Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002879.1 Hibiscus syriacus cultivar Beakdansim tig00005936_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: 492147
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 3 of 3
Found at i:460376 original size:112 final size:113
Alignment explanation
Indices: 459818--460377 Score: 643
Period size: 112 Copynumber: 4.9 Consensus size: 113
459808 GATTCAAATC
* **
459818 CATCACTT-GATGGATCAACATTTCCAG-AAGTGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 CATCA-TTCGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* *
459881 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATC
65 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATT
* * ** * *
459930 CATCACTT-GATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAG
1 CATCA-TTCGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* * * *
459994 AATAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
65 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATT
* *
460043 CATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG-AGGA
1 CATCATTCGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
**
460107 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTGCATGACTCTATCACAGAAGGA
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT---TG---C--T--C-GAA-TT
* ** * * *
460167 GAT-ATATC-A-ACATCAACTTTTCCAGAGAAAGTTTATAATGAGAAGAACTTATCTGAAG-AGG
1 CATCAT-TCGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* *
460228 AAGAAGAAGTTCATAATGATAAGAACTTGTTTAACCTTTTGCTCGAATT
65 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATT
* *
460277 CATCATTCGATGCATCAACTTTTCCAGAAAAAGTCCATAATGAGAAGAACTCATCTGAAGAAGG-
1 CATCATTCGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
460341 AGAAGAAGTTTATAATAAGAAGAACTTGTTCAACCTT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
460378 GCCTTAATTC
Statistics
Matches: 386, Mismatches: 43, Indels: 38
0.83 0.09 0.08
Matches are distributed among these distances:
110 4 0.01
111 6 0.02
112 143 0.37
113 131 0.34
114 1 0.00
115 2 0.01
116 1 0.00
118 1 0.00
119 2 0.01
120 1 0.00
122 85 0.22
123 5 0.01
124 4 0.01
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (113 bp):
CATCATTCGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATT
Found at i:460770 original size:3 final size:3
Alignment explanation
Indices: 460715--460756 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
460705 TCCATTTGAT
*
460715 TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
460757 AAAAAATTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:462223 original size:2 final size:2
Alignment explanation
Indices: 462216--462247 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
462206 TATATTAGTC
462216 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
462248 TTGTTTAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:466725 original size:15 final size:15
Alignment explanation
Indices: 466707--466778 Score: 62
Period size: 15 Copynumber: 5.0 Consensus size: 15
466697 AAATTTTAAA
466707 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
466722 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
** *
466737 TCA--TCGAT-AATA-
1 T-ATTTAAATAAAAAT
466749 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
466764 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
466779 CATCGATAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
11 1 0.02
12 1 0.02
13 6 0.14
14 6 0.14
15 29 0.66
16 1 0.02
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:466752 original size:42 final size:41
Alignment explanation
Indices: 466706--466793 Score: 167
Period size: 42 Copynumber: 2.1 Consensus size: 41
466696 GAAATTTTAA
466706 ATATTTAAATAAAAATTATTTATATAAAAATTCATCGATAAT
1 ATATTTAAATAAAAATTATTTATATAAAAA-TCATCGATAAT
466748 ATATTTAAATAAAAATTATTTATATAAAAATCATCGATAAT
1 ATATTTAAATAAAAATTATTTATATAAAAATCATCGATAAT
466789 ATATT
1 ATATT
466794 ATTTTATTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 16 0.35
42 30 0.65
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (41 bp):
ATATTTAAATAAAAATTATTTATATAAAAATCATCGATAAT
Found at i:469277 original size:37 final size:36
Alignment explanation
Indices: 469218--469337 Score: 181
Period size: 35 Copynumber: 3.3 Consensus size: 36
469208 ATCCCATTAT
* *
469218 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
469254 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
469290 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
469325 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
469338 TTGGTTACCA
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
35 35 0.45
36 13 0.17
37 29 0.38
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:469293 original size:21 final size:21
Alignment explanation
Indices: 469269--469329 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
469259 TTCAAAGAAA
469269 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
469290 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
469304 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
469325 CATTT
1 CATTT
469330 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:469346 original size:35 final size:36
Alignment explanation
Indices: 469220--469364 Score: 142
Period size: 35 Copynumber: 4.1 Consensus size: 36
469210 CCCATTATCA
*
469220 TTTTTCAACA-AACA-TCTACCAAACTTTGAAAAAC-T
1 TTTTTCAA-AGAACAGT-TACCAAACTTTGAAAACCAT
*
469255 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA-
1 -TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
*
469292 -TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
1 TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
***
469328 TTTTTCAAAG-TTGGTTACCAAAC-TTGAAAACCAT
1 TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
469362 TTT
1 TTT
469365 AATAATTTCA
Statistics
Matches: 98, Mismatches: 5, Indels: 14
0.84 0.04 0.12
Matches are distributed among these distances:
34 14 0.14
35 45 0.46
36 8 0.08
37 30 0.31
38 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.33
Consensus pattern (36 bp):
TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
Found at i:473419 original size:16 final size:16
Alignment explanation
Indices: 473395--473428 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
473385 TATCGCCGAC
*
473395 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
473411 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
473427 CG
1 CG
473429 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:473905 original size:36 final size:37
Alignment explanation
Indices: 473834--473918 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 37
473824 ATCCCATTAT
*
473834 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
* *
473870 TATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
1 CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
473906 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
473919 TTGGTTACCA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
36 13 0.30
37 30 0.70
ACGTcount: A:0.42, C:0.20, G:0.05, T:0.33
Consensus pattern (37 bp):
CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
Found at i:484393 original size:22 final size:23
Alignment explanation
Indices: 484365--484414 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
484355 TTTTATGAAT
*
484365 AGTGATGAACAGTACC-GTAAAC
1 AGTGATGAACAATACCTGTAAAC
*
484387 AGTGATGAACAATACCTGTGAAC
1 AGTGATGAACAATACCTGTAAAC
484410 AGTGA
1 AGTGA
484415 ACAGTGTACC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 15 0.60
23 10 0.40
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.20
Consensus pattern (23 bp):
AGTGATGAACAATACCTGTAAAC
Found at i:484953 original size:47 final size:46
Alignment explanation
Indices: 484879--485049 Score: 224
Period size: 47 Copynumber: 3.8 Consensus size: 46
484869 ATAAAATCTT
*
484879 TTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
1 TTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
* * *
484924 TTACCATTTAAATTCTATAAGCTCATAAGCTTATTTTATACAAAATAC
1 TTACCATTT-AATTCCATAAGCTCGTAAGCTTATTTTA-CCAAAATAC
* *
484972 TTACCATTTAA-TCCATAAGCTCGTAAGCTTATTTTACCCATATAC
1 TTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
* *
485017 TTGCCA-TT-ATTCCAAAAGCTCGTAAGCTTATTT
1 TTACCATTTAATTCCATAAGCTCGTAAGCTTATTT
485050 GTATGCTTAC
Statistics
Matches: 111, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
43 1 0.01
44 24 0.22
45 20 0.18
46 23 0.21
47 26 0.23
48 17 0.15
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.38
Consensus pattern (46 bp):
TTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
Done.