Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002705.1 Hibiscus syriacus cultivar Beakdansim tig00005582_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: 469953
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:467147 original size:33 final size:33
Alignment explanation
Indices: 467110--467189 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
467100 GCGATTTGTG
*
467110 TTTCGCGTTGCGATTTTGTCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCATTGCGATTTTCA
*
467143 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCATTGCGATTTTCA
467176 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
467190 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCATTGCGATTTTCA
Found at i:467153 original size:19 final size:19
Alignment explanation
Indices: 467129--467189 Score: 78
Period size: 19 Copynumber: 3.5 Consensus size: 19
467119 GCGATTTTGT
467129 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
*
467148 CATTGCGA-TTT--TGTCG
1 CATTGCGATTTTCATTTCG
467164 --TTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
467181 CATTGCGAT
1 CATTGCGAT
467190 AGCCATTTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 6 0.17
15 3 0.09
16 4 0.11
17 4 0.11
18 3 0.09
19 15 0.43
ACGTcount: A:0.15, C:0.20, G:0.20, T:0.46
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:467208 original size:20 final size:20
Alignment explanation
Indices: 467162--467248 Score: 104
Period size: 20 Copynumber: 4.4 Consensus size: 20
467152 GCGATTTTGT
**
467162 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
* *
467181 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
467201 CGTTGCGATAGTCATTTCCA
1 CGTTGCGATAGTCATTTCCG
* *
467221 CGGTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTCCG
467241 CGTTGCGA
1 CGTTGCGA
467249 AAGTAAGTTT
Statistics
Matches: 56, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
19 13 0.23
20 43 0.77
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:467259 original size:20 final size:20
Alignment explanation
Indices: 467236--467274 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
467226 CGATAGTCAT
467236 TTTCGCGTTGCGAAAGTAAG
1 TTTCGCGTTGCGAAAGTAAG
*
467256 TTTCGTGTTGCGAAAGTAA
1 TTTCGCGTTGCGAAAGTAA
467275 ACTATTATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.33
Consensus pattern (20 bp):
TTTCGCGTTGCGAAAGTAAG
Found at i:467268 original size:40 final size:40
Alignment explanation
Indices: 467183--467259 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
467173 TCATTTCGCA
* *
467183 TTGCGATAGCCATTTCCGCGTTGCGATAGTCATTTCCACG
1 TTGCGATAGCCATTTCCGCGTTGCGAAAGTAATTTCCACG
* * *
467223 GTGCGATAGTCATTTTCGCGTTGCGAAAGTAAGTTTC
1 TTGCGATAGCCATTTCCGCGTTGCGAAAGTAA-TTTC
467260 GTGTTGCGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
40 27 0.87
41 4 0.13
ACGTcount: A:0.19, C:0.22, G:0.25, T:0.34
Consensus pattern (40 bp):
TTGCGATAGCCATTTCCGCGTTGCGAAAGTAATTTCCACG
Found at i:467646 original size:21 final size:20
Alignment explanation
Indices: 467620--467689 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
467610 CTGCCATTCC
467620 TCAAGAGTCCCCTCCAATCGT
1 TCAAGAGTCCCCTCC-ATCGT
* * **
467641 TCAAGAGGCCCCTATCATCCC
1 TCAAGAGTCCCCT-CCATCGT
* *
467662 TCAAGAGTCCCCCCCCACCGT
1 TCAAGAGT-CCCCTCCATCGT
467683 TCAAGAG
1 TCAAGAG
467690 GCCACTGTCA
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
21 32 0.86
22 5 0.14
ACGTcount: A:0.24, C:0.41, G:0.16, T:0.19
Consensus pattern (20 bp):
TCAAGAGTCCCCTCCATCGT
Found at i:467722 original size:42 final size:42
Alignment explanation
Indices: 467618--467701 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
467608 ATCTGCCATT
* * *
467618 CCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTATCATC
1 CCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCATC
* *
467660 CCTCAAGAGTCCCCCCCCACCGTTCAAGAGGCCACTGTCATC
1 CCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCATC
467702 GTTGAAGAGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.23, C:0.43, G:0.15, T:0.19
Consensus pattern (42 bp):
CCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCATC
Found at i:469302 original size:18 final size:18
Alignment explanation
Indices: 469279--469328 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
469269 AACGAGAAAC
469279 ATCGCAACGCGAAATGAA
1 ATCGCAACGCGAAATGAA
*
469297 ATCGCAATGCGAAATGAA
1 ATCGCAACGCGAAATGAA
*
469315 ATCGCAACGAGAAA
1 ATCGCAACGCGAAA
469329 ATCGCAATGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (18 bp):
ATCGCAACGCGAAATGAA
Found at i:469384 original size:20 final size:20
Alignment explanation
Indices: 469367--469454 Score: 106
Period size: 20 Copynumber: 4.4 Consensus size: 20
469357 CGATTTTCTA
469367 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
* *** *
469387 GTTGCGCTTTTTCA-TTTCGA
1 GTTGCG-ATAGCCATTTTCGC
*
469407 ATTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
469427 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
469447 GTTGCGAT
1 GTTGCGAT
469455 TTCCCCGTTG
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
19 3 0.06
20 48 0.89
21 3 0.06
ACGTcount: A:0.15, C:0.23, G:0.24, T:0.39
Consensus pattern (20 bp):
GTTGCGATAGCCATTTTCGC
Found at i:469445 original size:40 final size:41
Alignment explanation
Indices: 469350--469454 Score: 115
Period size: 40 Copynumber: 2.6 Consensus size: 41
469340 ATTTTCATTT
* * *
469350 CGCATTGCGATTTTCTAGTTGCGATAGCCATTTTCGCGTTG
1 CGCATAGCCATTTTCGAGTTGCGATAGCCATTTTCGCGTTG
* *** *
469391 CGCTTTTTCA-TTTCGAATTGCGATAGCCATTTTCGCGTTG
1 CGCATAGCCATTTTCGAGTTGCGATAGCCATTTTCGCGTTG
*
469431 CG-ATAGCCATTTTCGCGTTGCGAT
1 CGCATAGCCATTTTCGAGTTGCGAT
469455 TTCCCCGTTG
Statistics
Matches: 51, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
39 3 0.06
40 42 0.82
41 6 0.12
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.39
Consensus pattern (41 bp):
CGCATAGCCATTTTCGAGTTGCGATAGCCATTTTCGCGTTG
Found at i:469689 original size:20 final size:20
Alignment explanation
Indices: 469664--469755 Score: 67
Period size: 20 Copynumber: 4.5 Consensus size: 20
469654 GTGAAGATGA
469664 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
469684 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
* * **
469704 TTGTGATTTTGTATTATCTCG
1 TTGCGATTTT-CAGAATCTCG
** * * *
469725 TTGCGATAGTCAGTATCGCA
1 TTGCGATTTTCAGAATCTCG
469745 TTGCGATTTTC
1 TTGCGATTTTC
469756 CAAATTCGCA
Statistics
Matches: 52, Mismatches: 19, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
20 38 0.73
21 14 0.27
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Done.