Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008469.1 Hibiscus syriacus cultivar Beakdansim tig00111290_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: 51992
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:5346 original size:38 final size:38
Alignment explanation
Indices: 5304--5470 Score: 144
Period size: 38 Copynumber: 4.5 Consensus size: 38
5294 CAATGTTCTA
* * * *
5304 TATTTAAGAATTTAAATTTAATTAAAATTTGAATATGT
1 TATTTAAGAATTTATATTTGATTAAAATATGAATATAT
* * *
5342 TATTTATGAATTTATATTCGATTGAAATATGAATATAT
1 TATTTAAGAATTTATATTTGATTAAAATATGAATATAT
***
5380 TATTTATA-AATTTATATTTGATT-AAATGCAAATATAT
1 TATTTA-AGAATTTATATTTGATTAAAATATGAATATAT
* * * **
5417 TATTTATGAATTTATA-TTCATTAAGATACAAATATAT
1 TATTTAAGAATTTATATTTGATTAAAATATGAATATAT
* *
5454 TA-TCATGAATTTATATT
1 TATTTAAGAATTTATATT
5471 AGTTTAGAAT
Statistics
Matches: 108, Mismatches: 17, Indels: 9
0.81 0.13 0.07
Matches are distributed among these distances:
36 17 0.16
37 40 0.37
38 51 0.47
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.48
Consensus pattern (38 bp):
TATTTAAGAATTTATATTTGATTAAAATATGAATATAT
Found at i:5423 original size:37 final size:37
Alignment explanation
Indices: 5335--5484 Score: 169
Period size: 37 Copynumber: 4.0 Consensus size: 37
5325 TTAAAATTTG
* * **
5335 AATATGTTATTTATGAATTTATATTCGATTGAAATATG
1 AATATATTATTTATGAATTTATATTTGATT-AAATACA
* *
5373 AATATATTATTTATAAATTTATATTTGATTAAATGCA
1 AATATATTATTTATGAATTTATATTTGATTAAATACA
*
5410 AATATATTATTTATGAATTTATA-TTCATTAAGATACA
1 AATATATTATTTATGAATTTATATTTGATTAA-ATACA
* * *
5447 AATATATTA-TCATGAATTTATATTAGTTTAGAATACA
1 AATATATTATTTATGAATTTATATTTGATTA-AATACA
5484 A
1 A
5485 TATTGTAGTT
Statistics
Matches: 96, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
36 19 0.20
37 49 0.51
38 28 0.29
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (37 bp):
AATATATTATTTATGAATTTATATTTGATTAAATACA
Found at i:5434 original size:17 final size:17
Alignment explanation
Indices: 5375--5434 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
5365 GAAATATGAA
*
5375 TATATTATTTATAAATT
1 TATATTATTTATGAATT
* *
5392 TATATTTGATTAAATGCAA-A
1 TATA-TT-ATT-TATG-AATT
5412 TATATTATTTATGAATT
1 TATATTATTTATGAATT
5429 TATATT
1 TATATT
5435 CATTAAGATA
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
16 2 0.06
17 13 0.39
18 5 0.15
19 5 0.15
20 6 0.18
21 2 0.06
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (17 bp):
TATATTATTTATGAATT
Found at i:17488 original size:3 final size:3
Alignment explanation
Indices: 17480--17539 Score: 95
Period size: 3 Copynumber: 20.0 Consensus size: 3
17470 AATTATTTTT
*
17480 TAA TAA TAA TAA T-A TATA TAA TAA TTA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
17525 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
17540 AATGAGTAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
2 2 0.04
3 48 0.91
4 3 0.06
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:18515 original size:112 final size:112
Alignment explanation
Indices: 17958--18720 Score: 1116
Period size: 112 Copynumber: 6.8 Consensus size: 112
17948 ATCTATCGAG
* * * * *
17958 TGATGAATTTGAGCAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTTTTCAGAT
1 TGATGAATTTAAGCAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT
* ** *
18023 GAGTTCTTCTCATTATGAACTCTTTCACTGGGGATGCTGATCCATCAAA
66 GAGTTCTTCTCATTATGAA--CTTTCTCTGGCAAAGCTGATCCATCAAA
* *
18072 TGATGAATTTAAACAAAAGGTTGAACAAATTCTTTTCATTATGAACTTCTTCTTCCTTCTTCAGA
1 TGATGAATTTAAGCAAAA-GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
* *
18137 TGAGTTCTTCTCATTATGAATTTTTTCTGG-AGAAGCTGATCCATCAAA
65 TGAGTTCTTCTCATTATGAACTTTCTCTGGCA-AAGCTGATCCATCAAA
* * *
18185 TGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGA
1 TGATGAATTTAAGCAAAA-GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
* *
18250 TGAGTTCTTCTCATTATGAACTTTCTCTGGCAAAGCTAATCCATCAAG
65 TGAGTTCTTCTCATTATGAACTTTCTCTGGCAAAGCTGATCCATCAAA
* * *
18298 TGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGA
1 TGATGAATTTAAGCAAAA-GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
18363 TGAGTTCTTCTCATTATGAACTTTCTCTGGCAAAGCTGATCCATCAAA
65 TGAGTTCTTCTCATTATGAACTTTCTCTGGCAAAGCTGATCCATCAAA
* * *
18411 TAATGAATTCAAGCAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAT
1 TGATGAATTTAAGCAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT
* *
18476 GAGTTCTTCTTATTATGAACTTTCTCTGGCAAAGTTGATCCATCAAA
66 GAGTTCTTCTCATTATGAACTTTCTCTGGCAAAGCTGATCCATCAAA
* * * *
18523 TAATGAATTCAAGCAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTT-CTCTCTTCAGA
1 TGATGAATTTAAGCAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCT-TCTTCAGA
*
18587 TGAGTTCTTCTTATTATGAACTTTCTCTGGCAAAGCTGATCCATCAAA
65 TGAGTTCTTCTCATTATGAACTTTCTCTGGCAAAGCTGATCCATCAAA
* * * * * *
18635 TGATGAATTCAAGCAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCTTTTTTCAGAC
1 TGATGAATTTAAGCAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT
18700 GAGTTCTTCTCATTATGAACT
66 GAGTTCTTCTCATTATGAACT
18721 CTAACTGACA
Statistics
Matches: 606, Mismatches: 38, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
111 2 0.00
112 276 0.46
113 250 0.41
114 17 0.03
115 61 0.10
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.39
Consensus pattern (112 bp):
TGATGAATTTAAGCAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT
GAGTTCTTCTCATTATGAACTTTCTCTGGCAAAGCTGATCCATCAAA
Found at i:20313 original size:19 final size:16
Alignment explanation
Indices: 20289--20333 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 16
20279 TTTCAAAATT
20289 ATAAATTGAATCTTCGAAA
1 ATAAATTGAATC-TC--AA
*
20308 ATAAATTAAATCTCAA
1 ATAAATTGAATCTCAA
20324 ATAAATTGAA
1 ATAAATTGAA
20334 CTTGGAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 11 0.46
18 2 0.08
19 11 0.46
ACGTcount: A:0.53, C:0.09, G:0.07, T:0.31
Consensus pattern (16 bp):
ATAAATTGAATCTCAA
Found at i:20681 original size:7 final size:7
Alignment explanation
Indices: 20665--20781 Score: 134
Period size: 7 Copynumber: 16.7 Consensus size: 7
20655 CTTGACCCCC
20665 TTTTTC-
1 TTTTTCT
20671 TTTTTCT
1 TTTTTCT
20678 TTTTTCT
1 TTTTTCT
*
20685 TTTCTCT
1 TTTTTCT
*
20692 TTTCTCT
1 TTTTTCT
20699 TTTTTC-
1 TTTTTCT
*
20705 TTTCT-T
1 TTTTTCT
20711 TTTTTCT
1 TTTTTCT
20718 CTTTTTCT
1 -TTTTTCT
20726 CTTTTTC-
1 -TTTTTCT
20733 TTTTTCT
1 TTTTTCT
20740 TTTTTCT
1 TTTTTCT
*
20747 TTTCTCT
1 TTTTTCT
20754 TTTTTCTT
1 TTTTTC-T
20762 TTCTTTCT
1 TT-TTTCT
20770 TTTTTCT
1 TTTTTCT
20777 TTTTT
1 TTTTT
20782 TGTTTTTTTT
Statistics
Matches: 98, Mismatches: 6, Indels: 13
0.84 0.05 0.11
Matches are distributed among these distances:
6 20 0.20
7 54 0.55
8 20 0.20
9 4 0.04
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTTCT
Found at i:20752 original size:55 final size:56
Alignment explanation
Indices: 20665--20795 Score: 189
Period size: 55 Copynumber: 2.4 Consensus size: 56
20655 CTTGACCCCC
20665 TTTTTCTTTTTCTTTTTTCTTTTCTCTTTTCTCTTTTTTC-TTTCTTT-TTTTCTCT
1 TTTTTCTTTTTC-TTTTTCTTTTCTCTTTTCTCTTTTTTCTTTTCTTTCTTTTCTCT
* *
20720 TTTTCTCTTTTTCTTTTTCTTTTTTCTTTTCTCTTTTTTCTTTTCTTTCTTTTTTCT
1 TTTT-TCTTTTTCTTTTTCTTTTCTCTTTTCTCTTTTTTCTTTTCTTTCTTTTCTCT
20777 TTTTT-TGTTTT-TTTTTCTT
1 TTTTTCT-TTTTCTTTTTCTT
20796 CAAGCATAAT
Statistics
Matches: 70, Mismatches: 2, Indels: 8
0.88 0.03 0.10
Matches are distributed among these distances:
55 39 0.56
56 20 0.29
57 11 0.16
ACGTcount: A:0.00, C:0.18, G:0.01, T:0.82
Consensus pattern (56 bp):
TTTTTCTTTTTCTTTTTCTTTTCTCTTTTCTCTTTTTTCTTTTCTTTCTTTTCTCT
Found at i:20762 original size:62 final size:59
Alignment explanation
Indices: 20664--20782 Score: 193
Period size: 62 Copynumber: 2.0 Consensus size: 59
20654 TCTTGACCCC
20664 CTTTTTCTTTTTCTTTTTTCTTTTCTCTTTTCTCTTTTTTCTTTCTTTTTTTCTCTTTTTCT
1 CTTTTTCTTTTTCTTTTTTCTTTTCTCTTTTCTC--TTTTCTTTC-TTTTTTCTCTTTTTCT
* *
20726 CTTTTTCTTTTTCTTTTTTCTTTTCTCTTTTTTCTTTTCTTTCTTTTTTCTTTTTTT
1 CTTTTTCTTTTTCTTTTTTCTTTTCTCTTTTCTCTTTTCTTTCTTTTTTCTCTTTTT
20783 GTTTTTTTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
59 13 0.24
60 9 0.16
62 33 0.60
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (59 bp):
CTTTTTCTTTTTCTTTTTTCTTTTCTCTTTTCTCTTTTCTTTCTTTTTTCTCTTTTTCT
Found at i:28012 original size:15 final size:15
Alignment explanation
Indices: 27989--28020 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
27979 TGAAATGAAT
27989 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
28004 AATGCATGTATGCAA
1 AATGAATGTATGCAA
28019 AA
1 AA
28021 AGATATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:33440 original size:3 final size:3
Alignment explanation
Indices: 33432--33491 Score: 95
Period size: 3 Copynumber: 20.0 Consensus size: 3
33422 AATTATTTTT
*
33432 TAA TAA TAA TAA T-A TATA TAA TAA TTA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
33477 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
33492 AATGAGTAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
2 2 0.04
3 48 0.91
4 3 0.06
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:39941 original size:2 final size:2
Alignment explanation
Indices: 39934--39967 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
39924 AATAGAAAAC
39934 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
39968 GTACCTAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:44269 original size:64 final size:62
Alignment explanation
Indices: 44201--44410 Score: 185
Period size: 65 Copynumber: 3.3 Consensus size: 62
44191 TGCACTAAGA
* *
44201 GTGCATCGATGCATCAAGTGCATTTGATGTTTCAAAATAGTCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATA-TCAGAGTGCATCGATGCATGG-TG
* * * **
44265 GTGCAACGATTCATCAAATGCATTCAATGTTTTCATAAA-ATCCTCAGTGCATCGATGCATGGTA
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAT-CAGAGTGCATCGATGCATGGT-
*
44329 T
62 G
* *
44330 GTGCATCGATGCATGAAATACATTCGATG-TTCAATTTAAT-TCATGA-TGCATCGATGCATGGA
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAA---AATATCA-GAGTGCATCGATGCATGG-
44392 TTG
61 -TG
*
44395 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
44411 CTATGAAAAA
Statistics
Matches: 117, Mismatches: 18, Indels: 21
0.75 0.12 0.13
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 42 0.36
65 66 0.56
66 4 0.03
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.31
Consensus pattern (62 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATATCAGAGTGCATCGATGCATGGTG
Found at i:45103 original size:14 final size:15
Alignment explanation
Indices: 45084--45113 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
45074 TTCAAACATT
45084 AAACAATCCA-AAAC
1 AAACAATCCAGAAAC
45098 AAACAATCCAGAAAC
1 AAACAATCCAGAAAC
45113 A
1 A
45114 TCAAAATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.63, C:0.27, G:0.03, T:0.07
Consensus pattern (15 bp):
AAACAATCCAGAAAC
Found at i:48316 original size:23 final size:24
Alignment explanation
Indices: 48286--48333 Score: 89
Period size: 23 Copynumber: 2.0 Consensus size: 24
48276 ATTTACCTTT
48286 ATGCTTTAAAAAC-ATGTAGTGTC
1 ATGCTTTAAAAACAATGTAGTGTC
48309 ATGCTTTAAAAACAATGTAGTGTC
1 ATGCTTTAAAAACAATGTAGTGTC
48333 A
1 A
48334 ACCTTCCCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 13 0.54
24 11 0.46
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (24 bp):
ATGCTTTAAAAACAATGTAGTGTC
Found at i:50858 original size:22 final size:21
Alignment explanation
Indices: 50816--50855 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
50806 ATATGAGTTT
*
50816 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
50837 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
50856 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Done.