Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014821.1 Corchorus olitorius cultivar O-4 contig14854, 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: 29329
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Found at i:599 original size:203 final size:206
Alignment explanation
Indices: 217--604 Score: 701
Period size: 206 Copynumber: 1.9 Consensus size: 206
207 GCTTAATAAC
*
217 TTTATGAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
* *
282 GATACAACACATTATTATTATTATATATATAACTATACCAAAAAAAAGTAGTTGAAACATTAGTG
66 GATACAACACATTACTATTATTATATATAGAACTATACCAAAAAAAAGTAGTTGAAACATTAGTG
*
347 GTTGGTTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAT
131 GTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAT
412 GATCCGATTTA
196 GATCCGATTTA
*
423 TTTATCAATGGTGAATGTTATTAATTTTTTATGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
*
488 GATACAACACATTACTATTA-TATATATAGAACTATACC-AAAAAAATTAGTTG-AACATTAGTG
66 GATACAACACATTACTATTATTATATATAGAACTATACCAAAAAAAAGTAGTTGAAACATTAGTG
550 GTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAA
131 GTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAA
605 TTAAAGATAT
Statistics
Matches: 176, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
203 64 0.36
204 13 0.07
205 17 0.10
206 82 0.47
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.37
Consensus pattern (206 bp):
TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
GATACAACACATTACTATTATTATATATAGAACTATACCAAAAAAAAGTAGTTGAAACATTAGTG
GTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAT
GATCCGATTTA
Found at i:736 original size:25 final size:24
Alignment explanation
Indices: 702--748 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
692 ACGTTTGCAC
*
702 AAATACCTAAGAGTTTGAATTAAAA
1 AAATACCTAAGAATTT-AATTAAAA
727 AAATACCTAAGAATTTAATTAA
1 AAATACCTAAGAATTTAATTAA
749 TGTAAGTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.30
Consensus pattern (24 bp):
AAATACCTAAGAATTTAATTAAAA
Found at i:794 original size:39 final size:40
Alignment explanation
Indices: 739--819 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
729 ATACCTAAGA
*
739 ATTTAATTAATGTAAGTATTTCAGTTATTA-TAATATTAC
1 ATTTAATTAATATAAGTATTTCAGTTATTATTAATATTAC
* *
778 ATTTAATTAATATAAGTATTTTAGTTATTATTTATATTAC
1 ATTTAATTAATATAAGTATTTCAGTTATTATTAATATTAC
818 AT
1 AT
820 CAGAATTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 28 0.74
40 10 0.26
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (40 bp):
ATTTAATTAATATAAGTATTTCAGTTATTATTAATATTAC
Found at i:1356 original size:56 final size:56
Alignment explanation
Indices: 1270--1383 Score: 219
Period size: 56 Copynumber: 2.0 Consensus size: 56
1260 TATCTGTTTC
*
1270 CTTTCATACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATT
1326 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATT
1382 CT
1 CT
1384 ACAAAATAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.33, C:0.25, G:0.02, T:0.40
Consensus pattern (56 bp):
CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATT
Found at i:1552 original size:42 final size:42
Alignment explanation
Indices: 1493--1573 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
1483 TAAGGATCAG
1493 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
*
1535 GATTTGAGTTGAGTATTTCTTAATTTACAGAGAATTTTC
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC
1574 AAGACTTAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.47
Consensus pattern (42 bp):
GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
Found at i:17483 original size:11 final size:11
Alignment explanation
Indices: 17467--17500 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
17457 TTTACTATGC
17467 AAAAACAGGGG
1 AAAAACAGGGG
*
17478 AAAAACAGAGG
1 AAAAACAGGGG
17489 -AAAACAGGGG
1 AAAAACAGGGG
17499 AA
1 AA
17501 GGGAAGGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.59, C:0.09, G:0.32, T:0.00
Consensus pattern (11 bp):
AAAAACAGGGG
Found at i:21084 original size:35 final size:36
Alignment explanation
Indices: 21024--21092 Score: 97
Period size: 35 Copynumber: 1.9 Consensus size: 36
21014 GAGATTTTGG
*
21024 AGAAATATGATAATCAAACCTACAAAA-ATGTAATA
1 AGAAATATGATAACCAAACCTACAAAAGATGTAATA
*
21059 AGAAATATGATAACCAAA-ATCACAAAAGATGTAA
1 AGAAATATGATAACCAAACCT-ACAAAAGATGTAA
21093 GGTTATTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
34 1 0.03
35 23 0.77
36 6 0.20
ACGTcount: A:0.58, C:0.12, G:0.10, T:0.20
Consensus pattern (36 bp):
AGAAATATGATAACCAAACCTACAAAAGATGTAATA
Found at i:22467 original size:58 final size:58
Alignment explanation
Indices: 22366--22478 Score: 167
Period size: 58 Copynumber: 1.9 Consensus size: 58
22356 AGCATCATGC
*
22366 CTCGGTCCTAAAACGTCTTTTTTAGACATCTAATAAAAAAACATGTCACTCGATAAGT
1 CTCGGTCCGAAAACGTCTTTTTTAGACATCTAATAAAAAAACATGTCACTCGATAAGT
* *
22424 CTCGGTCCGAAAACGTCTTTTCTTATG-CATCTAAT-AAAGAACATGTCACTTGATA
1 CTCGGTCCGAAAACGTCTTTT-TTA-GACATCTAATAAAAAAACATGTCACTCGATA
22479 TTTGATTAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
58 38 0.76
59 11 0.22
60 1 0.02
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (58 bp):
CTCGGTCCGAAAACGTCTTTTTTAGACATCTAATAAAAAAACATGTCACTCGATAAGT
Found at i:24726 original size:13 final size:13
Alignment explanation
Indices: 24697--24735 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
24687 ATAGTAATAG
24697 TAATAGTAATAATAA
1 TAATA-TAAT-ATAA
24712 TAATATAATATAA
1 TAATATAATATAA
*
24725 TAATATGATAT
1 TAATATAATAT
24736 TACTTGGTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 14 0.61
14 4 0.17
15 5 0.22
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (13 bp):
TAATATAATATAA
Done.