Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002920.1 Hibiscus syriacus cultivar Beakdansim tig00006037_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: 72164
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1708 original size:250 final size:245
Alignment explanation
Indices: 1195--1730 Score: 683
Period size: 251 Copynumber: 2.2 Consensus size: 245
1185 CTTATTCACA
* *
1195 TATTAAATAAAAATATTTTTTATTATTC-GAGTCGGGTC-GG-GTTTCTAATTCATTTATAGGGT
1 TATTAAATAAAAATATTTTTTATTATTCTGGGTCGGGTCGGGTGTTTCTAATTCATATATAGGGT
1257 CAGGTCGGTGAAACTTTATTTTGGTCGGGTCGGTTTTTTAAGTGTGATATTCGGGTAGGTCGAGT
66 CAGGTCGGTGAAACTTTATTTTGGTCGGGTCGGTTTTTTAAGTGTGATATTCGGGTAGG-CGAGT
*
1322 TGGGTTTAGAGTGAAAAATACCCGACCCGAAAATATATATAATTTTACCTTATATATTTAGATAT
130 TGGGTTTAGAGTGAAAAATACCCAACCCGAAAATATATATAATTTTACCTTATATATTTAGATAT
1387 AATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAGTCATTGTTT
195 AATTACAATAATACCCCTCTATATAT-ATTTTTTTCAATTAAGTCATTGTTT
1439 TA-TAAATAAAAATATTTTTTTATTATTCTGGGTCGGGTCGGGTCAGATTTCTAATTCATATATT
1 TATTAAATAAAAATA-TTTTTTATTATTCTGGGTCGGGTCGGGT--G-TTTCTAATTCATATA-T
* * *
1503 CGGGTC-GGTCAGGTGATACTTTATTTGGTCTGGTTGGGTCGGTTTTTTTTTAAGTGTGATATTC
61 AGGGTCAGGTC-GGTGAAACTTTA-TT--T-TGGTCGGGTCGG---TTTTTTAAGTGTGATATTC
* * *
1567 GGGTCGG-G-TTTGGG-TTAGGGTG-AAAATACCCAACCC-AAAA-ATATATAATTTTACCTTAT
118 GGGTAGGCGAGTTGGGTTTAGAGTGAAAAATACCCAACCCGAAAATATATATAATTTTACCTTAT
1626 ATATTTAAGA-ATAATTACAAT-ATACCCCTCTATATAT-TTTTTTTCAATTAAGTC--TGCTTT
183 ATATTT-AGATATAATTACAATAATACCCCTCTATATATATTTTTTTCAATTAAGTCATTG--TT
1686 T
245 T
* *
1687 TATTGAATAAAAATAATTTTTTATTATT-TCGGTCGGGTCGGGTG
1 TATTAAATAAAAAT-ATTTTTTATTATTCTGGGTCGGGTCGGGTG
1731 AAACTTTATT
Statistics
Matches: 260, Mismatches: 11, Indels: 40
0.84 0.04 0.13
Matches are distributed among these distances:
243 12 0.05
244 15 0.06
245 9 0.03
246 5 0.02
248 36 0.14
249 23 0.09
250 35 0.13
251 53 0.20
252 9 0.03
253 13 0.05
254 8 0.03
255 16 0.06
256 1 0.00
258 25 0.10
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.42
Consensus pattern (245 bp):
TATTAAATAAAAATATTTTTTATTATTCTGGGTCGGGTCGGGTGTTTCTAATTCATATATAGGGT
CAGGTCGGTGAAACTTTATTTTGGTCGGGTCGGTTTTTTAAGTGTGATATTCGGGTAGGCGAGTT
GGGTTTAGAGTGAAAAATACCCAACCCGAAAATATATATAATTTTACCTTATATATTTAGATATA
ATTACAATAATACCCCTCTATATATATTTTTTTCAATTAAGTCATTGTTT
Found at i:2129 original size:17 final size:18
Alignment explanation
Indices: 2104--2150 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
2094 TATGGAATTG
*
2104 GATTCCAATTCC-TGACA
1 GATTCCAATTCCTTCACA
*
2121 GATTTCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
2139 GATTCCAATTCC
1 GATTCCAATTCC
2151 ATCAGAAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.34
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:14413 original size:2 final size:2
Alignment explanation
Indices: 14408--14438 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
14398 TTCAAAATTC
14408 AT AT 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 AT AT A
14439 CAAACTCGAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19524 original size:3 final size:3
Alignment explanation
Indices: 19516--19550 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
19506 GAAACTCCAA
19516 AAG AAG AAGG AAG AAG AAG AA- AAG AAG AAG AAG AA
1 AAG AAG AA-G AAG AAG AAG AAG AAG AAG AAG AAG AA
19551 AAATGATGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.83
4 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:19542 original size:11 final size:11
Alignment explanation
Indices: 19514--19547 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
19504 GTGAAACTCC
19514 AAAAGAAGAAG
1 AAAAGAAGAAG
*
19525 -GAAGAAGAAG
1 AAAAGAAGAAG
19535 AAAAGAAGAAG
1 AAAAGAAGAAG
19546 AA
1 AA
19548 GAAAAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAAG
Found at i:19544 original size:14 final size:14
Alignment explanation
Indices: 19516--19552 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
19506 GAAACTCCAA
*
19516 AAGAAG-AAGGAAG
1 AAGAAGAAAAGAAG
19529 AAGAAGAAAAGAAG
1 AAGAAGAAAAGAAG
19543 AAGAAGAAAA
1 AAGAAGAAAA
19553 ATGATGTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 6 0.27
14 16 0.73
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (14 bp):
AAGAAGAAAAGAAG
Found at i:25314 original size:13 final size:12
Alignment explanation
Indices: 25294--25338 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
25284 ACAATACATA
25294 ACTTTCATATCTC
1 ACTTTCATAT-TC
* *
25307 ATTTTCATCTTTC
1 ACTTTCAT-ATTC
25320 ACTTTCATATTC
1 ACTTTCATATTC
25332 ACTTTCA
1 ACTTTCA
25339 CATTTATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
12 10 0.37
13 16 0.59
14 1 0.04
ACGTcount: A:0.22, C:0.27, G:0.00, T:0.51
Consensus pattern (12 bp):
ACTTTCATATTC
Found at i:29740 original size:17 final size:18
Alignment explanation
Indices: 29713--29747 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
29703 CTCTATGTTG
29713 TTTTATGTATGATACTTT
1 TTTTATGTATGATACTTT
*
29731 TTTTAT-TATGGTACTTT
1 TTTTATGTATGATACTTT
29748 ATGGATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.20, C:0.06, G:0.11, T:0.63
Consensus pattern (18 bp):
TTTTATGTATGATACTTT
Found at i:32859 original size:18 final size:18
Alignment explanation
Indices: 32836--32881 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
32826 TAAAAGGGAT
*
32836 TAATGATAATAATATTGA
1 TAATGATAATAATATTAA
* *
32854 TAATGATAAGAATGTTAA
1 TAATGATAATAATATTAA
*
32872 TGATGATAAT
1 TAATGATAAT
32882 GATGATATAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.37
Consensus pattern (18 bp):
TAATGATAATAATATTAA
Found at i:33139 original size:2 final size:2
Alignment explanation
Indices: 33132--33183 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
33122 AATTGAATAG
*
33132 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33173 TA TA TA TA TA T
1 TA TA TA TA TA T
33184 TGTTATATTG
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:45397 original size:16 final size:16
Alignment explanation
Indices: 45363--45407 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
45353 ACTTGGAGAG
*
45363 GAAAGTAAG-AGAAAA
1 GAAAATAAGAAGAAAA
*
45378 GAAAATAAGAAGAAAT
1 GAAAATAAGAAGAAAA
*
45394 GAAAATGAGAAGAA
1 GAAAATAAGAAGAA
45408 GATGGAATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 8 0.31
16 18 0.69
ACGTcount: A:0.67, C:0.00, G:0.24, T:0.09
Consensus pattern (16 bp):
GAAAATAAGAAGAAAA
Found at i:53693 original size:92 final size:92
Alignment explanation
Indices: 53536--53815 Score: 560
Period size: 92 Copynumber: 3.0 Consensus size: 92
53526 TATACAAAAT
53536 ATTTAAGGTATATGATAATATATATTTATTAAGAGTGATTGCCACAAATAGCTTTCCTTCTATCT
1 ATTTAAGGTATATGATAATATATATTTATTAAGAGTGATTGCCACAAATAGCTTTCCTTCTATCT
53601 ATCCTTGATCACATATAAATTCTTAAA
66 ATCCTTGATCACATATAAATTCTTAAA
53628 ATTTAAGGTATATGATAATATATATTTATTAAGAGTGATTGCCACAAATAGCTTTCCTTCTATCT
1 ATTTAAGGTATATGATAATATATATTTATTAAGAGTGATTGCCACAAATAGCTTTCCTTCTATCT
53693 ATCCTTGATCACATATAAATTCTTAAA
66 ATCCTTGATCACATATAAATTCTTAAA
53720 ATTTAAGGTATATGATAATATATATTTATTAAGAGTGATTGCCACAAATAGCTTTCCTTCTATCT
1 ATTTAAGGTATATGATAATATATATTTATTAAGAGTGATTGCCACAAATAGCTTTCCTTCTATCT
53785 ATCCTTGATCACATATAAATTCTTAAA
66 ATCCTTGATCACATATAAATTCTTAAA
53812 ATTT
1 ATTT
53816 TATTTTAATT
Statistics
Matches: 188, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 188 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.41
Consensus pattern (92 bp):
ATTTAAGGTATATGATAATATATATTTATTAAGAGTGATTGCCACAAATAGCTTTCCTTCTATCT
ATCCTTGATCACATATAAATTCTTAAA
Found at i:57673 original size:28 final size:30
Alignment explanation
Indices: 57610--57676 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 30
57600 TTCTGGGTTA
*
57610 AAAAAATATAATTAAATTGTTAATAAAAAT
1 AAAAATTATAATTAAATTGTTAATAAAAAT
* ***
57640 ATAAATTAT-ATTAAATT-TTAATATTTAT
1 AAAAATTATAATTAAATTGTTAATAAAAAT
57668 AAAAATTAT
1 AAAAATTAT
57677 GATCGTTTCC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
28 16 0.52
29 8 0.26
30 7 0.23
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (30 bp):
AAAAATTATAATTAAATTGTTAATAAAAAT
Found at i:59402 original size:16 final size:15
Alignment explanation
Indices: 59380--59422 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
59370 ATATATAATT
59380 ATATAAATATTTTAA
1 ATATAAATATTTTAA
*
59395 TATTTAAAATATTTTTAA
1 -ATAT-AAATA-TTTTAA
59413 ATATAAATAT
1 ATATAAATAT
59423 AATATATCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
15 1 0.04
16 8 0.35
17 8 0.35
18 6 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATATAAATATTTTAA
Found at i:59419 original size:17 final size:17
Alignment explanation
Indices: 59379--59419 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
59369 TATATATAAT
59379 TATAT-AAATATTTTAA
1 TATATAAAATATTTTAA
*
59395 TATTTAAAATATTTTTAA
1 TATATAAAATA-TTTTAA
59413 -ATATAAA
1 TATATAAA
59420 TATAATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 4 0.19
17 11 0.52
18 6 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TATATAAAATATTTTAA
Found at i:59605 original size:2 final size:2
Alignment explanation
Indices: 59598--59643 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
59588 CGCTAAAAAG
59598 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
59640 AT AT
1 AT AT
59644 TTCTAATAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60086 original size:64 final size:60
Alignment explanation
Indices: 59985--60150 Score: 233
Period size: 64 Copynumber: 2.7 Consensus size: 60
59975 TACACTGTAT
*
59985 ACTAACATTCCCCGTGCACTCCAAACGTTCAGCAAGCTTTTGGCTCCTCTCGTAAAGCAAGCAC
1 ACTAACATTCCCCATGCACTCCAAACGTTCAGCAAGCTTTTGGCTCCTCTCGT--A--AAGCAC
* *
60049 ACTAACATTCCCCATGCACTCCAAACGTTCAACAAGCTTTTGGCTTCTCTCGTAAAGCAC
1 ACTAACATTCCCCATGCACTCCAAACGTTCAGCAAGCTTTTGGCTCCTCTCGTAAAGCAC
* * *
60109 ATTAAAATTCCCCATGCACTCCAAAACGTTTAGCAAGCTTTT
1 ACTAACATTCCCCATGCACTCC-AAACGTTCAGCAAGCTTTT
60151 CAACACTCTT
Statistics
Matches: 94, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
60 26 0.28
61 17 0.18
62 1 0.01
64 50 0.53
ACGTcount: A:0.29, C:0.32, G:0.13, T:0.27
Consensus pattern (60 bp):
ACTAACATTCCCCATGCACTCCAAACGTTCAGCAAGCTTTTGGCTCCTCTCGTAAAGCAC
Found at i:66416 original size:27 final size:27
Alignment explanation
Indices: 66366--66419 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
66356 TCATAGAGAA
* *
66366 GTCACCCTCAAAAGTCGCATGCTCATT
1 GTCACCCTCAAAACTCGCAGGCTCATT
66393 GTCACCCTCATAAACT-GCAGGCTCATT
1 GTCACCCTCA-AAACTCGCAGGCTCATT
66420 CATCATTCTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.26, C:0.33, G:0.15, T:0.26
Consensus pattern (27 bp):
GTCACCCTCAAAACTCGCAGGCTCATT
Found at i:69325 original size:17 final size:17
Alignment explanation
Indices: 69303--69340 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
69293 TTTCTAGAGT
69303 AATTCTATCATTTTCAA
1 AATTCTATCATTTTCAA
69320 AATTCTATCATTTTCAA
1 AATTCTATCATTTTCAA
69337 AATT
1 AATT
69341 TGAATACATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.37, C:0.16, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTCTATCATTTTCAA
Done.