Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001076.1 Hibiscus syriacus cultivar Beakdansim tig00002131_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: 85692
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:2383 original size:16 final size:14
Alignment explanation
Indices: 2358--2396 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 14
2348 TTTACTTAAG
2358 TTAATATTTAATATTT
1 TTAAT-TTTAAT-TTT
2374 TTATATTTTAATTTT
1 TTA-ATTTTAATTTT
2389 TTAATTTT
1 TTAATTTT
2397 TTACTCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 5 0.23
15 6 0.27
16 9 0.41
17 2 0.09
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTAATTTTAATTTT
Found at i:2399 original size:16 final size:16
Alignment explanation
Indices: 2364--2396 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2354 TAAGTTAATA
2364 TTTAATATTTTTATAT
1 TTTAATATTTTTATAT
2380 TTTAAT-TTTTTA-AT
1 TTTAATATTTTTATAT
2394 TTT
1 TTT
2397 TTACTCTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 6 0.35
16 6 0.35
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTAATATTTTTATAT
Found at i:2820 original size:2 final size:2
Alignment explanation
Indices: 2813--2838 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2803 ATTTTATCCC
2813 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
2839 ATCATGTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3612 original size:423 final size:416
Alignment explanation
Indices: 2825--4063 Score: 1898
Period size: 423 Copynumber: 3.0 Consensus size: 416
2815 TATATATATA
* *
2825 TATATATATATATAATCATGTCTCTTAAAAAGAATGCCCACGGACTAGGTCAATCTAGTGCTCAA
1 TATATATATATATATTCATGTCTCTTAAAAAGAATGCCCATGGACTAGGTCAATCTAGTGCTCAA
*
2890 ATTTTTAAAAAATTCCAGGCCCAGGCCTATTCAAATTATCCAGCTCTTTTTTTTATCGTCAATAC
66 ATTTTTAAAAAA-T-CAGGCCCAGGCCTATTCAAATTATCCATCTCTTTTTTTTATCGTCAATAC
2955 ATGAATAAATTAGCCCATGGGTTAAAAAACTTTATTCATATTTAGAGTGGGCCTAGAGCCGTAAA
129 ATGAATAAATTAGCCCATGGGTTAAAAAACTTTATTCATATTTAGAGTGGGCCTAGAGCCGTAAA
*
3020 TGAGTCGTGTCGAGCTTGACTTAAATCAAAAACTTTAAAATTAAGTTCGATTCAACTCGAAAACT
194 TGAGTCGTGTCGAGCTTGACTTAAATCAAAAACTTTAAAATTAACTTCGATTCAACTCGAAAACT
*
3085 TACAAGCTTAAAATTGTCAAGCTCTACTCGATCTCGAAATAAAAAATTAAAGCTCGAATCGACTT
259 TGCAAGCTTAAAATTGTCAAGCTCTACTCGATCTCGAAATAAAAAATTAAAGCTCGAATCGACTT
3150 GAAAGCTCATAAGCTTAAAATTTTGAAGCTCCACTCGAAATAAAAAAAATAAGTTCGACTCAATC
324 GAAAGCTCATAAGCTTAAAATTTTGAAGCTCCACTCGAAATAAAAAAAATAAGTTCGACTCAATC
3215 TCGAACCCAAACATTAAATACGTAACAGACATG
389 TCGAACCCAAACATTAAATACGT-A-A-A-A-G
3248 TTATATATATATATATTTCATGTCTCTTAAAAAGAATGCCCATGGACTAGGTCAATCTAGTGCTC
1 -TATATATATATATA-TTCATGTCTCTTAAAAAGAATGCCCATGGACTAGGTCAATCTAGTGCTC
3313 AAATTTTTTAAAAAATCAGGCCCAGGCCTATTCAAATTATCCATCTCTTTTTTTTATCGTCAATA
64 AAA-TTTTTAAAAAATCAGGCCCAGGCCTATTCAAATTATCCATCTCTTTTTTTTATCGTCAATA
3378 CATGAATAAA-TAGCCCATGGGTTAAAAAACTTTATTCATATTTAGAGTGGGCCTAGAGCCGTAA
128 CATGAATAAATTAGCCCATGGGTTAAAAAACTTTATTCATATTTAGAGTGGGCCTAGAGCCGTAA
*
3442 ATGAGTCGTGTCGAGCTTGACTTAAATCAAAAACTTTAAAATTAATTTCGATTCAACTCGAAAAC
193 ATGAGTCGTGTCGAGCTTGACTTAAATCAAAAACTTTAAAATTAACTTCGATTCAACTCGAAAAC
*
3507 TTGCAAGTTTAAAATTGTCAAGCTCTACTCGATCTCGAAATAAAAAATTAAAGCTCGAATCGACT
258 TTGCAAGCTTAAAATTGTCAAGCTCTACTCGATCTCGAAATAAAAAATTAAAGCTCGAATCGACT
*
3572 TGAAAGCTTATAAGCTTAAAATTTTGAAGCTCCACTCGAAATAAAAAAAAAAATTAAGTTCGACT
323 TGAAAGCTCATAAGCTTAAAATTTTGAAGCTCCACTCGAAAT---AAAAAAAA-TAAGTTCGACT
* *
3637 CAATCTCGAACACAAACATTAAATATGTAAAAG
384 CAATCTCGAACCCAAACATTAAATACGTAAAAG
* * *
3670 -ACATAT-TGTATA-T-A-------T--AAAGAATGCCAATGGACTAGGTCAATCTAGTGCTCAA
1 TATATATATATATATTCATGTCTCTTAAAAAGAATGCCCATGGACTAGGTCAATCTAGTGCTCAA
* *
3722 ATTTTTAGAAAATTCAGGCCCAGGCCTATTCAAATTATCCATCTCTTTTTTTTATTGTCAATACA
66 ATTTTTA-AAAAATCAGGCCCAGGCCTATTCAAATTATCCATCTCTTTTTTTTATCGTCAATACA
* * *
3787 TTAATAAATTAGCCCATGGGTTAAAAAACTTTATTCATATTTAGTGTGGGCCTAGAGCCGTAAAC
130 TGAATAAATTAGCCCATGGGTTAAAAAACTTTATTCATATTTAGAGTGGGCCTAGAGCCGTAAAT
* * * ** * * *
3852 GAGTTGTGTTGAGCTCGACCCAAATCAAAAACATTAAAATTAAACTT-GATT-AACTTGAAAACA
195 GAGTCGTGTCGAGCTTGACTTAAATCAAAAACTTTAAAATT-AACTTCGATTCAACTCGAAAACT
* * * *
3915 TGCAAGCTTAAAATTATCAAGCTCTATTTGATCTCGAAATAAAAAAATTAAAGCTCGACTCGACT
259 TGCAAGCTTAAAATTGTCAAGCTCTACTCGATCTCGAAAT-AAAAAATTAAAGCTCGAATCGACT
* * * *
3980 TGAAAGCTCATAAGCTTAAAATTTTCAAACTCCACTCGAAATAAAAAAATTAAGCTCGACTCAAT
323 TGAAAGCTCATAAGCTTAAAATTTTGAAGCTCCACTCGAAATAAAAAAAATAAGTTCGACTCAAT
*
4045 CTCGAACCCAAACCTTAAA
388 CTCGAACCCAAACATTAAA
4064 CACATGAAAG
Statistics
Matches: 767, Mismatches: 38, Indels: 40
0.91 0.04 0.05
Matches are distributed among these distances:
404 31 0.04
405 7 0.01
406 6 0.01
407 145 0.19
408 155 0.20
409 5 0.01
416 1 0.00
417 1 0.00
419 5 0.01
420 5 0.01
422 1 0.00
423 223 0.29
424 73 0.10
425 52 0.07
426 20 0.03
427 37 0.05
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.30
Consensus pattern (416 bp):
TATATATATATATATTCATGTCTCTTAAAAAGAATGCCCATGGACTAGGTCAATCTAGTGCTCAA
ATTTTTAAAAAATCAGGCCCAGGCCTATTCAAATTATCCATCTCTTTTTTTTATCGTCAATACAT
GAATAAATTAGCCCATGGGTTAAAAAACTTTATTCATATTTAGAGTGGGCCTAGAGCCGTAAATG
AGTCGTGTCGAGCTTGACTTAAATCAAAAACTTTAAAATTAACTTCGATTCAACTCGAAAACTTG
CAAGCTTAAAATTGTCAAGCTCTACTCGATCTCGAAATAAAAAATTAAAGCTCGAATCGACTTGA
AAGCTCATAAGCTTAAAATTTTGAAGCTCCACTCGAAATAAAAAAAATAAGTTCGACTCAATCTC
GAACCCAAACATTAAATACGTAAAAG
Found at i:5842 original size:2 final size:2
Alignment explanation
Indices: 5835--5861 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5825 ACTTTTATTC
5835 AT 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 AT A
5862 ATTATTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15115 original size:2 final size:2
Alignment explanation
Indices: 15108--15138 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
15098 AAAATGTGAA
15108 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15139 GGTTAGAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:30817 original size:56 final size:56
Alignment explanation
Indices: 30749--30862 Score: 183
Period size: 56 Copynumber: 2.0 Consensus size: 56
30739 TTTCCTCGAT
* * *
30749 CAGGTAGGTTTAAATATAATATTTATTTCATAGAAAAATACCTTAAATAAATTTAA
1 CAGGTAAGTTTAAATATAATATTAATTTCATAGAAAAATACCTCAAATAAATTTAA
* *
30805 CAGGTAAGTTTAAATATAATATTAATTTCATCGAAAAATACCTCAAATAGATTTAA
1 CAGGTAAGTTTAAATATAATATTAATTTCATAGAAAAATACCTCAAATAAATTTAA
30861 CA
1 CA
30863 TGGGACTTTC
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.46, C:0.10, G:0.09, T:0.35
Consensus pattern (56 bp):
CAGGTAAGTTTAAATATAATATTAATTTCATAGAAAAATACCTCAAATAAATTTAA
Found at i:32417 original size:25 final size:24
Alignment explanation
Indices: 32389--32439 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
32379 TCTATCGATG
* *
32389 TATAATTTTGAACCTCTTGAAATTT
1 TATAATTTCGAA-CTCCTGAAATTT
*
32414 TATAATTTCGTACTCCTGAAATTT
1 TATAATTTCGAACTCCTGAAATTT
32438 TA
1 TA
32440 ATATAACTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (24 bp):
TATAATTTCGAACTCCTGAAATTT
Found at i:35851 original size:15 final size:15
Alignment explanation
Indices: 35831--35860 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
35821 AAATCCTTTT
35831 TTTTATTAAAAAATA
1 TTTTATTAAAAAATA
*
35846 TTTTATTATAAAATA
1 TTTTATTAAAAAATA
35861 CTTGTATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTTATTAAAAAATA
Found at i:46576 original size:33 final size:33
Alignment explanation
Indices: 46537--46613 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 33
46527 AATTCTCATC
* *
46537 ATTTTATTTGGGTATGTAAATCTACGAGTATTT
1 ATTTTATTTGGGTATGTAAATATACGAGTAATT
*
46570 ATTTTATTTGGGTATGTAAATATAGGAGTAATT
1 ATTTTATTTGGGTATGTAAATATACGAGTAATT
* *
46603 ACTTCATTTGG
1 ATTTTATTTGG
46614 TAAGCATGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.29, C:0.05, G:0.19, T:0.47
Consensus pattern (33 bp):
ATTTTATTTGGGTATGTAAATATACGAGTAATT
Found at i:46952 original size:31 final size:30
Alignment explanation
Indices: 46881--46952 Score: 90
Period size: 31 Copynumber: 2.4 Consensus size: 30
46871 TTTGGTAAAT
*
46881 AAGTTCTCAAATGATACAAAATAATCATCA
1 AAGTTATCAAATGATACAAAATAATCATCA
* * * *
46911 AAATTTTCAAATGATTACAAAATAGTCATTA
1 AAGTTATCAAATGA-TACAAAATAATCATCA
46942 AAGTTATCAAA
1 AAGTTATCAAA
46953 CTATGATGTG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
30 12 0.34
31 23 0.66
ACGTcount: A:0.50, C:0.12, G:0.07, T:0.31
Consensus pattern (30 bp):
AAGTTATCAAATGATACAAAATAATCATCA
Found at i:47005 original size:21 final size:22
Alignment explanation
Indices: 46980--47020 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
46970 AATTTTATAA
46980 CATTTTAATAA-ATT-TAATGGT
1 CATTTT-ATAATATTGTAATGGT
47001 CATTTTATAATATTGTAATG
1 CATTTTATAATATTGTAATG
47021 TTTTTTTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 9 0.50
22 5 0.28
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.49
Consensus pattern (22 bp):
CATTTTATAATATTGTAATGGT
Found at i:67323 original size:30 final size:30
Alignment explanation
Indices: 67282--67362 Score: 94
Period size: 30 Copynumber: 2.7 Consensus size: 30
67272 TTGATCTCTA
67282 AATTTTA-ATAAAATATTAACTTAACTT-TG
1 AATTTTAGATAAAATATTAACTTAA-TTATG
* * *
67311 ATTTTTAGATAAAATACTAATTTAATTCATG
1 AATTTTAGATAAAATATTAACTTAATT-ATG
67342 AATTTTAGATAAAAATATTAA
1 AATTTTAGAT-AAAATATTAA
67363 TATCATCCCT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
29 8 0.19
30 15 0.35
31 11 0.26
32 9 0.21
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (30 bp):
AATTTTAGATAAAATATTAACTTAATTATG
Found at i:68838 original size:23 final size:23
Alignment explanation
Indices: 68812--68872 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
68802 TAAACGGGAT
*
68812 TTAAATGAAAATGTTTACAAACG
1 TTAAATGAAAATGTTTACAAACA
**
68835 TTAAAT-AAATATGTTTATGAACA
1 TTAAATGAAA-ATGTTTACAAACA
*
68858 TTAAATGAACATGTT
1 TTAAATGAAAATGTT
68873 AGCACACGCT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 3 0.09
23 27 0.84
24 2 0.06
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.36
Consensus pattern (23 bp):
TTAAATGAAAATGTTTACAAACA
Found at i:69243 original size:30 final size:31
Alignment explanation
Indices: 69209--69268 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
69199 ATTTAATGAT
*
69209 CAAAATGTAAT-AATTAATAACATAAGTGAA
1 CAAAATGTAATAAATCAATAACATAAGTGAA
* *
69239 CAAAATTTAATAAATCAATAACGTAAGTGA
1 CAAAATGTAATAAATCAATAACATAAGTGA
69269 TTGAAACATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.55, C:0.08, G:0.10, T:0.27
Consensus pattern (31 bp):
CAAAATGTAATAAATCAATAACATAAGTGAA
Found at i:72984 original size:11 final size:11
Alignment explanation
Indices: 72970--73002 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
72960 ATGCTAACGG
72970 TATTATTTCCT
1 TATTATTTCCT
72981 TATTATTTCCT
1 TATTATTTCCT
*
72992 TATTCTTTCCT
1 TATTATTTCCT
73003 CGTATCTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.15, C:0.21, G:0.00, T:0.64
Consensus pattern (11 bp):
TATTATTTCCT
Found at i:74541 original size:18 final size:18
Alignment explanation
Indices: 74518--74576 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
74508 GTAATATTTC
74518 CTTTTTAATATTTTAATA
1 CTTTTTAATATTTTAATA
**
74536 CTTTTTTGTATTTTAATA
1 CTTTTTAATATTTTAATA
* *
74554 -TTTTGAAT-TTTAAATA
1 CTTTTTAATATTTTAATA
*
74570 ATTTTTA
1 CTTTTTA
74577 TTTAGATTAA
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
16 7 0.21
17 10 0.30
18 16 0.48
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (18 bp):
CTTTTTAATATTTTAATA
Found at i:82898 original size:17 final size:17
Alignment explanation
Indices: 82876--82909 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
82866 TCATTATTCA
*
82876 CGTGAATAGTGAAATTT
1 CGTGAATAGTAAAATTT
82893 CGTGAATAGTAAAATTT
1 CGTGAATAGTAAAATTT
82910 TGTCGGCGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.35
Consensus pattern (17 bp):
CGTGAATAGTAAAATTT
Done.