Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006524.1 Hibiscus syriacus cultivar Beakdansim tig00015899_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: 61893
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:4997 original size:25 final size:25
Alignment explanation
Indices: 4938--4998 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
4928 TTTCTTTGTT
*
4938 TTTCTTCTTCTTTTTGAGTGCTGAAA
1 TTTCTT-TTCTTTTGGAGTGCTGAAA
**
4964 TTT-TCTTTCTTTTGGAGTGCTTCAA
1 TTTCT-TTTCTTTTGGAGTGCTGAAA
4989 TTTCTTTTCT
1 TTTCTTTTCT
4999 GATTTTTCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 25 0.83
26 5 0.17
ACGTcount: A:0.11, C:0.16, G:0.13, T:0.59
Consensus pattern (25 bp):
TTTCTTTTCTTTTGGAGTGCTGAAA
Found at i:16532 original size:45 final size:45
Alignment explanation
Indices: 16462--16600 Score: 201
Period size: 45 Copynumber: 3.1 Consensus size: 45
16452 ATAACACACG
* *
16462 AAACTAACCCAAGAATGGCATAAGAACATTGTTTATTAAC-TACAT
1 AAACTTACCCAAGAATGGCCTAAGAACATTGTTTATTAACAT-CAT
* * *
16507 AAGCTTACCCAAGAATGGCCTAAGAACATGGTTCATTAACATCAT
1 AAACTTACCCAAGAATGGCCTAAGAACATTGTTTATTAACATCAT
16552 AAACTTACCCAAGAATGGCCTAAGAACA-TGTTTCATTAACATCAT
1 AAACTTACCCAAGAATGGCCTAAGAACATTGTTT-ATTAACATCAT
16597 AAAC
1 AAAC
16601 GTACACAAAA
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
44 3 0.04
45 80 0.95
46 1 0.01
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.25
Consensus pattern (45 bp):
AAACTTACCCAAGAATGGCCTAAGAACATTGTTTATTAACATCAT
Found at i:19230 original size:14 final size:17
Alignment explanation
Indices: 19194--19235 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 17
19184 TATATGATAT
19194 ATAATATATATTTTTGG
1 ATAATATATATTTTTGG
*
19211 A-AA-ATAT-TTTTTTG
1 ATAATATATATTTTTGG
19225 ATAATATATAT
1 ATAATATATAT
19236 AATATATAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 6
0.75 0.04 0.21
Matches are distributed among these distances:
14 7 0.33
15 6 0.29
16 6 0.29
17 2 0.10
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.52
Consensus pattern (17 bp):
ATAATATATATTTTTGG
Found at i:19287 original size:56 final size:58
Alignment explanation
Indices: 19192--19303 Score: 142
Period size: 56 Copynumber: 1.9 Consensus size: 58
19182 TATATATGAT
*
19192 ATATAATATATATTTTTGGAAAATATTTTTTTGATAATATATATA-ATATATAGTTTCAAAA
1 ATATAATATATATTTTTGGAAAACA--TTTTTGA-AATATATATATA-ATATAGTTTCAAAA
19253 ATATAATATATAGTTTTT-GAAAACA-TTTTG-AATATATATATAATATAGTTT
1 ATATAATATATA-TTTTTGGAAAACATTTTTGAAATATATATATAATATAGTTT
19304 TTGAAAATAT
Statistics
Matches: 48, Mismatches: 1, Indels: 9
0.83 0.02 0.16
Matches are distributed among these distances:
56 19 0.40
57 1 0.02
58 5 0.10
61 18 0.38
62 5 0.10
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (58 bp):
ATATAATATATATTTTTGGAAAACATTTTTGAAATATATATATAATATAGTTTCAAAA
Found at i:19299 original size:37 final size:37
Alignment explanation
Indices: 19253--19347 Score: 131
Period size: 35 Copynumber: 2.6 Consensus size: 37
19243 AGTTTCAAAA
*
19253 ATATAATATATAGTTTTTGAAAACATTTTGAATATAT
1 ATATAATATATAGTTTTTGAAAACATTTTGAAAATAT
*
19290 ATAT-A-ATATAGTTTTTGAAAATATTTTGAAAATAT
1 ATATAATATATAGTTTTTGAAAACATTTTGAAAATAT
* * *
19325 ATATATTTTATAGTTTTTAAAAA
1 ATATAATATATAGTTTTTGAAAA
19348 TATATTTATA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
35 32 0.63
36 1 0.02
37 18 0.35
ACGTcount: A:0.44, C:0.01, G:0.07, T:0.47
Consensus pattern (37 bp):
ATATAATATATAGTTTTTGAAAACATTTTGAAAATAT
Found at i:19342 original size:26 final size:27
Alignment explanation
Indices: 19313--19366 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
19303 TTTGAAAATA
* *
19313 TTTTGAAAATATA-TATATTTTATAGT
1 TTTTAAAAATATATTATATATTATAGT
19339 TTTTAAAAATATATTTATATATTATAGT
1 TTTTAAAAATATA-TTATATATTATAGT
19367 ATATGATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 12 0.50
28 12 0.50
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.54
Consensus pattern (27 bp):
TTTTAAAAATATATTATATATTATAGT
Found at i:19348 original size:37 final size:35
Alignment explanation
Indices: 19253--19350 Score: 128
Period size: 37 Copynumber: 2.8 Consensus size: 35
19243 AGTTTCAAAA
*
19253 ATATA-AT-ATATAGTTTTTGAAAACATTTTGAAT
1 ATATATATAATATAGTTTTTGAAAATATTTTGAAT
19286 ATATATATAATATAGTTTTTGAAAATATTTTGAAAAT
1 ATATATATAATATAGTTTTTGAAAATATTTTG--AAT
** *
19323 ATATATATTTTATAGTTTTTAAAAATAT
1 ATATATATAATATAGTTTTTGAAAATAT
19351 ATTTATATAT
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
33 5 0.09
34 2 0.04
35 22 0.39
37 28 0.49
ACGTcount: A:0.44, C:0.01, G:0.07, T:0.48
Consensus pattern (35 bp):
ATATATATAATATAGTTTTTGAAAATATTTTGAAT
Found at i:32853 original size:39 final size:39
Alignment explanation
Indices: 32794--32966 Score: 156
Period size: 39 Copynumber: 4.3 Consensus size: 39
32784 TTTTGAAAAC
* *
32794 ATATAATTTTTAAAAATATTTTGAATATATATATATATA
1 ATATAGTTTTTGAAAATATTTTGAATATATATATATATA
* * *
32833 ATATAGTTTTTGAAAGTATTTTGAAAACATATATA-AT-
1 ATATAGTTTTTGAAAATATTTTGAATATATATATATATA
*
32870 ATATAGTTTTTGAAAACATTTTGAATATGTATATATATATATATATACA
1 ATATAGTTTTTG-AAA-ATATT---T-TG-A-ATATATATATATAT--A
* *
32919 ATATAGTTTTTGAAAACATTTTGAA-A-ATATATATATT
1 ATATAGTTTTTGAAAATATTTTGAATATATATATATATA
32956 ATATAGTTTTT
1 ATATAGTTTTT
32967 TAGATATATT
Statistics
Matches: 110, Mismatches: 12, Indels: 26
0.74 0.08 0.18
Matches are distributed among these distances:
37 23 0.21
38 5 0.05
39 43 0.39
40 1 0.01
41 1 0.01
42 2 0.02
43 4 0.04
44 2 0.02
45 9 0.08
46 2 0.02
47 3 0.03
48 3 0.03
49 12 0.11
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (39 bp):
ATATAGTTTTTGAAAATATTTTGAATATATATATATATA
Found at i:32874 original size:37 final size:38
Alignment explanation
Indices: 32794--32912 Score: 159
Period size: 37 Copynumber: 3.1 Consensus size: 38
32784 TTTTGAAAAC
* *
32794 ATATAATTTTTAAAAATATTTTGAATATATATATATAT
1 ATATAGTTTTTGAAAATATTTTGAATATATATATATAT
* * *
32832 AATATAGTTTTTGAAAGTATTTTGAAAACATATATA-AT
1 -ATATAGTTTTTGAAAATATTTTGAATATATATATATAT
* *
32870 ATATAGTTTTTGAAAACATTTTGAATATGTATATATAT
1 ATATAGTTTTTGAAAATATTTTGAATATATATATATAT
32908 ATATA
1 ATATA
32913 TATACAATAT
Statistics
Matches: 69, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
37 30 0.43
38 9 0.13
39 30 0.43
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.46
Consensus pattern (38 bp):
ATATAGTTTTTGAAAATATTTTGAATATATATATATAT
Found at i:32923 original size:49 final size:48
Alignment explanation
Indices: 32861--32960 Score: 157
Period size: 49 Copynumber: 2.1 Consensus size: 48
32851 TTTTGAAAAC
* *
32861 ATATATAATATATAGTTTTTGAAAACATTTTGAATATGTATATATATAT
1 ATATATAATATATAGTTTTTGAAAACATTTTGAAAATATATATAT-TAT
32910 ATATATACA-ATATAGTTTTTGAAAACATTTTGAAAATATATATATTAT
1 ATATATA-ATATATAGTTTTTGAAAACATTTTGAAAATATATATATTAT
32958 ATA
1 ATA
32961 GTTTTTTAGA
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
48 6 0.12
49 41 0.85
50 1 0.02
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (48 bp):
ATATATAATATATAGTTTTTGAAAACATTTTGAAAATATATATATTAT
Found at i:36154 original size:59 final size:59
Alignment explanation
Indices: 36085--36412 Score: 470
Period size: 59 Copynumber: 5.6 Consensus size: 59
36075 TATATTTCCC
* ** * *
36085 ATACGGAAATTCATACACCTAAAATGAATTTCTTAACATGTTT-GTACACAAAGTGCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACAT-TTTAGCACACATAGTGCCCA
36144 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACA-TTTA--ACACATAGTGCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCA
* * *
36200 ATACGAAAATT-AGTGCACTTAGTTTGAATTTCTTAACATTTTAGCACACATAGTGCCCA
1 ATACGGAAATTCA-TACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCA
* * *
36259 ATACAGAAATT-ATTACATTTAATATGAATTTCTTAACATTTTAGCACACATAGTGCCCA
1 ATACGGAAATTCA-TACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCA
* *
36318 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACTCATAATGCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCA
36377 ATACGGAAATTCATACACTTAGTATGAATTTCTTAA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAA
36413 AAAATTCCAC
Statistics
Matches: 244, Mismatches: 19, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
55 1 0.00
56 46 0.19
57 7 0.03
59 189 0.77
60 1 0.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (59 bp):
ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCA
Found at i:36885 original size:17 final size:19
Alignment explanation
Indices: 36843--36879 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
36833 AGATTCGATG
36843 TTACC-TGGTATCGATACC
1 TTACCATGGTATCGATACC
36861 TTTACCATGGTATCGATAC
1 -TTACCATGGTATCGATAC
36880 TACCATACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.35
Consensus pattern (19 bp):
TTACCATGGTATCGATACC
Found at i:44305 original size:59 final size:59
Alignment explanation
Indices: 44234--44521 Score: 397
Period size: 59 Copynumber: 4.9 Consensus size: 59
44224 TATATTTCCC
* *
44234 ATACGGAAATTCATACACCTAGTATGAATTTCTTAACATGTTT-GCACACAAAGTGCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACAT-TTTAGCACACATAGTGCCCA
* *
44293 ATACGGAAATTCATACACTTAGTATGGATTTCTTAATATTTTAGCACACATAGTGCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCA
44352 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTA--ACAC--AGTGCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCA
** * ***
44407 ATATAGAAATTCATACACTTAGTAAGAATTTAAAAACATTTTAGCACACATAGTGCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCA
* * * *
44466 ATATGAAAATTCATAAACTTAGTATGAATTTCTTAACATTTTTAGCACACTTAGTG
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACA-TTTTAGCACACATAGTG
44522 TCATTTGGTA
Statistics
Matches: 203, Mismatches: 20, Indels: 11
0.87 0.09 0.05
Matches are distributed among these distances:
55 45 0.22
57 8 0.04
58 3 0.01
59 131 0.65
60 16 0.08
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.33
Consensus pattern (59 bp):
ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCA
Found at i:44451 original size:114 final size:116
Alignment explanation
Indices: 44234--44507 Score: 399
Period size: 114 Copynumber: 2.4 Consensus size: 116
44224 TATATTTCCC
* *
44234 ATACGGAAATTCATACACCTAGTATGAATTTCTTAACATGTTTGCACACAAAGTGCCCAATACGG
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACAT-TTT-CACACAAAGTGCCCAATACAG
* * *** *
44299 AAATTCATACACTTAGTATGGATTTCTTAATATTTTAGCACACATAGTGCCCA
64 AAATTCATACACTTAGTAAGAATTTAAAAACATTTTAGCACACATAGTGCCCA
* *
44352 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTT-A-ACACAGTGCCCAATATAGAA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTCACACAAAGTGCCCAATACAGAA
44415 ATTCATACACTTAGTAAGAATTTAAAAACATTTTAGCACACATAGTGCCCA
66 ATTCATACACTTAGTAAGAATTTAAAAACATTTTAGCACACATAGTGCCCA
* * *
44466 ATATGAAAATTCATAAACTTAGTATGAATTTCTTAACATTTT
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTT
44508 TAGCACACTT
Statistics
Matches: 143, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
114 101 0.71
115 1 0.01
117 3 0.02
118 38 0.27
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (116 bp):
ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTCACACAAAGTGCCCAATACAGAA
ATTCATACACTTAGTAAGAATTTAAAAACATTTTAGCACACATAGTGCCCA
Found at i:45319 original size:17 final size:17
Alignment explanation
Indices: 45279--45320 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
45269 AAGTATGTTG
*
45279 TTCATTAAAGCATGCAT
1 TTCATTTAAGCATGCAT
*
45296 TTCATTTAAGCATGTAT
1 TTCATTTAAGCATGCAT
45313 TTCATTTA
1 TTCATTTA
45321 GGGAAGTAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (17 bp):
TTCATTTAAGCATGCAT
Found at i:45347 original size:17 final size:17
Alignment explanation
Indices: 45327--45385 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
45317 TTTAGGGAAG
45327 TAGTTCATTTATGCATC
1 TAGTTCATTTATGCATC
* *
45344 TAGTT-ATTTAAT-AAAC
1 TAGTTCATTT-ATGCATC
* * *
45360 TAATTCATTCATGCATT
1 TAGTTCATTTATGCATC
45377 TAGTTCATT
1 TAGTTCATT
45386 GAATAAAGTT
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
16 12 0.39
17 19 0.61
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (17 bp):
TAGTTCATTTATGCATC
Found at i:45399 original size:18 final size:18
Alignment explanation
Indices: 45376--45421 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
45366 ATTCATGCAT
45376 TTAGTTCATTGAATAAAG
1 TTAGTTCATTGAATAAAG
*
45394 TTAGTTCATTGAATAATG
1 TTAGTTCATTGAATAAAG
*
45412 TTATTTCATT
1 TTAGTTCATT
45422 AATCAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.48
Consensus pattern (18 bp):
TTAGTTCATTGAATAAAG
Found at i:60441 original size:40 final size:40
Alignment explanation
Indices: 60382--60539 Score: 160
Period size: 40 Copynumber: 4.0 Consensus size: 40
60372 ACCGTAGTAC
* *
60382 TTACACATAAGATTC-TGCCCATCATATGCA-TCGAAGTGCA
1 TTACACATAAG-GTCGTGCCCACCATATGCACT-GAAGTGCA
* * * *
60422 TTGCACGTAATGTCGTGCCCACCATATGCACTAAAGTGCA
1 TTACACATAAGGTCGTGCCCACCATATGCACTGAAGTGCA
** * *
60462 TTACATTTAAGGACGT-CCCACCATATGCACCGAAGTGCA
1 TTACACATAAGGTCGTGCCCACCATATGCACTGAAGTGCA
* * *
60501 TTACACATAAGGTTGTGCCCATCATACGCACTGAAGTGC
1 TTACACATAAGGTCGTGCCCACCATATGCACTGAAGTGC
60540 TTAATTGATA
Statistics
Matches: 95, Mismatches: 20, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
39 35 0.37
40 59 0.62
41 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (40 bp):
TTACACATAAGGTCGTGCCCACCATATGCACTGAAGTGCA
Done.