Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021270.1 Corchorus olitorius cultivar O-4 contig21303, 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: 36252
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:16312 original size:17 final size:17
Alignment explanation
Indices: 16278--16323 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
16268 TTTTATCGTG
*
16278 TCAGTTTCTTTTCTAGTC
1 TCAGTTTC-TTTCGAGTC
16296 TCAGTTTCTTTCGAGTC
1 TCAGTTTCTTTCGAGTC
*
16313 TGAGTTTCTTT
1 TCAGTTTCTTT
16324 TCAAGTCTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 18 0.69
18 8 0.31
ACGTcount: A:0.11, C:0.20, G:0.15, T:0.54
Consensus pattern (17 bp):
TCAGTTTCTTTCGAGTC
Found at i:16332 original size:18 final size:18
Alignment explanation
Indices: 16280--16333 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 18
16270 TTATCGTGTC
* *
16280 AGTTTCTTTTCTAGTCTC
1 AGTTTCTTTTCAAGTCTG
*
16298 AGTTTC-TTTCGAGTCTG
1 AGTTTCTTTTCAAGTCTG
16315 AGTTTCTTTTCAAGTCTG
1 AGTTTCTTTTCAAGTCTG
16333 A
1 A
16334 ATCTTATGCT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
17 15 0.47
18 17 0.53
ACGTcount: A:0.15, C:0.19, G:0.17, T:0.50
Consensus pattern (18 bp):
AGTTTCTTTTCAAGTCTG
Found at i:19195 original size:13 final size:13
Alignment explanation
Indices: 19157--19198 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
19147 CACCTCAAAA
19157 ATCAAGAAAATT-
1 ATCAAGAAAATTC
*
19169 ATCAA-AACATTC
1 ATCAAGAAAATTC
*
19181 ATCAAGAATATTC
1 ATCAAGAAAATTC
19194 ATCAA
1 ATCAA
19199 AGAACTTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
11 5 0.19
12 10 0.38
13 11 0.42
ACGTcount: A:0.52, C:0.17, G:0.05, T:0.26
Consensus pattern (13 bp):
ATCAAGAAAATTC
Found at i:21246 original size:29 final size:29
Alignment explanation
Indices: 21213--21269 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
21203 TCTCTGTTCC
21213 TAAAACTATTTATTTAAATTCTTGCCAAA
1 TAAAACTATTTATTTAAATTCTTGCCAAA
21242 TAAAACTATTTATTTAAATTCTTGCCAA
1 TAAAACTATTTATTTAAATTCTTGCCAA
21270 TGAGAATTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.40, C:0.14, G:0.04, T:0.42
Consensus pattern (29 bp):
TAAAACTATTTATTTAAATTCTTGCCAAA
Found at i:21330 original size:3 final size:3
Alignment explanation
Indices: 21324--21375 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
21314 TAATACTCTC
21324 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
21372 TAA T
1 TAA T
21376 GTTAGTAAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:26023 original size:2 final size:2
Alignment explanation
Indices: 26016--26041 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
26006 AAATATAAGA
26016 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
26042 GTATGTATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26653 original size:2 final size:2
Alignment explanation
Indices: 26648--26683 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
26638 CTTTTGAAGA
26648 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26684 GTACTAGCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29640 original size:21 final size:21
Alignment explanation
Indices: 29614--29657 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
29604 AAAGATAATA
29614 TATTAACTAGTTAATTAAATT
1 TATTAACTAGTTAATTAAATT
29635 TATTAACTAGTTAATTAAATT
1 TATTAACTAGTTAATTAAATT
29656 TA
1 TA
29658 AAAATATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (21 bp):
TATTAACTAGTTAATTAAATT
Found at i:30544 original size:23 final size:23
Alignment explanation
Indices: 30517--30565 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
30507 TGTTATAAGG
30517 AAAATAAA-ATATTGGAAAAAAAT
1 AAAATAAATA-ATTGGAAAAAAAT
* *
30540 AAAATTACTAATTGGAAAAAAAT
1 AAAATAAATAATTGGAAAAAAAT
30563 AAA
1 AAA
30566 TACTACTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 22 0.96
24 1 0.04
ACGTcount: A:0.67, C:0.02, G:0.08, T:0.22
Consensus pattern (23 bp):
AAAATAAATAATTGGAAAAAAAT
Found at i:30572 original size:24 final size:23
Alignment explanation
Indices: 30527--30572 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
30517 AAAATAAAAT
*
30527 ATTGGAAAAAAATAAAATTACTA
1 ATTGGAAAAAAATAAAACTACTA
30550 ATTGGAAAAAAATAAATACTACT
1 ATTGGAAAAAAATAAA-ACTACT
30573 CATGTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.59, C:0.07, G:0.09, T:0.26
Consensus pattern (23 bp):
ATTGGAAAAAAATAAAACTACTA
Found at i:33198 original size:22 final size:24
Alignment explanation
Indices: 33155--33214 Score: 72
Period size: 22 Copynumber: 2.6 Consensus size: 24
33145 ATATTTTTAT
33155 AAAATTTTGATAA-CTACCCTAT-
1 AAAATTTTGATAATCTACCCTATA
* *
33177 TAAATTTTGATAATC-ACGCTATGA
1 AAAATTTTGATAATCTACCCTAT-A
33201 AAAATTTTGATAAT
1 AAAATTTTGATAAT
33215 TATCTAGTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 18 0.56
23 1 0.03
24 13 0.41
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (24 bp):
AAAATTTTGATAATCTACCCTATA
Found at i:33282 original size:22 final size:23
Alignment explanation
Indices: 33257--33301 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
33247 AATAACCTAA
33257 CTATGAAATTTTG-TAACCTTCC
1 CTATGAAATTTTGTTAACCTTCC
* *
33279 CTATGAGATTTTGTTAATCTTCC
1 CTATGAAATTTTGTTAACCTTCC
33302 TATAATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.44
Consensus pattern (23 bp):
CTATGAAATTTTGTTAACCTTCC
Found at i:34017 original size:2 final size:2
Alignment explanation
Indices: 34010--34041 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
34000 GTAGTTAGAA
34010 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
34042 GTTTGAGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.