Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008596.1 Hibiscus syriacus cultivar Beakdansim tig00111545_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: 280553
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:236225 original size:63 final size:64
Alignment explanation
Indices: 236158--236278 Score: 165
Period size: 64 Copynumber: 1.9 Consensus size: 64
236148 ACATAAATCC
* * * *
236158 CATTCGATG-TTTTATTTTAAGGGGGTGCATCAATGCACTACT-TGTGCATCGTTACACTGATGG
1 CATTCGATGTTTTTATTTTAAAGGAGTGCATCAATACACT-CTATGTGCATCGATACACTGATGG
* *
236221 CATTCGATGTTTTTATTTTAAAGGAGTGCATCGATACACTTTATGTGCATCGATACAC
1 CATTCGATGTTTTTATTTTAAAGGAGTGCATCAATACACTCTATGTGCATCGATACAC
236279 CTTGAACAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
63 10 0.20
64 40 0.80
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (64 bp):
CATTCGATGTTTTTATTTTAAAGGAGTGCATCAATACACTCTATGTGCATCGATACACTGATGG
Found at i:249305 original size:13 final size:14
Alignment explanation
Indices: 249287--249315 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
249277 TTAGCTCAAA
249287 CTTTGGTG-ACTCT
1 CTTTGGTGTACTCT
249300 CTTTGGTGTACTCT
1 CTTTGGTGTACTCT
249314 CT
1 CT
249316 CTATTATATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.07, C:0.24, G:0.21, T:0.48
Consensus pattern (14 bp):
CTTTGGTGTACTCT
Found at i:253227 original size:22 final size:22
Alignment explanation
Indices: 253202--253262 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
253192 TGAATAACAG
253202 AAGTGCCTTAGCACTAATACTA
1 AAGTGCCTTAGCACTAATACTA
* * *
253224 AAGTACAATT-GCACTGATACTA
1 AAGTGC-CTTAGCACTAATACTA
*
253246 AAGTGTCTTAGCACTAA
1 AAGTGCCTTAGCACTAA
253263 AAAAGAGAAT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
21 2 0.07
22 26 0.87
23 2 0.07
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.28
Consensus pattern (22 bp):
AAGTGCCTTAGCACTAATACTA
Found at i:271609 original size:416 final size:403
Alignment explanation
Indices: 270843--271627 Score: 1119
Period size: 416 Copynumber: 1.9 Consensus size: 403
270833 GGGTGGGTTC
* *
270843 TAATTTAGCTAAGAGACCAATTAGAAGTATCAGGTTAGAAATTGGCTTGTTATAGTTTGGGCTTA
1 TAATTTAGCTAAGAGACCAATTAGAAGTATCAGGTTAGAAATTGACTTGTTATAGTTTAGGCTTA
* * *
270908 AGCCCATTAAGGTATAAAAGTATTTTTGAATTGTGTAAGGAAGAGGGAGGACCAAAGGAGCAATT
66 AGCCCATTAAGGCATAAAAGTATTTTTGAAGTGTGTAAGGAAGAGGGAGGACCAAAGAAGCAATT
* * *
270973 AGACCCTAAACTATTTTTAAAGGTTGATTTTCTCTTTATGAAGCTTATGTCACCATGGGAATAAT
131 AGACCATAAACTACTTTTAAAGGTTGATTTTCTCTTTATGAAGCTTATGTCACCATGGAAATAAT
271038 CACATTTCTTATTCCTTCATTCAAAAGTTCTTCTCCACTATTACAAGTTCCAAAGGTGATAGCTT
196 CACATTTCTTATTCCTTCATTCAAAAGTTCTTCTCCACTATTACAAGTTCCAAAGGTGATAGCTT
*
271103 TGTGAATCCTTTATTTCCTATTTGAAAATCTAAGGTAACATTACTAATCTCCTCCACTAGAGCTT
261 TGTGAATCCTTTATTTCCTATTTGAAAATCTAAGGTAACATTAATAATCTCCTCCACTAGAGCTT
* *
271168 TCTTTTAAATTCTTAATCTCAAGGTTTGGTCATAGTGATCATATATGTTAGTAGTTTCAAGTAAT
326 TCTTTTAAACTCTTAATCTCAAGGTTTGGTCATAGTGACCATATATGTTAGTAGTTTCAAGTAAT
271233 CCCGGGTGAATTG
391 CCCGGGTGAATTG
** * *
271246 TAATTTAGGCTAAGAGATTAATTAGAAGTGTTAGGTTAGAAATTGACTTGTTATAGTTTAGGCTT
1 TAATTTA-GCTAAGAGACCAATTAGAAGTATCAGGTTAGAAATTGACTTGTTATAGTTTAGGCTT
* * *
271311 GAGCCCATTAAGGCATAAAAATGGTGTTTTTGAAGTGTGTAAGGAAGAGGGAGGACCAAAGAAGT
65 AAGCCCATTAAGGCAT-AAAA--GTATTTTTGAAGTGTGTAAGGAAGAGGGAGGACCAAAGAAGC
271376 AATTAGACCATAAACT-CTTTTAAAGGTTGATTTTCTCTTTATGAAGCTTATGTCA-CATGGAAA
127 AATTAGACCATAAACTACTTTTAAAGGTTGATTTTCTCTTTATGAAGCTTATGTCACCATGGAAA
* * * * *
271439 TCATC-CTATTTATTCTTGCCTTCCTCTTTCATTCAAAAGCTCTTCTTTTCCACTCTTGCAAGTT
192 TAATCAC-A--T-TTCTT--ATT-C-C-TTCATTCAAAAG---TTCTTCTCCACTATTACAAGTT
* * * *
271503 CCAATGGTGATAGCTTTGTGAATCCTTTATTTTCTTTTTGAAAATCTAAGGTAATATTAATAATC
245 CCAAAGGTGATAGCTTTGTGAATCCTTTATTTCCTATTTGAAAATCTAAGGTAACATTAATAATC
* * *
271568 TCCTCCCCTAGAGC-TTCATTTTGAACTCTTAATCTCAAGGTTTGGTCATGGTGACCATAT
310 TCCTCCACTAGAGCTTTC-TTTTAAACTCTTAATCTCAAGGTTTGGTCATAGTGACCATAT
271628 GGGGGCTTTA
Statistics
Matches: 335, Mismatches: 30, Indels: 21
0.87 0.08 0.05
Matches are distributed among these distances:
403 7 0.02
404 66 0.20
405 16 0.05
406 38 0.11
407 54 0.16
408 5 0.01
410 2 0.01
411 1 0.00
412 1 0.00
413 12 0.04
415 3 0.01
416 130 0.39
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.37
Consensus pattern (403 bp):
TAATTTAGCTAAGAGACCAATTAGAAGTATCAGGTTAGAAATTGACTTGTTATAGTTTAGGCTTA
AGCCCATTAAGGCATAAAAGTATTTTTGAAGTGTGTAAGGAAGAGGGAGGACCAAAGAAGCAATT
AGACCATAAACTACTTTTAAAGGTTGATTTTCTCTTTATGAAGCTTATGTCACCATGGAAATAAT
CACATTTCTTATTCCTTCATTCAAAAGTTCTTCTCCACTATTACAAGTTCCAAAGGTGATAGCTT
TGTGAATCCTTTATTTCCTATTTGAAAATCTAAGGTAACATTAATAATCTCCTCCACTAGAGCTT
TCTTTTAAACTCTTAATCTCAAGGTTTGGTCATAGTGACCATATATGTTAGTAGTTTCAAGTAAT
CCCGGGTGAATTG
Found at i:274763 original size:17 final size:17
Alignment explanation
Indices: 274743--274776 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
274733 ATAAATTTAT
274743 ATAAGG-CTTTATTTCTC
1 ATAAGGTCTTT-TTTCTC
274760 ATAAGGTCTTTTTTCTC
1 ATAAGGTCTTTTTTCTC
274777 TTCCCGAGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.21, C:0.18, G:0.12, T:0.50
Consensus pattern (17 bp):
ATAAGGTCTTTTTTCTC
Found at i:275096 original size:19 final size:20
Alignment explanation
Indices: 275059--275100 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
275049 AAAAATACAG
275059 ATGTGGTAATTAAAAAAAGTA
1 ATGTGGTAATT-AAAAAAGTA
275080 ATGTGGTAATT-AAAAAGTA
1 ATGTGGTAATTAAAAAAGTA
275099 AT
1 AT
275101 AAAAATGACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 10 0.48
21 11 0.52
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (20 bp):
ATGTGGTAATTAAAAAAGTA
Found at i:275972 original size:157 final size:157
Alignment explanation
Indices: 275730--276107 Score: 514
Period size: 157 Copynumber: 2.4 Consensus size: 157
275720 TGGGGTATAT
* * * *
275730 GAGCATGTGGTTCAAATTTGGTAAAGAAATGACTTAAAATAAATCACAAATTGAATG-AATAAGG
1 GAGCATGTGGTTCAAATTTGGTAAAAAAAAGACTTAAAATAAATCACGAATT-AAAGAAATAAGG
* * *
275794 AGATTATGAAAAATTGAAGGACTAAATTGAAAAATAAAAATTTGTAATCAA-AAAGAGAAATTG-
65 AGATTATAAAAAATTGAAGGACTAAATTAAAAAACAAAAATTTGTAATCAAGAAA-AGAAATTGA
275857 AATGTACACATGTATTCTACAATGGA-TTAG
129 AAT-TACACATGTATTCTACAAT-GATTTAG
* * *
275887 GAGCATGTTGCTCAAATTTGGTAAAAAAAAGACTTAAAATAAATGACGAATTAAAGAAATAAGGA
1 GAGCATGTGGTTCAAATTTGGTAAAAAAAAGACTTAAAATAAATCACGAATTAAAGAAATAAGGA
* *
275952 GATTATAAAAAATTGAAGGACTAAATTAAAAAACAAAAATTTGTTATCAAGAAAAGGAATTGAAA
66 GATTATAAAAAATTGAAGGACTAAATTAAAAAACAAAAATTTGTAATCAAGAAAAGAAATTGAAA
*
276017 TTACACATGTATTCTACTATGATTTAG
131 TTACACATGTATTCTACAATGATTTAG
* * *
276044 GAGCATGTGGTTCAAATTTAGTAAAAACAATAGACTTAAAATGAAA-CAGGAATTTAAGAAATAA
1 GAGCATGTGGTTCAAATTTGGTAAAAA-AA-AGACTTAAAAT-AAATCACGAATTAAAGAAATAA
276108 TGAAATCAGA
Statistics
Matches: 195, Mismatches: 19, Indels: 12
0.86 0.08 0.05
Matches are distributed among these distances:
156 5 0.03
157 153 0.78
158 8 0.04
159 26 0.13
160 3 0.02
ACGTcount: A:0.49, C:0.07, G:0.17, T:0.27
Consensus pattern (157 bp):
GAGCATGTGGTTCAAATTTGGTAAAAAAAAGACTTAAAATAAATCACGAATTAAAGAAATAAGGA
GATTATAAAAAATTGAAGGACTAAATTAAAAAACAAAAATTTGTAATCAAGAAAAGAAATTGAAA
TTACACATGTATTCTACAATGATTTAG
Found at i:276240 original size:9 final size:9
Alignment explanation
Indices: 276226--276250 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
276216 ATTCGAGTGG
276226 ACTCGAATA
1 ACTCGAATA
276235 ACTCGAATA
1 ACTCGAATA
276244 ACTCGAA
1 ACTCGAA
276251 ATTGAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.24, G:0.12, T:0.20
Consensus pattern (9 bp):
ACTCGAATA
Done.