Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020248.1 Corchorus olitorius cultivar O-4 contig20281, 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: 21675
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Found at i:191 original size:26 final size:27
Alignment explanation
Indices: 162--222 Score: 74
Period size: 25 Copynumber: 2.3 Consensus size: 27
152 AATTTCCTTA
*
162 TTTCTTTTTTTTTCCTTCC--TTTTTC
1 TTTCTTTTCTTTTCCTTCCTATTTTTC
*
187 TTT-TCTTTCTTTTCCTTTCTATTTTTC
1 TTTCT-TTTCTTTTCCTTCCTATTTTTC
214 TTTCTTTTC
1 TTTCTTTTC
223 CCTTTTTGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
24 1 0.03
25 15 0.50
27 13 0.43
28 1 0.03
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (27 bp):
TTTCTTTTCTTTTCCTTCCTATTTTTC
Found at i:281 original size:14 final size:14
Alignment explanation
Indices: 262--291 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
252 TTCTCTTCTC
262 TTCTTTTTTTTTTT
1 TTCTTTTTTTTTTT
276 TTCTTTTTTTTTTT
1 TTCTTTTTTTTTTT
290 TT
1 TT
292 TGGTTTGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (14 bp):
TTCTTTTTTTTTTT
Found at i:282 original size:13 final size:13
Alignment explanation
Indices: 266--290 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
256 CTTCTCTTCT
266 TTTTTTTTTTTTC
1 TTTTTTTTTTTTC
279 TTTTTTTTTTTT
1 TTTTTTTTTTTT
291 TTGGTTTGGT
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:0.00, C:0.04, G:0.00, T:0.96
Consensus pattern (13 bp):
TTTTTTTTTTTTC
Found at i:285 original size:17 final size:17
Alignment explanation
Indices: 260--292 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
250 TCTTCTCTTC
260 TCTTCTTTTTTTTTTTT
1 TCTTCTTTTTTTTTTTT
277 TCTT-TTTTTTTTTTTT
1 TCTTCTTTTTTTTTTTT
293 GGTTTGGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (17 bp):
TCTTCTTTTTTTTTTTT
Found at i:7123 original size:14 final size:15
Alignment explanation
Indices: 7103--7137 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
7093 GTTTGATAAA
7103 ACTGAAA-ATTAAGT
1 ACTGAAAGATTAAGT
*
7117 GCTGAAAGATTAAGT
1 ACTGAAAGATTAAGT
7132 ACTGAA
1 ACTGAA
7138 TTTTCAATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.46, C:0.09, G:0.20, T:0.26
Consensus pattern (15 bp):
ACTGAAAGATTAAGT
Found at i:19522 original size:248 final size:251
Alignment explanation
Indices: 19050--19553 Score: 712
Period size: 248 Copynumber: 2.0 Consensus size: 251
19040 ACAGGGGAAG
* * * * *
19050 AAGAATAAGAAGAATCGAAAAAGGAAGTAAGCCCCGCACGAAGGGAATGGAGGCAAGTGGCAGCA
1 AAGAAGAAGAAGAATCAAAAAAGGAAGTAAGCCCCGCACGAACGAAATGGAGGCAAGTAGCAGCA
* * *
19115 GCTGATCAATGGGTAGTTTTGCATTAATGGCTGAAATAACAATGGAATGGAACATATATCTTAGT
66 GCTGATCAAAGGGCAGTTTTGCATTAATGGCTGAAATAACAATGGAATGGAAC--A-ATCGTAGT
* * * *
19180 CTTAAAATGTACTAGCTTTCTCAAACCTATTTGGACAATCGTCTTTATGCTTAAAAATAGTAGTT
128 CTTAAAATGCACTAACTTTCTCAAACCTATTTGAACAATAGTCTTTATGCTTAAAAATAGTAGTT
* * *
19245 GAACTGAGTACTCTTCATGGATTGAAGATGTCGAAAT-AACGCAGCTATATATGGACCTC
193 GAAATGAGTACTCTCCATGGATTGAAGATGTCCAAATCAA-GCAGCTATATATGGACCTC
* *
19304 AAGAAGAAGAGGAATCAAAAAAGGAAGTAATCCCCGCACGAACGAAATGGAGGCAAGTAGCAGCA
1 AAGAAGAAGAAGAATCAAAAAAGGAAGTAAGCCCCGCACGAACGAAATGGAGGCAAGTAGCAGCA
* * *
19369 GCTGATCAAAGGGCGGTTTTGCATTAATGGTTGAAATAGCAATGGAATGGAAC-AT-GTA-TCTT
66 GCTGATCAAAGGGCAGTTTTGCATTAATGGCTGAAATAACAATGGAATGGAACAATCGTAGTCTT
* *
19431 AAAATGCACTAACTTTTTCAAACCTATTTGAACAATAGTCTTTATG-TTAGAAATTAGTAGTTGA
131 AAAATGCACTAACTTTCTCAAACCTATTTGAACAATAGTCTTTATGCTTA-AAAATAGTAGTTGA
**
19495 AATGAGTACTCTCCATGGATTGAAGATGTCCAAATCAAGTTGCTATATATGGACCTC
195 AATGAGTACTCTCCATGGATTGAAGATGTCCAAATCAAGCAGCTATATATGGACCTC
19552 AA
1 AA
19554 TGGTTCTTCT
Statistics
Matches: 224, Mismatches: 24, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
247 3 0.01
248 109 0.49
249 4 0.02
250 2 0.01
254 106 0.47
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (251 bp):
AAGAAGAAGAAGAATCAAAAAAGGAAGTAAGCCCCGCACGAACGAAATGGAGGCAAGTAGCAGCA
GCTGATCAAAGGGCAGTTTTGCATTAATGGCTGAAATAACAATGGAATGGAACAATCGTAGTCTT
AAAATGCACTAACTTTCTCAAACCTATTTGAACAATAGTCTTTATGCTTAAAAATAGTAGTTGAA
ATGAGTACTCTCCATGGATTGAAGATGTCCAAATCAAGCAGCTATATATGGACCTC
Done.