Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007150.1 Corchorus capsularis cultivar CVL-1 contig07171, 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: 20751
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:228 original size:22 final size:22
Alignment explanation
Indices: 203--246 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
193 AAAATTTGGC
*
203 TTTTAGTTTATGATTTATGAGT
1 TTTTAGTTTATGATTAATGAGT
225 TTTTAGTTTATGATTAATGAGT
1 TTTTAGTTTATGATTAATGAGT
247 AGATCTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.00, G:0.18, T:0.57
Consensus pattern (22 bp):
TTTTAGTTTATGATTAATGAGT
Found at i:731 original size:35 final size:34
Alignment explanation
Indices: 687--1125 Score: 481
Period size: 35 Copynumber: 12.9 Consensus size: 34
677 GTGAGTCAGT
* *
687 AGTAATCAACTTAATTCAAGGTAATTAAGTGAATC
1 AGTAAT-AACTTAATTCAGGGTAATTAAGTGAGTC
722 AGTAATCAACTTAATTCAGGGTAATTAAGT-AGTTC
1 AGTAAT-AACTTAATTCAGGGTAATTAAGTGAG-TC
*
757 AGTAATCAACTTAATTCAGGGTAATTAAGTGGGTC
1 AGTAAT-AACTTAATTCAGGGTAATTAAGTGAGTC
792 AGTAATCAACTTAATTCAGGGTAATTAAGTGAGTC
1 AGTAAT-AACTTAATTCAGGGTAATTAAGTGAGTC
* *
827 AGTGAATAAATTAATTCAGGGTAATTAAGTCAGT-
1 AGT-AATAACTTAATTCAGGGTAATTAAGTGAGTC
*
861 A--AATAGCTTAATTCAGGGTAATTAAGTGAGTC
1 AGTAATAACTTAATTCAGGGTAATTAAGTGAGTC
* *
893 AGCGAATAACTTAATTCAGGGTAATTAAGTCAGT-
1 AG-TAATAACTTAATTCAGGGTAATTAAGTGAGTC
* *
927 A--AATAGCTTAATTCAGGGTAATT-AGTGAGTT
1 AGTAATAACTTAATTCAGGGTAATTAAGTGAGTC
* *
958 AGTTAATGACTTAATTCAGGATAATT-A---AGTC
1 AG-TAATAACTTAATTCAGGGTAATTAAGTGAGTC
* *
989 AGTAAGTAGCTTAATTCAGGGTAATTAAGTGAATC
1 AGTAA-TAACTTAATTCAGGGTAATTAAGTGAGTC
*
1024 AGTAATCAACTTTAATTCAGGGTAATTAAGTGAGTT
1 AGTAAT-AAC-TTAATTCAGGGTAATTAAGTGAGTC
* *
1060 AATGAAAAACTTAATTCAGGGGTAATTAAGT-AGTTC
1 AGT-AATAACTTAATTCA-GGGTAATTAAGTGAG-TC
* *
1096 AATAAGTAACTTAATTCATGGTAATTAAGT
1 AGTAA-TAACTTAATTCAGGGTAATTAAGT
1126 TTAGTGAGCA
Statistics
Matches: 353, Mismatches: 29, Indels: 44
0.83 0.07 0.10
Matches are distributed among these distances:
30 9 0.03
31 71 0.20
32 2 0.01
34 24 0.07
35 186 0.53
36 59 0.17
37 2 0.01
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.33
Consensus pattern (34 bp):
AGTAATAACTTAATTCAGGGTAATTAAGTGAGTC
Found at i:891 original size:66 final size:65
Alignment explanation
Indices: 687--1125 Score: 483
Period size: 66 Copynumber: 6.4 Consensus size: 65
677 GTGAGTCAGT
*
687 AGTAATCAACTTAATTCAAGGTAATTAAGTGAATCAGT-AATCAACTTAATTCAGGGTAATTAAG
1 AGTAAT-AACTTAATTCAGGGTAATTAA--G--TCAGTAAAT-AACTTAATTCAGGGTAATTAAG
751 T-AGTTC
60 TGAG-TC
757 AGTAATCAACTTAATTCAGGGTAATTAAGTGGGTCAGT-AATCAACTTAATTCAGGGTAATTAAG
1 AGTAAT-AACTTAATTCAGGGTAATTAA----GTCAGTAAAT-AACTTAATTCAGGGTAATTAAG
821 TGAGTC
60 TGAGTC
* *
827 AGTGAATAAATTAATTCAGGGTAATTAAGTCAGTAAATAGCTTAATTCAGGGTAATTAAGTGAGT
1 AGT-AATAACTTAATTCAGGGTAATTAAGTCAGTAAATAACTTAATTCAGGGTAATTAAGTGAGT
892 C
65 C
* *
893 AGCGAATAACTTAATTCAGGGTAATTAAGTCAGTAAATAGCTTAATTCAGGGTAATT-AGTGAGT
1 AG-TAATAACTTAATTCAGGGTAATTAAGTCAGTAAATAACTTAATTCAGGGTAATTAAGTGAGT
*
957 T
65 C
* * * * *
958 AGTTAATGACTTAATTCAGGATAATTAAGTCAGTAAGTAGCTTAATTCAGGGTAATTAAGTGAAT
1 AG-TAATAACTTAATTCAGGGTAATTAAGTCAGTAAATAACTTAATTCAGGGTAATTAAGTGAGT
1023 C
65 C
* *
1024 AGTAATCAACTTTAATTCAGGGTAATTAAGTGAGTTAATGAAAAACTTAATTCAGGGGTAATTAA
1 AGTAAT-AAC-TTAATTCAGGGTAATTAAGTCAG-T-A--AATAACTTAATTCA-GGGTAATTAA
1089 GT-AGTTC
59 GTGAG-TC
* *
1096 AATAAGTAACTTAATTCATGGTAATTAAGT
1 AGTAA-TAACTTAATTCAGGGTAATTAAGT
1126 TTAGTGAGCA
Statistics
Matches: 330, Mismatches: 23, Indels: 31
0.86 0.06 0.08
Matches are distributed among these distances:
65 63 0.19
66 97 0.29
67 24 0.07
68 1 0.00
69 1 0.00
70 84 0.25
71 36 0.11
72 23 0.07
73 1 0.00
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.33
Consensus pattern (65 bp):
AGTAATAACTTAATTCAGGGTAATTAAGTCAGTAAATAACTTAATTCAGGGTAATTAAGTGAGTC
Found at i:2678 original size:2 final size:2
Alignment explanation
Indices: 2671--2719 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
2661 ACATTCAAAC
* * *
2671 TA TA TA TA TA AA TA TA TA TA TA TA TA TA TA CA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2713 TA TA TA T
1 TA TA TA T
2720 GACCTCTACA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:10982 original size:18 final size:20
Alignment explanation
Indices: 10941--10982 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
10931 TTTTTGCTTC
10941 TTTTTTTTTGTATTTTTGC-
1 TTTTTTTTTGTATTTTTGCG
* *
10960 TTTTTTTTT-TTTTTTTGGG
1 TTTTTTTTTGTATTTTTGCG
10979 TTTT
1 TTTT
10983 GCATGATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.02, C:0.02, G:0.12, T:0.83
Consensus pattern (20 bp):
TTTTTTTTTGTATTTTTGCG
Found at i:14024 original size:24 final size:24
Alignment explanation
Indices: 13992--14077 Score: 118
Period size: 24 Copynumber: 3.6 Consensus size: 24
13982 GGCCTTCCTA
*
13992 ACAACAACAATCCTCTGTATGAGG
1 ACAACAACAATGCTCTGTATGAGG
*
14016 ACAACAACAATGCTCTATATGAGG
1 ACAACAACAATGCTCTGTATGAGG
* * *
14040 ATAACAACAATGTTTTGTATGAGG
1 ACAACAACAATGCTCTGTATGAGG
*
14064 ACAAGAACAATGCT
1 ACAACAACAATGCT
14078 GACAACAACA
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (24 bp):
ACAACAACAATGCTCTGTATGAGG
Found at i:14455 original size:11 final size:11
Alignment explanation
Indices: 14430--14470 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
14420 AAAACAATTC
14430 TATAAAATAAAT
1 TATAAAAT-AAT
*
14442 TATCAAATAAT
1 TATAAAATAAT
14453 TATAAAATTAAT
1 TATAAAA-TAAT
14465 TATAAA
1 TATAAA
14471 CAAGAGGGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 9 0.35
12 17 0.65
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (11 bp):
TATAAAATAAT
Found at i:14833 original size:27 final size:27
Alignment explanation
Indices: 14803--14860 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
14793 AGTTTGGTGT
** * *
14803 AGTTTGGTGTTGTTAAGGAGTAGGAAC
1 AGTTTGGTAATGTAAAGGAGTAGGAAA
14830 AGTTTGGTAATGTAAAGGAGTAGGAAA
1 AGTTTGGTAATGTAAAGGAGTAGGAAA
14857 AGTT
1 AGTT
14861 GAGTAGCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.02, G:0.34, T:0.31
Consensus pattern (27 bp):
AGTTTGGTAATGTAAAGGAGTAGGAAA
Found at i:15272 original size:23 final size:22
Alignment explanation
Indices: 15225--15265 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
15215 TAAAGGGAAT
15225 TAAAAACCCACTTATAACATAA
1 TAAAAACCCACTTATAACATAA
15247 TAAAAACCCA-TT-TAACATA
1 TAAAAACCCACTTATAACATA
15266 TCAATAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.37
21 2 0.11
22 10 0.53
ACGTcount: A:0.54, C:0.22, G:0.00, T:0.24
Consensus pattern (22 bp):
TAAAAACCCACTTATAACATAA
Found at i:16035 original size:20 final size:20
Alignment explanation
Indices: 16010--16048 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
16000 CATATAAAAT
*
16010 AATAATAACTAATTTTTAAA
1 AATAATAACTAATTATTAAA
16030 AATAATAACTAATTATTAA
1 AATAATAACTAATTATTAA
16049 TTTAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
AATAATAACTAATTATTAAA
Found at i:17515 original size:1 final size:1
Alignment explanation
Indices: 17509--17536 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
17499 CATCATTGAT
17509 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
17537 CCCTAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:17755 original size:2 final size:2
Alignment explanation
Indices: 17748--17775 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
17738 CGGTGTGAAA
17748 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
17776 CTTTATACTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.