Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024731.1 Corchorus olitorius cultivar O-4 contig24764, 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: 35177
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:487 original size:10 final size:10
Alignment explanation
Indices: 442--506 Score: 57
Period size: 10 Copynumber: 6.7 Consensus size: 10
432 AAGTTCGTGT
442 TTGAAGACCA
1 TTGAAGACCA
**
452 TTTGAAGATAAA
1 -TTGAAGA-CCA
*
464 TTGGAGA-C-
1 TTGAAGACCA
472 TTGAAGACCA
1 TTGAAGACCA
482 TTGAAGA-C-
1 TTGAAGACCA
490 TTGAAGACCA
1 TTGAAGACCA
500 TTGAAGA
1 TTGAAGA
507 TTTATTTCAA
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
8 13 0.30
9 3 0.07
10 14 0.32
11 13 0.30
12 1 0.02
ACGTcount: A:0.40, C:0.12, G:0.23, T:0.25
Consensus pattern (10 bp):
TTGAAGACCA
Found at i:489 original size:18 final size:18
Alignment explanation
Indices: 463--506 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
453 TTGAAGATAA
*
463 ATTGGAGACTTGAAGACC
1 ATTGAAGACTTGAAGACC
481 ATTGAAGACTTGAAGACC
1 ATTGAAGACTTGAAGACC
499 ATTGAAGA
1 ATTGAAGA
507 TTTATTTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.23
Consensus pattern (18 bp):
ATTGAAGACTTGAAGACC
Found at i:1114 original size:11 final size:11
Alignment explanation
Indices: 1098--1123 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1088 AGATAATTTC
1098 TTTTCTTCTAG
1 TTTTCTTCTAG
1109 TTTTCTTCTAG
1 TTTTCTTCTAG
1120 TTTT
1 TTTT
1124 TAGGCAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:28001 original size:28 final size:28
Alignment explanation
Indices: 27968--28025 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
27958 TTTAGAAACA
27968 GCTATATCATCCGTCTTGAATTTACCAC
1 GCTATATCATCCGTCTTGAATTTACCAC
*
27996 GCTATATCATCCGTCTTGAATTTGCCAC
1 GCTATATCATCCGTCTTGAATTTACCAC
28024 GC
1 GC
28026 AACTCCTAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.22, C:0.29, G:0.14, T:0.34
Consensus pattern (28 bp):
GCTATATCATCCGTCTTGAATTTACCAC
Found at i:29117 original size:28 final size:29
Alignment explanation
Indices: 29066--29126 Score: 88
Period size: 28 Copynumber: 2.1 Consensus size: 29
29056 ATGGAAAAAT
* *
29066 ATTGAAATAGAACTAAGTGGT-AGAAACA
1 ATTGAAATAGAACTAAATGATAAGAAACA
29094 ATTGAAATAGAACTAAATGATAGAGAAACA
1 ATTGAAATAGAACTAAATGATA-AGAAACA
29124 ATT
1 ATT
29127 TAAACAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 19 0.66
30 10 0.34
ACGTcount: A:0.52, C:0.07, G:0.18, T:0.23
Consensus pattern (29 bp):
ATTGAAATAGAACTAAATGATAAGAAACA
Found at i:29335 original size:3 final size:3
Alignment explanation
Indices: 29327--29351 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
29317 TGTTTTCTTG
29327 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
29352 TCTCGAAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:31053 original size:97 final size:90
Alignment explanation
Indices: 30881--31080 Score: 238
Period size: 90 Copynumber: 2.1 Consensus size: 90
30871 CCCTATATGT
* *
30881 TGTTAAGACAATAATTACTTTGACAAAATCTATAACCAATCAAAGCACTTTGAGAAGTGGTCCCT
1 TGTTAAGACAATAATTACTTTGACAAAATCTATAACCAATCAAAGCACTTAGAGAAGTGGACCCT
30946 TAATAAAAAAAAACATATTTATTGC
66 TAATAAAAAAAAACATATTTATTGC
* *
30971 TGTTAAGGCAATAATTACTTTGGACAAAATCTATAATTATAACCCATCAAAGCACCTTAGAGAAG
1 TGTTAAGACAATAATTACTTT-GACAAAATC------TATAACCAATCAAAGCA-CTTAGAGAAG
* *
31036 TGGACCCTTAATTAAAAAAAAAAGACATACTTATTGT
58 TGGACCCTTAA-T--AAAAAAAA-ACATATTTATTGC
31073 TGTTAAGA
1 TGTTAAGA
31081 TAATTCTCTC
Statistics
Matches: 91, Mismatches: 7, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
90 20 0.22
91 9 0.10
97 16 0.18
98 19 0.21
99 1 0.01
101 8 0.09
102 18 0.20
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.29
Consensus pattern (90 bp):
TGTTAAGACAATAATTACTTTGACAAAATCTATAACCAATCAAAGCACTTAGAGAAGTGGACCCT
TAATAAAAAAAAACATATTTATTGC
Done.