Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013971.1 Corchorus capsularis cultivar CVL-1 contig13992, 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: 17918
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:825 original size:173 final size:178
Alignment explanation
Indices: 495--847 Score: 565
Period size: 173 Copynumber: 2.0 Consensus size: 178
485 ATGAAAGTTA
495 TAGACCATGAAATTACCTTTAAATAGACACTTGAATCACCTTGATCGGTCAAATAGAAAAAAAAT
1 TAGACCATGAAATTACCTTTAAATA-ACACTTGAATCACCTTGATCGGTCAAATAG--AAAAAAT
* * *
560 AAAAGAATTAAAGCCGAAACATTCAATCGTCCAACCCATAATTGTAAGTAATTAAATAGTATAAA
63 AAAACAATTAAAGCCGAAACATTCAATCGTCCAACACATAATTGTAAGTAATTAAATAGCATAAA
625 TTATAAAAGTATAAGGATCATTTAATAAATAATCCAACAAAAAAAATGATTG
128 TTATAAAAGTATAAGGATCATTTAATAAATAATCCAAC-AAAAAAATGATTG
*
677 TAGACCATGGAATTACCTTTAAAT-AC-C-TGAATCACCTTGATCGGTCAAATAG-AAAAA-AAA
1 TAGACCATGAAATTACCTTTAAATAACACTTGAATCACCTTGATCGGTCAAATAGAAAAAATAAA
* *
737 ACAATTAAAGCCGAAACATTCAATCGTCCAACATATAATTGTAAG-GATTAAATAGCATAAATTA
66 ACAATTAAAGCCGAAACATTCAATCGTCCAACACATAATTGTAAGTAATTAAATAGCATAAATTA
*
801 TAAAAGTATGAGGATCATTTAATAAATAATCCAACAAAAAAATGATT
131 TAAAAGTATAAGGATCATTTAATAAATAATCCAACAAAAAAATGATT
848 TGTTTATGGA
Statistics
Matches: 164, Mismatches: 7, Indels: 10
0.91 0.04 0.06
Matches are distributed among these distances:
172 12 0.07
173 51 0.31
174 45 0.27
175 5 0.03
178 25 0.15
179 1 0.01
180 2 0.01
182 23 0.14
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.26
Consensus pattern (178 bp):
TAGACCATGAAATTACCTTTAAATAACACTTGAATCACCTTGATCGGTCAAATAGAAAAAATAAA
ACAATTAAAGCCGAAACATTCAATCGTCCAACACATAATTGTAAGTAATTAAATAGCATAAATTA
TAAAAGTATAAGGATCATTTAATAAATAATCCAACAAAAAAATGATTG
Found at i:8035 original size:26 final size:27
Alignment explanation
Indices: 7968--8039 Score: 101
Period size: 27 Copynumber: 2.7 Consensus size: 27
7958 AGGGGCACAT
**
7968 AGGGGCATTTTGGTCATTTGTGCATTC
1 AGGGGCATTTTGGTCATTTGCACATTC
*
7995 AGGGGCATTTTGGTCATTTGCATATTC
1 AGGGGCATTTTGGTCATTTGCACATTC
*
8022 -GGGGCATTTCGGTCATTT
1 AGGGGCATTTTGGTCATTT
8040 TAGGTCTACT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
26 17 0.41
27 24 0.59
ACGTcount: A:0.15, C:0.15, G:0.29, T:0.40
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTGCACATTC
Found at i:13546 original size:18 final size:18
Alignment explanation
Indices: 13523--13573 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 18
13513 CATTAGTTAA
13523 CATTAGTTAATACTTATG
1 CATTAGTTAATACTTATG
13541 CATTAGTTAATATTACTTATG
1 CATTAGTT-A-A-TACTTATG
13562 CATTAGTTAATA
1 CATTAGTTAATA
13574 GGATACTTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
18 10 0.33
19 2 0.07
20 2 0.07
21 16 0.53
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (18 bp):
CATTAGTTAATACTTATG
Found at i:13559 original size:21 final size:21
Alignment explanation
Indices: 13533--13573 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
13523 CATTAGTTAA
13533 TACTTATGCATTAGTTAATAT
1 TACTTATGCATTAGTTAATAT
13554 TACTTATGCATTAGTTAATA
1 TACTTATGCATTAGTTAATA
13574 GGATACTTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (21 bp):
TACTTATGCATTAGTTAATAT
Found at i:17281 original size:43 final size:42
Alignment explanation
Indices: 17225--17547 Score: 190
Period size: 43 Copynumber: 7.7 Consensus size: 42
17215 CTGATTGTTC
* *
17225 TTTACTTTGTACTGATTACTATTTTACTCTTGTTGACTACCT
1 TTTACTTTTTACTGATTACTATTTTACTCTTGTTGATTACCT
* *
17267 TCTTACTTTTTACTGATTA-TCATTTTACACTTTTACTGATTA-CT
1 T-TTACTTTTTACTGATTACT-ATTTTACTCTTGT--TGATTACCT
* ** * **
17311 CTTTACTATTTT-CTGCTCCCCT-TTTT--TTTTACTGATTACTCT
1 -TTTACT-TTTTACTGAT-TACTATTTTACTCTTGTTGATTAC-CT
* * * * *
17353 TTTACTTTTTACTGATTGC-CTTTTGCTTCTTGCTGATTAGCTT
1 TTTACTTTTTACTGATTACTATTTTAC-TCTTGTTGATTA-CCT
* * *** *
17396 TTTACTCTTTACTGATCACCT-TTTTACTCTTACCGATTTCCT
1 TTTACTTTTTACTGATTA-CTATTTTACTCTTGTTGATTACCT
* * *
17438 TTTACTTCTTACTTATTACTTTTTTA--C----TGATTA-CT
1 TTTACTTTTTACTGATTACTATTTTACTCTTGTTGATTACCT
*
17473 ATTTACTTTTTACTGACTACTATTTTACTCTTGTTGATTACCT
1 -TTTACTTTTTACTGATTACTATTTTACTCTTGTTGATTACCT
*
17516 TCTTAATTTTTACTGATTACTATTTTACTCTT
1 T-TTACTTTTTACTGATTACTATTTTACTCTT
17548 TTACTGATTA
Statistics
Matches: 216, Mismatches: 37, Indels: 55
0.70 0.12 0.18
Matches are distributed among these distances:
35 2 0.01
36 26 0.12
38 1 0.00
40 16 0.07
41 12 0.06
42 34 0.16
43 92 0.43
44 22 0.10
45 10 0.05
46 1 0.00
ACGTcount: A:0.18, C:0.20, G:0.07, T:0.55
Consensus pattern (42 bp):
TTTACTTTTTACTGATTACTATTTTACTCTTGTTGATTACCT
Found at i:17461 original size:21 final size:21
Alignment explanation
Indices: 17212--17564 Score: 146
Period size: 21 Copynumber: 16.8 Consensus size: 21
17202 CATCACTATT
*
17212 TTACTGATT-GTTCTTTACTT-
1 TTACTGATTACTT-TTTACTTC
17232 TGTACTGATTACTATTTTAC-TC
1 T-TACTGATTACT-TTTTACTTC
** * * *
17254 TTGTTGACTACCTTCTTACTTT
1 TTACTGATTA-CTTTTTACTTC
*
17276 TTACTGATTATCATTTTACACTT-
1 TTACTGATTA-C-TTTT-TACTTC
*
17299 TTACTGATTACTCTTTACTAT-
1 TTACTGATTACTTTTTACT-TC
* * **
17320 TTTCTGCTCCCCTTTTT--TT-
1 TTACTGAT-TACTTTTTACTTC
*
17339 TTACTGATTACTCTTTTACTTT
1 TTACTGATTACT-TTTTACTTC
* * *
17361 TTACTGATTGCCTTTTGCTTC
1 TTACTGATTACTTTTTACTTC
*
17382 TTGCTGATTAGCTTTTTAC-TC
1 TTACTGATTA-CTTTTTACTTC
*
17403 TTTACTGATCACCTTTTTAC-TC
1 -TTACTGATTA-CTTTTTACTTC
* * *
17425 TTACCGATTTCCTTTTACTTC
1 TTACTGATTACTTTTTACTTC
*
17446 TTACTTATTAC---TT--TT-
1 TTACTGATTACTTTTTACTTC
* *
17461 TTACTGATTACTATTTACTTT
1 TTACTGATTACTTTTTACTTC
*
17482 TTACTGACTACTATTTTAC-TC
1 TTACTGATTACT-TTTTACTTC
** * * *
17503 TTGTTGATTACCTTCTTAATTT
1 TTACTGATTA-CTTTTTACTTC
*
17525 TTACTGATTACTATTTTACTCTT
1 TTACTGATTACT-TTTTACT-TC
17548 TTACTGATTACTCTTTT
1 TTACTGATTACT-TTTT
17565 TACCCTTTCA
Statistics
Matches: 249, Mismatches: 56, Indels: 53
0.70 0.16 0.15
Matches are distributed among these distances:
15 10 0.04
16 2 0.01
18 6 0.02
19 11 0.04
20 14 0.06
21 91 0.37
22 79 0.32
23 32 0.13
24 4 0.02
ACGTcount: A:0.18, C:0.20, G:0.07, T:0.55
Consensus pattern (21 bp):
TTACTGATTACTTTTTACTTC
Found at i:17597 original size:66 final size:64
Alignment explanation
Indices: 17453--17599 Score: 163
Period size: 66 Copynumber: 2.2 Consensus size: 64
17443 TTCTTACTTA
* * *
17453 TTACTTTTTTACTGATTACTATTTACTTTTTACTGACTACTATTTTACTCTTGTTGATTACCTTC
1 TTAC-TTTTTACTGATTACTATTTACTTTTTACTGACTACTATTTTACCCTTGTAGAGTACCTTC
* * * *
17518 TTAATTTTTACTGATTACTATTTTACTCTTTTACTGATTACTCTTTTTACCCTT-TCAG-GTATC
1 TTACTTTTTACTGATTACTA-TTTACT-TTTTACTGACTACT-ATTTTACCCTTGT-AGAGTACC
*
17581 TTT
62 TTC
17584 TTACTTTTTACTGATT
1 TTACTTTTTACTGATT
17600 GCCTGCTATT
Statistics
Matches: 69, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
64 16 0.23
65 9 0.13
66 34 0.49
67 10 0.14
ACGTcount: A:0.20, C:0.18, G:0.06, T:0.56
Consensus pattern (64 bp):
TTACTTTTTACTGATTACTATTTACTTTTTACTGACTACTATTTTACCCTTGTAGAGTACCTTC
Found at i:17852 original size:63 final size:62
Alignment explanation
Indices: 17785--17909 Score: 173
Period size: 63 Copynumber: 2.0 Consensus size: 62
17775 CATTTTAACT
* *
17785 CTTAATTA-TCGATTTACTGATTACTATTACT-TTGACTCTGATTAATCTCTTTTTACTTAATTA
1 CTTAATTACT-GATTTACTGATTACTATTACTCTTGA--CTGATTAATATCTTTTCACTTAATTA
* *
17848 CTTAATTACTGATTTACTGATTTCTATTACTCTTTACTGATTAATATCTTTTCACTTAATTA
1 CTTAATTACTGATTTACTGATTACTATTACTCTTGACTGATTAATATCTTTTCACTTAATTA
17910 TTGATTTAC
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
62 24 0.43
63 28 0.50
64 4 0.07
ACGTcount: A:0.27, C:0.16, G:0.06, T:0.51
Consensus pattern (62 bp):
CTTAATTACTGATTTACTGATTACTATTACTCTTGACTGATTAATATCTTTTCACTTAATTA
Done.