Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018801.1 Corchorus olitorius cultivar O-4 contig18834, 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: 41084
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:887 original size:34 final size:34
Alignment explanation
Indices: 804--893 Score: 114
Period size: 34 Copynumber: 2.7 Consensus size: 34
794 TTTAAAAAAC
804 TTTGAAAA--AAAACC-GAATGGGAACTTTCCCAA
1 TTTGAAAACTAAAACCTG-ATGGGAACTTTCCCAA
* *
836 TTTTAAAACTAAAACCTGGTGGGAACTTTCCCAA
1 TTTGAAAACTAAAACCTGATGGGAACTTTCCCAA
**
870 TTTGAAAACTAGGACCTGATGGGA
1 TTTGAAAACTAAAACCTGATGGGA
894 TTTTTTTGAA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
32 7 0.14
34 41 0.84
35 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.26
Consensus pattern (34 bp):
TTTGAAAACTAAAACCTGATGGGAACTTTCCCAA
Found at i:8740 original size:30 final size:30
Alignment explanation
Indices: 8701--8767 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
8691 GAGTATGACG
*
8701 AGGAGGAAGATTCCGATCTCTTTGTTTGTGA
1 AGGA-GAAGATTACGATCTCTTTGTTTGTGA
*
8732 AGGAGAAGATTATGATCTCTTTGTTTGTGA
1 AGGAGAAGATTACGATCTCTTTGTTTGTGA
8762 AGGAGA
1 AGGAGA
8768 GAATTCTGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 30 0.88
31 4 0.12
ACGTcount: A:0.27, C:0.09, G:0.30, T:0.34
Consensus pattern (30 bp):
AGGAGAAGATTACGATCTCTTTGTTTGTGA
Found at i:17917 original size:2 final size:2
Alignment explanation
Indices: 17910--17943 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
17900 TTTGTTTTCA
17910 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17944 TCTAGTAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20319 original size:30 final size:30
Alignment explanation
Indices: 20283--20343 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
20273 AAAGCTTCAA
*
20283 TTTAGGAGGATATTACCCACCAATTCCTTT
1 TTTAGGAGGATATTACCCACCAACTCCTTT
20313 TTTAGGAGGATATTACCCACCAACTCCTTT
1 TTTAGGAGGATATTACCCACCAACTCCTTT
20343 T
1 T
20344 GCTCCAAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.36
Consensus pattern (30 bp):
TTTAGGAGGATATTACCCACCAACTCCTTT
Found at i:25273 original size:126 final size:123
Alignment explanation
Indices: 25131--25419 Score: 389
Period size: 126 Copynumber: 2.3 Consensus size: 123
25121 CAAGGGTGGA
* * * * ** *
25131 ATGACTTGTTGTTGAATTGATAATTTAATTCAAGGGTGTTGACGACTTGACCTTGAATTGATAAT
1 ATGACTTGTTCTTGAATTGATAATTTAATTCAAGGGTCTCGAAGACTCAACCTTGAATCGATAAT
* ** *
25196 TTAATTCAAGGGTCTTGACGACTTGATCTTGAATTGATAATAATTCGATTCAAGGGTCTCG
66 TTAATTCAAGGGTCTCGACGACTCAATCTTGAATTGATAAT--TT-AATTCAAGGGTCTCG
*
25257 ATGACTTGTTCTTGAATTGATAATTTAATTCAAGGGTCTCGAAGACTCAATCTTGAATCGATAAT
1 ATGACTTGTTCTTGAATTGATAATTTAATTCAAGGGTCTCGAAGACTCAACCTTGAATCGATAAT
* *
25322 TTTATTCAAGGGTCTCGATGACTCAATCTTGAATTGATAATTTAATTCAAGGGTCTCG
66 TTAATTCAAGGGTCTCGACGACTCAATCTTGAATTGATAATTTAATTCAAGGGTCTCG
*** *
25380 ATGACTCAATCTTGAAATGATAATTTAATTCAAGGGTCTC
1 ATGACTTGTTCTTGAATTGATAATTTAATTCAAGGGTCTC
25420 AATGCCTTGA
Statistics
Matches: 145, Mismatches: 18, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
123 50 0.34
124 2 0.01
126 93 0.64
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.37
Consensus pattern (123 bp):
ATGACTTGTTCTTGAATTGATAATTTAATTCAAGGGTCTCGAAGACTCAACCTTGAATCGATAAT
TTAATTCAAGGGTCTCGACGACTCAATCTTGAATTGATAATTTAATTCAAGGGTCTCG
Found at i:25433 original size:41 final size:41
Alignment explanation
Indices: 25131--25436 Score: 387
Period size: 41 Copynumber: 7.4 Consensus size: 41
25121 CAAGGGTGGA
* * * *
25131 ATGACTTGTTGTTGAATTGATAATTTAATTCAAGGGTGTTG
1 ATGACTTGATCTTGAATTGATAATTTAATTCAAGGGTCTCG
* * *
25172 ACGACTTGACCTTGAATTGATAATTTAATTCAAGGGTCTTG
1 ATGACTTGATCTTGAATTGATAATTTAATTCAAGGGTCTCG
* *
25213 ACGACTTGATCTTGAATTGATAATAATTCGATTCAAGGGTCTCG
1 ATGACTTGATCTTGAATTGATAAT--TT-AATTCAAGGGTCTCG
*
25257 ATGACTTGTTCTTGAATTGATAATTTAATTCAAGGGTCTCG
1 ATGACTTGATCTTGAATTGATAATTTAATTCAAGGGTCTCG
* ** * *
25298 AAGACTCAATCTTGAATCGATAATTTTATTCAAGGGTCTCG
1 ATGACTTGATCTTGAATTGATAATTTAATTCAAGGGTCTCG
**
25339 ATGACTCAATCTTGAATTGATAATTTAATTCAAGGGTCTCG
1 ATGACTTGATCTTGAATTGATAATTTAATTCAAGGGTCTCG
** * *
25380 ATGACTCAATCTTGAAATGATAATTTAATTCAAGGGTCTCA
1 ATGACTTGATCTTGAATTGATAATTTAATTCAAGGGTCTCG
*
25421 ATGCCTTGATCTTGAA
1 ATGACTTGATCTTGAA
25437 CAAACGAAAA
Statistics
Matches: 237, Mismatches: 25, Indels: 6
0.88 0.09 0.02
Matches are distributed among these distances:
41 198 0.84
42 2 0.01
43 2 0.01
44 35 0.15
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (41 bp):
ATGACTTGATCTTGAATTGATAATTTAATTCAAGGGTCTCG
Found at i:26364 original size:65 final size:64
Alignment explanation
Indices: 26273--26453 Score: 182
Period size: 77 Copynumber: 2.6 Consensus size: 64
26263 GTCTAAGTTG
* *
26273 TCCTTTGCAGAATTTTCAACTTAGCGAGCTTTTTTTTTTTTCGCTATAACTTTTGCCTAAGCCA
1 TCCTTTACAGGATTTTCAACTTAGCGAGCTTTTTTTTTTTTCGCTATAACTTTTGCCTAAGCCA
*
26337 TCCTTTTACAGGATTTTCAACTTAGCGAGCCTTTTCTTTTTTTCTTTTTTTTTTCGCTCTAACTT
1 TCC-TTTACAGGATTTTCAACTTAGCGAG------C-----TT-TTTTTTTTTTCGCTATAACTT
* *
26402 TTGTCTAAGCCG
53 TTGCCTAAGCCA
* *
26414 TCCTTTATAGGATTTTCAACTTAGTGAGCTTTTTTTTTTT
1 TCCTTTACAGGATTTTCAACTTAGCGAGCTTTTTTTTTTT
26454 GTTGGGCAGT
Statistics
Matches: 97, Mismatches: 7, Indels: 26
0.75 0.05 0.20
Matches are distributed among these distances:
64 12 0.12
65 25 0.26
70 1 0.01
71 1 0.01
76 25 0.26
77 33 0.34
ACGTcount: A:0.17, C:0.20, G:0.12, T:0.51
Consensus pattern (64 bp):
TCCTTTACAGGATTTTCAACTTAGCGAGCTTTTTTTTTTTTCGCTATAACTTTTGCCTAAGCCA
Found at i:26453 original size:76 final size:77
Alignment explanation
Indices: 26304--26453 Score: 234
Period size: 77 Copynumber: 2.0 Consensus size: 77
26294 TAGCGAGCTT
26304 TTTTTTTTTTCGCTATAACTTTTGCCTAAGCCATCCTTTTACAGGATTTTCAACTTAGCGAGCCT
1 TTTTTTTTTTCGCTATAACTTTTGCCTAAGCCATCCTTTTACAGGATTTTCAACTTAGCGAGCCT
26369 TTTCTTTTTTTC
66 TTTCTTTTTTTC
* * * * *
26381 TTTTTTTTTTCGCTCTAACTTTTGTCTAAGCCGTCC-TTTATAGGATTTTCAACTTAGTGAG-CT
1 TTTTTTTTTTCGCTATAACTTTTGCCTAAGCCATCCTTTTACAGGATTTTCAACTTAGCGAGCCT
26444 TTT-TTTTTTT
66 TTTCTTTTTTT
26454 GTTGGGCAGT
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
74 7 0.10
75 5 0.07
76 23 0.34
77 33 0.49
ACGTcount: A:0.16, C:0.19, G:0.11, T:0.53
Consensus pattern (77 bp):
TTTTTTTTTTCGCTATAACTTTTGCCTAAGCCATCCTTTTACAGGATTTTCAACTTAGCGAGCCT
TTTCTTTTTTTC
Done.