Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002210.1 Hibiscus syriacus cultivar Beakdansim tig00004502_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: 328873
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:242452 original size:26 final size:26
Alignment explanation
Indices: 242423--242472 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
242413 ATAAATCAAA
242423 TTTAATAAATATCAATT-TTTTTATAT
1 TTTAATAAATA-CAATTATTTTTATAT
*
242449 TTTAATAAATACTATTATTTTTAT
1 TTTAATAAATACAATTATTTTTAT
242473 CAAGAGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (26 bp):
TTTAATAAATACAATTATTTTTATAT
Found at i:244215 original size:14 final size:14
Alignment explanation
Indices: 244193--244229 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
244183 TTAGTATGGC
*
244193 AAATAAAAATAAAG
1 AAATTAAAATAAAG
244207 AAATTAAAATAAAG
1 AAATTAAAATAAAG
244221 AAATTAAAA
1 AAATTAAAA
244230 CTTTAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (14 bp):
AAATTAAAATAAAG
Found at i:246879 original size:10 final size:9
Alignment explanation
Indices: 246857--246896 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
246847 ACTTGGTCTG
246857 TAAAAATAA
1 TAAAAATAA
*
246866 TAAAAATGA
1 TAAAAATAA
*
246875 TTAAAATAA
1 TAAAAATAA
*
246884 TAATAATAA
1 TAAAAATAA
246893 TAAA
1 TAAA
246897 CCCTGGGCAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (9 bp):
TAAAAATAA
Found at i:251668 original size:16 final size:16
Alignment explanation
Indices: 251647--251682 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
251637 TCTGAATCTT
251647 CTATTTTTGTACTATC
1 CTATTTTTGTACTATC
*
251663 CTATTTTTGTACTCTC
1 CTATTTTTGTACTATC
251679 CTAT
1 CTAT
251683 ATTGTCATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.17, C:0.22, G:0.06, T:0.56
Consensus pattern (16 bp):
CTATTTTTGTACTATC
Found at i:253905 original size:35 final size:35
Alignment explanation
Indices: 253828--253944 Score: 155
Period size: 35 Copynumber: 3.3 Consensus size: 35
253818 TACCATTCCT
* * *
253828 ATTTTC-AACAAACATCTAACAAACTTTGAAAAAAAC
1 ATTTTCAAAGAAACATTTAACAAACTTTG--AAAACC
253864 ATTTTTCAAAGAAACATTTAACAAACTTTGAAAACC
1 A-TTTTCAAAGAAACATTTAACAAACTTTGAAAACC
* *
253900 ATTTTCAAAGAAATATTTACCAAACTTTGAAAACC
1 ATTTTCAAAGAAACATTTAACAAACTTTGAAAACC
253935 ATTTTCAAAG
1 ATTTTCAAAG
253945 TTGGTTGCCA
Statistics
Matches: 74, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
35 42 0.57
36 7 0.09
37 5 0.07
38 20 0.27
ACGTcount: A:0.48, C:0.17, G:0.05, T:0.30
Consensus pattern (35 bp):
ATTTTCAAAGAAACATTTAACAAACTTTGAAAACC
Found at i:260306 original size:12 final size:12
Alignment explanation
Indices: 260289--260313 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
260279 TTATAAACAT
260289 AAATATTATAAA
1 AAATATTATAAA
260301 AAATATTATAAA
1 AAATATTATAAA
260313 A
1 A
260314 TTGTATTTGT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAATATTATAAA
Found at i:260415 original size:2 final size:2
Alignment explanation
Indices: 260408--260439 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
260398 GACCCACTTG
260408 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
260440 GTATGTATGA
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
Found at i:266148 original size:2 final size:2
Alignment explanation
Indices: 266141--266225 Score: 170
Period size: 2 Copynumber: 42.5 Consensus size: 2
266131 ACTCTGGATC
266141 AT AT AT AT AT 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 AT AT AT AT AT
266183 AT AT AT AT AT 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 AT AT AT AT AT
266225 A
1 A
266226 ATAAATTTAC
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 83 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:267363 original size:3 final size:3
Alignment explanation
Indices: 267357--267396 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
267347 TTATTAAATA
267357 AAT AAT AAT AAT AAT AAT AAT AAT AAT AGAT -AT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT A
267397 TTAAAGGTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 31 0.89
4 2 0.06
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:270257 original size:16 final size:15
Alignment explanation
Indices: 270232--270262 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
270222 ATTTTTTAAT
270232 AAATTTATTAACATA
1 AAATTTATTAACATA
270247 AAATGTTATTAACATA
1 AAAT-TTATTAACATA
270263 TACCAGCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (15 bp):
AAATTTATTAACATA
Found at i:278864 original size:6 final size:6
Alignment explanation
Indices: 278850--279062 Score: 282
Period size: 6 Copynumber: 35.5 Consensus size: 6
278840 TCTCTCGTCT
* * * * *
278850 TGTATA TGTACA TGTACA TGTACA TGTATA TGTATA TGTATA TGTATA
1 TGTACA TGTACA TGTACA TGTACA TGTACA TGTACA TGTACA TGTACA
* * *
278898 TGTATA TGTACA TGTACA TGTACA TGTATA TGTACA TGTACA TGTATA
1 TGTACA TGTACA TGTACA TGTACA TGTACA TGTACA TGTACA TGTACA
* * *
278946 TGTACA TGTACA TGTATA TGTACA TGTACA TGTATA TGTACA TGTATA
1 TGTACA TGTACA TGTACA TGTACA TGTACA TGTACA TGTACA TGTACA
* * *
278994 TGTATA TGTACA TGTACA TGTACA TGTATA TGTACA TGTACA TGTATA
1 TGTACA TGTACA TGTACA TGTACA TGTACA TGTACA TGTACA TGTACA
* *
279042 TGTACA TGTATA TGTATA TGT
1 TGTACA TGTACA TGTACA TGT
279063 TTTATTTAGG
Statistics
Matches: 189, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 189 1.00
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.41
Consensus pattern (6 bp):
TGTACA
Found at i:278876 original size:18 final size:18
Alignment explanation
Indices: 278850--279062 Score: 318
Period size: 18 Copynumber: 11.8 Consensus size: 18
278840 TCTCTCGTCT
278850 TGTATATGTACATGTACA
1 TGTATATGTACATGTACA
* * *
278868 TGTACATGTATATGTATA
1 TGTATATGTACATGTACA
* *
278886 TGTATATGTATATGTATA
1 TGTATATGTACATGTACA
*
278904 TGTACATGTACATGTACA
1 TGTATATGTACATGTACA
278922 TGTATATGTACATGTACA
1 TGTATATGTACATGTACA
278940 TGTATATGTACATGTACA
1 TGTATATGTACATGTACA
278958 TGTATATGTACATGTACA
1 TGTATATGTACATGTACA
*
278976 TGTATATGTACATGTATA
1 TGTATATGTACATGTACA
278994 TGTATATGTACATGTACA
1 TGTATATGTACATGTACA
* *
279012 TGTACATGTATATGTACA
1 TGTATATGTACATGTACA
* *
279030 TGTACATGTATATGTACA
1 TGTATATGTACATGTACA
*
279048 TGTATATGTATATGT
1 TGTATATGTACATGT
279063 TTTATTTAGG
Statistics
Matches: 182, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 182 1.00
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.41
Consensus pattern (18 bp):
TGTATATGTACATGTACA
Found at i:279325 original size:16 final size:17
Alignment explanation
Indices: 279290--279325 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
279280 ATTAATTTAA
279290 ATTTAAATAAAAAATAT
1 ATTTAAATAAAAAATAT
279307 ATTTAAATAAAAAAT-T
1 ATTTAAATAAAAAATAT
279323 ATT
1 ATT
279326 GATTTTAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATTTAAATAAAAAATAT
Found at i:284687 original size:63 final size:63
Alignment explanation
Indices: 284587--284715 Score: 186
Period size: 63 Copynumber: 2.0 Consensus size: 63
284577 CAAATATTGA
* *
284587 AAATCAAGTAGAGAAGTTGGAGGAGCCACCAGAAAAGAAACAATGCCATGAAACAGATACATC
1 AAATCAAGTAGAGAAGTCGGAGGAGCCACCAGAAAAGAAACAATGCCATGAAACAGATAAATC
* ** * * *
284650 AAATCAAGTAGATAAGTCGGAGGAGCTTCCAGCAAAGAAACAATGCCTTGAAACTGATAAATC
1 AAATCAAGTAGAGAAGTCGGAGGAGCCACCAGAAAAGAAACAATGCCATGAAACAGATAAATC
284713 AAA
1 AAA
284716 GAGTGCAACC
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.16
Consensus pattern (63 bp):
AAATCAAGTAGAGAAGTCGGAGGAGCCACCAGAAAAGAAACAATGCCATGAAACAGATAAATC
Found at i:293286 original size:23 final size:23
Alignment explanation
Indices: 293255--293320 Score: 96
Period size: 23 Copynumber: 2.9 Consensus size: 23
293245 CTGAATGATT
*
293255 CAGTACTGACTGATTCAGCAAAA
1 CAGTGCTGACTGATTCAGCAAAA
*
293278 CAGTGCTGACTGATTTAGCAAAA
1 CAGTGCTGACTGATTCAGCAAAA
* *
293301 TAGTGCTGAATGATTCAGCA
1 CAGTGCTGACTGATTCAGCA
293321 CATAAGTACA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (23 bp):
CAGTGCTGACTGATTCAGCAAAA
Found at i:293559 original size:21 final size:23
Alignment explanation
Indices: 293533--293588 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 23
293523 AAAAATATTA
*
293533 GATAATTTTTAGTT-ATATT-TAT
1 GATAATTTTTA-TTGATATTGGAT
293555 -ATAATTTATTATTGATATTGGAT
1 GATAATTT-TTATTGATATTGGAT
293578 GATAATTTTTA
1 GATAATTTTTA
293589 ATGGGTTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
21 9 0.31
22 8 0.28
23 5 0.17
24 7 0.24
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (23 bp):
GATAATTTTTATTGATATTGGAT
Found at i:296007 original size:15 final size:15
Alignment explanation
Indices: 295987--296015 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
295977 TTTTTATATT
295987 TTAAAATTATTTTTC
1 TTAAAATTATTTTTC
296002 TTAAAATTATTTTT
1 TTAAAATTATTTTT
296016 TAAAAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (15 bp):
TTAAAATTATTTTTC
Found at i:296020 original size:13 final size:13
Alignment explanation
Indices: 295980--296020 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
295970 ATATCACTTT
*
295980 TTATATTTTAAAA
1 TTATTTTTTAAAA
295993 TTATTTTTCTTAAAA
1 TTA-TTTT-TTAAAA
296008 TTATTTTTTAAAA
1 TTATTTTTTAAAA
296021 AATAATTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 9 0.36
14 7 0.28
15 9 0.36
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (13 bp):
TTATTTTTTAAAA
Found at i:296023 original size:15 final size:15
Alignment explanation
Indices: 295989--296021 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
295979 TTTATATTTT
*
295989 AAAATTATTTTTCTT
1 AAAATTATTTTTCTA
296004 AAAATTATTTTT-TA
1 AAAATTATTTTTCTA
296018 AAAA
1 AAAA
296022 ATAATTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (15 bp):
AAAATTATTTTTCTA
Found at i:301049 original size:12 final size:12
Alignment explanation
Indices: 301024--301118 Score: 59
Period size: 12 Copynumber: 7.8 Consensus size: 12
301014 ACGGAGATAT
* *
301024 CAGAAATCAAAA
1 CAGAATTCAGAA
301036 CAGAATTCAGAA
1 CAGAATTCAGAA
*
301048 CATATATATCAGAA
1 CAGA-AT-TCAGAA
*
301062 CAGAATCCA-AA
1 CAGAATTCAGAA
*
301073 TCAGAAATCAGAA
1 -CAGAATTCAGAA
* **
301086 CAAAATTCAGGT
1 CAGAATTCAGAA
*
301098 CATGTA-TCAGAA
1 CA-GAATTCAGAA
301110 CAGAATTCA
1 CAGAATTCA
301119 AGTCGGAAAT
Statistics
Matches: 61, Mismatches: 16, Indels: 12
0.69 0.18 0.13
Matches are distributed among these distances:
11 4 0.07
12 41 0.67
13 7 0.11
14 9 0.15
ACGTcount: A:0.51, C:0.18, G:0.13, T:0.19
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:301086 original size:24 final size:24
Alignment explanation
Indices: 301022--301132 Score: 91
Period size: 24 Copynumber: 4.5 Consensus size: 24
301012 AAACGGAGAT
*
301022 ATCAGAAATCAAAACAGAATTCAGA
1 ATCAGAAATCAGAACAGAATTCA-A
* *
301047 A-CATATATATCAGAACAGAATCCAA
1 ATCAGA-A-ATCAGAACAGAATTCAA
* *
301072 ATCAGAAATCAGAACAAAATTCAG
1 ATCAGAAATCAGAACAGAATTCAA
* *
301096 GTCATG-TATCAGAACAGAATTCAA
1 ATCA-GAAATCAGAACAGAATTCAA
* *
301120 GTCGGAAATCAGA
1 ATCAGAAATCAGA
301133 TAAAATATTT
Statistics
Matches: 68, Mismatches: 13, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
23 1 0.01
24 44 0.65
25 6 0.09
26 17 0.25
ACGTcount: A:0.50, C:0.17, G:0.14, T:0.19
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAA
Found at i:302414 original size:15 final size:15
Alignment explanation
Indices: 302394--302429 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
302384 TAATGAAGTT
302394 AAGTACAAATCTTCA
1 AAGTACAAATCTTCA
302409 AAGTACAAATCTTCA
1 AAGTACAAATCTTCA
302424 AAGTAC
1 AAGTAC
302430 TTTTTCATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.47, C:0.19, G:0.08, T:0.25
Consensus pattern (15 bp):
AAGTACAAATCTTCA
Found at i:302887 original size:36 final size:36
Alignment explanation
Indices: 302840--302912 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
302830 GATAAATTAT
*
302840 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
1 AATCTACATATCAATGGCTGATTCTTTTATCACTTA
302876 AATCTACATATCAATGGCTGATTCTTTTATCACTTA
1 AATCTACATATCAATGGCTGATTCTTTTATCACTTA
302912 A
1 A
302913 TTCCAGAACT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.30, C:0.21, G:0.08, T:0.41
Consensus pattern (36 bp):
AATCTACATATCAATGGCTGATTCTTTTATCACTTA
Found at i:303584 original size:18 final size:18
Alignment explanation
Indices: 303561--303596 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
303551 GCCGGTCAAC
303561 GGTCAACGGGTCAGGTTG
1 GGTCAACGGGTCAGGTTG
*
303579 GGTCAACGGGTCGGGTTG
1 GGTCAACGGGTCAGGTTG
303597 TAACCGGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.17, G:0.47, T:0.22
Consensus pattern (18 bp):
GGTCAACGGGTCAGGTTG
Found at i:306102 original size:18 final size:19
Alignment explanation
Indices: 306079--306115 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
306069 CGCATAACAC
306079 CCGTCATT-GTATAAAGCA
1 CCGTCATTGGTATAAAGCA
306097 CCGTCATTGGTATAAAGCA
1 CCGTCATTGGTATAAAGCA
306116 ATTGCAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (19 bp):
CCGTCATTGGTATAAAGCA
Found at i:324398 original size:22 final size:22
Alignment explanation
Indices: 324370--324416 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
324360 AAATTCAATA
*
324370 TTAAGGGTGAATTTATAAAATT
1 TTAAGGGTGAACTTATAAAATT
* *
324392 TTAAGGGTGGACTTGTAAAATT
1 TTAAGGGTGAACTTATAAAATT
324414 TTA
1 TTA
324417 GAGATTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.02, G:0.21, T:0.40
Consensus pattern (22 bp):
TTAAGGGTGAACTTATAAAATT
Found at i:326568 original size:17 final size:18
Alignment explanation
Indices: 326548--326585 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
326538 ATTAGCATGC
*
326548 CTTTCAAATAAGGTTA-G
1 CTTTCAAAGAAGGTTATG
*
326565 CTTTTAAAGAAGGTTATG
1 CTTTCAAAGAAGGTTATG
326583 CTT
1 CTT
326586 AAAGCTCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (18 bp):
CTTTCAAAGAAGGTTATG
Done.