Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002754.1 Hibiscus syriacus cultivar Beakdansim tig00005677_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: 59309
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:346 original size:75 final size:75
Alignment explanation
Indices: 244--448 Score: 258
Period size: 75 Copynumber: 2.8 Consensus size: 75
234 GACCGTTGAA
* *
244 CAGGGGGAATCGG-TAC-CCT-TGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAA
1 CAGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCAGAA
**
306 CAAAAATGTT
66 CAAAAACATT
* * *
316 TAGGGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCAGA
1 CA-GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCAGA
* * *
380 GCCAAACCATT
65 ACAAAAACATT
*
391 CAGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCA-ATCTGGAATT
1 CAGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATA-CTGGAATT
449 TTTTGGCTTT
Statistics
Matches: 113, Mismatches: 14, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
72 1 0.01
73 11 0.10
74 23 0.20
75 77 0.68
76 1 0.01
ACGTcount: A:0.22, C:0.23, G:0.30, T:0.24
Consensus pattern (75 bp):
CAGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCAGAA
CAAAAACATT
Found at i:3062 original size:20 final size:20
Alignment explanation
Indices: 3010--3070 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
3000 ATTCCCCTGT
3010 GGGGGGAATCGGTTCCCCTTCA
1 GGGGGGAATCGGTT-CCC-TCA
**
3032 AAGGGGAATCGGTTCCCTCA
1 GGGGGGAATCGGTTCCCTCA
* *
3052 GGGGGGGATCGATTCCCTC
1 GGGGGGAATCGGTTCCCTC
3071 TGCACCAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 18 0.55
21 3 0.09
22 12 0.36
ACGTcount: A:0.16, C:0.26, G:0.36, T:0.21
Consensus pattern (20 bp):
GGGGGGAATCGGTTCCCTCA
Found at i:8945 original size:75 final size:76
Alignment explanation
Indices: 8775--8979 Score: 283
Period size: 74 Copynumber: 2.8 Consensus size: 76
8765 GACCGTTGAA
* * *
8775 CAGGGGGGAATCGGTACC-CCT-TGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGA
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGA
**
8838 ACAAAAATGTT
66 ACAAAAACATT
*
8849 TA-GGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGA
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGA
* * *
8912 GCCAAACCATT
66 ACAAAAACATT
* *
8923 CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCAATCTGGAA
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAA
8980 TTTTTGGCTT
Statistics
Matches: 115, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
73 14 0.12
74 49 0.43
75 22 0.19
76 30 0.26
ACGTcount: A:0.22, C:0.24, G:0.31, T:0.23
Consensus pattern (76 bp):
CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGA
ACAAAAACATT
Found at i:9805 original size:256 final size:253
Alignment explanation
Indices: 9333--9837 Score: 631
Period size: 256 Copynumber: 2.0 Consensus size: 253
9323 TTCATTTCAA
* * * *
9333 TAAATTATAAAAATCATTTTTATTCAATAAAAATATTGACTTAATTGAAAAAAATTATATATAGG
1 TAAATAATAAAAATCATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAATTATATAGAGG
*
9398 GGGTATTATTATAATTATTCCTAAATATATAAGATAAATTATATTTTTTTCGGGTCGAGTCCGAT
66 GGGTATTATTATAATTATTCCTAAATATATAAGATAAATTATATTATTTTCGGGTCGAG--CGAT
*
9463 TTTTTTCACCTAAACCCAACCCAAATATCACACTTAAAAAAACCCGACCCGACTCGACCCGAACA
129 GTTTTTCACCTAAACCCAACCCAAATATCACACTTAAAAAAACCCGA-CC-ACTCGACCCGAACA
* *
9528 AAATAAAGTTTCACCCGACCCGATCCGAATATATGAATTAGAAA-TCTGACCCGACCTGACCC
192 AAATAAAGTTTCACCCGACCCGACCCGAATATATAAATTAGAAACTC-GACCCGACCTGACCC
9590 TAAATAATAAAAA--ATATTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAATTATATAGA-
1 TAAATAATAAAAATCAT-TTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAATTATATAGAG
* * *
9652 GGGTTATTATTGTAATTATTCCT-AA-ATATAAGGTAAAATTATATATATTTTCGGGTCG-G-G-
65 GGGGTATTATTATAATTATTCCTAAATATATAAGAT-AAATTATAT-TATTTTCGGGTCGAGCGA
9712 TGTTTTTCACCCTAAACCCGAACTCGACCCGACCCGAATATCACACTTAAAAAAA-CCGA-C-C-
128 TGTTTTTCA-CCTAAACCC--A----ACCC-A----AATATCACACTTAAAAAAACCCGACCACT
*
9773 CGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATAAATTAGAAACTCGACCCGA
181 CGACCCGAACAAAATAAAGTTTCACCCGACCCGACCCGAATATATAAATTAGAAACTCGACCCGA
9838 AATAATAAAA
Statistics
Matches: 220, Mismatches: 12, Indels: 33
0.83 0.05 0.12
Matches are distributed among these distances:
250 8 0.04
251 10 0.05
253 9 0.04
254 12 0.05
255 35 0.16
256 102 0.46
257 19 0.09
258 1 0.00
259 1 0.00
261 4 0.02
262 19 0.09
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (253 bp):
TAAATAATAAAAATCATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAATTATATAGAGG
GGGTATTATTATAATTATTCCTAAATATATAAGATAAATTATATTATTTTCGGGTCGAGCGATGT
TTTTCACCTAAACCCAACCCAAATATCACACTTAAAAAAACCCGACCACTCGACCCGAACAAAAT
AAAGTTTCACCCGACCCGACCCGAATATATAAATTAGAAACTCGACCCGACCTGACCC
Found at i:10265 original size:8 final size:8
Alignment explanation
Indices: 10254--10326 Score: 60
Period size: 8 Copynumber: 9.4 Consensus size: 8
10244 TAAATTCATA
*
10254 AAATTTAT
1 AAATATAT
*
10262 AAATAAAT
1 AAATATAT
10270 AAATATAT
1 AAATATAT
*
10278 ATATATAT
1 AAATATAT
*
10286 ATATATAT
1 AAATATAT
*
10294 ATATATAT
1 AAATATAT
* *
10302 ATATTTAT
1 AAATATAT
10310 AAA-AT-T
1 AAATATAT
*
10316 AAAAATAT
1 AAATATAT
10324 AAA
1 AAA
10327 AAAGTTTAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
6 4 0.07
7 3 0.05
8 49 0.88
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
AAATATAT
Found at i:10279 original size:2 final size:2
Alignment explanation
Indices: 10272--10310 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
10262 AAATAAATAA
*
10272 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10311 AAATTAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:14385 original size:112 final size:112
Alignment explanation
Indices: 14257--14483 Score: 445
Period size: 112 Copynumber: 2.0 Consensus size: 112
14247 CACACTTCGG
*
14257 TTTCTTGATTACATTTTACATGTAGCTAAAATGAATGGTTCTTTTCTGGAGGTGTGGTGGTCCCT
1 TTTCTTGATTACATTTTACATGTAGCTAAAATGAATGGTTCTTTTCTGGAGGTGTGCTGGTCCCT
14322 TTTCTTCTCTTGAAGAGGAGAGGTCATGTTTCTGTCTAGCACAGTGC
66 TTTCTTCTCTTGAAGAGGAGAGGTCATGTTTCTGTCTAGCACAGTGC
14369 TTTCTTGATTACATTTTACATGTAGCTAAAATGAATGGTTCTTTTCTGGAGGTGTGCTGGTCCCT
1 TTTCTTGATTACATTTTACATGTAGCTAAAATGAATGGTTCTTTTCTGGAGGTGTGCTGGTCCCT
14434 TTTCTTCTCTTGAAGAGGAGAGGTCATGTTTCTGTCTAGCACAGTGC
66 TTTCTTCTCTTGAAGAGGAGAGGTCATGTTTCTGTCTAGCACAGTGC
14481 TTT
1 TTT
14484 AAAAATCATT
Statistics
Matches: 114, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
112 114 1.00
ACGTcount: A:0.19, C:0.16, G:0.23, T:0.41
Consensus pattern (112 bp):
TTTCTTGATTACATTTTACATGTAGCTAAAATGAATGGTTCTTTTCTGGAGGTGTGCTGGTCCCT
TTTCTTCTCTTGAAGAGGAGAGGTCATGTTTCTGTCTAGCACAGTGC
Found at i:21092 original size:31 final size:31
Alignment explanation
Indices: 21054--21112 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
21044 AAACCCAAGA
21054 GGTTCCTAGTGAGAAGGACATATTGAATGGG
1 GGTTCCTAGTGAGAAGGACATATTGAATGGG
*
21085 GGTTCCTAGTGAGAAGGGCATATTGAAT
1 GGTTCCTAGTGAGAAGGACATATTGAAT
21113 TAACCGAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.29, C:0.10, G:0.34, T:0.27
Consensus pattern (31 bp):
GGTTCCTAGTGAGAAGGACATATTGAATGGG
Found at i:41329 original size:2 final size:2
Alignment explanation
Indices: 41322--41348 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
41312 TTAAATTTAT
41322 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 T
41349 GAATTTTGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.