Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004386.1 Hibiscus syriacus cultivar Beakdansim tig00009617_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: 67248
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:4172 original size:20 final size:20
Alignment explanation
Indices: 4147--4196 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
4137 ATACTGAAAG
4147 TATCGATACTAGCCCAAGAC
1 TATCGATACTAGCCCAAGAC
4167 TATCGATACTAGCCCAAGAC
1 TATCGATACTAGCCCAAGAC
4187 TATCGATACT
1 TATCGATACT
4197 CCAGTAAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (20 bp):
TATCGATACTAGCCCAAGAC
Found at i:5599 original size:12 final size:12
Alignment explanation
Indices: 5582--5607 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5572 ATTGCATCAG
5582 CAATGACAACAT
1 CAATGACAACAT
5594 CAATGACAACAT
1 CAATGACAACAT
5606 CA
1 CA
5608 GTCCTAAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.27, G:0.08, T:0.15
Consensus pattern (12 bp):
CAATGACAACAT
Found at i:17375 original size:15 final size:16
Alignment explanation
Indices: 17345--17377 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
17335 GGCATTAGCA
17345 TCAGAAAGGGTATTCT
1 TCAGAAAGGGTATTCT
*
17361 TCAGAAA-GTTATTCT
1 TCAGAAAGGGTATTCT
17376 TC
1 TC
17378 TCAGAAAGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.36
Consensus pattern (16 bp):
TCAGAAAGGGTATTCT
Found at i:26782 original size:18 final size:19
Alignment explanation
Indices: 26746--26782 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
26736 TTAGGGTTTG
*
26746 TGGTATAATCTTTAGATTT
1 TGGTATAATCTTTAAATTT
26765 TGGTATAAT-TTTAAATTT
1 TGGTATAATCTTTAAATTT
26783 ACTTTTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.30, C:0.03, G:0.14, T:0.54
Consensus pattern (19 bp):
TGGTATAATCTTTAAATTT
Found at i:26823 original size:49 final size:49
Alignment explanation
Indices: 26766--26860 Score: 165
Period size: 49 Copynumber: 1.9 Consensus size: 49
26756 TTTAGATTTT
*
26766 GGTATAATTTTAAATTTACTTTT-TGATTTTAATTATATATTAATAATTG
1 GGTATAATTTTAAATTTAATTTTCT-ATTTTAATTATATATTAATAATTG
26815 GGTATAATTTTAAATTTAATTTTCTATTTTAATTATATATTAATAA
1 GGTATAATTTTAAATTTAATTTTCTATTTTAATTATATATTAATAA
26861 AATAATAATA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
49 43 0.98
50 1 0.02
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55
Consensus pattern (49 bp):
GGTATAATTTTAAATTTAATTTTCTATTTTAATTATATATTAATAATTG
Found at i:29781 original size:3 final size:3
Alignment explanation
Indices: 29775--29820 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
29765 ATAGTAGTAG
*
29775 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-T TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
29821 TTCTTTAACC
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 1 0.03
3 39 0.98
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:30348 original size:91 final size:92
Alignment explanation
Indices: 30189--30363 Score: 273
Period size: 91 Copynumber: 1.9 Consensus size: 92
30179 GTGATAGGTC
*
30189 GAACAAGCTCTTCTCATTATGAACTTATTCTCTCTCTTTCAGACGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTATTCTCTCTCGTTCAGACGAGTTCTTCTCATTATGAACT
30254 CTCCATTGAAAATATTGATGCGAAGTT
66 CTCCATTGAAAATATTGATGCGAAGTT
* * * *
30281 GAACAAGTTCTTCTCATTATGAACTTCTTCT-TCCTCGTT-GGATGAGTTCTTCTCATTATGAAC
1 GAACAAGCTCTTCTCATTATGAACTTATTCTCT-CTCGTTCAGACGAGTTCTTCTCATTATGAAC
*
30344 TCTCCATTGGAAATATTGAT
65 TCTCCATTGAAAATATTGAT
30364 CCATCTCTTT
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
91 42 0.55
92 34 0.45
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (92 bp):
GAACAAGCTCTTCTCATTATGAACTTATTCTCTCTCGTTCAGACGAGTTCTTCTCATTATGAACT
CTCCATTGAAAATATTGATGCGAAGTT
Found at i:30712 original size:240 final size:240
Alignment explanation
Indices: 30282--30838 Score: 934
Period size: 240 Copynumber: 2.3 Consensus size: 240
30272 TGCGAAGTTG
* *
30282 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAACTCT
1 AACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCT
*
30347 CCATTGGAAATATTGATCCATCTCTTTCTGTGATGGACTTGAAAGGAACAAGTTCTTCTCATCAT
66 CCATTGGAAATATTGATCCATCTCTTTCTGTGATGGACTTGAAAGGAACAAGTTATTCTCATCAT
* *
30412 GAACTTTCTCCTTTAGGACGAGTTTTTCTCATTATGAACTCTTTTGAAAGTGTCAATCCCTCAAG
131 GAACTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTTTGAAAATGTCAATCCCTCAAG
* *
30477 CGAGGTGTCCCTGATTCGAAATGTCATGAATCGAGTGATAGGTCA
196 CGAGGTGTCACTGATTCAAAATGTCATGAATCGAGTGATAGGTCA
* *
30522 AACAAGCTCTTCTCATTATGAACTTTTTATCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCT
1 AACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCT
* * *
30587 CCATTGGAAATTTTGATCCATCTCTTTCTGTGATGGACTTGAAAGGAATAAGTTATTCTCATTAT
66 CCATTGGAAATATTGATCCATCTCTTTCTGTGATGGACTTGAAAGGAACAAGTTATTCTCATCAT
*
30652 GAACTTTCTCTTTTAGGACGAGTTCTTCTCATTATGAACTCTTTTGAAAATGTCAATCCCTCAAG
131 GAACTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTTTGAAAATGTCAATCCCTCAAG
* * **
30717 CGAGGTGTCACTGATTTAAAATGTCGTGAATCGAGTGATAGGTTG
196 CGAGGTGTCACTGATTCAAAATGTCATGAATCGAGTGATAGGTCA
**
30762 AACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCAGATGAGTTCTTCTCATTATGAACTC
1 AACAAGCTCTTCTCATTATGAACTTCTTCTCCCTC-GTTGGATGAGTTCTTCTCATTATGAACTC
30827 TCCATTGGAAAT
65 TCCATTGGAAAT
30839 GTTGGTTCAC
Statistics
Matches: 295, Mismatches: 21, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
240 256 0.87
241 39 0.13
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (240 bp):
AACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCT
CCATTGGAAATATTGATCCATCTCTTTCTGTGATGGACTTGAAAGGAACAAGTTATTCTCATCAT
GAACTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTTTGAAAATGTCAATCCCTCAAG
CGAGGTGTCACTGATTCAAAATGTCATGAATCGAGTGATAGGTCA
Found at i:31778 original size:10 final size:8
Alignment explanation
Indices: 31719--31783 Score: 73
Period size: 8 Copynumber: 8.1 Consensus size: 8
31709 TATTTTTCTC
31719 TTTTCATT
1 TTTTCATT
31727 TTTTCATT
1 TTTTCATT
*
31735 TCTT--TT
1 TTTTCATT
31741 TTTTCATT
1 TTTTCATT
31749 TTTTCATTTT
1 TTTTCA--TT
31759 TTTTCATT
1 TTTTCATT
31767 TTTTCATCT
1 TTTTCAT-T
31776 TTTT-ATT
1 TTTTCATT
31783 T
1 T
31784 ATTACTTTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 11
0.79 0.03 0.17
Matches are distributed among these distances:
6 5 0.10
7 2 0.04
8 30 0.60
9 5 0.10
10 8 0.16
ACGTcount: A:0.11, C:0.12, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTCATT
Found at i:31778 original size:18 final size:18
Alignment explanation
Indices: 31719--31779 Score: 77
Period size: 18 Copynumber: 3.2 Consensus size: 18
31709 TATTTTTCTC
31719 TTTTCATTTTTTCATTTCTTTT
1 TTTTCATTTTTTCA--TC--TT
*
31741 TTTTCATTTTTTCATTTT
1 TTTTCATTTTTTCATCTT
31759 TTTTCATTTTTTCATCTT
1 TTTTCATTTTTTCATCTT
31777 TTT
1 TTT
31780 ATTTATTACT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
18 22 0.59
20 1 0.03
22 14 0.38
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTCATTTTTTCATCTT
Found at i:44916 original size:3 final size:3
Alignment explanation
Indices: 44901--44982 Score: 139
Period size: 3 Copynumber: 27.7 Consensus size: 3
44891 TAAACACACT
*
44901 TAA TAA TAT TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
44949 TAA TAA TAA TAA TAA TAA TAA TAA T-T TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
44983 TTCTTTAACC
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
2 1 0.01
3 73 0.99
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:46420 original size:20 final size:20
Alignment explanation
Indices: 46397--46435 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
46387 ATCAGAACTT
46397 ACCCATGACTATCGATACTC
1 ACCCATGACTATCGATACTC
* **
46417 ACCCTTGGGTATCGATACT
1 ACCCATGACTATCGATACT
46436 ATAAGATTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.28
Consensus pattern (20 bp):
ACCCATGACTATCGATACTC
Found at i:48111 original size:18 final size:18
Alignment explanation
Indices: 48085--48122 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
48075 GTCGAATAGT
48085 CCTTCTTCTTCTCCTTTC
1 CCTTCTTCTTCTCCTTTC
* *
48103 CCTTGTTCTTCTTCTTTC
1 CCTTCTTCTTCTCCTTTC
48121 CC
1 CC
48123 GGCTCTCACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.00, C:0.42, G:0.03, T:0.55
Consensus pattern (18 bp):
CCTTCTTCTTCTCCTTTC
Found at i:49842 original size:31 final size:30
Alignment explanation
Indices: 49770--49856 Score: 92
Period size: 31 Copynumber: 3.0 Consensus size: 30
49760 CTTTTTCATT
*
49770 TAAGTATCT-AAAGTATTTTTTGGTCAAAA
1 TAAGTATCTAAAATTATTTTTTGGTCAAAA
*
49799 TAAATA-CATAAAATTATCTTTTTGGTCAAAA
1 TAAGTATC-TAAAATTAT-TTTTTGGTCAAAA
* *
49830 TAGGTATCTAAAA-TATTTTGT-GTCAAA
1 TAAGTATCTAAAATTATTTTTTGGTCAAA
49857 CTAGGTTCCT
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
28 7 0.14
29 10 0.20
30 9 0.18
31 22 0.45
32 1 0.02
ACGTcount: A:0.40, C:0.08, G:0.11, T:0.40
Consensus pattern (30 bp):
TAAGTATCTAAAATTATTTTTTGGTCAAAA
Found at i:58273 original size:17 final size:17
Alignment explanation
Indices: 58253--58298 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
58243 GTTATGTATT
58253 TTCGTATTTTATCATTA
1 TTCGTATTTTATCATTA
* *
58270 TTCGTATTTCATCGTTA
1 TTCGTATTTTATCATTA
*
58287 TTCATATTTTAT
1 TTCGTATTTTAT
58299 TTACCGGAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.22, C:0.13, G:0.07, T:0.59
Consensus pattern (17 bp):
TTCGTATTTTATCATTA
Found at i:59451 original size:20 final size:21
Alignment explanation
Indices: 59410--59451 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
59400 ATTCTCTCTT
*
59410 ATTTTATTAATTGTATTTTTA
1 ATTTTATTAATTGTATTATTA
59431 ATTTT-TTAATT-TACTTATTA
1 ATTTTATTAATTGTA-TTATTA
59451 A
1 A
59452 ACTTTCAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 2 0.11
20 12 0.63
21 5 0.26
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (21 bp):
ATTTTATTAATTGTATTATTA
Found at i:59555 original size:23 final size:23
Alignment explanation
Indices: 59529--59581 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
59519 TTTATTTAAT
59529 ATAAAAATAATTTAAA-A-TAAAAA
1 ATAAAAAT-A-TTAAATATTAAAAA
*
59552 ATAAAAATATTAAATATTAAATA
1 ATAAAAATATTAAATATTAAAAA
59575 ATAAAAA
1 ATAAAAA
59582 ATAGTACATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 5 0.19
22 2 0.07
23 20 0.74
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (23 bp):
ATAAAAATATTAAATATTAAAAA
Found at i:65348 original size:22 final size:22
Alignment explanation
Indices: 65307--65348 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
65297 ATAAATATTA
* *
65307 AAAATTCTAACAATAGTAAACT
1 AAAATTCTAACAAAAATAAACT
*
65329 AAAATTCTAAGAAAAATAAA
1 AAAATTCTAACAAAAATAAA
65349 TTCCTAATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.62, C:0.10, G:0.05, T:0.24
Consensus pattern (22 bp):
AAAATTCTAACAAAAATAAACT
Done.