Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016742.1 Corchorus olitorius cultivar O-4 contig16775, 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: 14134
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:2125 original size:21 final size:19
Alignment explanation
Indices: 2080--2137 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
2070 CTGTTTAACA
2080 ACTGTACAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
* *
2099 ACTGTACAGATTAGATTAGGT
1 ACTGTACAGATGAGATTA--C
2120 ACTGTACAGATGAGATTA
1 ACTGTACAGATGAGATTA
2138 TTAGAACAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.29
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:2526 original size:53 final size:53
Alignment explanation
Indices: 2469--2575 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
2459 AACAAGAAAA
*
2469 TCTGACAGTGAAAGAATGAAGAGAGAAAGGGGAAATGGAAGAGAGGCGATGGG
1 TCTGACAGTGAAAGAATAAAGAGAGAAAGGGGAAATGGAAGAGAGGCGATGGG
2522 TCTGACAGTGAAAGAATAAAGAGAGAAAGGGGAAATGGAAGAGAGGCGATGGG
1 TCTGACAGTGAAAGAATAAAGAGAGAAAGGGGAAATGGAAGAGAGGCGATGGG
2575 T
1 T
2576 GGTTTCGTGA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.42, C:0.06, G:0.40, T:0.12
Consensus pattern (53 bp):
TCTGACAGTGAAAGAATAAAGAGAGAAAGGGGAAATGGAAGAGAGGCGATGGG
Found at i:9565 original size:12 final size:12
Alignment explanation
Indices: 9543--9576 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
9533 TACAGACATA
9543 CCTGCAAGAGCTG
1 CCTG-AAGAGCTG
9556 CCTGAAGAGCTG
1 CCTGAAGAGCTG
9568 CCTGAAGAG
1 CCTGAAGAG
9577 GTAACTTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 17 0.81
13 4 0.19
ACGTcount: A:0.26, C:0.26, G:0.32, T:0.15
Consensus pattern (12 bp):
CCTGAAGAGCTG
Found at i:10336 original size:22 final size:22
Alignment explanation
Indices: 10307--10431 Score: 123
Period size: 22 Copynumber: 5.7 Consensus size: 22
10297 TGAATATTTT
10307 TATGAAATTTTGATAATTACCC
1 TATGAAATTTTGATAATTACCC
* **
10329 TATTAAATTTTGATAACCACCC
1 TATGAAATTTTGATAATTACCC
10351 TATGAAATTTTGATAATTA-CC
1 TATGAAATTTTGATAATTACCC
*
10372 TATGAAATTGTGATAA--ACTCC
1 TATGAAATTTTGATAATTAC-CC
* * *
10393 ATATGAAACTTTGATAACCTA-AC
1 -TATGAAATTTTGATAA-TTACCC
*
10416 TATGAAATTTTAATAA
1 TATGAAATTTTGATAA
10432 ACCTTTCTAT
Statistics
Matches: 85, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.01
21 19 0.22
22 63 0.74
23 1 0.01
25 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAATTACCC
Found at i:10386 original size:65 final size:65
Alignment explanation
Indices: 10307--10431 Score: 157
Period size: 65 Copynumber: 1.9 Consensus size: 65
10297 TGAATATTTT
* * * * *
10307 TATGAAATTTTGATAATTAC-CC-TATTAAATTTTGATAACC-ACCCTATGAAATTTTGATAATT
1 TATGAAATTGTGATAA--ACTCCATATGAAACTTTGATAACCTA-ACTATGAAATTTTAATAATT
10369 ACC
63 ACC
10372 TATGAAATTGTGATAAACTCCATATGAAACTTTGATAACCTAACTATGAAATTTTAATAA
1 TATGAAATTGTGATAAACTCCATATGAAACTTTGATAACCTAACTATGAAATTTTAATAA
10432 ACCTTTCTAT
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
63 2 0.04
64 2 0.04
65 47 0.90
66 1 0.02
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.38
Consensus pattern (65 bp):
TATGAAATTGTGATAAACTCCATATGAAACTTTGATAACCTAACTATGAAATTTTAATAATTACC
Found at i:10463 original size:44 final size:43
Alignment explanation
Indices: 10307--10474 Score: 164
Period size: 44 Copynumber: 3.9 Consensus size: 43
10297 TGAATATTTT
* *
10307 TATGAAATTTTGATAATTACCCTATTAAATTTTGAT-AACCACCC
1 TATGAAATTTTGATAATTA-CCTATGAAATTTTGATAAACC-TCC
*
10351 TATGAAATTTTGATAATTACCTATGAAATTGTGATAAA-CTCC
1 TATGAAATTTTGATAATTACCTATGAAATTTTGATAAACCTCC
* * * * *
10393 ATATGAAACTTTGATAACCTAACTATGAAATTTTAATAAACCTTTC
1 -TATGAAATTTTGATAA-TTACCTATGAAATTTTGATAAACC-TCC
* *
10439 TATGAAATTTTG-TAATCTTCCTATG-ATTTTTGATAA
1 TATGAAATTTTGATAAT-TACCTATGAAATTTTGATAA
10475 TATCCATGTG
Statistics
Matches: 103, Mismatches: 15, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
42 2 0.02
43 39 0.38
44 48 0.47
45 12 0.12
46 2 0.02
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (43 bp):
TATGAAATTTTGATAATTACCTATGAAATTTTGATAAACCTCC
Found at i:12382 original size:56 final size:56
Alignment explanation
Indices: 12296--12409 Score: 210
Period size: 56 Copynumber: 2.0 Consensus size: 56
12286 TATCCATTTC
* *
12296 CTTTCATACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCATATCTCTACTTAATTATT
12352 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCATATCTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCATATCTCTACTTAATTATT
12408 CT
1 CT
12410 ATAAAATAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.40
Consensus pattern (56 bp):
CTTTCACACAATAAATGTTATAATAAATCCTATCCCCATATCTCTACTTAATTATT
Done.