Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006743.1 Hibiscus syriacus cultivar Beakdansim tig00016935_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: 431342
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 3 of 3
Found at i:420805 original size:19 final size:20
Alignment explanation
Indices: 420777--420820 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
420767 AATTTTAAAA
*
420777 TAAATTATATAAAAAT-ATT
1 TAAATAATATAAAAATAATT
* *
420796 TAAATAATATTATAATAATT
1 TAAATAATATAAAAATAATT
420816 TAAAT
1 TAAAT
420821 TATTTATGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAATAATATAAAAATAATT
Found at i:420857 original size:17 final size:17
Alignment explanation
Indices: 420837--420869 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
420827 TGTTAAGAAC
420837 ATATTAATATAATTTAA
1 ATATTAATATAATTTAA
*
420854 ATATTAATATTATTTA
1 ATATTAATATAATTTA
420870 TTATATAGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATATTAATATAATTTAA
Found at i:421209 original size:13 final size:14
Alignment explanation
Indices: 421191--421219 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
421181 AATATATTAA
421191 TATAATTTAAA-AT
1 TATAATTTAAATAT
421204 TATAATTTAAATAT
1 TATAATTTAAATAT
421218 TA
1 TA
421220 ATATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TATAATTTAAATAT
Found at i:421467 original size:355 final size:352
Alignment explanation
Indices: 420796--421562 Score: 1022
Period size: 355 Copynumber: 2.2 Consensus size: 352
420786 TAAAAATATT
* *
420796 TAAATAATATTATAATAATTTAAATTATTT-ATGTTAAGAACATATTAATATAATTT--AAATAT
1 TAAA-AATATTATAATAATTTAAATAATTTAAT-TTAAGAATATATTAATATAATTTAAAAATAT
* * *
420858 TAATATTATTTATTATATAGGGCAGGATCCAATTATAATGTGTAAAACTCTTTTAATTTATACCA
64 TAATATTATTTATTATATAGGGCAAGATCCAATTATAATGTATAAAACTCTTTTAATTTACACCA
* * * *
420923 TTTTAAGACCATTTGATGAGAGAAATTAAAGACTGACATTAATCGTGGAAAATGAAAAGATATTC
129 TTTTAAGACCATTTGATGAAAGAAATTAAAGACTAACATTAACCATGGAAAATGAAAAGATATTC
* * *
420988 ACTAAAAAAACGAATTAATCTCAATCTTTGATTTCTCTCAATCCAATGGCTCTAAAAATGTGTAA
194 ACTAAAAAAACGAATTAATCTCAACCTTTGATTTCTCTCAATCCAATGGCACTAAAAATGTGCAA
* * *
421053 AACTAAAAGAGTTTTACATAGTGTAAATGGATCTTAATCCTTATTATATTTAAAAA-T-TAT-AT
259 AACTAAAAGAGTTTTACACAATATAAATGGATCTTAATCCTTATTATATTTAAAAATTATATAAT
421115 TAATTAA-TTAATTTAAGAATAAATTATA
324 TAATTAATTTAATTTAAGAATAAATTATA
421143 TAAAAATATTATAATAATTTAAATCAATTTAATTTAAGAATATATTAATATAATTTAAAATTATA
1 TAAAAATATTATAATAATTTAAAT-AATTTAATTTAAGAATATATTAATATAATTTAAAA--AT-
* * * *
421208 ATTTAAATATTAATATTATTATATGGGGCAAGATCCAATTATAGTGTATAAAGCTC-TTTAGTTT
62 A-TT-AATATT-AT-TTATTATATAGGGCAAGATCCAATTATAATGTATAAAACTCTTTTA-ATT
* * *
421272 TACACCATTTTAGGACCA-TTGAATGAAAGAAATTAAAGACTAAGATTAACCATGGAAAATGAAC
122 TACACCATTTTAAGACCATTTG-ATGAAAGAAATTAAAGACTAACATTAACCATGGAAAATGAAA
421336 AGATATTCACT-AAAAAACGAATTAATCTCAACCTTTGATTTCTCTCAATCCAATGAG-ACTAAA
186 AGATATTCACTAAAAAAACGAATTAATCTCAACCTTTGATTTCTCTCAATCCAATG-GCACTAAA
* * *
421399 AA-GATGC-AAACATAAAAGAGTTTTACACAATATAAGTGTATCTTAATCCTTATTATATTTATA
250 AATG-TGCAAAAC-TAAAAGAGTTTTACACAATATAAATGGATCTTAATCCTTATTATATTTAAA
421462 AATTATATAAATTAATTAATTTAATTTAAGAATAAATTATA
313 AATTATAT-AATTAATTAATTTAATTTAAGAATAAATTATA
* *
421503 T-AAAATATTTTAAATAATATTAGAATAATTTATTTTAAGAATATATTAATATAATTTAAA
1 TAAAAATATTAT-AATAAT-TTA-AATAATTTAATTTAAGAATATATTAATATAATTTAAA
421563 TTAATATATT
Statistics
Matches: 369, Mismatches: 27, Indels: 34
0.86 0.06 0.08
Matches are distributed among these distances:
346 20 0.05
347 30 0.08
348 2 0.01
349 2 0.01
351 2 0.01
352 1 0.00
353 2 0.01
354 11 0.03
355 108 0.29
356 103 0.28
357 3 0.01
359 18 0.05
360 28 0.08
361 36 0.10
362 3 0.01
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.38
Consensus pattern (352 bp):
TAAAAATATTATAATAATTTAAATAATTTAATTTAAGAATATATTAATATAATTTAAAAATATTA
ATATTATTTATTATATAGGGCAAGATCCAATTATAATGTATAAAACTCTTTTAATTTACACCATT
TTAAGACCATTTGATGAAAGAAATTAAAGACTAACATTAACCATGGAAAATGAAAAGATATTCAC
TAAAAAAACGAATTAATCTCAACCTTTGATTTCTCTCAATCCAATGGCACTAAAAATGTGCAAAA
CTAAAAGAGTTTTACACAATATAAATGGATCTTAATCCTTATTATATTTAAAAATTATATAATTA
ATTAATTTAATTTAAGAATAAATTATA
Found at i:421496 original size:25 final size:26
Alignment explanation
Indices: 421468--421566 Score: 91
Period size: 26 Copynumber: 3.9 Consensus size: 26
421458 TATAAATTAT
421468 ATAAATTAAT-TAATTTAATTTAAGA
1 ATAAATTAATATAATTTAATTTAAGA
** *
421493 ATAAATT-ATATAAAAT-ATTTTA-A
1 ATAAATTAATATAATTTAATTTAAGA
*
421516 ATAATATTAGA-ATAATTTATTTTAAGA
1 ATAA-ATTA-ATATAATTTAATTTAAGA
* *
421543 ATATATTAATATAATTTAAATTAA
1 ATAAATTAATATAATTTAATTTAA
421567 TATATTCTTA
Statistics
Matches: 57, Mismatches: 10, Indels: 13
0.71 0.12 0.16
Matches are distributed among these distances:
23 5 0.09
24 10 0.18
25 17 0.30
26 21 0.37
27 4 0.07
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (26 bp):
ATAAATTAATATAATTTAATTTAAGA
Found at i:421528 original size:34 final size:34
Alignment explanation
Indices: 421459--421561 Score: 102
Period size: 34 Copynumber: 2.9 Consensus size: 34
421449 TATTATATTT
* *
421459 ATAAATTATATAAATTAATTAATTTAATTTAAGA
1 ATAAATTATATAAAATAATTAATATAATTTAAGA
*
421493 ATAAATTATATAAAATATTTTAA-ATAATATT-AGA
1 ATAAATTATATAAAATA-ATTAATATAAT-TTAAGA
* *
421527 ATAATTTATTTTAAGAATATATTAATATAATTTAA
1 ATAAATTA-TATAA-AATA-ATTAATATAATTTAA
421562 ATTAATATAT
Statistics
Matches: 57, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
34 30 0.53
35 10 0.18
36 11 0.19
37 6 0.11
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (34 bp):
ATAAATTATATAAAATAATTAATATAATTTAAGA
Found at i:421556 original size:26 final size:26
Alignment explanation
Indices: 421472--421560 Score: 89
Period size: 25 Copynumber: 3.5 Consensus size: 26
421462 AATTATATAA
* *
421472 ATTAAT-TAATTTAATTTAAGAATAA
1 ATTAATATAATTTATTTTAAGAATAT
**
421497 ATT-ATATAAAATATTTT-A-AATAAT
1 ATTAATATAATTTATTTTAAGAAT-AT
421521 ATTAGA-ATAATTTATTTTAAGAATAT
1 ATTA-ATATAATTTATTTTAAGAATAT
421547 ATTAATATAATTTA
1 ATTAATATAATTTA
421561 AATTAATATA
Statistics
Matches: 51, Mismatches: 6, Indels: 13
0.73 0.09 0.19
Matches are distributed among these distances:
23 3 0.06
24 7 0.14
25 22 0.43
26 16 0.31
27 3 0.06
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (26 bp):
ATTAATATAATTTATTTTAAGAATAT
Found at i:421610 original size:23 final size:21
Alignment explanation
Indices: 421584--421628 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 21
421574 TTATGATATT
421584 TTATATTTATAATATAATTATCA
1 TTATATTTATAA-ATAA-TATCA
421607 TTATATTTATAAATAATATCA
1 TTATATTTATAAATAATATCA
421628 T
1 T
421629 AGTAAATGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 6 0.27
22 4 0.18
23 12 0.55
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (21 bp):
TTATATTTATAAATAATATCA
Found at i:428280 original size:26 final size:26
Alignment explanation
Indices: 428230--428280 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
428220 CACAATTCAT
* * *
428230 ATCATAGTCCATATCAACCAATAATA
1 ATCATAATCCAAATCAAACAATAATA
*
428256 ATCATAATCCAAATCAAACATTAAT
1 ATCATAATCCAAATCAAACAATAAT
428281 CAGTCCTAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.49, C:0.22, G:0.02, T:0.27
Consensus pattern (26 bp):
ATCATAATCCAAATCAAACAATAATA
Found at i:429617 original size:25 final size:26
Alignment explanation
Indices: 429566--429619 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
429556 CACAATTCAC
* *
429566 ATCATAATCCGAATCAAACAATGATA
1 ATCATAATCCAAATCAAACAATAATA
* *
429592 ATCATTATCCAAATC-AACATTAATA
1 ATCATAATCCAAATCAAACAATAATA
429617 ATC
1 ATC
429620 CGAGTTTGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 11 0.46
26 13 0.54
ACGTcount: A:0.48, C:0.20, G:0.04, T:0.28
Consensus pattern (26 bp):
ATCATAATCCAAATCAAACAATAATA
Found at i:429771 original size:25 final size:26
Alignment explanation
Indices: 429738--429802 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 26
429728 TATTAACATA
429738 ATTTA-AATTAATATATT-CTATGAT
1 ATTTATAATTAATATATTACTATGAT
* *
429762 ATTTATAATTAA-ATATTATTATTAT
1 ATTTATAATTAATATATTACTATGAT
429787 ATTTATAAATT-ATATA
1 ATTTAT-AATTAATATA
429803 AATAATTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
24 10 0.29
25 18 0.51
26 7 0.20
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (26 bp):
ATTTATAATTAATATATTACTATGAT
Done.