Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002432.1 Hibiscus syriacus cultivar Beakdansim tig00004973_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: 75479
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:8157 original size:21 final size:22
Alignment explanation
Indices: 8140--8180 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
8130 AGATTTATTA
*
8140 AAAAATATTAATATTTTA-AAT
1 AAAAATAATAATATTTTATAAT
8161 AAAAATAATAATATTTTATA
1 AAAAATAATAATATTTTATA
8181 TCATTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
AAAAATAATAATATTTTATAAT
Found at i:8450 original size:30 final size:31
Alignment explanation
Indices: 8415--8493 Score: 76
Period size: 30 Copynumber: 2.6 Consensus size: 31
8405 TGGTGACGGT
8415 TATTAAAATTAATATAATTATA-TAAT-TAA
1 TATTAAAATTAATATAATTATATTAATATAA
* *
8444 TCATTAATACTT-ATAT-ATTCTATTAATATAA
1 T-ATTAA-AATTAATATAATTATATTAATATAA
* *
8475 TATTAATATTAATTTAATT
1 TATTAAAATTAATATAATT
8494 CTTAAAATAA
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
29 8 0.21
30 21 0.54
31 10 0.26
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (31 bp):
TATTAAAATTAATATAATTATATTAATATAA
Found at i:8478 original size:11 final size:12
Alignment explanation
Indices: 8439--8492 Score: 51
Period size: 11 Copynumber: 4.5 Consensus size: 12
8429 TAATTATATA
8439 ATTAATCATTAAT
1 ATTAAT-ATTAAT
*
8452 ACTTATATATT-CT
1 A-TTA-ATATTAAT
8465 ATTAATA-TAAT
1 ATTAATATTAAT
8476 ATTAATATTAAT
1 ATTAATATTAAT
8488 -TTAAT
1 ATTAAT
8493 TCTTAAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
10 1 0.03
11 16 0.46
12 7 0.20
13 3 0.09
14 6 0.17
15 2 0.06
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (12 bp):
ATTAATATTAAT
Found at i:8884 original size:61 final size:62
Alignment explanation
Indices: 8818--8998 Score: 197
Period size: 61 Copynumber: 2.9 Consensus size: 62
8808 ATATATAAAC
* *
8818 AAATTCTAATAAATAAATTAAATTAAAATTTTCTTTTTTATAATTATTTTTAAATGATTC-C
1 AAATTCTAATAAATAAATTAAATTAAAATTTTCTTTTTTATAGTTATTTTTAAATGATTCAA
* * *** ** *
8879 GAATTCTAACAAATAAATTAAATTATTTTTTTCAGTTTTACT-GTTACTTTTAAATGATTCAA
1 AAATTCTAATAAATAAATTAAATTAAAATTTTCTTTTTTA-TAGTTATTTTTAAATGATTCAA
* * * *
8941 AAATTTTAATAAATAAA-TAAAATAAAATAATTCTTTTTTATAGTAATTTTTAAATGAT
1 AAATTCTAATAAATAAATTAAATTAAAAT-TTTCTTTTTTATAGTTATTTTTAAATGAT
8999 AAATGAATAA
Statistics
Matches: 94, Mismatches: 22, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
61 57 0.61
62 37 0.39
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (62 bp):
AAATTCTAATAAATAAATTAAATTAAAATTTTCTTTTTTATAGTTATTTTTAAATGATTCAA
Found at i:15054 original size:22 final size:24
Alignment explanation
Indices: 15016--15060 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
15006 GATGAGGAAG
*
15016 TATTTTTTATTTTTGG-AAGTAAA
1 TATTTGTTATTTTTGGAAAGTAAA
15039 TATTTGTTA-TTTTGGAAAGTAA
1 TATTTGTTATTTTTGGAAAGTAA
15061 TGGAATGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.53
Consensus pattern (24 bp):
TATTTGTTATTTTTGGAAAGTAAA
Found at i:18782 original size:91 final size:92
Alignment explanation
Indices: 18679--18864 Score: 322
Period size: 91 Copynumber: 2.0 Consensus size: 92
18669 CAATTAGAAG
*
18679 AGCTGGTATATTTTCCA-CTGAGAGAGAAAAAGGAGTCACTTATGTCCCATTAGACCCTCACATA
1 AGCTGGTATATTTTCCACCT-AGAGAGAAAAAGCAGTCACTTATGTCCCATTAGACCCTCACATA
18743 GAAAAAGGG-AAGCTATCTGAGCCAGCT
65 GAAAAAGGGAAAGCTATCTGAGCCAGCT
* *
18770 AGCTGGTATATTTTTCACCTAGAGAGAAAAAGCAGTCACTTATGTCCCATTAGGCCCTCACATAG
1 AGCTGGTATATTTTCCACCTAGAGAGAAAAAGCAGTCACTTATGTCCCATTAGACCCTCACATAG
18835 AAAAAGGGAAAGCTATCTGAGCCAGCT
66 AAAAAGGGAAAGCTATCTGAGCCAGCT
18862 AGC
1 AGC
18865 CTATCTGGTC
Statistics
Matches: 90, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
91 67 0.74
92 23 0.26
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.23
Consensus pattern (92 bp):
AGCTGGTATATTTTCCACCTAGAGAGAAAAAGCAGTCACTTATGTCCCATTAGACCCTCACATAG
AAAAAGGGAAAGCTATCTGAGCCAGCT
Found at i:22245 original size:18 final size:18
Alignment explanation
Indices: 22222--22256 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
22212 CGTACAAATT
*
22222 TGTCCCGTAGGACCACTA
1 TGTCCCGAAGGACCACTA
22240 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
22257 CCTTAAGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.34, G:0.23, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:24882 original size:2 final size:2
Alignment explanation
Indices: 24875--24905 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
24865 GCTCTGACTT
24875 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
24906 CTTATACGCT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27199 original size:21 final size:21
Alignment explanation
Indices: 27173--27215 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
27163 ATTCTGGGTT
* *
27173 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
27194 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
27215 A
1 A
27216 CGAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:27290 original size:67 final size:68
Alignment explanation
Indices: 27195--27346 Score: 209
Period size: 68 Copynumber: 2.2 Consensus size: 68
27185 ACCCATTCAA
* * *
27195 GGGGAACCGATACCCCTTCAACGAATATG-ATTTCCAGAATG-TTAGAGGGGAATCGGTACCCCC
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTT-GAGGGGAATCGATACCCCC
27258 AGGG
65 AGGG
* * * *
27262 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGGGGAATCGATACCCCTA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTTGAGGGGAATCGATACCCCCA
27327 GGG
66 GGG
*
27330 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
27347 ATGAGAAAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
67 26 0.35
68 47 0.63
69 2 0.03
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTTGAGGGGAATCGATACCCCCA
GGG
Found at i:27683 original size:29 final size:29
Alignment explanation
Indices: 27649--27720 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
27639 CATATTATGA
**
27649 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
* *
27678 TACATGACATGAATTCATCTTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
27707 TACATGACATGAAT
1 TACATGACATGAAT
27721 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:27784 original size:30 final size:30
Alignment explanation
Indices: 27735--27792 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
27725 AGAAAAGTTC
*
27735 TATGCACTATGTGATAAGGTATGTAAATGA
1 TATGCACTATGTGATAAGGTATGGAAATGA
*
27765 TATGC-CTATGTGTTAAAGGTATGGAAAT
1 TATGCACTATGTGAT-AAGGTATGGAAAT
27793 ACTATGTCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.32
30 17 0.68
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.34
Consensus pattern (30 bp):
TATGCACTATGTGATAAGGTATGGAAATGA
Found at i:28086 original size:22 final size:22
Alignment explanation
Indices: 28012--28078 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
28002 TTATGGACAT
28012 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
28034 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
28056 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
28078 A
1 A
28079 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:33462 original size:36 final size:36
Alignment explanation
Indices: 33415--33554 Score: 212
Period size: 36 Copynumber: 3.9 Consensus size: 36
33405 TGAATAAGAA
*
33415 GAACGAAAGGAAGCATCAGCACTTTCGATTCAAAAT
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAAAT
*
33451 GAACGGAAGGAAGCATCGGCACTTTCGATTCAAGAA-
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAA-AAT
*
33487 GAACGAAAGGAAGCATCGGCACTTTCGATTC-AAGT
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAAAT
* *
33522 GAACGGAAGGAAGCATCCGCACTTTCGATTCAA
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAA
33555 TTGTTCATCT
Statistics
Matches: 95, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
34 1 0.01
35 30 0.32
36 62 0.65
37 2 0.02
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.19
Consensus pattern (36 bp):
GAACGAAAGGAAGCATCGGCACTTTCGATTCAAAAT
Found at i:37888 original size:36 final size:36
Alignment explanation
Indices: 37785--37891 Score: 153
Period size: 36 Copynumber: 3.0 Consensus size: 36
37775 TCTGCAGGAG
**
37785 ATAGTTATTCTTCT-AAATATCTCATGCATCTATGGT
1 ATAGTTATTCTT-TGAAATATCTCATGCATCTGGGGT
* * *
37821 ATATTTATTCTTCGAAATATCTCATGAATCTGGGGT
1 ATAGTTATTCTTTGAAATATCTCATGCATCTGGGGT
37857 ATAGTTATTCTTTGAAATATCTCATGCATCTGGGG
1 ATAGTTATTCTTTGAAATATCTCATGCATCTGGGG
37892 CGTTTCCCAG
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
36 62 1.00
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (36 bp):
ATAGTTATTCTTTGAAATATCTCATGCATCTGGGGT
Found at i:56370 original size:15 final size:15
Alignment explanation
Indices: 56350--56392 Score: 68
Period size: 15 Copynumber: 2.8 Consensus size: 15
56340 CTGGAAGTTC
56350 CGGGTACCCGAAAAT
1 CGGGTACCCGAAAAT
*
56365 CGGGTATCCGAAAAT
1 CGGGTACCCGAAAAT
56380 CGGGTTACCCGAA
1 CGGG-TACCCGAA
56393 TTTGCACTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 18 0.72
16 7 0.28
ACGTcount: A:0.30, C:0.26, G:0.28, T:0.16
Consensus pattern (15 bp):
CGGGTACCCGAAAAT
Found at i:56473 original size:29 final size:29
Alignment explanation
Indices: 56431--56491 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
56421 GTTTAAATTA
56431 ACAATTAATGTTTACGTCGATACATTGAT
1 ACAATTAATGTTTACGTCGATACATTGAT
*
56460 ACAATTAATGTTTACGTTGATACATTGAT
1 ACAATTAATGTTTACGTCGATACATTGAT
56489 ACA
1 ACA
56492 TTGAGGTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (29 bp):
ACAATTAATGTTTACGTCGATACATTGAT
Found at i:64090 original size:7 final size:7
Alignment explanation
Indices: 64057--64088 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
64047 TTAGATGCCA
64057 AATGTTT
1 AATGTTT
64064 AATGTTT
1 AATGTTT
64071 AATGTTT
1 AATGTTT
*
64078 AATGCTT
1 AATGTTT
64085 AATG
1 AATG
64089 CTCAGCTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.31, C:0.03, G:0.16, T:0.50
Consensus pattern (7 bp):
AATGTTT
Found at i:67682 original size:25 final size:25
Alignment explanation
Indices: 67636--67684 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
67626 TAATATCTTT
*
67636 TCATCTCCTAAAAATTATAAATTTA
1 TCATCTCCTAAAAATTAAAAATTTA
* * *
67661 TCATCTCTTAAGACTTAAAAATTT
1 TCATCTCCTAAAAATTAAAAATTT
67685 TCTATCTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.41, C:0.16, G:0.02, T:0.41
Consensus pattern (25 bp):
TCATCTCCTAAAAATTAAAAATTTA
Found at i:75334 original size:28 final size:27
Alignment explanation
Indices: 75274--75338 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
75264 TAAATTCATA
*
75274 ATATTTATATATCTTAACTTTTAAAAT
1 ATATTTATTTATCTTAACTTTTAAAAT
*
75301 ATATTTATTTGTCTTAACTTATT-AAAT
1 ATATTTATTTATCTTAACTT-TTAAAAT
75328 ATAATTTATTT
1 AT-ATTTATTT
75339 TTTAATACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 24 0.71
28 10 0.29
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.55
Consensus pattern (27 bp):
ATATTTATTTATCTTAACTTTTAAAAT
Done.