Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004219.1 Hibiscus syriacus cultivar Beakdansim tig00009239_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: 55877
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:3277 original size:20 final size:20
Alignment explanation
Indices: 3252--3360 Score: 152
Period size: 20 Copynumber: 5.5 Consensus size: 20
3242 ATTAAGGCAA
3252 TATCGATACTCTAGGATGAG
1 TATCGATACTCTAGGATGAG
3272 TATCGATACTCTAGGATGAG
1 TATCGATACTCTAGGATGAG
3292 TATCGATACTCTAGGATGAG
1 TATCGATACTCTAGGATGAG
* *
3312 TATCGATACTCTAGTGTAGGGG
1 TATCGATACTCTAG-G-ATGAG
3334 TATCGATA--CTA-GACTGAG
1 TATCGATACTCTAGGA-TGAG
3352 TATCGATAC
1 TATCGATAC
3361 CAAAATTGGA
Statistics
Matches: 81, Mismatches: 4, Indels: 9
0.86 0.04 0.10
Matches are distributed among these distances:
17 1 0.01
18 11 0.14
20 57 0.70
21 1 0.01
22 11 0.14
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (20 bp):
TATCGATACTCTAGGATGAG
Found at i:5296 original size:60 final size:59
Alignment explanation
Indices: 5163--5531 Score: 512
Period size: 60 Copynumber: 6.2 Consensus size: 59
5153 TCTAAAATAA
* *
5163 AAGTTAGATGAAAAGTAAAATGCCTAACAGTGCATTTTGGTAGAAA----CACTAATGC
1 AAGTTAGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGTAGAAAGGTGCACTAATGC
5218 AAGTTAGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGTAGAAAGGTGTCACTAATGC
1 AAGTTAGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGTAGAAAGGTG-CACTAATGC
* * *
5278 AAGTTAGATGAAAAGTTAAATGCCTAATGGTGCATTTTGGCAAAAAGGTGCAACTAATGC
1 AAGTTAGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGTAGAAAGGTGC-ACTAATGC
* * * *
5338 AAGTTAGATGAAAAGTTAAATGCCTAACGGTGTATTTTGGAATAAATGTGTCACTAATGC
1 AAGTTAGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGTAGAAAGGTG-CACTAATGC
*
5398 AAGTTAGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGTAGAAAGGTGCCACTAAAGC
1 AAGTTAGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGTAGAAAGGTG-CACTAATGC
* * * * * *
5458 AAGTTAGATGAAAAGTTAAATGCATAATGGTTCATTTTGGCAGAAAGGTGCCACAAACGC
1 AAGTTAGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGTAGAAAGGTG-CACTAATGC
*
5518 AAGTTAAATGAAAA
1 AAGTTAGATGAAAA
5532 ATAGTGGATT
Statistics
Matches: 284, Mismatches: 23, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
55 44 0.15
59 1 0.00
60 238 0.84
61 1 0.00
ACGTcount: A:0.39, C:0.12, G:0.23, T:0.27
Consensus pattern (59 bp):
AAGTTAGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGTAGAAAGGTGCACTAATGC
Found at i:5462 original size:180 final size:175
Alignment explanation
Indices: 5163--5531 Score: 567
Period size: 180 Copynumber: 2.1 Consensus size: 175
5153 TCTAAAATAA
*
5163 AAGTTAGATGAAAAGTAAAATGCCTAACAGTGCATTTTGGTAGAAACACTAATGCAAGTTAGATG
1 AAGTTAGATGAAAAGTAAAATGCCTAACAGTGCATTTTGGAAGAAACACTAATGCAAGTTAGATG
* *
5228 AAAAGTTAAATGCCTAACGGTGCATTTTGGTAGAAAGGTGTCACTAATGCAAGTTAGATGAAAAG
66 AAAAGTTAAATGCCTAACGGTGCATTTTGGTAGAAAGGTGCCACTAAAGCAAGTTAGATGAAAAG
* * *
5293 TTAAATGCCTAATGGTGCATTTTGGCAAAAAGGTGCAACTAATGC
131 TTAAATGCATAATGGTGCATTTTGGCAAAAAGGTGCAACAAACGC
* * * *
5338 AAGTTAGATGAAAAGTTAAATGCCTAACGGTGTATTTTGGAATAAATGTGTCACTAATGCAAGTT
1 AAGTTAGATGAAAAGTAAAATGCCTAACAGTGCATTTTGGAAGAAA-----CACTAATGCAAGTT
5403 AGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGTAGAAAGGTGCCACTAAAGCAAGTTAGATG
61 AGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGTAGAAAGGTGCCACTAAAGCAAGTTAGATG
* * *
5468 AAAAGTTAAATGCATAATGGTTCATTTTGGCAGAAAGGTGCCACAAACGC
126 AAAAGTTAAATGCATAATGGTGCATTTTGGCAAAAAGGTGCAACAAACGC
*
5518 AAGTTAAATGAAAA
1 AAGTTAGATGAAAA
5532 ATAGTGGATT
Statistics
Matches: 175, Mismatches: 14, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
175 41 0.23
180 134 0.77
ACGTcount: A:0.39, C:0.12, G:0.23, T:0.27
Consensus pattern (175 bp):
AAGTTAGATGAAAAGTAAAATGCCTAACAGTGCATTTTGGAAGAAACACTAATGCAAGTTAGATG
AAAAGTTAAATGCCTAACGGTGCATTTTGGTAGAAAGGTGCCACTAAAGCAAGTTAGATGAAAAG
TTAAATGCATAATGGTGCATTTTGGCAAAAAGGTGCAACAAACGC
Found at i:10388 original size:17 final size:17
Alignment explanation
Indices: 10330--10382 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
10320 TGAATAAAGT
10330 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* *
10347 TAGTTCATTCATGAAAC
1 TAGTTCATTAATTAAAC
*
10364 TAGTTCATTTATTAAAC
1 TAGTTCATTAATTAAAC
10381 TA
1 TA
10383 ACTCATAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.42
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:14109 original size:60 final size:60
Alignment explanation
Indices: 14036--14527 Score: 761
Period size: 60 Copynumber: 8.2 Consensus size: 60
14026 AAAATAAAAT
* *
14036 TTAGATGAAAAGTTAAATGCCTAATGGTGCATTTTGGCATAAAGGTGCCACTAATGCAAG
1 TTAGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGCAGAAAGGTGCCACTAATGCAAG
* *
14096 TTAGATGAAAAGTTAAATGCCTAACGATGCATTTTGGCATAAAGGTGCCACTAATGCAAG
1 TTAGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGCAGAAAGGTGCCACTAATGCAAG
* *
14156 TTAGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGTAGAAAGGTGTCACTAATGCAAG
1 TTAGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGCAGAAAGGTGCCACTAATGCAAG
* *
14216 TTAGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGCAGAAAGGTACCACTAAAGCAAG
1 TTAGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGCAGAAAGGTGCCACTAATGCAAG
* * * *
14276 TTAGATGAAAAGTTAAATGCCTAACGGTGTATTTTGGCAGAAAGGTGTCACAAATGGAAG
1 TTAGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGCAGAAAGGTGCCACTAATGCAAG
* * * *
14336 TTAGCTGAAACGTTAAATGCCTAACGGTGTATTTTGGCAGAAACGTGCCACTAATGCAAG
1 TTAGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGCAGAAAGGTGCCACTAATGCAAG
* * * *
14396 TTAGATGAAAAGTT-AATGCCTAAAGGTGCATTTTTGGAAGAAAGGTGCCATTAATCCAAG
1 TTAGATGAAAAGTTAAATGCCTAACGGTGCA-TTTTGGCAGAAAGGTGCCACTAATGCAAG
* *
14456 TTAGATGAAAAGTTAAATGCATAACGGTGCATTTCTGGTAGAAAGGTGCCACTAATGCAAG
1 TTAGATGAAAAGTTAAATGCCTAACGGTGCATTT-TGGCAGAAAGGTGCCACTAATGCAAG
14517 TTAGATGAAAA
1 TTAGATGAAAA
14528 ACAATGCATT
Statistics
Matches: 394, Mismatches: 35, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
59 14 0.04
60 332 0.84
61 48 0.12
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (60 bp):
TTAGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGCAGAAAGGTGCCACTAATGCAAG
Found at i:19162 original size:19 final size:19
Alignment explanation
Indices: 19138--19177 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
19128 ATTGAGGGCT
19138 CAAATGAAAGCTCTAAAGA
1 CAAATGAAAGCTCTAAAGA
19157 CAAATGAAAGCTCTAAAGA
1 CAAATGAAAGCTCTAAAGA
19176 CA
1 CA
19178 CTGAATTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.53, C:0.17, G:0.15, T:0.15
Consensus pattern (19 bp):
CAAATGAAAGCTCTAAAGA
Found at i:22836 original size:17 final size:17
Alignment explanation
Indices: 22814--22848 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
22804 TTCATAATGG
22814 CCCTTTACCATTATAAT
1 CCCTTTACCATTATAAT
22831 CCCTTTACCATTATAAT
1 CCCTTTACCATTATAAT
22848 C
1 C
22849 ATTTCACATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.31, G:0.00, T:0.40
Consensus pattern (17 bp):
CCCTTTACCATTATAAT
Found at i:28295 original size:59 final size:59
Alignment explanation
Indices: 28212--28332 Score: 188
Period size: 59 Copynumber: 2.1 Consensus size: 59
28202 AGTATATGGA
* ** *
28212 TAAGTGTCCTATCGAACCCTCCTAGTCGTAATGAAAAGGCAAACTCGATAATATGGCTC
1 TAAGTGTCATATCGAACCCTCCTAGTCACAATGAAAAGGCAAACTCGATAATATGACTC
* *
28271 TAAGTGTCATATTGAACCCTCCTAGTCACAATGAAAAGGCAAACTCGATAGTATGACTC
1 TAAGTGTCATATCGAACCCTCCTAGTCACAATGAAAAGGCAAACTCGATAATATGACTC
28330 TAA
1 TAA
28333 CCAACCCTCC
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (59 bp):
TAAGTGTCATATCGAACCCTCCTAGTCACAATGAAAAGGCAAACTCGATAATATGACTC
Found at i:33032 original size:20 final size:20
Alignment explanation
Indices: 33001--33051 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
32991 TTGTTTTAGT
* *
33001 ATGTTAGAAATTAATGTTGGA
1 ATGTT-GAAATTAATGATAGA
*
33022 ATGTTGAAATTGATGATAGA
1 ATGTTGAAATTAATGATAGA
33042 ATG-TGAAATT
1 ATGTTGAAATT
33052 GGGTCATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 7 0.26
20 15 0.56
21 5 0.19
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.37
Consensus pattern (20 bp):
ATGTTGAAATTAATGATAGA
Found at i:34423 original size:24 final size:23
Alignment explanation
Indices: 34396--34595 Score: 100
Period size: 24 Copynumber: 8.3 Consensus size: 23
34386 TCAATCATGT
34396 TTAGTGCATTCGTGCACTCTAGTA
1 TTAGTGCATTCGTGCACTCT-GTA
* *
34420 TTAGTGCATTTGTTGCACTCCTGTT
1 TTAGTGCATTCG-TGCACT-CTGTA
* *
34445 TTAGTGCCTT-GATGCACTCCAGT-
1 TTAGTGCATTCG-TGCACT-CTGTA
* *
34468 TATAGTGTATTTGTGCACTCCTGTA
1 T-TAGTGCATTCGTGCACT-CTGTA
* *
34493 TAAGTGCATACGTGCACTCTTGTA
1 TTAGTGCATTCGTGCACTC-TGTA
* * * * * * *
34517 TTATTACTTTTGGGTACTCCTGCA
1 TTAGTGCATTCGTGCACT-CTGTA
* *
34541 TTAGTGCATCCGTGCACTCCTGAA
1 TTAGTGCATTCGTGCACT-CTGTA
* *
34565 TCAGTGCCATT-GAGCACTCATGTA
1 TTAGTG-CATTCGTGCACTC-TGTA
34589 TTAGTGC
1 TTAGTGC
34596 TAGTATGCAT
Statistics
Matches: 133, Mismatches: 34, Indels: 19
0.72 0.18 0.10
Matches are distributed among these distances:
23 4 0.03
24 104 0.78
25 23 0.17
26 2 0.02
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.38
Consensus pattern (23 bp):
TTAGTGCATTCGTGCACTCTGTA
Found at i:34461 original size:49 final size:48
Alignment explanation
Indices: 34395--34511 Score: 139
Period size: 49 Copynumber: 2.4 Consensus size: 48
34385 ATCAATCATG
*
34395 TTTAGTGCATTCGTGCACTCTAG-TATTAGTGCATTTGTTGCACTCCTGT
1 TTTAGTGCATTCGTGCACTCCAGTTA-TAGTGCATTTG-TGCACTCCTGT
* *
34444 TTTAGTGCCTT-GATGCACTCCAGTTATAGTGTATTTGTGCACTCCTGT
1 TTTAGTGCATTCG-TGCACTCCAGTTATAGTGCATTTGTGCACTCCTGT
* * *
34492 ATAAGTGCATACGTGCACTC
1 TTTAGTGCATTCGTGCACTC
34512 TTGTATTATT
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
48 26 0.45
49 30 0.52
50 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (48 bp):
TTTAGTGCATTCGTGCACTCCAGTTATAGTGCATTTGTGCACTCCTGT
Found at i:38708 original size:21 final size:21
Alignment explanation
Indices: 38683--38744 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
38673 CCATAATAAG
38683 GGGTATCGGTACCCCTTCATA
1 GGGTATCGGTACCCCTTCATA
* *
38704 GGGTATAGGTACCCCTTAATA
1 GGGTATCGGTACCCCTTCATA
* *
38725 GGGTATCAGTACACCTTCAT
1 GGGTATCGGTACCCCTTCAT
38745 TAAATTCAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (21 bp):
GGGTATCGGTACCCCTTCATA
Found at i:38955 original size:36 final size:37
Alignment explanation
Indices: 38885--38955 Score: 101
Period size: 36 Copynumber: 1.9 Consensus size: 37
38875 GCAGTCATAG
* *
38885 GTGTATGGATACACCTGCAGGGGGTATCGGTACACCA
1 GTGTATGGATACACCTGCAAGGGGTATCGATACACCA
38922 GTGTATGGATACA-CT-CATAGGGGTATCGATACAC
1 GTGTATGGATACACCTGCA-AGGGGTATCGATACAC
38956 ATTTGCCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
35 2 0.06
36 16 0.52
37 13 0.42
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.24
Consensus pattern (37 bp):
GTGTATGGATACACCTGCAAGGGGTATCGATACACCA
Found at i:43271 original size:32 final size:31
Alignment explanation
Indices: 43226--43288 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 31
43216 TGCTCACGTT
43226 GATCTTACCTTAGTTACTCTCGAACACTAAG
1 GATCTTACCTTAGTTACTCTCGAACACTAAG
* *
43257 GATCTTTCACTTAGTTTCTCTCGAACACTAAG
1 GATCTTAC-CTTAGTTACTCTCGAACACTAAG
43289 ATTTAAACCT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 7 0.24
32 22 0.76
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.35
Consensus pattern (31 bp):
GATCTTACCTTAGTTACTCTCGAACACTAAG
Found at i:55832 original size:2 final size:2
Alignment explanation
Indices: 55825--55865 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
55815 AATTAAAATC
55825 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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
55866 CAAATATACA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.