Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008149.1 Hibiscus syriacus cultivar Beakdansim tig00110715_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: 174755
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 2 of 2
Found at i:148357 original size:37 final size:38
Alignment explanation
Indices: 148284--148364 Score: 128
Period size: 37 Copynumber: 2.2 Consensus size: 38
148274 AGTTGTAGAT
*
148284 TTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGGA
1 TTTGATTTCCTTTTGCTTGGCAACATATGAGATTTGGA
* *
148322 TTTGATTTCGTTTTGCTTGG-AACATATGAGCTTTGGA
1 TTTGATTTCCTTTTGCTTGGCAACATATGAGATTTGGA
148359 TTTGAT
1 TTTGAT
148365 GAGCATCGGA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
37 21 0.52
38 19 0.47
ACGTcount: A:0.19, C:0.12, G:0.22, T:0.47
Consensus pattern (38 bp):
TTTGATTTCCTTTTGCTTGGCAACATATGAGATTTGGA
Found at i:148690 original size:18 final size:18
Alignment explanation
Indices: 148667--148703 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
148657 TGAAATTTAT
148667 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
148685 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
148703 A
1 A
148704 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:149115 original size:24 final size:25
Alignment explanation
Indices: 149083--149131 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
149073 ATTATTTTTC
*
149083 CAAATAATGTA-CCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
149107 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
149132 TAATTGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.45, C:0.20, G:0.08, T:0.27
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:149220 original size:20 final size:20
Alignment explanation
Indices: 149197--149263 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
149187 TGTTAAAGGT
* *
149197 AAATTTGCAACACGAAAGTC
1 AAATTCGCAACGCGAAAGTC
* *
149217 AAATTCGCTACGCGATAGTC
1 AAATTCGCAACGCGAAAGTC
149237 AAATTCGCAACGCGAAAGTC
1 AAATTCGCAACGCGAAAGTC
149257 AAATTCG
1 AAATTCG
149264 GTTTGCGATT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (20 bp):
AAATTCGCAACGCGAAAGTC
Found at i:149608 original size:18 final size:18
Alignment explanation
Indices: 149585--149620 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
149575 AAGCCGGTTG
*
149585 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
149603 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
149621 CCTTTTGCTT
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:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:151851 original size:22 final size:23
Alignment explanation
Indices: 151826--151877 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 23
151816 TTCCATCACC
151826 ATCAAAATCC-GTATTGACCAAG
1 ATCAAAATCCGGTATTGACCAAG
* *
151848 ATCAAAGTCCGGGTATTGGCCAAG
1 ATCAAAATCC-GGTATTGACCAAG
151872 ATCAAA
1 ATCAAA
151878 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 9 0.35
24 17 0.65
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.21
Consensus pattern (23 bp):
ATCAAAATCCGGTATTGACCAAG
Found at i:152030 original size:12 final size:12
Alignment explanation
Indices: 151997--152031 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
151987 AAGGTTGTGG
*
151997 GTTTGAGATTGT
1 GTTTGATATTGT
152009 GTTTGATATTGT
1 GTTTGATATTGT
*
152021 GTTTGGTATTG
1 GTTTGATATTG
152032 GAAATGTGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.31, T:0.54
Consensus pattern (12 bp):
GTTTGATATTGT
Found at i:152639 original size:22 final size:22
Alignment explanation
Indices: 152613--152655 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
152603 ATGTAAAAAA
*
152613 TAGATATGGGGAA-GGATGTCGT
1 TAGATAT-AGGAACGGATGTCGT
152635 TAGATATAGGAACGGATGTCG
1 TAGATATAGGAACGGATGTCG
152656 CCGGAGAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.30, C:0.07, G:0.37, T:0.26
Consensus pattern (22 bp):
TAGATATAGGAACGGATGTCGT
Found at i:152808 original size:20 final size:20
Alignment explanation
Indices: 152783--152838 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
152773 GAAATTAAAT
152783 TCGCGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
* * *
152803 TCGCGTTACAAATTTGACTT
1 TCGCGTTGCGAATTTGACTA
152823 TCGCGTTGCGAATTTG
1 TCGCGTTGCGAATTTG
152839 TTGGTCATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGACTA
Found at i:156172 original size:26 final size:26
Alignment explanation
Indices: 156141--156202 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
156131 CATTATGCCA
*
156141 AATGCACTTTATCATTGCTGCCAACT
1 AATGCACTTTATCATTACTGCCAACT
*
156167 AATGCACTTTATCATTACTGTCAACT
1 AATGCACTTTATCATTACTGCCAACT
156193 AATGCACTTT
1 AATGCACTTT
156203 CGGTGCATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (26 bp):
AATGCACTTTATCATTACTGCCAACT
Found at i:163033 original size:32 final size:32
Alignment explanation
Indices: 162997--163064 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 32
162987 TAATATATCA
*
162997 TTTCTAATATTATTTAT-GTTCAATCTTTAAAC
1 TTTCTAATATTATTTATAATTCAAT-TTTAAAC
* *
163029 TTTCTAATTTTATTTATAATTCGATTTTAAAC
1 TTTCTAATATTATTTATAATTCAATTTTAAAC
163061 TTTC
1 TTTC
163065 AATTCCAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 27 0.84
33 5 0.16
ACGTcount: A:0.29, C:0.12, G:0.03, T:0.56
Consensus pattern (32 bp):
TTTCTAATATTATTTATAATTCAATTTTAAAC
Found at i:165361 original size:19 final size:19
Alignment explanation
Indices: 165339--165376 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
165329 TTCTTTACCA
165339 CAAAATGATATATTTATAG
1 CAAAATGATATATTTATAG
165358 CAAAATGATATATTTATAG
1 CAAAATGATATATTTATAG
165377 GGACAATTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.37
Consensus pattern (19 bp):
CAAAATGATATATTTATAG
Found at i:168093 original size:24 final size:24
Alignment explanation
Indices: 168066--168111 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
168056 CTGTTTTGTT
168066 TGGTGTGTT-GTGCTTTTCTCTTGG
1 TGGT-TGTTCGTGCTTTTCTCTTGG
*
168090 TGGTTGTTCGTGTTTTTCTCTT
1 TGGTTGTTCGTGCTTTTCTCTT
168112 TCGCAGGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.00, C:0.13, G:0.28, T:0.59
Consensus pattern (24 bp):
TGGTTGTTCGTGCTTTTCTCTTGG
Found at i:168534 original size:3 final size:3
Alignment explanation
Indices: 168528--168556 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
168518 TTAATAATAA
168528 TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
168557 ATTTTATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:168544 original size:14 final size:14
Alignment explanation
Indices: 168527--168563 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
168517 TTTAATAATA
168527 ATATTATTATTATT
1 ATATTATTATTATT
168541 ATATTATTATTATT
1 ATATTATTATTATT
168555 ATATT-TTAT
1 ATATTATTAT
168564 AATAATAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 4 0.17
14 19 0.83
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
ATATTATTATTATT
Found at i:168568 original size:3 final size:3
Alignment explanation
Indices: 168562--168591 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
168552 ATTATATTTT
168562 ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
168592 ATGGGCAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:170718 original size:12 final size:13
Alignment explanation
Indices: 170701--170731 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
170691 ACATAATCTG
170701 AAAATT-ATTTTT
1 AAAATTCATTTTT
170713 AAAATTCATTTTT
1 AAAATTCATTTTT
170726 AAAATT
1 AAAATT
170732 TATAAAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (13 bp):
AAAATTCATTTTT
Found at i:174253 original size:45 final size:43
Alignment explanation
Indices: 174203--174505 Score: 195
Period size: 44 Copynumber: 6.9 Consensus size: 43
174193 TATATTTTAG
* * *
174203 TATATAGAATTTGATAAATAATTATACAG-TTTTAAAAACATATAA
1 TATATAG-TTTTGA-AAATAATTATATAGTTTTTAAAAA-AAATAA
174248 TATATAGTTTTTGAAAAT-A-TATATAGTTTTTAAAAAAACAT-A
1 TATATAG-TTTTGAAAATAATTATATAGTTTTTAAAAAAA-ATAA
*
174290 TATATAGTTTTGAAAACATATTATATAGTTTTTAAAAAAAATATA
1 TATATAGTTTTGAAAATA-ATTATATAGTTTTTAAAAAAAATA-A
* *
174335 TATATAGTTTT-AAAAT-ATATAGTGTAG-TTTT-AAAAACAT-A
1 TATATAGTTTTGAAAATAAT-TA-TATAGTTTTTAAAAAAAATAA
* *
174375 TAGTATAGTTTTGAAAA-CA-TATTATAG-CTTT--AAAAAATAA
1 TA-TATAGTTTTGAAAATAATTA-TATAGTTTTTAAAAAAAATAA
* **
174415 TAATATAGTATTTGAAAAT-ATATAGTATAGTTTTTAAAAACATATTGT
1 T-ATATAGT-TTTGAAAATAAT-TA-TATAGTTTTTAAAAA-A-AATAA
*
174463 TATATAGTTTTGAAAACATAAAATATATATAGTTTTTGAAAAA
1 TATATAGTTTTG-AAA-AT--AAT-TATATAGTTTTTAAAAAA
174506 CATATGTAAT
Statistics
Matches: 212, Mismatches: 18, Indels: 52
0.75 0.06 0.18
Matches are distributed among these distances:
39 6 0.03
40 20 0.09
41 28 0.13
42 29 0.14
43 28 0.13
44 34 0.16
45 24 0.11
46 7 0.03
47 11 0.05
48 5 0.02
49 1 0.00
50 14 0.07
51 5 0.02
ACGTcount: A:0.48, C:0.03, G:0.09, T:0.41
Consensus pattern (43 bp):
TATATAGTTTTGAAAATAATTATATAGTTTTTAAAAAAAATAA
Found at i:174256 original size:23 final size:22
Alignment explanation
Indices: 174225--174510 Score: 197
Period size: 23 Copynumber: 13.0 Consensus size: 22
174215 GATAAATAAT
*
174225 TATACAGTTTTAAAAACATATAA
1 TATATAGTTTTAAAAACATAT-A
**
174248 TATATAGTTTT-TGAA-A-ATA
1 TATATAGTTTTAAAAACATATA
* *
174267 TATATAGTTTTTAAAAAAACATA
1 TATATAG-TTTTAAAAACATATA
*
174290 TATATAGTTTTGAAAACATAT-
1 TATATAGTTTTAAAAACATATA
*
174311 TATATAGTTTTTAAAAAAAATATA
1 TATATAG-TTTT-AAAAACATATA
174335 TATATAGTTTT--AAA-ATATA
1 TATATAGTTTTAAAAACATATA
*
174354 TAGTGTAGTTTTAAAAACATATA
1 TA-TATAGTTTTAAAAACATATA
* *
174377 -GTATAGTTTTGAAAAC--ATA
1 TATATAGTTTTAAAAACATATA
*
174396 T-TATAGCTTTAAAAA-ATA-A
1 TATATAGTTTTAAAAACATATA
*
174415 TAATATAGTATTT-GAAA-ATATA
1 T-ATATAGT-TTTAAAAACATATA
*
174437 TAGTATAGTTTTTAAAAACATATTGT
1 TA-TATAG-TTTTAAAAACATA-T-A
*
174463 TATATAGTTTTGAAAACATAAAATA
1 TATATAGTTTTAAAAACAT---ATA
174488 TATATAGTTTTTGAAAAACATAT
1 TATATAG-TTTT-AAAAACATAT
174511 GTAATATATA
Statistics
Matches: 211, Mismatches: 23, Indels: 57
0.73 0.08 0.20
Matches are distributed among these distances:
19 32 0.15
20 18 0.09
21 35 0.17
22 34 0.16
23 41 0.19
24 23 0.11
25 13 0.06
26 7 0.03
27 8 0.04
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.41
Consensus pattern (22 bp):
TATATAGTTTTAAAAACATATA
Found at i:174280 original size:43 final size:42
Alignment explanation
Indices: 174232--174478 Score: 217
Period size: 43 Copynumber: 5.8 Consensus size: 42
174222 AATTATACAG
174232 TTTTAAAAACATATAATATATAGTTTTTGAAAATATATATAGT
1 TTTTAAAAACATATAATATATAG-TTTTGAAAATATATATAGT
* *
174275 TTTTAAAAAAACAT-ATATATAGTTTTGAAAACATATTATATAGT
1 TTTTAAAAACATATAATATATAGTTTTG-AAA-ATA-TATATAGT
*
174319 TTTTAAAAA-AAATATATATATAGTTTT-AAAATATATAGT-GT
1 TTTTAAAAACATATA-ATATATAGTTTTGAAAATATATA-TAGT
* *
174360 AGTTTTAAAAACATAT-A-GTATAGTTTTGAAAACATATTATAG-
1 --TTTTAAAAACATATAATATATAGTTTTGAAAATATA-TATAGT
*
174402 CTTT-AAAA-A-ATAATAATATAGTATTTGAAAATATATAGTATAGT
1 TTTTAAAAACATATAAT-ATATAGT-TTTG-AAA-ATATA-TATAGT
**
174446 TTTTAAAAACATATTGTTATATAGTTTTGAAAA
1 TTTTAAAAACATA-TAATATATAGTTTTGAAAA
174479 CATAAAATAT
Statistics
Matches: 168, Mismatches: 13, Indels: 45
0.74 0.06 0.20
Matches are distributed among these distances:
37 2 0.01
38 2 0.01
39 4 0.02
40 9 0.05
41 24 0.14
42 27 0.16
43 42 0.25
44 24 0.14
45 19 0.11
46 5 0.03
47 8 0.05
48 2 0.01
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.42
Consensus pattern (42 bp):
TTTTAAAAACATATAATATATAGTTTTGAAAATATATATAGT
Found at i:174285 original size:21 final size:21
Alignment explanation
Indices: 174232--174510 Score: 153
Period size: 21 Copynumber: 12.7 Consensus size: 21
174222 AATTATACAG
174232 TTTTAAAAACATATAATATATAGT
1 TTTTAAAAA-A-AT-ATATATAGT
*
174256 TTTT--GAAAATATATATAGT
1 TTTTAAAAAAATATATATAGT
174275 TTTTAAAAAAACATATATATAG-
1 TTTT-AAAAAA-ATATATATAGT
* *
174297 TTTTGAAAACATATTATATAGT
1 TTTTAAAAAAATA-TATATAGT
174319 TTTTAAAAAAAATATATATA-T
1 TTTT-AAAAAAATATATATAGT
* *
174340 AGTTTT-AAAATATATAGTGTAG-
1 --TTTTAAAAAAATATA-TATAGT
*
174362 TTTTAAAAACATATAGTATAG-
1 TTTTAAAAAAATATA-TATAGT
* * *
174383 TTTTGAAAACATAT-TATAGC
1 TTTTAAAAAAATATATATAGT
*
174403 TTTAAAAAATAATA-ATATAGT
1 TTTTAAAAA-AATATATATAGT
* * *
174424 ATTTGAAAATATATAGTATAGT
1 TTTTAAAAAAATATA-TATAGT
*
174446 TTTTAAAAACATATTGTTATATAGT
1 TTTTAAAAA-A-A-T-ATATATAGT
*
174471 TTTGAAAACATAAAATATATATAGT
1 TTT--TAA-A-AAAATATATATAGT
*
174496 TTTTGAAAAACATAT
1 TTTT-AAAAAAATAT
174511 GTAATATATA
Statistics
Matches: 202, Mismatches: 27, Indels: 54
0.71 0.10 0.19
Matches are distributed among these distances:
19 18 0.09
20 19 0.09
21 64 0.32
22 41 0.20
23 22 0.11
24 7 0.03
25 21 0.10
26 3 0.01
27 3 0.01
28 2 0.01
29 2 0.01
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.41
Consensus pattern (21 bp):
TTTTAAAAAAATATATATAGT
Found at i:174517 original size:27 final size:27
Alignment explanation
Indices: 174440--174520 Score: 84
Period size: 27 Copynumber: 3.1 Consensus size: 27
174430 AAATATATAG
174440 TATAGTTTTT-AAAAACATATTGT--TA
1 TATAGTTTTTGAAAAACATA-TGTAATA
**
174465 TATAG-TTTTG-AAAACATA-AAATATA
1 TATAGTTTTTGAAAAACATATGTA-ATA
174490 TATAGTTTTTGAAAAACATATGTAATA
1 TATAGTTTTTGAAAAACATATGTAATA
174517 TATA
1 TATA
174521 TATATATAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
24 12 0.27
25 12 0.27
26 5 0.11
27 15 0.33
28 1 0.02
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.42
Consensus pattern (27 bp):
TATAGTTTTTGAAAAACATATGTAATA
Done.