Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008749.1 Hibiscus syriacus cultivar Beakdansim tig00111840_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: 379273
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
File 3 of 3
Found at i:342715 original size:225 final size:225
Alignment explanation
Indices: 342321--342773 Score: 870
Period size: 225 Copynumber: 2.0 Consensus size: 225
342311 TAAGAAACTG
342321 ATTTTCAAAGGTTTTTTTATCTTAAGACCTCAGAGTCATTCATAAGACCTCTGGGCAGAATGTTT
1 ATTTTCAAAGGTTTTTTTATCTTAAGACCTCAGAGTCATTCATAAGACCTCTGGGCAGAATGTTT
*
342386 TCAACATTTCCATCCTACTCAAAAGAAGCCAAATGAAAAAATTATAGTCTTTTTCGTCTTTGCTC
66 TCAACATTTCCATCATACTCAAAAGAAGCCAAATGAAAAAATTATAGTCTTTTTCGTCTTTGCTC
* *
342451 TATTCTTGTTAACACAAGAATGAGCAAAGAGGTGCAGCTGTAGACTTTAATTTTTTCATCTTTTT
131 TATTCTTGTTAACACAAGAATGAGCAAAGAGGGGCAGCTGTAGACATTAATTTTTTCATCTTTTT
342516 ATTAATATTATTATTGTTATTATTATAATT
196 ATTAATATTATTATTGTTATTATTATAATT
342546 ATTTTCAAAGGTTTTTTTATCTTAAGACCTCAGAGTCATTCATAAGACCTCTGGGCAGAATGTTT
1 ATTTTCAAAGGTTTTTTTATCTTAAGACCTCAGAGTCATTCATAAGACCTCTGGGCAGAATGTTT
342611 TCAACATTTCCATCATACTCAAAAGAAGCCAAATGAAAAAATTATAGTCTTTTTCGTCTTTGCTC
66 TCAACATTTCCATCATACTCAAAAGAAGCCAAATGAAAAAATTATAGTCTTTTTCGTCTTTGCTC
*
342676 TATTCTTGTTAACATAAGAATGAGCAAAGAGGGGCAGCTGTAGACATTAATTTTTTCATCTTTTT
131 TATTCTTGTTAACACAAGAATGAGCAAAGAGGGGCAGCTGTAGACATTAATTTTTTCATCTTTTT
342741 ATTAATATTATTATTGTTATTATTATAATT
196 ATTAATATTATTATTGTTATTATTATAATT
342771 ATT
1 ATT
342774 ATAATAATAA
Statistics
Matches: 224, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
225 224 1.00
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (225 bp):
ATTTTCAAAGGTTTTTTTATCTTAAGACCTCAGAGTCATTCATAAGACCTCTGGGCAGAATGTTT
TCAACATTTCCATCATACTCAAAAGAAGCCAAATGAAAAAATTATAGTCTTTTTCGTCTTTGCTC
TATTCTTGTTAACACAAGAATGAGCAAAGAGGGGCAGCTGTAGACATTAATTTTTTCATCTTTTT
ATTAATATTATTATTGTTATTATTATAATT
Found at i:344310 original size:12 final size:11
Alignment explanation
Indices: 344289--344328 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
344279 TTTTTCAATA
344289 TATTTAAATTAT
1 TATTT-AATTAT
344301 TACTTTAATTAT
1 TA-TTTAATTAT
*
344313 TATTTTATTAT
1 TATTTAATTAT
344324 TATTT
1 TATTT
344329 TCATATTAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 13 0.50
12 10 0.38
13 3 0.12
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTTAATTAT
Found at i:346530 original size:24 final size:25
Alignment explanation
Indices: 346486--346533 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
346476 AAAGTAATTC
*
346486 TTTTAAAAATATTTATGAAATAATA
1 TTTTAAAAATATTTATAAAATAATA
346511 TTTT-AAAA-ATTTATCAAAATAAT
1 TTTTAAAAATATTTAT-AAAATAAT
346534 GTAAAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 6 0.29
24 11 0.52
25 4 0.19
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (25 bp):
TTTTAAAAATATTTATAAAATAATA
Found at i:347432 original size:3 final size:3
Alignment explanation
Indices: 347421--347473 Score: 63
Period size: 3 Copynumber: 18.0 Consensus size: 3
347411 TTTTTTTCCG
** * *
347421 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TCG TTA TTT TTT TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
347468 TTA TTA
1 TTA TTA
347474 ATTAATTACA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:347944 original size:11 final size:11
Alignment explanation
Indices: 347928--347962 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
347918 AGAGATTTCG
347928 AAACAGAAAAA
1 AAACAGAAAAA
347939 AAACAGAAGAAA
1 AAACAGAA-AAA
*
347951 AAAAAGAAAAA
1 AAACAGAAAAA
347962 A
1 A
347963 GAAAAGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (11 bp):
AAACAGAAAAA
Found at i:360982 original size:16 final size:16
Alignment explanation
Indices: 360947--361011 Score: 51
Period size: 16 Copynumber: 4.0 Consensus size: 16
360937 TATTACACTT
** *
360947 AAAAAAAAAATGATGG
1 AAAAAAAAAAAAATGA
360963 AAAAAAAAAAAAATGA
1 AAAAAAAAAAAAATGA
**
360979 AAAAATGAAAAAA-GA
1 AAAAAAAAAAAAATGA
*
360994 AGAAAAATAAATAAATGA
1 A-AAAAA-AAAAAAATGA
361012 GGGTTCAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
15 3 0.08
16 28 0.74
17 5 0.13
18 2 0.05
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.11
Consensus pattern (16 bp):
AAAAAAAAAAAAATGA
Found at i:360991 original size:25 final size:25
Alignment explanation
Indices: 360963--361011 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
360953 AAAATGATGG
360963 AAAAAAAAAAAAATGAAA-AAATGAA
1 AAAAAAAAAAAAAT-AAATAAATGAA
* *
360988 AAAAGAAGAAAAATAAATAAATGA
1 AAAAAAAAAAAAATAAATAAATGA
361012 GGGTTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 3 0.14
25 18 0.86
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (25 bp):
AAAAAAAAAAAAATAAATAAATGAA
Found at i:361992 original size:43 final size:43
Alignment explanation
Indices: 361945--362321 Score: 268
Period size: 43 Copynumber: 8.7 Consensus size: 43
361935 ACATCAACTG
* *
361945 ACCAGACTTCCTCATCACGTAGGAGCCGTGTCAACCATAGATA
1 ACCAGACGTCCTCATCACGTAGGAACCGTGTCAACCATAGATA
* * * *
361988 ACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATG
1 ACCAGACGTCCTCATCACGTAGGAACCGTGTCA--ACC-ATAGATA
* * *
362034 GCCAGATC-TCTTCATCACGTAGGAGCCGTGTCAACCATAGATA
1 ACCAGA-CGTCCTCATCACGTAGGAACCGTGTCAACCATAGATA
* * * *
362077 ACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATG
1 ACCAGACGTCCTCATCACGTAGGAACCGTGTCA--ACC-ATAGATA
* * * *
362123 GCCAGATC-TCTTCATCACGTATGAGCCGTGTCAACCATAGATA
1 ACCAGA-CGTCCTCATCACGTAGGAACCGTGTCAACCATAGATA
* * * * *
362166 ACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGGTG
1 ACCAGACGTCCTCATCACGTAGGAACCGTGTCA--ACC-ATAGATA
* * * * * **
362212 GCCAGA-GT-TTCATCAGGTATGAACCGTGTCATCCCCAG---
1 ACCAGACGTCCTCATCACGTAGGAACCGTGTCAACCATAGATA
* * *
362250 ACCAGATC-TCTTCATCACGTAAGAGCCGTGTCAA-CATTAGGATA
1 ACCAGA-CGTCCTCATCACGTAGGAACCGTGTCAACCA-TA-GATA
*
362294 ACCAGCCGTCCTCATCACGTAGGAACCG
1 ACCAGACGTCCTCATCACGTAGGAACCG
362322 AGTTATCACC
Statistics
Matches: 255, Mismatches: 57, Indels: 43
0.72 0.16 0.12
Matches are distributed among these distances:
38 5 0.02
39 2 0.01
40 21 0.08
41 3 0.01
42 4 0.02
43 91 0.36
44 47 0.18
45 11 0.04
46 69 0.27
47 2 0.01
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (43 bp):
ACCAGACGTCCTCATCACGTAGGAACCGTGTCAACCATAGATA
Found at i:362097 original size:89 final size:89
Alignment explanation
Indices: 361956--362242 Score: 506
Period size: 89 Copynumber: 3.2 Consensus size: 89
361946 CCAGACTTCC
361956 TCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTA
1 TCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTA
362021 TCACCTTTAGATGGCCAGATCTCT
66 TCACCTTTAGATGGCCAGATCTCT
362045 TCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTA
1 TCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTA
362110 TCACCTTTAGATGGCCAGATCTCT
66 TCACCTTTAGATGGCCAGATCTCT
*
362134 TCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTA
1 TCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTA
* *
362199 TCACCTTTAGGTGGCCAGA-GT-T
66 TCACCTTTAGATGGCCAGATCTCT
* * *
362221 TCATCAGGTATGAACCGTGTCA
1 TCATCACGTAGGAGCCGTGTCA
362243 TCCCCAGACC
Statistics
Matches: 193, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
87 21 0.11
88 1 0.01
89 171 0.89
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (89 bp):
TCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTA
TCACCTTTAGATGGCCAGATCTCT
Found at i:362584 original size:3 final size:3
Alignment explanation
Indices: 362573--362625 Score: 63
Period size: 3 Copynumber: 18.0 Consensus size: 3
362563 TTTTTTTCCG
** * *
362573 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TCG TTA TTT TTT TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
362620 TTA TTA
1 TTA TTA
362626 ATTAATTACA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:363106 original size:19 final size:19
Alignment explanation
Indices: 363079--363116 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
363069 GAGAGATTTC
*
363079 GAAACAAAAA-AAAACAGAA
1 GAAA-AAAAAGAAAAAAGAA
363098 GAAAAAAAAGAAAAAAGAA
1 GAAAAAAAAGAAAAAAGAA
363117 AAGTTTTACC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.82, C:0.05, G:0.13, T:0.00
Consensus pattern (19 bp):
GAAAAAAAAGAAAAAAGAA
Found at i:371508 original size:30 final size:29
Alignment explanation
Indices: 371472--371536 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
371462 AAAGGACGAG
371472 TTGTAACATATGAATAGTCGAG-TGACTATT
1 TTGTAAC-TATGAATAGTCG-GTTGACTATT
* *
371502 TTGTAACTTTTAATAGTCGGTTGACTATT
1 TTGTAACTATGAATAGTCGGTTGACTATT
371531 TTGTAA
1 TTGTAA
371537 ATTTTAATAG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
28 1 0.03
29 24 0.75
30 7 0.22
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.43
Consensus pattern (29 bp):
TTGTAACTATGAATAGTCGGTTGACTATT
Found at i:371519 original size:29 final size:29
Alignment explanation
Indices: 371484--371547 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
371474 GTAACATATG
*
371484 AATAGTCGAG-TGACTATTTTGTAACTTTT
1 AATAGTCG-GTTGACTATTTTGTAAATTTT
371513 AATAGTCGGTTGACTATTTTGTAAATTTT
1 AATAGTCGGTTGACTATTTTGTAAATTTT
371542 AATAGT
1 AATAGT
371548 TAAAGGAATC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
28 1 0.03
29 32 0.97
ACGTcount: A:0.30, C:0.08, G:0.17, T:0.45
Consensus pattern (29 bp):
AATAGTCGGTTGACTATTTTGTAAATTTT
Found at i:373295 original size:15 final size:16
Alignment explanation
Indices: 373275--373307 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
373265 TTAACTCGAG
373275 CTCAAAAATTAT-AAA
1 CTCAAAAATTATCAAA
*
373290 CTCAAATATTATCAAA
1 CTCAAAAATTATCAAA
373306 CT
1 CT
373308 TAGTTCGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.52, C:0.18, G:0.00, T:0.30
Consensus pattern (16 bp):
CTCAAAAATTATCAAA
Found at i:373946 original size:29 final size:30
Alignment explanation
Indices: 373888--373948 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
373878 ATTGAAAGGG
* *
373888 TATTAAAAATTTGAGGACTCAATTAAAATA
1 TATTAAAAATTTAACGACTCAATTAAAATA
*
373918 TATT-AAAATTTAACGAC-CAATTTAGAATA
1 TATTAAAAATTTAACGACTCAA-TTAAAATA
373947 TA
1 TA
373949 AGTATAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 3 0.11
29 20 0.74
30 4 0.15
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.34
Consensus pattern (30 bp):
TATTAAAAATTTAACGACTCAATTAAAATA
Found at i:377018 original size:12 final size:12
Alignment explanation
Indices: 377003--377048 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
376993 CGGTTTTTTT
*
377003 ACCGGATAAAAA
1 ACCGGTTAAAAA
377015 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
377030 ACCGGTTAAAAA
1 ACCGGTTAAAAA
377042 ACCGGTT
1 ACCGGTT
377049 TTTATCCGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 17 0.57
13 1 0.03
14 2 0.07
15 10 0.33
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:377030 original size:15 final size:13
Alignment explanation
Indices: 377009--377049 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
376999 TTTTACCGGA
377009 TAAAAAACCGGTT
1 TAAAAAACCGGTT
377022 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
377036 TAAAAAACCGGTT
1 TAAAAAACCGGTT
377049 T
1 T
377050 TTATCCGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Done.