Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000200.1 Hibiscus syriacus cultivar Beakdansim tig00000357_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: 60479
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:2026 original size:21 final size:22
Alignment explanation
Indices: 1962--2079 Score: 131
Period size: 21 Copynumber: 5.6 Consensus size: 22
1952 TTCAATATTT
* *
1962 GTCCTGAAGGACCACTGG--AC
1 GTCCCGAAGGACTACTGGATAC
* * *
1982 GTCCTGAAAGAC-ACTGGATTC
1 GTCCCGAAGGACTACTGGATAC
*
2003 GTCCCGAATGACTACT-GATAC
1 GTCCCGAAGGACTACTGGATAC
2024 GTCCCGAAGGACTACTGGATA-
1 GTCCCGAAGGACTACTGGATAC
*
2045 GTCCCGAA-GACCACTGGATAC
1 GTCCCGAAGGACTACTGGATAC
2066 GTCCCGAAGGACTA
1 GTCCCGAAGGACTA
2080 ATATACCTCG
Statistics
Matches: 84, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
19 5 0.06
20 22 0.26
21 46 0.55
22 11 0.13
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.19
Consensus pattern (22 bp):
GTCCCGAAGGACTACTGGATAC
Found at i:2079 original size:63 final size:62
Alignment explanation
Indices: 1962--2079 Score: 157
Period size: 63 Copynumber: 1.9 Consensus size: 62
1952 TTCAATATTT
* * * * *
1962 GTCCTGAAGGACCACTGGACGTCCTGAAAGACACTGGATTCGTCCCGAATGACTACTGATAC
1 GTCCCGAAGGACCACTGGAAGTCCCGAAAGACACTGGATACGTCCCGAAGGACTACTGATAC
*
2024 GTCCCGAAGGACTACTGGATAGTCCCG-AAGACCACTGGATACGTCCCGAAGGACTA
1 GTCCCGAAGGACCACTGGA-AGTCCCGAAAGA-CACTGGATACGTCCCGAAGGACTA
2080 ATATACCTCG
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
62 21 0.44
63 27 0.56
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.19
Consensus pattern (62 bp):
GTCCCGAAGGACCACTGGAAGTCCCGAAAGACACTGGATACGTCCCGAAGGACTACTGATAC
Found at i:8967 original size:22 final size:22
Alignment explanation
Indices: 8939--9058 Score: 177
Period size: 22 Copynumber: 5.5 Consensus size: 22
8929 ACCACTATGC
*
8939 CCCGAAGAACCACTGGATACGT
1 CCCGAAGGACCACTGGATACGT
*
8961 CCCGAAGGACCACTGGATACAT
1 CCCGAAGGACCACTGGATACGT
* *
8983 CCCGAAGGACTACTGGATGCGT
1 CCCGAAGGACCACTGGATACGT
*
9005 CCCGAATGACCACTGGATACGT
1 CCCGAAGGACCACTGGATACGT
**
9027 CATGAAGGACCACTGGATACGT
1 CCCGAAGGACCACTGGATACGT
9049 CCCGAAGGAC
1 CCCGAAGGAC
9059 TAATATACCC
Statistics
Matches: 85, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 85 1.00
ACGTcount: A:0.29, C:0.30, G:0.26, T:0.15
Consensus pattern (22 bp):
CCCGAAGGACCACTGGATACGT
Found at i:14158 original size:2 final size:2
Alignment explanation
Indices: 14151--14196 Score: 83
Period size: 2 Copynumber: 22.5 Consensus size: 2
14141 ATGGATTACT
14151 TA TA TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14194 TA T
1 TA T
14197 TAGTATTATG
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 41 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14256 original size:2 final size:2
Alignment explanation
Indices: 14249--14285 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
14239 TCAATCTACA
14249 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 A
14286 ATTTACGACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:14458 original size:85 final size:85
Alignment explanation
Indices: 14303--14470 Score: 189
Period size: 85 Copynumber: 2.0 Consensus size: 85
14293 ACATACAATC
* ** * * *
14303 ATGACACACGAATGTGTGTCATCTTTTCTAATGGTGTGTGCTTCAATGACACGCAATGTAAGTCA
1 ATGACACACAAATGTGTGTCATCTTTTCTAATGACGAGGGCTTCAATGACACGCAATGTAAGTAA
* *
14368 TAAATGCGTGTCATAAATTT
66 AAAATGCGCGTCATAAATTT
* *
14388 ATGACACACAAATGTGTGTCATCTTCATT-T-ATGACGAGGGCTTCAATGGCACGCAATG-AGCG
1 ATGACACACAAATGTGTGTCATCTT--TTCTAATGACGAGGGCTTCAATGACACGCAATGTA-AG
*
14450 TAAAAAATGTGCGTCATAAAT
63 TAAAAAATGCGCGTCATAAAT
14471 GCGTGTCATA
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
84 1 0.01
85 65 0.94
86 1 0.01
87 2 0.03
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (85 bp):
ATGACACACAAATGTGTGTCATCTTTTCTAATGACGAGGGCTTCAATGACACGCAATGTAAGTAA
AAAATGCGCGTCATAAATTT
Found at i:14470 original size:13 final size:13
Alignment explanation
Indices: 14454--14496 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
14444 TGAGCGTAAA
*
14454 AAATGTGCGTCAT
1 AAATGCGCGTCAT
*
14467 AAATGCGTGTCAT
1 AAATGCGCGTCAT
*
14480 AAATACGCGTCAT
1 AAATGCGCGTCAT
14493 AAAT
1 AAAT
14497 TCATGATGCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (13 bp):
AAATGCGCGTCAT
Found at i:20663 original size:24 final size:24
Alignment explanation
Indices: 20636--20709 Score: 76
Period size: 24 Copynumber: 3.1 Consensus size: 24
20626 TATATCAAAA
*
20636 ATCAAAACATAATACAGGTCAAGT
1 ATCAAAACAAAATACAGGTCAAGT
* * *
20660 ATCATATCAAAATCCAGGTCAAGT
1 ATCAAAACAAAATACAGGTCAAGT
* * * *
20684 ATCATATCAAAATCCAGGTCAGGT
1 ATCAAAACAAAATACAGGTCAAGT
20708 AT
1 AT
20710 TATAATAGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (24 bp):
ATCAAAACAAAATACAGGTCAAGT
Found at i:23205 original size:18 final size:18
Alignment explanation
Indices: 23182--23220 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
23172 CAACGGTCAA
23182 CGGGTCGGGTCAACGGAT
1 CGGGTCGGGTCAACGGAT
*
23200 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGAT
23218 CGG
1 CGG
23221 ATTGTGACCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.13, C:0.23, G:0.49, T:0.15
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGAT
Found at i:23220 original size:13 final size:13
Alignment explanation
Indices: 23176--23205 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
23166 GCCGGTCAAC
*
23176 GGTCAACGGGTCG
1 GGTCAACGGATCG
23189 GGTCAACGGATCG
1 GGTCAACGGATCG
23202 GGTC
1 GGTC
23206 GGGTCAACGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.43, T:0.17
Consensus pattern (13 bp):
GGTCAACGGATCG
Found at i:24113 original size:60 final size:61
Alignment explanation
Indices: 24036--24155 Score: 224
Period size: 60 Copynumber: 2.0 Consensus size: 61
24026 TGCTCTGAAG
24036 TGGAGAAGTTAGATGGAGTTGTAATACCACAAAAATTTAGACAATGACCAAAATGAAAATT
1 TGGAGAAGTTAGATGGAGTTGTAATACCACAAAAATTTAGACAATGACCAAAATGAAAATT
*
24097 TGGAG-AGTTAGATGGAGTTGTAATACCACAAAAATTTAGACAATGACCAAAATTAAAAT
1 TGGAGAAGTTAGATGGAGTTGTAATACCACAAAAATTTAGACAATGACCAAAATGAAAAT
24156 ACATATTTTA
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
60 53 0.91
61 5 0.09
ACGTcount: A:0.46, C:0.10, G:0.19, T:0.25
Consensus pattern (61 bp):
TGGAGAAGTTAGATGGAGTTGTAATACCACAAAAATTTAGACAATGACCAAAATGAAAATT
Found at i:24932 original size:22 final size:22
Alignment explanation
Indices: 24885--24932 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
24875 GGTATCCTGT
* *
24885 TTTTGTGTTATTTCGGATTTAT
1 TTTTGTGTTATTTCGGAGTTAG
* *
24907 TTTTGTGTTATTTTGGGGTTAG
1 TTTTGTGTTATTTCGGAGTTAG
24929 TTTT
1 TTTT
24933 AGGGGTTTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.10, C:0.02, G:0.23, T:0.65
Consensus pattern (22 bp):
TTTTGTGTTATTTCGGAGTTAG
Found at i:32043 original size:23 final size:21
Alignment explanation
Indices: 32008--32051 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
31998 TTAATTATTT
32008 AAAAAATTAAATAAAAATATAA
1 AAAAAATTAAATAAAAA-ATAA
*
32030 AAAAACATTTAATAAAAAATAA
1 AAAAA-ATTAAATAAAAAATAA
32052 TTTTTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAAAATTAAATAAAAAATAA
Found at i:32390 original size:70 final size:70
Alignment explanation
Indices: 32268--32446 Score: 304
Period size: 70 Copynumber: 2.6 Consensus size: 70
32258 ATTTTTTTTA
* * * * *
32268 AAAAAAATCTCACATAGCTAAGAAACATAGAATAGCATTACAAAAGTTTAAAGAGTAAAAATATG
1 AAAACAATCTCACATGGCTAAGAAACATAGAAGAGCATCACAAAAGTCTAAAGAGTAAAAATATG
32333 AAAAC
66 AAAAC
*
32338 AAAACAATCTCACATGGCTAAGAAACATAGAAGAACATCACAAAAGTCTAAAGAGTAAAAATATG
1 AAAACAATCTCACATGGCTAAGAAACATAGAAGAGCATCACAAAAGTCTAAAGAGTAAAAATATG
32403 AAAAC
66 AAAAC
32408 AAAACAATCTCACATGGCTAAGAAACATAGAAGAGCATC
1 AAAACAATCTCACATGGCTAAGAAACATAGAAGAGCATC
32447 CCAATTGACT
Statistics
Matches: 102, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 102 1.00
ACGTcount: A:0.55, C:0.15, G:0.13, T:0.17
Consensus pattern (70 bp):
AAAACAATCTCACATGGCTAAGAAACATAGAAGAGCATCACAAAAGTCTAAAGAGTAAAAATATG
AAAAC
Found at i:33967 original size:73 final size:73
Alignment explanation
Indices: 33885--34030 Score: 247
Period size: 73 Copynumber: 2.0 Consensus size: 73
33875 CGTAGTAAAC
* *
33885 GAATTGTAGAGAAAATTGAAAAAATTAAAATAATTGTTGAAAATGTTGATTTCGATGGTTTAAAT
1 GAATTGTAGAGAAAACTAAAAAAATTAAAATAATTGTTGAAAATGTTGATTTCGATGGTTTAAAT
33950 ATATGTAT
66 ATATGTAT
** *
33958 GAATTGTAGAGAATGCTAAAAAAATTAAAATAATTGTTGAAAATGTTGATTTTGATGGTTTAAAT
1 GAATTGTAGAGAAAACTAAAAAAATTAAAATAATTGTTGAAAATGTTGATTTCGATGGTTTAAAT
34023 ATATGTAT
66 ATATGTAT
34031 TGATAAATTT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
73 68 1.00
ACGTcount: A:0.43, C:0.01, G:0.18, T:0.38
Consensus pattern (73 bp):
GAATTGTAGAGAAAACTAAAAAAATTAAAATAATTGTTGAAAATGTTGATTTCGATGGTTTAAAT
ATATGTAT
Found at i:39170 original size:15 final size:14
Alignment explanation
Indices: 39131--39170 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
39121 TTTTTTATAT
*
39131 AATTATACATATTAA
1 AATTATA-ATTTTAA
39146 AATTATAATTTTGAA
1 AATTATAATTTT-AA
39161 AATTATAATT
1 AATTATAATT
39171 CAAATTTAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 4 0.17
15 19 0.83
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (14 bp):
AATTATAATTTTAA
Found at i:39640 original size:28 final size:28
Alignment explanation
Indices: 39595--39662 Score: 118
Period size: 28 Copynumber: 2.4 Consensus size: 28
39585 TTGAACCCTT
*
39595 CTTCTTTCTTCTTTAACTCCCATTGACCC
1 CTTC-TTCTTCTTCAACTCCCATTGACCC
39624 CTTCTTCTTCTTCAACTCCCATTGACCC
1 CTTCTTCTTCTTCAACTCCCATTGACCC
39652 CTTCTTCTTCT
1 CTTCTTCTTCT
39663 CTCCTAATCC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
28 34 0.89
29 4 0.11
ACGTcount: A:0.12, C:0.40, G:0.03, T:0.46
Consensus pattern (28 bp):
CTTCTTCTTCTTCAACTCCCATTGACCC
Found at i:42750 original size:4 final size:4
Alignment explanation
Indices: 42741--42767 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
42731 CAATGCATGT
42741 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
42768 CATAGTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:52997 original size:74 final size:74
Alignment explanation
Indices: 52856--53002 Score: 179
Period size: 74 Copynumber: 2.0 Consensus size: 74
52846 GGGTACAAAT
* * * *
52856 AAAATTTCAGGGTAGATACCATTCATAAAATAGGTAACTAATCGAAGAAAACTTAAATTTCATGG
1 AAAATTTCAAGGTAGACACCATTCATAAAATAAGTAACTAATCGAAGAAAACTTAAATTTCAAGG
*
52921 TGGGCACGA
66 TGGACACGA
* * * ** *
52930 AAAATTTCAAGGTGGACACCA-TCAGTAAAATAAGTAATTAATCGAAGAAAATTTGGATTTTAAG
1 AAAATTTCAAGGTAGACACCATTCA-TAAAATAAGTAACTAATCGAAGAAAACTTAAATTTCAAG
52994 GTGGACACG
65 GTGGACACG
53003 TGCCCACCCC
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
73 3 0.05
74 58 0.95
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.26
Consensus pattern (74 bp):
AAAATTTCAAGGTAGACACCATTCATAAAATAAGTAACTAATCGAAGAAAACTTAAATTTCAAGG
TGGACACGA
Found at i:57588 original size:18 final size:20
Alignment explanation
Indices: 57568--57604 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 20
57558 ATCATTATTC
57568 AAAAGAATGT-ATTTTTTCA
1 AAAAGAATGTCATTTTTTCA
57587 AAAAGAATGTCATTTTTT
1 AAAAGAATGTCATTTTTT
57605 TTTTGAGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (20 bp):
AAAAGAATGTCATTTTTTCA
Done.