Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001350.1 Hibiscus syriacus cultivar Beakdansim tig00002631_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: 43304
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:6445 original size:24 final size:24
Alignment explanation
Indices: 6414--6505 Score: 94
Period size: 24 Copynumber: 3.8 Consensus size: 24
6404 CGGAGATATC
* *
6414 AGAAATCAAAATAGAATTCAGATT
1 AGAAATCAAAACAGAATTCAGATA
* * * *
6438 AGATATCATAACAGAATCCAGATC
1 AGAAATCAAAACAGAATTCAGATA
* *
6462 AGAAATCAGAACAAAATTCAGATA
1 AGAAATCAAAACAGAATTCAGATA
* *
6486 AGAAATCAGAACATAATTCA
1 AGAAATCAAAACAGAATTCA
6506 AATCGAAAAT
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.53, C:0.14, G:0.12, T:0.21
Consensus pattern (24 bp):
AGAAATCAAAACAGAATTCAGATA
Found at i:6471 original size:12 final size:12
Alignment explanation
Indices: 6411--6495 Score: 50
Period size: 12 Copynumber: 7.1 Consensus size: 12
6401 AAACGGAGAT
*
6411 ATCAGAAATCAAA
1 ATCAGAAATC-AG
*
6424 AT-AGAATTCAG
1 ATCAGAAATCAG
* * *
6435 ATTAGATATCAT
1 ATCAGAAATCAG
*
6447 AACAG-AATCCAG
1 ATCAGAAAT-CAG
6459 ATCAGAAATCAG
1 ATCAGAAATCAG
*
6471 AACA-AAATTCAG
1 ATCAGAAA-TCAG
*
6483 ATAAGAAATCAG
1 ATCAGAAATCAG
6495 A
1 A
6496 ACATAATTCA
Statistics
Matches: 54, Mismatches: 13, Indels: 11
0.69 0.17 0.14
Matches are distributed among these distances:
11 8 0.15
12 38 0.70
13 8 0.15
ACGTcount: A:0.53, C:0.14, G:0.13, T:0.20
Consensus pattern (12 bp):
ATCAGAAATCAG
Found at i:8011 original size:10 final size:10
Alignment explanation
Indices: 7987--8016 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
7977 CCCAAAAAAA
7987 GTCAACGGTCG
1 GTCAACGG-CG
7998 GTCAACGGCG
1 GTCAACGGCG
8008 GTCAACGGC
1 GTCAACGGC
8017 AATCAACATC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.58
11 8 0.42
ACGTcount: A:0.20, C:0.30, G:0.37, T:0.13
Consensus pattern (10 bp):
GTCAACGGCG
Found at i:10185 original size:24 final size:24
Alignment explanation
Indices: 10156--10245 Score: 99
Period size: 24 Copynumber: 3.8 Consensus size: 24
10146 AAGATATCTG
* *
10156 AAATCAAAACAGAATTTAGATCAA
1 AAATCAAAACAGAATTCAGATAAA
* * *
10180 ATATCATAACAGAATCCAGATAAA
1 AAATCAAAACAGAATTCAGATAAA
* *
10204 AAATCAGAACAGAATTCAGATAAG
1 AAATCAAAACAGAATTCAGATAAA
* *
10228 AAATCAGAATAGAATTCA
1 AAATCAAAACAGAATTCA
10246 AATAGGAAAT
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 56 1.00
ACGTcount: A:0.56, C:0.13, G:0.11, T:0.20
Consensus pattern (24 bp):
AAATCAAAACAGAATTCAGATAAA
Found at i:10254 original size:24 final size:24
Alignment explanation
Indices: 10155--10255 Score: 87
Period size: 24 Copynumber: 4.2 Consensus size: 24
10145 GAAGATATCT
* * *
10155 GAAATCAAAACAGAATTTAGATCAA
1 GAAATCAGAACAGAATTCAAAT-AA
* * * *
10180 -ATATCATAACAGAATCCAGATAA
1 GAAATCAGAACAGAATTCAAATAA
* *
10203 AAAATCAGAACAGAATTCAGATAA
1 GAAATCAGAACAGAATTCAAATAA
* *
10227 GAAATCAGAATAGAATTCAAATAG
1 GAAATCAGAACAGAATTCAAATAA
10251 GAAAT
1 GAAAT
10256 AAGATAAAAC
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
23 2 0.03
24 62 0.97
ACGTcount: A:0.55, C:0.12, G:0.13, T:0.20
Consensus pattern (24 bp):
GAAATCAGAACAGAATTCAAATAA
Found at i:11756 original size:16 final size:17
Alignment explanation
Indices: 11724--11756 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
11714 CCGGTCAACG
*
11724 GCGATCAACATCGGTCA
1 GCGATCAACAGCGGTCA
11741 GCGATCAAC-GCGGTCA
1 GCGATCAACAGCGGTCA
11757 ACGGCTCGGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.15
Consensus pattern (17 bp):
GCGATCAACAGCGGTCA
Found at i:20579 original size:32 final size:34
Alignment explanation
Indices: 20543--20627 Score: 86
Period size: 34 Copynumber: 2.6 Consensus size: 34
20533 AAGTTAAGAG
20543 TCTAATATAAAAGTGTGCATG-T-TAATAGATAT
1 TCTAATATAAAAGTGTGCATGTTATAATAGATAT
* *** *
20575 TCTAA-AGAAACAAAATGAATGTTATAATAGATAT
1 TCTAATATAAA-AGTGTGCATGTTATAATAGATAT
*
20609 TCAAATATAAAAGTGTGCA
1 TCTAATATAAAAGTGTGCA
20628 CGAATTAAGT
Statistics
Matches: 38, Mismatches: 11, Indels: 6
0.69 0.20 0.11
Matches are distributed among these distances:
31 4 0.11
32 11 0.29
33 1 0.03
34 18 0.47
35 4 0.11
ACGTcount: A:0.47, C:0.07, G:0.14, T:0.32
Consensus pattern (34 bp):
TCTAATATAAAAGTGTGCATGTTATAATAGATAT
Found at i:20663 original size:25 final size:25
Alignment explanation
Indices: 20629--20682 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
20619 AAGTGTGCAC
20629 GAATTAAGTGACTTTCGTGGTAAAA
1 GAATTAAGTGACTTTCGTGGTAAAA
20654 GAATTAAGTGACTTTCGTGGTAAAA
1 GAATTAAGTGACTTTCGTGGTAAAA
20679 GAAT
1 GAAT
20683 AATTATTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.31
Consensus pattern (25 bp):
GAATTAAGTGACTTTCGTGGTAAAA
Found at i:29355 original size:59 final size:60
Alignment explanation
Indices: 29287--29403 Score: 164
Period size: 60 Copynumber: 2.0 Consensus size: 60
29277 TTTTTGGATG
* * * * * *
29287 TTTATTTGATTGC-AAAAGATTAAAATGTTTGAGCTATGGTGAATTATGAAAATCTTGTT
1 TTTATTTGATTCCAAAAAGATTAAAAAGTTTGAGCAACGATGAATTACGAAAATCTTGTT
*
29346 TTTATTTGATTCCAAAAAGATTAAAAAGTTTGGGCAACGATGAATTACGAAAATCTTG
1 TTTATTTGATTCCAAAAAGATTAAAAAGTTTGAGCAACGATGAATTACGAAAATCTTG
29404 CATAAATATT
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
59 12 0.24
60 38 0.76
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.38
Consensus pattern (60 bp):
TTTATTTGATTCCAAAAAGATTAAAAAGTTTGAGCAACGATGAATTACGAAAATCTTGTT
Found at i:31477 original size:63 final size:64
Alignment explanation
Indices: 31343--31500 Score: 162
Period size: 63 Copynumber: 2.5 Consensus size: 64
31333 TTCAATGTGC
* * * * * *
31343 ATCGATGCACATGAAGTGTATCGATGCACTCCTTTAAAATAAATACATCGAATGTCATCAGTGT
1 ATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAATACATCGAATGGCATCAGTGT
* * *
31407 ATCGATGCACAAGTGGTGCATCGATGCACCCCCTT-AAATACAA-ACATCGAATGGGATTTA-TG
1 ATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATA-AATACATCGAATGGCA-TCAGTG
31469 T
64 T
* *
31470 ATCGATGCA-TAGATTGTGCATCGATGCACCC
1 ATCGATGCACAAG-TAGTGCATCGATGCACCC
31501 GTCAAGGGAT
Statistics
Matches: 80, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
62 2 0.03
63 45 0.56
64 33 0.41
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.27
Consensus pattern (64 bp):
ATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAATACATCGAATGGCATCAGTGT
Found at i:32089 original size:18 final size:18
Alignment explanation
Indices: 32066--32156 Score: 92
Period size: 18 Copynumber: 4.9 Consensus size: 18
32056 AGGGATTATC
*
32066 AGTGGTCCTACGGGATAT
1 AGTGGTCCTTCGGGATAT
* * *
32084 AGTGGTTCTTCGGAACAAT
1 AGTGGTCCTTCGGGA-TAT
*
32103 CAGTGGTCCTTCGGGACAT
1 -AGTGGTCCTTCGGGATAT
*
32122 AGTGGTCTTTCGGGATAT
1 AGTGGTCCTTCGGGATAT
* *
32140 AGTGGTCTTTTGGGATA
1 AGTGGTCCTTCGGGATA
32157 AATATTCAGT
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
18 44 0.72
19 4 0.07
20 13 0.21
ACGTcount: A:0.20, C:0.15, G:0.32, T:0.33
Consensus pattern (18 bp):
AGTGGTCCTTCGGGATAT
Found at i:37966 original size:19 final size:18
Alignment explanation
Indices: 37927--37968 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
37917 TGAATGGAAT
*
37927 TTTGAAATAGAGTTCATA
1 TTTGAAATAGAGTTCAAA
37945 TTTGAAATCAGAGGTT-AAA
1 TTTGAAAT-AGA-GTTCAAA
37964 TTTGA
1 TTTGA
37969 CTTGTCATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 8 0.38
19 10 0.48
20 3 0.14
ACGTcount: A:0.38, C:0.05, G:0.19, T:0.38
Consensus pattern (18 bp):
TTTGAAATAGAGTTCAAA
Found at i:38413 original size:64 final size:64
Alignment explanation
Indices: 38297--38436 Score: 151
Period size: 64 Copynumber: 2.2 Consensus size: 64
38287 CATGAAGTGT
* * *
38297 ATCGATGCACTCATTTAAAATAAAAACATTGAATGTCATCAGTGTATCGATGCACAAG-TGGTGC
1 ATCGATGCACCCATTTAAAATAAAAACATCGAATGGCATCAGTGTATCGATGCA-AAGATGGTGC
* * * * * *
38361 ATCGATGCACCCCTTTAAAATACAAACATCGAATGGGATTTA-TGTA-CTGATGCATAGATTGTG
1 ATCGATGCACCCATTTAAAATAAAAACATCGAATGGCA-TCAGTGTATC-GATGCAAAGATGGTG
38424 C
64 C
38425 ATCGATGCACCC
1 ATCGATGCACCC
38437 GTCAAGGGAT
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
63 3 0.05
64 59 0.92
65 2 0.03
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.28
Consensus pattern (64 bp):
ATCGATGCACCCATTTAAAATAAAAACATCGAATGGCATCAGTGTATCGATGCAAAGATGGTGC
Found at i:39320 original size:2 final size:2
Alignment explanation
Indices: 39313--39345 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
39303 AATGCATTGT
39313 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39346 TTATTTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.