Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015794.1 Corchorus olitorius cultivar O-4 contig15827, 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: 18024
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.30
Found at i:489 original size:12 final size:12
Alignment explanation
Indices: 472--496 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
462 GAATGTGTGT
472 GATTTTGTTAAA
1 GATTTTGTTAAA
484 GATTTTGTTAAA
1 GATTTTGTTAAA
496 G
1 G
497 GGGTGATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (12 bp):
GATTTTGTTAAA
Found at i:874 original size:211 final size:211
Alignment explanation
Indices: 504--1077 Score: 1040
Period size: 211 Copynumber: 2.7 Consensus size: 211
494 AAGGGGTGAT
* * *
504 ATTAAGTATCCCCAAAGTAAAATACTTTATACCCAAATTCTTTCTCATCATCTCCAAATAATCTT
1 ATTAAGTATCCCCAAAGTAATATACTTTATACCCAAATTCTTTCTCATCATCCCCAAATAATCAT
* *
569 ATGCACTATCCCCAAATTCTTTAGAGATGGACATTTTTTCTCATATACCCAAAATTGACTTTAAA
66 ATGCACCATCCCCAAATTCTTTAGAGATGGACATTTTTTCCCATATACCCAAAATTGACTTTAAA
* * * *
634 AGGTGTTTTAATCCATTTATCATTTGAATAAACCCCATCTATATGATTTTAGTGCCATCTACTAA
131 ATGTGTTTTAATCCATATATTAATTGAATAAACCCCATCTATATGATTTTAGTGCCATCTACTAA
699 TTAAACAAAATGCAAA
196 TTAAACAAAATGCAAA
715 ATTAAGTATCCCCAAAGTAATATACTTTATACCCAAATTCTTTCTCATCATCCCCAAATAATCAT
1 ATTAAGTATCCCCAAAGTAATATACTTTATACCCAAATTCTTTCTCATCATCCCCAAATAATCAT
780 ATGCACCATCCCCAAATTCTTTAGAGATGGACATTTTTTCCCATATACCCAAAATTGACTTTAAA
66 ATGCACCATCCCCAAATTCTTTAGAGATGGACATTTTTTCCCATATACCCAAAATTGACTTTAAA
845 ATGTGTTTTAATCCATATATTAATTGAATAAACCCCATCTATATGATTTTAGTGCCATCTACTAA
131 ATGTGTTTTAATCCATATATTAATTGAATAAACCCCATCTATATGATTTTAGTGCCATCTACTAA
910 TTAAACAAAATGCAAA
196 TTAAACAAAATGCAAA
*
926 ATTAAGTATCCCCAAAGTAATATACTTTATGCCCAAATTCTTTCTCATCATCCCCAAATAATCAT
1 ATTAAGTATCCCCAAAGTAATATACTTTATACCCAAATTCTTTCTCATCATCCCCAAATAATCAT
* *
991 ATGCACCATCCCCAAATTCTTTAGAGATGGATATTTTTTCCCATATACCCAAAATTGACCTTAAA
66 ATGCACCATCCCCAAATTCTTTAGAGATGGACATTTTTTCCCATATACCCAAAATTGACTTTAAA
1056 ATGTGTTTTAATCCATATATTA
131 ATGTGTTTTAATCCATATATTA
1078 TTCATAATCT
Statistics
Matches: 351, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
211 351 1.00
ACGTcount: A:0.36, C:0.22, G:0.07, T:0.35
Consensus pattern (211 bp):
ATTAAGTATCCCCAAAGTAATATACTTTATACCCAAATTCTTTCTCATCATCCCCAAATAATCAT
ATGCACCATCCCCAAATTCTTTAGAGATGGACATTTTTTCCCATATACCCAAAATTGACTTTAAA
ATGTGTTTTAATCCATATATTAATTGAATAAACCCCATCTATATGATTTTAGTGCCATCTACTAA
TTAAACAAAATGCAAA
Found at i:3645 original size:59 final size:59
Alignment explanation
Indices: 3573--3695 Score: 201
Period size: 59 Copynumber: 2.1 Consensus size: 59
3563 AAATAATTCA
* ** *
3573 AGATTATGTTTTCAAATTTTTTGTTTGATGTTGGAGATTTCGATATTTATAGACCATTG
1 AGATTATGTTTTCAAATTTTTGGTGAGATGTTGGAGATTTCGATATTTATAGACCATGG
*
3632 AGATTATGTTTTCAAATTTTTGGTGAGATGTTGGAGATTTCGATATTTATCGACCATGG
1 AGATTATGTTTTCAAATTTTTGGTGAGATGTTGGAGATTTCGATATTTATAGACCATGG
3691 AGATT
1 AGATT
3696 GGAGAAATTA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.26, C:0.07, G:0.21, T:0.46
Consensus pattern (59 bp):
AGATTATGTTTTCAAATTTTTGGTGAGATGTTGGAGATTTCGATATTTATAGACCATGG
Found at i:3842 original size:21 final size:21
Alignment explanation
Indices: 3790--3842 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
3780 CACATAAGTT
* * * *
3790 TTTGGGTATAATGAGATTTAT
1 TTTGGGTATGATAAGATATAA
*
3811 TTTGGGAATGATAAGATATAA
1 TTTGGGTATGATAAGATATAA
3832 TTTGGGTATGA
1 TTTGGGTATGA
3843 AGTTATCACG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.42
Consensus pattern (21 bp):
TTTGGGTATGATAAGATATAA
Found at i:3952 original size:21 final size:20
Alignment explanation
Indices: 3907--3954 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
3897 CATATAAGTT
*
3907 TTTGGGTATAATGAGATATAT
1 TTTGGGTATAA-GAGATATAC
3928 TTTGGGTATAA-AGTATATTAC
1 TTTGGGTATAAGAG-ATA-TAC
3949 TTTGGG
1 TTTGGG
3955 GATACTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 2 0.08
20 3 0.12
21 19 0.79
ACGTcount: A:0.29, C:0.02, G:0.25, T:0.44
Consensus pattern (20 bp):
TTTGGGTATAAGAGATATAC
Found at i:4176 original size:21 final size:20
Alignment explanation
Indices: 4131--4188 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 20
4121 CATATAAGTT
*
4131 TTTGGGTATAATGAG-ATATAT
1 TTTGGGTATAA--AGTATATAC
4152 TTTGGGTATAAAGTATATTAC
1 TTTGGGTATAAAGTATA-TAC
*
4173 TTTGGGTATGAAGTAT
1 TTTGGGTATAAAGTAT
4189 CCAATTGGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.06
20 3 0.09
21 28 0.85
ACGTcount: A:0.31, C:0.02, G:0.24, T:0.43
Consensus pattern (20 bp):
TTTGGGTATAAAGTATATAC
Found at i:8763 original size:47 final size:47
Alignment explanation
Indices: 8685--8780 Score: 167
Period size: 47 Copynumber: 2.0 Consensus size: 47
8675 TGAGGGAATG
8685 GCAAATGGGTACAGAATCTTTGTAAAATTTGAAAGAAAGAACGATTT
1 GCAAATGGGTACAGAATCTTTGTAAAATTTGAAAGAAAGAACGATTT
*
8732 GCAAATGGGTACAGAATTTTTG-AAAATTTTGAAAGAAAGAACGATTT
1 GCAAATGGGTACAGAATCTTTGTAAAA-TTTGAAAGAAAGAACGATTT
8779 GC
1 GC
8781 CCAAAACGAT
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 4 0.09
47 43 0.91
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (47 bp):
GCAAATGGGTACAGAATCTTTGTAAAATTTGAAAGAAAGAACGATTT
Found at i:8790 original size:14 final size:14
Alignment explanation
Indices: 8771--8800 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
8761 TGAAAGAAAG
8771 AACGATTTGCCCAA
1 AACGATTTGCCCAA
8785 AACGATTTGCCCAA
1 AACGATTTGCCCAA
8799 AA
1 AA
8801 ATTTGATGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.27, G:0.13, T:0.20
Consensus pattern (14 bp):
AACGATTTGCCCAA
Found at i:9518 original size:26 final size:26
Alignment explanation
Indices: 9482--9535 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
9472 CATATCGCCT
*
9482 AATAATTATGGGCAGAATTAAATTCG
1 AATAATTATGGGAAGAATTAAATTCG
9508 AATAATTATGGGAAGAATTAAATTCG
1 AATAATTATGGGAAGAATTAAATTCG
9534 AA
1 AA
9536 GTTTAGCCCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.46, C:0.06, G:0.19, T:0.30
Consensus pattern (26 bp):
AATAATTATGGGAAGAATTAAATTCG
Found at i:14739 original size:7 final size:7
Alignment explanation
Indices: 14727--14751 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
14717 TTCAATTAAT
14727 AAAAATA
1 AAAAATA
14734 AAAAATA
1 AAAAATA
14741 AAAAATA
1 AAAAATA
14748 AAAA
1 AAAA
14752 CTCTGTCCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Done.