Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021056.1 Corchorus olitorius cultivar O-4 contig21089, 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: 12550
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Found at i:2100 original size:59 final size:58
Alignment explanation
Indices: 1989--2102 Score: 160
Period size: 59 Copynumber: 1.9 Consensus size: 58
1979 ATTAATCAAA
1989 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTCAGACCGAGACT
1 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTCAGACCGAGACT
* * *
2047 TATCGAGTGACATGTTTTTTTTATTAGATGCCT-AAAAAAGACGTTTT-AGGACCGAG
1 TATCAAGTGACATG--TTCTTTATTAGATGCATAAAAAAAGACGTTTTCA-GACCGAG
2103 GCATGATGCT
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
58 14 0.28
59 21 0.42
60 15 0.30
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.33
Consensus pattern (58 bp):
TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTCAGACCGAGACT
Found at i:4322 original size:203 final size:202
Alignment explanation
Indices: 3920--4331 Score: 763
Period size: 203 Copynumber: 2.0 Consensus size: 202
3910 GCTTAATAAT
*
3920 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGTTTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
*
3985 GATACAACACATTATTATTATATATAAAACTATACCAAAAAAAAAATTAGTTGAACATTAGTGGT
66 GATACAACACATTACTATTATATATAAAACTATACC--AAAAAAAATTAGTTGAACATTAGTGGT
4050 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGA
129 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGA
4115 TCCGATTTA
194 TCCGATTTA
4124 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
4189 GATACAACACATTACTATTATATATATAGAACTATACC-AAAAAAATTAGTTGAACATTAGTGGT
66 GATACAACACATTACTATTATATATA-A-AACTATACCAAAAAAAATTAGTTGAACATTAGTGGT
4253 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGA
129 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGA
4318 TCCGATTTA
194 TCCGATTTA
4327 TTTAT
1 TTTAT
4332 TATTAAGGAA
Statistics
Matches: 204, Mismatches: 2, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
203 105 0.51
204 89 0.44
205 1 0.00
206 9 0.04
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (202 bp):
TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
GATACAACACATTACTATTATATATAAAACTATACCAAAAAAAATTAGTTGAACATTAGTGGTTG
ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATC
CGATTTA
Found at i:4458 original size:25 final size:25
Alignment explanation
Indices: 4404--4450 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
4394 ACGTTTGCAC
4404 AAATACCTAAGAATTTGAATTAAAA
1 AAATACCTAAGAATTTGAATTAAAA
4429 AAATACCTAAGAATTT-AATTAA
1 AAATACCTAAGAATTTGAATTAA
4451 TGTAAATATT
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 (25 bp):
AAATACCTAAGAATTTGAATTAAAA
Found at i:4500 original size:39 final size:40
Alignment explanation
Indices: 4441--4521 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
4431 ATACCTAAGA
*
4441 ATTTAATTAATGTAAATATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAATATTTCAGTTATTATATATATTAC
* *
4480 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAATATTTCAGTTATTATATATATTAC
4520 AT
1 AT
4522 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:0.38, C:0.04, G:0.07, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATGTAAATATTTCAGTTATTATATATATTAC
Found at i:8551 original size:22 final size:22
Alignment explanation
Indices: 8519--8641 Score: 113
Period size: 22 Copynumber: 5.5 Consensus size: 22
8509 CTCCAATGTA
*
8519 AAAATATTGATAACCACATTTTG
1 AAAAT-TTGATAACCACATTATG
*
8542 AAAATTTGATAACCTCATTATG
1 AAAATTTGATAACCACATTATG
* *
8564 -AAATTTCGATAACCTCCTTATG
1 AAAATTT-GATAACCACATTATG
* *
8586 AAAATTTGATAAGCACACTATG
1 AAAATTTGATAACCACATTATG
* * * *
8608 AAATTTTGGTAACCATACTATG
1 AAAATTTGATAACCACATTATG
**
8630 AAGTTTTGATAA
1 AAAATTTGATAA
8642 ACTCAGTGTG
Statistics
Matches: 85, Mismatches: 13, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
21 6 0.07
22 68 0.80
23 11 0.13
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (22 bp):
AAAATTTGATAACCACATTATG
Found at i:8577 original size:44 final size:44
Alignment explanation
Indices: 8520--8663 Score: 144
Period size: 44 Copynumber: 3.3 Consensus size: 44
8510 TCCAATGTAA
* * * *
8520 AAATATTGATAACCACATTTTGAAAATTTGATAACCTCATTATG
1 AAATTTTGATAACCACATTATGAAAATTTGATAAACTCACTATG
* * * * *
8564 AAATTTCGATAACCTCCTTATGAAAATTTGATAAGCACACTATG
1 AAATTTTGATAACCACATTATGAAAATTTGATAAACTCACTATG
* * * ** * *
8608 AAATTTTGGTAACCATACTATGAAGTTTTGATAAACTCAGTGTG
1 AAATTTTGATAACCACATTATGAAAATTTGATAAACTCACTATG
8652 AAATTTTGATAA
1 AAATTTTGATAA
8664 TCTGCCTATA
Statistics
Matches: 79, Mismatches: 21, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
44 79 1.00
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.35
Consensus pattern (44 bp):
AAATTTTGATAACCACATTATGAAAATTTGATAAACTCACTATG
Found at i:8838 original size:22 final size:21
Alignment explanation
Indices: 8813--8887 Score: 89
Period size: 22 Copynumber: 3.4 Consensus size: 21
8803 CTCTATGTAT
8813 TTTTGATAACCTCACCATAAAA
1 TTTTGATAACCTC-CCATAAAA
*
8835 TTTTCATAACCTCCCTATAAAA
1 TTTTGATAACCTCCC-ATAAAA
*
8857 TTTTGTTAACCT-CCATAGGAAA
1 TTTTGATAACCTCCCATA--AAA
8879 TTTTGATAA
1 TTTTGATAA
8888 GCACAAATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
20 3 0.07
21 4 0.09
22 39 0.85
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.37
Consensus pattern (21 bp):
TTTTGATAACCTCCCATAAAA
Found at i:8952 original size:22 final size:22
Alignment explanation
Indices: 8910--9013 Score: 111
Period size: 22 Copynumber: 4.7 Consensus size: 22
8900 GTAACCTCCC
**
8910 TCTCTATGAAATTTTATTAACA
1 TCTCTATGAAATTTTGGTAACA
* *
8932 TCCCTAAGAAATTTTGGTAACA
1 TCTCTATGAAATTTTGGTAACA
* * *
8954 TTTTTATGAAATTTTGGTAACC
1 TCTCTATGAAATTTTGGTAACA
*
8976 TCTGTATGAAATTTTGGTAAC-
1 TCTCTATGAAATTTTGGTAACA
*
8997 TACACTATGAAATTTTG
1 T-CTCTATGAAATTTTG
9014 ATAATCTTTC
Statistics
Matches: 68, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
21 1 0.01
22 67 0.99
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (22 bp):
TCTCTATGAAATTTTGGTAACA
Found at i:9026 original size:22 final size:21
Alignment explanation
Indices: 8909--9037 Score: 105
Period size: 22 Copynumber: 5.9 Consensus size: 21
8899 GGTAACCTCC
**
8909 CTCTCTATGAAATTTTATTAA
1 CTCTCTATGAAATTTTGGTAA
* *
8930 CATCCCTAAGAAATTTTGGTAA
1 C-TCTCTATGAAATTTTGGTAA
* *
8952 CATTTTTATGAAATTTTGGTAA
1 C-TCTCTATGAAATTTTGGTAA
*
8974 CCTCTGTATGAAATTTTGGTAA
1 -CTCTCTATGAAATTTTGGTAA
* *
8996 CTACACTATGAAATTTTGATAA
1 CT-CTCTATGAAATTTTGGTAA
* **
9018 TCTTTCTATGTGATTTTGGT
1 -CTCTCTATGAAATTTTGGT
9038 TTGATTGTCA
Statistics
Matches: 86, Mismatches: 18, Indels: 7
0.77 0.16 0.06
Matches are distributed among these distances:
21 3 0.03
22 80 0.93
23 3 0.03
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.44
Consensus pattern (21 bp):
CTCTCTATGAAATTTTGGTAA
Done.