Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014805.1 Corchorus olitorius cultivar O-4 contig14838, 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: 18754
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1706 original size:205 final size:202
Alignment explanation
Indices: 1329--1740 Score: 704
Period size: 205 Copynumber: 2.0 Consensus size: 202
1319 CTTAATAACT
*
1329 TTTATCAATGGTGAATGTTATTAATTTTTTTGAGTCTAAGATTACTAACAAAGTTGTAGTGAATA
1 TTTATCAATGGTGAATGTTATTAATTTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATA
*
1394 AGATACAACACATTATTATTATATATATAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTT
66 AGATACAACACATTATTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTT
*
1459 GATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGAT
131 GATTTATTAAATTAAATTAGATCAATGGCAAACAAAATTTCAAAATTATAAAAGATATT-AAGAT
1524 CCGATTTA
195 CCGATTTA
*
1532 TTTATCAATGGTGAATGTTATTAA-TTTTTTAAGTCTAAGATTACTAACAAAGTTTTAGTGAATA
1 TTTATCAATGGTGAATGTTATTAATTTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATA
*
1596 AGATACAACACATTACTATTATATATATATAAAACTATACC-AAAAAAATTAGTTGAACATTAGT
66 AGATACAACACA-T--TATTAT-TATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGT
1660 GGTTGATTTATTAAATTAAATTAGATCAATGGCAAA-AAAGATTTCAAAATTATAAAAGATATTA
127 GGTTGATTTATTAAATTAAATTAGATCAATGGCAAACAAA-ATTTCAAAATTATAAAAGATATTA
1724 AGATCCGATTTA
191 AGATCCGATTTA
1736 TTTAT
1 TTTAT
1741 TATTAAGGAA
Statistics
Matches: 199, Mismatches: 5, Indels: 9
0.93 0.02 0.04
Matches are distributed among these distances:
202 50 0.25
203 25 0.13
204 21 0.11
205 86 0.43
206 17 0.09
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.37
Consensus pattern (202 bp):
TTTATCAATGGTGAATGTTATTAATTTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATA
AGATACAACACATTATTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTT
GATTTATTAAATTAAATTAGATCAATGGCAAACAAAATTTCAAAATTATAAAAGATATTAAGATC
CGATTTA
Found at i:1892 original size:39 final size:40
Alignment explanation
Indices: 1849--1929 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
1839 ATACCTAAGA
* *
1849 ATTTAATTAATTTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
*
1888 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
1928 AT
1 AT
1930 AGGAATTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Found at i:2404 original size:119 final size:116
Alignment explanation
Indices: 2175--2414 Score: 345
Period size: 119 Copynumber: 2.0 Consensus size: 116
2165 CTTTATAGAG
* * ** *
2175 ATAGGAGAAAAATTACTCTTATTTTTATGGATCCAACCGGTTGAACCAATTTGGACATTGAATCG
1 ATAGTAGAAAAATTACTCATATTTTTATGGATCCAACCGGTTGAACCAAAATGGACATAGAATCG
* * *
2240 ATCCGACTCTGTCATTAACTCATATAATGTTATTATCAGGATTTGAATCGT
66 ATCCGAATCTGACATTAACTCATATAATGTTATTATCAGGATTTGAATCAT
* *
2291 ATAGTAGAAAAATTACTCATATTTTTATGGATCCAACCGGTTGAATCGATGAAATGGATATAGAA
1 ATAGTAGAAAAATTACTCATATTTTTATGGATCCAACCGGTTGAA-CCA--AAATGGACATAGAA
* *
2356 TCGATCTGAATCTGACATTAACTCATATAATGTTATTATCAGGGTTTGAATCAT
63 TCGATCCGAATCTGACATTAACTCATATAATGTTATTATCAGGATTTGAATCAT
2410 ATAGT
1 ATAGT
2415 TGAGTGACTT
Statistics
Matches: 109, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
116 43 0.39
117 2 0.02
119 64 0.59
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (116 bp):
ATAGTAGAAAAATTACTCATATTTTTATGGATCCAACCGGTTGAACCAAAATGGACATAGAATCG
ATCCGAATCTGACATTAACTCATATAATGTTATTATCAGGATTTGAATCAT
Found at i:9588 original size:40 final size:40
Alignment explanation
Indices: 9533--9614 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
9523 GCTACATGAT
9533 TAGCTACATTACCGAAATGTTAATCTATGAGCCAATAAAC
1 TAGCTACATTACCGAAATGTTAATCTATGAGCCAATAAAC
9573 TAGCTACATTACCGAAATGTTAATCTATGAGCCAATAAAC
1 TAGCTACATTACCGAAATGTTAATCTATGAGCCAATAAAC
9613 TA
1 TA
9615 ACCCCTTCCC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.28
Consensus pattern (40 bp):
TAGCTACATTACCGAAATGTTAATCTATGAGCCAATAAAC
Found at i:9716 original size:24 final size:24
Alignment explanation
Indices: 9684--9740 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
9674 ACCCACAAAC
*
9684 CAAA-TAAACAAATAAACAAATTA
1 CAAATTAAACAAACAAACAAATTA
**
9707 CAAATTAAACTCACAAACAAATTA
1 CAAATTAAACAAACAAACAAATTA
*
9731 TAAATTAAAC
1 CAAATTAAAC
9741 TCACATTTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 4 0.14
24 25 0.86
ACGTcount: A:0.63, C:0.16, G:0.00, T:0.21
Consensus pattern (24 bp):
CAAATTAAACAAACAAACAAATTA
Found at i:9741 original size:24 final size:24
Alignment explanation
Indices: 9697--9745 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
9687 ATAAACAAAT
9697 AAACAAATTACAAATTAAACTCAC
1 AAACAAATTACAAATTAAACTCAC
*
9721 AAACAAATTATAAATTAAACTCAC
1 AAACAAATTACAAATTAAACTCAC
9745 A
1 A
9746 TTTTGTGAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.59, C:0.18, G:0.00, T:0.22
Consensus pattern (24 bp):
AAACAAATTACAAATTAAACTCAC
Done.