Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017073.1 Corchorus olitorius cultivar O-4 contig17106, 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: 23525
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:5613 original size:15 final size:16
Alignment explanation
Indices: 5589--5626 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
5579 AAAGGTTGAA
*
5589 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
5604 AGAAAACAATTAAACT
1 AGAAAACAATTAAACT
5620 AGAAAAC
1 AGAAAAC
5627 TAAGCAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.63, C:0.13, G:0.11, T:0.13
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:7743 original size:16 final size:15
Alignment explanation
Indices: 7705--7746 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
7695 ACAGAGATTG
*
7705 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
7720 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
7735 ACTAGAAAACAA
1 AC-AGAAAACAA
7747 AACAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:10605 original size:14 final size:15
Alignment explanation
Indices: 10586--10615 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
10576 CAATCAAAGC
10586 AATAAT-CAAGGAAA
1 AATAATGCAAGGAAA
10600 AATAATGCAAGGAAA
1 AATAATGCAAGGAAA
10615 A
1 A
10616 TTAAAAAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.63, C:0.07, G:0.17, T:0.13
Consensus pattern (15 bp):
AATAATGCAAGGAAA
Found at i:10994 original size:21 final size:21
Alignment explanation
Indices: 10970--11042 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
10960 GGCACTGAAT
10970 GGTGATGGCACGGGCATGGCC
1 GGTGATGGCACGGGCATGGCC
* * **
10991 GGTGGTGGCACGGGCTTAACC
1 GGTGATGGCACGGGCATGGCC
* *
11012 GGTGGTGGCACGGTGAATGGCC
1 GGTGATGGCACGG-GCATGGCC
*
11034 GGTAATGGC
1 GGTGATGGC
11043 TTGGTAGTGG
Statistics
Matches: 41, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
21 30 0.73
22 11 0.27
ACGTcount: A:0.15, C:0.21, G:0.47, T:0.18
Consensus pattern (21 bp):
GGTGATGGCACGGGCATGGCC
Found at i:14045 original size:16 final size:15
Alignment explanation
Indices: 14007--14048 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
13997 ACAGAGATTG
*
14007 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
14022 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
14037 ACTAGAAAACAA
1 AC-AGAAAACAA
14049 AACAAAACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:14783 original size:12 final size:13
Alignment explanation
Indices: 14766--14795 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
14756 CCCTTTGCCT
14766 AAAAACTAGA-AG
1 AAAAACTAGATAG
14778 AAAAACTAGATAG
1 AAAAACTAGATAG
14791 AAAAA
1 AAAAA
14796 AATAAATCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.70, C:0.07, G:0.13, T:0.10
Consensus pattern (13 bp):
AAAAACTAGATAG
Found at i:18252 original size:33 final size:32
Alignment explanation
Indices: 18213--18366 Score: 158
Period size: 33 Copynumber: 4.9 Consensus size: 32
18203 CGTTTTAAAA
* * *
18213 GGACAAACGCCACTAAATTGGGGTGTTTTTGGT
1 GGACAAACGCC-CTAAATTGGGGCGTTTCTGAT
* *
18246 GTACAAACGGCCCTAAATTGGGGCGATTCTGAT
1 GGACAAAC-GCCCTAAATTGGGGCGTTTCTGAT
18279 GGACAAACGCCCCTAAATTGGGGCGTTTCTGAT
1 GGACAAACG-CCCTAAATTGGGGCGTTTCTGAT
* *
18312 GG-----C-CCTTAAATTGGGGCGTTTCCGAT
1 GGACAAACGCCCTAAATTGGGGCGTTTCTGAT
*
18338 GGACAAACGCCCCTAAATTGGAGCGTTTC
1 GGACAAACG-CCCTAAATTGGGGCGTTTC
18367 CTTTTACAAA
Statistics
Matches: 101, Mismatches: 11, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
26 23 0.23
28 1 0.01
31 1 0.01
32 1 0.01
33 72 0.71
34 3 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (32 bp):
GGACAAACGCCCTAAATTGGGGCGTTTCTGAT
Found at i:18323 original size:26 final size:26
Alignment explanation
Indices: 18287--18339 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
18277 ATGGACAAAC
*
18287 GCCCCTAAATTGGGGCGTTTCTGATG
1 GCCCCTAAATTGGGGCGTTTCCGATG
*
18313 GCCCTTAAATTGGGGCGTTTCCGATG
1 GCCCCTAAATTGGGGCGTTTCCGATG
18339 G
1 G
18340 ACAAACGCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.15, C:0.23, G:0.32, T:0.30
Consensus pattern (26 bp):
GCCCCTAAATTGGGGCGTTTCCGATG
Found at i:18345 original size:59 final size:58
Alignment explanation
Indices: 18254--18366 Score: 190
Period size: 59 Copynumber: 1.9 Consensus size: 58
18244 GTGTACAAAC
* *
18254 GGCCCTAAATTGGGGCGATTCTGATGGACAAACGCCCCTAAATTGGGGCGTTTCTGAT
1 GGCCCTAAATTGGGGCGATTCCGATGGACAAACGCCCCTAAATTGGAGCGTTTCTGAT
*
18312 GGCCCTTAAATTGGGGCGTTTCCGATGGACAAACGCCCCTAAATTGGAGCGTTTC
1 GGCCC-TAAATTGGGGCGATTCCGATGGACAAACGCCCCTAAATTGGAGCGTTTC
18367 CTTTTACAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
58 5 0.10
59 46 0.90
ACGTcount: A:0.22, C:0.24, G:0.28, T:0.26
Consensus pattern (58 bp):
GGCCCTAAATTGGGGCGATTCCGATGGACAAACGCCCCTAAATTGGAGCGTTTCTGAT
Done.