Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009043.1 Hibiscus syriacus cultivar Beakdansim tig00112453_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: 500226
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:461300 original size:21 final size:24
Alignment explanation
Indices: 461256--461548 Score: 88
Period size: 23 Copynumber: 13.0 Consensus size: 24
461246 GATAAGATGT
461256 CATAATTGAAATGAATATAGGTG-
1 CATAATTGAAATGAATATAGGTGC
* *
461279 CATTATTGACATGAA-A-AGGTGC
1 CATAATTGAAATGAATATAGGTGC
*
461301 CATAATTGAAATGCATAT-GGATG-
1 CATAATTGAAATGAATATAGG-TGC
** ** *
461324 CATTGTTGGCATGAA-AT-GATGC
1 CATAATTGAAATGAATATAGGTGC
* *
461346 CATAATTGAAATGCATATGGGTG-
1 CATAATTGAAATGAATATAGGTGC
** **
461369 CATTGTTGCCATG-A-A-AGGATGC
1 CATAATTGAAATGAATATAGG-TGC
*
461391 CATAATTGAAATGCATATAGGTG-
1 CATAATTGAAATGAATATAGGTGC
** ** * *
461414 CATTGTTGGCATGAA-AT-GATGA
1 CATAATTGAAATGAATATAGGTGC
* * *
461436 TATAATTGAAATGCATATGGGTG-
1 CATAATTGAAATGAATATAGGTGC
* **
461459 CATTATTGGCATG-A-A-AGGATGC
1 CATAATTGAAATGAATATAGG-TGC
* *
461481 CATAATTGAAATGCATATGGGTG-
1 CATAATTGAAATGAATATAGGTGC
* ** * *
461504 CATTATTGGCATGAA-AGA-ATGC
1 CATAATTGAAATGAATATAGGTGC
* *
461526 CATAATTGAAATGCATATGGGTG
1 CATAATTGAAATGAATATAGGTG
461549 TATTGTTGGC
Statistics
Matches: 185, Mismatches: 62, Indels: 45
0.63 0.21 0.15
Matches are distributed among these distances:
20 4 0.02
21 18 0.10
22 70 0.38
23 72 0.39
24 16 0.09
25 5 0.03
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (24 bp):
CATAATTGAAATGAATATAGGTGC
Found at i:461623 original size:22 final size:22
Alignment explanation
Indices: 461598--461668 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
461588 TGGGTGCATT
461598 ATTGGCATGAAATGATGTCATA
1 ATTGGCATGAAATGATGTCATA
** * * *
461620 ATTGAAATGCATATG-GGTGCATT
1 ATTGGCATG-AAATGATGT-CATA
*
461643 ATTGGCATGAAATGATGTTATA
1 ATTGGCATGAAATGATGTCATA
461665 ATTG
1 ATTG
461669 AAAATGCATA
Statistics
Matches: 35, Mismatches: 11, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
22 19 0.54
23 16 0.46
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.35
Consensus pattern (22 bp):
ATTGGCATGAAATGATGTCATA
Found at i:468921 original size:200 final size:198
Alignment explanation
Indices: 468362--468940 Score: 697
Period size: 200 Copynumber: 2.9 Consensus size: 198
468352 TCGATCGTTG
* * * * *
468362 GGCATTCATTCTGGAAAAAAGTATCGACACAAACTTAAAAAGTGTCAATACATTAT-TCAGACCT
1 GGCATTCATTCTGGACAAAAGTATCGACACAAACTTAACAAGTGTCGATACATTATGT-TGACAT
* * * * * *
468426 ATTTTCTCATAAAACTGGTATATTTCTATCGGGTACATTGTAAATTTACCTATCACATTGTAATG
65 ATTTTCTCATAAAACCGGTATATTTATATCGGTTACATTGTAAATTTACCTATTACATTATAATT
* * *
468491 ATCAGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATATATTGACACTTTATGCATGCACCT
130 ATAAGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCATGCACCT
*
468556 GTTT
195 ATTT
* * * * *
468560 GGCATTCATTATGGACAAAATGTATCGACACAAATTTAACAAGTGTCGATACTTTATGCTGACTT
1 GGCATTCATTCTGGACAAAA-GTATCGACACAAACTTAACAAGTGTCGATACATTATGTTGACAT
* * * * *
468625 ATTTTCTCATAAAACCGATATATCTATATCGGTTACATTGTAAATTTACATATTATA-TACAAAT
65 ATTTTCTCATAAAACCGGTATATTTATATCGGTTACATTGTAAATTTACCTATTACATTA-TAA-
* * *
468689 TTAAAAGTATCGAT-TTTATTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCA
128 TTATAAGTTTCGATGTTT-TTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCATGCA
468753 CCTCATTT
192 CCT-ATTT
468761 GGACATTCATTCTGGACAATAAGTATCGACACAAA-TTACACAAGTGTCGATACATTATGTTGAC
1 GG-CATTCATTCTGGACAA-AAGTATCGACACAAACTTA-ACAAGTGTCGATACATTATGTTGAC
* *
468825 ATATTTTCT-A-AATAACCGGTATATTTATA-CTGGTTGCATTGTTAATTTACCTATTACATTAT
63 ATATTTTCTCATAA-AACCGGTATATTTATATC-GGTTACATTGTAAATTTACCTATTACATTAT
** *
468887 AATTATTGGTTTCGATGTTTTTGGGGTCGATACTTTTAGA-AAATGTATCGACAC
126 AATTATAAGTTTCGATGTTTTTGGGATCGATACTTTTA-ATAAATGTATCGACAC
468941 ATATTTAGGT
Statistics
Matches: 324, Mismatches: 43, Indels: 26
0.82 0.11 0.07
Matches are distributed among these distances:
198 19 0.06
199 90 0.28
200 100 0.31
201 52 0.16
202 61 0.19
203 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.38
Consensus pattern (198 bp):
GGCATTCATTCTGGACAAAAGTATCGACACAAACTTAACAAGTGTCGATACATTATGTTGACATA
TTTTCTCATAAAACCGGTATATTTATATCGGTTACATTGTAAATTTACCTATTACATTATAATTA
TAAGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCATGCACCTA
TTT
Found at i:471465 original size:19 final size:19
Alignment explanation
Indices: 471420--471468 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
471410 TTACATTCAC
471420 ATACAAAATTATAAATCAT
1 ATACAAAATTATAAATCAT
** *
471439 ATGTAAAATTATAAATCTT
1 ATACAAAATTATAAATCAT
471458 ATACAAAATTA
1 ATACAAAATTA
471469 ACCCTACGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.35
Consensus pattern (19 bp):
ATACAAAATTATAAATCAT
Found at i:474001 original size:58 final size:58
Alignment explanation
Indices: 473932--474075 Score: 261
Period size: 58 Copynumber: 2.5 Consensus size: 58
473922 CATTTATACA
* *
473932 ACCTATAATATCATTTTCTACCTATAATATTTAATAAAAGTATCGATATTTATATTTT
1 ACCTAGAATATCACTTTCTACCTATAATATTTAATAAAAGTATCGATATTTATATTTT
473990 ACCTAGAATATCACTTTCTACCTATAATATTTAATAAAAGTATCGATATTTATATTTT
1 ACCTAGAATATCACTTTCTACCTATAATATTTAATAAAAGTATCGATATTTATATTTT
*
474048 ACCTAGAATATCACTTTCTACCTGTAAT
1 ACCTAGAATATCACTTTCTACCTATAAT
474076 CGGTCTCAAA
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 83 1.00
ACGTcount: A:0.37, C:0.15, G:0.05, T:0.43
Consensus pattern (58 bp):
ACCTAGAATATCACTTTCTACCTATAATATTTAATAAAAGTATCGATATTTATATTTT
Found at i:474720 original size:20 final size:20
Alignment explanation
Indices: 474670--474720 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
474660 GTCGCTCTAT
*
474670 ACCGATTTTATCCTTTAGAG
1 ACCGATTTTGTCCTTTAGAG
*
474690 ACCG-GTTTGTCCTTTAGAG
1 ACCGATTTTGTCCTTTAGAG
474709 ACCGATTTTGTC
1 ACCGATTTTGTC
474721 ATATTTTTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.39
Consensus pattern (20 bp):
ACCGATTTTGTCCTTTAGAG
Found at i:475009 original size:182 final size:180
Alignment explanation
Indices: 474690--475048 Score: 556
Period size: 182 Copynumber: 2.0 Consensus size: 180
474680 TCCTTTAGAG
* ** * *
474690 ACCGGTTTGTCCTTTAGAGACCGATTTTGTCATATTTTTACCTGTTATATTATTTTGGATCGATA
1 ACCGGTTTGTCCTTTAGAGACCGATTTTATCATATTTTTAAATGTTATATCATTGTGGATCGATA
** * *
474755 CATTGTTATAAAGTATCGACACTTTATGGGCGCTAAAACTGCTTCTCTTTTAAATTCATAAAGTG
66 CATTGTTATAAAGTATCGACACTTTATAAGCGCTAAAACTACTTCTCTTTTAAATTCACAAAGTG
*
474820 TCGATACTTATATTAAAGTATAGATACTTTCAATATATCTGGTCGCTCTAT
131 TCGATACTTATATTAAAGTATAGACACTTTCAATATAT-TGGTCGCTCTAT
* * *
474871 ACCGGTTTTGTCTTTTAGAGACCGGTTTTATCATATTTTTAAATGTTATATCGTTGTGGATCGAT
1 ACCGG-TTTGTCCTTTAGAGACCGATTTTATCATATTTTTAAATGTTATATCATTGTGGATCGAT
*
474936 ACATTGTTATAAAGTATCGACACTTTATAAGCGCTAAAATTACTTCTCTTTTAAATTCACAAAGT
65 ACATTGTTATAAAGTATCGACACTTTATAAGCGCTAAAACTACTTCTCTTTTAAATTCACAAAGT
* *
475001 GTCGATACTTATATTAAAGTATCGACACTTTCTATATATTGGTCGCTC
130 GTCGATACTTATATTAAAGTATAGACACTTTCAATATATTGGTCGCTC
475049 CGGTTTTGTC
Statistics
Matches: 161, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
181 14 0.09
182 147 0.91
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (180 bp):
ACCGGTTTGTCCTTTAGAGACCGATTTTATCATATTTTTAAATGTTATATCATTGTGGATCGATA
CATTGTTATAAAGTATCGACACTTTATAAGCGCTAAAACTACTTCTCTTTTAAATTCACAAAGTG
TCGATACTTATATTAAAGTATAGACACTTTCAATATATTGGTCGCTCTAT
Found at i:481015 original size:18 final size:17
Alignment explanation
Indices: 480966--481016 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
480956 ATAATTAAAT
480966 TTATAATATTTTAACAAA
1 TTATAATATTTTAA-AAA
* **
480984 TTAAAATAAATTAAAAA
1 TTATAATATTTTAAAAA
481001 TTATAATGATTTTAAA
1 TTATAAT-ATTTTAAA
481017 TTTTCAGACA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
17 9 0.35
18 17 0.65
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (17 bp):
TTATAATATTTTAAAAA
Found at i:482926 original size:31 final size:31
Alignment explanation
Indices: 482889--482956 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
482879 CAAGTGACTT
* * *
482889 AACTTAATAAAACGATAATGTAAGTGACCAA
1 AACTTAATAAAACAATAACGCAAGTGACCAA
*
482920 AACTTAATGAAACAATAACGCAAGTGACCAA
1 AACTTAATAAAACAATAACGCAAGTGACCAA
482951 AACTTA
1 AACTTA
482957 TATTTTTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.51, C:0.16, G:0.12, T:0.21
Consensus pattern (31 bp):
AACTTAATAAAACAATAACGCAAGTGACCAA
Found at i:484530 original size:15 final size:16
Alignment explanation
Indices: 484510--484542 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
484500 CATTTGTTAG
484510 TAATG-AATAATTTTT
1 TAATGAAATAATTTTT
484525 TAATGAAATAATTTTT
1 TAATGAAATAATTTTT
484541 TA
1 TA
484543 GGATATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (16 bp):
TAATGAAATAATTTTT
Found at i:489833 original size:21 final size:21
Alignment explanation
Indices: 489803--489850 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
489793 GCAAGGGTAC
* *
489803 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
*
489824 ATGCCAAGCCCACCAGTTCAT
1 ATGCCAAGCCCACCACTTCAT
489845 ATGCCA
1 ATGCCA
489851 TCTCCGCAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.25, C:0.42, G:0.12, T:0.21
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:489880 original size:21 final size:21
Alignment explanation
Indices: 489854--489947 Score: 118
Period size: 21 Copynumber: 4.5 Consensus size: 21
489844 TATGCCATCT
489854 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
*
489875 CCGCAGGGTTACATTTCGAGC
1 CCGCAGGGTTACATTCCGAGC
**
489896 CCGCAGGGTTACATTCATAGC
1 CCGCAGGGTTACATTCCGAGC
* *
489917 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCGAGC
*
489938 CCGTAGGGTT
1 CCGCAGGGTT
489948 TTATACTATA
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
20 1 0.02
21 61 0.95
22 2 0.03
ACGTcount: A:0.19, C:0.31, G:0.28, T:0.22
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCGAGC
Found at i:490573 original size:34 final size:34
Alignment explanation
Indices: 490468--490574 Score: 151
Period size: 34 Copynumber: 3.1 Consensus size: 34
490458 ATAAATGTTT
*
490468 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAAA
* * *
490502 TAAAAATAAAAATAATATTATTTGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAAA
* * *
490536 TTAAAATATAAATTATAGTATTCGAAATTTAACA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAAA
490570 TTAAA
1 TTAAA
490575 TTTCAACTTA
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 63 1.00
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (34 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAAA
Found at i:491198 original size:128 final size:128
Alignment explanation
Indices: 490970--491576 Score: 1097
Period size: 128 Copynumber: 4.7 Consensus size: 128
490960 ACAATCCATC
490970 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*
491035 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCACTGAGAAATAATAGGTACTGATATGAA
*
491098 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTTTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* * *
491163 GGAAGGCGAGCCCCCGGGAATGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCACTGAGAAATAATAGGTACTGATATGAA
* * *
491226 CAGTGTCCCTGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTTTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
491291 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCACTGAGAAATAATAGGTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCACTGAGAAATAATAGGTACTGATATGAA
491354 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*
491419 GGAAGGCGCGCCCCCGGGAATGCGCCTTCAAGTCCACTGAGAAATAATAGGTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCACTGAGAAATAATAGGTACTGATATGAA
*
491482 TAGTGTCCCCGAGGGACATGAGTGATATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* * *
491547 GGAAGACGCGTCCCCGGGAACACGCCTTCA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCA
491577 TATGAATAGT
Statistics
Matches: 462, Mismatches: 17, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
128 462 1.00
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (128 bp):
TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCACTGAGAAATAATAGGTACTGATATGAA
Found at i:491670 original size:8 final size:8
Alignment explanation
Indices: 491657--491697 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
491647 TCACAAGCTT
491657 TCAAATTC
1 TCAAATTC
491665 TCAAATTC
1 TCAAATTC
* *
491673 CCAAACTC
1 TCAAATTC
491681 T-AAATTC
1 TCAAATTC
491688 TCAAATTC
1 TCAAATTC
491696 TC
1 TC
491698 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:495923 original size:26 final size:26
Alignment explanation
Indices: 495887--495940 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
495877 CTTCCCACCG
495887 TTGCCTTCTGCGTGGGATTGCTTTTT
1 TTGCCTTCTGCGTGGGATTGCTTTTT
495913 TTGCCTTCTGCGTGGGATTGCTTTTT
1 TTGCCTTCTGCGTGGGATTGCTTTTT
495939 TT
1 TT
495941 TAACCTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.04, C:0.19, G:0.26, T:0.52
Consensus pattern (26 bp):
TTGCCTTCTGCGTGGGATTGCTTTTT
Found at i:497956 original size:46 final size:46
Alignment explanation
Indices: 497902--497994 Score: 168
Period size: 46 Copynumber: 2.0 Consensus size: 46
497892 TTAGAGTGGT
497902 TCAACTTCTTCAATGAAGTCTACATCTACTACCTTAGAATACGCAC
1 TCAACTTCTTCAATGAAGTCTACATCTACTACCTTAGAATACGCAC
* *
497948 TCAACTTCTTCAATGAAGTCTACATCTACTACCTTAGATTCCGCAC
1 TCAACTTCTTCAATGAAGTCTACATCTACTACCTTAGAATACGCAC
497994 T
1 T
497995 AAGGATTTCA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.30, C:0.29, G:0.09, T:0.32
Consensus pattern (46 bp):
TCAACTTCTTCAATGAAGTCTACATCTACTACCTTAGAATACGCAC
Done.