Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008375.1 Hibiscus syriacus cultivar Beakdansim tig00111132_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: 1210889
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 7
Found at i:1171382 original size:20 final size:20
Alignment explanation
Indices: 1171359--1171434 Score: 125
Period size: 20 Copynumber: 3.8 Consensus size: 20
1171349 TGTGACAGTC
1171359 AGAATCGCGTTGCGATAGTA
1 AGAATCGCGTTGCGATAGTA
* *
1171379 AGAATCTCGTTGCGATAGTC
1 AGAATCGCGTTGCGATAGTA
1171399 AGAATCGCGTTGCGATAGTA
1 AGAATCGCGTTGCGATAGTA
*
1171419 AGAATCGCATTGCGAT
1 AGAATCGCGTTGCGAT
1171435 TTACATATTT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (20 bp):
AGAATCGCGTTGCGATAGTA
Found at i:1171410 original size:40 final size:40
Alignment explanation
Indices: 1171355--1171434 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
1171345 GTGTTGTGAC
* *
1171355 AGTCAGAATCGCGTTGCGATAGTAAGAATCTCGTTGCGAT
1 AGTCAGAATCGCGTTGCGATAGTAAGAATCGCATTGCGAT
1171395 AGTCAGAATCGCGTTGCGATAGTAAGAATCGCATTGCGAT
1 AGTCAGAATCGCGTTGCGATAGTAAGAATCGCATTGCGAT
1171435 TTACATATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (40 bp):
AGTCAGAATCGCGTTGCGATAGTAAGAATCGCATTGCGAT
Found at i:1171448 original size:20 final size:20
Alignment explanation
Indices: 1171423--1171473 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
1171413 ATAGTAAGAA
1171423 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
*
1171443 TTGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
1171463 TCGCATTGCGA
1 TCGCATTGCGA
1171474 ATTCGGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:1171494 original size:21 final size:21
Alignment explanation
Indices: 1171470--1171515 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1171460 TATTCGCATT
1171470 GCGAATTCGGAAAATCGCAAC
1 GCGAATTCGGAAAATCGCAAC
* * *
1171491 GCGAATTTGGAAATTCGCAAT
1 GCGAATTCGGAAAATCGCAAC
1171512 GCGA
1 GCGA
1171516 TAGTGAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.20
Consensus pattern (21 bp):
GCGAATTCGGAAAATCGCAAC
Found at i:1175683 original size:18 final size:19
Alignment explanation
Indices: 1175662--1175705 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1175652 GTTGTTTTTA
*
1175662 AAATAAAAG-ATAAGAATT
1 AAATAAAAGAAAAAGAATT
*
1175680 AAATAAAAGAAAAATAATT
1 AAATAAAAGAAAAAGAATT
1175699 AAATAAA
1 AAATAAA
1175706 CAAATTAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (19 bp):
AAATAAAAGAAAAAGAATT
Found at i:1178155 original size:19 final size:19
Alignment explanation
Indices: 1178131--1178180 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
1178121 TAAGCATCTG
1178131 ATGAAATAAAATAAA-ATAA
1 ATGAAATAAAATAAATA-AA
*
1178150 ATGAAATGAAATAAATAAA
1 ATGAAATAAAATAAATAAA
1178169 ATGAAAATAAAA
1 ATG-AAATAAAA
1178181 CGAAATGGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 19 0.70
20 8 0.30
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.20
Consensus pattern (19 bp):
ATGAAATAAAATAAATAAA
Found at i:1178156 original size:14 final size:14
Alignment explanation
Indices: 1178134--1178179 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
1178124 GCATCTGATG
1178134 AAATAAAATAAAAT
1 AAATAAAATAAAAT
* *
1178148 AAATGAAATGAAAT
1 AAATAAAATAAAAT
1178162 AAATAAAATGAAAAT
1 AAATAAAAT-AAAAT
1178177 AAA
1 AAA
1178180 ACGAAATGGG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
14 20 0.74
15 7 0.26
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.20
Consensus pattern (14 bp):
AAATAAAATAAAAT
Found at i:1178165 original size:4 final size:5
Alignment explanation
Indices: 1178134--1178180 Score: 53
Period size: 5 Copynumber: 9.6 Consensus size: 5
1178124 GCATCTGATG
* *
1178134 AAATA AAATA AAAT- AAATG AAATG AAAT- AAATA AAATGA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAAT-A AAATA AAA
1178181 CGAAATGGGT
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
4 8 0.21
5 26 0.67
6 5 0.13
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:1183580 original size:18 final size:18
Alignment explanation
Indices: 1183557--1183591 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1183547 AGGGATTAAC
1183557 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
1183575 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
1183592 AATTCTATGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.23, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:1188019 original size:18 final size:18
Alignment explanation
Indices: 1187996--1188030 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1187986 AGGGATTAAC
1187996 AGTGGTCCTTCAGGACAT
1 AGTGGTCCTTCAGGACAT
*
1188014 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCAGGACA
1188031 AATTCTATGC
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:0.20, C:0.23, G:0.31, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCAGGACAT
Found at i:1188323 original size:12 final size:12
Alignment explanation
Indices: 1188306--1188333 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1188296 AATAAGATTA
1188306 ATGAAGTAAATG
1 ATGAAGTAAATG
1188318 ATGAAGTAAATG
1 ATGAAGTAAATG
1188330 ATGA
1 ATGA
1188334 GTGGTATGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (12 bp):
ATGAAGTAAATG
Found at i:1190452 original size:17 final size:18
Alignment explanation
Indices: 1190432--1190473 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
1190422 AAAGATATAT
*
1190432 TAAAATAAA-ATAAATAA
1 TAAAATAAAGAAAAATAA
1190449 TAAAA-AAAGAAAAATAA
1 TAAAATAAAGAAAAATAA
*
1190466 TATAATAA
1 TAAAATAA
1190474 TAAATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 3 0.14
17 16 0.76
18 2 0.10
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.21
Consensus pattern (18 bp):
TAAAATAAAGAAAAATAA
Found at i:1193268 original size:29 final size:29
Alignment explanation
Indices: 1193236--1193340 Score: 74
Period size: 29 Copynumber: 3.6 Consensus size: 29
1193226 CAAAAAAGGT
*
1193236 ATAATTTAGAGACTTATTTTGATCAAAAA
1 ATAATTTAGAGACTTAATTTGATCAAAAA
* **
1193265 ATAA-TTAGATACTTAAAAT-AGTCACATAAA
1 ATAATTTAGAGACTTAATTTGA-TCA-A-AAA
* *
1193295 ATATTTTA-AGTA-TCTAGTTTGATCAAAAA
1 ATAATTTAGAG-ACT-TAATTTGATCAAAAA
*
1193324 ATAATTTAGATACTTAA
1 ATAATTTAGAGACTTAA
1193341 AGCAAAAAAT
Statistics
Matches: 55, Mismatches: 12, Indels: 18
0.65 0.14 0.21
Matches are distributed among these distances:
27 1 0.02
28 14 0.25
29 18 0.33
30 11 0.20
31 10 0.18
32 1 0.02
ACGTcount: A:0.47, C:0.08, G:0.09, T:0.37
Consensus pattern (29 bp):
ATAATTTAGAGACTTAATTTGATCAAAAA
Found at i:1193365 original size:59 final size:59
Alignment explanation
Indices: 1193253--1193365 Score: 138
Period size: 59 Copynumber: 1.9 Consensus size: 59
1193243 AGAGACTTAT
* ** * * *
1193253 TTTGATCAAAAAATAATTAGATACTTAAAATAGTCACATAAAATATTTTAAGTATCTAG
1 TTTGATCAAAAAATAATTAGATACTTAAAACAGAAAAATAAAATAATTCAAGTATCTAG
* *
1193312 TTTGATCAAAAAATAATTTAGATACTTAAAGCA-AAAAATAACATAATTCAAGTA
1 TTTGATCAAAAAATAA-TTAGATACTTAAAACAGAAAAATAAAATAATTCAAGTA
1193366 ATTTTTTAGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
59 31 0.69
60 14 0.31
ACGTcount: A:0.50, C:0.09, G:0.08, T:0.33
Consensus pattern (59 bp):
TTTGATCAAAAAATAATTAGATACTTAAAACAGAAAAATAAAATAATTCAAGTATCTAG
Found at i:1193689 original size:27 final size:28
Alignment explanation
Indices: 1193648--1193712 Score: 105
Period size: 27 Copynumber: 2.3 Consensus size: 28
1193638 TAAGGGTTAG
1193648 AAAATAAAAACTTTAAATCTCAAACATAA
1 AAAAT-AAAACTTTAAATCTCAAACATAA
1193677 AAAATAAAA-TTTAAATCTCAAACATAA
1 AAAATAAAACTTTAAATCTCAAACATAA
*
1193704 AGAATAAAA
1 AAAATAAAA
1193713 AGAATTATTG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 26 0.74
28 4 0.11
29 5 0.14
ACGTcount: A:0.65, C:0.11, G:0.02, T:0.23
Consensus pattern (28 bp):
AAAATAAAACTTTAAATCTCAAACATAA
Found at i:1200360 original size:2 final size:2
Alignment explanation
Indices: 1200355--1200396 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1200345 ATACACATTC
1200355 AT AT AT AT AT 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 AT AT
1200397 TTCTTACACA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1200701 original size:31 final size:31
Alignment explanation
Indices: 1200663--1200728 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
1200653 TCCCACATTA
1200663 AGTGGGAAATAATTCTTGCAAGGGTATTTAT
1 AGTGGGAAATAATTCTTGCAAGGGTATTTAT
1200694 AGTGGGAAATAATTCTTGCAAGGGTATTTAT
1 AGTGGGAAATAATTCTTGCAAGGGTATTTAT
1200725 AGTG
1 AGTG
1200729 TTCATTCTGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.32, C:0.06, G:0.27, T:0.35
Consensus pattern (31 bp):
AGTGGGAAATAATTCTTGCAAGGGTATTTAT
Found at i:1205536 original size:21 final size:21
Alignment explanation
Indices: 1205512--1205551 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1205502 CAGGAGAAAA
1205512 AATAAAAATAAAACAAAATGG
1 AATAAAAATAAAACAAAATGG
1205533 AATAAAAATAAAACAAAAT
1 AATAAAAATAAAACAAAAT
1205552 AATGTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.15
Consensus pattern (21 bp):
AATAAAAATAAAACAAAATGG
Found at i:1206367 original size:21 final size:21
Alignment explanation
Indices: 1206343--1206384 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1206333 GGGGCCATTT
1206343 TCGATTACTTTGGGGTTGTTC
1 TCGATTACTTTGGGGTTGTTC
**
1206364 TCGATTGTTTTGGGGTTGTTC
1 TCGATTACTTTGGGGTTGTTC
1206385 CCAGTTATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.07, C:0.12, G:0.31, T:0.50
Consensus pattern (21 bp):
TCGATTACTTTGGGGTTGTTC
Found at i:1206796 original size:30 final size:30
Alignment explanation
Indices: 1206762--1206828 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
1206752 CCCTAACATA
1206762 TCTCGGGTCTCTTATTTACCCGGTTTACCC
1 TCTCGGGTCTCTTATTTACCCGGTTTACCC
1206792 TCTCGGGTCTCTTATTTACCCGGTTTACCC
1 TCTCGGGTCTCTTATTTACCCGGTTTACCC
1206822 TCT-GGGT
1 TCTCGGGT
1206829 ATTCGGACTA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 4 0.11
30 33 0.89
ACGTcount: A:0.09, C:0.31, G:0.19, T:0.40
Consensus pattern (30 bp):
TCTCGGGTCTCTTATTTACCCGGTTTACCC
Found at i:1206956 original size:11 final size:11
Alignment explanation
Indices: 1206937--1206994 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
1206927 AAAAAAGAAA
1206937 ATAAA-AAAAT
1 ATAAATAAAAT
*
1206947 ATTAATAAAAT
1 ATAAATAAAAT
1206958 AATAAATAACAA-
1 -ATAAATAA-AAT
1206970 ATAAATAAAAT
1 ATAAATAAAAT
*
1206981 -T-AATATAAT
1 ATAAATAAAAT
1206990 ATAAA
1 ATAAA
1206995 AATTAAAATC
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
9 7 0.18
10 8 0.21
11 15 0.38
12 7 0.18
13 2 0.05
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.28
Consensus pattern (11 bp):
ATAAATAAAAT
Found at i:1207074 original size:36 final size:35
Alignment explanation
Indices: 1207030--1207373 Score: 349
Period size: 36 Copynumber: 9.6 Consensus size: 35
1207020 TTATACATGC
*
1207030 TTTCAAAAATAGTTTTCAAAACCATATAATATATAT
1 TTTCAAAAAT-GTTTTCAAAACTATATAATATATAT
* *
1207066 TTTAAAAAATTGTTTTTAAAACTATATAATATATAT
1 TTTCAAAAA-TGTTTTCAAAACTATATAATATATAT
* * *
1207102 TTTCAAAACT-TTTCCAAAATTATATATTATATATAT
1 TTTCAAAAATGTTTTCAAAACTATATA--ATATATAT
* *
1207138 TTTCAAAAATGTTTTCAAAATTATATAATATATGT
1 TTTCAAAAATGTTTTCAAAACTATATAATATATAT
* *
1207173 TTTC-AAAATGTTTTCGAAACTATATAACATATAT
1 TTTCAAAAATGTTTTCAAAACTATATAATATATAT
*
1207207 TTTCAAAAAT-TTTCCAAAACTATATATTATATATAT
1 TTTCAAAAATGTTTTCAAAACTATATA--ATATATAT
* *
1207243 TTT-TAAAATGTTTTCAAAAGCCATATATTATATATATGT
1 TTTCAAAAATGTTTTCAAAA--C-TATA-TA-ATATATAT
*
1207282 TTTC-AAAATGCTTTCAAAACTATATAATATATAT
1 TTTCAAAAATGTTTTCAAAACTATATAATATATAT
* * *
1207316 ATTATCGAAAATTGTTTTAATAAACTATATATTATAT-T
1 -TT-TC-AAAAATGTTTTCA-AAACTATATAATATATAT
*
1207354 TTTCAAAAATATTTTCAAAA
1 TTTCAAAAATGTTTTCAAAA
1207374 AAAATTATTC
Statistics
Matches: 260, Mismatches: 30, Indels: 38
0.79 0.09 0.12
Matches are distributed among these distances:
34 67 0.26
35 36 0.14
36 81 0.31
37 19 0.07
38 11 0.04
39 44 0.17
40 2 0.01
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (35 bp):
TTTCAAAAATGTTTTCAAAACTATATAATATATAT
Found at i:1207400 original size:2 final size:2
Alignment explanation
Indices: 1207393--1207426 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1207383 CTATATTAAC
1207393 AT 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
1207427 TAAAGTAACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1210038 original size:50 final size:50
Alignment explanation
Indices: 1209979--1210077 Score: 146
Period size: 50 Copynumber: 2.0 Consensus size: 50
1209969 AATGAAAGTA
** *
1209979 AGGTTTTCTCTTGGAAATTAACTTTCTTGGTG-TGAATTTTATACCTGTTT
1 AGGTTTTCTCTTCCAAAATAACTTTCTTGGTGCT-AATTTTATACCTGTTT
*
1210029 AGGTTTTCTCTTCCAAAATAACTTTCTTGGTGCTAATTTTATGCCTGTT
1 AGGTTTTCTCTTCCAAAATAACTTTCTTGGTGCTAATTTTATACCTGTT
1210078 CTACATTTGG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
50 43 0.98
51 1 0.02
ACGTcount: A:0.20, C:0.15, G:0.16, T:0.48
Consensus pattern (50 bp):
AGGTTTTCTCTTCCAAAATAACTTTCTTGGTGCTAATTTTATACCTGTTT
Done.