Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000587.1 Hibiscus syriacus cultivar Beakdansim tig00001143_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: 57666
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.35
Found at i:12943 original size:6 final size:6
Alignment explanation
Indices: 12932--12961 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
12922 AGATGGAATA
12932 CATTGG CATTGG CATTGG CATTGG CATTGG
1 CATTGG CATTGG CATTGG CATTGG CATTGG
12962 GAGTTGGGGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.33, T:0.33
Consensus pattern (6 bp):
CATTGG
Found at i:15339 original size:25 final size:26
Alignment explanation
Indices: 15293--15345 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
15283 TTTTTAACTT
*
15293 AAAATATATTAAATTATAAGATATATA
1 AAAATATATTAAA-TATAAGATAAATA
*
15320 AAAATATATTAAA-ATTAGATAAATA
1 AAAATATATTAAATATAAGATAAATA
15345 A
1 A
15346 TCATACTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 11 0.46
27 13 0.54
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (26 bp):
AAAATATATTAAATATAAGATAAATA
Found at i:15377 original size:20 final size:19
Alignment explanation
Indices: 15351--15399 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
15341 AATAATCATA
*
15351 CTATTTTTTTGTAATTTTT
1 CTATTTTTTTATAATTTTT
*
15370 CGTATTTTTTTATATTTTTT
1 C-TATTTTTTTATAATTTTT
15390 CTGATTTTTT
1 CT-ATTTTTT
15400 ATATCCGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 2 0.08
20 24 0.92
ACGTcount: A:0.14, C:0.06, G:0.06, T:0.73
Consensus pattern (19 bp):
CTATTTTTTTATAATTTTT
Found at i:22443 original size:16 final size:16
Alignment explanation
Indices: 22422--22456 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
22412 TTTTATATAA
22422 TTTTCTGTGTTCTTGT
1 TTTTCTGTGTTCTTGT
*
22438 TTTTCTTTGTTCTTGT
1 TTTTCTGTGTTCTTGT
22454 TTT
1 TTT
22457 GCAATAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.00, C:0.11, G:0.14, T:0.74
Consensus pattern (16 bp):
TTTTCTGTGTTCTTGT
Found at i:24864 original size:19 final size:19
Alignment explanation
Indices: 24821--24868 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
24811 ACCTGACATC
24821 TGCAGCA-GGGCAGCATGG
1 TGCAGCATGGGCAGCATGG
* *
24839 TCCCAGCATGGGCGGCATGG
1 T-GCAGCATGGGCAGCATGG
24859 TGCAGCATGG
1 TGCAGCATGG
24869 CATTTGCAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 1 0.04
19 13 0.52
20 11 0.44
ACGTcount: A:0.19, C:0.25, G:0.42, T:0.15
Consensus pattern (19 bp):
TGCAGCATGGGCAGCATGG
Found at i:36103 original size:3 final size:3
Alignment explanation
Indices: 36095--36309 Score: 182
Period size: 3 Copynumber: 73.7 Consensus size: 3
36085 ATCACCATTT
* * *
36095 TTA TTA TTA TTA TT- CTA CTA CTA TTA TTA TTA TTA TTA TTA TCT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* * * * * *
36139 TT- TTCA TCA TCA TAA TTA TCA TTA TTA TTA TT- TTA TT- TTG CTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
36182 TTA TTA TT- TTG TTA TTA TTA TT- CTA TT- TTA TTA TTA TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
36226 CTA TTA TTA TTA TTA TTA GTTA TT- TTA TTA TTA TTA TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
36270 TTA CTA TTA TTA TTTA TTTA TTA TTA TTA TTG TTA TTA TT
1 TTA TTA TTA TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TT
36310 GTTGTTGTTG
Statistics
Matches: 179, Mismatches: 19, Indels: 28
0.79 0.08 0.12
Matches are distributed among these distances:
2 18 0.10
3 149 0.83
4 12 0.07
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:36190 original size:14 final size:14
Alignment explanation
Indices: 36166--36324 Score: 116
Period size: 14 Copynumber: 11.6 Consensus size: 14
36156 ATCATTATTA
36166 TTATT-TTATTTTG
1 TTATTATTATTTTG
*
36179 CTATTATTATTTTG
1 TTATTATTATTTTG
* *
36193 TTATTATTATTCTA
1 TTATTATTATTTTG
*
36207 TT-TTATTA--TTA
1 TTATTATTATTTTG
* * *
36218 TTATTATTCTATTA
1 TTATTATTATTTTG
*
36232 TTATTATTA-TTAG
1 TTATTATTATTTTG
*
36245 TTATT-TTATTATTA
1 TTATTATTATT-TTG
*
36259 TTATTATTATTTTA
1 TTATTATTATTTTG
*
36273 CTATTATTATTTAT-
1 TTATTATTATTT-TG
36287 TTATTATTATTATTG
1 TTATTATTATT-TTG
*
36302 TTATTATTGTTGTTG
1 TTATTATTATT-TTG
*
36317 TTGTTATT
1 TTATTATT
36325 TCAAAAAAAA
Statistics
Matches: 119, Mismatches: 17, Indels: 18
0.77 0.11 0.12
Matches are distributed among these distances:
11 4 0.03
12 8 0.07
13 17 0.14
14 63 0.53
15 27 0.23
ACGTcount: A:0.25, C:0.03, G:0.05, T:0.68
Consensus pattern (14 bp):
TTATTATTATTTTG
Found at i:36215 original size:58 final size:60
Alignment explanation
Indices: 36153--36324 Score: 195
Period size: 64 Copynumber: 2.8 Consensus size: 60
36143 CATCATCATA
* *
36153 ATTATCATTATTATTATTTTATT-TTGCTATTATTATTTTGTTATTATTATT-CTATTTT
1 ATTATTATTATTATTATTTTATTATTGTTATTATTATTTTGTTATTATTATTACTATTTT
* * * * *
36211 ATTATTATTATTATTCTATTATTATTATTATTAGTTATTTTATTATTATTATTATTATTTT
1 ATTATTATTATTATTATTTTATTATTGTTATTA-TTATTTTGTTATTATTATTACTATTTT
* * *
36272 ACTATTATTATTTATTTATTATTATTATTGTTATTATTGTTGTTGTTGTTATT
1 ATTATTATTA-TTA-TTATT-TTATTATTGTTATTATTATT-TTGTTATTATT
36325 TCAAAAAAAA
Statistics
Matches: 93, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
58 20 0.22
59 7 0.08
60 18 0.19
61 15 0.16
62 3 0.03
63 7 0.08
64 23 0.25
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.67
Consensus pattern (60 bp):
ATTATTATTATTATTATTTTATTATTGTTATTATTATTTTGTTATTATTATTACTATTTT
Found at i:37405 original size:194 final size:194
Alignment explanation
Indices: 37076--37468 Score: 786
Period size: 194 Copynumber: 2.0 Consensus size: 194
37066 AATGAAGATG
37076 TAAATCTTGTAAGTCTTGGTGCTCTTCCTGATCTTCTTCTTCCCTAAACGAAATCAAGGATTTGA
1 TAAATCTTGTAAGTCTTGGTGCTCTTCCTGATCTTCTTCTTCCCTAAACGAAATCAAGGATTTGA
37141 AAGAAGGCGAGTTGAATCAGGAGATAAGGAATTGAGGGGGTTCGGCGGGGGCAGCTTTTGGTGGC
66 AAGAAGGCGAGTTGAATCAGGAGATAAGGAATTGAGGGGGTTCGGCGGGGGCAGCTTTTGGTGGC
37206 GTTGATGGAAGCAGTAGCGGCGGAGGCATCTACGGGGAGGAAATGGCGTCGGAGATTCGAAGGC
131 GTTGATGGAAGCAGTAGCGGCGGAGGCATCTACGGGGAGGAAATGGCGTCGGAGATTCGAAGGC
37270 TAAATCTTGTAAGTCTTGGTGCTCTTCCTGATCTTCTTCTTCCCTAAACGAAATCAAGGATTTGA
1 TAAATCTTGTAAGTCTTGGTGCTCTTCCTGATCTTCTTCTTCCCTAAACGAAATCAAGGATTTGA
37335 AAGAAGGCGAGTTGAATCAGGAGATAAGGAATTGAGGGGGTTCGGCGGGGGCAGCTTTTGGTGGC
66 AAGAAGGCGAGTTGAATCAGGAGATAAGGAATTGAGGGGGTTCGGCGGGGGCAGCTTTTGGTGGC
37400 GTTGATGGAAGCAGTAGCGGCGGAGGCATCTACGGGGAGGAAATGGCGTCGGAGATTCGAAGGC
131 GTTGATGGAAGCAGTAGCGGCGGAGGCATCTACGGGGAGGAAATGGCGTCGGAGATTCGAAGGC
37464 TAAAT
1 TAAAT
37469 TGGAAGCGGC
Statistics
Matches: 199, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
194 199 1.00
ACGTcount: A:0.25, C:0.16, G:0.34, T:0.25
Consensus pattern (194 bp):
TAAATCTTGTAAGTCTTGGTGCTCTTCCTGATCTTCTTCTTCCCTAAACGAAATCAAGGATTTGA
AAGAAGGCGAGTTGAATCAGGAGATAAGGAATTGAGGGGGTTCGGCGGGGGCAGCTTTTGGTGGC
GTTGATGGAAGCAGTAGCGGCGGAGGCATCTACGGGGAGGAAATGGCGTCGGAGATTCGAAGGC
Found at i:40152 original size:309 final size:309
Alignment explanation
Indices: 39593--40211 Score: 1229
Period size: 309 Copynumber: 2.0 Consensus size: 309
39583 GTATTGCTTT
39593 TATTTTTTGTATTTCAGTACAAAATGTGTCTTGTTTTCCCTTTTTTATTTTCTAAATTAAATAAA
1 TATTTTTTGTATTTCAGTACAAAATGTGTCTTGTTTTCCCTTTTTTATTTTCTAAATTAAATAAA
39658 CTGATACTATTATTTTTCATGTTTGCTCGGTTGTCAAAGTGAAGCATGCAGGGCTTTGGGGATCA
66 CTGATACTATTATTTTTCATGTTTGCTCGGTTGTCAAAGTGAAGCATGCAGGGCTTTGGGGATCA
39723 TATGGTGTTCAAATCAATCACTTCCATAATGAATTCTGGTTTGCTAAAGCACCTTGACTTTGATG
131 TATGGTGTTCAAATCAATCACTTCCATAATGAATTCTGGTTTGCTAAAGCACCTTGACTTTGATG
*
39788 ATTTGCTTTTGCTTCTGGCTGATATGGATCCTTCTACATGTCATGAAAAATTATTAAGTTGCTGG
196 ATTTGCTTTTGATTCTGGCTGATATGGATCCTTCTACATGTCATGAAAAATTATTAAGTTGCTGG
39853 CAAGATCAGCAAAATAATTCTTGCTTAAAATCATCATTGTTTAGAGCAA
261 CAAGATCAGCAAAATAATTCTTGCTTAAAATCATCATTGTTTAGAGCAA
39902 TATTTTTTGTATTTCAGTACAAAATGTGTCTTGTTTTCCCTTTTTTATTTTCTAAATTAAATAAA
1 TATTTTTTGTATTTCAGTACAAAATGTGTCTTGTTTTCCCTTTTTTATTTTCTAAATTAAATAAA
39967 CTGATACTATTATTTTTCATGTTTGCTCGGTTGTCAAAGTGAAGCATGCAGGGCTTTGGGGATCA
66 CTGATACTATTATTTTTCATGTTTGCTCGGTTGTCAAAGTGAAGCATGCAGGGCTTTGGGGATCA
40032 TATGGTGTTCAAATCAATCACTTCCATAATGAATTCTGGTTTGCTAAAGCACCTTGACTTTGATG
131 TATGGTGTTCAAATCAATCACTTCCATAATGAATTCTGGTTTGCTAAAGCACCTTGACTTTGATG
40097 ATTTGCTTTTGATTCTGGCTGATATGGATCCTTCTACATGTCATGAAAAATTATTAAGTTGCTGG
196 ATTTGCTTTTGATTCTGGCTGATATGGATCCTTCTACATGTCATGAAAAATTATTAAGTTGCTGG
40162 CAAGATCAGCAAAATAATTCTTGCTTAAAATCATCATTGTTTAGAGCAA
261 CAAGATCAGCAAAATAATTCTTGCTTAAAATCATCATTGTTTAGAGCAA
40211 T
1 T
40212 CTTCTATGCT
Statistics
Matches: 309, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
309 309 1.00
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.41
Consensus pattern (309 bp):
TATTTTTTGTATTTCAGTACAAAATGTGTCTTGTTTTCCCTTTTTTATTTTCTAAATTAAATAAA
CTGATACTATTATTTTTCATGTTTGCTCGGTTGTCAAAGTGAAGCATGCAGGGCTTTGGGGATCA
TATGGTGTTCAAATCAATCACTTCCATAATGAATTCTGGTTTGCTAAAGCACCTTGACTTTGATG
ATTTGCTTTTGATTCTGGCTGATATGGATCCTTCTACATGTCATGAAAAATTATTAAGTTGCTGG
CAAGATCAGCAAAATAATTCTTGCTTAAAATCATCATTGTTTAGAGCAA
Found at i:41049 original size:122 final size:122
Alignment explanation
Indices: 40832--41078 Score: 449
Period size: 122 Copynumber: 2.0 Consensus size: 122
40822 CATATGAGAT
40832 GATAAAGAAAGTTTAACAAAAGGTTTCTTAGTATACTAAGATTTTGGGTTCCTACCAGTTTCTAA
1 GATAAAGAAAGTTTAACAAAAGGTTTCTTAGTATACTAAGATTTTGGGTTCCTACCAGTTTCTAA
40897 AGGAAGAACTGGTGTTCCTGATCGCCTCTCAAGAAAAAACATCCTTGTCATTAGCAG
66 AGGAAGAACTGGTGTTCCTGATCGCCTCTCAAGAAAAAACATCCTTGTCATTAGCAG
* * *
40954 GATAAAGAAAGTTTAACAAAATGTTTCTTAGTATATTAGGATTTTGGGTTCCTACCAGTTTCTAA
1 GATAAAGAAAGTTTAACAAAAGGTTTCTTAGTATACTAAGATTTTGGGTTCCTACCAGTTTCTAA
* *
41019 AGGAAGAACTTGTGTTCCTGATCGCCTCTCAAGAAAAAGCATCCTTGTCATTAGCAG
66 AGGAAGAACTGGTGTTCCTGATCGCCTCTCAAGAAAAAACATCCTTGTCATTAGCAG
41076 GAT
1 GAT
41079 TTGATGGGAT
Statistics
Matches: 120, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
122 120 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32
Consensus pattern (122 bp):
GATAAAGAAAGTTTAACAAAAGGTTTCTTAGTATACTAAGATTTTGGGTTCCTACCAGTTTCTAA
AGGAAGAACTGGTGTTCCTGATCGCCTCTCAAGAAAAAACATCCTTGTCATTAGCAG
Found at i:44063 original size:306 final size:298
Alignment explanation
Indices: 43507--44070 Score: 862
Period size: 306 Copynumber: 1.9 Consensus size: 298
43497 TGGGCCCTGA
* *
43507 CTGATGAACCACTCTGCAAATTCTCCCAAAAACCATGCGAGTAAGAACGAATTACTCTTTTCCTT
1 CTGATGAACCACTCTGCAAACTCTCCCAAAAACCATGCGAGTAAGAACGAATTACTCTTTTCCTG
* *
43572 TACCATTTGTCACTGGCTTTCTTAATGTCTTCAGAGGGAGCAATGCCAAGATTCCTCAATATTTT
66 TACCATTTGTCACTGGCTTTCTT-ATGTCTTCAGAGGGAGAAATGCCAAGATTCATCAATATTTT
* *
43637 GAGGATCTTTTTTGTAATATTGGCTGCTGCGAAGAATACGGCCTAAGAACTAGTAACAAATTCCT
130 GAGGATCTTTTTTGTAATATTGGCTGCTGCGAAAAATACGGCCTAAGAACTAGCAACAAATTCCT
* * * *
43702 CCGTGAGGTTTGGTCACAATGTTTCTTTACTACTAGACCATTTTTTTCGTCTTTCAAGTTTTCCT
195 CCCTGAGGTTTGGTCACAATGTTTCTTTACTACTAGACCATTTTATCCATCTTTCAAGTTTTCCT
43767 CTTTGAAGAGCATGCTTTATATTTTCAGGGACTTTTTCG
260 CTTTGAAGAGCATGCTTTATATTTTCAGGGACTTTTTCG
* **
43806 CTGATGAACCACTCTGCAAACTCTCCCATAAACCATGCGAGTAAGAATTAATTACTCTTTTCCTG
1 CTGATGAACCACTCTGCAAACTCTCCCAAAAACCATGCGAGTAAGAACGAATTACTCTTTTCCTG
* *
43871 TACCATTTGTCACATATGTCACTGGCTTTCTT-TGTCTTCAGGGGGAGAAATGCCAATATTCATC
66 TACCA----T----T-TGTCACTGGCTTTCTTATGTCTTCAGAGGGAGAAATGCCAAGATTCATC
*
43935 AGTATTTTGAGGATCTTTTTTTGTAATATTGGCTGCTGC-AAAAATACGGCCTAAGAACTAGCAA
122 AATATTTTGAGGATC-TTTTTTGTAATATTGGCTGCTGCGAAAAATACGGCCTAAGAACTAGCAA
*
43999 CAAATTCCTCCCTGAGGTTTGGTCACAATGTTTCTTTACTACTTGACCATTTTATCCATCTTTCA
186 CAAATTCCTCCCTGAGGTTTGGTCACAATGTTTCTTTACTACTAGACCATTTTATCCATCTTTCA
44064 AGTTTTC
251 AGTTTTC
44071 ACCTTTTAAG
Statistics
Matches: 238, Mismatches: 17, Indels: 13
0.89 0.06 0.05
Matches are distributed among these distances:
299 65 0.27
303 1 0.00
306 132 0.55
307 24 0.10
308 16 0.07
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (298 bp):
CTGATGAACCACTCTGCAAACTCTCCCAAAAACCATGCGAGTAAGAACGAATTACTCTTTTCCTG
TACCATTTGTCACTGGCTTTCTTATGTCTTCAGAGGGAGAAATGCCAAGATTCATCAATATTTTG
AGGATCTTTTTTGTAATATTGGCTGCTGCGAAAAATACGGCCTAAGAACTAGCAACAAATTCCTC
CCTGAGGTTTGGTCACAATGTTTCTTTACTACTAGACCATTTTATCCATCTTTCAAGTTTTCCTC
TTTGAAGAGCATGCTTTATATTTTCAGGGACTTTTTCG
Found at i:50090 original size:13 final size:13
Alignment explanation
Indices: 50072--50097 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
50062 TTGGTAGTTA
50072 CCGAGGAAAAGGG
1 CCGAGGAAAAGGG
50085 CCGAGGAAAAGGG
1 CCGAGGAAAAGGG
50098 GAAACCCGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.46, T:0.00
Consensus pattern (13 bp):
CCGAGGAAAAGGG
Found at i:55280 original size:17 final size:17
Alignment explanation
Indices: 55258--55290 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
55248 GATATCTTCT
55258 TTCTTTCATTATAAATC
1 TTCTTTCATTATAAATC
55275 TTCTTTCATTATAAAT
1 TTCTTTCATTATAAAT
55291 GACTTCAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.15, G:0.00, T:0.55
Consensus pattern (17 bp):
TTCTTTCATTATAAATC
Done.