Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017956.1 Corchorus olitorius cultivar O-4 contig17989, 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: 23195
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Found at i:8 original size:3 final size:3
Alignment explanation
Indices: 1--75 Score: 150
Period size: 3 Copynumber: 25.0 Consensus size: 3
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
49 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
76 AATTTACTAA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2053 original size:19 final size:19
Alignment explanation
Indices: 2029--2065 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2019 GTATAGTACC
*
2029 TAATCTAATTTGTACAGTG
1 TAATCTAATCTGTACAGTG
*
2048 TAATCTCATCTGTACAGT
1 TAATCTAATCTGTACAGT
2066 TGCTAAACAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.41
Consensus pattern (19 bp):
TAATCTAATCTGTACAGTG
Found at i:3245 original size:26 final size:21
Alignment explanation
Indices: 3205--3264 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
3195 GCTGCTCTAA
* *
3205 TAATCTCATTTGTACAGTA-T
1 TAATCTAATCTGTACAGTACT
3225 CTAATCTAATCTGTACAGTACT
1 -TAATCTAATCTGTACAGTACT
3247 TAATCTAATCTGTACAGT
1 TAATCTAATCTGTACAGT
3265 GTAATCTCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 35 0.97
22 1 0.03
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.40
Consensus pattern (21 bp):
TAATCTAATCTGTACAGTACT
Found at i:13817 original size:48 final size:48
Alignment explanation
Indices: 13746--13840 Score: 163
Period size: 48 Copynumber: 2.0 Consensus size: 48
13736 TAAGCAGATC
*
13746 TCAAGTTCGAAATCCTGCGTACACAGTTATCCCTGATTTTTTTTTTTT
1 TCAAGTTCGAAATCCTGCGTACACAATTATCCCTGATTTTTTTTTTTT
* *
13794 TCAAGTTCGAAATCCTGCGTACACAATTATTCCTGGTTTTTTTTTTT
1 TCAAGTTCGAAATCCTGCGTACACAATTATCCCTGATTTTTTTTTTT
13841 GGAAAGATAG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.21, C:0.20, G:0.13, T:0.46
Consensus pattern (48 bp):
TCAAGTTCGAAATCCTGCGTACACAATTATCCCTGATTTTTTTTTTTT
Found at i:13923 original size:112 final size:113
Alignment explanation
Indices: 13802--14023 Score: 401
Period size: 113 Copynumber: 2.0 Consensus size: 113
13792 TTTCAAGTTC
*
13802 GAAATCCTGCGTACACAATTATTCCTGG-TTTTTTTTTTTGGAAAGATAGAATATTATTGAGAGA
1 GAAATCCTGCGTACACAATTATCCCTGGCTTTTTTTTTTTGGAAAGATAGAATATTATTGAGAGA
13866 AGAGGGGGTACATAGGGGTGTCTCATTAAAACCTCCATAAGGAAACTT
66 AGAGGGGGTACATAGGGGTGTCTCATTAAAACCTCCATAAGGAAACTT
* * *
13914 GAAATCCTGCGTACATAGTTATCCCTGGCTTTTTTTTTTTTGAAAGATAGAATATTATTGAGAGA
1 GAAATCCTGCGTACACAATTATCCCTGGCTTTTTTTTTTTGGAAAGATAGAATATTATTGAGAGA
13979 AGAGGGGGTACATAGGGGTGTCTCATTAAAACCTCCATAAGGAAA
66 AGAGGGGGTACATAGGGGTGTCTCATTAAAACCTCCATAAGGAAA
14024 AACCCTGTGG
Statistics
Matches: 105, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
112 25 0.24
113 80 0.76
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (113 bp):
GAAATCCTGCGTACACAATTATCCCTGGCTTTTTTTTTTTGGAAAGATAGAATATTATTGAGAGA
AGAGGGGGTACATAGGGGTGTCTCATTAAAACCTCCATAAGGAAACTT
Found at i:21345 original size:18 final size:18
Alignment explanation
Indices: 21324--21360 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
21314 CTCCTTCTCC
* *
21324 TTATGCTGCTGGTCCTTA
1 TTATGCAGCGGGTCCTTA
21342 TTATGCAGCGGGTCCTTA
1 TTATGCAGCGGGTCCTTA
21360 T
1 T
21361 GCCGCCGGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.22, G:0.24, T:0.41
Consensus pattern (18 bp):
TTATGCAGCGGGTCCTTA
Found at i:21371 original size:33 final size:33
Alignment explanation
Indices: 21321--21441 Score: 104
Period size: 33 Copynumber: 3.7 Consensus size: 33
21311 CTGCTCCTTC
* *
21321 TCCTTATGCTGCTGGTCCTTATTATGCAGCGGG
1 TCCTTATGCTGCTGGTCCTTATCATGCAGCAGG
* * * * *
21354 TCCTTATGCCGCCGGTCCTCATCGTGCTGCAGG
1 TCCTTATGCTGCTGGTCCTTATCATGCAGCAGG
*
21387 TCCCTATGCTGCTGGTCC-T-T-ATGCAGCAGG
1 TCCTTATGCTGCTGGTCCTTATCATGCAGCAGG
* *
21417 GCCTCACCGTGCTGCTGGTCCTTAT
1 TCCTTA---TGCTGCTGGTCCTTAT
21442 GCCGCCGGTC
Statistics
Matches: 67, Mismatches: 16, Indels: 8
0.74 0.18 0.09
Matches are distributed among these distances:
30 11 0.16
31 1 0.01
33 53 0.79
34 1 0.01
35 1 0.01
ACGTcount: A:0.11, C:0.31, G:0.26, T:0.31
Consensus pattern (33 bp):
TCCTTATGCTGCTGGTCCTTATCATGCAGCAGG
Found at i:21404 original size:48 final size:48
Alignment explanation
Indices: 21343--21453 Score: 132
Period size: 48 Copynumber: 2.3 Consensus size: 48
21333 TGGTCCTTAT
* * * * *
21343 TATGCAGCGGGTCCTTATGCCGCCGGTCCTCATCGTGCTGCAGGTCCC
1 TATGCAGCCGGTCCTTATGCAGCAGGGCCTCACCGTGCTGCAGGTCCC
* * * *
21391 TATGCTGCTGGTCCTTATGCAGCAGGGCCTCACCGTGCTGCTGGTCCT
1 TATGCAGCCGGTCCTTATGCAGCAGGGCCTCACCGTGCTGCAGGTCCC
*
21439 TATGCCGCCGGTCCT
1 TATGCAGCCGGTCCT
21454 CATCGTGCTG
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 53 1.00
ACGTcount: A:0.10, C:0.34, G:0.29, T:0.27
Consensus pattern (48 bp):
TATGCAGCCGGTCCTTATGCAGCAGGGCCTCACCGTGCTGCAGGTCCC
Found at i:21442 original size:33 final size:33
Alignment explanation
Indices: 21393--21498 Score: 158
Period size: 33 Copynumber: 3.2 Consensus size: 33
21383 CAGGTCCCTA
*
21393 TGCTGCTGGTCCTTATGCAGCAGGGCCTCACCG
1 TGCTGCTGGTCCTTATGCAGCAGGGCCTCATCG
* * *
21426 TGCTGCTGGTCCTTATGCCGCCGGTCCTCATCG
1 TGCTGCTGGTCCTTATGCAGCAGGGCCTCATCG
* *
21459 TGCTGCAGGTCCTTATGCAGCGGGGCCTCATCG
1 TGCTGCTGGTCCTTATGCAGCAGGGCCTCATCG
21492 TGCTGCT
1 TGCTGCT
21499 CCTTATGCCG
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 64 1.00
ACGTcount: A:0.09, C:0.33, G:0.30, T:0.27
Consensus pattern (33 bp):
TGCTGCTGGTCCTTATGCAGCAGGGCCTCATCG
Found at i:21542 original size:63 final size:63
Alignment explanation
Indices: 21393--21531 Score: 167
Period size: 66 Copynumber: 2.2 Consensus size: 63
21383 CAGGTCCCTA
* *
21393 TGCTGCTGGTCCTTATGCAGCAGGGCCTCACCGTGCTGCTGGTCCTTATGCCGCCGGTCCTCATC
1 TGCTGCAGATCCTTATGCAGCAGGGCCTCACCGTGCTGC--GTCCTTATGCCGCCGGT-CTCATC
21458 G
63 G
* * * * *
21459 TGCTGCAGGTCCTTATGCAGCGGGGCCTCATCGTGCTGC-TCCTTATGCCGGCGGT-TC-TGG
1 TGCTGCAGATCCTTATGCAGCAGGGCCTCACCGTGCTGCGTCCTTATGCCGCCGGTCTCATCG
21519 TGCTGCAGATCCT
1 TGCTGCAGATCCT
21532 CATCATGCAG
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
60 14 0.21
61 2 0.03
63 15 0.22
66 36 0.54
ACGTcount: A:0.09, C:0.32, G:0.30, T:0.28
Consensus pattern (63 bp):
TGCTGCAGATCCTTATGCAGCAGGGCCTCACCGTGCTGCGTCCTTATGCCGCCGGTCTCATCG
Done.