Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019900.1 Corchorus olitorius cultivar O-4 contig19933, 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: 27965
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:6255 original size:12 final size:13
Alignment explanation
Indices: 6237--6266 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
6227 GTTTTCTTTA
6237 ATTTTCTTGATTG
1 ATTTTCTTGATTG
6250 -TTTTCTTGATTG
1 ATTTTCTTGATTG
6262 ATTTT
1 ATTTT
6267 AATTACTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.13, C:0.07, G:0.13, T:0.67
Consensus pattern (13 bp):
ATTTTCTTGATTG
Found at i:13113 original size:18 final size:19
Alignment explanation
Indices: 13090--13126 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
13080 CACCCTAGCC
13090 CTAAAACTAGAAGA-AAAA
1 CTAAAACTAGAAGAGAAAA
13108 CTAAAACTAGAAGAGAAAA
1 CTAAAACTAGAAGAGAAAA
13127 AGAAGAAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.65, C:0.11, G:0.14, T:0.11
Consensus pattern (19 bp):
CTAAAACTAGAAGAGAAAA
Found at i:18027 original size:22 final size:24
Alignment explanation
Indices: 17989--18033 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
17979 TTTTTTAAAA
17989 ACGCAGAAACAAATTTT-TTTTTG
1 ACGCAGAAACAAATTTTGTTTTTG
18012 ACGCA-AAA-AAACTTTTGTTTTT
1 ACGCAGAAACAAA-TTTTGTTTTT
18034 CAAAAACGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 3 0.15
22 7 0.35
23 10 0.50
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (24 bp):
ACGCAGAAACAAATTTTGTTTTTG
Found at i:18075 original size:29 final size:28
Alignment explanation
Indices: 18043--18138 Score: 90
Period size: 27 Copynumber: 3.4 Consensus size: 28
18033 TCAAAAACGC
*
18043 AAAACACAAAATTTTTTTTTTTAAGATTA
1 AAAACGCAAAA-TTTTTTTTTTAAGATTA
** *
18072 AAAACGCAAAACAAATTTTTATTATAGA--A
1 AAAACGC-AAA-ATTTTTTTTTTA-AGATTA
*
18101 AAAACGCAGAATTTTTTTTTTAA-ATTA
1 AAAACGCAAAATTTTTTTTTTAAGATTA
18128 AAAACGCAAAA
1 AAAACGCAAAA
18139 GAAATTTTTT
Statistics
Matches: 53, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
25 1 0.02
26 1 0.02
27 20 0.38
28 2 0.04
29 14 0.26
30 11 0.21
31 4 0.08
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.34
Consensus pattern (28 bp):
AAAACGCAAAATTTTTTTTTTAAGATTA
Found at i:18146 original size:27 final size:27
Alignment explanation
Indices: 18059--18148 Score: 72
Period size: 27 Copynumber: 3.2 Consensus size: 27
18049 CAAAATTTTT
18059 TTTTTTAAGATTAAAAACGCAAAACAAA
1 TTTTTTAA-ATTAAAAACGCAAAACAAA
* ** * ****
18087 TTTTTATTATAGAAAAAACGCAGAATTTT
1 -TTTT-TTAAATTAAAAACGCAAAACAAA
*
18116 TTTTTTAAATTAAAAACGCAAAAGAAA
1 TTTTTTAAATTAAAAACGCAAAACAAA
18143 TTTTTT
1 TTTTTT
18149 TTTTGTAGGG
Statistics
Matches: 44, Mismatches: 16, Indels: 4
0.69 0.25 0.06
Matches are distributed among these distances:
27 21 0.48
28 4 0.09
29 16 0.36
30 3 0.07
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.38
Consensus pattern (27 bp):
TTTTTTAAATTAAAAACGCAAAACAAA
Found at i:18151 original size:30 final size:30
Alignment explanation
Indices: 18056--18151 Score: 103
Period size: 30 Copynumber: 3.3 Consensus size: 30
18046 ACACAAAATT
*
18056 TTTTTTTTTAAGATTAAAAACGCAAAACAAA
1 TTTTTTTTTAA-ATTAAAAACGCAAAAGAAA
* * *
18087 TTTTTATTATAGA--AAAAACGC---AGAAT
1 TTTTT-TTTTAAATTAAAAACGCAAAAGAAA
18113 TTTTTTTTTAAATTAAAAACGCAAAAGAAA
1 TTTTTTTTTAAATTAAAAACGCAAAAGAAA
18143 TTTTTTTTT
1 TTTTTTTTT
18152 TGTAGGGAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
25 5 0.10
26 8 0.15
27 8 0.15
29 8 0.15
30 13 0.25
31 6 0.12
32 4 0.08
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (30 bp):
TTTTTTTTTAAATTAAAAACGCAAAAGAAA
Found at i:19859 original size:11 final size:12
Alignment explanation
Indices: 19831--19874 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
19821 CAATTCTTCC
* *
19831 TCTTGAAATAAT
1 TCTTCAAATAAA
19843 TCTTCAAA-AAA
1 TCTTCAAATAAA
*
19854 TCTTCAAATAAG
1 TCTTCAAATAAA
19866 TCTTCAAAT
1 TCTTCAAAT
19875 GGTCTTCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 10 0.36
12 18 0.64
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (12 bp):
TCTTCAAATAAA
Found at i:19879 original size:11 final size:12
Alignment explanation
Indices: 19831--19884 Score: 58
Period size: 11 Copynumber: 4.7 Consensus size: 12
19821 CAATTCTTCC
* *
19831 TCTTGAAATAAT
1 TCTTCAAATAAG
*
19843 TCTTCAAA-AAA
1 TCTTCAAATAAG
19854 TCTTCAAATAAG
1 TCTTCAAATAAG
*
19866 TCTTCAAAT-GG
1 TCTTCAAATAAG
19877 TCTTCAAA
1 TCTTCAAA
19885 CACGAACTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
11 19 0.51
12 18 0.49
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.35
Consensus pattern (12 bp):
TCTTCAAATAAG
Found at i:22534 original size:25 final size:26
Alignment explanation
Indices: 22506--22562 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 26
22496 TAACTCTCAC
* * *
22506 TCAATCTCTCAACCCAATCTAA-CAA
1 TCAATCTCTAAACCAAACCTAATCAA
22531 TCAATC-CTAAACCAAACCTAATCAA
1 TCAATCTCTAAACCAAACCTAATCAA
22556 TCAATCT
1 TCAATCT
22563 TGAGCACTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.42, C:0.33, G:0.00, T:0.25
Consensus pattern (26 bp):
TCAATCTCTAAACCAAACCTAATCAA
Found at i:22596 original size:25 final size:25
Alignment explanation
Indices: 22562--22610 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
22552 TCAATCAATC
*
22562 TTGAGCACTCTCGCTCGGTCTCTAT
1 TTGAGCACTCTCGCTCAGTCTCTAT
22587 TTGAGCACTCTCGCTCAGTCTCTA
1 TTGAGCACTCTCGCTCAGTCTCTA
22611 CAAACTAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.14, C:0.33, G:0.18, T:0.35
Consensus pattern (25 bp):
TTGAGCACTCTCGCTCAGTCTCTAT
Found at i:27045 original size:11 final size:11
Alignment explanation
Indices: 27029--27065 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
27019 TTGCCATAAA
27029 AGCCCGGCCCG
1 AGCCCGGCCCG
27040 AGCCCGGCCCG
1 AGCCCGGCCCG
*
27051 -GCCCGACCCG
1 AGCCCGGCCCG
27061 A-CCCG
1 AGCCCG
27066 TATACTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 13 0.54
11 11 0.46
ACGTcount: A:0.11, C:0.57, G:0.32, T:0.00
Consensus pattern (11 bp):
AGCCCGGCCCG
Found at i:27051 original size:16 final size:15
Alignment explanation
Indices: 27030--27065 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
27020 TGCCATAAAA
27030 GCCCGGCCCGAGCCCG
1 GCCCGGCCCGA-CCCG
27046 GCCCGGCCCGACCCG
1 GCCCGGCCCGACCCG
*
27061 ACCCG
1 GCCCG
27066 TATACTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.08, C:0.58, G:0.33, T:0.00
Consensus pattern (15 bp):
GCCCGGCCCGACCCG
Done.