Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004960.1 Hibiscus syriacus cultivar Beakdansim tig00011148_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: 50625
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:446 original size:18 final size:18
Alignment explanation
Indices: 425--464 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
415 TCATATAGGT
*
425 TTATTTTTTAAATTATTA
1 TTATTTATTAAATTATTA
*
443 TTATTTATTATATTATTA
1 TTATTTATTAAATTATTA
461 TTAT
1 TTAT
465 ATACTTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTATTTATTAAATTATTA
Found at i:2506 original size:19 final size:19
Alignment explanation
Indices: 2484--2570 Score: 124
Period size: 19 Copynumber: 4.6 Consensus size: 19
2474 GGACTCCTAT
*
2484 TGCATCGGTGCACTAAGAG
1 TGCATCGATGCACTAAGAG
2503 TGCATCGATGCACTAAGAG
1 TGCATCGATGCACTAAGAG
*
2522 TGCATCGATGCA-TGA-AG
1 TGCATCGATGCACTAAGAG
*
2539 TGCATTCGATGTACTAAGAG
1 TGCA-TCGATGCACTAAGAG
2559 TGCATCGATGCA
1 TGCATCGATGCA
2571 TGAAGTGCAT
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
17 6 0.10
18 9 0.15
19 39 0.65
20 6 0.10
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.24
Consensus pattern (19 bp):
TGCATCGATGCACTAAGAG
Found at i:2555 original size:37 final size:37
Alignment explanation
Indices: 2501--2587 Score: 158
Period size: 37 Copynumber: 2.4 Consensus size: 37
2491 GTGCACTAAG
*
2501 AGTGCA-TCGATGCACTAAGAGTGCATCGATGCATGA
1 AGTGCATTCGATGTACTAAGAGTGCATCGATGCATGA
2537 AGTGCATTCGATGTACTAAGAGTGCATCGATGCATGA
1 AGTGCATTCGATGTACTAAGAGTGCATCGATGCATGA
2574 AGTGCATTCGATGT
1 AGTGCATTCGATGT
2588 TTGAAAAATA
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
36 6 0.12
37 43 0.88
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (37 bp):
AGTGCATTCGATGTACTAAGAGTGCATCGATGCATGA
Found at i:2592 original size:18 final size:17
Alignment explanation
Indices: 2501--2586 Score: 91
Period size: 19 Copynumber: 4.7 Consensus size: 17
2491 GTGCACTAAG
*
2501 AGTGCATCGATGCACTAA
1 AGTGCATCGATGCA-TGA
2519 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
* *
2537 AGTGCATTCGATGTACTAA
1 AGTGCA-TCGATGCA-TGA
2556 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
2574 AGTGCATTCGATG
1 AGTGCA-TCGATG
2587 TTTGAAAAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
17 12 0.21
18 17 0.29
19 23 0.40
20 6 0.10
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:2612 original size:64 final size:60
Alignment explanation
Indices: 2537--2717 Score: 168
Period size: 64 Copynumber: 2.8 Consensus size: 60
2527 CGATGCATGA
*
2537 AGTGCATTCGATGTACTAAGAGTGCATCGATGCATGAAGTGCATTCGATGTTTGAA-AAAT-AG
1 AGTGCA-TCGATGCA-T-AGAGTGCATCGATGCATGAA-TGCATTCGATGTTTGAATAAATCAG
* * * *
2599 CCTGGTGCATCGATGCATGGATTGTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATC
1 ---AGTGCATCGATGCATAGA--GTGCATCGATGCAT-GAATGCATTCGATGTTTGAA-TAAATC
2664 AG
59 AG
*
2666 AGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATGTTT
1 AGTGCATCGATGCAT--AGAGTGCATCGATGCAT-GAATGCATTCGATGTTT
2718 CAATTTATTC
Statistics
Matches: 98, Mismatches: 10, Indels: 17
0.78 0.08 0.14
Matches are distributed among these distances:
62 2 0.02
63 1 0.01
64 80 0.82
65 7 0.07
66 6 0.06
67 2 0.02
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (60 bp):
AGTGCATCGATGCATAGAGTGCATCGATGCATGAATGCATTCGATGTTTGAATAAATCAG
Found at i:2688 original size:19 final size:19
Alignment explanation
Indices: 2664--2714 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
2654 TAATTAAATC
2664 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
2683 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
2702 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
2715 TTTCAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:5368 original size:24 final size:23
Alignment explanation
Indices: 5297--5376 Score: 94
Period size: 24 Copynumber: 3.5 Consensus size: 23
5287 CATGGTCTTG
*
5297 TGCATCGATGCACATTCAAGGCA
1 TGCATCGATGCACATTCAAGGGA
* *
5320 TGCATCGGTG--CA-TCATGCGGA
1 TGCATCGATGCACATTCAAG-GGA
5341 TGCATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTC-AAGGGA
5365 TGCATCGATGCA
1 TGCATCGATGCA
5377 TTATTAAGTG
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
20 4 0.09
21 13 0.28
23 11 0.23
24 17 0.36
25 2 0.04
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.23
Consensus pattern (23 bp):
TGCATCGATGCACATTCAAGGGA
Found at i:5389 original size:44 final size:41
Alignment explanation
Indices: 5274--5381 Score: 117
Period size: 45 Copynumber: 2.5 Consensus size: 41
5264 AAAACCCGAC
*
5274 GGATGCATCGATGCATGGTCTTGTGCATCGATGCACATTCAAG
1 GGATGCATCGATGCAT--TATTGTGCATCGATGCACATTCAAG
* * * *
5317 GCATGCATCGGTGCATCATGCGGATGCATCGATGCACATTCAAAG
1 GGATGCATCGATGCATTAT--TG-TGCATCGATGCACATTC-AAG
5362 GGATGCATCGATGCATTATT
1 GGATGCATCGATGCATTATT
5382 AAGTGCATTG
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
41 1 0.02
43 15 0.29
44 17 0.33
45 19 0.37
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (41 bp):
GGATGCATCGATGCATTATTGTGCATCGATGCACATTCAAG
Found at i:11296 original size:64 final size:65
Alignment explanation
Indices: 11228--11391 Score: 197
Period size: 64 Copynumber: 2.5 Consensus size: 65
11218 AAATACCCTG
* * *
11228 GTGCATCGATGCATGGATTGTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATCA-GA
1 GTGCATCGATGCATGGATTGTGCATCGGTGCATCAAATGAATTCGATGTTTCAATTAAATCATGA
** ** * * *
11292 GTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGAATTTGATGTTTCAATTTATTCATTG
1 GTGCATCGATGCATGGATTGTGCATCGGTGCATCAAATGAATTCGATGTTTCAATTAAATCA-TG
11357 A
65 A
11358 -TGCATCGATGCATGGTATTGATGCATCGGTGCAT
1 GTGCATCGATGCATGG-ATTG-TGCATCGGTGCAT
11392 GCCTTTGAAA
Statistics
Matches: 84, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
64 52 0.62
65 15 0.18
66 4 0.05
67 13 0.15
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.34
Consensus pattern (65 bp):
GTGCATCGATGCATGGATTGTGCATCGGTGCATCAAATGAATTCGATGTTTCAATTAAATCATGA
Found at i:11313 original size:19 final size:19
Alignment explanation
Indices: 11289--11327 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
11279 TAATTAAATC
11289 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
11308 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
11327 A
1 A
11328 ATGAATTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.15, G:0.38, T:0.21
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:11379 original size:21 final size:21
Alignment explanation
Indices: 11353--11392 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
11343 CAATTTATTC
11353 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
11374 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
11393 CCTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:15583 original size:22 final size:22
Alignment explanation
Indices: 15558--15599 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
15548 CACCATATGC
*
15558 ACTAGGTATCCTTTAATGTTGT
1 ACTAAGTATCCTTTAATGTTGT
*
15580 ACTAAGTATCCTTTAGTGTT
1 ACTAAGTATCCTTTAATGTT
15600 AAACTGATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.24, C:0.14, G:0.17, T:0.45
Consensus pattern (22 bp):
ACTAAGTATCCTTTAATGTTGT
Found at i:23959 original size:37 final size:39
Alignment explanation
Indices: 23869--23972 Score: 124
Period size: 39 Copynumber: 2.7 Consensus size: 39
23859 TTATAATTAT
* * * * *
23869 ATTT-TTAACCTAATCACCATAATTAATATAGAGAGCAA
1 ATTTATTAATCTAATGATCATAATTAATATAGAAAACAA
*
23907 ATTTATTAATCTAATGATCATAATTGATATAGAAAAC-A
1 ATTTATTAATCTAATGATCATAATTAATATAGAAAACAA
*
23945 A-TTATTAATCTAATGATTATAATTAATA
1 ATTTATTAATCTAATGATCATAATTAATA
23973 ATTTATTTTA
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
37 25 0.44
38 6 0.11
39 26 0.46
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.38
Consensus pattern (39 bp):
ATTTATTAATCTAATGATCATAATTAATATAGAAAACAA
Found at i:28548 original size:30 final size:30
Alignment explanation
Indices: 28512--28625 Score: 219
Period size: 30 Copynumber: 3.8 Consensus size: 30
28502 TTGTCAATGT
*
28512 CTTAACATATTTGATATACCGAACTGAAGC
1 CTTAACATATTTGATATACCGAACCGAAGC
28542 CTTAACATATTTGATATACCGAACCGAAGC
1 CTTAACATATTTGATATACCGAACCGAAGC
28572 CTTAACATATTTGATATACCGAACCGAAGC
1 CTTAACATATTTGATATACCGAACCGAAGC
28602 CTTAACATATTTGATATACCGAAC
1 CTTAACATATTTGATATACCGAAC
28626 TGATGGGACT
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 83 1.00
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.29
Consensus pattern (30 bp):
CTTAACATATTTGATATACCGAACCGAAGC
Found at i:29499 original size:20 final size:20
Alignment explanation
Indices: 29474--29526 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
29464 TCCAAAGTAA
29474 GCAGTATCGATACTCTACTT
1 GCAGTATCGATACTCTACTT
29494 GCAGTATCGATACTCTACTT
1 GCAGTATCGATACTCTACTT
* *
29514 GAAGTGTCGATAC
1 GCAGTATCGATAC
29527 CCCTATGAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (20 bp):
GCAGTATCGATACTCTACTT
Found at i:40620 original size:2 final size:2
Alignment explanation
Indices: 40613--40644 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
40603 AAAATTACTC
40613 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40645 TAATATTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.