Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021444.1 Corchorus olitorius cultivar O-4 contig21477, 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: 14185
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Found at i:7487 original size:51 final size:50
Alignment explanation
Indices: 7380--7509 Score: 154
Period size: 51 Copynumber: 2.6 Consensus size: 50
7370 CCAAATCAAC
* * * *
7380 TTCTTTGAATTGCCTTCCAA-TCTAATATTAAAAGGATCGTATTCCGCTTA
1 TTCTTTGAACTGTCTTCCAATTC-AATCTTAAAAGGACCGTATTCCGCTTA
* *
7430 TCCTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTA
1 TTCTTTGAACTGTCTTCCAATTCAATCTT-AAAAGGACCGTATTCCGCTTA
* * *
7481 TTCTTTGGACTATCCTCCAATTCAATCTT
1 TTCTTTGAACTGTCTTCCAATTCAATCTT
7510 GAGAAAATCA
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
50 22 0.32
51 46 0.68
ACGTcount: A:0.25, C:0.25, G:0.11, T:0.39
Consensus pattern (50 bp):
TTCTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTATTCCGCTTA
Found at i:7877 original size:64 final size:64
Alignment explanation
Indices: 7707--8444 Score: 941
Period size: 64 Copynumber: 11.9 Consensus size: 64
7697 AGTTCTAAAT
* * * * * *
7707 AACCGTCTTCCGGTGTA-TCTCTTAACAAGATCGTCTTCCGAGCAACTTCTG-AAATCTTTTCGA
1 AACCATCTTCTGGTGTACT-TCTTGACAAGATCGTCTTCCGATCAATTTCTGAAAAT-TGTT-GA
*
7770 AA
63 GA
* * * * * *
7772 AACTATCTTCTGGTGTACTTTTTAACAAGATCGTCTTCCGATCAACTTCTGAAATTTTTTGAGA
1 AACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAATTTCTGAAAATTGTTGAGA
* * * * * * * *
7836 AACCATCTTCTTGCGTACTTCTTGACACGATCATCTTCCGATTC-ACTCCTGAAAACTCTTGAGA
1 AACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGA-TCAATTTCTGAAAATTGTTGAGA
* * *
7900 AACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGA
1 AACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAATTTCTGAAAATTGTTGAGA
* * * *
7964 AACCATCTTCTAGTGTACTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGA
1 AACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAATTTCTGAAAATTGTTGAGA
*
8028 AACCATCTTCTGGTGTGCTTCTTGACAAGATCGTCTTCCGATCAATTTCTGAAAATTGTTGAGA
1 AACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAATTTCTGAAAATTGTTGAGA
*
8092 AACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAATTTCTCAAAATTGTTGAGA
1 AACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAATTTCTGAAAATTGTTGAGA
*
8156 AACCATCTTCTGGTGTACTTCTTGAC-A-A---------GATCAATTTATGAAAATTGTTGAGA
1 AACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAATTTCTGAAAATTGTTGAGA
8209 AACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAATTTCTGAAAATTGTTGAGA
1 AACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAATTTCTGAAAATTGTTGAGA
8273 AACCATCTTCTGGTGTACTTCTTGACAAGA--------C---CAATTTCTGAAAATTGTTGAGA
1 AACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAATTTCTGAAAATTGTTGAGA
*
8326 AACCATCTTCTGTTGTACTTCTTGACAAGATCGTCTTCCGATCAATTTCTGAAAATTGTTGAGA
1 AACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAATTTCTGAAAATTGTTGAGA
* * **
8390 AACCATATTCTGGTGAACTTCTTGACAAGATCGTCTTTTGATCAATTTCTGAAAA
1 AACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAATTTCTGAAAA
8445 CTCTTTCTAG
Statistics
Matches: 607, Mismatches: 40, Indels: 53
0.87 0.06 0.08
Matches are distributed among these distances:
53 100 0.16
54 1 0.00
55 1 0.00
56 1 0.00
61 1 0.00
62 1 0.00
63 3 0.00
64 445 0.73
65 50 0.08
66 4 0.01
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (64 bp):
AACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAATTTCTGAAAATTGTTGAGA
Found at i:8200 original size:53 final size:53
Alignment explanation
Indices: 8131--8421 Score: 330
Period size: 53 Copynumber: 5.1 Consensus size: 53
8121 ATCGTCTTCC
*
8131 GATCAATTTCTCAAAATTGTTGAGAAACCATCTTCTGGTGTACTTCTTGACAA
1 GATCAATTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACTTCTTGACAA
*
8184 GATCAATTTATGAAAATTGTTGAGAAACCATCTTCTGGTGTACTTCTTGACAAGA
1 GATCAATTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACTTCTTGAC-A-A
8239 TCGTCTTCCGATCAATTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACTTCTTGACAA
1 ---------GATCAATTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACTTCTTGACAA
* *
8301 GACCAATTTCTGAAAATTGTTGAGAAACCATCTTCTGTTGTACTTCTTGACAAGA
1 GATCAATTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACTTCTTGAC-A-A
* *
8356 TCGTCTTCCGATCAATTTCTGAAAATTGTTGAGAAACCATATTCTGGTGAACTTCTTGACAA
1 ---------GATCAATTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACTTCTTGACAA
8418 GATC
1 GATC
8422 GTCTTTTGAT
Statistics
Matches: 207, Mismatches: 9, Indels: 44
0.80 0.03 0.17
Matches are distributed among these distances:
53 102 0.49
54 2 0.01
55 2 0.01
62 2 0.01
63 2 0.01
64 97 0.47
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (53 bp):
GATCAATTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACTTCTTGACAA
Found at i:8251 original size:117 final size:117
Alignment explanation
Indices: 8067--8421 Score: 656
Period size: 117 Copynumber: 3.0 Consensus size: 117
8057 ATCGTCTTCC
8067 GATCAATTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCG
1 GATCAATTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCG
*
8132 ATCAATTTCTCAAAATTGTTGAGAAACCATCTTCTGGTGTACTTCTTGACAA
66 ATCAATTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACTTCTTGACAA
*
8184 GATCAATTTATGAAAATTGTTGAGAAACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCG
1 GATCAATTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCG
8249 ATCAATTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACTTCTTGACAA
66 ATCAATTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACTTCTTGACAA
* *
8301 GACCAATTTCTGAAAATTGTTGAGAAACCATCTTCTGTTGTACTTCTTGACAAGATCGTCTTCCG
1 GATCAATTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCG
* *
8366 ATCAATTTCTGAAAATTGTTGAGAAACCATATTCTGGTGAACTTCTTGACAA
66 ATCAATTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACTTCTTGACAA
8418 GATC
1 GATC
8422 GTCTTTTGAT
Statistics
Matches: 230, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
117 230 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (117 bp):
GATCAATTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCG
ATCAATTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACTTCTTGACAA
Found at i:8283 original size:25 final size:25
Alignment explanation
Indices: 8255--8337 Score: 78
Period size: 25 Copynumber: 3.2 Consensus size: 25
8245 TCCGATCAAT
8255 TTCTGAAAATTGTTGAGAAACCATC
1 TTCTGAAAATTGTTGAGAAACCATC
** * * *
8280 TTCTGGTGTACTTCTTGACAAGACCAAT-
1 TTCT-G-AAAATTGTTGAGAA-ACC-ATC
8308 TTCTGAAAATTGTTGAGAAACCATC
1 TTCTGAAAATTGTTGAGAAACCATC
8333 TTCTG
1 TTCTG
8338 TTGTACTTCT
Statistics
Matches: 43, Mismatches: 10, Indels: 10
0.68 0.16 0.16
Matches are distributed among these distances:
24 2 0.05
25 12 0.28
26 10 0.23
27 10 0.23
28 7 0.16
29 2 0.05
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (25 bp):
TTCTGAAAATTGTTGAGAAACCATC
Found at i:8517 original size:67 final size:67
Alignment explanation
Indices: 8439--8606 Score: 309
Period size: 67 Copynumber: 2.5 Consensus size: 67
8429 GATCAATTTC
*
8439 TGAAAACTCTTTCTAGCAAACCGTCTTCTGATGTATTCCTTAATGAGATTGTCTTCCAATCAGCA
1 TGAAAATTCTTTCTAGCAAACCGTCTTCTGATGTATTCCTTAATGAGATTGTCTTCCAATCAGCA
8504 CT
66 CT
*
8506 TGAAAATTCTTTCTAGCAAACCGTCTTCTGATGTATTCCTTAGTGAGATTGTCTTCCAATCAGCA
1 TGAAAATTCTTTCTAGCAAACCGTCTTCTGATGTATTCCTTAATGAGATTGTCTTCCAATCAGCA
8571 CT
66 CT
*
8573 TGAAAATTCTTTCTAGCAAACCGTCTTCCGATGT
1 TGAAAATTCTTTCTAGCAAACCGTCTTCTGATGT
8607 TCTTCTAAAA
Statistics
Matches: 98, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 98 1.00
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.36
Consensus pattern (67 bp):
TGAAAATTCTTTCTAGCAAACCGTCTTCTGATGTATTCCTTAATGAGATTGTCTTCCAATCAGCA
CT
Found at i:10282 original size:14 final size:15
Alignment explanation
Indices: 10244--10285 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
10234 TAGAGCTTTA
10244 TCTCTTCTTTTTTTC
1 TCTCTTCTTTTTTTC
*
10259 T-TTTTCTTTTTTTC
1 TCTCTTCTTTTTTTC
10273 TCTCTT-TTTTTTT
1 TCTCTTCTTTTTTT
10286 ACTTCACCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 20 0.83
15 4 0.17
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (15 bp):
TCTCTTCTTTTTTTC
Done.