Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008590.1 Hibiscus syriacus cultivar Beakdansim tig00111539_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: 253679
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:236356 original size:36 final size:36
Alignment explanation
Indices: 236316--236390 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
236306 GGTCAACAGT
236316 GGTCAACGACGGTCA-AT-GGGTCAACGGGTCGGGTCG
1 GGTCAACG--GGTCAGATCGGGTCAACGGGTCGGGTCG
*
236352 GGTCAACGGGTCAGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCAGATCGGGTCAACGGGTCGGGTCG
236388 GGT
1 GGT
236391 TGTGACAGGT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
34 5 0.14
35 1 0.03
36 30 0.83
ACGTcount: A:0.16, C:0.21, G:0.45, T:0.17
Consensus pattern (36 bp):
GGTCAACGGGTCAGATCGGGTCAACGGGTCGGGTCG
Found at i:239679 original size:29 final size:28
Alignment explanation
Indices: 239635--239724 Score: 89
Period size: 26 Copynumber: 3.1 Consensus size: 28
239625 TAGAAAAGCC
239635 AGAATGAGAAATAGCTTAGCAAAGCTATTAG
1 AGAATGA-AAA-AGCTTAGCAAAGCTA-TAG
239666 AGAATGAAAAAGCTTAGCAAAGC-A-AG
1 AGAATGAAAAAGCTTAGCAAAGCTATAG
*
239692 -GACGA-GAAATAGCTTAGCAAAGCTATGAG
1 AGA--ATGAAAAAGCTTAGCAAAGCTAT-AG
239721 AGAA
1 AGAA
239725 AAGGTGAAGC
Statistics
Matches: 52, Mismatches: 1, Indels: 15
0.76 0.01 0.22
Matches are distributed among these distances:
25 2 0.04
26 19 0.37
27 2 0.04
28 2 0.04
29 15 0.29
30 5 0.10
31 7 0.13
ACGTcount: A:0.48, C:0.11, G:0.24, T:0.17
Consensus pattern (28 bp):
AGAATGAAAAAGCTTAGCAAAGCTATAG
Found at i:239699 original size:55 final size:55
Alignment explanation
Indices: 239616--239724 Score: 164
Period size: 55 Copynumber: 2.0 Consensus size: 55
239606 AGGAATATGA
* * * *
239616 GAAAAGGCTTAGAAAAGCCAGAATGAGAAATAGCTTAGCAAAGCTATTAGAGAAT
1 GAAAAAGCTTAGAAAAGCAAGAACGAGAAATAGCTTAGCAAAGCTATGAGAGAAT
* *
239671 GAAAAAGCTTAGCAAAGCAAGGACGAGAAATAGCTTAGCAAAGCTATGAGAGAA
1 GAAAAAGCTTAGAAAAGCAAGAACGAGAAATAGCTTAGCAAAGCTATGAGAGAA
239725 AAGGTGAAGC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.48, C:0.12, G:0.25, T:0.16
Consensus pattern (55 bp):
GAAAAAGCTTAGAAAAGCAAGAACGAGAAATAGCTTAGCAAAGCTATGAGAGAAT
Found at i:239707 original size:26 final size:25
Alignment explanation
Indices: 239614--239725 Score: 84
Period size: 26 Copynumber: 4.2 Consensus size: 25
239604 AAAGGAATAT
* * *
239614 GAGAAA-AGGCTTAGAAAAGCCAGAA
1 GAGAAATA-GCTTAGCAAAGCAAGGA
239639 TGAGAAATAGCTTAGCAAAGCTATTA-GA
1 -GAGAAATAGCTTAGCAAAGC-A--AGGA
*
239667 GAATGAAAAAGCTTAGCAAAGCAAGGA
1 G-A-GAAATAGCTTAGCAAAGCAAGGA
* *
239694 CGAGAAATAGCTTAGCAAAGCTATGA
1 -GAGAAATAGCTTAGCAAAGCAAGGA
239720 GAGAAA
1 GAGAAA
239726 AGGTGAAGCT
Statistics
Matches: 71, Mismatches: 7, Indels: 17
0.75 0.07 0.18
Matches are distributed among these distances:
25 6 0.08
26 38 0.54
27 5 0.07
28 4 0.06
29 18 0.25
ACGTcount: A:0.48, C:0.12, G:0.25, T:0.15
Consensus pattern (25 bp):
GAGAAATAGCTTAGCAAAGCAAGGA
Found at i:242900 original size:12 final size:13
Alignment explanation
Indices: 242869--242894 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
242859 AGAAGTGAGC
242869 AATTATTTAAAAA
1 AATTATTTAAAAA
242882 AATTATTTAAAAA
1 AATTATTTAAAAA
242895 TTTATTGGTC
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AATTATTTAAAAA
Found at i:243288 original size:5 final size:5
Alignment explanation
Indices: 243278--243306 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
243268 TTTCAAAAAA
243278 AATTC AATTC AATTC AATTC AATTC AATT
1 AATTC AATTC AATTC AATTC AATTC AATT
243307 ATTCTAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (5 bp):
AATTC
Found at i:251686 original size:462 final size:466
Alignment explanation
Indices: 250528--251900 Score: 2024
Period size: 462 Copynumber: 3.0 Consensus size: 466
250518 AATTATTTCT
*
250528 AAATAGATAAAGTAAAATTATATTTTTTCGGGTCGGGTCGGGTATTTTTACCCTAAACCCGAACC
1 AAATAGATAAAGTAAAATTATATTTTTTCGGGTCGAGTCGGGTATTTTTACCCTAAACCCGAACC
* *
250593 GACCCGAACATTACACTTAAAAAAATCCGACCCGACCCCGAATTATTTTAA-ATAACCCGAGCCG
66 GACCCGAACATTACACTTAAAAAAATCCGACCCGA-CCCGAATTATTTTAAGAAAACTCGAGCCG
* * * *
250657 ATCGAGTC-GGATCAAATCGAAACCCGTCGAATTCGAGTCTCATACCCATCCTTATGAATACATA
130 ATCGGGTCAGG-TCAAATCGAAACCCATCGAATTCGA-TCTCATGCCCAT-CTTATGAATACCTA
* * * *
250721 TTTTGATATCTTAATAAAGTAAAAGGCATAAGGAAAAATTATCACTTTTTTTCAGAAATAGTTAT
192 TTTTGATATCTTGATAAAGTCAAAGGCATAAGGAAAAATTAT--CGTTTTTTCATAAATAGTTAT
*
250786 TTTC-TTCTATACTTCTTTTT-ATATTTTAGTTGTTAAT-TTTATTTTTTTTGTCAAAATAATCC
255 TTTCTTTCTATACTTCTTTTTAATATTTTAGTTGTTAATATTT-TATTTTTTGTCAAAATAATCC
*
250848 GTATTGAATGAAAATTATTACTAATTGTCAATATATGTTACTGACGTGTTATTTTCATATGTGTT
319 TTATTGAATGAAAATTATTA-TAATTGTCAATATATGTTACTGACGTGTTATTTTCATATGTGTT
250913 CAATTGTTAATGTAAAATATATTATGTCATTATTTTAGTGACGCGATAATTTATGATGATATAAC
383 CAATTGTTAATGTAAAATATATTATGTCATTATTTTAGTGACGCGATAATTTATGATGATATAAC
*
250978 ACATGTCATATCATTGAGTA
448 ACATGTCA-ATCATAGAGTA
*
250998 AAATATATAAAGTAAAA--ATATTTTTTCGGGTC-AGGTCGGGTCAGGTATTTTTACCCTAAACC
1 AAATAGATAAAGTAAAATTATATTTTTTCGGGTCGA-GTC--G---GGTATTTTTACCCTAAACC
* * *
251060 CGAATCGACCCGAACATTACACTT-AAAAAATCCGACCCGACCCAAATTATTTTGAGAAAACTCG
60 CGAACCGACCCGAACATTACACTTAAAAAAATCCGACCCGACCCGAATTATTTTAAGAAAACTCG
* * *
251124 AGCCGATCGGGTAAGATCAAATCGAAACCTATCGAATT---TC-CTATGCCCATCTTTATGAATA
125 AGCCGATCGGGTCAGGTCAAATCGAAACCCATCGAATTCGATCTC-ATGCCCATC-TTATGAATA
* *
251185 CCTATTTTGATATCTTGATAAAGTCAAAGGTAAAAGGAAAAATTATCGTTTTTTCATAAATAGTT
188 CCTATTTTGATATCTTGATAAAGTCAAAGGCATAAGGAAAAATTATCGTTTTTTCATAAATAGTT
251250 ATTTTCTTCTCTATACTTCTTTTTAATATTTTAGTTGTTAATATTTTATTTTTTGTC-AAATAAT
253 ATTTTCTT-TCTATACTTCTTTTTAATATTTTAGTTGTTAATATTTTATTTTTTGTCAAAATAAT
*
251314 CCTTATTGAATGAAAATTA-T-TAATTGTCAATATATATTACTGACGTGTTATTTTCATATGTGT
317 CCTTATTGAATGAAAATTATTATAATTGTCAATATATGTTACTGACGTGTTATTTTCATATGTGT
251377 TCAATTGTTAATGTAAAATA-ATTATGTCATTA-TTTAGTGACGCGATAATTTATGATGATATAA
382 TCAATTGTTAATGTAAAATATATTATGTCATTATTTTAGTGACGCGATAATTTATGATGATATAA
251440 CACATGTC-A-CATAGAGTA
447 CACATGTCAATCATAGAGTA
*
251458 AAATAGATAAAGTAAAATTATATTTTTTCGGGTCGAGTCGGGTATTTTTACCCTAAATCCGAACC
1 AAATAGATAAAGTAAAATTATATTTTTTCGGGTCGAGTCGGGTATTTTTACCCTAAACCCGAACC
* * *
251523 GACCCGAACATTACATTTAAAAAAATCCGACCTGACCCTGAATTATTTTAAGAAAACTCGAGCCT
66 GACCCGAACATTACACTTAAAAAAATCCGACCCGACCC-GAATTATTTTAAGAAAACTCGAGCCG
* *
251588 ATCGGGTCAGGTCGAATCAAAACCCATCGAATTCGAATCTCATGCCCATCTTATGAATACCTATT
130 ATCGGGTCAGGTCAAATCGAAACCCATCGAATTCG-ATCTCATGCCCATCTTATGAATACCTATT
* * * *
251653 TTGATGTCTTGATAAAATCAAAGGCATAAGGAAAAAATATTGTTTTTTCATAAATAGTTATTTTC
194 TTGATATCTTGATAAAGTCAAAGGCATAAGGAAAAATTATCGTTTTTTCATAAATAGTTATTTTC
251718 TTTTCTATACTTC-TTTTAATATTTTAGTTGTTAATATTTTATTTTTTGTCAAAATAATCCTTAT
259 -TTTCTATACTTCTTTTTAATATTTTAGTTGTTAATATTTTATTTTTTGTCAAAATAATCCTTAT
* * *
251782 TGAATGAAAATTATTACTAATTGTCAATATATGTTATTGAAGTGTTATTTTTATATGTGTTCAAT
323 TGAATGAAAATTATTA-TAATTGTCAATATATGTTACTGACGTGTTATTTTCATATGTGTTCAAT
*
251847 TGCTAATGT-AAATATATTA--TCATTATTTTAGTGACGCGATAATTTAT--TGATATA
387 TGTTAATGTAAAATATATTATGTCATTATTTTAGTGACGCGATAATTTATGATGATATA
251901 CATGTCACAT
Statistics
Matches: 824, Mismatches: 48, Indels: 70
0.87 0.05 0.07
Matches are distributed among these distances:
457 40 0.05
458 18 0.02
459 51 0.06
460 25 0.03
461 38 0.05
462 135 0.16
463 60 0.07
464 39 0.05
465 118 0.14
466 23 0.03
467 4 0.00
468 117 0.14
469 27 0.03
470 20 0.02
471 13 0.02
472 53 0.06
473 43 0.05
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (466 bp):
AAATAGATAAAGTAAAATTATATTTTTTCGGGTCGAGTCGGGTATTTTTACCCTAAACCCGAACC
GACCCGAACATTACACTTAAAAAAATCCGACCCGACCCGAATTATTTTAAGAAAACTCGAGCCGA
TCGGGTCAGGTCAAATCGAAACCCATCGAATTCGATCTCATGCCCATCTTATGAATACCTATTTT
GATATCTTGATAAAGTCAAAGGCATAAGGAAAAATTATCGTTTTTTCATAAATAGTTATTTTCTT
TCTATACTTCTTTTTAATATTTTAGTTGTTAATATTTTATTTTTTGTCAAAATAATCCTTATTGA
ATGAAAATTATTATAATTGTCAATATATGTTACTGACGTGTTATTTTCATATGTGTTCAATTGTT
AATGTAAAATATATTATGTCATTATTTTAGTGACGCGATAATTTATGATGATATAACACATGTCA
ATCATAGAGTA
Done.