Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019932.1 Corchorus olitorius cultivar O-4 contig19965, 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: 33224
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:692 original size:179 final size:178
Alignment explanation
Indices: 422--760 Score: 506
Period size: 179 Copynumber: 1.9 Consensus size: 178
412 TCAATTAAGG
*
422 TGATTTAAGTCTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
1 TGATTCAAGTCTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
* * * * *
487 AATTTAATGTTTCAAGTATCAAAAATGTTTTCGAAA-AATTTGTTGTTTCGTTTAACGAGAAATA
66 AATTTAATGTTTCAAGTATAAAAAATG-CTTCCAAAGAATTAGTTGTTTCGGTTAAC-AGAAATA
*
551 GACGGT-TCACTTAATATTATATAACTTT-TGCTCCAGATATCTGATTGAGA
129 GACGGTCT-ACTTAATATTACATAA-TTTGTGCTCCAGATATCTGATTGAGA
* * * *
601 TGATTCAAGTGTCTCTTGAAAGGTTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
1 TGATTCAAGTCTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
666 AATTTAATG-TTCAAGGTATAAAAAATGCTTCCAAAGAATTAGTTGTTTCGGTTAACAGAAATAG
66 AATTTAATGTTTCAA-GTATAAAAAATGCTTCCAAAGAATTAGTTGTTTCGGTTAACAGAAATAG
730 ACGGTCTACTTAATATTACATAATTTGTGCT
130 ACGGTCTACTTAATATTACATAATTTGTGCT
761 TATGGTGGAA
Statistics
Matches: 145, Mismatches: 11, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
177 3 0.02
178 43 0.30
179 99 0.68
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.36
Consensus pattern (178 bp):
TGATTCAAGTCTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
AATTTAATGTTTCAAGTATAAAAAATGCTTCCAAAGAATTAGTTGTTTCGGTTAACAGAAATAGA
CGGTCTACTTAATATTACATAATTTGTGCTCCAGATATCTGATTGAGA
Found at i:1185 original size:2 final size:2
Alignment explanation
Indices: 1180--1217 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1170 AAGGGGGTGC
1180 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1218 GTACTTGAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3365 original size:2 final size:2
Alignment explanation
Indices: 3358--3384 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3348 CTAAGCACGC
3358 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
3385 TTGATTACTG
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:3630 original size:36 final size:36
Alignment explanation
Indices: 3589--3660 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
3579 GTAAGGAAAA
3589 TTCCATTGAACTTTATGATGCCAAAGAGATTAAGAG
1 TTCCATTGAACTTTATGATGCCAAAGAGATTAAGAG
3625 TTCCATTGAACTTTATGATGCCAAAGAGATTAAGAG
1 TTCCATTGAACTTTATGATGCCAAAGAGATTAAGAG
3661 AGTAACAACG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (36 bp):
TTCCATTGAACTTTATGATGCCAAAGAGATTAAGAG
Found at i:3857 original size:103 final size:103
Alignment explanation
Indices: 3678--3884 Score: 387
Period size: 103 Copynumber: 2.0 Consensus size: 103
3668 ACGGAGCGAT
* *
3678 CGATATTTAAGTGGACATTTTTTCGACTTATACGGTGGTGATTTCTTGGAGGGTGTTACGGTTTC
1 CGATATCTAAGTGGACATTTTTTCGACTTATACGGTGGTGATTTCTTGAAGGGTGTTACGGTTTC
3743 CATTAAAAAATACAACACAAATCATTGTGATCTCGACA
66 CATTAAAAAATACAACACAAATCATTGTGATCTCGACA
*
3781 CGATATCTAAGTGGACATTTTTTCGACTTATACGGTGGTGATTTCTTGAAGGTTGTTACGGTTTC
1 CGATATCTAAGTGGACATTTTTTCGACTTATACGGTGGTGATTTCTTGAAGGGTGTTACGGTTTC
3846 CATTAAAAAATACAACACAAATCATTGTGATCTCGACA
66 CATTAAAAAATACAACACAAATCATTGTGATCTCGACA
3884 C
1 C
3885 CATTTTCAAC
Statistics
Matches: 101, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 101 1.00
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.35
Consensus pattern (103 bp):
CGATATCTAAGTGGACATTTTTTCGACTTATACGGTGGTGATTTCTTGAAGGGTGTTACGGTTTC
CATTAAAAAATACAACACAAATCATTGTGATCTCGACA
Found at i:4210 original size:20 final size:20
Alignment explanation
Indices: 4164--4211 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
4154 CGAAGAAAAA
4164 AAAATAAAAAATAAAAAAGTT
1 AAAA-AAAAAATAAAAAAGTT
* *
4185 AGAAAAAAAATAAATCAAG-T
1 AAAAAAAAAATAAA-AAAGTT
4205 AAAAAAA
1 AAAAAAA
4212 GTAATTGATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.77, C:0.02, G:0.06, T:0.15
Consensus pattern (20 bp):
AAAAAAAAAATAAAAAAGTT
Found at i:9726 original size:11 final size:11
Alignment explanation
Indices: 9706--9740 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
9696 TTGACAACGC
9706 AACAAAAACAA
1 AACAAAAACAA
*
9717 AACGAAAACAA
1 AACAAAAACAA
*
9728 AATAAAAACAA
1 AACAAAAACAA
9739 AA
1 AA
9741 AATAGAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.80, C:0.14, G:0.03, T:0.03
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:10807 original size:27 final size:29
Alignment explanation
Indices: 10777--10839 Score: 76
Period size: 32 Copynumber: 2.1 Consensus size: 29
10767 AAAGCTTCTC
*
10777 ATTTTC-TT-AAATAGGATTATATTATAT
1 ATTTTCTTTAAAAAAGGATTATATTATAT
10804 ATTTTCTTTCAAAAAAAAGGATTATATTATAT
1 ATTTTCTTT---AAAAAAGGATTATATTATAT
10836 ATTT
1 ATTT
10840 AAACTTAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 6 0.20
28 2 0.07
32 22 0.73
ACGTcount: A:0.40, C:0.05, G:0.06, T:0.49
Consensus pattern (29 bp):
ATTTTCTTTAAAAAAGGATTATATTATAT
Found at i:16837 original size:2 final size:2
Alignment explanation
Indices: 16830--16857 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
16820 TCCACAGCCC
16830 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16858 AAGAGATTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18828 original size:24 final size:24
Alignment explanation
Indices: 18796--18843 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
18786 TTTTAGATAC
18796 GACGATTAAGATTCAGCCTTCAAT
1 GACGATTAAGATTCAGCCTTCAAT
18820 GACGATTAAGATTCAGCCTTCAAT
1 GACGATTAAGATTCAGCCTTCAAT
18844 AAAGTTGTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (24 bp):
GACGATTAAGATTCAGCCTTCAAT
Found at i:31811 original size:39 final size:39
Alignment explanation
Indices: 31756--31838 Score: 114
Period size: 39 Copynumber: 2.1 Consensus size: 39
31746 ATATAGTATT
* *
31756 TTAGAGATTGCAAGAACTTTAGAA-GAGATGAAAGGGAAA
1 TTAGAGATTCCAAGAACTTT-GAATGAGATGAAAAGGAAA
*
31795 TTAGGGATTCCAAGAACTTTGAATGAGATGAAAAGGAAA
1 TTAGAGATTCCAAGAACTTTGAATGAGATGAAAAGGAAA
*
31834 GTAGA
1 TTAGA
31839 AGGTGGAGGA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
38 3 0.08
39 35 0.92
ACGTcount: A:0.45, C:0.06, G:0.28, T:0.22
Consensus pattern (39 bp):
TTAGAGATTCCAAGAACTTTGAATGAGATGAAAAGGAAA
Done.