Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023045.1 Corchorus olitorius cultivar O-4 contig23078, 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: 32772
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:2185 original size:12 final size:12
Alignment explanation
Indices: 2168--2197 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
2158 CAAAACAGGA
2168 TGTATGTGATTC
1 TGTATGTGATTC
2180 TGTATGTGATTC
1 TGTATGTGATTC
2192 TGTATG
1 TGTATG
2198 GATGGATGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.17, C:0.07, G:0.27, T:0.50
Consensus pattern (12 bp):
TGTATGTGATTC
Found at i:13263 original size:19 final size:18
Alignment explanation
Indices: 13230--13265 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
13220 TTGAAATTAT
13230 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
13248 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
13266 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:14132 original size:18 final size:18
Alignment explanation
Indices: 14109--14145 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
14099 CTCCTCTATC
*
14109 ATGAAAACACTTCTTTTT
1 ATGAAAACAATTCTTTTT
*
14127 ATGAAAACAATTTTTTTT
1 ATGAAAACAATTCTTTTT
14145 A
1 A
14146 GATTACCCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (18 bp):
ATGAAAACAATTCTTTTT
Found at i:14511 original size:22 final size:22
Alignment explanation
Indices: 14483--14528 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
14473 AAAATTGGGG
14483 AAAATAAGATTAATCCAAAAAC
1 AAAATAAGATTAATCCAAAAAC
14505 AAAATAAGATTAATCCAAAAAC
1 AAAATAAGATTAATCCAAAAAC
14527 AA
1 AA
14529 TCAAATTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.65, C:0.13, G:0.04, T:0.17
Consensus pattern (22 bp):
AAAATAAGATTAATCCAAAAAC
Found at i:14847 original size:30 final size:30
Alignment explanation
Indices: 14808--14866 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
14798 GTTTATTAAT
14808 GAAACTTGAAAATTAAAGACATAAAATAAAG
1 GAAACTTGAAAATTAAAG-CATAAAATAAAG
*
14839 GAAA-TTGAAAATTAAAGCATAAAGTAAA
1 GAAACTTGAAAATTAAAGCATAAAATAAA
14867 TAACTAATCC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 10 0.37
30 13 0.48
31 4 0.15
ACGTcount: A:0.61, C:0.05, G:0.14, T:0.20
Consensus pattern (30 bp):
GAAACTTGAAAATTAAAGCATAAAATAAAG
Found at i:19463 original size:18 final size:18
Alignment explanation
Indices: 19426--19463 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
19416 CTAGCCCTAA
*
19426 AACTAGAAGAAAAACTAG
1 AACTAGAAGAAAAACAAG
19444 AACTAGAAGAGAAAA-AAG
1 AACTAGAAGA-AAAACAAG
19462 AA
1 AA
19464 GAAGAGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.66, C:0.08, G:0.18, T:0.08
Consensus pattern (18 bp):
AACTAGAAGAAAAACAAG
Found at i:20079 original size:19 final size:18
Alignment explanation
Indices: 20046--20081 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
20036 TTGAAATTAT
20046 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
20064 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
20082 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:22580 original size:5 final size:5
Alignment explanation
Indices: 22565--22619 Score: 64
Period size: 5 Copynumber: 11.6 Consensus size: 5
22555 ATGCAAAGAG
*
22565 ACAAA AAAAA ACAAA A-AACA A-AAA ACAAA A-AAA A-AAA ACAAA ACAAA
1 ACAAA ACAAA ACAAA ACAA-A ACAAA ACAAA ACAAA ACAAA ACAAA ACAAA
22612 ACAAA ACA
1 ACAAA ACA
22620 TTGTTCCTAC
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
4 12 0.27
5 33 0.73
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (5 bp):
ACAAA
Found at i:22582 original size:7 final size:7
Alignment explanation
Indices: 22570--22607 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
22560 AAGAGACAAA
22570 AAAAAAC
1 AAAAAAC
22577 AAAAAAC
1 AAAAAAC
22584 AAAAAAC
1 AAAAAAC
22591 AAAAAA-
1 AAAAAAC
22597 AAAAAAC
1 AAAAAAC
22604 AAAA
1 AAAA
22608 CAAAACAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.20
7 24 0.80
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:22589 original size:14 final size:13
Alignment explanation
Indices: 22567--22619 Score: 79
Period size: 14 Copynumber: 3.8 Consensus size: 13
22557 GCAAAGAGAC
22567 AAAAAAAAACAAA
1 AAAAAAAAACAAA
22580 AAACAAAAAACAAA
1 AAA-AAAAAACAAA
22594 AAAAAAAAACAAA
1 AAAAAAAAACAAA
22607 ACAAAACAAAACA
1 A-AAAA-AAAACA
22620 TTGTTCCTAC
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
13 14 0.38
14 17 0.46
15 6 0.16
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAACAAA
Found at i:22594 original size:13 final size:13
Alignment explanation
Indices: 22570--22612 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
22560 AAGAGACAAA
22570 AAAAAACAAAAAAC
1 AAAAAAC-AAAAAC
*
22584 AAAAAACAAAAAA
1 AAAAAACAAAAAC
22597 AAAAAAC-AAAAC
1 AAAAAACAAAAAC
22609 AAAA
1 AAAA
22613 CAAAACATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
12 8 0.30
13 12 0.44
14 7 0.26
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAACAAAAAC
Found at i:30246 original size:15 final size:15
Alignment explanation
Indices: 30226--30260 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
30216 AGAGGGCTTA
*
30226 TCAGCAGCAACTTTC
1 TCAGCAGCAACCTTC
*
30241 TCAGCAGGAACCTTC
1 TCAGCAGCAACCTTC
30256 TCAGC
1 TCAGC
30261 TGAAGCTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.34, G:0.17, T:0.23
Consensus pattern (15 bp):
TCAGCAGCAACCTTC
Found at i:32552 original size:28 final size:30
Alignment explanation
Indices: 32512--32584 Score: 107
Period size: 29 Copynumber: 2.5 Consensus size: 30
32502 GTTAAAAGGG
*
32512 TAAAACTGTAAATTTAAC-C-TTCTTAGGA
1 TAAAACGGTAAATTTAACTCATTCTTAGGA
32540 TAAAACGGTAAATTT-ACTCATTCTTAGGA
1 TAAAACGGTAAATTTAACTCATTCTTAGGA
*
32569 TAAAACGGTAATTTTA
1 TAAAACGGTAAATTTA
32585 TGCCTATACA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
27 2 0.05
28 15 0.38
29 23 0.57
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (30 bp):
TAAAACGGTAAATTTAACTCATTCTTAGGA
Done.