Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015973.1 Corchorus olitorius cultivar O-4 contig16006, 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: 8487
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:2132 original size:2 final size:2
Alignment explanation
Indices: 2125--2165 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
2115 TAATATGTAG
2125 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2166 CATAATAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2967 original size:22 final size:22
Alignment explanation
Indices: 2907--2996 Score: 64
Period size: 22 Copynumber: 4.1 Consensus size: 22
2897 CAAATTTCCC
2907 TATAAAATTT--ATTAACCTCCT
1 TATAAAATTTGGA-TAACCTCCT
* *
2928 TATAAAATTTTGAAAACCT-CT
1 TATAAAATTTGGATAACCTCCT
* *
2949 ATATATAATTTGGATAACCACAC-
1 -TATAAAATTTGGATAACCTC-CT
*
2972 TATGAAATGTT-GATAACCTCCT
1 TATAAAAT-TTGGATAACCTCCT
2994 TAT
1 TAT
2997 GAATTTTTTA
Statistics
Matches: 54, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
21 13 0.24
22 37 0.69
23 3 0.06
24 1 0.02
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.38
Consensus pattern (22 bp):
TATAAAATTTGGATAACCTCCT
Found at i:3152 original size:23 final size:22
Alignment explanation
Indices: 2919--3247 Score: 120
Period size: 22 Copynumber: 15.1 Consensus size: 22
2909 TAAAATTTAT
*
2919 TAACCTC-CTTATAAAATTTTGA
1 TAACCTCAC-TATGAAATTTTGA
* *
2941 AAACCTCTA-TAT-ATAATTTGGA
1 TAACCTC-ACTATGA-AATTTTGA
* *
2963 TAACCACACTATGAAATGTTGA
1 TAACCTCACTATGAAATTTTGA
*
2985 TAACCTC-CTTATG-AATTTT-T
1 TAACCTCAC-TATGAAATTTTGA
* *
3005 TAA---AACTATTAAATTTTGA
1 TAACCTCACTATGAAATTTTGA
* * *
3024 TAACGACT-A-TACGGAATTTCGA
1 TAAC--CTCACTATGAAATTTTGA
* * * *
3046 GAACC-CACCTATAAAAATTTGT
1 TAACCTCA-CTATGAAATTTTGA
* *
3068 TAACTTCCCTATGAAATTTTG-
1 TAACCTCACTATGAAATTTTGA
* **
3089 TGAGCCTCTTTATGAAATTTTGA
1 T-AACCTCACTATGAAATTTTGA
*
3112 AAACCTCACTATGAAATTTTGA
1 TAACCTCACTATGAAATTTTGA
3134 TAACCTC-CTAAATGAAATTTTGA
1 TAACCTCACT--ATGAAATTTTGA
*
3157 TAA--TGATCT-TGCAAAATTTTGA
1 TAACCTCA-CTATG--AAATTTTGA
***
3179 TAATGACACTATGAAATTTTGA
1 TAACCTCACTATGAAATTTTGA
* * *
3201 TAACCTC-CAAGTGGAATGTTCG-
1 TAACCTCACTA-TGAAAT-TTTGA
* *
3223 TAAGCACACTATGAAATTTTGA
1 TAACCTCACTATGAAATTTTGA
3245 TAA
1 TAA
3248 TCTCCCAAAA
Statistics
Matches: 223, Mismatches: 51, Indels: 66
0.66 0.15 0.19
Matches are distributed among these distances:
17 3 0.01
18 7 0.03
19 3 0.01
20 7 0.03
21 17 0.08
22 156 0.70
23 27 0.12
24 3 0.01
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.36
Consensus pattern (22 bp):
TAACCTCACTATGAAATTTTGA
Found at i:5307 original size:29 final size:29
Alignment explanation
Indices: 5274--5341 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
5264 ACTTGTACGA
* *
5274 TTTGGACGTTTTGTCCCCTGAACT-TTAAT
1 TTTGGACGTTTTG-CCCCTAAACTCTCAAT
5303 TTTGGACGTTTTGCCCCTAAACTCTCAAT
1 TTTGGACGTTTTGCCCCTAAACTCTCAAT
*
5332 TTTGAACGTT
1 TTTGGACGTT
5342 GTAGTCCATC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
28 9 0.26
29 26 0.74
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.43
Consensus pattern (29 bp):
TTTGGACGTTTTGCCCCTAAACTCTCAAT
Found at i:7701 original size:15 final size:15
Alignment explanation
Indices: 7671--7712 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
7661 TTACTTTGTT
7671 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
7687 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
7702 TTGTTTTCTGT
1 TTGTTTTCTGT
7713 CAACCTCTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:8290 original size:55 final size:55
Alignment explanation
Indices: 8184--8290 Score: 153
Period size: 55 Copynumber: 1.9 Consensus size: 55
8174 CAATAAACGC
*** *
8184 TTTTAATTTTGTGTGTTTTGCGTCGTTTTGATTTAAAAAAAAAATTATTTTGCCT
1 TTTTAATTTTGTGTGTTTTGCGTCGTTTTGAAAAAAAAAAAAAAATATTTTGCCT
*
8239 TTTTAATTTTGTGTTTTTTGCGTCGTTTTGAAAAAAAAAATAAAAAT-TTTTG
1 TTTTAATTTTGTGTGTTTTGCGTCGTTTTGAAAAAAAAAA-AAAAATATTTTG
8291 TTTTGTGTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
55 41 0.89
56 5 0.11
ACGTcount: A:0.29, C:0.06, G:0.14, T:0.51
Consensus pattern (55 bp):
TTTTAATTTTGTGTGTTTTGCGTCGTTTTGAAAAAAAAAAAAAAATATTTTGCCT
Found at i:8453 original size:27 final size:26
Alignment explanation
Indices: 8352--8455 Score: 81
Period size: 25 Copynumber: 3.9 Consensus size: 26
8342 TTTTTGAGTC
*
8352 TTGCGTCAAAAAAAAAAGTTTTGTGTT
1 TTGCGTCATAAAAAAAAGTTTT-TGTT
* *
8379 TTGCGTC--AAAAAAAA-TATAT-TT
1 TTGCGTCATAAAAAAAAGTTTTTGTT
**
8401 TTGCGTCATAACAAAAATTTTTTTTTTGTT
1 TTGCGTCATAA-AAAAA---AGTTTTTGTT
8431 TCTGCGTCATAAAAAAAAGTTTTTG
1 T-TGCGTCATAAAAAAAAGTTTTTG
8456 CGTTTTTCCA
Statistics
Matches: 61, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
22 9 0.15
23 1 0.02
24 4 0.07
25 13 0.21
27 13 0.21
29 3 0.05
30 8 0.13
31 10 0.16
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (26 bp):
TTGCGTCATAAAAAAAAGTTTTTGTT
Done.