Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000714.1 Hibiscus syriacus cultivar Beakdansim tig00001386_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: 53537
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:130 original size:23 final size:23
Alignment explanation
Indices: 104--152 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
94 TGGTGGTTAA
104 TTTAATGGTTGT-TTGAACTTTAT
1 TTTAATGG-TGTATTGAACTTTAT
* *
127 TTTAATGGTGTATTTAAGTTTAT
1 TTTAATGGTGTATTGAACTTTAT
150 TTT
1 TTT
153 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 3 0.13
23 20 0.87
ACGTcount: A:0.22, C:0.02, G:0.16, T:0.59
Consensus pattern (23 bp):
TTTAATGGTGTATTGAACTTTAT
Found at i:7018 original size:25 final size:24
Alignment explanation
Indices: 6957--7030 Score: 75
Period size: 20 Copynumber: 3.2 Consensus size: 24
6947 CCTCTTAAAT
*
6957 TTTTAACTTTTTCTTTTCTCTTTC
1 TTTTAACTTTTACTTTTCTCTTTC
* *
6981 -TTT-A--TTAATTTTTCTCTTTC
1 TTTTAACTTTTACTTTTCTCTTTC
*
7001 ATTTTAACTTTTACTTTTCTATTTC
1 -TTTTAACTTTTACTTTTCTCTTTC
7026 TTTTA
1 TTTTA
7031 CTCATCTTCT
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
20 13 0.33
22 4 0.10
23 4 0.10
24 5 0.13
25 13 0.33
ACGTcount: A:0.15, C:0.16, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTTAACTTTTACTTTTCTCTTTC
Found at i:10321 original size:24 final size:24
Alignment explanation
Indices: 10294--10343 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
10284 TGGTGGTTGA
10294 TTTAATGGTTGT-TTGAACTTTATT
1 TTTAATGG-TGTATTGAACTTTATT
* *
10318 TTTAATGGTGTATTTAAGTTTATT
1 TTTAATGGTGTATTGAACTTTATT
10342 TT
1 TT
10344 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.22, C:0.02, G:0.16, T:0.60
Consensus pattern (24 bp):
TTTAATGGTGTATTGAACTTTATT
Found at i:12348 original size:2 final size:2
Alignment explanation
Indices: 12341--12370 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12331 AAACTGCGTC
12341 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
12371 TTGCATGGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:12370 original size:151 final size:153
Alignment explanation
Indices: 12205--12503 Score: 478
Period size: 151 Copynumber: 2.0 Consensus size: 153
12195 CTACGTCGTC
*
12205 AGAGAGAGAGAGAGATTGCATGGATAAACCTCAAATGAGATGATATTATCAAAATATGTGTAGTG
1 AGAGAGAGAGAGAGATTGCATGGATAAACCTCAAATGAGATGATATTATCAAAATATGTGTAGTC
* * *
12270 GACGAAATGATAAGATTGTCAGCTCCATCCAAAATATGCTTTCAAACAGTAATCCTTTCTGAAA-
66 GACGAAATGATAAGATTGTCAACTCCATCCAAAATAAGCTTTCAAACAATAATCCTTTCTGAAAC
12334 C-TG-CGTCGAGAGAGAGAGAGAG
131 CATGTCGT-GAGAGAGAGAGAGAG
*
12356 AGAGAGAGAGAGAGATTGCATGGATAAACCTCAAATGAGATGATATTATTAAAATATGTGTAGTC
1 AGAGAGAGAGAGAGATTGCATGGATAAACCTCAAATGAGATGATATTATCAAAATATGTGTAGTC
* * * * *
12421 GATGAAATGATAGGGTTGTCAACTCCATCCAGAATAAGCTTTCAAACAATCATCCTTTCTGAAAC
66 GACGAAATGATAAGATTGTCAACTCCATCCAAAATAAGCTTTCAAACAATAATCCTTTCTGAAAC
12486 CATGTCGTGAGAGAGAGA
131 CATGTCGTGAGAGAGAGA
12504 TTGCATGGAT
Statistics
Matches: 135, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
151 119 0.88
152 1 0.01
153 12 0.09
154 3 0.02
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.25
Consensus pattern (153 bp):
AGAGAGAGAGAGAGATTGCATGGATAAACCTCAAATGAGATGATATTATCAAAATATGTGTAGTC
GACGAAATGATAAGATTGTCAACTCCATCCAAAATAAGCTTTCAAACAATAATCCTTTCTGAAAC
CATGTCGTGAGAGAGAGAGAGAG
Found at i:12504 original size:133 final size:133
Alignment explanation
Indices: 12361--12620 Score: 448
Period size: 133 Copynumber: 2.0 Consensus size: 133
12351 GAGAGAGAGA
* *
12361 GAGAGAGAGATTGCATGGATAAACCTCAAATGAGATGATATTATTAAAATATGTGTAGTCGATGA
1 GAGAGAGAGATTGCATGGATAAACCTCAAATGAGATGATATTATCAAAATATGTGTAGTCGACGA
* * *
12426 AATGATAGGGTTGTCAACTCCATCCAGAATAAGCTTTCAAACAATCATCCTTTCTGAAACCATGT
66 AATGATAAGGTTGTCAACTCCATCCAAAATAAGCTTTCAAACAACCATCCTTTCTGAAACCATGT
12491 CGT
131 CGT
* *
12494 GAGAGAGAGATTGCATGGATAAACCTCAAATGAGATGATATTGTCAAAATATGTGTAGTGGACGA
1 GAGAGAGAGATTGCATGGATAAACCTCAAATGAGATGATATTATCAAAATATGTGTAGTCGACGA
*
12559 AATGATAAGGTTGTCAGCTCCATCCAAAATAAGCTTTCAAACAACCATCCTTTCTGAAACCA
66 AATGATAAGGTTGTCAACTCCATCCAAAATAAGCTTTCAAACAACCATCCTTTCTGAAACCA
12621 CGTCATGTAC
Statistics
Matches: 119, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
133 119 1.00
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.27
Consensus pattern (133 bp):
GAGAGAGAGATTGCATGGATAAACCTCAAATGAGATGATATTATCAAAATATGTGTAGTCGACGA
AATGATAAGGTTGTCAACTCCATCCAAAATAAGCTTTCAAACAACCATCCTTTCTGAAACCATGT
CGT
Found at i:12597 original size:284 final size:287
Alignment explanation
Indices: 12098--12618 Score: 805
Period size: 284 Copynumber: 1.8 Consensus size: 287
12088 TGCATAGATA
* * * * *
12098 AAATGAGATGATATTGTCAACATATGTGTAGTGGGCGAAATGATAAGGTTGTCAATTCCATCCAA
1 AAATGAGATGATATTATCAAAATATGTGTAGTCGACGAAATGATAAGGTTGTCAACTCCATCCAA
** * *
12163 AATAAGCTTTCAAACCGCCATTCTTTCTGAAACTACGTCGTCAGAGAGAGAGAGAGATTGCATGG
66 AATAAGCTTTCAAACAACCATCCTTTCTGAAAC-ACATCGTC--AGAGAGAGAGAGATTGCATGG
12228 ATAAACCTCAAATGAGATGATATTATCAAAATATGTGTAGTGGACGAAATGATAAGATTGTCAGC
128 ATAAACCTCAAATGAGATGATATTATCAAAATATGTGTAGTGGACGAAATGATAAGATTGTCAGC
* **
12293 TCCATCCAAAATATGCTTTCAAACAGTAATCCTTTCTGAAACTGCGTCGAGAGAGAGAGAGAGAG
193 TCCATCCAAAATAAGCTTTCAAACAACAATCCTTTCTGAAACTGCGTCGAGAGAGAGAGAGAGAG
12358 AGAGAGAGAGAGATTGCATGGATAAACCTC
258 AGAGAGAGAGAGATTGCATGGATAAACCTC
* * * *
12388 AAATGAGATGATATTATTAAAATATGTGTAGTCGATGAAATGATAGGGTTGTCAACTCCATCCAG
1 AAATGAGATGATATTATCAAAATATGTGTAGTCGACGAAATGATAAGGTTGTCAACTCCATCCAA
* *
12453 AATAAGCTTTCAAACAATCATCCTTTCTGAAAC-CAT-GTC-GTGAGAGAGAGATTGCATGGATA
66 AATAAGCTTTCAAACAACCATCCTTTCTGAAACACATCGTCAGAGAGAGAGAGATTGCATGGATA
* *
12515 AACCTCAAATGAGATGATATTGTCAAAATATGTGTAGTGGACGAAATGATAAGGTTGTCAGCTCC
131 AACCTCAAATGAGATGATATTATCAAAATATGTGTAGTGGACGAAATGATAAGATTGTCAGCTCC
*
12580 ATCCAAAATAAGCTTTCAAACAACCATCCTTTCTGAAAC
196 ATCCAAAATAAGCTTTCAAACAACAATCCTTTCTGAAAC
12619 CACGTCATGT
Statistics
Matches: 210, Mismatches: 21, Indels: 6
0.89 0.09 0.03
Matches are distributed among these distances:
284 120 0.57
287 3 0.01
288 2 0.01
290 85 0.40
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (287 bp):
AAATGAGATGATATTATCAAAATATGTGTAGTCGACGAAATGATAAGGTTGTCAACTCCATCCAA
AATAAGCTTTCAAACAACCATCCTTTCTGAAACACATCGTCAGAGAGAGAGAGATTGCATGGATA
AACCTCAAATGAGATGATATTATCAAAATATGTGTAGTGGACGAAATGATAAGATTGTCAGCTCC
ATCCAAAATAAGCTTTCAAACAACAATCCTTTCTGAAACTGCGTCGAGAGAGAGAGAGAGAGAGA
GAGAGAGAGATTGCATGGATAAACCTC
Found at i:24888 original size:54 final size:54
Alignment explanation
Indices: 24796--25502 Score: 661
Period size: 54 Copynumber: 13.3 Consensus size: 54
24786 ATGTCCACCG
* * * ** *
24796 CCACTGGAACTTGGACCTGAGTTGGTCACAGCATCAACGAATGCATTACCATGT
1 CCACCGGAACTTGGACCCGAGTTGGTGACAGCATCAACGAATGCATGGCCTTGT
* * * * *
24850 CCTCCGGAGCTTGGACCCGAGTTGGTGACGGCAACAACGAGTGCATGGCCTTGT
1 CCACCGGAACTTGGACCCGAGTTGGTGACAGCATCAACGAATGCATGGCCTTGT
*** * * * * *
24904 CCTTTGGAACTAGGAACCGAGTCGGTGACAGCATCAACGAATGTATGGCCTTTT
1 CCACCGGAACTTGGACCCGAGTTGGTGACAGCATCAACGAATGCATGGCCTTGT
* * * *
24958 CCACCGAAACTTGGACCTGAGTTGGTGACAGCATCAATGAATGCATGGCCTTTT
1 CCACCGGAACTTGGACCCGAGTTGGTGACAGCATCAACGAATGCATGGCCTTGT
* * ** ** *
25012 CCACCAGAGCTTGGACTTGAGTTGGTGACCA-CATCAACGAATGCATTACCATGT
1 CCACCGGAACTTGGACCCGAGTTGGTGA-CAGCATCAACGAATGCATGGCCTTGT
* * * * **
25066 CCTCTGGAACTTGGACCTGAGTTTGTGACAGCATCAACGAATGCATTACCTTGT
1 CCACCGGAACTTGGACCCGAGTTGGTGACAGCATCAACGAATGCATGGCCTTGT
* * * * * * *
25120 CCTCCGGAGCTTGGACCCGAGTTGCTGACTGCAACAACTAGTGCATGGCCTTGT
1 CCACCGGAACTTGGACCCGAGTTGGTGACAGCATCAACGAATGCATGGCCTTGT
* * * * *
25174 CCTCTGGAACTAGGAACCGAGTTGGTGACAGCATCAACGAATGCATGGCCTTTT
1 CCACCGGAACTTGGACCCGAGTTGGTGACAGCATCAACGAATGCATGGCCTTGT
* *
25228 CCACCGGAACTTGGACCTGAGTTGGTGACAGCATCAAAGAATGCATGGCCTT-T
1 CCACCGGAACTTGGACCCGAGTTGGTGACAGCATCAACGAATGCATGGCCTTGT
** *
25281 ACCACCGGAACTTGGACCCGAGACGGTGACAGCATCAACGAATGCATGGCCTTTT
1 -CCACCGGAACTTGGACCCGAGTTGGTGACAGCATCAACGAATGCATGGCCTTGT
*
25336 CCACCGGAGCTTGGACCCGAGTTGGTGACCA-CATCAACG-A---AT--CC---T
1 CCACCGGAACTTGGACCCGAGTTGGTGA-CAGCATCAACGAATGCATGGCCTTGT
* * * * * ** *
25381 ---CTGGAACTTGGACCTGAGTTGTTGACAGCATCAAAGAAAGCATTCCCCTGT
1 CCACCGGAACTTGGACCCGAGTTGGTGACAGCATCAACGAATGCATGGCCTTGT
** * * * * *
25432 CCTTCGGAGCATGGACCAGAGTTGGCGACAGCATCAACGAATGCATGGCCTTTT
1 CCACCGGAACTTGGACCCGAGTTGGTGACAGCATCAACGAATGCATGGCCTTGT
25486 CCACCGGAACTTGGACC
1 CCACCGGAACTTGGACC
25503 ACCGGTCTTG
Statistics
Matches: 531, Mismatches: 104, Indels: 36
0.79 0.15 0.05
Matches are distributed among these distances:
41 2 0.00
42 28 0.05
43 1 0.00
45 1 0.00
46 2 0.00
48 4 0.01
50 2 0.00
51 1 0.00
53 4 0.01
54 481 0.91
55 5 0.01
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.23
Consensus pattern (54 bp):
CCACCGGAACTTGGACCCGAGTTGGTGACAGCATCAACGAATGCATGGCCTTGT
Found at i:29368 original size:2 final size:2
Alignment explanation
Indices: 29361--29394 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
29351 TTGATTCATT
29361 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29395 GAGAGAGAGA
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):
TA
Found at i:29399 original size:2 final size:2
Alignment explanation
Indices: 29394--29427 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
29384 ATATATATAT
29394 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
29428 TAGGTTAGTA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:30076 original size:6 final size:6
Alignment explanation
Indices: 30065--30098 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
30055 GTTGTCGCTC
30065 GGCCCT GGCCCT GGCCCT GGCCCT GGCCCT GGCC
1 GGCCCT GGCCCT GGCCCT GGCCCT GGCCCT GGCC
30099 TGGTTTGAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.35, T:0.15
Consensus pattern (6 bp):
GGCCCT
Found at i:30309 original size:26 final size:25
Alignment explanation
Indices: 30265--30316 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
30255 ATTTATAATT
* * *
30265 ATAAATATAAAAGAATTAAAGATAA
1 ATAAAAATAAAAAAATTAAAAATAA
30290 ATAAAAATAAAAAATATTAAAAATAA
1 ATAAAAATAAAAAA-ATTAAAAATAA
30316 A
1 A
30317 CTATAAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (25 bp):
ATAAAAATAAAAAAATTAAAAATAA
Found at i:30324 original size:27 final size:27
Alignment explanation
Indices: 30259--30324 Score: 73
Period size: 26 Copynumber: 2.4 Consensus size: 27
30249 ACTAAGATTT
* *
30259 ATAATTATAAATATAAAAGAATTAAAG
1 ATAAATATAAATATAAAAGAATTAAAA
*
30286 ATAAATA-AAA-ATAAAAAATATTAAAA
1 ATAAATATAAATATAAAAGA-ATTAAAA
30312 ATAAACTATAAAT
1 ATAAA-TATAAAT
30325 TTAATCAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
25 7 0.22
26 14 0.44
27 8 0.25
28 3 0.09
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (27 bp):
ATAAATATAAATATAAAAGAATTAAAA
Found at i:40088 original size:21 final size:21
Alignment explanation
Indices: 40059--40103 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
40049 CGGATAAAAA
* * *
40059 TTATTTAAAATATTATTATTT
1 TTATCTAAAACATTAATATTT
*
40080 TTATCTAAAACATTAATGTTT
1 TTATCTAAAACATTAATATTT
40101 TTA
1 TTA
40104 ATATTTTCGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (21 bp):
TTATCTAAAACATTAATATTT
Found at i:41851 original size:30 final size:30
Alignment explanation
Indices: 41815--41882 Score: 136
Period size: 30 Copynumber: 2.3 Consensus size: 30
41805 TTAGTCTTTA
41815 AGCTTCAACTATAAATACCCTAGCTCATTT
1 AGCTTCAACTATAAATACCCTAGCTCATTT
41845 AGCTTCAACTATAAATACCCTAGCTCATTT
1 AGCTTCAACTATAAATACCCTAGCTCATTT
41875 AGCTTCAA
1 AGCTTCAA
41883 AATCATCCCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.34, C:0.26, G:0.07, T:0.32
Consensus pattern (30 bp):
AGCTTCAACTATAAATACCCTAGCTCATTT
Done.