Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018986.1 Corchorus olitorius cultivar O-4 contig19019, 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: 19986
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Found at i:1278 original size:37 final size:37
Alignment explanation
Indices: 1231--1313 Score: 134
Period size: 37 Copynumber: 2.3 Consensus size: 37
1221 TAAAGGAGCT
1231 AAAAAA-AAACTGGGCCTAAAATAGAAAGAGGTC-GA
1 AAAAAAGAAACTGGGCCTAAAATAGAAAGAGGTCAGA
*
1266 AAAAGAAGAAACTTGGCCTAAAATAGAAAGAGGTCAGA
1 AAAA-AAGAAACTGGGCCTAAAATAGAAAGAGGTCAGA
1304 AAAAAAGAAA
1 AAAAAAGAAA
1314 TAAATAAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
35 4 0.09
36 2 0.05
37 32 0.73
38 6 0.14
ACGTcount: A:0.58, C:0.10, G:0.22, T:0.11
Consensus pattern (37 bp):
AAAAAAGAAACTGGGCCTAAAATAGAAAGAGGTCAGA
Found at i:2203 original size:59 final size:58
Alignment explanation
Indices: 2134--2624 Score: 775
Period size: 59 Copynumber: 8.3 Consensus size: 58
2124 TTTCAAATCT
* *
2134 AATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTATTTTGTTTCTAA
1 AATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCCTATCTTGTTT-TAA
*
2193 AATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTAAAAATCCTATCTTGTTTTTAA
1 AATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCCTATCTTG-TTTTAA
* * *
2252 AATTCTGATCGAGGTCTCTGGTAGAGAGTTTTTAATTCAAAATCCTATTTTTTGTTTTAA
1 AATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCCTA--TCTTGTTTTAA
2312 AATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCCTATCTTGTTTTTAA
1 AATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCCTATCTTG-TTTTAA
* *
2371 AATCCTGAACGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCCTATTTTGTTTTAA
1 AATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCCTATCTTGTTTTAA
*
2429 AATCCTGATCGAGGTCTCTGGTAGAGAGTTTGCAATTCAAAATCCTATCTTGTTTTCAA
1 AATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCCTATCTTGTTTT-AA
* * *
2488 AATCCTGATCGAGGTCTCTGGTAGAAAGTTTTCAATTCAAAATTCTATCTTATTTTTAA
1 AATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCCTATCTT-GTTTTAA
* * *
2547 AATCCTGTTCGAGATCTCTGGTAGAGAGTTTTCAATTCAAAATCTTATCTTGTTTTAA
1 AATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCCTATCTTGTTTTAA
*
2605 AATCCTGGTCGAGGTCTCTG
1 AATCCTGATCGAGGTCTCTG
2625 ATTGAAGGTC
Statistics
Matches: 399, Mismatches: 27, Indels: 13
0.91 0.06 0.03
Matches are distributed among these distances:
58 87 0.22
59 250 0.63
60 58 0.15
61 4 0.01
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (58 bp):
AATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCCTATCTTGTTTTAA
Found at i:2483 original size:117 final size:117
Alignment explanation
Indices: 2134--2624 Score: 806
Period size: 117 Copynumber: 4.2 Consensus size: 117
2124 TTTCAAATCT
*
2134 AATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTATTTTGTTTCTAAAATCCT
1 AATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCCTATTTTGTTT-TAAAATCCT
*
2199 GATCGAGGTCTCTGGTAGAGAGTTTTCAATTAAAAATCCTATCTTGTTTTTAA
65 GATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCCTATCTTGTTTTTAA
* *
2252 AATTCTGATCGAGGTCTCTGGTAGAGAGTTTTTAATTCAAAATCCTATTTTTTGTTTTAAAATCC
1 AATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCCTA--TTTTGTTTTAAAATCC
2317 TGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCCTATCTTGTTTTTAA
64 TGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCCTATCTTGTTTTTAA
*
2371 AATCCTGAACGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCCTATTTTGTTTTAAAATCCTG
1 AATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCCTATTTTGTTTTAAAATCCTG
* *
2436 ATCGAGGTCTCTGGTAGAGAGTTTGCAATTCAAAATCCTATCTTGTTTTCAA
66 ATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCCTATCTTGTTTTTAA
* *
2488 AATCCTGATCGAGGTCTCTGGTAGAAAGTTTTCAATTCAAAATTCTATCTTAT-TTTTAAAATCC
1 AATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCCTAT-TT-TGTTTTAAAATCC
* * *
2552 TGTTCGAGATCTCTGGTAGAGAGTTTTCAATTCAAAATCTTATCTTG-TTTTAA
64 TGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCCTATCTTGTTTTTAA
*
2605 AATCCTGGTCGAGGTCTCTG
1 AATCCTGATCGAGGTCTCTG
2625 ATTGAAGGTC
Statistics
Matches: 351, Mismatches: 18, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
117 137 0.39
118 100 0.28
119 106 0.30
120 8 0.02
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (117 bp):
AATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCCTATTTTGTTTTAAAATCCTG
ATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCCTATCTTGTTTTTAA
Found at i:2947 original size:27 final size:27
Alignment explanation
Indices: 2869--2952 Score: 125
Period size: 28 Copynumber: 3.1 Consensus size: 27
2859 TATTTCTTAA
2869 TTGGTCATTTGCACTCTCAGGGGCATT
1 TTGGTCATTTGCACTCTCAGGGGCATT
*
2896 TTGGGTCATTTGCACTCTCATGGGCATT
1 TT-GGTCATTTGCACTCTCAGGGGCATT
*
2924 TTGGTCATTTGCA-TATTCAGGGGCATT
1 TTGGTCATTTGCACT-CTCAGGGGCATT
2951 TT
1 TT
2953 TGTCGTAACG
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
26 1 0.02
27 25 0.48
28 26 0.50
ACGTcount: A:0.15, C:0.19, G:0.25, T:0.40
Consensus pattern (27 bp):
TTGGTCATTTGCACTCTCAGGGGCATT
Found at i:11940 original size:4 final size:4
Alignment explanation
Indices: 11931--12157 Score: 64
Period size: 4 Copynumber: 57.5 Consensus size: 4
11921 AGATTTTTTG
* * * *
11931 TTAT TTAT TTA- TTAT TT-T TATTT TTAT TTAT TAAT TTAA CTA- TTAT
1 TTAT TTAT TTAT TTAT TTAT T-TAT TTAT TTAT TTAT TTAT TTAT TTAT
* * * * *
11977 CTAT TTAT TTA- CTAT TTAT CTT-T TTAT TTAT TAAT TTAG CTA- TTAT
1 TTAT TTAT TTAT TTAT TTAT -TTAT TTAT TTAT TTAT TTAT TTAT TTAT
* * * * * * * *
12023 CTAT TTAT TTACT ATTAT CTAC TT-T TT-T TTAC TTAC CTAT TTAT CTAA
1 TTAT TTAT TTA-T -TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
* * * * * * *
12071 TTAT CTAT ATAC CTAT TTAT CTT-T TTAT TTAT CTAT TATTT TTAC TTAT
1 TTAT TTAT TTAT TTAT TTAT -TTAT TTAT TTAT TTAT T-TAT TTAT TTAT
*
12120 TT-T TCTAT TTAT TTAT CTA- TTACT TT-T TTATT TTAT TT
1 TTAT T-TAT TTAT TTAT TTAT TTA-T TTAT TTA-T TTAT TT
12158 TAATATTTTT
Statistics
Matches: 160, Mismatches: 43, Indels: 40
0.66 0.18 0.16
Matches are distributed among these distances:
3 27 0.17
4 111 0.69
5 19 0.12
6 3 0.02
ACGTcount: A:0.25, C:0.10, G:0.00, T:0.65
Consensus pattern (4 bp):
TTAT
Found at i:11976 original size:19 final size:18
Alignment explanation
Indices: 11935--11992 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 18
11925 TTTTTGTTAT
* * *
11935 TTATTTATTATTTTTATTT
1 TTATTTATTA-ATTTACTA
11954 TTATTTATTAATTTAACTA
1 TTATTTATTAATTT-ACTA
* *
11973 TTATCTATTTATTTACTA
1 TTATTTATTAATTTACTA
11991 TT
1 TT
11993 TATCTTTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
18 9 0.27
19 24 0.73
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (18 bp):
TTATTTATTAATTTACTA
Found at i:11983 original size:27 final size:27
Alignment explanation
Indices: 11953--12033 Score: 79
Period size: 27 Copynumber: 3.3 Consensus size: 27
11943 TATTTTTATT
11953 TTTATTTATTAATTTAACTATTATCTA
1 TTTATTTATTAATTTAACTATTATCTA
* *
11980 TTTA--T-TT-A-CT-A-T-TTATCTT
1 TTTATTTATTAATTTAACTATTATCTA
*
11999 TTTATTTATTAATTTAGCTATTATCTA
1 TTTATTTATTAATTTAACTATTATCTA
12026 TTTATTTA
1 TTTATTTA
12034 CTATTATCTA
Statistics
Matches: 41, Mismatches: 5, Indels: 16
0.66 0.08 0.26
Matches are distributed among these distances:
19 10 0.24
20 1 0.02
21 2 0.05
22 3 0.07
23 2 0.05
24 3 0.07
25 1 0.02
26 1 0.02
27 18 0.44
ACGTcount: A:0.28, C:0.07, G:0.01, T:0.63
Consensus pattern (27 bp):
TTTATTTATTAATTTAACTATTATCTA
Found at i:12001 original size:46 final size:46
Alignment explanation
Indices: 11932--12102 Score: 181
Period size: 46 Copynumber: 3.7 Consensus size: 46
11922 GATTTTTTGT
* * *
11932 TATTTATTTATTATTTTTATTTTTATTTATTAATTTAACTATTATC
1 TATTTATTTACTATTTATCTTTTTATTTATTAATTTAACTATTATC
*
11978 TATTTATTTACTATTTATCTTTTTATTTATTAATTTAGCTATTATC
1 TATTTATTTACTATTTATCTTTTTATTTATTAATTTAACTATTATC
* *
12024 TATTTATTTACTA-TTATCTACTTTTTTTTACTTACCTATTTATCTAATTATC
1 TATTTATTTACTATTTATCT--TTTTATTTA-TTA---ATTTAACT-ATTATC
12076 TA--TA--TACCTATTTATCTTTTTATTTAT
1 TATTTATTTA-CTATTTATCTTTTTATTTAT
12103 CTATTATTTT
Statistics
Matches: 109, Mismatches: 7, Indels: 17
0.82 0.05 0.13
Matches are distributed among these distances:
45 6 0.06
46 55 0.50
47 9 0.08
48 13 0.12
49 3 0.03
50 8 0.07
51 7 0.06
52 8 0.07
ACGTcount: A:0.26, C:0.10, G:0.01, T:0.63
Consensus pattern (46 bp):
TATTTATTTACTATTTATCTTTTTATTTATTAATTTAACTATTATC
Found at i:15072 original size:26 final size:25
Alignment explanation
Indices: 15021--15079 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
15011 CAAAAGAAGG
*
15021 AGAAAAAAAAGAAAAGAATTGAAAA
1 AGAAAAAAAAGAAAAGAACTGAAAA
*
15046 AGAAAAAGAAAG-AAAGAAGCTGGAAA
1 AGAAAAA-AAAGAAAAGAA-CTGAAAA
*
15072 AGTAAAAA
1 AGAAAAAA
15080 TGGAGGAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 14 0.48
26 15 0.52
ACGTcount: A:0.71, C:0.02, G:0.20, T:0.07
Consensus pattern (25 bp):
AGAAAAAAAAGAAAAGAACTGAAAA
Found at i:16385 original size:22 final size:22
Alignment explanation
Indices: 16360--16407 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
16350 AGACAACAGC
* *
16360 CAAGAATGGGTAAA-GAAGAAGT
1 CAAGAAAGGATAAATGAAG-AGT
16382 CAAGAAAGGATAAATGAAGAGT
1 CAAGAAAGGATAAATGAAGAGT
16404 CAAG
1 CAAG
16408 TACAGATCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.52, C:0.06, G:0.29, T:0.12
Consensus pattern (22 bp):
CAAGAAAGGATAAATGAAGAGT
Found at i:16520 original size:54 final size:54
Alignment explanation
Indices: 16437--16578 Score: 137
Period size: 54 Copynumber: 2.6 Consensus size: 54
16427 CGATATGTCT
* * *
16437 TTCATAGAAGTTTTCAGAA-ATCTA-AGTTGATCTTCAGATGACCCCGTGCGGTCT-
1 TTCAAAGAAGTTTTCA-AAGATC-AGAGTTGATCTCCAGATAACCCCGTGCGGT-TG
* * * * *
16491 TTCAAAGAAGTTTTTAAAGATCAGGGTTGATCCCCAGATAATCCGGTGCGGTTG
1 TTCAAAGAAGTTTTCAAAGATCAGAGTTGATCTCCAGATAACCCCGTGCGGTTG
* * *
16545 TTCCAAGAAGTTTTCGATGATCAGAGTTGATCTC
1 TTCAAAGAAGTTTTCAAAGATCAGAGTTGATCTC
16579 ATTTCAAGAA
Statistics
Matches: 71, Mismatches: 14, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
53 4 0.06
54 67 0.94
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (54 bp):
TTCAAAGAAGTTTTCAAAGATCAGAGTTGATCTCCAGATAACCCCGTGCGGTTG
Found at i:16701 original size:37 final size:36
Alignment explanation
Indices: 16548--17047 Score: 574
Period size: 35 Copynumber: 13.9 Consensus size: 36
16538 GCGGTTGTTC
**
16548 CAAGAAG-TTTTCGATGATCAGAGTTGATCTCATTT
1 CAAGAAGTTTTTTTATGATCAGAGTTGATCTCATTT
*
16583 CAAGAAG--TTTTTATGATCAGAGTTGTTCTCATTT
1 CAAGAAGTTTTTTTATGATCAGAGTTGATCTCATTT
* *
16617 CAAGAAGTTTTTTTATGATCAGAGTTAATCTCGTTT
1 CAAGAAGTTTTTTTATGATCAGAGTTGATCTCATTT
*
16653 CAAGAAGTTTTTTTATGATCAGAGTTGATCTCGTTT
1 CAAGAAGTTTTTTTATGATCAGAGTTGATCTCATTT
16689 CAAGAAGTTTTTTTTATGATCAGAGTTGATCTCATTT
1 CAAGAAG-TTTTTTTATGATCAGAGTTGATCTCATTT
*
16726 CAAGAAGTTTTTTTAATGATTC-GAGTTGATCTCGTTT
1 CAAGAAGTTTTTTT-ATGA-TCAGAGTTGATCTCATTT
*** *
16763 CAAGAAG-TTTTCGGTGATCAGAGTTGATCTCCTTT
1 CAAGAAGTTTTTTTATGATCAGAGTTGATCTCATTT
* * *
16798 CAGGAAG-TTTTTTGTGATCAGAGTTCATCTCATTTT
1 CAAGAAGTTTTTTTATGATCAGAGTTGATCTCA-TTT
* *
16834 CAAGACG--TTTTTATGGTCAGAGTTGATCTCATTT
1 CAAGAAGTTTTTTTATGATCAGAGTTGATCTCATTT
** *
16868 CAAGAAG-TTTTCGATGATCAGAGTTGATCTCGTTT
1 CAAGAAGTTTTTTTATGATCAGAGTTGATCTCATTT
**
16903 CAA-AGAGTTTTCGT-TGATCAGAGTTGATCTCATTT
1 CAAGA-AGTTTTTTTATGATCAGAGTTGATCTCATTT
* *
16938 CAAGAAGTTTTTTATATGGTCAGAGTTGATCTCCTTT
1 CAAGAAGTTTTTT-TATGATCAGAGTTGATCTCATTT
16975 CAAGAAGTTTTTTTTCTTTTTATGATCAGAGTTGATCTCATTT
1 CAAGAAG------TT-TTTTTATGATCAGAGTTGATCTCATTT
**
17018 CAAGAAG-TTTTCGATGATCAGAGTTGATCT
1 CAAGAAGTTTTTTTATGATCAGAGTTGATCT
17048 TCATATTGAT
Statistics
Matches: 405, Mismatches: 40, Indels: 40
0.84 0.08 0.08
Matches are distributed among these distances:
34 43 0.11
35 149 0.37
36 91 0.22
37 86 0.21
38 2 0.00
43 30 0.07
44 4 0.01
ACGTcount: A:0.25, C:0.13, G:0.19, T:0.42
Consensus pattern (36 bp):
CAAGAAGTTTTTTTATGATCAGAGTTGATCTCATTT
Found at i:17831 original size:16 final size:15
Alignment explanation
Indices: 17793--17834 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
17783 ACAGAGGTTG
17793 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
17808 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
17823 ACTAGAAAACAA
1 AC-AGAAAACAA
17835 AACAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Done.