Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006889.1 Hibiscus syriacus cultivar Beakdansim tig00017575_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: 33567
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.30
Found at i:80 original size:52 final size:50
Alignment explanation
Indices: 1--146 Score: 210
Period size: 52 Copynumber: 2.9 Consensus size: 50
1 TTTGTTTAACATGTCTTGGAAACTGATTTTTTGTATATATATATATATATA
1 TTTGTTTAACATGTCTTGGAAACTGATTTTTTGT-TATATATATATATATA
*
52 TATTGTTTAACATGTCTTGGAAACTGATTTTTTG-T-T-CATATATATATA
1 T-TTGTTTAACATGTCTTGGAAACTGATTTTTTGTTATATATATATATATA
* *
100 TTTGTTTAACATGTC-TGGAAACTGATTCTTTGTTCATATACATATAT
1 TTTGTTTAACATGTCTTGGAAACTGATTTTTTGTT-ATATATATATAT
147 TTGTTTAATG
Statistics
Matches: 86, Mismatches: 4, Indels: 11
0.85 0.04 0.11
Matches are distributed among these distances:
46 16 0.19
47 15 0.17
48 12 0.14
49 2 0.02
50 8 0.09
51 1 0.01
52 32 0.37
ACGTcount: A:0.29, C:0.09, G:0.12, T:0.49
Consensus pattern (50 bp):
TTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTATATATATATATATA
Found at i:119 original size:46 final size:47
Alignment explanation
Indices: 1--154 Score: 229
Period size: 46 Copynumber: 3.2 Consensus size: 47
*
1 TTTGTTTAACATGTCTTGGAAACTGATTTTTTGTATATATATATATATATA
1 TTTGTTTAACATGTCTTGGAAACTGATTTTTTG--T-T-CATATATATATA
52 TATTGTTTAACATGTCTTGGAAACTGATTTTTTGTTCATATATATATA
1 T-TTGTTTAACATGTCTTGGAAACTGATTTTTTGTTCATATATATATA
* *
100 TTTGTTTAACATGTC-TGGAAACTGATTCTTTGTTCATATACATATA
1 TTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTCATATATATATA
146 TTTGTTTAA
1 TTTGTTTAA
155 TGTGTCTAGG
Statistics
Matches: 99, Mismatches: 3, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
46 38 0.38
47 14 0.14
48 12 0.12
49 1 0.01
50 1 0.01
51 1 0.01
52 32 0.32
ACGTcount: A:0.29, C:0.08, G:0.12, T:0.50
Consensus pattern (47 bp):
TTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTCATATATATATA
Found at i:345 original size:53 final size:52
Alignment explanation
Indices: 221--345 Score: 166
Period size: 53 Copynumber: 2.4 Consensus size: 52
211 TTGTTAAACG
*
221 TATATATATTTTTATTTAATGTGTCTTGGAAAACTGATTTTTGTTCATATATA
1 TATATATATATTTATTTAATGTG-CTTGGAAAACTGATTTTTGTTCATATATA
274 TATAT-TATATATTATTTAATGTG-TTGG-AAACTGATTTTTTTTGTTCATATATA
1 TATATATATAT-TTATTTAATGTGCTTGGAAAACTGA---TTTTTGTTCATATATA
*
327 TATATATATATTTGTTTAA
1 TATATATATATTTATTTAA
346 CATGTCTTAG
Statistics
Matches: 65, Mismatches: 2, Indels: 10
0.84 0.03 0.13
Matches are distributed among these distances:
50 7 0.11
51 4 0.06
52 4 0.06
53 45 0.69
54 5 0.08
ACGTcount: A:0.31, C:0.04, G:0.10, T:0.54
Consensus pattern (52 bp):
TATATATATATTTATTTAATGTGCTTGGAAAACTGATTTTTGTTCATATATA
Found at i:550 original size:22 final size:24
Alignment explanation
Indices: 509--552 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
499 TATATTCTTA
509 TATCATTTATTTAATAAGTATAGT
1 TATCATTTATTTAATAAGTATAGT
533 TATC-TTTATTT-ATAAGTATA
1 TATCATTTATTTAATAAGTATA
553 ATGTTCCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 9 0.45
23 7 0.35
24 4 0.20
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52
Consensus pattern (24 bp):
TATCATTTATTTAATAAGTATAGT
Found at i:12242 original size:17 final size:16
Alignment explanation
Indices: 12218--12304 Score: 79
Period size: 16 Copynumber: 5.0 Consensus size: 16
12208 AAAAGGGAAC
12218 AAAT-AAAAAGATAAAA
1 AAATGAAAAAGA-AAAA
12234 AAATGAAAAAGAAAAA
1 AAATGAAAAAGAAAAA
12250 AAATGAAAAA-AAATGAA
1 AAATGAAAAAGAAA--AA
12267 AAATGAAAAAAAGAAATGAAA
1 AAATG--AAAAAG-AA--AAA
12288 AAATGAAAAGAGAAAAA
1 AAATGAAAA-AGAAAAA
12305 GGAGGGTTTG
Statistics
Matches: 61, Mismatches: 0, Indels: 19
0.76 0.00 0.24
Matches are distributed among these distances:
15 3 0.05
16 18 0.30
17 17 0.28
19 11 0.18
20 2 0.03
21 9 0.15
23 1 0.02
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.09
Consensus pattern (16 bp):
AAATGAAAAAGAAAAA
Found at i:12243 original size:10 final size:10
Alignment explanation
Indices: 12239--12290 Score: 56
Period size: 10 Copynumber: 5.3 Consensus size: 10
12229 TAAAAAAATG
12239 AAAAA-GAAA
1 AAAAATGAAA
12248 AAAAATGAAA
1 AAAAATGAAA
12258 AAAAATGAAA
1 AAAAATGAAA
12268 AATGAAA--AAA
1 AA--AAATGAAA
*
12278 AGAAATGAAA
1 AAAAATGAAA
12288 AAA
1 AAA
12291 TGAAAAGAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
8 3 0.08
9 5 0.14
10 25 0.69
12 3 0.08
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.08
Consensus pattern (10 bp):
AAAAATGAAA
Found at i:12252 original size:27 final size:27
Alignment explanation
Indices: 12222--12304 Score: 107
Period size: 28 Copynumber: 3.0 Consensus size: 27
12212 GGGAACAAAT
12222 AAAAAGATAAAAAAATGAAAAAGAAAA
1 AAAAAGATAAAAAAATGAAAAAGAAAA
*
12249 AAAATGA-AAAAAAATGAAAAATGAAAA
1 AAAAAGATAAAAAAATGAAAAA-GAAAA
*
12276 AAAGAA-ATGAAAAAATGAAAAGAGAAAA
1 AAA-AAGATAAAAAAATGAAAA-AGAAAA
12304 A
1 A
12305 GGAGGGTTTG
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
26 14 0.29
27 15 0.31
28 19 0.39
29 1 0.02
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.08
Consensus pattern (27 bp):
AAAAAGATAAAAAAATGAAAAAGAAAA
Found at i:12261 original size:28 final size:26
Alignment explanation
Indices: 12222--12304 Score: 105
Period size: 26 Copynumber: 3.1 Consensus size: 26
12212 GGGAACAAAT
12222 AAAAAGATAAAAAAATGAAAAAGAAA
1 AAAAAGATAAAAAAATGAAAAAGAAA
12248 AAAAATGA-AAAAAAATGAAAAATGAAA
1 AAAAA-GATAAAAAAATGAAAAA-GAAA
* *
12275 AAAAGAAATGAAAAAATGAAAAGAGAAA
1 AAAA-AGATAAAAAAATGAAAA-AGAAA
12303 AA
1 AA
12305 GGAGGGTTTG
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
26 19 0.38
27 11 0.22
28 19 0.38
29 1 0.02
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.08
Consensus pattern (26 bp):
AAAAAGATAAAAAAATGAAAAAGAAA
Found at i:12267 original size:20 final size:18
Alignment explanation
Indices: 12230--12296 Score: 59
Period size: 17 Copynumber: 3.7 Consensus size: 18
12220 ATAAAAAGAT
*
12230 AAAAAAATG--AAAAAGA
1 AAAAAAATGAAAAAAAAA
12246 AAAAAAATG-AAAAAAAA
1 AAAAAAATGAAAAAAAAA
**
12263 TGAAAAATGAAAAAAAGAA
1 AAAAAAATGAAAAAAA-AA
12282 ATGAAAAAATGAAAA
1 A--AAAAAATGAAAA
12297 GAGAAAAAGG
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
16 9 0.22
17 13 0.32
18 6 0.15
19 2 0.05
21 11 0.27
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (18 bp):
AAAAAAATGAAAAAAAAA
Found at i:12291 original size:8 final size:8
Alignment explanation
Indices: 12218--12296 Score: 53
Period size: 8 Copynumber: 10.1 Consensus size: 8
12208 AAAAGGGAAC
12218 AAAT-AAA
1 AAATGAAA
*
12225 AAGATAAAA
1 AA-ATGAAA
12234 AAATGAAA
1 AAATGAAA
*
12242 AAGA-AAAA
1 AA-ATGAAA
12250 AAATGAAAAA
1 AAATG--AAA
12260 AAATG-AA
1 AAATGAAA
12267 AAATG-AA
1 AAATGAAA
*
12274 AAA--AAG
1 AAATGAAA
12280 AAATGAAA
1 AAATGAAA
12288 AAATGAAA
1 AAATGAAA
12296 A
1 A
12297 GAGAAAAAGG
Statistics
Matches: 58, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
6 4 0.07
7 15 0.26
8 25 0.43
9 6 0.10
10 8 0.14
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.10
Consensus pattern (8 bp):
AAATGAAA
Found at i:12301 original size:20 final size:19
Alignment explanation
Indices: 12231--12302 Score: 82
Period size: 16 Copynumber: 3.9 Consensus size: 19
12221 TAAAAAGATA
12231 AAAAAATGAAAAAG-AA--
1 AAAAAATGAAAAAGAAATG
12247 AAAAAATGAAAAA-AAATG
1 AAAAAATGAAAAAGAAATG
12265 -AAAAATGAAAAAAAGAAATG
1 AAAAAATG--AAAAAGAAATG
12285 AAAAAATGAAAAGAGAAA
1 AAAAAATGAAAA-AGAAA
12303 AAGGAGGGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
16 15 0.31
17 7 0.15
19 9 0.19
20 10 0.21
21 7 0.15
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (19 bp):
AAAAAATGAAAAAGAAATG
Found at i:12303 original size:13 final size:13
Alignment explanation
Indices: 12231--12304 Score: 55
Period size: 13 Copynumber: 5.5 Consensus size: 13
12221 TAAAAAGATA
12231 AAAAAATGAAAAAG
1 AAAAAATG-AAAAG
12245 AAAAAA--AATGAA-
1 AAAAAATGAA--AAG
12257 AAAAAATGAAAAATG
1 AAAAAATG-AAAA-G
* *
12272 AAAAAAAGAAATG
1 AAAAAATGAAAAG
12285 AAAAAATGAAAAG
1 AAAAAATGAAAAG
12298 AGAAAAA
1 A-AAAAA
12305 GGAGGGTTTG
Statistics
Matches: 48, Mismatches: 4, Indels: 16
0.71 0.06 0.24
Matches are distributed among these distances:
11 2 0.04
12 6 0.12
13 17 0.35
14 14 0.29
15 9 0.19
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (13 bp):
AAAAAATGAAAAG
Found at i:13504 original size:35 final size:35
Alignment explanation
Indices: 13458--13542 Score: 170
Period size: 35 Copynumber: 2.4 Consensus size: 35
13448 TCCAGTGAAG
13458 AGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAA
1 AGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAA
13493 AGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAA
1 AGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAA
13528 AGTTCATAATGAGAA
1 AGTTCATAATGAGAA
13543 AAACATGTTC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 50 1.00
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.21
Consensus pattern (35 bp):
AGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAA
Found at i:13675 original size:105 final size:105
Alignment explanation
Indices: 13489--13723 Score: 436
Period size: 105 Copynumber: 2.2 Consensus size: 105
13479 GTCCTAAAGG
13489 AGAA-AGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATGAGAAAAACATGTTC
1 AGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATGAGAAAAACATGTTC
13553 TTTCTAAGTCCACCGCAAAAGGATTTGGATCAACATTTCC
66 TTTCTAAGTCCACCGCAAAAGGATTTGGATCAACATTTCC
*
13593 AGAAGAGTTCATAATGAGAAGAACTCGTCCTAAATGAGAAAGTTCATAATGAGAAAAACATGTTC
1 AGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATGAGAAAAACATGTTC
*
13658 TTTCTAAGTCCACCGCAAAAGGATTTGGATCAACGTTTCC
66 TTTCTAAGTCCACCGCAAAAGGATTTGGATCAACATTTCC
*
13698 AAAAGAGTTCATAATGAGAAGAACTC
1 AGAAGAGTTCATAATGAGAAGAACTC
13724 ATCCACGAGA
Statistics
Matches: 127, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
104 4 0.03
105 123 0.97
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.25
Consensus pattern (105 bp):
AGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATGAGAAAAACATGTTC
TTTCTAAGTCCACCGCAAAAGGATTTGGATCAACATTTCC
Found at i:13902 original size:3 final size:3
Alignment explanation
Indices: 13894--13958 Score: 121
Period size: 3 Copynumber: 21.7 Consensus size: 3
13884 AGTTAAAAAA
13894 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
13942 TAT TAT TAG TAT TAT TA
1 TAT TAT TAT TAT TAT TA
13959 AGTGTATTTA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:15326 original size:14 final size:16
Alignment explanation
Indices: 15302--15334 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
15292 GTTTATTTTG
15302 TTTTAAGTATTT-TAT
1 TTTTAAGTATTTATAT
15317 TTTTAA-TATTTATAT
1 TTTTAAGTATTTATAT
15332 TTT
1 TTT
15335 AGTCACACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (16 bp):
TTTTAAGTATTTATAT
Found at i:15884 original size:2 final size:2
Alignment explanation
Indices: 15877--15907 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
15867 GTTAAACGTG
15877 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
15908 TTATTTAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15998 original size:49 final size:49
Alignment explanation
Indices: 15894--16111 Score: 359
Period size: 49 Copynumber: 4.4 Consensus size: 49
15884 ATATATATAT
* **
15894 ATATATATATATATTTATTTAATGTGTCTTGGAAACTGATTTTTTGTTC
1 ATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTC
15943 ATATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTC
1 --ATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTC
15994 ATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTC
1 ATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTC
*
16043 ATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTCTTTGTTC
1 ATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTC
*
16092 --ATATACATATATTTGTTTAA
1 ATATATATATATATTTGTTTAA
16112 TGTGTCTTAG
Statistics
Matches: 162, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
47 19 0.12
49 97 0.60
51 46 0.28
ACGTcount: A:0.30, C:0.08, G:0.11, T:0.51
Consensus pattern (49 bp):
ATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTC
Found at i:16282 original size:58 final size:58
Alignment explanation
Indices: 16179--16309 Score: 230
Period size: 58 Copynumber: 2.3 Consensus size: 58
16169 TTGTTAAACG
*
16179 TATATATATAT-TTTTATTTAATGTGTCTTGGAAACTGATTTTTTGTTCATATATATA
1 TATATATATATATATTATTTAATGTGTCTTGGAAACTGATTTTTTGTTCATATATATA
16236 TATATATATATATATTATTTAATG-GTCTTGGAAACTGATTTTTTTGTTCATATATATA
1 TATATATATATATATTATTTAATGTGTCTTGGAAACTGA-TTTTTTGTTCATATATATA
16294 TATATATATATATATT
1 TATATATATATATATT
16310 TGTTTAACAT
Statistics
Matches: 71, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
57 25 0.35
58 46 0.65
ACGTcount: A:0.33, C:0.05, G:0.09, T:0.53
Consensus pattern (58 bp):
TATATATATATATATTATTTAATGTGTCTTGGAAACTGATTTTTTGTTCATATATATA
Found at i:16378 original size:2 final size:2
Alignment explanation
Indices: 16371--16449 Score: 151
Period size: 2 Copynumber: 40.0 Consensus size: 2
16361 GCTTAGCTGG
16371 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
16413 AT AT AT AT AT AT AT -T 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
16450 TGCCATAAAA
Statistics
Matches: 76, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 75 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:23373 original size:23 final size:23
Alignment explanation
Indices: 23347--23407 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 23
23337 CCAAGTGTTT
23347 GTGAACATGTTCGTTTAACATTC
1 GTGAACATGTTCGTTTAACATTC
** * * *
23370 GTGAGTATATTTGTTTAATATTC
1 GTGAACATGTTCGTTTAACATTC
**
23393 ACGAACATGTTCGTT
1 GTGAACATGTTCGTT
23408 ATATATTTCG
Statistics
Matches: 27, Mismatches: 11, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.43
Consensus pattern (23 bp):
GTGAACATGTTCGTTTAACATTC
Found at i:23397 original size:81 final size:81
Alignment explanation
Indices: 23259--23419 Score: 259
Period size: 81 Copynumber: 2.0 Consensus size: 81
23249 TGATTCGTTT
* * * *
23259 AGTGTTTGTGAACTTATTCGTTTAACATTCGTGAGCATATTTGTTTATTGTTTACGAACATGTTC
1 AGTGTTTGTGAACATATTCGTTTAACATTCGTGAGCATATTTGTTTAATATTCACGAACATGTTC
*
23324 GTTATATGTTTCGCCA
66 GTTATATATTTCGCCA
* *
23340 AGTGTTTGTGAACATGTTCGTTTAACATTCGTGAGTATATTTGTTTAATATTCACGAACATGTTC
1 AGTGTTTGTGAACATATTCGTTTAACATTCGTGAGCATATTTGTTTAATATTCACGAACATGTTC
23405 GTTATATATTTCGCC
66 GTTATATATTTCGCC
23420 GACATATTCA
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 73 1.00
ACGTcount: A:0.24, C:0.14, G:0.18, T:0.45
Consensus pattern (81 bp):
AGTGTTTGTGAACATATTCGTTTAACATTCGTGAGCATATTTGTTTAATATTCACGAACATGTTC
GTTATATATTTCGCCA
Done.