Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006819.1 Hibiscus syriacus cultivar Beakdansim tig00017327_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: 60439
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:4379 original size:23 final size:23
Alignment explanation
Indices: 4335--4379 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
4325 ATTATTATAT
*
4335 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
4358 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
4380 AGCTGTGGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:5288 original size:22 final size:24
Alignment explanation
Indices: 5260--5317 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
5250 GACATGTGAA
*
5260 ATATGTCCCGAAGGA-C-CTATGC
1 ATATGTCCCGAAGGACCACTATCC
*
5282 ATATGTCTCGAAGGACCACTATCC
1 ATATGTCCCGAAGGACCACTATCC
*
5306 ATATGTTCCGAA
1 ATATGTCCCGAA
5318 TAACATAGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 14 0.47
23 1 0.03
24 15 0.50
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (24 bp):
ATATGTCCCGAAGGACCACTATCC
Found at i:5339 original size:30 final size:30
Alignment explanation
Indices: 5303--5360 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
5293 AGGACCACTA
*
5303 TCCATATGT-TCCGAATAACATAGGTAACTG
1 TCCATATGTCT-CGAAGAACATAGGTAACTG
*
5333 TCCATATGTCTCGAAGGACATAGGTAAC
1 TCCATATGTCTCGAAGAACATAGGTAAC
5361 CCTCGACTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.28
Consensus pattern (30 bp):
TCCATATGTCTCGAAGAACATAGGTAACTG
Found at i:12706 original size:23 final size:23
Alignment explanation
Indices: 12663--12708 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
12653 ATGTTCATTT
*
12663 TACATAACTTAGAAAGAAAAAAA
1 TACATAACTTACAAAGAAAAAAA
* *
12686 TACATAAC-TACAAATATAAAAA
1 TACATAACTTACAAAGAAAAAAA
12708 T
1 T
12709 TATATATCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.63, C:0.11, G:0.04, T:0.22
Consensus pattern (23 bp):
TACATAACTTACAAAGAAAAAAA
Found at i:13096 original size:16 final size:16
Alignment explanation
Indices: 13072--13106 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
13062 AGATATGAAA
13072 AAATCAATTTAAATTT
1 AAATCAATTTAAATTT
* *
13088 AAATTAATTTAATTTT
1 AAATCAATTTAAATTT
13104 AAA
1 AAA
13107 ATAACGTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (16 bp):
AAATCAATTTAAATTT
Found at i:15125 original size:25 final size:23
Alignment explanation
Indices: 15061--15135 Score: 71
Period size: 24 Copynumber: 3.2 Consensus size: 23
15051 TTTTTATTTA
* *
15061 ATTTTTAAAATTTATTTAATCTG
1 ATTTTTAAAATTTATTTAATATT
** * *
15084 A-AATTAAATTTTATTTATTTATT
1 ATTTTTAAAATTTATTTA-ATATT
15107 ATTTTTAAAATTTAGTTTAATATT
1 ATTTTTAAAATTTA-TTTAATATT
15131 ATTTT
1 ATTTT
15136 CATTTATTAT
Statistics
Matches: 39, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
22 13 0.33
23 4 0.10
24 18 0.46
25 4 0.10
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (23 bp):
ATTTTTAAAATTTATTTAATATT
Found at i:15328 original size:21 final size:21
Alignment explanation
Indices: 15289--15328 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
15279 TTAATTAATT
*
15289 TAAATTATATTTATATATTCA
1 TAAATTATATTAATATATTCA
15310 TAAATTAATATTAAT-TATT
1 TAAATT-ATATTAATATATT
15329 TTTTCTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (21 bp):
TAAATTATATTAATATATTCA
Found at i:25396 original size:67 final size:67
Alignment explanation
Indices: 25318--25452 Score: 252
Period size: 67 Copynumber: 2.0 Consensus size: 67
25308 TGGAGTATAA
*
25318 TTATATTTTAATTTTTGTATGTCATTTTTGATTGTAATTAAATTAGACGAGTTAATTACATCACA
1 TTATATTTTAATTTTTGTATGTCATATTTGATTGTAATTAAATTAGACGAGTTAATTACATCACA
25383 TG
66 TG
*
25385 TTATATTTTAATTTTTGTATGTCATATTTGATTGTAATTAAATTAGACGAGTTAATTACTTCACA
1 TTATATTTTAATTTTTGTATGTCATATTTGATTGTAATTAAATTAGACGAGTTAATTACATCACA
25450 TG
66 TG
25452 T
1 T
25453 CTTTCAATTA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (67 bp):
TTATATTTTAATTTTTGTATGTCATATTTGATTGTAATTAAATTAGACGAGTTAATTACATCACA
TG
Found at i:26903 original size:16 final size:16
Alignment explanation
Indices: 26882--26912 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
26872 GGTTGGGTTT
26882 ATATTTTTTAAAAAAA
1 ATATTTTTTAAAAAAA
26898 ATATTTTTTAAAAAA
1 ATATTTTTTAAAAAA
26913 GTTCAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATATTTTTTAAAAAAA
Found at i:29471 original size:15 final size:15
Alignment explanation
Indices: 29451--29481 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
29441 TTACTGTGCA
29451 TTATTTAATCTAATT
1 TTATTTAATCTAATT
*
29466 TTATTTAATTTAATT
1 TTATTTAATCTAATT
29481 T
1 T
29482 ATTAAATGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (15 bp):
TTATTTAATCTAATT
Found at i:32308 original size:26 final size:25
Alignment explanation
Indices: 32275--32334 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
32265 AAGGAAACAA
*
32275 AATT-AATTAATTTTCTTAAATATCC
1 AATTGAATTAATATTC-TAAATATCC
* *
32300 AATTGAATTTATATTCTAAATATTC
1 AATTGAATTAATATTCTAAATATCC
32325 AATATGAATT
1 AAT-TGAATT
32335 CACTCACTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
25 15 0.50
26 15 0.50
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (25 bp):
AATTGAATTAATATTCTAAATATCC
Found at i:37521 original size:106 final size:106
Alignment explanation
Indices: 37336--37760 Score: 697
Period size: 106 Copynumber: 4.0 Consensus size: 106
37326 TGTATTGTTC
* * * *
37336 CGAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACA
*
37401 ACCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
37442 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGTTCTAAAATTAGGAAATTGTTTGTTGGCA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACA
*
37507 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
** * * *
37548 CGAGTCCAATGCCCTTCACTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACA
37613 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
** *
37654 TAAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACA
37719 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
37760 C
1 C
37761 AGGTGGCGCG
Statistics
Matches: 292, Mismatches: 27, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
106 292 1.00
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACA
ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:38474 original size:37 final size:37
Alignment explanation
Indices: 38392--38476 Score: 91
Period size: 37 Copynumber: 2.3 Consensus size: 37
38382 GTTTCATGAG
* * * * **
38392 AAACAGTCTCAAGGGAGACAAAATTTTGTTTTAAGAA
1 AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAGAA
38429 AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAA-AA
1 AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAGAA
*
38465 TAAATTGTCTCA
1 -AAACTGTCTCA
38477 CGGGGAGATG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
36 2 0.05
37 38 0.95
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (37 bp):
AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAGAA
Found at i:38612 original size:36 final size:38
Alignment explanation
Indices: 38558--38639 Score: 123
Period size: 36 Copynumber: 2.2 Consensus size: 38
38548 GAAACAATTT
* *
38558 CAAAGGTTTTTTTCCAAGGGAAACTGTCTCAAGAGAGA
1 CAAAGGTTTGTTTCCAAGGGAAACTATCTCAAGAGAGA
38596 CAAA-GTTTGTTT-CAAGGGAAACTATCTCAAGAGAGA
1 CAAAGGTTTGTTTCCAAGGGAAACTATCTCAAGAGAGA
*
38632 CAATGGTT
1 CAAAGGTT
38640 AGCACGATTC
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
36 26 0.65
37 10 0.25
38 4 0.10
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (38 bp):
CAAAGGTTTGTTTCCAAGGGAAACTATCTCAAGAGAGA
Found at i:39097 original size:18 final size:18
Alignment explanation
Indices: 39070--39105 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
39060 TGTTGAATCC
*
39070 CCAAAGATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
39088 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
39106 TTGATGTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.33, G:0.08, T:0.17
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:40199 original size:16 final size:16
Alignment explanation
Indices: 40192--40222 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40182 TTCTTTTTTG
40192 TTCTTTTTTGCTTCTT
1 TTCTTTTTTGCTTCTT
40208 TTCTTTTTTG-TTCTT
1 TTCTTTTTTGCTTCTT
40223 GATTGAATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.00, C:0.16, G:0.06, T:0.77
Consensus pattern (16 bp):
TTCTTTTTTGCTTCTT
Found at i:40200 original size:26 final size:26
Alignment explanation
Indices: 40170--40222 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
40160 TTCCTTTTGA
*
40170 TTTTTGTTTCTTTTCTTTTTTGTTCT
1 TTTTTGCTTCTTTTCTTTTTTGTTCT
40196 TTTTTGCTTCTTTTCTTTTTTGTTCT
1 TTTTTGCTTCTTTTCTTTTTTGTTCT
40222 T
1 T
40223 GATTGAATCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.79
Consensus pattern (26 bp):
TTTTTGCTTCTTTTCTTTTTTGTTCT
Found at i:40233 original size:26 final size:26
Alignment explanation
Indices: 40178--40233 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
40168 GATTTTTGTT
** **
40178 TCTTTTCTTTTTTGTTCTTTTTTGCT
1 TCTTTTCTTTTTTGTTCTTGATTGAA
40204 TCTTTTCTTTTTTGTTCTTGATTGAA
1 TCTTTTCTTTTTTGTTCTTGATTGAA
40230 TCTT
1 TCTT
40234 CGCACTTGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.05, C:0.14, G:0.09, T:0.71
Consensus pattern (26 bp):
TCTTTTCTTTTTTGTTCTTGATTGAA
Found at i:43135 original size:19 final size:19
Alignment explanation
Indices: 43111--43150 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
43101 TTACCCATCT
43111 TTCGTCAACCCCAGCAACC
1 TTCGTCAACCCCAGCAACC
43130 TTCGTCAACCCCAGCAACC
1 TTCGTCAACCCCAGCAACC
43149 TT
1 TT
43151 GGCTAGTGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.45, G:0.10, T:0.20
Consensus pattern (19 bp):
TTCGTCAACCCCAGCAACC
Found at i:44977 original size:2 final size:2
Alignment explanation
Indices: 44970--45013 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
44960 ATAACGTAAA
44970 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45011 AT A
1 AT A
45014 ACATATAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45025 original size:16 final size:18
Alignment explanation
Indices: 44968--45024 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
44958 AAATAACGTA
44968 AAATATATATATATATAT
1 AAATATATATATATATAT
*
44986 ATATATATATATATATAT
1 AAATATATATATATATAT
* *
45004 ATATA-ATATA-ACATAT
1 AAATATATATATATATAT
45020 AAATA
1 AAATA
45025 AAATAAGTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
16 9 0.25
17 5 0.14
18 22 0.61
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATATATATATATATAT
Found at i:45114 original size:24 final size:23
Alignment explanation
Indices: 45087--45143 Score: 55
Period size: 24 Copynumber: 2.4 Consensus size: 23
45077 GGAAATAAAT
45087 AATAATAATATAGGA-GTAATATCA
1 AATAATAATATA--ATGTAATATCA
* *
45111 AATATATACTATAATGTAATATTA
1 AATA-ATAATATAATGTAATATCA
45135 AATAA-AATA
1 AATAATAATA
45144 AGAAGAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
22 3 0.11
23 2 0.07
24 16 0.57
25 7 0.25
ACGTcount: A:0.56, C:0.04, G:0.07, T:0.33
Consensus pattern (23 bp):
AATAATAATATAATGTAATATCA
Found at i:46260 original size:17 final size:17
Alignment explanation
Indices: 46219--46260 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
46209 TATGAATCTG
*
46219 ATAAATTTAGTTTTAAT
1 ATAAATTTAATTTTAAT
*
46236 ATATATTTAATTTTAA-
1 ATAAATTTAATTTTAAT
46252 AGTAAATTT
1 A-TAAATTT
46261 CAATGGTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 1 0.05
17 20 0.95
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (17 bp):
ATAAATTTAATTTTAAT
Found at i:48195 original size:17 final size:18
Alignment explanation
Indices: 48146--48195 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
48136 TTTAGCTTCG
* *
48146 GATTCAATTTGGTTTTTC
1 GATTAAATTTAGTTTTTC
*
48164 GATTAAGTTTAGTTTTT-
1 GATTAAATTTAGTTTTTC
48181 GATGTAAATTT-GTTT
1 GAT-TAAATTTAGTTT
48196 GCTATGTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 7 0.26
18 20 0.74
ACGTcount: A:0.22, C:0.04, G:0.18, T:0.56
Consensus pattern (18 bp):
GATTAAATTTAGTTTTTC
Found at i:59329 original size:13 final size:13
Alignment explanation
Indices: 59311--59335 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59301 TAATTCACTC
59311 AAATTTAAAAAAT
1 AAATTTAAAAAAT
59324 AAATTTAAAAAA
1 AAATTTAAAAAA
59336 CACAAAAACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATTTAAAAAAT
Done.