Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002186.1 Hibiscus syriacus cultivar Beakdansim tig00004454_pilon, 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: 50539
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1519 original size:18 final size:18
Alignment explanation
Indices: 1488--1533 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
1478 TTAATTTCCG
1488 ATCGAAT-ATCTAAAAAAA
1 ATCGAATAAT-TAAAAAAA
*
1506 ATTGAATAATTAAAAAAA
1 ATCGAATAATTAAAAAAA
1524 ATCGAATAAT
1 ATCGAATAAT
1534 CGAATTGGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 23 0.92
19 2 0.08
ACGTcount: A:0.61, C:0.07, G:0.07, T:0.26
Consensus pattern (18 bp):
ATCGAATAATTAAAAAAA
Found at i:13465 original size:26 final size:24
Alignment explanation
Indices: 13433--13500 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
13423 ATTAAATTTA
*
13433 ATATATAATTAAAATATAATAAACAT
1 ATATATAATTAAAA-ATAAT-AACAG
* *
13459 ATATATATATAAAAAAT-ATAATAG
1 ATATATA-ATTAAAAATAATAACAG
13483 ATATATAATTAAAAATAA
1 ATATATAATTAAAAATAA
13501 AGCCGGTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
23 8 0.22
24 11 0.31
25 2 0.06
26 9 0.25
27 6 0.17
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (24 bp):
ATATATAATTAAAAATAATAACAG
Found at i:14404 original size:39 final size:39
Alignment explanation
Indices: 14350--14547 Score: 317
Period size: 39 Copynumber: 5.1 Consensus size: 39
14340 GTCACTAAAC
* * *
14350 CTGAGGGAGTGGTTAATGTTGCAA-TCAATTCTTCAAAAT
1 CTGAGGGAGAGGTTAATGTGGCAACT-GATTCTTCAAAAT
*
14389 CTGAGGGAGAGGTTAATGTGGCAACTGATTCTACAAAAT
1 CTGAGGGAGAGGTTAATGTGGCAACTGATTCTTCAAAAT
* *
14428 CTGAGGGAGAGGTTAATGTTGCAACTGATTCTACAAAAT
1 CTGAGGGAGAGGTTAATGTGGCAACTGATTCTTCAAAAT
14467 CTGAGGGAGAGGTTAATGTGGCAACTGATTCTTCAAAAT
1 CTGAGGGAGAGGTTAATGTGGCAACTGATTCTTCAAAAT
*
14506 CTGAGGGAGAGGTTAATGTGGCAACTGATTCTTCAAAGT
1 CTGAGGGAGAGGTTAATGTGGCAACTGATTCTTCAAAAT
14545 CTG
1 CTG
14548 CTGTTATTGA
Statistics
Matches: 150, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
39 149 0.99
40 1 0.01
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (39 bp):
CTGAGGGAGAGGTTAATGTGGCAACTGATTCTTCAAAAT
Found at i:28395 original size:9 final size:8
Alignment explanation
Indices: 28363--28394 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
28353 ATTAATTAAA
28363 TTTAAAATT
1 TTTAAAA-T
28372 TTTAAAAT
1 TTTAAAAT
28380 TTTAAAAT
1 TTTAAAAT
28388 TTTAAAA
1 TTTAAAA
28395 AATAAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
TTTAAAAT
Found at i:28395 original size:17 final size:17
Alignment explanation
Indices: 28363--28395 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28353 ATTAATTAAA
*
28363 TTTAAAATTTTTAAAAT
1 TTTAAAATTTTAAAAAT
28380 TTTAAAATTTTAAAAA
1 TTTAAAATTTTAAAAA
28396 ATAAAATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTAAAATTTTAAAAAT
Found at i:28409 original size:9 final size:9
Alignment explanation
Indices: 28362--28410 Score: 52
Period size: 8 Copynumber: 5.9 Consensus size: 9
28352 TATTAATTAA
28362 ATTTAAAAT
1 ATTTAAAAT
*
28371 TTTTAAAAT
1 ATTTAAAAT
28380 -TTTAAAAT
1 ATTTAAAAT
28388 -TTTAAAA-
1 ATTTAAAAT
*
28395 A-ATAAAAT
1 ATTTAAAAT
28403 ATTTAAAA
1 ATTTAAAA
28411 AAAATTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
7 5 0.15
8 16 0.47
9 13 0.38
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
ATTTAAAAT
Found at i:32378 original size:97 final size:93
Alignment explanation
Indices: 32233--32423 Score: 346
Period size: 97 Copynumber: 2.0 Consensus size: 93
32223 TTTTGAATAA
32233 ATATTATCTTATAATCATCTCAAAACATAAAAAATAATATAGGACAGGTAGAACCGATTTTCTTT
1 ATATTATCTTATAATCATCTCAAAACATAAAAAATAATATAGGACAGGTAGAACCGATTTTCTTT
32298 CGGTTATTGAGAATGAAGCGATTAAGGT
66 CGGTTATTGAGAATGAAGCGATTAAGGT
32326 ATATTATCTTATAATCATCTCAAATTATCCATAAAAAATAATATAGGACAGGTAGAACCGATTTT
1 ATATTATCTTATAATCATCTCAAA--A--CATAAAAAATAATATAGGACAGGTAGAACCGATTTT
32391 CTTTCGGTTATTGAGAATGAAGCGATTAAGGT
62 CTTTCGGTTATTGAGAATGAAGCGATTAAGGT
32423 A
1 A
32424 ATACTTTATC
Statistics
Matches: 94, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
93 24 0.26
95 1 0.01
97 69 0.73
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (93 bp):
ATATTATCTTATAATCATCTCAAAACATAAAAAATAATATAGGACAGGTAGAACCGATTTTCTTT
CGGTTATTGAGAATGAAGCGATTAAGGT
Found at i:32564 original size:31 final size:31
Alignment explanation
Indices: 32529--32599 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 31
32519 GAATAAATAT
* *
32529 AATTTGATCCTCGAACTTTTGAGAAATTGCA
1 AATTTGATCCTCAAAATTTTGAGAAATTGCA
32560 AATTTGATCCTCAAAATTTTGAGAAATTGCA
1 AATTTGATCCTCAAAATTTTGAGAAATTGCA
*
32591 AATTGGATC
1 AATTTGATC
32600 ATAAATGATT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.35
Consensus pattern (31 bp):
AATTTGATCCTCAAAATTTTGAGAAATTGCA
Found at i:37031 original size:22 final size:22
Alignment explanation
Indices: 36979--37031 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
36969 ACAGGAGTTA
** *
36979 CAAGAGTTATTTGATTTAATTC
1 CAAGAGTTACATGATATAATTC
* * *
37001 CAGGGGTTACATGATATAATTT
1 CAAGAGTTACATGATATAATTC
37023 CAAGAGTTA
1 CAAGAGTTA
37032 TAACAGCTGA
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (22 bp):
CAAGAGTTACATGATATAATTC
Found at i:46402 original size:2 final size:2
Alignment explanation
Indices: 46395--46458 Score: 85
Period size: 2 Copynumber: 31.5 Consensus size: 2
46385 ACATATTCAA
* *
46395 AT AT AT AT AA AT A- AT AT AA AT AGT AT CAT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT -AT AT AT AT AT AT AT AT
46438 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
46459 CCACACACAC
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
1 1 0.02
2 50 0.91
3 4 0.07
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:46405 original size:25 final size:29
Alignment explanation
Indices: 46391--46458 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
46381 AATTACATAT
46391 TCAAATATATATAAATAATATAAATAGTA
1 TCAAATATATATAAATAATATAAATAGTA
* * *
46420 TCATATATATATATAT-ATATATATA-TA
1 TCAAATATATATAAATAATATAAATAGTA
*
46447 T-ATATATATATA
1 TCAAATATATATA
46459 CCACACACAC
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
26 11 0.31
27 3 0.08
28 8 0.22
29 14 0.39
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (29 bp):
TCAAATATATATAAATAATATAAATAGTA
Done.