Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000938.1 Hibiscus syriacus cultivar Beakdansim tig00001873_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: 37157
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:9833 original size:31 final size:31
Alignment explanation
Indices: 9795--9856 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
9785 TACCTAGAGA
9795 TCAGCCTTAGGCTTTAAGGTTTTTGGTTCTC
1 TCAGCCTTAGGCTTTAAGGTTTTTGGTTCTC
9826 TCAGCCTTAGGCTTTAAGGTTTTTGGTTCTC
1 TCAGCCTTAGGCTTTAAGGTTTTTGGTTCTC
9857 CCATTGGCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.13, C:0.19, G:0.23, T:0.45
Consensus pattern (31 bp):
TCAGCCTTAGGCTTTAAGGTTTTTGGTTCTC
Found at i:10234 original size:29 final size:29
Alignment explanation
Indices: 10201--10265 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
10191 ATAACTTAGC
*
10201 TAGGTTATTCTAATATGATTAAAACCCTA
1 TAGGTTATTCTAATAGGATTAAAACCCTA
* *
10230 TAGGTTATTCTAATAGGATTAGAAGCCTA
1 TAGGTTATTCTAATAGGATTAAAACCCTA
*
10259 GAGGTTA
1 TAGGTTA
10266 AATATTTGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.35
Consensus pattern (29 bp):
TAGGTTATTCTAATAGGATTAAAACCCTA
Found at i:12166 original size:127 final size:127
Alignment explanation
Indices: 11926--12182 Score: 471
Period size: 127 Copynumber: 2.0 Consensus size: 127
11916 CATAAAGATG
*
11926 GATTATTAGATTCATTTGTTTTCGAACAATATGATGTATATGAGTCTTGCTTGTTGGGAAAATGA
1 GATTATTAGATTCATTTGTTTTCGAACAATATGATATATATGAGTCTTGCTTGTTGGGAAAATGA
11991 TTAATGCTCCTTTTAATAGTAAAGGTGAGCAAGCAAGTGATTTATTGGGGTTAATACA-AGT
66 TTAATGCTCCTTTTAATAGTAAAGGTGAGCAAGCAAGTGATTTATTGGGGTTAATACATAGT
* *
12052 GATTATTAGATTTATTTGTTTTCGAACAATATGATATATGTGAGTCTTGCTTGTTGGGAAAAATG
1 GATTATTAGATTCATTTGTTTTCGAACAATATGATATATATGAGTCTTGCTTGTTGGG-AAAATG
12117 ATTAATGCTCCTTTTAATAGTAAAGGTGAGCAAGCAAGTGATTTATTGGGGTTAATACATAGT
65 ATTAATGCTCCTTTTAATAGTAAAGGTGAGCAAGCAAGTGATTTATTGGGGTTAATACATAGT
12180 GAT
1 GAT
12183 GTATGTGAAC
Statistics
Matches: 126, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
126 55 0.44
127 65 0.52
128 6 0.05
ACGTcount: A:0.31, C:0.08, G:0.22, T:0.39
Consensus pattern (127 bp):
GATTATTAGATTCATTTGTTTTCGAACAATATGATATATATGAGTCTTGCTTGTTGGGAAAATGA
TTAATGCTCCTTTTAATAGTAAAGGTGAGCAAGCAAGTGATTTATTGGGGTTAATACATAGT
Found at i:18238 original size:29 final size:29
Alignment explanation
Indices: 18094--18260 Score: 126
Period size: 29 Copynumber: 5.6 Consensus size: 29
18084 TGAAAATTAT
* * * *
18094 TTTATAAATTATAATAAAGGATACAATTT
1 TTTATAAATTACAATAAAGGATAAAACTA
*
18123 TTTCATAAATTACAAT-AA-TATACACAACTA
1 TTT-ATAAATTACAATAAAGGATA-A-AACTA
* * *
18153 TTTATAAATTACAATAGAGTACAAAA-TCA
1 TTTATAAATTACAATAAAGGATAAAACT-A
**
18182 TTTATAAATTACAATAAAATAAAATAAAACTA
1 TTTATAAATTACAAT--AA-AGGATAAAACTA
*
18214 TTTATAAATTATAATAAAGGATAAAACCT-
1 TTTATAAATTACAATAAAGGATAAAA-CTA
*
18243 TTTATAAATTATAATAAA
1 TTTATAAATTACAATAAA
18261 AAGAGATAAT
Statistics
Matches: 113, Mismatches: 14, Indels: 22
0.76 0.09 0.15
Matches are distributed among these distances:
28 4 0.04
29 60 0.53
30 23 0.20
31 4 0.04
32 21 0.19
33 1 0.01
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (29 bp):
TTTATAAATTACAATAAAGGATAAAACTA
Found at i:19832 original size:2 final size:2
Alignment explanation
Indices: 19825--19855 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
19815 TTTCCATAAC
19825 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
19856 AGTATCTAGG
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:28258 original size:29 final size:29
Alignment explanation
Indices: 28224--28282 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
28214 CCTAAATTAA
28224 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
28253 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
28282 T
1 T
28283 ATGTGCAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:28602 original size:40 final size:41
Alignment explanation
Indices: 28552--28651 Score: 157
Period size: 41 Copynumber: 2.5 Consensus size: 41
28542 TGATTAAACA
* *
28552 TGCTTTTGTTCACATTGGA-GGCACCATTTGGAGACATGAT
1 TGCTTTTGTTCACATTGGACGACACCATGTGGAGACATGAT
* *
28592 TGCTTGTGTTCAAATTGGACGACACCATGTGGAGACATGAT
1 TGCTTTTGTTCACATTGGACGACACCATGTGGAGACATGAT
28633 TGCTTTTGTTCACATTGGA
1 TGCTTTTGTTCACATTGGA
28652 TGACTATTAA
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 17 0.32
41 36 0.68
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (41 bp):
TGCTTTTGTTCACATTGGACGACACCATGTGGAGACATGAT
Found at i:29935 original size:65 final size:64
Alignment explanation
Indices: 29811--29964 Score: 202
Period size: 65 Copynumber: 2.4 Consensus size: 64
29801 TACACTAGGG
* * * *
29811 GTGCATCGGTACACTAATTACATTCGATGTTTCAAAGATCCAAGAGTGCATCAATGCATGG-TCT
1 GTGCATCGGTACACAAAATGCATTCGATGATTCAAAGATCCAAGAGTGCATCAATGCATGGCT-T
* * * *
29875 GTGCATCGGTACACAAAATGCATTTGATGATTCAAGATATTCAAGAGTGCATCGATGCATGGCTT
1 GTGCATCGGTACACAAAATGCATTCGATGATTCAA-AGATCCAAGAGTGCATCAATGCATGGCTT
*
29940 CTGCATCGGTACACAAAATGCATTC
1 GTGCATCGGTACACAAAATGCATTC
29965 AAAATGGGTA
Statistics
Matches: 78, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
64 30 0.38
65 47 0.60
66 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.29
Consensus pattern (64 bp):
GTGCATCGGTACACAAAATGCATTCGATGATTCAAAGATCCAAGAGTGCATCAATGCATGGCTT
Found at i:30693 original size:21 final size:22
Alignment explanation
Indices: 30668--30712 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
30658 CCAAAATAAA
*
30668 ACAATC-CAAAAACATCAATCC
1 ACAATCACAAAAACATAAATCC
*
30689 ACAATCATCAAAAATATAAATCC
1 ACAATCA-CAAAAACATAAATCC
30712 A
1 A
30713 AAAATATTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
23 14 0.70
ACGTcount: A:0.56, C:0.27, G:0.00, T:0.18
Consensus pattern (22 bp):
ACAATCACAAAAACATAAATCC
Found at i:32349 original size:15 final size:15
Alignment explanation
Indices: 32329--32359 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
32319 ACTAATCAAA
32329 ACTTGTCCTAAGTTC
1 ACTTGTCCTAAGTTC
32344 ACTTGTCCTAAGTTC
1 ACTTGTCCTAAGTTC
32359 A
1 A
32360 AAAATCAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.39
Consensus pattern (15 bp):
ACTTGTCCTAAGTTC
Found at i:32701 original size:43 final size:43
Alignment explanation
Indices: 32635--32734 Score: 125
Period size: 43 Copynumber: 2.3 Consensus size: 43
32625 TGCACAGTAG
*
32635 AGTGAATCGATGCACATTCAAGGG-CGCATCAGTACA-TCT-T
1 AGTGTATCGATGCACATTCAAGGGACGCATCAGTACACTCTCT
* *
32675 CATGATGTATCGATGCACATTCAAGGGATGCATCGGTACACTCTCT
1 -A-G-TGTATCGATGCACATTCAAGGGACGCATCAGTACACTCTCT
32721 AGTGTATCGATGCA
1 AGTGTATCGATGCA
32735 TGAAGCACAA
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
41 1 0.02
42 1 0.02
43 33 0.65
44 11 0.22
45 4 0.08
46 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (43 bp):
AGTGTATCGATGCACATTCAAGGGACGCATCAGTACACTCTCT
Found at i:36396 original size:20 final size:21
Alignment explanation
Indices: 36360--36399 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
36350 GAAGCTTTAA
*
36360 GATCATCAATTTTCTTTTGAT
1 GATCATCAATTTACTTTTGAT
36381 GATCAT-AATTTACTTTTGA
1 GATCATCAATTTACTTTTGA
36400 AAGTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.28, C:0.12, G:0.10, T:0.50
Consensus pattern (21 bp):
GATCATCAATTTACTTTTGAT
Done.