Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001726.1 Hibiscus syriacus cultivar Beakdansim tig00003490_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: 55388
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Found at i:11699 original size:18 final size:18
Alignment explanation
Indices: 11676--11710 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
11666 ATATGTTATT
*
11676 TAAAAAAAATTAAATAAC
1 TAAAAAAAACTAAATAAC
11694 TAAAAAAAACTAAATAA
1 TAAAAAAAACTAAATAA
11711 TAGGTGGGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.20
Consensus pattern (18 bp):
TAAAAAAAACTAAATAAC
Found at i:12506 original size:2 final size:2
Alignment explanation
Indices: 12495--12531 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
12485 TATACATTCA
12495 AT AT -T 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
12532 TGATAATCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:12792 original size:15 final size:15
Alignment explanation
Indices: 12759--12792 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
12749 GTTTGGTCTG
*
12759 TTTAATTTTATTGGA
1 TTTAATTTTATTCGA
*
12774 TTTAATTTTATTCGT
1 TTTAATTTTATTCGA
12789 TTTA
1 TTTA
12793 CTATATATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.03, G:0.09, T:0.65
Consensus pattern (15 bp):
TTTAATTTTATTCGA
Found at i:17043 original size:2 final size:2
Alignment explanation
Indices: 17031--17066 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
17021 TCCCAAGAGA
17031 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17067 CCTCGTAGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:17627 original size:2 final size:2
Alignment explanation
Indices: 17620--17652 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
17610 ATGAAAATCA
*
17620 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17653 CAACTATCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17725 original size:26 final size:26
Alignment explanation
Indices: 17696--17745 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
17686 GGATTTGAAA
17696 AAAGATGCTTCATCATCGAGAAATTT
1 AAAGATGCTTCATCATCGAGAAATTT
*
17722 AAAGATGCTTCATCATCGATAAAT
1 AAAGATGCTTCATCATCGAGAAAT
17746 ACAAGTGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (26 bp):
AAAGATGCTTCATCATCGAGAAATTT
Found at i:18682 original size:27 final size:28
Alignment explanation
Indices: 18629--18682 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
18619 CTCTATTTAT
* * *
18629 ATTATGTTGTTGAGTCAGTGTTTGAAAC
1 ATTATGTTGTTCAGCCAGTGTTCGAAAC
18657 ATTATGTTG-TCAGCCAGTGTTCGAAA
1 ATTATGTTGTTCAGCCAGTGTTCGAAA
18683 GCAACAACGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.26, C:0.11, G:0.24, T:0.39
Consensus pattern (28 bp):
ATTATGTTGTTCAGCCAGTGTTCGAAAC
Found at i:34005 original size:24 final size:24
Alignment explanation
Indices: 33977--34107 Score: 129
Period size: 24 Copynumber: 5.5 Consensus size: 24
33967 ATGTTTTATC
* *
33977 TGATTTCTTATTTGAATTCTGTTA
1 TGATTTCTGATCTGAATTCTGTTA
* * * *
34001 TGATTTCCGATTTGAATTATGTTC
1 TGATTTCTGATCTGAATTCTGTTA
* * * *
34025 TAATTTCTGATATGAATTATGTTC
1 TGATTTCTGATCTGAATTCTGTTA
*
34049 TGATTTCTGATCTGGATTCTGTTA
1 TGATTTCTGATCTGAATTCTGTTA
* *
34073 TGATATT-TGATCTGAATTCCGTTT
1 TGAT-TTCTGATCTGAATTCTGTTA
34097 TGATTTCTGAT
1 TGATTTCTGAT
34108 ATCTCCGTTT
Statistics
Matches: 90, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
23 2 0.02
24 86 0.96
25 2 0.02
ACGTcount: A:0.21, C:0.11, G:0.16, T:0.52
Consensus pattern (24 bp):
TGATTTCTGATCTGAATTCTGTTA
Found at i:34103 original size:72 final size:72
Alignment explanation
Indices: 33975--34109 Score: 173
Period size: 72 Copynumber: 1.9 Consensus size: 72
33965 GAATGTTTTA
* * * *
33975 TCTGATTTCTTATTTGAATTCTGTTATGATTTCCGATTTGAATTATGTTCTAATTTCTGATATGA
1 TCTGATTTCTGATCTGAATTCTGTTATGATTTCCGATCTGAATTACGTTCTAATTTCTGATATGA
34040 ATTATGT
66 ATTATGT
* * * * *
34047 TCTGATTTCTGATCTGGATTCTGTTATGATATT-TGATCTGAATTCCGTTTTGATTTCTGATAT
1 TCTGATTTCTGATCTGAATTCTGTTATGAT-TTCCGATCTGAATTACGTTCTAATTTCTGATAT
34110 CTCCGTTTAC
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
72 51 0.96
73 2 0.04
ACGTcount: A:0.21, C:0.11, G:0.16, T:0.52
Consensus pattern (72 bp):
TCTGATTTCTGATCTGAATTCTGTTATGATTTCCGATCTGAATTACGTTCTAATTTCTGATATGA
ATTATGT
Found at i:38205 original size:17 final size:17
Alignment explanation
Indices: 38183--38220 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
38173 TTCCTAAAAT
38183 TTTTAAATTCTTATATA
1 TTTTAAATTCTTATATA
* *
38200 TTTTAAATTTTTATGTA
1 TTTTAAATTCTTATATA
38217 TTTT
1 TTTT
38221 TTATTAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (17 bp):
TTTTAAATTCTTATATA
Found at i:38258 original size:28 final size:25
Alignment explanation
Indices: 38227--38283 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 25
38217 TTTTTTATTA
*
38227 ATAATTTATTTTTATTCTCTAAAATTTT
1 ATAATTTA-TATTA-TCTCT-AAATTTT
38255 ATAAATTTATATTATCTCTAAATTTT
1 AT-AATTTATATTATCTCTAAATTTT
38281 ATA
1 ATA
38284 CGTTCGTTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 1 0.04
26 9 0.33
27 5 0.19
28 6 0.22
29 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (25 bp):
ATAATTTATATTATCTCTAAATTTT
Found at i:41507 original size:2 final size:2
Alignment explanation
Indices: 41500--41538 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
41490 TTTTTCACGA
41500 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
41539 ATCATTTTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:45072 original size:16 final size:17
Alignment explanation
Indices: 45051--45088 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
45041 TTTTATTATT
*
45051 ATTTAAGATA-AAAATA
1 ATTTAAAATATAAAATA
*
45067 ATTTAAAATATAAAATT
1 ATTTAAAATATAAAATA
45084 ATTTA
1 ATTTA
45089 TTATTATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
ATTTAAAATATAAAATA
Found at i:45087 original size:17 final size:16
Alignment explanation
Indices: 45048--45088 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
45038 ATTTTTTATT
*
45048 ATTATTTAAGATAAAA
1 ATTATTTAAAATAAAA
*
45064 ATAATTTAAAATATAAA
1 ATTATTTAAAATA-AAA
45081 ATTATTTA
1 ATTATTTA
45089 TTATTATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (16 bp):
ATTATTTAAAATAAAA
Found at i:54148 original size:58 final size:60
Alignment explanation
Indices: 54022--54157 Score: 179
Period size: 58 Copynumber: 2.3 Consensus size: 60
54012 ACTAGTTGGG
* *
54022 TGACCATTTTGTAACTTTTAATAGTTGAGGGACTCTACAAAATAATATCCTATAATTGAA
1 TGACCATTTTGTAACTTTTAATAGTTGAGAGACTCTACAAAATAATATCCTATAATAGAA
* * * * *
54082 TGACCATTTTGTAACTTTTAGTAGTT-AGAGATTC-ATAAAGTAATATCTTATAATAGAA
1 TGACCATTTTGTAACTTTTAATAGTTGAGAGACTCTACAAAATAATATCCTATAATAGAA
54140 TGACCATTTGTGT-ACTTT
1 TGACCATTT-TGTAACTTT
54158 ACCCTAAATC
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
58 34 0.50
59 9 0.13
60 25 0.37
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.40
Consensus pattern (60 bp):
TGACCATTTTGTAACTTTTAATAGTTGAGAGACTCTACAAAATAATATCCTATAATAGAA
Done.