Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012401.1 Corchorus olitorius cultivar O-4 contig12434, 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: 22094
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Found at i:1539 original size:24 final size:23
Alignment explanation
Indices: 1485--1566 Score: 128
Period size: 23 Copynumber: 3.5 Consensus size: 23
1475 TTAATAACAC
* * *
1485 CTTGGGCCATTTTATTTCCTTCA
1 CTTGGTCCATTTTATTTTCTTTA
1508 CTTGGTCCATTTTATTTTTCTTTA
1 CTTGGTCCATTTTA-TTTTCTTTA
1532 CTTGGTCCATTTTATTTTCTTTA
1 CTTGGTCCATTTTATTTTCTTTA
1555 CTTGGTCCATTT
1 CTTGGTCCATTT
1567 CTTTATTTCC
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
23 34 0.62
24 21 0.38
ACGTcount: A:0.12, C:0.21, G:0.11, T:0.56
Consensus pattern (23 bp):
CTTGGTCCATTTTATTTTCTTTA
Found at i:8830 original size:11 final size:11
Alignment explanation
Indices: 8814--8839 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
8804 CCTTGCCTAA
8814 AAAACTAGAAG
1 AAAACTAGAAG
8825 AAAACTAGAAG
1 AAAACTAGAAG
8836 AAAA
1 AAAA
8840 GATCTAAAAC
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:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:11477 original size:54 final size:50
Alignment explanation
Indices: 11348--11478 Score: 147
Period size: 50 Copynumber: 2.5 Consensus size: 50
11338 AAATATCTAG
* * * *
11348 AAGAGTGAATTGGAAGACAGTTTAAAGGATAAGCGGAAGACGGTCCTTTT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCAGAAGACGATCCTTTT
* *
11398 AAGATTAAATTGGAAGACAGTTCAAAGGATGAGCAGAAGACGATCCTTTTTT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCAGAAGACGATCC--TTTT
*
11450 ATATATTTGAATTGGAAGAC-GATTCAAAG
1 A-AGA-TTGAATTGGAAGACAG-TTCAAAG
11479 AAGTTGATTC
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
50 40 0.59
52 5 0.07
53 3 0.04
54 20 0.29
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.27
Consensus pattern (50 bp):
AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCAGAAGACGATCCTTTT
Found at i:11492 original size:26 final size:26
Alignment explanation
Indices: 11463--11550 Score: 81
Period size: 26 Copynumber: 3.4 Consensus size: 26
11453 TATTTGAATT
11463 GGAAGACGATTCAAAGAAGTTGATTC
1 GGAAGACGATTCAAAGAAGTTGATTC
***
11489 GGAAGACGATTCCTCGAAGATTGAATT-
1 GGAAGACGATTCAAAGAAG-TTG-ATTC
** * *
11516 GGAAGATAATTCGAAGAAGTTGATCC
1 GGAAGACGATTCAAAGAAGTTGATTC
11542 GG-AGACGAT
1 GGAAGACGAT
11551 CCATTTCAAA
Statistics
Matches: 48, Mismatches: 11, Indels: 7
0.73 0.17 0.11
Matches are distributed among these distances:
25 7 0.15
26 21 0.44
27 17 0.35
28 3 0.06
ACGTcount: A:0.36, C:0.12, G:0.28, T:0.23
Consensus pattern (26 bp):
GGAAGACGATTCAAAGAAGTTGATTC
Found at i:11839 original size:29 final size:28
Alignment explanation
Indices: 11751--11845 Score: 127
Period size: 28 Copynumber: 3.4 Consensus size: 28
11741 TTTACTTCTT
11751 ATTTTGGTCATTTTGCATGTCCAGGGGC
1 ATTTTGGTCATTTTGCATGTCCAGGGGC
* * *
11779 ATTTTGGTCCTTTTGCATGTCCATGGGT
1 ATTTTGGTCATTTTGCATGTCCAGGGGC
**
11807 ATTTTGGTCATTTTTGCACATCCAGGGGC
1 ATTTTGGTCA-TTTTGCATGTCCAGGGGC
*
11836 ATTTTAGTCA
1 ATTTTGGTCA
11846 CTTCAAGTAC
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
28 34 0.60
29 23 0.40
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.42
Consensus pattern (28 bp):
ATTTTGGTCATTTTGCATGTCCAGGGGC
Found at i:12642 original size:17 final size:17
Alignment explanation
Indices: 12616--12653 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
12606 CTTATCAGCA
*
12616 GCAAATACAGAGTCAAG
1 GCAAACACAGAGTCAAG
12633 GCAAACACAGAGTCAAG
1 GCAAACACAGAGTCAAG
12650 GCAA
1 GCAA
12654 GTCAAGTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.47, C:0.21, G:0.24, T:0.08
Consensus pattern (17 bp):
GCAAACACAGAGTCAAG
Found at i:18154 original size:29 final size:29
Alignment explanation
Indices: 18095--18472 Score: 424
Period size: 29 Copynumber: 13.0 Consensus size: 29
18085 GCACGCTCAA
*
18095 GGGCATTTTGGTCA-TTTTGCATATTCT-G
1 GGGCATTTTGGTCATTTTTGCACA-TCTAG
* *
18123 GGGCAGTTTGGTTATTTTTGCACATCTAG
1 GGGCATTTTGGTCATTTTTGCACATCTAG
* * *
18152 GGGTATTATGGTCATTTTTGCATATCTAG
1 GGGCATTTTGGTCATTTTTGCACATCTAG
* * *
18181 GGGCATTTTGGTCATTTTTGTATATTCT-T
1 GGGCATTTTGGTCATTTTTGCACA-TCTAG
* * *
18210 GGGCAGTTTGGTTATTTTTGCACATCAAG
1 GGGCATTTTGGTCATTTTTGCACATCTAG
* * * *
18239 GGGTATTATGGTCATTTTTGCACATCCAA
1 GGGCATTTTGGTCATTTTTGCACATCTAG
18268 GGGCATTTTGGTCATTTTTGCACATCTAG
1 GGGCATTTTGGTCATTTTTGCACATCTAG
*
18297 GGGCATTTTGGTCATTTTTGCATATTCT-G
1 GGGCATTTTGGTCATTTTTGCACA-TCTAG
* *
18326 GGGCAGTTTGGTTATTTTTGCACATCTAG
1 GGGCATTTTGGTCATTTTTGCACATCTAG
* * *
18355 GGGTATTATGGTCATTTTTGCGCATCTAG
1 GGGCATTTTGGTCATTTTTGCACATCTAG
* *
18384 GGGCATTTTGGTCATTTTTGCCCATCCAG
1 GGGCATTTTGGTCATTTTTGCACATCTAG
* *
18413 GGGCATTATGGTCATTTTTACACATTCT-G
1 GGGCATTTTGGTCATTTTTGCACA-TCTAG
* *
18442 GGGCAGTTTGGTCATTTTTGCATACTCTAG
1 GGGCATTTTGGTCATTTTTGCACA-TCTAG
18472 G
1 G
18473 TTCTCTTTGG
Statistics
Matches: 292, Mismatches: 50, Indels: 14
0.82 0.14 0.04
Matches are distributed among these distances:
28 20 0.07
29 262 0.90
30 10 0.03
ACGTcount: A:0.17, C:0.15, G:0.25, T:0.43
Consensus pattern (29 bp):
GGGCATTTTGGTCATTTTTGCACATCTAG
Found at i:18298 original size:116 final size:116
Alignment explanation
Indices: 18131--18463 Score: 522
Period size: 116 Copynumber: 2.9 Consensus size: 116
18121 TGGGGCAGTT
* * * *
18131 TGGTTATTTTTGCACATCTAGGGGTATTATGGTCATTTTTGCATATCTAGGGGCATTTTGGTCAT
1 TGGTCATTTTTGCACATCTAGGGGCATTTTGGTCATTTTTGCACATCTAGGGGCATTTTGGTCAT
* *
18196 TTTTGTATATTCTTGGGCAGTTTGGTTATTTTTGCACATCAAGGGGTATTA
66 TTTTGCATATTCTGGGGCAGTTTGGTTATTTTTGCACATCAAGGGGTATTA
* *
18247 TGGTCATTTTTGCACATCCAAGGGCATTTTGGTCATTTTTGCACATCTAGGGGCATTTTGGTCAT
1 TGGTCATTTTTGCACATCTAGGGGCATTTTGGTCATTTTTGCACATCTAGGGGCATTTTGGTCAT
*
18312 TTTTGCATATTCTGGGGCAGTTTGGTTATTTTTGCACATCTAGGGGTATTA
66 TTTTGCATATTCTGGGGCAGTTTGGTTATTTTTGCACATCAAGGGGTATTA
* * * *
18363 TGGTCATTTTTGCGCATCTAGGGGCATTTTGGTCATTTTTGCCCATCCAGGGGCATTATGGTCAT
1 TGGTCATTTTTGCACATCTAGGGGCATTTTGGTCATTTTTGCACATCTAGGGGCATTTTGGTCAT
* * *
18428 TTTTACACATTCTGGGGCAGTTTGGTCATTTTTGCA
66 TTTTGCATATTCTGGGGCAGTTTGGTTATTTTTGCA
18464 TACTCTAGGT
Statistics
Matches: 199, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
116 199 1.00
ACGTcount: A:0.18, C:0.15, G:0.24, T:0.43
Consensus pattern (116 bp):
TGGTCATTTTTGCACATCTAGGGGCATTTTGGTCATTTTTGCACATCTAGGGGCATTTTGGTCAT
TTTTGCATATTCTGGGGCAGTTTGGTTATTTTTGCACATCAAGGGGTATTA
Found at i:22062 original size:2 final size:2
Alignment explanation
Indices: 22055--22094 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
22045 ATACGTCATA
22055 AT AT AT 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 AT AT AT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.