Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015857.1 Corchorus capsularis cultivar CVL-1 contig15878, 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: 6748
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Found at i:3842 original size:10 final size:10
Alignment explanation
Indices: 3829--3867 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
3819 AAAAATTCCC
3829 AAAAAAAATG
1 AAAAAAAATG
3839 AAAAAAAATG
1 AAAAAAAATG
*
3849 AATGAAAAATG
1 AA-AAAAAATG
3860 AAAAAAAA
1 AAAAAAAA
3868 AAAGCACTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.10
Consensus pattern (10 bp):
AAAAAAAATG
Found at i:3843 original size:11 final size:11
Alignment explanation
Indices: 3829--3868 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
3819 AAAAATTCCC
3829 AAAAAAAATG-
1 AAAAAAAATGA
3839 AAAAAAAATGA
1 AAAAAAAATGA
**
3850 ATGAAAAATGA
1 AAAAAAAATGA
3861 AAAAAAAA
1 AAAAAAAA
3869 AAGCACTTGG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
10 10 0.40
11 15 0.60
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (11 bp):
AAAAAAAATGA
Found at i:4287 original size:22 final size:21
Alignment explanation
Indices: 4259--4323 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 21
4249 TTTTCAAAAA
4259 AAAAAATTCAAAAAAATCAAAT
1 AAAAAATT-AAAAAAATCAAAT
4281 AAAAAATT-AAAAAA-CAAAT
1 AAAAAATTAAAAAAATCAAAT
*
4300 AAATAAATAAAAATAAAT-AAAT
1 AAA-AAATTAAAA-AAATCAAAT
4322 AA
1 AA
4324 TAATAAAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
19 8 0.21
20 10 0.26
21 3 0.08
22 17 0.45
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (21 bp):
AAAAAATTAAAAAAATCAAAT
Found at i:4298 original size:19 final size:20
Alignment explanation
Indices: 4259--4334 Score: 70
Period size: 18 Copynumber: 3.8 Consensus size: 20
4249 TTTTCAAAAA
4259 AAAAAATTCAAAAAAATCAAAT
1 AAAAAATT--AAAAAATCAAAT
4281 AAAAAATTAAAAAA-CAAAT
1 AAAAAATTAAAAAATCAAAT
4300 AAATAAA-T-AAAAAT-AAAT
1 AAA-AAATTAAAAAATCAAAT
*
4318 AAATAATAATAAAAAAT
1 AAA-AA-ATTAAAAAAT
4335 GATGATGAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 11
0.82 0.00 0.18
Matches are distributed among these distances:
18 15 0.31
19 10 0.20
20 10 0.20
21 6 0.12
22 8 0.16
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (20 bp):
AAAAAATTAAAAAATCAAAT
Found at i:4305 original size:4 final size:4
Alignment explanation
Indices: 4272--4334 Score: 50
Period size: 4 Copynumber: 17.0 Consensus size: 4
4262 AAATTCAAAA
*
4272 AAAT CAAAT AAA- AAATT AAA- AAAC AAAT AAAT AAAT -AA- AAAT AAAT
1 AAAT -AAAT AAAT AAA-T AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
4318 AAAT -AAT -AAT AAA- AAAT
1 AAAT AAAT AAAT AAAT AAAT
4335 GATGATGAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 15
0.76 0.02 0.23
Matches are distributed among these distances:
3 19 0.38
4 24 0.48
5 7 0.14
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:4313 original size:10 final size:10
Alignment explanation
Indices: 4300--4332 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
4290 AAAAACAAAT
4300 AAATAAATAA
1 AAATAAATAA
4310 AAATAAATAA
1 AAATAAATAA
4320 ATAAT-AATAA
1 A-AATAAATAA
4330 AAA
1 AAA
4333 ATGATGATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 2 0.09
10 17 0.77
11 3 0.14
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
AAATAAATAA
Found at i:5227 original size:104 final size:104
Alignment explanation
Indices: 5047--5250 Score: 390
Period size: 104 Copynumber: 2.0 Consensus size: 104
5037 TTTGTGAGCC
*
5047 AAGGGTTAAGTATGCCGATTACTTCCAAATTGTTAAAGTCCATTGATTAAGGGGCATTCTGAATG
1 AAGGGTGAAGTATGCCGATTACTTCCAAATTGTTAAAGTCCATTGATTAAGGGGCATTCTGAATG
5112 GTGTTCATCAATCCTCTTGAAAAATAATTGAAATTGTTA
66 GTGTTCATCAATCCTCTTGAAAAATAATTGAAATTGTTA
*
5151 AAGGGTGAAGTATGTCGATTACTTCCAAATTGTTAAAGTCCATTGATTAAGGGGCATTCTGAATG
1 AAGGGTGAAGTATGCCGATTACTTCCAAATTGTTAAAGTCCATTGATTAAGGGGCATTCTGAATG
5216 GTGTTCATCAATCCTCTTGAAAAATAATTGAAATT
66 GTGTTCATCAATCCTCTTGAAAAATAATTGAAATT
5251 TTCACAAAGT
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
104 98 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (104 bp):
AAGGGTGAAGTATGCCGATTACTTCCAAATTGTTAAAGTCCATTGATTAAGGGGCATTCTGAATG
GTGTTCATCAATCCTCTTGAAAAATAATTGAAATTGTTA
Found at i:6187 original size:22 final size:22
Alignment explanation
Indices: 6162--6235 Score: 85
Period size: 22 Copynumber: 3.2 Consensus size: 22
6152 TTCGGGCACA
6162 AATTCAGAAACCTCCGGGTATT
1 AATTCAGAAACCTCCGGGTATT
* * **
6184 AATTCTGATAAGTCCTCCGGGCACA
1 AATTCAGA-AA--CCTCCGGGTATT
6209 AATTCAGAAACCTCCGGGTATT
1 AATTCAGAAACCTCCGGGTATT
6231 AATTC
1 AATTC
6236 TGATAAGTCC
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
22 21 0.51
23 2 0.05
24 2 0.05
25 16 0.39
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (22 bp):
AATTCAGAAACCTCCGGGTATT
Found at i:6201 original size:25 final size:25
Alignment explanation
Indices: 6172--6251 Score: 103
Period size: 25 Copynumber: 3.3 Consensus size: 25
6162 AATTCAGAAA
6172 CCTCCGGGTATTAATTCTGATAAGT
1 CCTCCGGGTATTAATTCTGATAAGT
* ** *
6197 CCTCCGGGCACAAATTCAGA-AA--
1 CCTCCGGGTATTAATTCTGATAAGT
6219 CCTCCGGGTATTAATTCTGATAAGT
1 CCTCCGGGTATTAATTCTGATAAGT
6244 CCTCCGGG
1 CCTCCGGG
6252 CAATTGGTAA
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
22 16 0.36
23 2 0.05
24 2 0.05
25 24 0.55
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (25 bp):
CCTCCGGGTATTAATTCTGATAAGT
Found at i:6214 original size:47 final size:47
Alignment explanation
Indices: 6145--6253 Score: 209
Period size: 47 Copynumber: 2.3 Consensus size: 47
6135 TTTGCATTGG
*
6145 TAAGTCCTTCGGGCACAAATTCAGAAACCTCCGGGTATTAATTCTGA
1 TAAGTCCTCCGGGCACAAATTCAGAAACCTCCGGGTATTAATTCTGA
6192 TAAGTCCTCCGGGCACAAATTCAGAAACCTCCGGGTATTAATTCTGA
1 TAAGTCCTCCGGGCACAAATTCAGAAACCTCCGGGTATTAATTCTGA
6239 TAAGTCCTCCGGGCA
1 TAAGTCCTCCGGGCA
6254 ATTGGTAAAA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 61 1.00
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (47 bp):
TAAGTCCTCCGGGCACAAATTCAGAAACCTCCGGGTATTAATTCTGA
Found at i:6256 original size:22 final size:23
Alignment explanation
Indices: 6184--6256 Score: 64
Period size: 22 Copynumber: 3.2 Consensus size: 23
6174 TCCGGGTATT
6184 AATTCTGATAAGTCCTCCGGGCAC
1 AATTCTGATAAGTCCTCCGGG-AC
* *
6208 AAATTCAGA-AA--CCTCCGGGTATT
1 -AATTCTGATAAGTCCTCCGGG-A-C
6231 AATTCTGATAAGTCCTCCGGG-C
1 AATTCTGATAAGTCCTCCGGGAC
6253 AATT
1 AATT
6257 GGTAAAACCT
Statistics
Matches: 39, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
22 20 0.51
23 2 0.05
24 2 0.05
25 15 0.38
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (23 bp):
AATTCTGATAAGTCCTCCGGGAC
Found at i:6403 original size:22 final size:22
Alignment explanation
Indices: 6378--6451 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 22
6368 TCCGGGCACA
6378 AATTCAGAAACCTCAGGGTATT
1 AATTCAGAAACCTCAGGGTATT
* * * **
6400 AATTCTGATAAGTCCTCCGGGCACA
1 AATTCAGA-AA--CCTCAGGGTATT
*
6425 AATTCAGAAACCTCTGGGTATT
1 AATTCAGAAACCTCAGGGTATT
6447 AATTC
1 AATTC
6452 TGATAAGTCC
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
22 20 0.51
23 2 0.05
24 2 0.05
25 15 0.38
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (22 bp):
AATTCAGAAACCTCAGGGTATT
Found at i:6430 original size:47 final size:47
Alignment explanation
Indices: 6361--6469 Score: 209
Period size: 47 Copynumber: 2.3 Consensus size: 47
6351 TTTGCATTGG
6361 TAAGTCCTCCGGGCACAAATTCAGAAACCTCAGGGTATTAATTCTGA
1 TAAGTCCTCCGGGCACAAATTCAGAAACCTCAGGGTATTAATTCTGA
*
6408 TAAGTCCTCCGGGCACAAATTCAGAAACCTCTGGGTATTAATTCTGA
1 TAAGTCCTCCGGGCACAAATTCAGAAACCTCAGGGTATTAATTCTGA
6455 TAAGTCCTCCGGGCA
1 TAAGTCCTCCGGGCA
6470 ATTGGTGAAA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 61 1.00
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (47 bp):
TAAGTCCTCCGGGCACAAATTCAGAAACCTCAGGGTATTAATTCTGA
Found at i:6469 original size:216 final size:216
Alignment explanation
Indices: 6090--6736 Score: 1062
Period size: 216 Copynumber: 3.0 Consensus size: 216
6080 CAAGTTTTAA
* * *
6090 TCATATTTAAGTTTAAAATCCTTGATCGAAGTTGTCAATTCAGAGTTTGCATTGGTAAGTCCTTC
1 TCATGTTTAAGTTTAAAATCCTTGATCGAAGGTGTCAATTCAGAGTTTGCATTGGTAAGTCCTCC
6155 GGGCACAAATTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCACAAATTCAGAAAC
66 GGGCACAAATTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCACAAATTCAGAAAC
6220 CTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGGTAAAACCTCCGGGTGCCATTTCATTT
131 CTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGGTAAAACCTCCGGGTGCCATTTCATTT
6285 CACCAAGTTTTCATCAAAAAT
196 CACCAAGTTTTCATCAAAAAT
6306 TCATGTTTAAGTTTAAAATCCTTGATCGAAGGTGTCAATTCAGAGTTTGCATTGGTAAGTCCTCC
1 TCATGTTTAAGTTTAAAATCCTTGATCGAAGGTGTCAATTCAGAGTTTGCATTGGTAAGTCCTCC
*
6371 GGGCACAAATTCAGAAACCTCAGGGTATTAATTCTGATAAGTCCTCCGGGCACAAATTCAGAAAC
66 GGGCACAAATTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCACAAATTCAGAAAC
* *
6436 CTCTGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGGTGAAACCTCCGGGTGCCATTTCATTT
131 CTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGGTAAAACCTCCGGGTGCCATTTCATTT
6501 CACCAAGTTTTCAAT-AAAAAT
196 CACCAAGTTTTC-ATCAAAAAT
* * * *
6522 TCATGTTTAAGCTTAAAATCCTCGACCGAAGGTGCCAATTCAGAGTTTGCATTGGTAAGTCCTCC
1 TCATGTTTAAGTTTAAAATCCTTGATCGAAGGTGTCAATTCAGAGTTTGCATTGGTAAGTCCTCC
* * *
6587 GGGCACAAATTCAGAAACCTCCGGATTTTAATTCTGAGAAGTCCTCCGGGCACAAATTCAGAAAC
66 GGGCACAAATTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCACAAATTCAGAAAC
* * * *
6652 CTCCGTGTATTAATTCTGATATATAAGTCCTCCGGGCAATTGGTAAAACCTTCAGGTACCATTTC
131 CTCCGGGTATTAATTCTG----ATAAGTCCTCCGGGCAATTGGTAAAACCTCCGGGTGCCATTTC
* * *
6717 ATTCCATCAAGTTTTTATCA
192 ATTTCACCAAGTTTTCATCA
6737 TATTTAAGTT
Statistics
Matches: 402, Mismatches: 23, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
216 345 0.86
217 2 0.00
219 2 0.00
220 53 0.13
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (216 bp):
TCATGTTTAAGTTTAAAATCCTTGATCGAAGGTGTCAATTCAGAGTTTGCATTGGTAAGTCCTCC
GGGCACAAATTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCACAAATTCAGAAAC
CTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGGTAAAACCTCCGGGTGCCATTTCATTT
CACCAAGTTTTCATCAAAAAT
Found at i:6610 original size:22 final size:22
Alignment explanation
Indices: 6582--6656 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
6572 ATTGGTAAGT
6582 CCTCCGGGCACAAATTCAGAAA
1 CCTCCGGGCACAAATTCAGAAA
***** *
6604 CCTCCGGATTTTAATTCTGAGAAGT
1 CCTCCGGGCACAAATTC--AGAA-A
6629 CCTCCGGGCACAAATTCAGAAA
1 CCTCCGGGCACAAATTCAGAAA
6651 CCTCCG
1 CCTCCG
6657 TGTATTAATT
Statistics
Matches: 38, Mismatches: 12, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
22 18 0.47
23 4 0.11
24 4 0.11
25 12 0.32
ACGTcount: A:0.29, C:0.31, G:0.19, T:0.21
Consensus pattern (22 bp):
CCTCCGGGCACAAATTCAGAAA
Found at i:6647 original size:47 final size:47
Alignment explanation
Indices: 6578--6670 Score: 161
Period size: 47 Copynumber: 2.0 Consensus size: 47
6568 TTGCATTGGT
*
6578 AAGTCCTCCGGGCACAAATTCAGAAACCTCCG-GATTTTAATTCTGAG
1 AAGTCCTCCGGGCACAAATTCAGAAACCTCCGTG-TATTAATTCTGAG
6625 AAGTCCTCCGGGCACAAATTCAGAAACCTCCGTGTATTAATTCTGA
1 AAGTCCTCCGGGCACAAATTCAGAAACCTCCGTGTATTAATTCTGA
6671 TATATAAGTC
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
47 43 0.98
48 1 0.02
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (47 bp):
AAGTCCTCCGGGCACAAATTCAGAAACCTCCGTGTATTAATTCTGAG
Done.