Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022351.1 Corchorus olitorius cultivar O-4 contig22384, 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: 41545
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.31
Found at i:18247 original size:43 final size:43
Alignment explanation
Indices: 18200--18529 Score: 442
Period size: 43 Copynumber: 7.8 Consensus size: 43
18190 ATAAGGAAAA
*
18200 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
*
18243 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTG-ATATA-A-
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTA-ATAGAG
***
18284 ATGCATTTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
* * *
18327 TTGCCCCTGTGTTATATATGTGTTTGGGGACTTTG--ATATAG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
*
18368 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
* *
18411 GTGCCCCTGTGTTATATATGTGTTTGGGGACTTTGTAAT--AG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
* **
18452 TTGCCTTTGTGTTATATATGTGTTTGAGGACTTT-TAGAATAGAG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGT--AATAGAG
*
18496 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTT
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTT
18530 TTGTTATTGG
Statistics
Matches: 250, Mismatches: 27, Indels: 19
0.84 0.09 0.06
Matches are distributed among these distances:
40 1 0.00
41 103 0.41
42 7 0.03
43 107 0.43
44 32 0.13
ACGTcount: A:0.21, C:0.10, G:0.26, T:0.43
Consensus pattern (43 bp):
ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
Found at i:18312 original size:84 final size:84
Alignment explanation
Indices: 18198--18529 Score: 551
Period size: 84 Copynumber: 3.9 Consensus size: 84
18188 CCATAAGGAA
18198 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATG
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATG
18263 TGTTTGGGGACTTTGATAT
66 TGTTTGGGGACTTTGATAT
* * *
18282 AAATGCATTTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGTTGCCCCTGTGTTATATATG
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATG
18347 TGTTTGGGGACTTTGATAT
66 TGTTTGGGGACTTTGATAT
* *
18366 AGATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGGTGCCCCTGTGTTATATATG
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATG
18431 TGTTTGGGGACTTTG-TAAT
66 TGTTTGGGGACTTTGAT-AT
** *
18450 AGTTGCCTTTGTGTTATATATGTGTTTGAGGACTTT-TAGAATAGAGATGCCCCTGTGTTATATA
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGT--AATAGAGATGCCCCTGTGTTATATA
18514 TGTGTTTGGGGACTTT
64 TGTGTTTGGGGACTTT
18530 TTGTTATTGG
Statistics
Matches: 235, Mismatches: 10, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
83 2 0.01
84 193 0.82
85 40 0.17
ACGTcount: A:0.21, C:0.10, G:0.26, T:0.43
Consensus pattern (84 bp):
AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATG
TGTTTGGGGACTTTGATAT
Found at i:31100 original size:43 final size:43
Alignment explanation
Indices: 31036--31363 Score: 417
Period size: 41 Copynumber: 7.8 Consensus size: 43
31026 ATAAGGAGAA
* *
31036 ATGCCTCTGTG-T-TATATGTGTTTGAAGACTTTGTAATAGAG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
* * *
31077 ACGCCCATGTGTTATATATGTGTTTGGGGACTTTG-ATATA-A-
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTA-ATAGAG
*
31118 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
* *
31161 TTGCCCCTGTGTTATATATGTGTTTGAGGACTTTG--ATATAG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
*
31202 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTTATAGAG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
* *
31245 GTGCCCCTGTGTTATATATGTGTTTGGGGACTTTGTAAT--AG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
* **
31286 TTGCGTCTGTGTTATATATGTGTTTGAGGACTTT-TAGAATAGAG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGT--AATAGAG
31330 ATGCCCCTGTGTTATATATGTGTTTTG-GGACTTT
1 ATGCCCCTGTGTTATATATGTG-TTTGAGGACTTT
31364 TGGTTATTGG
Statistics
Matches: 250, Mismatches: 24, Indels: 23
0.84 0.08 0.08
Matches are distributed among these distances:
40 1 0.00
41 113 0.45
42 8 0.03
43 96 0.38
44 28 0.11
45 4 0.02
ACGTcount: A:0.21, C:0.11, G:0.26, T:0.42
Consensus pattern (43 bp):
ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
Found at i:31151 original size:84 final size:84
Alignment explanation
Indices: 31034--31363 Score: 488
Period size: 84 Copynumber: 3.9 Consensus size: 84
31024 CCATAAGGAG
* * *
31034 AAATGCCTCTGTG-T-TATATGTGTTTGAAGACTTTGTAATAGAGACGCCCATGTGTTATATATG
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATG
31097 TGTTTGGGGACTTTGATAT
66 TGTTTGGGGACTTTGATAT
*
31116 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGTTGCCCCTGTGTTATATATG
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATG
*
31181 TGTTTGAGGACTTTGATAT
66 TGTTTGGGGACTTTGATAT
* * * *
31200 AGATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTTATAGAGGTGCCCCTGTGTTATATATG
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATG
31265 TGTTTGGGGACTTTG-TAAT
66 TGTTTGGGGACTTTGAT-AT
** *
31284 AGTTGCGTCTGTGTTATATATGTGTTTGAGGACTTT-TAGAATAGAGATGCCCCTGTGTTATATA
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGT--AATAGAGATGCCCCTGTGTTATATA
*
31348 TGTGTTTTGGGACTTT
64 TGTGTTTGGGGACTTT
31364 TGGTTATTGG
Statistics
Matches: 227, Mismatches: 16, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
82 13 0.06
83 3 0.01
84 173 0.76
85 38 0.17
ACGTcount: A:0.22, C:0.11, G:0.25, T:0.42
Consensus pattern (84 bp):
AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATG
TGTTTGGGGACTTTGATAT
Found at i:38085 original size:23 final size:23
Alignment explanation
Indices: 38059--38103 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
38049 TTTCGAAATT
38059 AAAGGATTT-TCTCAAAACTAAAA
1 AAAGG-TTTCTCTCAAAACTAAAA
* *
38082 AAAGGTTTCTTTCAAAATTAAA
1 AAAGGTTTCTCTCAAAACTAAA
38104 GAGAATTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.49, C:0.11, G:0.09, T:0.31
Consensus pattern (23 bp):
AAAGGTTTCTCTCAAAACTAAAA
Found at i:39602 original size:19 final size:20
Alignment explanation
Indices: 39555--39602 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 20
39545 TTTAATCTGG
39555 GTATACTTGTTTATACATGT
1 GTATACTTGTTTATACATGT
*
39575 -TAT--TTGTTT-TGCATGT
1 GTATACTTGTTTATACATGT
39591 GTATACTTGTTT
1 GTATACTTGTTT
39603 CCACACCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
16 6 0.25
17 9 0.38
19 9 0.38
ACGTcount: A:0.19, C:0.08, G:0.17, T:0.56
Consensus pattern (20 bp):
GTATACTTGTTTATACATGT
Found at i:40223 original size:25 final size:25
Alignment explanation
Indices: 40184--40235 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 25
40174 CTCAAGAATT
*
40184 TTCTCTATTTTTGCG-TTAAAAAAA
1 TTCTCTATTTCTGCGTTTAAAAAAA
40208 TTCTCTTATTTCTGCGTTTTAAAAAAA
1 TTCTC-TATTTCTGCG-TTTAAAAAAA
40235 T
1 T
40236 ATATTTCTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 5 0.21
25 9 0.38
27 10 0.42
ACGTcount: A:0.31, C:0.13, G:0.08, T:0.48
Consensus pattern (25 bp):
TTCTCTATTTCTGCGTTTAAAAAAA
Found at i:40248 original size:34 final size:35
Alignment explanation
Indices: 40209--40276 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
40199 TTAAAAAAAT
*
40209 TCTCTTA-TTT-CTGCGTTTTAAAAAAATATATTTC
1 TCTCTTATTTTCCTG-GTTTAAAAAAAATATATTTC
*
40243 TCTCTTATTTTCCTGGTTTAAAAAAAATTTATTT
1 TCTCTTATTTTCCTGGTTTAAAAAAAATATATTT
40277 TCTGTTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
34 7 0.23
35 20 0.67
36 3 0.10
ACGTcount: A:0.29, C:0.13, G:0.06, T:0.51
Consensus pattern (35 bp):
TCTCTTATTTTCCTGGTTTAAAAAAAATATATTTC
Done.