Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012841.1 Corchorus olitorius cultivar O-4 contig12874, 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: 26616
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--27 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
28 CAATGCCCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1741 original size:20 final size:20
Alignment explanation
Indices: 1716--1754 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1706 GACTATCTAC
1716 ATAAATCTAATAATAGATAG
1 ATAAATCTAATAATAGATAG
1736 ATAAATCTAATAATAGATA
1 ATAAATCTAATAATAGATA
1755 AAAGCTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.56, C:0.05, G:0.08, T:0.31
Consensus pattern (20 bp):
ATAAATCTAATAATAGATAG
Found at i:4422 original size:24 final size:24
Alignment explanation
Indices: 4395--4455 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
4385 TTTTTTTACC
* *
4395 TACCTATTTATCTATTTATCTCTA
1 TACCTATTTATCTACTTATCTATA
*
4419 TACCTCTTTATCTACTTATCTATA
1 TACCTATTTATCTACTTATCTATA
4443 TACCTATTTATCT
1 TACCTATTTATCT
4456 TTTTCTTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.25, C:0.23, G:0.00, T:0.52
Consensus pattern (24 bp):
TACCTATTTATCTACTTATCTATA
Found at i:4497 original size:16 final size:16
Alignment explanation
Indices: 4353--4511 Score: 69
Period size: 16 Copynumber: 10.1 Consensus size: 16
4343 TTTATTATAG
*
4353 TTATTTATCTA-CTAT
1 TTATTTATTTATCTAT
*
4368 GTATTTACTATTATCTAT
1 TTATTTA-T-TTATCTAT
* ** *
4386 TTTTTTACCTACCTAT
1 TTATTTATTTATCTAT
* *
4402 TTATCTATTTATCTCT
1 TTATTTATTTATCTAT
* ** * *
4418 ATACCTCTTTATCTAC
1 TTATTTATTTATCTAT
* * *
4434 TTATCTATATACCTAT
1 TTATTTATTTATCTAT
* *
4450 TTATCTT-TTTCTTTAT
1 TTAT-TTATTTATCTAT
*
4466 CTA-TTATTT-T-TAT
1 TTATTTATTTATCTAT
4479 TTATTT-TTCTATCTAT
1 TTATTTATT-TATCTAT
4495 TTATTTATTTATCTAT
1 TTATTTATTTATCTAT
4511 T
1 T
4512 GCGTTTTTTT
Statistics
Matches: 103, Mismatches: 31, Indels: 19
0.67 0.20 0.12
Matches are distributed among these distances:
13 7 0.07
14 6 0.06
15 10 0.10
16 66 0.64
17 5 0.05
18 9 0.09
ACGTcount: A:0.23, C:0.16, G:0.01, T:0.61
Consensus pattern (16 bp):
TTATTTATTTATCTAT
Found at i:14878 original size:54 final size:54
Alignment explanation
Indices: 14790--15258 Score: 453
Period size: 54 Copynumber: 8.7 Consensus size: 54
14780 TTTTGTAGAA
* * * *
14790 AGTTGATTCTCAAATGATCCAGTGCGGTCCTTCCAAGAAGTTTTTAATGATCAG
1 AGTTGATCCTCAGATGATCCAGTGCGATCATTCCAAGAAGTTTTTAATGATCAG
* * *
14844 AGTTGATCCTCTGATGATCCAGTGCGATTATTCCAAGAAG-TTTTGA-GATCAG
1 AGTTGATCCTCAGATGATCCAGTGCGATCATTCCAAGAAGTTTTTAATGATCAG
*
14896 AGTTGATCC-CTAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTTAGA-GATCAG
1 AGTTGATCCTC-AGATGATCCAGTGCGATCATTCCAAGAAGTTTTTA-ATGATCAG
** *
14950 AGTTGATTCCT-AGATGATCCAGTGC-AGTCA-TCACAAGAAGTTTCCAAGTGATTAG
1 AGTTGA-TCCTCAGATGATCCAGTGCGA-TCATTC-CAAGAAGTTTTTAA-TGATCAG
* * * * *
15005 AGTTAATCCCCAGATGATCCACTGC-AGTCATTTCAAGAAGTTTTCAATGATCAG
1 AGTTGATCCTCAGATGATCCAGTGCGA-TCATTCCAAGAAGTTTTTAATGATCAG
* * * *
15059 AGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAAAAAATTTTTAGA-GATCAG
1 AGTTGATCCTCAGATGATCCAGTGCGATCATTCCAAGAAGTTTTTA-ATGATCAG
* *
15113 AGTTGATCCTTAGATGATCCAGTGCGATCATTCCAAGAAGTTTTCAATGATCAG
1 AGTTGATCCTCAGATGATCCAGTGCGATCATTCCAAGAAGTTTTTAATGATCAG
* * * * *
15167 AGTTAAT-CTCCA-ATTGATACAATGC-AGTCA-TCCAAGAAGTTTTTGATGATTAG
1 AGTTGATCCT-CAGA-TGATCCAGTGCGA-TCATTCCAAGAAGTTTTTAATGATCAG
* * *
15220 AGTTGAT-CTTAAATTTGATCCAGTGCGGTCATTCCAAGA
1 AGTTGATCCTCAGA--TGATCCAGTGCGATCATTCCAAGA
15259 GAAGTTTCCG
Statistics
Matches: 348, Mismatches: 46, Indels: 41
0.80 0.11 0.09
Matches are distributed among these distances:
51 1 0.00
52 42 0.12
53 46 0.13
54 206 0.59
55 52 0.15
56 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (54 bp):
AGTTGATCCTCAGATGATCCAGTGCGATCATTCCAAGAAGTTTTTAATGATCAG
Found at i:15084 original size:163 final size:159
Alignment explanation
Indices: 14790--15258 Score: 565
Period size: 163 Copynumber: 2.9 Consensus size: 159
14780 TTTTGTAGAA
* * * * *
14790 AGTTGATT-CTCAAATGATCCAGTGCGGTCCTTCCAAGAAGTTTTTAATGATCAGAGTTGATCCT
1 AGTTGATTCCT-AGATGATCCAGTGC-GT-CATCCAAGAAGTTTTCAATGATCAGAGTTAATCCC
* * *
14854 CTGATGATCCAGTGC-GATTATTCCAAGAAGTTTTGA-GATCAGAGTTGATCCCTAGATGATCCA
63 CAGATGATCCAATGCAG-TCATTCCAAGAAGTTTTGATGATCAGAGTTGATCCCTAGATGATCCA
*
14917 GTGCGGTCATTCCAAGAAGTTTTTAGAGATCAG
127 GTGCGGTCATTCCAAGAAATTTTTAGAGATCAG
* *
14950 AGTTGATTCCTAGATGATCCAGTGCAGTCATCACAAGAAGTTTCCAAGTGATTAGAGTTAATCCC
1 AGTTGATTCCTAGATGATCCAGTGC-GTCATC-CAAGAAGTTTTCAA-TGATCAGAGTTAATCCC
* * * *
15015 CAGATGATCCACTGCAGTCATTTCAAGAAGTTTTCAATGATCAGAGTTGATCCCCAGATGATCCA
63 CAGATGATCCAATGCAGTCATTCCAAGAAGTTTT-GATGATCAGAGTTGATCCCTAGATGATCCA
*
15080 GTGCGGTCATTCCAAAAAATTTTTAGAGATCAG
127 GTGCGGTCATTCCAAGAAATTTTTAGAGATCAG
*
15113 AGTTGA-TCCTTAGATGATCCAGTGCGATCATTCCAAGAAGTTTTCAATGATCAGAGTTAATCTC
1 AGTTGATTCC-TAGATGATCCAGTGCG-TCA-TCCAAGAAGTTTTCAATGATCAGAGTTAATCCC
* * * *
15177 CA-ATTGATACAATGCAGTCA-TCCAAGAAGTTTTTGATGATTAGAGTTGAT-CTTAAATTTGAT
63 CAGA-TGATCCAATGCAGTCATTCCAAGAAG-TTTTGATGATCAGAGTTGATCCCTAGA--TGAT
15239 CCAGTGCGGTCATTCCAAGA
124 CCAGTGCGGTCATTCCAAGA
15259 GAAGTTTCCG
Statistics
Matches: 268, Mismatches: 28, Indels: 24
0.84 0.09 0.08
Matches are distributed among these distances:
159 3 0.01
160 38 0.14
161 67 0.25
162 64 0.24
163 94 0.35
164 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (159 bp):
AGTTGATTCCTAGATGATCCAGTGCGTCATCCAAGAAGTTTTCAATGATCAGAGTTAATCCCCAG
ATGATCCAATGCAGTCATTCCAAGAAGTTTTGATGATCAGAGTTGATCCCTAGATGATCCAGTGC
GGTCATTCCAAGAAATTTTTAGAGATCAG
Found at i:15303 original size:217 final size:215
Alignment explanation
Indices: 14800--15208 Score: 565
Period size: 217 Copynumber: 1.9 Consensus size: 215
14790 AGTTGATTCT
* * * * * **
14800 CAAATGATCCAGTGCGGTCCTTCCAAGAAGTTTTTAATGATCAGAGTTGATCCTCTGATGATCCA
1 CAAATGATCCACTGCAGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCCCAAATGATCCA
* * * *
14865 GTGCGATTATTCCAAGAAGTTTTGAGATCAGAGTTGATCCCTAGATGATCCAGTGCGGTCATTCC
66 GTGCGGTCATTCCAAAAAGTTTTGAGATCAGAGTTGATCCCTAGATGATCCAGTGCGATCATTCC
* * * *
14930 AAGAAGTTTTTAGAGATCAGAGTTGATTCCTAGATGATCCAGTGCAGTCATCACAAGAAGTTTCC
131 AAGAAGTTTTCAGAGATCAGAGTTAATTCCTAGATGATACAATGCAGTCATCACAAGAAGTTTCC
14995 AAGTGATTAGAGTTAATCCC
196 AAGTGATTAGAGTTAATCCC
* * *
15015 CAGATGATCCACTGCAGTCATTTCAAGAAGTTTTCAATGATCAGAGTTGATCCCCAGATGATCCA
1 CAAATGATCCACTGCAGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCCCAAATGATCCA
* *
15080 GTGCGGTCATTCCAAAAAATTTTTAGAGATCAGAGTTGATCCTTAGATGATCCAGTGCGATCATT
66 GTGCGGTCATTCC-AAAAAGTTTT-GAGATCAGAGTTGATCCCTAGATGATCCAGTGCGATCATT
15145 CCAAGAAGTTTTCA-ATGATCAGAGTTAATCTCC-A-ATTGATACAATGCAGTCATC-CAAGAAG
129 CCAAGAAGTTTTCAGA-GATCAGAGTTAAT-TCCTAGA-TGATACAATGCAGTCATCACAAGAAG
15206 TTT
191 TTT
15209 TTGATGATTA
Statistics
Matches: 171, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
215 68 0.40
216 20 0.12
217 80 0.47
218 3 0.02
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.30
Consensus pattern (215 bp):
CAAATGATCCACTGCAGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCCCAAATGATCCA
GTGCGGTCATTCCAAAAAGTTTTGAGATCAGAGTTGATCCCTAGATGATCCAGTGCGATCATTCC
AAGAAGTTTTCAGAGATCAGAGTTAATTCCTAGATGATACAATGCAGTCATCACAAGAAGTTTCC
AAGTGATTAGAGTTAATCCC
Found at i:16672 original size:14 final size:15
Alignment explanation
Indices: 16646--16805 Score: 70
Period size: 16 Copynumber: 10.9 Consensus size: 15
16636 TTATTATAGT
16646 TATTTATCTATTATC
1 TATTTATCTATTATC
16661 TATTTA-CTATTATC
1 TATTTATCTATTATC
* * ** *
16675 TATTTTTTTTACCCACC
1 TA-TTTATCTA-TTATC
16692 TATTTATCTATTTATC
1 TATTTATCTA-TTATC
* *
16708 TCTATACCTCT-TTATC
1 TATTTA--TCTATTATC
* *
16724 TACTTATCTATATACC
1 TATTTATCTAT-TATC
16740 TATTTATCT-TT-T-
1 TATTTATCTATTATC
*
16752 TCTTTATCTATTAT-
1 TATTTATCTATTATC
*
16766 T-TTTATTTATT-T-
1 TATTTATCTATTATC
* *
16778 T-TCTATCTATTTATT
1 TATTTATCTA-TTATC
16793 TATTTATCTATTA
1 TATTTATCTATTA
16806 CTTTTTTTAT
Statistics
Matches: 108, Mismatches: 24, Indels: 26
0.68 0.15 0.16
Matches are distributed among these distances:
12 16 0.15
13 13 0.12
14 17 0.16
15 15 0.14
16 40 0.37
17 4 0.04
18 3 0.03
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTTATCTATTATC
Found at i:16704 original size:8 final size:8
Alignment explanation
Indices: 16691--16804 Score: 76
Period size: 8 Copynumber: 14.6 Consensus size: 8
16681 TTTTACCCAC
16691 CTATTTAT
1 CTATTTAT
16699 CTATTTAT
1 CTATTTAT
* * *
16707 CTCTATAC
1 CTATTTAT
*
16715 CTCTTTAT
1 CTATTTAT
*
16723 CTACTTAT
1 CTATTTAT
* *
16731 CTATATAC
1 CTATTTAT
16739 CTATTTAT
1 CTATTTAT
16747 CT-TTT-T
1 CTATTTAT
16753 C--TTTAT
1 CTATTTAT
*
16759 CTATTATTT
1 CTATT-TAT
*
16768 TTATTTAT
1 CTATTTAT
*
16776 -TTTTCTAT
1 CTATT-TAT
16784 CTATTTAT
1 CTATTTAT
*
16792 TTATTTAT
1 CTATTTAT
16800 CTATT
1 CTATT
16805 ACTTTTTTTA
Statistics
Matches: 81, Mismatches: 19, Indels: 12
0.72 0.17 0.11
Matches are distributed among these distances:
5 3 0.04
6 4 0.05
7 6 0.07
8 59 0.73
9 9 0.11
ACGTcount: A:0.22, C:0.16, G:0.00, T:0.62
Consensus pattern (8 bp):
CTATTTAT
Found at i:16716 original size:24 final size:24
Alignment explanation
Indices: 16689--16748 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
16679 TTTTTTACCC
* *
16689 ACCTATTTATCTATTTATCTCTAT
1 ACCTATTTATCTACTTATCTATAT
*
16713 ACCTCTTTATCTACTTATCTATAT
1 ACCTATTTATCTACTTATCTATAT
16737 ACCTATTTATCT
1 ACCTATTTATCT
16749 TTTTCTTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.25, C:0.23, G:0.00, T:0.52
Consensus pattern (24 bp):
ACCTATTTATCTACTTATCTATAT
Found at i:16792 original size:20 final size:20
Alignment explanation
Indices: 16767--16818 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
16757 ATCTATTATT
16767 TTTATTTATTTTTCTATCTA-
1 TTTATTTATTTTTCTAT-TAC
*
16787 TTTATTTATTTATCTATTAC
1 TTTATTTATTTTTCTATTAC
*
16807 TTTTTTTATTTT
1 TTTATTTATTTT
16819 ATTTCAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 2 0.07
20 26 0.93
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTATTTATTTTTCTATTAC
Found at i:16804 original size:12 final size:12
Alignment explanation
Indices: 16740--16799 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
16730 TCTATATACC
*
16740 TATTTATCTTTT
1 TATTTATCTATT
*
16752 TCTTTATCTA-T
1 TATTTATCTATT
16763 TATTT-T-TATT
1 TATTTATCTATT
* *
16773 TATTTTTCTATC
1 TATTTATCTATT
*
16785 TATTTATTTATT
1 TATTTATCTATT
16797 TAT
1 TAT
16800 CTATTACTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
9 2 0.05
10 7 0.18
11 6 0.16
12 23 0.61
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (12 bp):
TATTTATCTATT
Found at i:16814 original size:16 final size:16
Alignment explanation
Indices: 16769--16815 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
16759 CTATTATTTT
*
16769 TATTTATTTTTCTATC
1 TATTTATTTTTTTATC
*
16785 TATTTATTTATTTATC
1 TATTTATTTTTTTATC
16801 TA-TTACTTTTTTTAT
1 TATTTA-TTTTTTTAT
16816 TTTATTTCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 3 0.11
16 24 0.89
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTTATTTTTTTATC
Found at i:21837 original size:29 final size:29
Alignment explanation
Indices: 21805--21882 Score: 120
Period size: 29 Copynumber: 2.7 Consensus size: 29
21795 TAGGGTCATC
* *
21805 CAGGGGAATTTTGGTCATTTTTGCATATT
1 CAGGGGAATTTTGGTCATTTTTCCACATT
*
21834 CAGGGGCATTTTGGTCATTTTTCCACATT
1 CAGGGGAATTTTGGTCATTTTTCCACATT
*
21863 CAGGGGTATTTTGGTCATTT
1 CAGGGGAATTTTGGTCATTT
21883 GTACTCCAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.18, C:0.14, G:0.24, T:0.44
Consensus pattern (29 bp):
CAGGGGAATTTTGGTCATTTTTCCACATT
Done.