Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017234.1 Corchorus olitorius cultivar O-4 contig17267, 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: 13472
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Found at i:4820 original size:18 final size:18
Alignment explanation
Indices: 4792--4826 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
4782 TGTTTAAATA
4792 AATTGAAAATTAAATTAAT
1 AATTGAAAATT-AATTAAT
4811 AATT-AAAATTAATTAA
1 AATTGAAAATTAATTAA
4827 CACCATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 6 0.38
19 4 0.25
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (18 bp):
AATTGAAAATTAATTAAT
Found at i:5562 original size:77 final size:78
Alignment explanation
Indices: 5471--5630 Score: 259
Period size: 77 Copynumber: 2.1 Consensus size: 78
5461 GTTTTCTAGT
* * * *
5471 TAAAATAGTTAAATGGTAAACTGAAATAGTTATAAAGATGTTAAATTTAATTAAATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTAAATTTAATTAAATAAAAATAGA
*
5536 G-TTTTAGTTGAG
66 GTTTTTAATTGAG
*
5548 TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTAGATTTAATTAAATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTAAATTTAATTAAATAAAAATAGA
5613 GTTTTTAATTGAG
66 GTTTTTAATTGAG
5626 TAAAA
1 TAAAA
5631 CTATAAATTT
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
77 61 0.80
78 15 0.20
ACGTcount: A:0.51, C:0.01, G:0.14, T:0.34
Consensus pattern (78 bp):
TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTAAATTTAATTAAATAAAAATAGA
GTTTTTAATTGAG
Found at i:6369 original size:15 final size:14
Alignment explanation
Indices: 6337--6395 Score: 50
Period size: 15 Copynumber: 4.1 Consensus size: 14
6327 GTTTTTTAAA
* *
6337 TTAAGTCCTGGAAAT
1 TTAAGTACT-GAATT
6352 TTAAGTACTGAATCT
1 TTAAGTACTGAAT-T
6367 TTATAGCTACTGAA-T
1 TTA-AG-TACTGAATT
6382 TTAA-TACTGAATT
1 TTAAGTACTGAATT
6395 T
1 T
6396 ATGGTGAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
12 7 0.18
13 2 0.05
14 4 0.11
15 16 0.42
16 2 0.05
17 7 0.18
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.41
Consensus pattern (14 bp):
TTAAGTACTGAATT
Found at i:10689 original size:58 final size:58
Alignment explanation
Indices: 10599--10708 Score: 177
Period size: 58 Copynumber: 1.9 Consensus size: 58
10589 TCAAATATCA
*
10599 AGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTCGGACCGAGGCTTATTG
1 AGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCGAGGCTTATTG
* *
10657 AGTGACATGTTTTTTGATTAGATGCCT-AAAAAAGACGTTTTAGGACCGAGGC
1 AGTGACATGTTCTTT-ATTAGATGCATAAAAAAAGACGTTTTAGGACCGAGGC
10709 ATGATGCTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
58 38 0.79
59 10 0.21
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.32
Consensus pattern (58 bp):
AGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCGAGGCTTATTG
Found at i:12003 original size:36 final size:36
Alignment explanation
Indices: 11962--12031 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
11952 TTCAATAACC
* *
11962 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
11998 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
12032 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:12872 original size:197 final size:196
Alignment explanation
Indices: 12517--12920 Score: 661
Period size: 195 Copynumber: 2.0 Consensus size: 196
12507 GCTTAATAAC
*
12517 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATTAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
* *
12582 GATACAACACATTATTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTG
66 GATACAACACATTACTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGATTG
12647 ATTAATTAAATTAAATTAGATCAATGT-C-AAA-CAAAATTATAAAAGATATTAAAGATCCGATT
131 ATTAATTAAATTAAATTAGATCAATGTACAAAATCAAAATTATAAAAGATATT-AAGATCCGATT
12709 TA
195 TA
12711 TTTATTAATGGTGAATGTTATTAATTTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATA
1 TTTATTAATGGTGAATGTTATTAA-TTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATA
*
12776 AGATACAACACATTACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGA
65 AGATACAACACATTACTATTATATATA-A-AACTATACCAAAAAAAAGTAGTTGAACATTAGTGA
* *
12841 TTGGTTTATTAAATTAAATTAGATCAATGTCAACAAAATTTCAAAATTATAAAAGATATTAAGAT
128 TTGATTAATTAAATTAAATTAGATCAATGT--ACAAAA--TCAAAATTATAAAAGATATTAAGAT
12906 CCGATTTA
189 CCGATTTA
12914 TTTATTA
1 TTTATTA
12921 TTAAGGAAAC
Statistics
Matches: 194, Mismatches: 6, Indels: 11
0.92 0.03 0.05
Matches are distributed among these distances:
194 23 0.12
195 66 0.34
196 1 0.01
197 61 0.31
200 1 0.01
201 3 0.02
203 20 0.10
204 19 0.10
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (196 bp):
TTTATTAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
GATACAACACATTACTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGATTG
ATTAATTAAATTAAATTAGATCAATGTACAAAATCAAAATTATAAAAGATATTAAGATCCGATTT
A
Found at i:13022 original size:25 final size:24
Alignment explanation
Indices: 12988--13034 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
12978 ACGTTTGCAC
12988 AAATACCTAAGAATTTGAATTAAAA
1 AAATACCTAAGAATTT-AATTAAAA
13013 AAATACCTAAGAATTTAATTAA
1 AAATACCTAAGAATTTAATTAA
13035 TGTAAGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (24 bp):
AAATACCTAAGAATTTAATTAAAA
Done.