Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014164.1 Corchorus olitorius cultivar O-4 contig14197, 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: 34459
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:59 original size:39 final size:39
Alignment explanation
Indices: 5--409 Score: 693
Period size: 39 Copynumber: 10.4 Consensus size: 39
1 AGAT
*
5 AGGCCATCTTTTCAGCATTTATCAAAGTTGGTTGGAGAC
1 AGGCCATCTTTTCAGCATTTATCAAAGTTGGTTGGAAAC
* *
44 AGGCCATCTCTTCAGCATTTATCAAAGTTGGTTGGACAC
1 AGGCCATCTTTTCAGCATTTATCAAAGTTGGTTGGAAAC
*
83 AGGCCATCTTTTCAGCATTTATCAAAGTTGGTTGGAAAT
1 AGGCCATCTTTTCAGCATTTATCAAAGTTGGTTGGAAAC
*
122 AGGCCATCTTTTCAGCATTTATCAAAGTTGGTTGGAAAT
1 AGGCCATCTTTTCAGCATTTATCAAAGTTGGTTGGAAAC
161 AGGCCATCTTTTCAGCATTTATCAAAGTTGGTTGGAAAC
1 AGGCCATCTTTTCAGCATTTATCAAAGTTGGTTGGAAAC
200 AGGCCATCTTTTCAGCATTTATCAAAGTTGGTTGGAAAC
1 AGGCCATCTTTTCAGCATTTATCAAAGTTGGTTGGAAAC
239 AGGCCATCTTTTCAGCATTTATCAAAGTTGGTTGGAAAC
1 AGGCCATCTTTTCAGCATTTATCAAAGTTGGTTGGAAAC
278 AGGCCATCTTTTCAGCATTTATCAAAGTTGGTTGGAAAC
1 AGGCCATCTTTTCAGCATTTATCAAAGTTGGTTGGAAAC
* **
317 AGGCCAACTTTTCAGCATTTATCAAAGTTGACTGGAAAC
1 AGGCCATCTTTTCAGCATTTATCAAAGTTGGTTGGAAAC
* **
356 AGGTCATCTTTTCAGCATTTATCAAAGTTGACTGGAAAC
1 AGGCCATCTTTTCAGCATTTATCAAAGTTGGTTGGAAAC
* *
395 AGGTCAACTTTTCAG
1 AGGCCATCTTTTCAG
410 TTTTATGTTG
Statistics
Matches: 354, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 354 1.00
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (39 bp):
AGGCCATCTTTTCAGCATTTATCAAAGTTGGTTGGAAAC
Found at i:663 original size:46 final size:46
Alignment explanation
Indices: 607--723 Score: 139
Period size: 45 Copynumber: 2.5 Consensus size: 46
597 TCCATTTTAA
*
607 TAAAGCCCATTTCCTCATTAGTTTCATTCAAAGTCCATTACCATTT
1 TAAAGCCCATTTCCTTATTAGTTTCATTCAAAGTCCATTACCATTT
* * * * **
653 TAGAGCCCATTCCCTTATTTAG--TAATTCAAAGTCCATTTCTTTTT
1 TAAAGCCCATTTCCTTA-TTAGTTTCATTCAAAGTCCATTACCATTT
698 TAAAGACCCATTTCCTTATTAGTTTC
1 TAAAG-CCCATTTCCTTATTAGTTTC
724 TCAAAATGTT
Statistics
Matches: 57, Mismatches: 10, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
45 27 0.47
46 25 0.44
47 5 0.09
ACGTcount: A:0.26, C:0.24, G:0.08, T:0.42
Consensus pattern (46 bp):
TAAAGCCCATTTCCTTATTAGTTTCATTCAAAGTCCATTACCATTT
Found at i:789 original size:13 final size:15
Alignment explanation
Indices: 761--793 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
751 GGTCTTCTCC
761 CTTTTTTCCTTCTTT
1 CTTTTTTCCTTCTTT
776 CTTTTTT-CTT-TTT
1 CTTTTTTCCTTCTTT
789 CTTTT
1 CTTTT
794 CTTTTGGGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.44
14 3 0.17
15 7 0.39
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
CTTTTTTCCTTCTTT
Found at i:4502 original size:34 final size:34
Alignment explanation
Indices: 4460--4537 Score: 129
Period size: 34 Copynumber: 2.3 Consensus size: 34
4450 TTTTATTGGA
**
4460 AAAGTTCCCACCAGTTTTAAGTTTTGTAATCGGG
1 AAAGTTCCCACCAGTTTTAAGTTTTCAAATCGGG
*
4494 AAAGTTCCCACCGGTTTTAAGTTTTCAAATCGGG
1 AAAGTTCCCACCAGTTTTAAGTTTTCAAATCGGG
4528 AAAGTTCCCA
1 AAAGTTCCCA
4538 TTCAATTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (34 bp):
AAAGTTCCCACCAGTTTTAAGTTTTCAAATCGGG
Found at i:7590 original size:47 final size:47
Alignment explanation
Indices: 7539--8057 Score: 738
Period size: 47 Copynumber: 11.0 Consensus size: 47
7529 TTACTGTTTA
* *
7539 CTTCTCCTTTTACTATTTAGTTTAATTACACAGAATTAAACTAACCT
1 CTTCTTCTTTTACTATTTAGTTTAATTACTCAGAATTAAACTAACCT
*
7586 CTTCTTCTTTTCCTATTTAGTTTAATTACTCAGAATTAAACTAACCT
1 CTTCTTCTTTTACTATTTAGTTTAATTACTCAGAATTAAACTAACCT
*
7633 CTTCTTCTTTTCCTATTTAGTTTAATTACTCAGAATTAAACTAACCT
1 CTTCTTCTTTTACTATTTAGTTTAATTACTCAGAATTAAACTAACCT
** *
7680 CTTCTTCTTTTACTGCTTAGTTTAATTAC-CTAGAATTAAACTAATCT
1 CTTCTTCTTTTACTATTTAGTTTAATTACTC-AGAATTAAACTAACCT
* * *
7727 CTTCTTCTTTTCCTATTTAGTTTAATTACTTAGAATTAAACTAATCT
1 CTTCTTCTTTTACTATTTAGTTTAATTACTCAGAATTAAACTAACCT
* * *
7774 CTTCCTCTTCTACTATTTAGTTTAATTACTCAGAATTAAACTAATCT
1 CTTCTTCTTTTACTATTTAGTTTAATTACTCAGAATTAAACTAACCT
* * *
7821 CTTCCTCTTTTACTACTTAGTTTAATTACCCAGAATTAAACTAACCT
1 CTTCTTCTTTTACTATTTAGTTTAATTACTCAGAATTAAACTAACCT
* *
7868 CTTCTTCTTTTACTCTTTAGTTTAATTAC-CTAGAATTAAACTAATCT
1 CTTCTTCTTTTACTATTTAGTTTAATTACTC-AGAATTAAACTAACCT
* * * *
7915 CTTCCTCTTTTACTACTTAGTTTAATTACCCAGAATTGAACTAACCT
1 CTTCTTCTTTTACTATTTAGTTTAATTACTCAGAATTAAACTAACCT
* * *
7962 CTTCTTTTTTTACTCTTTAGTTTAATTAC-CTAGAATTAAACTAATCT
1 CTTCTTCTTTTACTATTTAGTTTAATTACTC-AGAATTAAACTAACCT
* * *
8009 CTTCCTCTTTTACTACTTAGTTTAATTACCCAGAATTAAACTAACCT
1 CTTCTTCTTTTACTATTTAGTTTAATTACTCAGAATTAAACTAACCT
8056 CT
1 CT
8058 GTTTTACTTC
Statistics
Matches: 427, Mismatches: 39, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
46 3 0.01
47 422 0.99
48 2 0.00
ACGTcount: A:0.29, C:0.21, G:0.05, T:0.45
Consensus pattern (47 bp):
CTTCTTCTTTTACTATTTAGTTTAATTACTCAGAATTAAACTAACCT
Found at i:8144 original size:22 final size:23
Alignment explanation
Indices: 8104--8146 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
8094 TACTCCTCTA
*
8104 ATTACTCATTTCTTTTACTTCTG
1 ATTACTCATTTCTTCTACTTCTG
8127 ATTACTC-TTTCTTCTACTTC
1 ATTACTCATTTCTTCTACTTC
8147 CTAGCTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.16, C:0.26, G:0.02, T:0.56
Consensus pattern (23 bp):
ATTACTCATTTCTTCTACTTCTG
Found at i:16699 original size:21 final size:21
Alignment explanation
Indices: 16675--16725 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
16665 GAAAGGAACG
16675 AGAGAAAAAAGAAGAAGAAAA
1 AGAGAAAAAAGAAGAAGAAAA
** * * *
16696 AGAGTTATAAGAAGAATAAGA
1 AGAGAAAAAAGAAGAAGAAAA
16717 AGAGAAAAA
1 AGAGAAAAA
16726 TGTCGAAAGA
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.69, C:0.00, G:0.24, T:0.08
Consensus pattern (21 bp):
AGAGAAAAAAGAAGAAGAAAA
Found at i:22927 original size:2 final size:2
Alignment explanation
Indices: 22920--22950 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
22910 TTATTTGTCC
*
22920 TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
22951 TTGTCCTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:24275 original size:2 final size:2
Alignment explanation
Indices: 24270--24306 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
24260 CTCTCTAGTT
24270 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
24307 AAACATCCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:27364 original size:5 final size:5
Alignment explanation
Indices: 27354--27381 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
27344 CCTTTTAATT
27354 TTTCC TTTCC TTTCC TTTCC TTTCC TTT
1 TTTCC TTTCC TTTCC TTTCC TTTCC TTT
27382 TGTGGGGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTCC
Found at i:30970 original size:14 final size:14
Alignment explanation
Indices: 30951--30978 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
30941 GATCTCTGAT
30951 GCAAAAAATAAGAA
1 GCAAAAAATAAGAA
30965 GCAAAAAATAAGAA
1 GCAAAAAATAAGAA
30979 TAAGATTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.07, G:0.14, T:0.07
Consensus pattern (14 bp):
GCAAAAAATAAGAA
Found at i:32956 original size:36 final size:36
Alignment explanation
Indices: 32902--32971 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
32892 TTCAATAACC
* *
32902 TTACATCTTCTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTCTGTAATTTTGATTATCATATTTCTTA
* *
32938 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTCTGTAATTTTGATTATCATATTTCT
32972 CCAAAATCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.21, C:0.11, G:0.09, T:0.59
Consensus pattern (36 bp):
TTACATCTTCTGTAATTTTGATTATCATATTTCTTA
Found at i:33834 original size:205 final size:199
Alignment explanation
Indices: 33471--33879 Score: 710
Period size: 205 Copynumber: 2.0 Consensus size: 199
33461 GCTTAATAAC
*
33471 TTTATCAATGGTGAATGTTATAATTTTTAATTCTAAGATTACTAACAAAGTTGTAGTGAATAAGA
1 TTTATCAATGGTGAATGTTATAATTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGA
* * * *
33536 TATAACACATTATTATTATATAAAAAATTATACCAAAAAAAAGTATTTGAACATTAGTGGTTGAT
66 TACAACACATTACTATTATATAAAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTGAT
33601 TTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCCG
131 TTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT-AAGATCCG
33666 ATTTA
195 ATTTA
33671 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTA-TAA-TTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
*
33736 GATACAACACATTACTATTATATAATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGG
64 GATACAACACATTACTATTATATAA-A-A-AACTATACCAAAAAAAAGTAGTTGAACATTAGTGG
33801 TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGA
126 TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGA
33866 TCCGATTTA
191 TCCGATTTA
33875 TTTAT
1 TTTAT
33880 TATTAAGGAA
Statistics
Matches: 198, Mismatches: 6, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
200 20 0.10
201 3 0.02
202 62 0.31
203 1 0.01
204 19 0.10
205 93 0.47
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (199 bp):
TTTATCAATGGTGAATGTTATAATTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGA
TACAACACATTACTATTATATAAAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTGAT
TTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCCGA
TTTA
Found at i:33985 original size:25 final size:24
Alignment explanation
Indices: 33951--33997 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
33941 ACGTCTGCAC
33951 AAATACCTAAGAATTTGAATTAAAA
1 AAATACCTAAGAATTT-AATTAAAA
33976 AAATACCTAAGAATTTAATTAA
1 AAATACCTAAGAATTTAATTAA
33998 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
Found at i:34042 original size:39 final size:40
Alignment explanation
Indices: 33988--34068 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
33978 ATACCTAAGA
* *
33988 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTCACTTATTATATATATTAC
*
34027 ATTTAATTAATGTAAGTATTTTACTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCACTTATTATATATATTAC
34067 AT
1 AT
34069 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:0.05, G:0.07, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCACTTATTATATATATTAC
Done.