Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000558.1 Hibiscus syriacus cultivar Beakdansim tig00001091_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: 180436
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:159983 original size:44 final size:44
Alignment explanation
Indices: 159920--160009 Score: 162
Period size: 44 Copynumber: 2.0 Consensus size: 44
159910 AGTCGAGGGT
*
159920 TATACAGTGGTCCTTCGGGACATATACAGTGGTCTTTCGGGACA
1 TATACAGTGGTCCTTCGGGACATATACAATGGTCTTTCGGGACA
*
159964 TATACAGTGGTCCTTCGGGACATATACAATGGTTTTTCGGGACA
1 TATACAGTGGTCCTTCGGGACATATACAATGGTCTTTCGGGACA
160008 TA
1 TA
160010 ATGGTCCTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (44 bp):
TATACAGTGGTCCTTCGGGACATATACAATGGTCTTTCGGGACA
Found at i:160020 original size:18 final size:19
Alignment explanation
Indices: 159927--160021 Score: 75
Period size: 22 Copynumber: 4.6 Consensus size: 19
159917 GGTTATACAG
159927 TGGTCCTTCGGGACATATACA
1 TGGTCCTTCGGGACA-ATA-A
*
159948 GTGGTCTTTCGGGACATATACA
1 -TGGTCCTTCGGGACA-ATA-A
159970 GTGGTCCTTCGGGACATATACAA
1 -TGGTCCTTCGGGACA-AT--AA
**
159993 TGGTTTTTCGGGAC-ATAA
1 TGGTCCTTCGGGACAATAA
160011 TGGTCCTTCGG
1 TGGTCCTTCGG
160022 CAGATAGTGG
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
18 11 0.17
20 2 0.03
22 50 0.77
23 1 0.02
24 1 0.02
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (19 bp):
TGGTCCTTCGGGACAATAA
Found at i:164477 original size:65 final size:64
Alignment explanation
Indices: 164407--164562 Score: 242
Period size: 65 Copynumber: 2.4 Consensus size: 64
164397 TGCACTAAGG
* *
164407 GTGCATCGATGCATAAATTGCATTCGATGTTTCAA-ACAAGCTTGGAGTGCATCGATGCATGATA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAATAAAAGCTT-GAGTGCATCGATGCATGA-A
164471 T
64 T
* * *
164472 GTGCATCGATGCATAAAATGCATTCGATGTTTTAATAAAATCTTGAGTGCATCGATGCATGACT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAATAAAAGCTTGAGTGCATCGATGCATGAAT
164536 GTGCATCGATGCATAAAATGCATTCGA
1 GTGCATCGATGCATAAAATGCATTCGA
164563 AATGGGGTGT
Statistics
Matches: 85, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
64 28 0.33
65 51 0.60
66 6 0.07
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCAATAAAAGCTTGAGTGCATCGATGCATGAAT
Found at i:167279 original size:45 final size:44
Alignment explanation
Indices: 167200--167295 Score: 133
Period size: 45 Copynumber: 2.2 Consensus size: 44
167190 TGCTAAATGC
* *
167200 ATCGATATACATTCAAGGAGTGCATCGGTGCATCTTCAT-GATGT
1 ATCGATGTACATTCAAGGAGTGCATCGATGCATCTTCATAG-TGT
167244 ATCGATGTACATTCATAGG-GATGCATCGATGCATCTTCATAGTGT
1 ATCGATGTACATTCA-AGGAG-TGCATCGATGCATCTTCATAGTGT
167289 ATCGATG
1 ATCGATG
167296 CATTATGCAC
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
44 15 0.32
45 31 0.66
46 1 0.02
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (44 bp):
ATCGATGTACATTCAAGGAGTGCATCGATGCATCTTCATAGTGT
Found at i:167282 original size:24 final size:23
Alignment explanation
Indices: 167211--167298 Score: 71
Period size: 21 Copynumber: 4.0 Consensus size: 23
167201 TCGATATACA
*
167211 TTCA-AGGAGTGCATCGGTGCATC
1 TTCATAGGA-TGCATCGATGCATC
* *
167234 TTCAT--GATGTATCGATGTA-C
1 TTCATAGGATGCATCGATGCATC
167254 ATTCATAGGGATGCATCGATGCATC
1 -TTCATA-GGATGCATCGATGCATC
*
167279 TTCATA-G-TGTATCGATGCAT
1 TTCATAGGATGCATCGATGCAT
167299 TATGCACAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
20 1 0.02
21 26 0.49
22 3 0.06
23 4 0.08
24 18 0.34
25 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (23 bp):
TTCATAGGATGCATCGATGCATC
Found at i:167294 original size:21 final size:22
Alignment explanation
Indices: 167220--167298 Score: 74
Period size: 21 Copynumber: 3.6 Consensus size: 22
167210 ATTCAAGGAG
*
167220 TGCATCGGTGCATCTTCAT-GA
1 TGCATCGATGCATCTTCATAGA
* *
167241 TGTATCGATGTA-CATTCATAGGGA
1 TGCATCGATGCATC-TTCATA--GA
167265 TGCATCGATGCATCTTCATAG-
1 TGCATCGATGCATCTTCATAGA
*
167286 TGTATCGATGCAT
1 TGCATCGATGCAT
167299 TATGCACAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
20 1 0.02
21 26 0.55
22 1 0.02
24 18 0.38
25 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (22 bp):
TGCATCGATGCATCTTCATAGA
Found at i:172943 original size:21 final size:21
Alignment explanation
Indices: 172919--172967 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
172909 TGGGTGCATT
*
172919 GATGCATAGTCAAGGTGAATC
1 GATGCATAGTCAAAGTGAATC
*
172940 GATGCATAGTCAAAGTGCATC
1 GATGCATAGTCAAAGTGAATC
172961 GATGCAT
1 GATGCAT
172968 CAAGTGTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (21 bp):
GATGCATAGTCAAAGTGAATC
Found at i:173182 original size:64 final size:65
Alignment explanation
Indices: 173027--173182 Score: 192
Period size: 65 Copynumber: 2.4 Consensus size: 65
173017 TGCACTAAGG
* * * * **
173027 GTGCATCGATGCATAAATTGCTTTCGATGTTTCAAACTAGCATGGAGTGCATCGATGCATGGTAT
1 GTGCATCAATGCATAAAATGCATTCGATGTTTAAAAAAAGCATGGAGTGCATCGATGCATGGTAT
* * *
173092 GTGCATCAATGCATAAAATGAATTCGATGTTTTAAAAAAATCCT-GAGTGCATCGATGCAT-G-A
1 GTGCATCAATGCATAAAATGCATTCGATG-TTTAAAAAAAGCATGGAGTGCATCGATGCATGGTA
173154 CT
65 -T
173156 GTGCATCAATGCATAAAATGCATTCGA
1 GTGCATCAATGCATAAAATGCATTCGA
173183 AATGGGGTGT
Statistics
Matches: 79, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
63 1 0.01
64 28 0.35
65 41 0.52
66 9 0.11
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (65 bp):
GTGCATCAATGCATAAAATGCATTCGATGTTTAAAAAAAGCATGGAGTGCATCGATGCATGGTAT
Found at i:173614 original size:2 final size:2
Alignment explanation
Indices: 173607--173688 Score: 155
Period size: 2 Copynumber: 40.5 Consensus size: 2
173597 CATGTAAAAT
173607 TA TA TA TA 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 TA TA TA TA
173649 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
173689 TCAATTGTAC
Statistics
Matches: 79, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 77 0.97
3 2 0.03
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
TA
Found at i:174212 original size:2 final size:2
Alignment explanation
Indices: 174205--174234 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
174195 TACCCTAACA
174205 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
174235 TTCATTATTA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:179441 original size:124 final size:120
Alignment explanation
Indices: 179236--179516 Score: 372
Period size: 124 Copynumber: 2.3 Consensus size: 120
179226 TCTTCTCTTT
* * * * *
179236 CTTCGGATGAGTTCTTCTCATTATGAACTTTTCGCTGG---GGATGATGTTGACCTATTTCCTTC
1 CTTCAGATGAGTTCTTCTCATTATGAAC-TTTCTCTGGAAAGGATGATGCTAACCTATCTCCTTC
* *
179298 TGTGATAGAGTCATTCAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTCTTCTTTCTC
65 TGTGATAGAATCATGCAAAAGGTTGAATAAGCTCTTCTCATTATGAA---CTT-TTTCTC
* * *
179358 CTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGTTGATGCTAATCTATCTGCTTCT
1 CTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGATGATGCTAACCTATCTCCTTCT
* * *
179423 GTGATAGAATTATGCAAAAGGTTGAATAAGCTCTTCTCATTGTGAACTTTTTCTT
66 GTGATAGAATCATGCAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTTTTCTC
179478 CTTCAGATGAGTTCTTCTCATTATGAAC-TTCTCTGGAAA
1 CTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA
179517 AAACTGATCC
Statistics
Matches: 143, Mismatches: 13, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
119 11 0.08
120 33 0.23
121 11 0.08
122 27 0.19
124 61 0.43
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.41
Consensus pattern (120 bp):
CTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGATGATGCTAACCTATCTCCTTCT
GTGATAGAATCATGCAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTTTTCTC
Found at i:179920 original size:110 final size:113
Alignment explanation
Indices: 179436--180097 Score: 779
Period size: 110 Copynumber: 6.0 Consensus size: 113
179426 ATAGAATTAT
* ** *
179436 GCAAAAGGTTGAATAAGCTCTTCTCATTGTGAAC-T-TT-TT-CTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
179497 ATTATGAAC-TTCTCTGGAAAAAACTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTTTCTGG-AAAAGCTGATCCATCAAATGATGGATTTGA
*
179545 GCAAAA-GTTAAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
**** *
179609 ATTATGAACTCAAACTGGAAAAGCTGATCCATCAAGTGATGGA-TTGA
66 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
*
179656 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGATGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC--A-GATGAGTTCTT
* ** * * * * * *
179721 CTCATTATGAACTCTACCTGGCAATGTTAATCCATC-AATGATGAATTTAA
63 CTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
*
179771 ACAAAAGGTTGAAC-AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
179835 ATTATGAACTTTTTCTGGAAAAGCTGAT-CTTCAAATGA-GGATTTGA
66 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
* * * **
179881 GCGAAAGG-TGAATAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAATGA-TGAGTTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG-ATGAGT-TCTTC
* * * * *
179944 TCATTATGAACTTTCTTC----AATGTTAATCCATCAAATGATGAATTTAA
64 TCATTATGAACTTT-TTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
* * *
179991 ACAAAAGGTTGAACAAATT-TTCTCATTTTGAACTTCTTCTTCCTTCTTCAGATGAATT-TTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
180054 ATTATGAACTTTTTC-GGAAAAGCTGATCCATCAAATGATGGATT
66 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATT
180098 GAATCTTTGC
Statistics
Matches: 476, Mismatches: 55, Indels: 43
0.83 0.10 0.07
Matches are distributed among these distances:
107 3 0.01
108 45 0.09
109 24 0.05
110 119 0.25
111 82 0.17
112 100 0.21
113 4 0.01
114 42 0.09
115 57 0.12
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
Done.