Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006478.1 Corchorus capsularis cultivar CVL-1 contig06499, 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: 54781
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Found at i:5390 original size:45 final size:46
Alignment explanation
Indices: 5308--5410 Score: 165
Period size: 45 Copynumber: 2.3 Consensus size: 46
5298 AAAACACAAC
* *
5308 TTTGGAAAACCATTTTATCAAAACCTTTTTGAAAACCATGACTCTT
1 TTTGAAAAACCATTTTATCAAAACCTTTTTAAAAACCATGACTCTT
*
5354 TTTGAAAAACCGTTTTATCAAAACC-TTTTAAAAACCATGACTCTT
1 TTTGAAAAACCATTTTATCAAAACCTTTTTAAAAACCATGACTCTT
5399 TTTG-AAAACCAT
1 TTTGAAAAACCAT
5411 CGTTGCTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
44 7 0.13
45 23 0.43
46 23 0.43
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.36
Consensus pattern (46 bp):
TTTGAAAAACCATTTTATCAAAACCTTTTTAAAAACCATGACTCTT
Found at i:5435 original size:11 final size:11
Alignment explanation
Indices: 5419--5443 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5409 ATCGTTGCTT
5419 TTTCTCTTTTC
1 TTTCTCTTTTC
5430 TTTCTCTTTTC
1 TTTCTCTTTTC
5441 TTT
1 TTT
5444 TATTATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTCTCTTTTC
Found at i:5973 original size:75 final size:75
Alignment explanation
Indices: 5881--6020 Score: 208
Period size: 75 Copynumber: 1.9 Consensus size: 75
5871 CCTTGAAATC
* *
5881 ATTGCTTTGACTAAAACTGATTTGGAAACATCTTTTGATTAAAACTCATCATTCTTTTGCCCACA
1 ATTGCTTTGACTAAAACTGATTTGGAAACATCTTTTGATTAAAACCCATCATTCCTTTGCCCACA
5946 CCTCGAAACA
66 CCTCGAAACA
* * * * * *
5956 ATTGCTTTGATTGAAACTGATTTTGAAACCTGTTTTGATTAAAACCCATCATTCCTTTGCTCACA
1 ATTGCTTTGACTAAAACTGATTTGGAAACATCTTTTGATTAAAACCCATCATTCCTTTGCCCACA
6021 GTCTAGATAA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
75 57 1.00
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.37
Consensus pattern (75 bp):
ATTGCTTTGACTAAAACTGATTTGGAAACATCTTTTGATTAAAACCCATCATTCCTTTGCCCACA
CCTCGAAACA
Found at i:6163 original size:3 final size:3
Alignment explanation
Indices: 6155--6202 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
6145 TTTTATCCCT
6155 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
6203 GTTAATGCAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:10486 original size:26 final size:25
Alignment explanation
Indices: 10442--10540 Score: 87
Period size: 26 Copynumber: 3.8 Consensus size: 25
10432 TACTCTTTTT
*
10442 TACCATTTTTATCCCTTTTTACTGAA
1 TACCATTTTTA-CCTTTTTTACTGAA
10468 TACCACTTTTTACCTTTTTTACTG-A
1 TACCA-TTTTTACCTTTTTTACTGAA
*
10493 TCACCATTTCTTACTCTTTATTACT-AA
1 T-ACCATTT-TTAC-CTTTTTTACTGAA
10520 TTACTC-TCTTTTACCTTTTTT
1 -TAC-CAT-TTTTACCTTTTTT
10541 TATCTTACTT
Statistics
Matches: 62, Mismatches: 3, Indels: 16
0.77 0.04 0.20
Matches are distributed among these distances:
25 5 0.08
26 30 0.48
27 23 0.37
28 4 0.06
ACGTcount: A:0.20, C:0.24, G:0.02, T:0.54
Consensus pattern (25 bp):
TACCATTTTTACCTTTTTTACTGAA
Found at i:10999 original size:72 final size:68
Alignment explanation
Indices: 10902--11068 Score: 199
Period size: 72 Copynumber: 2.4 Consensus size: 68
10892 ACTCTTTAAT
* * * * *
10902 TACTGATTAATCTCTTACCTTGACTCTTAATTATCAATTTACTGATTGCTTATCTTTTTACTTAA
1 TACTGATT-A-CTATTACCTGGACTCTTAATTATCAATTTACTAATT-CCTATCTTTTTACCTAA
*
10967 TTACTAATT
63 TTAC---TG
* *
10976 TACTGATTACTATTATCTGGACTCTTAATTATCAATTTACTAATTCCTATCTTTTTACCTGATTA
1 TACTGATTACTATTACCTGGACTCTTAATTATCAATTTACTAATTCCTATCTTTTTACCTAATTA
11041 CTG
66 CTG
*
11044 TACTGATTACTATTACCTTGACTCT
1 TACTGATTACTATTACCTGGACTCT
11069 GATTAATCTC
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
68 24 0.29
71 18 0.22
72 32 0.39
73 1 0.01
74 8 0.10
ACGTcount: A:0.26, C:0.19, G:0.07, T:0.48
Consensus pattern (68 bp):
TACTGATTACTATTACCTGGACTCTTAATTATCAATTTACTAATTCCTATCTTTTTACCTAATTA
CTG
Found at i:11114 original size:55 final size:55
Alignment explanation
Indices: 11044--11494 Score: 796
Period size: 55 Copynumber: 8.2 Consensus size: 55
11034 CTGATTACTG
*
11044 TACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTAATTACTGATT
1 TACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTCACTTAATTACTGATT
11099 TACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTCACTTAATTACTGATT
1 TACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTCACTTAATTACTGATT
11154 TACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTCACTTAATTACTGATT
1 TACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTCACTTAATTACTGATT
11209 TACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTCACTTAATTACTGATT
1 TACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTCACTTAATTACTGATT
*
11264 TACTGATTACAATTACCTTGACTCTGATTAATCTCTTTTCACTTAATTACTGATT
1 TACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTCACTTAATTACTGATT
11319 TACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTCACTTAATTACTGATT
1 TACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTCACTTAATTACTGATT
* * * * *
11374 TACTGATTACCATTACTTTGACTCCGATTAATCTCTTTTTACTTAATTACTAATT
1 TACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTCACTTAATTACTGATT
* *
11429 TACTAATTACCCT-TTACCTTGACTCTGATTAATCTCTTTTTACTTAATTACTGATT
1 TACTGATTA--CTATTACCTTGACTCTGATTAATCTCTTTTCACTTAATTACTGATT
11485 TACTGATTAC
1 TACTGATTAC
11495 CTTTTTACTT
Statistics
Matches: 380, Mismatches: 14, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
54 1 0.00
55 330 0.87
56 48 0.13
57 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.07, T:0.47
Consensus pattern (55 bp):
TACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTCACTTAATTACTGATT
Found at i:13095 original size:23 final size:23
Alignment explanation
Indices: 13065--13108 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
13055 CAGGAAAAAA
*
13065 CCCAAAACCCTAGTTGTTTTTGC
1 CCCAAAACCCTAGCTGTTTTTGC
13088 CCCAAAACCCTAGCTGTTTTT
1 CCCAAAACCCTAGCTGTTTTT
13109 TCTCTCCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.23, C:0.32, G:0.11, T:0.34
Consensus pattern (23 bp):
CCCAAAACCCTAGCTGTTTTTGC
Found at i:15088 original size:27 final size:27
Alignment explanation
Indices: 15058--15132 Score: 96
Period size: 27 Copynumber: 2.8 Consensus size: 27
15048 AAGTGAACTT
* *
15058 AAAATGACCAAAATACCCCTAAATGCA
1 AAAATGACCAAAATGCCCCTAAACGCA
* * **
15085 AAAATGACCAAAATGCCCGTGAACGTG
1 AAAATGACCAAAATGCCCCTAAACGCA
15112 AAAATGACCAAAATGCCCCTA
1 AAAATGACCAAAATGCCCCTA
15133 TGTGACCCTA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.47, C:0.25, G:0.13, T:0.15
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTAAACGCA
Found at i:25372 original size:3 final size:3
Alignment explanation
Indices: 25364--25403 Score: 71
Period size: 3 Copynumber: 13.0 Consensus size: 3
25354 AAAATATTAC
25364 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT
25404 GCATCATTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:27589 original size:16 final size:16
Alignment explanation
Indices: 27568--27602 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
27558 ATCGAGTTCA
*
27568 GTCATTTTGGGTTTGG
1 GTCATTTCGGGTTTGG
27584 GTCATTTCGGGTTTGG
1 GTCATTTCGGGTTTGG
27600 GTC
1 GTC
27603 GTTTACATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.06, C:0.11, G:0.37, T:0.46
Consensus pattern (16 bp):
GTCATTTCGGGTTTGG
Found at i:29330 original size:24 final size:25
Alignment explanation
Indices: 29286--29339 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
29276 TCCTATTAGT
** *
29286 AATTTT-GTTTATTTTCTTTTCTTG
1 AATTTTCGTTTATTTTAGTTTCGTG
29310 AATTTTCG-TTATTTTAGTTTCGTG
1 AATTTTCGTTTATTTTAGTTTCGTG
29334 -ATTTTC
1 AATTTTC
29340 TCTAGGGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 6 0.23
24 19 0.73
25 1 0.04
ACGTcount: A:0.15, C:0.09, G:0.11, T:0.65
Consensus pattern (25 bp):
AATTTTCGTTTATTTTAGTTTCGTG
Found at i:42703 original size:1 final size:1
Alignment explanation
Indices: 42697--42728 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
42687 CCAAGTGAAG
42697 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
42729 CCCTTCTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:54440 original size:16 final size:16
Alignment explanation
Indices: 54386--54441 Score: 67
Period size: 16 Copynumber: 3.5 Consensus size: 16
54376 TTTCGGATTT
54386 GGGTTCGGGTTTTTTC
1 GGGTTCGGGTTTTTTC
* *
54402 GGGTTTGAGTTTTTTC
1 GGGTTCGGGTTTTTTC
***
54418 ATATTCGGGTTTTTTC
1 GGGTTCGGGTTTTTTC
54434 GGGTTCGG
1 GGGTTCGG
54442 ATTCGGGCGG
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.05, C:0.11, G:0.34, T:0.50
Consensus pattern (16 bp):
GGGTTCGGGTTTTTTC
Done.