Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001875.1 Hibiscus syriacus cultivar Beakdansim tig00003802_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: 58781
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:2512 original size:18 final size:18
Alignment explanation
Indices: 2489--2529 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
2479 ATAAATGTTG
2489 TTTTAATTATTATTAATA
1 TTTTAATTATTATTAATA
*
2507 TTTTAATTATTATTAATT
1 TTTTAATTATTATTAATA
2525 TTTTA
1 TTTTA
2530 CTGCTATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTAATTATTATTAATA
Found at i:6393 original size:15 final size:15
Alignment explanation
Indices: 6373--6404 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
6363 TATAAAATTT
*
6373 TAAAAATAAAATAAA
1 TAAAAATAAAACAAA
6388 TAAAAATAAAACAAA
1 TAAAAATAAAACAAA
6403 TA
1 TA
6405 TAGATTTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (15 bp):
TAAAAATAAAACAAA
Found at i:8142 original size:12 final size:12
Alignment explanation
Indices: 8125--8149 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
8115 TTTAGATAAA
8125 AAATAATTTTTT
1 AAATAATTTTTT
8137 AAATAATTTTTT
1 AAATAATTTTTT
8149 A
1 A
8150 TCAAAATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
AAATAATTTTTT
Found at i:8951 original size:30 final size:30
Alignment explanation
Indices: 8915--8972 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
8905 TTTTATTAAA
8915 TTTTAAAATATTGTAAATTTAATCATTTAG
1 TTTTAAAATATTGTAAATTTAATCATTTAG
* * * *
8945 TTTTAAATTATTTTTATTTTAATCATTT
1 TTTTAAAATATTGTAAATTTAATCATTT
8973 TGATCGATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (30 bp):
TTTTAAAATATTGTAAATTTAATCATTTAG
Found at i:17560 original size:93 final size:92
Alignment explanation
Indices: 17396--17568 Score: 328
Period size: 93 Copynumber: 1.9 Consensus size: 92
17386 AAGCAAATAG
17396 TCTATCAAAAGAGGAAAAACCTGAGGTGGTGAAGTAAATGATCAGATTCCAGTGGATAATAGCTC
1 TCTATCAAAAGAGGAAAAACCTGAGGTGGTGAAGTAAATGATCAGATTCCAGTGGATAATAGCTC
*
17461 AGAAGATGATAAACTGGAAGTGAATGA
66 AGAAGATGACAAACTGGAAGTGAATGA
17488 TCTATCAAAAGAGGAAAAACCTGAGGTGGTGGAAGTAAATGATCAGATTCCAGTGGATAATAGCT
1 TCTATCAAAAGAGGAAAAACCTGAGGTGGT-GAAGTAAATGATCAGATTCCAGTGGATAATAGCT
17553 CAGAAGATGACAAACT
65 CAGAAGATGACAAACT
17569 TAGCTCATTA
Statistics
Matches: 79, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
92 30 0.38
93 49 0.62
ACGTcount: A:0.41, C:0.12, G:0.25, T:0.21
Consensus pattern (92 bp):
TCTATCAAAAGAGGAAAAACCTGAGGTGGTGAAGTAAATGATCAGATTCCAGTGGATAATAGCTC
AGAAGATGACAAACTGGAAGTGAATGA
Found at i:19325 original size:26 final size:24
Alignment explanation
Indices: 19263--19325 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
19253 CATTTTCATC
19263 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
19287 AAAATATAT-TTATTAATAT-TTAT
1 AAAATATATATTATTAAAATATT-T
19310 AATAATATAATATTAT
1 AA-AATAT-ATATTAT
19326 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 12 0.36
25 3 0.09
26 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:19327 original size:22 final size:23
Alignment explanation
Indices: 19280--19340 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 23
19270 TAATTATTAA
* *
19280 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
19301 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
* *
19324 -ATATTTTTAATATTATA
1 AATATTTATAATAATATA
19341 TAAAATAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 11 0.32
22 19 0.56
23 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:19336 original size:31 final size:31
Alignment explanation
Indices: 19291--19369 Score: 90
Period size: 31 Copynumber: 2.5 Consensus size: 31
19281 ATATTTAAAA
*
19291 TATATTTATTAATATTTATAATAATATAAT-AT
1 TATATTT-TTAATATTTAT-ATAAAATAATAAT
19323 TATATTTTTAATA-TTATATAAAATAATCAAT
1 TATATTTTTAATATTTATATAAAATAAT-AAT
19354 TATATTATTATAATAT
1 TATATT-TT-TAATAT
19370 AAGATATTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
29 9 0.22
30 4 0.10
31 14 0.34
32 9 0.22
33 5 0.12
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (31 bp):
TATATTTTTAATATTTATATAAAATAATAAT
Found at i:19400 original size:24 final size:23
Alignment explanation
Indices: 19368--19414 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
19358 TTATTATAAT
* *
19368 ATAAGATATTATATTTTTATTTTA
1 ATAAGATATAATAATTTT-TTTTA
*
19392 ATAATATATAATAATTTTTTTTA
1 ATAAGATATAATAATTTTTTTTA
19415 TATATTTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
ATAAGATATAATAATTTTTTTTA
Found at i:19424 original size:28 final size:28
Alignment explanation
Indices: 19393--19456 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 28
19383 TTTATTTTAA
* *
19393 TAATATAT-AATAATTTTTTTTATATATT
1 TAATA-ATGAATAATATTATTTATATATT
19421 TAATAATGAATAATATTATTTATATATT
1 TAATAATGAATAATATTATTTATATATT
19449 TCAATAAT
1 T-AATAAT
19457 ATTTTAGTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
27 2 0.06
28 24 0.75
29 6 0.19
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (28 bp):
TAATAATGAATAATATTATTTATATATT
Found at i:19701 original size:20 final size:20
Alignment explanation
Indices: 19623--19692 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
19613 TTTCCAGATG
19623 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
19643 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
19663 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
19683 TTTTCCAGAA
1 TTTTCCAGAA
19693 TTCAAATTCT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:19701 original size:40 final size:40
Alignment explanation
Indices: 19623--19701 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
19613 TTTCCAGATG
* **
19623 TTTTCCAGAAATGTAATTCATTTTCCAGAAATGTAATTCA
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
*
19663 TTTTACAGAAATGTAATTCATTTTCCAGAATTCAAATTC
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTC
19702 TAGTAATTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (40 bp):
TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
Found at i:19711 original size:15 final size:15
Alignment explanation
Indices: 19675--19741 Score: 82
Period size: 15 Copynumber: 4.5 Consensus size: 15
19665 TTACAGAAAT
**
19675 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
*
19690 G-AATTCAAATTCTA
1 GTAATTCAAATTCCA
**
19704 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
19719 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
19734 GTAATTCA
1 GTAATTCA
19742 TTTTCTGAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
14 11 0.26
15 32 0.74
ACGTcount: A:0.34, C:0.18, G:0.07, T:0.40
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:19717 original size:29 final size:30
Alignment explanation
Indices: 19675--19746 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
19665 TTACAGAAAT
*
19675 GTAATTCATTTTCCAG-AATTCAAATTCTA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
19704 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
19734 GTAATTCATTTTC
1 GTAATTCATTTTC
19747 TGAAAAACCA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
29 16 0.39
30 25 0.61
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.43
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:20582 original size:2 final size:2
Alignment explanation
Indices: 20575--20599 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20565 TTGAATGAAC
20575 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
20600 GTATCTAGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29228 original size:12 final size:11
Alignment explanation
Indices: 29211--29294 Score: 78
Period size: 12 Copynumber: 7.1 Consensus size: 11
29201 GTAAATGAAC
29211 TTATAAACGAG
1 TTATAAACGAG
*
29222 TTGATAAATGAG
1 TT-ATAAACGAG
29234 CTTATAAACGAG
1 -TTATAAACGAG
*
29246 TTGATAAATGAG
1 TT-ATAAACGAG
*
29258 CTTATAAACGAA
1 -TTATAAACGAG
*
29270 TTGATAAATGAG
1 TT-ATAAACGAG
29282 CTTATAAACGAG
1 -TTATAAACGAG
29294 T
1 T
29295 CAATAAATGA
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
11 7 0.12
12 46 0.78
13 6 0.10
ACGTcount: A:0.43, C:0.08, G:0.19, T:0.30
Consensus pattern (11 bp):
TTATAAACGAG
Found at i:29230 original size:24 final size:24
Alignment explanation
Indices: 29202--29305 Score: 172
Period size: 24 Copynumber: 4.3 Consensus size: 24
29192 TAAAACCGAG
*
29202 TAAATGAACTTATAAACGAGTTGA
1 TAAATGAGCTTATAAACGAGTTGA
29226 TAAATGAGCTTATAAACGAGTTGA
1 TAAATGAGCTTATAAACGAGTTGA
*
29250 TAAATGAGCTTATAAACGAATTGA
1 TAAATGAGCTTATAAACGAGTTGA
**
29274 TAAATGAGCTTATAAACGAGTCAA
1 TAAATGAGCTTATAAACGAGTTGA
29298 TAAATGAG
1 TAAATGAG
29306 ATTGTTGTGA
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 75 1.00
ACGTcount: A:0.45, C:0.09, G:0.18, T:0.28
Consensus pattern (24 bp):
TAAATGAGCTTATAAACGAGTTGA
Found at i:30084 original size:6 final size:6
Alignment explanation
Indices: 30073--30097 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
30063 GACACGTATT
30073 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
30098 GACGGGACGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:33512 original size:22 final size:22
Alignment explanation
Indices: 33468--33513 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
33458 TTTTTAAATT
*
33468 AAAATTCATATTTTTATATAAA
1 AAAATTCATATTTTTATAAAAA
* *
33490 AAAATTCCTATTTTT-CAAAAA
1 AAAATTCATATTTTTATAAAAA
33511 AAA
1 AAA
33514 CCCAAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAATTCATATTTTTATAAAAA
Found at i:35622 original size:13 final size:14
Alignment explanation
Indices: 35596--35624 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
35586 CCGCATTTTC
35596 TAAAATATTTTATT
1 TAAAATATTTTATT
35610 TAAAATA-TTTATT
1 TAAAATATTTTATT
35623 TA
1 TA
35625 TTTTAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TAAAATATTTTATT
Found at i:35923 original size:7 final size:7
Alignment explanation
Indices: 35911--35940 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
35901 TAATCTATCT
35911 ATACTAA
1 ATACTAA
35918 ATACTAA
1 ATACTAA
35925 ATACTAA
1 ATACTAA
*
35932 ATACAAA
1 ATACTAA
35939 AT
1 AT
35941 TTATTTCGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.27
Consensus pattern (7 bp):
ATACTAA
Found at i:37032 original size:21 final size:21
Alignment explanation
Indices: 36987--37033 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
36977 TATTTTAATA
* *
36987 TATAAAAATATCAAATTAAAT
1 TATAAAAATATCAAATAAAAC
37008 TATAAAAATAT-AAATAACAAC
1 TATAAAAATATCAAATAA-AAC
37029 TATAA
1 TATAA
37034 TTATAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (21 bp):
TATAAAAATATCAAATAAAAC
Found at i:53562 original size:2 final size:2
Alignment explanation
Indices: 53555--53584 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
53545 TACCTAAATG
53555 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
53585 TAAGTAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.