Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019241.1 Corchorus olitorius cultivar O-4 contig19274, 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: 77402
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:10934 original size:20 final size:20
Alignment explanation
Indices: 10909--10947 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
10899 CTTTATCACC
10909 TTTGCTTGGTCCTTAACTTT
1 TTTGCTTGGTCCTTAACTTT
10929 TTTGCTTGGTCCTTAACTT
1 TTTGCTTGGTCCTTAACTT
10948 ATGCACCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.21, G:0.15, T:0.54
Consensus pattern (20 bp):
TTTGCTTGGTCCTTAACTTT
Found at i:21220 original size:65 final size:67
Alignment explanation
Indices: 21151--21288 Score: 183
Period size: 71 Copynumber: 2.0 Consensus size: 67
21141 GTAAGTTAGA
*
21151 TAGGGAAAATAACTTT-C-CTGGTTGGAGG-AATCTAATTTTAGGTGAAAATGTTATTCCCATCA
1 TAGGGAAAATAACTTTCCTCTGGTTGG-GGAAATCTAATTTTAGGTGAAAATGTCATTCCCATCA
21213 CTT
65 CTT
**
21216 TAGGGAAAATAACTTTCCCATGTCTGGTTGGGGAAATCTAATTTTAGGTGGGAATGTCATTCCCA
1 TAGGGAAAATAACTTT-CC---TCTGGTTGGGGAAATCTAATTTTAGGTGAAAATGTCATTCCCA
21281 TCACTT
62 TCACTT
21287 TA
1 TA
21289 CCATATTCTC
Statistics
Matches: 63, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
65 16 0.25
67 1 0.02
70 2 0.03
71 44 0.70
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (67 bp):
TAGGGAAAATAACTTTCCTCTGGTTGGGGAAATCTAATTTTAGGTGAAAATGTCATTCCCATCAC
TT
Found at i:26340 original size:39 final size:39
Alignment explanation
Indices: 26262--26343 Score: 119
Period size: 39 Copynumber: 2.1 Consensus size: 39
26252 CAAGAACAGG
** * *
26262 TGTTATGAGATTTCAATTGTATTTGTTGGGGGAGGGGTT
1 TGTTATGAGATTTCAATTGTATTTGTTAAGGAAGAGGTT
*
26301 TGTTATGAGATTTTAATTGTATTTGTTAAGGAAGAGGTT
1 TGTTATGAGATTTCAATTGTATTTGTTAAGGAAGAGGTT
26340 TGTT
1 TGTT
26344 GGCTTATAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.22, C:0.01, G:0.30, T:0.46
Consensus pattern (39 bp):
TGTTATGAGATTTCAATTGTATTTGTTAAGGAAGAGGTT
Found at i:26589 original size:34 final size:32
Alignment explanation
Indices: 26518--26598 Score: 94
Period size: 34 Copynumber: 2.5 Consensus size: 32
26508 AAAAAAAATT
* *
26518 AAGTACTAGTAGTA-ATTTTTTCGTTGGCACA
1 AAGTACTAGTAGTATTTTTTTTCGTTGACACA
**
26549 AA-TACTAGTAGTATTTTTTTTTTTATGACATCA
1 AAGTACTAGTAGTATTTTTTTTCGT-TGACA-CA
26582 AAGTACTAGTAGTATTT
1 AAGTACTAGTAGTATTT
26599 AGGAGGAGTA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
30 11 0.26
31 9 0.21
32 4 0.10
33 4 0.10
34 14 0.33
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (32 bp):
AAGTACTAGTAGTATTTTTTTTCGTTGACACA
Found at i:34241 original size:16 final size:17
Alignment explanation
Indices: 34220--34252 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
34210 TGAGAGATGA
34220 AGAGAAGAA-AGATTTG
1 AGAGAAGAAGAGATTTG
34236 AGAGAAGAAGAGATTTG
1 AGAGAAGAAGAGATTTG
34253 TAACAAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.48, C:0.00, G:0.33, T:0.18
Consensus pattern (17 bp):
AGAGAAGAAGAGATTTG
Found at i:34245 original size:24 final size:22
Alignment explanation
Indices: 34198--34248 Score: 68
Period size: 24 Copynumber: 2.3 Consensus size: 22
34188 GCAGCAGAGA
*
34198 AAGA-AAGAAAATTGAGAGATG
1 AAGAGAAGAAAATTGAGAGAAG
34219 AAGAGAAGAAAGATTTGAGAGAAG
1 AAGAGAAGAAA-A-TTGAGAGAAG
34243 AAGAGA
1 AAGAGA
34249 TTTGTAACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 4 0.15
22 6 0.23
23 1 0.04
24 15 0.58
ACGTcount: A:0.57, C:0.00, G:0.31, T:0.12
Consensus pattern (22 bp):
AAGAGAAGAAAATTGAGAGAAG
Found at i:38419 original size:13 final size:13
Alignment explanation
Indices: 38401--38426 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38391 GATGGGCTTT
38401 ACCCTTATAATAG
1 ACCCTTATAATAG
38414 ACCCTTATAATAG
1 ACCCTTATAATAG
38427 GCTAACTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (13 bp):
ACCCTTATAATAG
Found at i:62605 original size:2 final size:2
Alignment explanation
Indices: 62598--62629 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
62588 AATCCGAATC
62598 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
62630 GATGATTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.