTATG
1 ACACCAGTTGTGTGCCTGAGGTCAAATGAGGACTCCATTATG
25258 ACACCAGTTGTGTGCCTGAGGTCAAATGAGGACTCCATTATG
1 ACACCAGTTGTGTGCCTGAGGTCAAATGAGGACTCCATTATG
25300 ACACCAGTTGTGTGCCTGAGGTCAAATGAGGACTCCATTATG
1 ACACCAGTTGTGTGCCTGAGGTCAAATGAGGACTCCATTATG
25342 ACA
1 ACA
25345 AGAAATATTG
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 87 1.00
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.26
Consensus pattern (42 bp):
ACACCAGTTGTGTGCCTGAGGTCAAATGAGGACTCCATTATG
Found at i:29602 original size:20 final size:19
Alignment explanation
Indices: 29566--29604 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
29556 TTAGCGGAGA
* *
29566 AGAAGATAAGGGTAAAAAT
1 AGAAAATAAAGGTAAAAAT
29585 AGAAAATAAAGGTAAAAAT
1 AGAAAATAAAGGTAAAAAT
29604 A
1 A
29605 CATAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.21, T:0.15
Consensus pattern (19 bp):
AGAAAATAAAGGTAAAAAT
Found at i:38784 original size:30 final size:30
Alignment explanation
Indices: 38748--38804 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
38738 TTAGAAATCT
38748 TCATCATCACTAGCATTGTCGGACTCAAAG
1 TCATCATCACTAGCATTGTCGGACTCAAAG
*
38778 TCATCATCACTAGCATTGTCGGTCTCA
1 TCATCATCACTAGCATTGTCGGACTCA
38805 GAATCACTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (30 bp):
TCATCATCACTAGCATTGTCGGACTCAAAG
Done.