Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024162.1 Corchorus olitorius cultivar O-4 contig24195, 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: 6497
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Found at i:289 original size:17 final size:17
Alignment explanation
Indices: 245--316 Score: 71
Period size: 16 Copynumber: 4.5 Consensus size: 17
235 GTCGGGTTGA
*
245 TCGGGTTCGGTTCATTT
1 TCGGGTTCGGGTCATTT
*
262 T-GGGTTTGGGTCATTT
1 TCGGGTTCGGGTCATTT
*
278 TCGGGTTCGGGTC-GTT
1 TCGGGTTCGGGTCATTT
* *
294 T-GGATTCGGGT-AATT
1 TCGGGTTCGGGTCATTT
309 TCGGGTTC
1 TCGGGTTC
317 TGGTACCCAA
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
15 12 0.27
16 22 0.49
17 11 0.24
ACGTcount: A:0.07, C:0.14, G:0.36, T:0.43
Consensus pattern (17 bp):
TCGGGTTCGGGTCATTT
Found at i:369 original size:17 final size:17
Alignment explanation
Indices: 329--369 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
319 GTACCCAAAA
329 TTTCGGGTCATTTCTGG
1 TTTCGGGTCATTTCTGG
*
346 GTT-GGGTCAGTTTC-GG
1 TTTCGGGTCA-TTTCTGG
362 TTTCGGGT
1 TTTCGGGT
370 TGGGCGGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.05, C:0.15, G:0.37, T:0.44
Consensus pattern (17 bp):
TTTCGGGTCATTTCTGG
Found at i:1702 original size:21 final size:21
Alignment explanation
Indices: 1678--1718 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1668 TGGTCTATCC
1678 TCAAACTCTCAAAGCATTTTA
1 TCAAACTCTCAAAGCATTTTA
* *
1699 TCAAAGTCTCAAGGCATTTT
1 TCAAACTCTCAAAGCATTTT
1719 TTCGAAGAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.34
Consensus pattern (21 bp):
TCAAACTCTCAAAGCATTTTA
Found at i:2115 original size:19 final size:19
Alignment explanation
Indices: 2091--2128 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2081 TGATGCTCCA
*
2091 GGGAACCTTCTAGGTAATC
1 GGGAACCTTCCAGGTAATC
*
2110 GGGAACTTTCCAGGTAATC
1 GGGAACCTTCCAGGTAATC
2129 TCCTTGTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (19 bp):
GGGAACCTTCCAGGTAATC
Found at i:3581 original size:11 final size:11
Alignment explanation
Indices: 3565--3589 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3555 TTTATTATCT
3565 TAATTCTCAAA
1 TAATTCTCAAA
3576 TAATTCTCAAA
1 TAATTCTCAAA
3587 TAA
1 TAA
3590 GATTAAATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (11 bp):
TAATTCTCAAA
Found at i:4277 original size:16 final size:16
Alignment explanation
Indices: 4258--4359 Score: 80
Period size: 16 Copynumber: 6.4 Consensus size: 16
4248 GGGCGGGTTT
4258 GGGTTCGGGTTTTTTC
1 GGGTTCGGGTTTTTTC
*
4274 GGGTTCGGGTATTTTC
1 GGGTTCGGGTTTTTTC
* ****
4290 GGGCTCGGGTCAAGTC
1 GGGTTCGGGTTTTTTC
* *
4306 GGGTTCGCGTATTTTC
1 GGGTTCGGGTTTTTTC
** * *
4322 GGACTCGGGTTATGTC
1 GGGTTCGGGTTTTTTC
4338 GGGTTCGGGTATTTTT-
1 GGGTTCGGGT-TTTTTC
4354 GGGTTC
1 GGGTTC
4360 AATCTCGGAT
Statistics
Matches: 63, Mismatches: 22, Indels: 2
0.72 0.25 0.02
Matches are distributed among these distances:
16 60 0.95
17 3 0.05
ACGTcount: A:0.07, C:0.16, G:0.38, T:0.39
Consensus pattern (16 bp):
GGGTTCGGGTTTTTTC
Found at i:4298 original size:32 final size:32
Alignment explanation
Indices: 4262--4352 Score: 128
Period size: 32 Copynumber: 2.8 Consensus size: 32
4252 GGGTTTGGGT
* * *
4262 TCGGGTTTTTTCGGGTTCGGGTATTTTCGGGC
1 TCGGGTTATGTCGGGTTCGGGTATTTTCGGAC
* * *
4294 TCGGGTCAAGTCGGGTTCGCGTATTTTCGGAC
1 TCGGGTTATGTCGGGTTCGGGTATTTTCGGAC
4326 TCGGGTTATGTCGGGTTCGGGTATTTT
1 TCGGGTTATGTCGGGTTCGGGTATTTT
4353 TGGGTTCAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.08, C:0.16, G:0.36, T:0.40
Consensus pattern (32 bp):
TCGGGTTATGTCGGGTTCGGGTATTTTCGGAC
Found at i:4547 original size:5 final size:5
Alignment explanation
Indices: 4530--4586 Score: 50
Period size: 5 Copynumber: 11.8 Consensus size: 5
4520 AAGTTTATTG
* *
4530 ATAAT AT-AT ATAAT AT-A- ATAAT ATAAT ATAAC ATTATT ATCAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A-TAAT AT-AAT ATAAT
4579 AT-AT ATAA
1 ATAAT ATAA
4587 AGATTGAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
3 2 0.05
4 10 0.24
5 23 0.55
6 7 0.17
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:4555 original size:13 final size:14
Alignment explanation
Indices: 4530--4586 Score: 71
Period size: 13 Copynumber: 3.9 Consensus size: 14
4520 AAGTTTATTG
4530 ATAATATATATAAT
1 ATAATATATATAAT
4544 ATAATA-ATATAAT
1 ATAATATATATAAT
*
4557 ATAACATTATTATCAAT
1 ATAATA-TA-TAT-AAT
4574 ATAATATATATAA
1 ATAATATATATAA
4587 AGATTGAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
13 12 0.32
14 8 0.22
15 4 0.11
16 5 0.14
17 8 0.22
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (14 bp):
ATAATATATATAAT
Found at i:4555 original size:22 final size:23
Alignment explanation
Indices: 4530--4586 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 23
4520 AAGTTTATTG
4530 ATAATATATATAATATAAT-AAT
1 ATAATATATATAATATAATCAAT
* * *
4552 ATAATATA-ACATTATTATCAAT
1 ATAATATATATAATATAATCAAT
4574 ATAATATATATAA
1 ATAATATATATAA
4587 AGATTGAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 7 0.25
22 19 0.68
23 2 0.07
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (23 bp):
ATAATATATATAATATAATCAAT
Found at i:5427 original size:16 final size:16
Alignment explanation
Indices: 5384--5427 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
5374 GTTCGGGCTG
*
5384 TTTAGGGTTCGGGTAT
1 TTTAGGGTTCGGGTAA
* *
5400 TTTCGGGCTCGGGTAA
1 TTTAGGGTTCGGGTAA
5416 TTTAGGGTTCGG
1 TTTAGGGTTCGG
5428 ATTCGGGCGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.11, C:0.11, G:0.39, T:0.39
Consensus pattern (16 bp):
TTTAGGGTTCGGGTAA
Done.