Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012423.1 Corchorus olitorius cultivar O-4 contig12456, 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: 12407
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Found at i:317 original size:65 final size:67
Alignment explanation
Indices: 248--388 Score: 223
Period size: 67 Copynumber: 2.1 Consensus size: 67
238 TCAATATTCA
*
248 AATCAATCAATTTAATATCA-TTAGTACTAATTGATTCTAATTGGATC-AAGATATTCAAATCAA
1 AATCAATCAATTTAATATCATTTAGTACTAATTGATTCTAATTGAATCAAAGATATTCAAATCAA
311 TC
66 TC
* *
313 AATCAATCAATTTAATATCATTTTAGTACTAATTGATTCTAATTGAATCAAAATATATTCAAATG
1 AATCAATCAATTTAATATCA-TTTAGTACTAATTGATTCTAATTGAATC-AAAGATATTCAAATC
378 AATC
64 AATC
382 AATCAAT
1 AATCAAT
389 TTAATATATA
Statistics
Matches: 69, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
65 20 0.29
67 26 0.38
69 23 0.33
ACGTcount: A:0.43, C:0.13, G:0.06, T:0.38
Consensus pattern (67 bp):
AATCAATCAATTTAATATCATTTAGTACTAATTGATTCTAATTGAATCAAAGATATTCAAATCAA
TC
Found at i:389 original size:65 final size:64
Alignment explanation
Indices: 248--395 Score: 210
Period size: 65 Copynumber: 2.3 Consensus size: 64
238 TCAATATTCA
* *
248 AATCAATCAATTTAATATCATTAGTACTAATTGATTCTAATTGGATCAAGATATTCAAATCAATC
1 AATCAATCAATTTAATATCATTAGTACTAATTGATTCTAATTGAATCAAAATATT-AAATCAATC
*
313 AATCAATCAATTTAATATCATTTTAGTACTAATTGATTCTAATTGAATCAAAATA-T-ATTCAAA
1 AATCAATCAATTTAATATCA--TTAGTACTAATTGATTCTAATTGAATCAAAATATTAAATC-AA
*
376 TG
63 TC
378 AATCAATCAATTTAATAT
1 AATCAATCAATTTAATAT
396 ATATAAATTG
Statistics
Matches: 76, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
64 3 0.04
65 41 0.54
66 1 0.01
67 31 0.41
ACGTcount: A:0.43, C:0.12, G:0.06, T:0.39
Consensus pattern (64 bp):
AATCAATCAATTTAATATCATTAGTACTAATTGATTCTAATTGAATCAAAATATTAAATCAATC
Found at i:506 original size:2 final size:2
Alignment explanation
Indices: 499--544 Score: 76
Period size: 2 Copynumber: 23.0 Consensus size: 2
489 ATAGTTTTAA
499 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
541 AT AT
1 AT AT
545 GATTAGCTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.02
2 39 0.93
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1334 original size:17 final size:17
Alignment explanation
Indices: 1312--1363 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
1302 TGCTAATTTC
1312 TATTATCCTTTTGCTTT
1 TATTATCCTTTTGCTTT
**
1329 TATTAT-AATTT-C---
1 TATTATCCTTTTGCTTT
1341 TATTATCCTTTTGCTTT
1 TATTATCCTTTTGCTTT
1358 TATTAT
1 TATTAT
1364 TGGTTTATTC
Statistics
Matches: 26, Mismatches: 4, Indels: 10
0.65 0.10 0.25
Matches are distributed among these distances:
12 6 0.23
13 3 0.12
14 1 0.04
15 1 0.04
16 3 0.12
17 12 0.46
ACGTcount: A:0.19, C:0.13, G:0.04, T:0.63
Consensus pattern (17 bp):
TATTATCCTTTTGCTTT
Found at i:1341 original size:29 final size:29
Alignment explanation
Indices: 1305--1363 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1295 TCTCAACTGC
1305 TAATTTCTATTATCCTTTTGCTTTTATTA
1 TAATTTCTATTATCCTTTTGCTTTTATTA
1334 TAATTTCTATTATCCTTTTGCTTTTATTA
1 TAATTTCTATTATCCTTTTGCTTTTATTA
1363 T
1 T
1364 TGGTTTATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.20, C:0.14, G:0.03, T:0.63
Consensus pattern (29 bp):
TAATTTCTATTATCCTTTTGCTTTTATTA
Found at i:4511 original size:28 final size:28
Alignment explanation
Indices: 4471--4528 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
4461 GTGAGAGCAA
4471 ATGGGGGAAGATTTATGTTCTATTACCC
1 ATGGGGGAAGATTTATGTTCTATTACCC
4499 ATGGGGGAAGATTTATGTTCTATTACCC
1 ATGGGGGAAGATTTATGTTCTATTACCC
4527 AT
1 AT
4529 ATGTATAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (28 bp):
ATGGGGGAAGATTTATGTTCTATTACCC
Found at i:5839 original size:114 final size:114
Alignment explanation
Indices: 5639--5863 Score: 441
Period size: 114 Copynumber: 2.0 Consensus size: 114
5629 AATGTCAGGT
*
5639 TTTAATGAGCTTCAGTTGCTATTGAATATAAAAGTTCTGAGCTTATAATGCTTAGTTTCAGTAGT
1 TTTAATGAGCTTCAGTAGCTATTGAATATAAAAGTTCTGAGCTTATAATGCTTAGTTTCAGTAGT
5704 GAAACACATGAAACATGAACCCACATATAAGCGTAGTTCAAATTTTGTA
66 GAAACACATGAAACATGAACCCACATATAAGCGTAGTTCAAATTTTGTA
5753 TTTAATGAGCTTCAGTAGCTATTGAATATAAAAGTTCTGAGCTTATAATGCTTAGTTTCAGTAGT
1 TTTAATGAGCTTCAGTAGCTATTGAATATAAAAGTTCTGAGCTTATAATGCTTAGTTTCAGTAGT
5818 GAAACACATGAAACATGAACCCACATATAAGCGTAGTTCAAATTTT
66 GAAACACATGAAACATGAACCCACATATAAGCGTAGTTCAAATTTT
5864 ATTTTGATGT
Statistics
Matches: 110, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
114 110 1.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (114 bp):
TTTAATGAGCTTCAGTAGCTATTGAATATAAAAGTTCTGAGCTTATAATGCTTAGTTTCAGTAGT
GAAACACATGAAACATGAACCCACATATAAGCGTAGTTCAAATTTTGTA
Done.