Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020363.1 Corchorus olitorius cultivar O-4 contig20396, 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: 39880
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:3099 original size:5 final size:5
Alignment explanation
Indices: 3091--3123 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
3081 TGCAAAATAA
3091 AAAAG AAAAG AAAAG AAAAG -AAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
3124 ACATAGGCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:3116 original size:9 final size:9
Alignment explanation
Indices: 3092--3122 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
3082 GCAAAATAAA
3092 AAAGAAAAG
1 AAAGAAAAG
3101 AAAAGAAAAG
1 -AAAGAAAAG
3111 AAAGAAAAG
1 AAAGAAAAG
3120 AAA
1 AAA
3123 AACATAGGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (9 bp):
AAAGAAAAG
Found at i:3116 original size:14 final size:15
Alignment explanation
Indices: 3091--3123 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
3081 TGCAAAATAA
3091 AAAAGAAAAGAAAAG
1 AAAAGAAAAGAAAAG
3106 AAAAG-AAAGAAAAG
1 AAAAGAAAAGAAAAG
3120 AAAA
1 AAAA
3124 ACATAGGCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAGAAAAG
Found at i:18648 original size:2 final size:2
Alignment explanation
Indices: 18641--18669 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18631 TTAAAGCTTG
18641 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
18670 AAAACAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:27907 original size:17 final size:17
Alignment explanation
Indices: 27881--27933 Score: 88
Period size: 17 Copynumber: 3.1 Consensus size: 17
27871 GAACAAAAAA
27881 AAAAAGTAGATGAGTTTC
1 AAAAA-TAGATGAGTTTC
27899 AAAAATAGATGAGTTTC
1 AAAAATAGATGAGTTTC
*
27916 AAAAATAAATGAGTTTC
1 AAAAATAGATGAGTTTC
27933 A
1 A
27934 TGTTAATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 29 0.85
18 5 0.15
ACGTcount: A:0.49, C:0.06, G:0.17, T:0.28
Consensus pattern (17 bp):
AAAAATAGATGAGTTTC
Found at i:28261 original size:45 final size:45
Alignment explanation
Indices: 28212--28345 Score: 196
Period size: 45 Copynumber: 3.0 Consensus size: 45
28202 TGATCAAACG
*
28212 GTTTGATGGAGGTAAAGTTAGATTCCCTGAAATTTCTTGTCAACA
1 GTTTGATTGAGGTAAAGTTAGATTCCCTGAAATTTCTTGTCAACA
* * * **
28257 GTTTGATTGAGGTAAAGTTAGATTCCCAGACATTTCTTATCAATG
1 GTTTGATTGAGGTAAAGTTAGATTCCCTGAAATTTCTTGTCAACA
* *
28302 GTTTGATTGAGGTAAAGTTTGGTTCCCTGAAATTTCTTGTCAAC
1 GTTTGATTGAGGTAAAGTTAGATTCCCTGAAATTTCTTGTCAAC
28346 TTTGCATATT
Statistics
Matches: 77, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 77 1.00
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (45 bp):
GTTTGATTGAGGTAAAGTTAGATTCCCTGAAATTTCTTGTCAACA
Found at i:28550 original size:132 final size:134
Alignment explanation
Indices: 28302--28611 Score: 489
Period size: 132 Copynumber: 2.3 Consensus size: 134
28292 CTTATCAATG
* * * * *
28302 GTTTGATTGAGGTAAAGTTTGGTTCCCTGAAATTTCTTGTCAACTTTGCATATTTTGACTTCCTT
1 GTTTGATAGAAGTAAAGTTAGATTCCCTGAAATTTCTTGTCAACTTTGCATATTCTGACTTCCTT
* *
28367 GGGTATTGTGTAAAAGTGTTCAGAATTCAAATGGACGGTTAAGATGAG-TTTTACATTTTGATCC
66 GGGTATGGTGTAAAAGTGTTCAGAATTCAAATGGACGATTAAGATGAGTTTTTACATTTTGATCC
*
28431 AATA
131 AACA
*
28435 G-TTGGTAGAAGTAAAGTTAGATTCCCTGAAATTTCTTGTCAACTTTGCATATTCTGACTTCCTT
1 GTTTGATAGAAGTAAAGTTAGATTCCCTGAAATTTCTTGTCAACTTTGCATATTCTGACTTCCTT
*
28499 GGGTATGGTGTAAAAGTGTTCAGAATTCAAATGGACGATTAAGATGAGTTTTTACTTTTTGATCC
66 GGGTATGGTGTAAAAGTGTTCAGAATTCAAATGGACGATTAAGATGAGTTTTTACATTTTGATCC
*
28564 AACG
131 AACA
* *
28568 GTTTGATGGAGGTAAAGTTAGATTCCCTGAAATTTCTTGTCAAC
1 GTTTGATAGAAGTAAAGTTAGATTCCCTGAAATTTCTTGTCAAC
28612 GGTTTGGTTG
Statistics
Matches: 161, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
132 103 0.64
133 19 0.12
134 39 0.24
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (134 bp):
GTTTGATAGAAGTAAAGTTAGATTCCCTGAAATTTCTTGTCAACTTTGCATATTCTGACTTCCTT
GGGTATGGTGTAAAAGTGTTCAGAATTCAAATGGACGATTAAGATGAGTTTTTACATTTTGATCC
AACA
Found at i:31402 original size:12 final size:13
Alignment explanation
Indices: 31374--31407 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
31364 TTTATTTAAC
31374 TGCTTTGGATCAT
1 TGCTTTGGATCAT
31387 TGCTTTGGAT-AT
1 TGCTTTGGATCAT
31399 TGCTGTTGG
1 TGCT-TTGG
31408 TTTGTTATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 6 0.30
13 14 0.70
ACGTcount: A:0.12, C:0.12, G:0.29, T:0.47
Consensus pattern (13 bp):
TGCTTTGGATCAT
Done.