Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000421.1 Hibiscus syriacus cultivar Beakdansim tig00000770_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: 41833
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:5124 original size:25 final size:26
Alignment explanation
Indices: 5080--5128 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
5070 ATAATAACAA
5080 TAATAATAATATAAAAAAATTTGATT
1 TAATAATAATATAAAAAAATTTGATT
* *
5106 TAATAA-AATATTAATAAATTTGA
1 TAATAATAATATAAAAAAATTTGA
5129 ATAGTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (26 bp):
TAATAATAATATAAAAAAATTTGATT
Found at i:5160 original size:9 final size:9
Alignment explanation
Indices: 5146--5186 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
5136 AAATTATTTT
5146 ATATTTATA
1 ATATTTATA
5155 ATATTTATA
1 ATATTTATA
5164 ATA-TTA-A
1 ATATTTATA
*
5171 TTATTTATA
1 ATATTTATA
5180 AT-TTTAT
1 ATATTTAT
5187 GAGGTGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
7 3 0.11
8 11 0.39
9 14 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
ATATTTATA
Found at i:9476 original size:26 final size:26
Alignment explanation
Indices: 9437--9486 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
9427 AATATATGAT
9437 CACTCACCGATAAAAAACTAACAAAA
1 CACTCACCGATAAAAAACTAACAAAA
* * *
9463 CACTCACCGTTAAAAGATTAACAA
1 CACTCACCGATAAAAAACTAACAA
9487 CACTATCGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.52, C:0.26, G:0.06, T:0.16
Consensus pattern (26 bp):
CACTCACCGATAAAAAACTAACAAAA
Found at i:17044 original size:23 final size:24
Alignment explanation
Indices: 17024--17075 Score: 61
Period size: 23 Copynumber: 2.1 Consensus size: 24
17014 TGTGTTAGGA
*
17024 GATACGAACTTA-AAAATTTAGAG
1 GATACGAAATTATAAAATTTAGAG
*
17047 GATATGAAATTATAAAATTTCAAGAG
1 GATACGAAATTATAAAATTT--AGAG
17073 GAT
1 GAT
17076 GATATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 10 0.42
24 7 0.29
26 7 0.29
ACGTcount: A:0.48, C:0.06, G:0.17, T:0.29
Consensus pattern (24 bp):
GATACGAAATTATAAAATTTAGAG
Found at i:22370 original size:199 final size:201
Alignment explanation
Indices: 22016--22409 Score: 621
Period size: 199 Copynumber: 2.0 Consensus size: 201
22006 TATTATTAGC
* * * * *
22016 TTCTTAATCATTCTCATTGTTATGTTCATCAATCACTGCATCGTTGGGATTAAAAACCAGCATAT
1 TTCTTAATCATTCTCATTGCTATGTTCATCAATCACTACATAGTTGGGATTAAAAACCAACACAT
* *
22081 AGTTCCTTTTTTCAACCTTCTCTTCATCCCAATTCCAACTTGCATCTTCATTAAACTCCACATTT
66 AGTTCCATTTTTCAACCTTCTCTTCATCCCAATTCCAACTTGCATCTTCATTAAACTCCACATCT
* * *
22146 CTACTGATCGTGATCTTCCCAGTGTCAAGATTGAAAATTCGGTAGCCTTTTGCTTGAGAATCATA
131 CTACTGATCATGATATTCCCAGTGTCAAGATTGAAAATTCGGTAGCCTTTGGCTTGAGAATCATA
22211 TCTAGT
196 TCTAGT
* *
22217 TTCTTCATCATTCTCATTGCTATGTTCATCACTCACTACATAGTTGGGATTAAAAA-CAACACAT
1 TTCTTAATCATTCTCATTGCTATGTTCATCAATCACTACATAGTTGGGATTAAAAACCAACACAT
* * *
22281 AGTT-CATTTTTCAACCTTCTCTTTATCCCAATTCCAGCTTGCATCTTCATTAAACTGCACATCT
66 AGTTCCATTTTTCAACCTTCTCTTCATCCCAATTCCAACTTGCATCTTCATTAAACTCCACATCT
* *
22345 CTATTGATCATGATATTCTCAGTGTCAAGATTGAAAATTCGGTAGCCTTTGGCTTGAGAATCATA
131 CTACTGATCATGATATTCCCAGTGTCAAGATTGAAAATTCGGTAGCCTTTGGCTTGAGAATCATA
22410 GCCAATGAAG
Statistics
Matches: 176, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
199 115 0.65
200 10 0.06
201 51 0.29
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (201 bp):
TTCTTAATCATTCTCATTGCTATGTTCATCAATCACTACATAGTTGGGATTAAAAACCAACACAT
AGTTCCATTTTTCAACCTTCTCTTCATCCCAATTCCAACTTGCATCTTCATTAAACTCCACATCT
CTACTGATCATGATATTCCCAGTGTCAAGATTGAAAATTCGGTAGCCTTTGGCTTGAGAATCATA
TCTAGT
Found at i:31283 original size:25 final size:25
Alignment explanation
Indices: 31254--31302 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
31244 ACGAGAATAA
* *
31254 AAAAATATTATAGAAATGATTCATT
1 AAAAATATTATACAAATAATTCATT
31279 AAAAATATTATACAAATAATTCAT
1 AAAAATATTATACAAATAATTCAT
31303 GAATAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.35
Consensus pattern (25 bp):
AAAAATATTATACAAATAATTCATT
Found at i:32627 original size:24 final size:21
Alignment explanation
Indices: 32595--32647 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
32585 AATGTGATTT
*
32595 AAATTGAAAACAGAAGAATCCCAG
1 AAATGGAAAACA-AA-AA-CCCAG
* *
32619 AAATGGAAAGCAAAAAGCCAG
1 AAATGGAAAACAAAAACCCAG
32640 AAATGGAA
1 AAATGGAA
32648 TGAAATAACG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 12 0.46
22 2 0.08
23 2 0.08
24 10 0.38
ACGTcount: A:0.57, C:0.13, G:0.21, T:0.09
Consensus pattern (21 bp):
AAATGGAAAACAAAAACCCAG
Found at i:38431 original size:20 final size:20
Alignment explanation
Indices: 38406--38445 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
38396 GGAATAGTAC
*
38406 AATATTAAATTATGTTTTTA
1 AATATTAAATTATGGTTTTA
*
38426 AATATTACATTATGGTTTTA
1 AATATTAAATTATGGTTTTA
38446 TGCGATTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.53
Consensus pattern (20 bp):
AATATTAAATTATGGTTTTA
Found at i:38841 original size:2 final size:2
Alignment explanation
Indices: 38834--38873 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
38824 TAGGTTTGAA
*
38834 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA 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
38874 TATCAACAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.