Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024143.1 Corchorus olitorius cultivar O-4 contig24176, 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: 20843
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Found at i:2666 original size:125 final size:125
Alignment explanation
Indices: 2402--2655 Score: 490
Period size: 125 Copynumber: 2.0 Consensus size: 125
2392 TTAGATTTCA
2402 TTAAATAAAAATAGAGTTTTTAGTAGAATAAAACTATAATAGTTTAAGTAATGGTATTTAAGAAA
1 TTAAATAAAAATAGAGTTTTTAGTAGAATAAAACTATAATAGTTTAAGTAATGGTATTTAAGAAA
2467 TATATTCGAAAAATAAGGGTATAATGGACGATTCAAAAGTTTTACAGGTGAACGTACTTT
66 TATATTCGAAAAATAAGGGTATAATGGACGATTCAAAAGTTTTACAGGTGAACGTACTTT
2527 TTAAATAAAAATAGAGTTTTTAGTAGAATAAAACTATAATAGTTTAAGTAATGGTATTTAAGAAA
1 TTAAATAAAAATAGAGTTTTTAGTAGAATAAAACTATAATAGTTTAAGTAATGGTATTTAAGAAA
* *
2592 TATATTCGAAAAATAAGGGTATAATGGGCGATTCAAAAGTTTTACAGGTGATCGTACTTT
66 TATATTCGAAAAATAAGGGTATAATGGACGATTCAAAAGTTTTACAGGTGAACGTACTTT
2652 TTAA
1 TTAA
2656 TATAGTATAG
Statistics
Matches: 127, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
125 127 1.00
ACGTcount: A:0.43, C:0.06, G:0.17, T:0.34
Consensus pattern (125 bp):
TTAAATAAAAATAGAGTTTTTAGTAGAATAAAACTATAATAGTTTAAGTAATGGTATTTAAGAAA
TATATTCGAAAAATAAGGGTATAATGGACGATTCAAAAGTTTTACAGGTGAACGTACTTT
Found at i:11099 original size:3 final size:3
Alignment explanation
Indices: 11091--11115 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
11081 TATCTATCCA
11091 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
11116 ACTCAACAAA
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:13775 original size:4 final size:4
Alignment explanation
Indices: 13766--13792 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
13756 TCAGAGCTAA
13766 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
13793 ATTTTTAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:15636 original size:33 final size:33
Alignment explanation
Indices: 15594--15662 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
15584 ACAAAGTTTA
* *
15594 TTTATCATGCATGATCTCCTTCTTCTACCTTTC
1 TTTATCATGCATAATCTCCTCCTTCTACCTTTC
*
15627 TTTATCATGCATAATCTCCTCCTTGTACCTTTC
1 TTTATCATGCATAATCTCCTCCTTCTACCTTTC
15660 TTT
1 TTT
15663 TATTATTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.16, C:0.29, G:0.06, T:0.49
Consensus pattern (33 bp):
TTTATCATGCATAATCTCCTCCTTCTACCTTTC
Found at i:16638 original size:12 final size:12
Alignment explanation
Indices: 16601--16639 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
16591 ACTATAATTA
*
16601 TGGACGTGGTCA
1 TGGACGTGGTCG
*
16613 TGGACGTGGACG
1 TGGACGTGGTCG
*
16625 TGGCCGTGGTCG
1 TGGACGTGGTCG
16637 TGG
1 TGG
16640 TTTTGGCTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.10, C:0.18, G:0.49, T:0.23
Consensus pattern (12 bp):
TGGACGTGGTCG
Found at i:16638 original size:18 final size:18
Alignment explanation
Indices: 16601--16639 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
16591 ACTATAATTA
*
16601 TGGACGTGGTCATGGACG
1 TGGACGTGGCCATGGACG
* *
16619 TGGACGTGGCCGTGGTCG
1 TGGACGTGGCCATGGACG
16637 TGG
1 TGG
16640 TTTTGGCTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.10, C:0.18, G:0.49, T:0.23
Consensus pattern (18 bp):
TGGACGTGGCCATGGACG
Found at i:17079 original size:25 final size:25
Alignment explanation
Indices: 17051--17107 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
17041 AATAAACTCT
17051 TTATGTC-CTATATGTTTTATCTTCC
1 TTATGTCTC-ATATGTTTTATCTTCC
* *
17076 TTATATTTCATATGTTTTATCTTCC
1 TTATGTCTCATATGTTTTATCTTCC
17101 TATATGT
1 T-TATGT
17108 TTTAATCTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 22 0.81
26 5 0.19
ACGTcount: A:0.19, C:0.16, G:0.07, T:0.58
Consensus pattern (25 bp):
TTATGTCTCATATGTTTTATCTTCC
Found at i:18982 original size:15 final size:15
Alignment explanation
Indices: 18958--19003 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
18948 GGATAAGGTT
18958 ACTCCAGAAGAGTCC
1 ACTCCAGAAGAGTCC
* *
18973 ACTCCTGAAGAGAT-T
1 ACTCCAGAAGAG-TCC
18988 ACTCCAGAAGAGTCC
1 ACTCCAGAAGAGTCC
19003 A
1 A
19004 TAGGCATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 1 0.04
15 23 0.92
16 1 0.04
ACGTcount: A:0.35, C:0.28, G:0.20, T:0.17
Consensus pattern (15 bp):
ACTCCAGAAGAGTCC
Done.