Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008012.1 Hibiscus syriacus cultivar Beakdansim tig00110475_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: 62157
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:8532 original size:20 final size:21
Alignment explanation
Indices: 8478--8540 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
8468 GATTCCCATG
8478 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
8502 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
8522 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
8541 GCACAAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:15456 original size:35 final size:35
Alignment explanation
Indices: 15410--15480 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
15400 TATGCCTTCC
15410 ACGGTGGTTGACGCTTCACATCATAAATCATCTCA
1 ACGGTGGTTGACGCTTCACATCATAAATCATCTCA
15445 ACGGTGGTTGACGCTTCACATCATAAATCATCTCA
1 ACGGTGGTTGACGCTTCACATCATAAATCATCTCA
15480 A
1 A
15481 TCATCTGAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (35 bp):
ACGGTGGTTGACGCTTCACATCATAAATCATCTCA
Found at i:33392 original size:22 final size:22
Alignment explanation
Indices: 33367--33412 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
33357 GCATTCGATA
33367 CTTTAAATTTTTACTAATTATT
1 CTTTAAATTTTTACTAATTATT
* * **
33389 CTTTGATTTTTTTTTAATTATT
1 CTTTAAATTTTTACTAATTATT
33411 CT
1 CT
33413 AATATCACTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.24, C:0.09, G:0.02, T:0.65
Consensus pattern (22 bp):
CTTTAAATTTTTACTAATTATT
Found at i:43041 original size:21 final size:21
Alignment explanation
Indices: 43004--43043 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
42994 AAAAAAGGAA
*
43004 AAAGACAAAAAATGAAAAATG
1 AAAGACAAAAAAAGAAAAATG
43025 AAAGA-AAAAGAAAGAAAAA
1 AAAGACAAAA-AAAGAAAAA
43044 AAAATAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.78, C:0.03, G:0.15, T:0.05
Consensus pattern (21 bp):
AAAGACAAAAAAAGAAAAATG
Found at i:44257 original size:48 final size:48
Alignment explanation
Indices: 44181--44709 Score: 597
Period size: 48 Copynumber: 11.3 Consensus size: 48
44171 CAAGTCTGCC
* * * *
44181 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCAA
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCTTCTCCA
* *
44229 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTCTTCTCAA
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCTTCTCCA
* *
44277 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAATCTATCTTCTCCA
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCTTCTCCA
* * *
44325 AGATCTGATATTTCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCA
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCTTCTCCA
* *
44373 AGATTTGATATTCCCTTTAGAGTAAGTGGAACAAG----TC-T-GCC-
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCTTCTCCA
* * * * *
44414 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTTTTCTCAA
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCTTCTCCA
* *
44462 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAATCTATCTTCTCCA
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCTTCTCCA
* * * * *
44510 AGATCTGATATTTCCTTCAGAGTAAGCGAAACATGTCTCTCTTCTCCA
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCTTCTCCA
*
44558 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAG----TC-T-ACC-
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCTTCTCCA
* * * *
44599 AGATCTGACATTCCCTTCAGAGTAAGTGGAACAGGTCTCT-TTTTCCA
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCTTCTCCA
* * * *
44646 TGATTTGATATTCCCTTCAGAAG-AAGCGGAACATA-TCTCTTTTTTCCA
1 AGATTTGATATTCCCTTCAG-AGTAAGTGGAACA-AGTCTCTCTTCTCCA
* *
44694 AGGTTTGGTATTCCCT
1 AGATTTGATATTCCCT
44710 GTGACAGCGG
Statistics
Matches: 409, Mismatches: 55, Indels: 34
0.82 0.11 0.07
Matches are distributed among these distances:
41 63 0.15
42 4 0.01
43 2 0.00
44 4 0.01
45 3 0.01
46 3 0.01
47 32 0.08
48 298 0.73
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.33
Consensus pattern (48 bp):
AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCTTCTCCA
Found at i:44432 original size:185 final size:184
Alignment explanation
Indices: 44093--44683 Score: 804
Period size: 185 Copynumber: 3.2 Consensus size: 184
44083 CAAGATTTTC
* ** *
44093 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCAAGAT-TGATATTTCCTT
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAATCTATCTTCTCCAAGATCTGATATTTCCTT
* * * * *
44157 TAGAGTAAGTGGAACAAG----TC-T-GCC-AGATCTGATATTCCCTTCAGAGTAAGCGGAACAG
66 CAGAGTAAGTGGAACAAGTCTCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAA
* * *
44215 GTCTCTCTTCTCAAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTCTTCTCAA
131 G----TCTAC-C--AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCT-TTCTCAA
44277 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAATCTATCTTCTCCAAGATCTGATATTTCCTT
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAATCTATCTTCTCCAAGATCTGATATTTCCTT
* *
44342 CAGAGTAAGTGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCCTTTAGAGTAAGTGGAACAA
66 CAGAGTAAGTGGAACAAGTCTCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAA
*
44407 GTCTGCCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTTTTCTCAA
131 GTCTACCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTC-TTTCTCAA
44462 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAATCTATCTTCTCCAAGATCTGATATTTCCTT
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAATCTATCTTCTCCAAGATCTGATATTTCCTT
* * *
44527 CAGAGTAAGCGAAACATGTCTCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAA
66 CAGAGTAAGTGGAACAAGTCTCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAA
* * * *
44592 GTCTACCAGATCTGACATTCCCTTCAGAGTAAGTGGAACAGGTCTCTTTTTCCA
131 GTCTACCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTTTCTCAA
* * *
44646 TGATTTGATATTCCCTTCAGAAG-AAGCGGAACATATCT
1 AGATTTGATATTCCCTTCAG-AGTAAGTGGAACAAATCT
44684 CTTTTTTCCA
Statistics
Matches: 371, Mismatches: 26, Indels: 20
0.89 0.06 0.05
Matches are distributed among these distances:
184 86 0.23
185 243 0.65
186 1 0.00
187 1 0.00
188 4 0.01
189 2 0.01
190 1 0.00
191 2 0.01
192 31 0.08
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (184 bp):
AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAATCTATCTTCTCCAAGATCTGATATTTCCTT
CAGAGTAAGTGGAACAAGTCTCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAA
GTCTACCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTTTCTCAA
Found at i:44476 original size:89 final size:89
Alignment explanation
Indices: 44325--44666 Score: 488
Period size: 89 Copynumber: 3.8 Consensus size: 89
44315 ATCTTCTCCA
* *
44325 AGATCTGATATTTCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCCTT
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCCTT
* *
44390 TAGAGTAAGTGGAACAAGTCTGCC
66 CAGAGTAAGTGGAACAAGTCTACC
* *
44414 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTTTTCTCAAAGATTTGATATTCCCTT
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCCTT
*
44479 CAGAGTAAGTGGAACAAATCTATCTTCTCC
66 CAGAGTAAGTGGAACAAGTCTA------CC
* * *
44509 AAGATCTGATATTTCCTTCAGAGTAAGCGAAACATGTCTCTCTTCTCCAAGATTTGATATTCCCT
1 -AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCCT
44574 TCAGAGTAAGTGGAACAAGTCTACC
65 TCAGAGTAAGTGGAACAAGTCTACC
* * * *
44599 AGATCTGACATTCCCTTCAGAGTAAGTGGAACAGGTCTCT-TTTTCCATGATTTGATATTCCCTT
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCCTT
44663 CAGA
66 CAGA
44667 AGAAGCGGAA
Statistics
Matches: 226, Mismatches: 20, Indels: 15
0.87 0.08 0.06
Matches are distributed among these distances:
88 26 0.12
89 115 0.51
90 2 0.01
95 2 0.01
96 81 0.36
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.33
Consensus pattern (89 bp):
AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCCTT
CAGAGTAAGTGGAACAAGTCTACC
Found at i:44507 original size:233 final size:232
Alignment explanation
Indices: 44093--44595 Score: 853
Period size: 233 Copynumber: 2.2 Consensus size: 232
44083 CAAGATTTTC
*
44093 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCAAGATTGATATTTCCTTT
1 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCAAGATTGATATTCCCTTT
44158 AGAGTAAGTGGAACAAGTCTGCCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCT
66 AGAGTAAGTGGAACAAGTCTGCCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCT
* * *
44223 TCTCAAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTCTTCTCAAAGATTTGATAT
131 TCTCAAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAAATCTATCTTCTCAAAGATCTGATAT
* *
44288 TCCCTTCAGAGTAAGTGGAACAAATCTATCTTCTCCA
196 TCCCTTCAGAGTAAGCGAAACAAATCTATCTTCTCCA
*
44325 AGATCTGATATTTCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCCTT
1 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCAAGA-TTGATATTCCCTT
*
44390 TAGAGTAAGTGGAACAAGTCTGCCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTT
65 TAGAGTAAGTGGAACAAGTCTGCCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTC
* *
44455 TTCTCAAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAATCTATCTTCTCCAAGATCTGATA
130 TTCTCAAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAAATCTATCTTCTCAAAGATCTGATA
* ** *
44520 TTTCCTTCAGAGTAAGCGAAACATGTCTCTCTTCTCCA
195 TTCCCTTCAGAGTAAGCGAAACAAATCTATCTTCTCCA
* *
44558 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCT
1 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCT
44596 ACCAGATCTG
Statistics
Matches: 253, Mismatches: 17, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
232 50 0.20
233 203 0.80
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.32
Consensus pattern (232 bp):
AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCAAGATTGATATTCCCTTT
AGAGTAAGTGGAACAAGTCTGCCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCT
TCTCAAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAAATCTATCTTCTCAAAGATCTGATAT
TCCCTTCAGAGTAAGCGAAACAAATCTATCTTCTCCA
Found at i:52135 original size:28 final size:29
Alignment explanation
Indices: 52104--52159 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
52094 TAATAATTCG
52104 AAAGTTAAATGACT-AAATTAAAAATATT
1 AAAGTTAAATGACTAAAATTAAAAATATT
* *
52132 AAAGTTGAATGACTAAAATTAAGAATAT
1 AAAGTTAAATGACTAAAATTAAAAATAT
52160 AGTCAAGTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.55, C:0.04, G:0.11, T:0.30
Consensus pattern (29 bp):
AAAGTTAAATGACTAAAATTAAAAATATT
Found at i:53616 original size:7 final size:7
Alignment explanation
Indices: 53604--53671 Score: 91
Period size: 7 Copynumber: 9.7 Consensus size: 7
53594 ACACAGAACT
*
53604 GCCTATG
1 GCCTATA
*
53611 GCCTATG
1 GCCTATA
*
53618 GCCTATG
1 GCCTATA
* *
53625 GACTATG
1 GCCTATA
53632 GCCTATA
1 GCCTATA
53639 GCCTATA
1 GCCTATA
53646 GCCTATA
1 GCCTATA
53653 GCCTATA
1 GCCTATA
53660 GCCTATA
1 GCCTATA
53667 GCCTA
1 GCCTA
53672 CAGGTGGTGG
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 58 1.00
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.28
Consensus pattern (7 bp):
GCCTATA
Done.