Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015408.1 Corchorus olitorius cultivar O-4 contig15441, 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: 78693
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:380 original size:15 final size:15
Alignment explanation
Indices: 336--383 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
326 ACCATCTTCC
336 TTCCTTCCCATTTCT
1 TTCCTTCCCATTTCT
* *
351 TTCC-CCCCCTCTTCT
1 TTCCTTCCCAT-TTCT
366 TTCCTTCCCATTTCT
1 TTCCTTCCCATTTCT
381 TTC
1 TTC
384 GTACCAAACA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
14 4 0.15
15 19 0.70
16 4 0.15
ACGTcount: A:0.04, C:0.46, G:0.00, T:0.50
Consensus pattern (15 bp):
TTCCTTCCCATTTCT
Found at i:13322 original size:15 final size:15
Alignment explanation
Indices: 13294--13362 Score: 68
Period size: 15 Copynumber: 4.5 Consensus size: 15
13284 CATGGAAAGT
* *
13294 ACTCTCTTGGGAATC
1 ACTCTCCTGAGAATC
* *
13309 ACTCTCCTTAGAATG
1 ACTCTCCTGAGAATC
13324 ACTCTCCATGGAGAA-C
1 ACTCTCC-T-GAGAATC
*
13340 ACTCTCCCGAGAATC
1 ACTCTCCTGAGAATC
13355 ACTCTCCT
1 ACTCTCCT
13363 TTGAAAGCAC
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
14 5 0.12
15 26 0.60
16 8 0.19
17 4 0.09
ACGTcount: A:0.25, C:0.33, G:0.14, T:0.28
Consensus pattern (15 bp):
ACTCTCCTGAGAATC
Found at i:13344 original size:31 final size:31
Alignment explanation
Indices: 13308--13378 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
13298 TCTTGGGAAT
* *
13308 CACTCTCCTTAGAATGACTCTCCATGGAGAA-
1 CACTCTCCTGAGAATCACTCTCCATGGA-AAG
* * *
13339 CACTCTCCCGAGAATCACTCTCCTTTGAAAG
1 CACTCTCCTGAGAATCACTCTCCATGGAAAG
13370 CACTCTCCT
1 CACTCTCCT
13379 CGGAAAGTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
30 2 0.06
31 31 0.94
ACGTcount: A:0.25, C:0.35, G:0.13, T:0.27
Consensus pattern (31 bp):
CACTCTCCTGAGAATCACTCTCCATGGAAAG
Found at i:21011 original size:21 final size:20
Alignment explanation
Indices: 20985--21027 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
20975 AAAAGTACTT
20985 TTTTATTAAATTTTACACAAA
1 TTTTATTAAATTTTAC-CAAA
**
21006 TTTTATTTCATTTTACCAAA
1 TTTTATTAAATTTTACCAAA
21026 TT
1 TT
21028 GTCTTACATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTTATTAAATTTTACCAAA
Found at i:21037 original size:20 final size:21
Alignment explanation
Indices: 20988--21038 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
20978 AGTACTTTTT
* *
20988 TATTAAATTTTACACAAATTT
1 TATTACATTTTACACAAATTG
*
21009 TATTTCATTTTAC-CAAATTG
1 TATTACATTTTACACAAATTG
*
21029 TCTTACATTT
1 TATTACATTT
21039 AATTGATACA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.33, C:0.14, G:0.02, T:0.51
Consensus pattern (21 bp):
TATTACATTTTACACAAATTG
Found at i:26232 original size:13 final size:13
Alignment explanation
Indices: 26214--26238 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26204 TGTATATGTA
26214 TATATATATACAC
1 TATATATATACAC
26227 TATATATATACA
1 TATATATATACA
26239 TATTAACTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (13 bp):
TATATATATACAC
Found at i:27580 original size:66 final size:66
Alignment explanation
Indices: 27470--27594 Score: 187
Period size: 66 Copynumber: 1.9 Consensus size: 66
27460 TTTGCATTCC
* * *
27470 CGAGTTGTTAACTCAATTGGTAGATGTACCGTGTCTGGATCGTGAGGTCCTGGGTTAAAATCTCT
1 CGAGTTGTTAACTCAACTGGTAGATGCACCGTGTCTGGACCGTGAGGTCCTGGGTTAAAATCTCT
27535 T
66 T
* * * *
27536 CGAGTTGTTAATTCAACTGGTAGGTGCATCGTGTCTGGACCGTGAGGTCCTGTGTTAAA
1 CGAGTTGTTAACTCAACTGGTAGATGCACCGTGTCTGGACCGTGAGGTCCTGGGTTAAA
27595 GTTTCATGCA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
66 52 1.00
ACGTcount: A:0.21, C:0.17, G:0.29, T:0.34
Consensus pattern (66 bp):
CGAGTTGTTAACTCAACTGGTAGATGCACCGTGTCTGGACCGTGAGGTCCTGGGTTAAAATCTCT
T
Found at i:39560 original size:14 final size:14
Alignment explanation
Indices: 39529--39558 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
39519 CGGTCTCACA
39529 TTTCTTTTTCTTTT
1 TTTCTTTTTCTTTT
39543 TTTC-TTTTCTTTT
1 TTTCTTTTTCTTTT
39556 TTT
1 TTT
39559 TCAATTACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (14 bp):
TTTCTTTTTCTTTT
Found at i:52230 original size:12 final size:12
Alignment explanation
Indices: 52213--52239 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
52203 TGATATATAA
52213 TAATTAACGTTG
1 TAATTAACGTTG
52225 TAATTAACGTTG
1 TAATTAACGTTG
52237 TAA
1 TAA
52240 GAGTTCTGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (12 bp):
TAATTAACGTTG
Found at i:52532 original size:60 final size:60
Alignment explanation
Indices: 52461--52596 Score: 166
Period size: 60 Copynumber: 2.3 Consensus size: 60
52451 AAGATTTGCC
* * * * *
52461 AAAATGTTCAAATAAGAGCCCAATCTTTTAATTTGGCCAAATAAGGGTCTAA-TGTTATTG
1 AAAATGCTCAAATAAGAGCCCAATCTTTTAATTTGGCCAAATAAAGGCCTAACAG-TATCG
* ** **
52521 AAAATGCTCAAATAAGGGTTCGGTCTTTTAATTTGGCCAAATAAAGGCCTAACAGTATCG
1 AAAATGCTCAAATAAGAGCCCAATCTTTTAATTTGGCCAAATAAAGGCCTAACAGTATCG
52581 AAAATGCTCAAATAAG
1 AAAATGCTCAAATAAG
52597 GGTCTGTCGT
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
60 64 0.98
61 1 0.02
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (60 bp):
AAAATGCTCAAATAAGAGCCCAATCTTTTAATTTGGCCAAATAAAGGCCTAACAGTATCG
Found at i:52597 original size:60 final size:60
Alignment explanation
Indices: 52484--52599 Score: 180
Period size: 60 Copynumber: 1.9 Consensus size: 60
52474 AAGAGCCCAA
* * * *
52484 TCTTTTAATTTGGCCAAATAAGGGTCTAATGTTATTGAAAATGCTCAAATAAGGGTTCGG
1 TCTTTTAATTTGGCCAAATAAAGGCCTAAAGTTATCGAAAATGCTCAAATAAGGGTTCGG
52544 TCTTTTAATTTGGCCAAATAAAGGCCTAACAG-TATCGAAAATGCTCAAATAAGGGT
1 TCTTTTAATTTGGCCAAATAAAGGCCTAA-AGTTATCGAAAATGCTCAAATAAGGGT
52600 CTGTCGTCAG
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
60 50 0.98
61 1 0.02
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (60 bp):
TCTTTTAATTTGGCCAAATAAAGGCCTAAAGTTATCGAAAATGCTCAAATAAGGGTTCGG
Done.