Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018286.1 Corchorus olitorius cultivar O-4 contig18319, 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: 41166
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3304 original size:36 final size:36
Alignment explanation
Indices: 3257--3330 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
3247 AACGGTACAA
3257 AATCAACACTAATGAGCTAAATGGAGAAAATCAAGC
1 AATCAACACTAATGAGCTAAATGGAGAAAATCAAGC
3293 AATCAACACTAATGAGCTAAATGGAGAAAATCAAGC
1 AATCAACACTAATGAGCTAAATGGAGAAAATCAAGC
3329 AA
1 AA
3331 CGACACAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.51, C:0.16, G:0.16, T:0.16
Consensus pattern (36 bp):
AATCAACACTAATGAGCTAAATGGAGAAAATCAAGC
Found at i:8983 original size:21 final size:21
Alignment explanation
Indices: 8959--8998 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
8949 ATATACGGTT
*
8959 AATCAATCAATTTTTTTTGGC
1 AATCAATCAATTATTTTTGGC
8980 AATCAATCAATTATTTTTG
1 AATCAATCAATTATTTTTG
8999 AAATAGTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.47
Consensus pattern (21 bp):
AATCAATCAATTATTTTTGGC
Found at i:9286 original size:14 final size:14
Alignment explanation
Indices: 9242--9292 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
9232 TAAGAGGGAA
9242 AATTCATTAAAACT
1 AATTCATTAAAACT
*
9256 AATT--TTGAGAACAT
1 AATTCATT-AAAAC-T
9270 AATTCATTAAAACT
1 AATTCATTAAAACT
*
9284 AATTGATTA
1 AATTCATTA
9293 TAAATTAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
12 2 0.07
13 4 0.13
14 18 0.60
15 4 0.13
16 2 0.07
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.37
Consensus pattern (14 bp):
AATTCATTAAAACT
Found at i:10446 original size:15 final size:16
Alignment explanation
Indices: 10407--10447 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
10397 AACGAAACCA
10407 TTCTTTC-TTCCTTTC
1 TTCTTTCTTTCCTTTC
10422 TTCTTTCTTTCCTTT-
1 TTCTTTCTTTCCTTTC
*
10437 TTTTTTCTTTC
1 TTCTTTCTTTC
10448 TCTCTCTGGC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 17 0.71
16 7 0.29
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (16 bp):
TTCTTTCTTTCCTTTC
Found at i:11439 original size:29 final size:28
Alignment explanation
Indices: 11388--11442 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
11378 AACTTGTATG
* *
11388 ATTTTGACGTTTTGCCCCTTAAACTTTA
1 ATTTTGACATTTTACCCCTTAAACTTTA
*
11416 ATTTTGGACATTTTACCCTTTAAACTT
1 ATTTT-GACATTTTACCCCTTAAACTT
11443 GCAATTTGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 5 0.22
29 18 0.78
ACGTcount: A:0.24, C:0.20, G:0.09, T:0.47
Consensus pattern (28 bp):
ATTTTGACATTTTACCCCTTAAACTTTA
Found at i:11652 original size:28 final size:30
Alignment explanation
Indices: 11601--11658 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 30
11591 AATATGTTTT
11601 CAAATTACAAGTTTAGGGGGCAAAAAGTCA
1 CAAATTACAAGTTTAGGGGGCAAAAAGTCA
* *
11631 CAAATTA-AATTTTA-GGGGCAAAATGTCA
1 CAAATTACAAGTTTAGGGGGCAAAAAGTCA
11659 ATTTTAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 13 0.50
29 6 0.23
30 7 0.27
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.24
Consensus pattern (30 bp):
CAAATTACAAGTTTAGGGGGCAAAAAGTCA
Found at i:13421 original size:30 final size:31
Alignment explanation
Indices: 13385--13453 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
13375 GTGCAAATGG
*
13385 GTCCCTGAAGTGAACTT-AGTGAGTAATTGA
1 GTCCCTGAAATGAACTTAAGTGAGTAATTGA
* * * *
13415 GTCCCTGAAATGGAGTTAATTGAGTAATTGG
1 GTCCCTGAAATGAACTTAAGTGAGTAATTGA
13446 GTCCCTGA
1 GTCCCTGA
13454 CTCATTTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
30 14 0.42
31 19 0.58
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (31 bp):
GTCCCTGAAATGAACTTAAGTGAGTAATTGA
Found at i:13491 original size:21 final size:20
Alignment explanation
Indices: 13458--13498 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
13448 CCCTGACTCA
*
13458 TTTTTAAAAAAAAAATATAT
1 TTTTTAAAAAAAAAAAATAT
*
13478 TTTTTAAATCAAAAAAAATAT
1 TTTTTAAA-AAAAAAAAATAT
13499 GACGTGGCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
TTTTTAAAAAAAAAAAATAT
Found at i:13990 original size:25 final size:26
Alignment explanation
Indices: 13936--13990 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
13926 GTTCGCCTAT
*
13936 ATTT-ATTTTTTAAAATAAAATAATA
1 ATTTAATTTTTTAAAATAAAACAATA
13961 A-TTAATTTTTTAATAA-AAAACAA-A
1 ATTTAATTTTTTAA-AATAAAACAATA
13985 ATTTAA
1 ATTTAA
13991 ATATTAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
24 4 0.15
25 20 0.77
26 2 0.08
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (26 bp):
ATTTAATTTTTTAAAATAAAACAATA
Found at i:19976 original size:3 final size:3
Alignment explanation
Indices: 19968--20000 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
19958 CTTCCCTTTG
19968 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
20001 TTGTAATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:31196 original size:106 final size:106
Alignment explanation
Indices: 31011--31215 Score: 401
Period size: 106 Copynumber: 1.9 Consensus size: 106
31001 ATATAACCGG
31011 TAAAATGTGATTCAACGTCCAATTTGAAGTGCACTAATTCACCAAACCGAACTCGACCTAATCCG
1 TAAAATGTGATTCAACGTCCAATTTGAAGTGCACTAATTCACCAAACCGAACTCGACCTAATCCG
31076 ATTTTTAAAATAAAAGTAAACAATCTAAACAAGCCGATTTT
66 ATTTTTAAAATAAAAGTAAACAATCTAAACAAGCCGATTTT
*
31117 TAAAATGTGATTCAACGTCCAATTTGAAGTGCACTAATTCACCAAACCGAACTCGACCTAATTCG
1 TAAAATGTGATTCAACGTCCAATTTGAAGTGCACTAATTCACCAAACCGAACTCGACCTAATCCG
31182 ATTTTTAAAATAAAAGTAAACAATCTAAACAAGC
66 ATTTTTAAAATAAAAGTAAACAATCTAAACAAGC
31216 AGGTCGGCTT
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
106 98 1.00
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.27
Consensus pattern (106 bp):
TAAAATGTGATTCAACGTCCAATTTGAAGTGCACTAATTCACCAAACCGAACTCGACCTAATCCG
ATTTTTAAAATAAAAGTAAACAATCTAAACAAGCCGATTTT
Found at i:31438 original size:42 final size:44
Alignment explanation
Indices: 31391--31478 Score: 135
Period size: 45 Copynumber: 2.0 Consensus size: 44
31381 TTACCTAAAC
*
31391 TCTACT-C-CATCTCTAGGTAATTCATCAAAACAAAGCTAATAT
1 TCTACTCCACATCTCTAGATAATTCATCAAAACAAAGCTAATAT
*
31433 TCTACTCCTACATCTCTAGATAATTCATCAAAATAAAGCTAATAT
1 TCTACTCC-ACATCTCTAGATAATTCATCAAAACAAAGCTAATAT
31478 T
1 T
31479 AATTGTTGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
42 6 0.15
43 1 0.02
45 34 0.83
ACGTcount: A:0.39, C:0.23, G:0.06, T:0.33
Consensus pattern (44 bp):
TCTACTCCACATCTCTAGATAATTCATCAAAACAAAGCTAATAT
Done.