Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016377.1 Corchorus olitorius cultivar O-4 contig16410, 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: 68736
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:2922 original size:69 final size:72
Alignment explanation
Indices: 2771--2954 Score: 234
Period size: 69 Copynumber: 2.6 Consensus size: 72
2761 AAATGATGTC
* *
2771 GAGGAGGGACAACAGGGAGCATCCACAACTAATATTGAGGAGGAACAAGAGGGAACATCCACAAG
1 GAGGAGGGACAACAAGGAGCATCCACAACTAATATTGAGGAGGAACAAGAGGGAACATCCACAAC
*
2836 TAATATT
66 TAATACT
* * * * *
2843 GAGGATGGACAACATGGAACATCCAGAACTAATGA-TGA-G-GG-AC-AGAAGGGAGCATCCACA
1 GAGGAGGGACAACAAGGAGCATCCACAACTAAT-ATTGAGGAGGAACAAG-AGGGAACATCCACA
2903 ACTAATACT
64 ACTAATACT
*
2912 GAGGAGGGACAAGAAGGAGCATCCACAACTAATATTGAGGAGG
1 GAGGAGGGACAACAAGGAGCATCCACAACTAATATTGAGGAGG
2955 GACGACCGGG
Statistics
Matches: 95, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
68 3 0.03
69 53 0.56
70 3 0.03
71 3 0.03
72 32 0.34
73 1 0.01
ACGTcount: A:0.41, C:0.17, G:0.29, T:0.14
Consensus pattern (72 bp):
GAGGAGGGACAACAAGGAGCATCCACAACTAATATTGAGGAGGAACAAGAGGGAACATCCACAAC
TAATACT
Found at i:2955 original size:36 final size:36
Alignment explanation
Indices: 2771--2957 Score: 220
Period size: 36 Copynumber: 5.3 Consensus size: 36
2761 AAATGATGTC
* *
2771 GAGGAGGGACAACAGGGAGCATCCACAACTAATATT
1 GAGGAGGGACAAGAAGGAGCATCCACAACTAATATT
* * * *
2807 GAGGAGGAACAAGAGGGAACATCCACAAGTAATATT
1 GAGGAGGGACAAGAAGGAGCATCCACAACTAATATT
* * * * *
2843 GAGGATGGACAACATGGAACATCCAGAACT-A-A-T
1 GAGGAGGGACAAGAAGGAGCATCCACAACTAATATT
* *
2876 GATGAGGGAC-AGAAGGGAGCATCCACAACTAATACT
1 GAGGAGGGACAAGAA-GGAGCATCCACAACTAATATT
2912 GAGGAGGGACAAGAAGGAGCATCCACAACTAATATT
1 GAGGAGGGACAAGAAGGAGCATCCACAACTAATATT
2948 GAGGAGGGAC
1 GAGGAGGGAC
2958 GACCGGGACC
Statistics
Matches: 128, Mismatches: 18, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
32 2 0.02
33 22 0.17
34 2 0.02
35 2 0.02
36 96 0.75
37 4 0.03
ACGTcount: A:0.41, C:0.17, G:0.29, T:0.13
Consensus pattern (36 bp):
GAGGAGGGACAAGAAGGAGCATCCACAACTAATATT
Found at i:17344 original size:13 final size:12
Alignment explanation
Indices: 17335--17397 Score: 58
Period size: 12 Copynumber: 5.2 Consensus size: 12
17325 TAAAAAAATT
17335 AAAAAA-AAAAA
1 AAAAAACAAAAA
*
17346 CAAAAACAAAAA
1 AAAAAACAAAAA
17358 AACAAAACAAAACA
1 AA-AAAACAAAA-A
*
17372 AAACAAA-ACAAA
1 AAA-AAACAAAAA
*
17384 ACAAAACAAAAA
1 AAAAAACAAAAA
17396 AA
1 AA
17398 TGTGCAAACA
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
11 8 0.20
12 14 0.34
13 13 0.32
14 6 0.15
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAACAAAAA
Found at i:17345 original size:5 final size:5
Alignment explanation
Indices: 17337--17394 Score: 84
Period size: 5 Copynumber: 11.8 Consensus size: 5
17327 AAAAAATTAA
*
17337 AAAAA AAAAC AAAA- ACAAA- AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC
1 AAAAC AAAAC AAAAC A-AAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC
17386 AAAAC AAAA
1 AAAAC AAAA
17395 AAATGTGCAA
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
4 4 0.08
5 46 0.92
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:21655 original size:21 final size:20
Alignment explanation
Indices: 21621--21680 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
21611 ACTGGTCTAA
* *
21621 TAATCTCATTTGTACAATAGC
1 TAATATCATCTGTACAATA-C
21642 TAAT-TCGATCTGTACAATA-
1 TAATATC-ATCTGTACAATAC
*
21661 TAATATCATCTATACAATAC
1 TAATATCATCTGTACAATAC
21681 CTAAACAGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
19 15 0.44
20 4 0.12
21 15 0.44
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.37
Consensus pattern (20 bp):
TAATATCATCTGTACAATAC
Found at i:23210 original size:30 final size:30
Alignment explanation
Indices: 23111--23211 Score: 78
Period size: 30 Copynumber: 3.2 Consensus size: 30
23101 TGGGTTACTG
*
23111 TCACAGTAAATGGTTTGTTTTGAGTCACCA
1 TCACAGTAAATGATTTGTTTTGAGTCACCA
* * * * *
23141 TCACAATAACCTAATCTGTTTGTGATCTGTTCTA-GA
1 TCACAGTAA-ATGATTTGTTT-TGA---G-TC-ACCA
23177 TCACAGTAAATGATTTGTTTTGAGTCACCA
1 TCACAGTAAATGATTTGTTTTGAGTCACCA
23207 TCACA
1 TCACA
23212 ATAACCTAAT
Statistics
Matches: 52, Mismatches: 11, Indels: 16
0.66 0.14 0.20
Matches are distributed among these distances:
29 1 0.02
30 16 0.31
31 8 0.15
32 3 0.06
34 3 0.06
35 9 0.17
36 11 0.21
37 1 0.02
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.37
Consensus pattern (30 bp):
TCACAGTAAATGATTTGTTTTGAGTCACCA
Found at i:23963 original size:2 final size:2
Alignment explanation
Indices: 23948--23984 Score: 56
Period size: 2 Copynumber: 17.5 Consensus size: 2
23938 GTATTAAGCC
23948 TA TA TA TCA CTA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA T-A -TA TA TA TA TA TA TA TA TA TA TA TA TA T
23985 GCATTTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 30 0.91
3 2 0.06
4 1 0.03
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:38281 original size:17 final size:17
Alignment explanation
Indices: 38259--38293 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
38249 TCAAGGTGGG
38259 TGAGGAAACATAATTTT
1 TGAGGAAACATAATTTT
38276 TGAGGAAACATAATTTT
1 TGAGGAAACATAATTTT
38293 T
1 T
38294 TAGAAGAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.37
Consensus pattern (17 bp):
TGAGGAAACATAATTTT
Found at i:48951 original size:15 final size:15
Alignment explanation
Indices: 48931--48964 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
48921 TGTAAGCATT
48931 ATTTTTATTATTATTA
1 ATTTTTA-TATTATTA
48947 ATTTTTATATT-TTA
1 ATTTTTATATTATTA
48961 ATTT
1 ATTT
48965 GTTAAAGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 4 0.22
16 7 0.39
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
ATTTTTATATTATTA
Found at i:50466 original size:21 final size:21
Alignment explanation
Indices: 50441--50480 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
50431 TAAAGTGGGA
50441 AAAGTTGGGTCTGAACAAAAG
1 AAAGTTGGGTCTGAACAAAAG
* *
50462 AAAGTTGGGTTTGGACAAA
1 AAAGTTGGGTCTGAACAAA
50481 CAAAAACCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.07, G:0.30, T:0.23
Consensus pattern (21 bp):
AAAGTTGGGTCTGAACAAAAG
Found at i:59251 original size:29 final size:29
Alignment explanation
Indices: 59209--59266 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
59199 TTCGATTCTT
*
59209 TATGTCTTTCTTACAGTTTTGTTTTGAGG
1 TATGCCTTTCTTACAGTTTTGTTTTGAGG
59238 TATGCCTTTCTTACAGTTTTGTTTTGAGG
1 TATGCCTTTCTTACAGTTTTGTTTTGAGG
59267 AAGACATCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.14, C:0.12, G:0.21, T:0.53
Consensus pattern (29 bp):
TATGCCTTTCTTACAGTTTTGTTTTGAGG
Found at i:62620 original size:63 final size:63
Alignment explanation
Indices: 62521--62651 Score: 262
Period size: 63 Copynumber: 2.1 Consensus size: 63
62511 GAACTCCTCA
62521 ATAATGGAGAATGACAATTCTGTTGGAAAAGCTCAAACTAAAATAGTTACTGAATATTGTAAT
1 ATAATGGAGAATGACAATTCTGTTGGAAAAGCTCAAACTAAAATAGTTACTGAATATTGTAAT
62584 ATAATGGAGAATGACAATTCTGTTGGAAAAGCTCAAACTAAAATAGTTACTGAATATTGTAAT
1 ATAATGGAGAATGACAATTCTGTTGGAAAAGCTCAAACTAAAATAGTTACTGAATATTGTAAT
62647 ATAAT
1 ATAAT
62652 TGAGCAGACT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 68 1.00
ACGTcount: A:0.44, C:0.09, G:0.17, T:0.31
Consensus pattern (63 bp):
ATAATGGAGAATGACAATTCTGTTGGAAAAGCTCAAACTAAAATAGTTACTGAATATTGTAAT
Done.