Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000781.1 Hibiscus syriacus cultivar Beakdansim tig00001517_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: 44105
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:7476 original size:32 final size:32
Alignment explanation
Indices: 7407--7468 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
7397 AGTCTAGTTT
* * * *
7407 AAATAATTTAGGTTTTAGATTTAAAATAATTC
1 AAATAATCTAAGTTTTAAATTTAAAATAATAC
7439 AAATAATCTAAGTTTTAAATTTAAAA-AATA
1 AAATAATCTAAGTTTTAAATTTAAAATAATA
7469 AGAAATAAGG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 3 0.12
32 23 0.88
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.40
Consensus pattern (32 bp):
AAATAATCTAAGTTTTAAATTTAAAATAATAC
Found at i:8050 original size:20 final size:20
Alignment explanation
Indices: 8008--8050 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
7998 CTTAGTCTTT
*
8008 ATTATTTATTTATAAAGATA
1 ATTATTTATTTATAAAGAAA
*
8028 ATTATTTGA-TTATAAATAAA
1 ATTATTT-ATTTATAAAGAAA
8048 ATT
1 ATT
8051 TGTGATGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
ATTATTTATTTATAAAGAAA
Found at i:19772 original size:2 final size:2
Alignment explanation
Indices: 19695--19759 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
19685 ATTTCGTGTG
19695 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
19737 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
19760 TTCGAACATA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:25590 original size:89 final size:89
Alignment explanation
Indices: 25435--25675 Score: 351
Period size: 89 Copynumber: 2.7 Consensus size: 89
25425 AGCTGGTAAG
* * **
25435 ACCTTACGGACCTAAGGATACTC-TTGGGTAGTCCCATAGGCCCCAAGGCATATTATTAGGTTGG
1 ACCTTACGGATCTAAGGATAC-CATTGGGTAGGCCCATAGGCCCCAAGGCATATCCTTAGGTTGG
25499 TTCTCTTTCCTGTGTGCTTAGGGTA
65 TTCTCTTTCCTGTGTGCTTAGGGTA
*
25524 GCGC-TACGGATCTAAGGATACCATTGGGTAGGCCCATAGGCCCCAAGGCATATCCTTAGGTTGG
1 AC-CTTACGGATCTAAGGATACCATTGGGTAGGCCCATAGGCCCCAAGGCATATCCTTAGGTTGG
**
25588 TTCTCTTTGTTGTGTGCTTAGGGTA
65 TTCTCTTTCCTGTGTGCTTAGGGTA
* * * *
25613 ACCTTACAGATCTAAGGATACCATTGGTTAGGCCCATAGGCCCCAAAGAATATCCTTAGGTTG
1 ACCTTACGGATCTAAGGATACCATTGGGTAGGCCCATAGGCCCCAAGGCATATCCTTAGGTTG
25676 TCCCCTTGCT
Statistics
Matches: 137, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
88 2 0.01
89 134 0.98
90 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.30
Consensus pattern (89 bp):
ACCTTACGGATCTAAGGATACCATTGGGTAGGCCCATAGGCCCCAAGGCATATCCTTAGGTTGGT
TCTCTTTCCTGTGTGCTTAGGGTA
Found at i:26906 original size:29 final size:28
Alignment explanation
Indices: 26874--26936 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 28
26864 AATTTCAAAT
26874 TTAATCTTTTATTTTAATTAAAAATATTA
1 TTAATC-TTTATTTTAATTAAAAATATTA
* *
26903 TTAAAACTTTATTTTAATTAACAATATTA
1 TT-AATCTTTATTTTAATTAAAAATATTA
26932 TTAAT
1 TTAAT
26937 TTCGAATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 2 0.07
29 25 0.83
30 3 0.10
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (28 bp):
TTAATCTTTATTTTAATTAAAAATATTA
Found at i:26937 original size:16 final size:15
Alignment explanation
Indices: 26883--26937 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
26873 TTTAATCTTT
*
26883 TATTTTAATTAAAAA
1 TATTTTAATTAACAA
**
26898 TATTATTAA--AACTT
1 TATT-TTAATTAACAA
26912 TATTTTAATTAACAA
1 TATTTTAATTAACAA
26927 TATTATTAATT
1 TATT-TTAATT
26938 TCGAATTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
13 4 0.13
14 6 0.19
15 11 0.35
16 10 0.32
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (15 bp):
TATTTTAATTAACAA
Found at i:28282 original size:363 final size:361
Alignment explanation
Indices: 27547--28547 Score: 1364
Period size: 363 Copynumber: 2.7 Consensus size: 361
27537 ATCAGATTTC
* * * * * *
27547 ATTATACCAACTTAATATTGATACTATATTTGAACCATAGATATTGTATGAACAGTTATTGGTAG
1 ATTACACCAACTTAATATTGATACTATATTTGAACTATCGATCTTGTATGAACAATTATTGGTAC
* **
27612 TCATTCAATGGTATTGATACCATTAGTATAAAATATGTAAA-TATACAATTAGTCCCTGGATTAT
66 CCATTCAATGGTATTGATACCATTAGTATAAAATATAAAAATTATACAATTAGTCCCTGGATTAT
* **
27676 GTATTACTCATGCTAAGACCTTTTAAGTAGTGATATAGTATGTAATTGTTAATAGAATCGGTCTT
131 GTATTACTCATGCTAAGACCTTTTAAGTAGTGATATAGTATGTAACTGTTAATAGAATTAGTCTT
* * * * * *
27741 CAGAATAATTTATTACATAATCCCTAATCTTTTATATAATTACATGCCCATCCCTAAAAGTTTGT
196 TAGAATAATTTACTATATAATCCCTAATCTTTTACAT-GTT--A-----ATCCCTAAAAGTTTGA
* * * *
27806 AAAGTTTTAATTTGGTCCTTGTCATATCAAAGTATAACATTAGTAATATGATGATATATATAATT
253 AAAGTCTTAAATTAGTCCTTGTCATATCAAAGTATAACATTAGCAATATGATGATATATATAATT
27871 TAAAATCAATAATTAAATGTTCGTTTAGCAAGGTATGATCAATT
318 TAAAATCAATAATTAAATGTTCGTTTAGCAAGGTATGATCAATT
* *
27915 ATTACACCAACTTAATATTGATATTATATTCGAACTATCGATCTTGTATGAACAATTATTGGTAC
1 ATTACACCAACTTAATATTGATACTATATTTGAACTATCGATCTTGTATGAACAATTATTGGTAC
* * * *
27980 CCATTCAACGGTATTGATACCAATAGTATAAAATATACAAATTATACAATTAGTCCCTGGATCAT
66 CCATTCAATGGTATTGATACCATTAGTATAAAATATAAAAATTATACAATTAGTCCCTGGATTAT
*
28045 GTATTACTCATGCTAAGACCTTTTAAGTAGTGATACAGTATGTAA-T-TT-ATAGAATTAGTCTT
131 GTATTACTCATGCTAAGACCTTTTAAGTAGTGATATAGTATGTAACTGTTAATAGAATTAGTCTT
28107 TAGAATAATTTACTATATAATCCCTAATCTTTTACATGTTAATCCCTAAAAGTTTGAAAAGTCTT
196 TAGAATAATTTACTATATAATCCCTAATCTTTTACATGTTAATCCCTAAAAGTTTGAAAAGTCTT
* ** *
28172 AAATTAGTCCTTGTCATATCAAATTAAAGTATAGCATTAGCGTTATGATGATATATATGATTTAA
261 AAATTAGTCCTTGTCATATC-----AAAGTATAACATTAGCAATATGATGATATATATAATTTAA
* * *
28237 AATGAGTAATTAAATGTTTGTTTAGCAAGGTATGATCAATT
321 AATCAATAATTAAATGTTCGTTTAGCAAGGTATGATCAATT
*
28278 ATTACACCAACTTAATATTGATACTATATTTGAACTATCGA-CATTGTATGAACAATTATTTGTA
1 ATTACACCAACTTAATATTGATACTATATTTGAACTATCGATC-TTGTATGAACAATTATTGGTA
* * * * *
28342 TCCATTCAATAGTATCGATAACATTAGTATAAAATATAAAAATTATACAATTAGTCCCTAGATTA
65 CCCATTCAATGGTATTGATACCATTAGTATAAAATATAAAAATTATACAATTAGTCCCTGGATTA
* *
28407 TGTATTACTCATGCTAAGACCTTTTAAGTAGTGATATAATATGTAACTGTTAATGGAATTAGTCT
130 TGTATTACTCATGCTAAGACCTTTTAAGTAGTGATATAGTATGTAACTGTTAATAGAATTAGTCT
*
28472 TTAGAATAATTTACTATACAATCCCTAATCTTTTAGATAATTACATGTTAATCCCTAAAAGTTTG
195 TTAGAATAATTTACTATATAATCCCTAATC---T---T--TTACATGTTAATCCCTAAAAGTTTG
28537 AAAAGTCTTAA
252 AAAAGTCTTAA
28548 TGTAACACCC
Statistics
Matches: 565, Mismatches: 50, Indels: 30
0.88 0.08 0.05
Matches are distributed among these distances:
358 40 0.07
362 1 0.00
363 233 0.41
364 1 0.00
365 4 0.01
366 86 0.15
367 2 0.00
368 94 0.17
369 67 0.12
372 1 0.00
374 36 0.06
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (361 bp):
ATTACACCAACTTAATATTGATACTATATTTGAACTATCGATCTTGTATGAACAATTATTGGTAC
CCATTCAATGGTATTGATACCATTAGTATAAAATATAAAAATTATACAATTAGTCCCTGGATTAT
GTATTACTCATGCTAAGACCTTTTAAGTAGTGATATAGTATGTAACTGTTAATAGAATTAGTCTT
TAGAATAATTTACTATATAATCCCTAATCTTTTACATGTTAATCCCTAAAAGTTTGAAAAGTCTT
AAATTAGTCCTTGTCATATCAAAGTATAACATTAGCAATATGATGATATATATAATTTAAAATCA
ATAATTAAATGTTCGTTTAGCAAGGTATGATCAATT
Found at i:29331 original size:30 final size:30
Alignment explanation
Indices: 29295--29366 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
29285 CCCGCAGGAC
*
29295 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
29325 CTATCCAGAGGTCATAAAGATCCTCGGCAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
* *
29355 CTGTCCATAGGT
1 CTATCCAGAGGT
29367 TTCGAAGAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGCAA
Found at i:29391 original size:31 final size:30
Alignment explanation
Indices: 29353--29540 Score: 130
Period size: 31 Copynumber: 6.0 Consensus size: 30
29343 GATCCTCGGC
* *
29353 AACTGTCCATAGGTTTCGAAGAACCTAGGT
1 AACTGTCCATATGTTTCGAAGAACATAGGT
* **
29383 GAACTGTCCATATGTTCCTTAGAACATAGGT
1 -AACTGTCCATATGTTTCGAAGAACATAGGT
*
29414 ATACTGTCCATATGTCTCGAA-AGACATAGGT
1 A-ACTGTCCATATGTTTCGAAGA-ACATAGGT
* ** *
29445 AATTCTATCCATATG-TTCTTTATAACATAGGT
1 AA--CTGTCCATATGTTTC-GAAGAACATAGGT
* *
29477 ATATTGTCCATATGTCTCGAA-AGACATAGGT
1 A-ACTGTCCATATGTTTCGAAGA-ACATAGGT
* **
29508 AATTCTGTCCATATGTTCCTTAGAACATAGGT
1 AA--CTGTCCATATGTTTCGAAGAACATAGGT
29540 A
1 A
29541 TACCCTCAAC
Statistics
Matches: 122, Mismatches: 23, Indels: 23
0.73 0.14 0.14
Matches are distributed among these distances:
30 5 0.04
31 70 0.57
32 44 0.36
33 3 0.02
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Consensus pattern (30 bp):
AACTGTCCATATGTTTCGAAGAACATAGGT
Found at i:29476 original size:63 final size:63
Alignment explanation
Indices: 29389--29543 Score: 274
Period size: 63 Copynumber: 2.5 Consensus size: 63
29379 AGGTGAACTG
29389 TCCATATGTTCCTTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACATAGGTAATTCTA
1 TCCATATGTTCCTTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACATAGGTAATTCTA
* * * *
29452 TCCATATGTTCTTTATAACATAGGTATATTGTCCATATGTCTCGAAAGACATAGGTAATTCTG
1 TCCATATGTTCCTTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACATAGGTAATTCTA
29515 TCCATATGTTCCTTAGAACATAGGTATAC
1 TCCATATGTTCCTTAGAACATAGGTATAC
29544 CCTCAACTCT
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 85 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.35
Consensus pattern (63 bp):
TCCATATGTTCCTTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACATAGGTAATTCTA
Found at i:29536 original size:32 final size:32
Alignment explanation
Indices: 29386--29540 Score: 158
Period size: 32 Copynumber: 4.9 Consensus size: 32
29376 CCTAGGTGAA
*
29386 CTGTCCATATGTTCCTTAGAACATAGGT-ATA
1 CTGTCCATATGTTCCTTAGAACATAGGTAATT
***
29417 CTGTCCATATGTCTCGAAAG-ACATAGGTAATT
1 CTGTCCATATGT-TCCTTAGAACATAGGTAATT
* * *
29449 CTATCCATATGTTCTTTATAACATAGGT-ATAT
1 CTGTCCATATGTTCCTTAGAACATAGGTAAT-T
***
29481 -TGTCCATATGTCTCGAAAG-ACATAGGTAATT
1 CTGTCCATATGT-TCCTTAGAACATAGGTAATT
29512 CTGTCCATATGTTCCTTAGAACATAGGTA
1 CTGTCCATATGTTCCTTAGAACATAGGTA
29541 TACCCTCAAC
Statistics
Matches: 99, Mismatches: 17, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
31 48 0.48
32 51 0.52
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.35
Consensus pattern (32 bp):
CTGTCCATATGTTCCTTAGAACATAGGTAATT
Done.