Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014459.1 Corchorus olitorius cultivar O-4 contig14492, 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: 4766
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Found at i:4375 original size:33 final size:33
Alignment explanation
Indices: 4317--4533 Score: 380
Period size: 33 Copynumber: 6.5 Consensus size: 33
4307 AATGTGAGTG
*
4317 AAGGCAAGTTCAATGTTTTTTGGATGTGAGAAAT
1 AAGGCAAGTTCAATG-TTTTTGGATGTGAGAATT
*
4351 AAGGCAAGTTCAATGTTTTTGGATGTGAGAAAT
1 AAGGCAAGTTCAATGTTTTTGGATGTGAGAATT
4384 AAGGCAAGTTCAATGTTTTTGGATTGTGAGAATT
1 AAGGCAAGTTCAATGTTTTTGGA-TGTGAGAATT
*
4418 AAGGCAAGTTCAATGTTTTTGGATGTGGGAATT
1 AAGGCAAGTTCAATGTTTTTGGATGTGAGAATT
4451 AAGGCAAGTTCAATGTTTTTGGATTGTGAGAATT
1 AAGGCAAGTTCAATGTTTTTGGA-TGTGAGAATT
4485 AAGGCAAGTTCAATGTTTTTGGATGTGAGAATT
1 AAGGCAAGTTCAATGTTTTTGGATGTGAGAATT
4518 AAGGCAAGTTCAATGT
1 AAGGCAAGTTCAATGT
4534 CAATTGGGAA
Statistics
Matches: 178, Mismatches: 3, Indels: 5
0.96 0.02 0.03
Matches are distributed among these distances:
33 99 0.56
34 79 0.44
ACGTcount: A:0.31, C:0.06, G:0.27, T:0.35
Consensus pattern (33 bp):
AAGGCAAGTTCAATGTTTTTGGATGTGAGAATT
Found at i:4425 original size:67 final size:67
Alignment explanation
Indices: 4317--4533 Score: 391
Period size: 67 Copynumber: 3.2 Consensus size: 67
4307 AATGTGAGTG
*
4317 AAGGCAAGTTCAATGTTTTTTGGA-TGTGAGAAATAAGGCAAGTTCAATGTTTTTGGATGTGAGA
1 AAGGCAAGTTCAATG-TTTTTGGATTGTGAGAATTAAGGCAAGTTCAATGTTTTTGGATGTGAGA
*
4381 AAT
65 ATT
*
4384 AAGGCAAGTTCAATGTTTTTGGATTGTGAGAATTAAGGCAAGTTCAATGTTTTTGGATGTGGGAA
1 AAGGCAAGTTCAATGTTTTTGGATTGTGAGAATTAAGGCAAGTTCAATGTTTTTGGATGTGAGAA
4449 TT
66 TT
4451 AAGGCAAGTTCAATGTTTTTGGATTGTGAGAATTAAGGCAAGTTCAATGTTTTTGGATGTGAGAA
1 AAGGCAAGTTCAATGTTTTTGGATTGTGAGAATTAAGGCAAGTTCAATGTTTTTGGATGTGAGAA
4516 TT
66 TT
4518 AAGGCAAGTTCAATGT
1 AAGGCAAGTTCAATGT
4534 CAATTGGGAA
Statistics
Matches: 145, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
66 8 0.06
67 137 0.94
ACGTcount: A:0.31, C:0.06, G:0.27, T:0.35
Consensus pattern (67 bp):
AAGGCAAGTTCAATGTTTTTGGATTGTGAGAATTAAGGCAAGTTCAATGTTTTTGGATGTGAGAA
TT
Found at i:4568 original size:22 final size:22
Alignment explanation
Indices: 4503--4569 Score: 57
Period size: 20 Copynumber: 3.1 Consensus size: 22
4493 TTCAATGTTT
4503 TTGGATGTGAGAATTAAGGCAAG
1 TTGGATGTGAGAA-TAAGGCAAG
** * ** *
4526 TTCAATGT--CAATTGGGAAAG
1 TTGGATGTGAGAATAAGGCAAG
4546 TTGGATGTGAGAATAAGGCAAG
1 TTGGATGTGAGAATAAGGCAAG
4568 TT
1 TT
4570 CAATGTCAAT
Statistics
Matches: 30, Mismatches: 12, Indels: 5
0.64 0.26 0.11
Matches are distributed among these distances:
20 12 0.40
21 2 0.07
22 10 0.33
23 6 0.20
ACGTcount: A:0.34, C:0.06, G:0.31, T:0.28
Consensus pattern (22 bp):
TTGGATGTGAGAATAAGGCAAG
Found at i:4575 original size:22 final size:22
Alignment explanation
Indices: 4507--4575 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 22
4497 ATGTTTTTGG
4507 ATGTGAGAATTAAGGCAAGTTCA
1 ATGTGAGAA-TAAGGCAAGTTCA
* ** * **
4530 ATGT--CAATTGGGAAAGTTGG
1 ATGTGAGAATAAGGCAAGTTCA
4550 ATGTGAGAATAAGGCAAGTTCA
1 ATGTGAGAATAAGGCAAGTTCA
4572 ATGT
1 ATGT
4576 CAATTGGGAA
Statistics
Matches: 32, Mismatches: 12, Indels: 5
0.65 0.24 0.10
Matches are distributed among these distances:
20 12 0.38
21 2 0.06
22 14 0.44
23 4 0.12
ACGTcount: A:0.36, C:0.07, G:0.29, T:0.28
Consensus pattern (22 bp):
ATGTGAGAATAAGGCAAGTTCA
Found at i:4614 original size:83 final size:82
Alignment explanation
Indices: 4513--4667 Score: 240
Period size: 83 Copynumber: 1.9 Consensus size: 82
4503 TTGGATGTGA
* * *
4513 GAATTAAGGCAAGTTCAATGTCAATTGGGAAAGTTGGATGTGAGAAT-AAGGCAAGTTCAATGTC
1 GAATCAAGGCAAGTTCAATGTCAATTGGGAAAGTTGAATGT--GAATCAAGGAAAGTTCAATGTC
4577 AATTGGGAATGTTGAAAGT
64 AATTGGGAATGTTGAAAGT
* *
4596 GAATCAAGGCAAGTTCAATGTTAATTGGGAATGTTGAATGTGAATCAAGGAAAGTTCAATGTCAA
1 GAATCAAGGCAAGTTCAATGTCAATTGGGAAAGTTGAATGTGAATCAAGGAAAGTTCAATGTCAA
4661 TTGGGAA
66 TTGGGAA
4668 ATTCAATGTG
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 4 0.06
82 25 0.38
83 37 0.56
ACGTcount: A:0.37, C:0.08, G:0.28, T:0.28
Consensus pattern (82 bp):
GAATCAAGGCAAGTTCAATGTCAATTGGGAAAGTTGAATGTGAATCAAGGAAAGTTCAATGTCAA
TTGGGAATGTTGAAAGT
Found at i:4622 original size:41 final size:41
Alignment explanation
Indices: 4513--4680 Score: 232
Period size: 41 Copynumber: 4.1 Consensus size: 41
4503 TTGGATGTGA
* * *
4513 GAATTAAGGCAAGTTCAATGTCAATTGGGAAAGTTGGATGT
1 GAATCAAGGCAAGTTCAATGTCAATTGGGAATGTTGAATGT
*
4554 GAGAAT-AAGGCAAGTTCAATGTCAATTGGGAATGTTGAAAGT
1 --GAATCAAGGCAAGTTCAATGTCAATTGGGAATGTTGAATGT
*
4596 GAATCAAGGCAAGTTCAATGTTAATTGGGAATGTTGAATGT
1 GAATCAAGGCAAGTTCAATGTCAATTGGGAATGTTGAATGT
* * *
4637 GAATCAAGGAAAGTTCAATGTCAATTGGGAA-ATTCAATGT
1 GAATCAAGGCAAGTTCAATGTCAATTGGGAATGTTGAATGT
4677 GAAT
1 GAAT
4681 GCGCCGCGTA
Statistics
Matches: 115, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
40 15 0.13
41 63 0.55
42 33 0.29
43 4 0.03
ACGTcount: A:0.37, C:0.08, G:0.27, T:0.29
Consensus pattern (41 bp):
GAATCAAGGCAAGTTCAATGTCAATTGGGAATGTTGAATGT
Done.