Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003679.1 Hibiscus syriacus cultivar Beakdansim tig00007859_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: 27335
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:1192 original size:29 final size:29
Alignment explanation
Indices: 1114--1332 Score: 164
Period size: 29 Copynumber: 7.7 Consensus size: 29
1104 TGATTCTGTA
*
1114 GGGATTATATCCCT-TCCTGACTCTATAT
1 GGGATTATATCCCTGTCCTGACTCTACAT
* *
1142 AGGATTATATCTCC-AT--TGACTCTACAT
1 GGGATTATATC-CCTGTCCTGACTCTACAT
** * *
1169 GAAATTGTATCCCTGTCCTGACTCTGCAT
1 GGGATTATATCCCTGTCCTGACTCTACAT
* * **
1198 GGGATTATATCTCAGTATTGACTCTACAT
1 GGGATTATATCCCTGTCCTGACTCTACAT
* * * * * *
1227 GGTATTGTATACATGTCCCGACTCTGCAT
1 GGGATTATATCCCTGTCCTGACTCTACAT
* * *
1256 GTGATTATATCCCCGTCCTGATTCTACAT
1 GGGATTATATCCCTGTCCTGACTCTACAT
**
1285 GGGATTATATCACC-GTCCT-ACTCTGTAT
1 GGGATTATATC-CCTGTCCTGACTCTACAT
1313 GGGATTATATTCCC-GTCCTG
1 GGGATTATA-TCCCTGTCCTG
1333 TTTCCGTTTG
Statistics
Matches: 144, Mismatches: 39, Indels: 15
0.73 0.20 0.08
Matches are distributed among these distances:
26 2 0.01
27 18 0.12
28 32 0.22
29 90 0.62
30 2 0.01
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (29 bp):
GGGATTATATCCCTGTCCTGACTCTACAT
Found at i:2832 original size:19 final size:20
Alignment explanation
Indices: 2792--2834 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
2782 CACACATATT
2792 AAAAAATTCAAATTTCAAAGA
1 AAAAAATTCAAATTTC-AAGA
2813 AAAAAATT-AGAATTTC-AGA
1 AAAAAATTCA-AATTTCAAGA
2832 AAA
1 AAA
2835 CTTCAAGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 6 0.29
20 1 0.05
21 14 0.67
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.23
Consensus pattern (20 bp):
AAAAAATTCAAATTTCAAGA
Found at i:7750 original size:35 final size:35
Alignment explanation
Indices: 7711--7783 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
7701 TAAATAATCG
7711 AATATTCTTTATCTTTCTAATGATTTGATAGTTTT
1 AATATTCTTTATCTTTCTAATGATTTGATAGTTTT
*
7746 AATATTTTTTATCTTTCTAATGATTTGATAGTTTT
1 AATATTCTTTATCTTTCTAATGATTTGATAGTTTT
7781 AAT
1 AAT
7784 TAAATCTATT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.27, C:0.07, G:0.08, T:0.58
Consensus pattern (35 bp):
AATATTCTTTATCTTTCTAATGATTTGATAGTTTT
Found at i:13130 original size:27 final size:27
Alignment explanation
Indices: 13093--13147 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
13083 AAAATTAAAT
* *
13093 ATTTTATGTACTTATTTTAACAAAAAA
1 ATTTTACGTACTCATTTTAACAAAAAA
* *
13120 ATTTTACGTACTCATTTTGACCAAAAA
1 ATTTTACGTACTCATTTTAACAAAAAA
13147 A
1 A
13148 GTAATTTTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.42, C:0.13, G:0.05, T:0.40
Consensus pattern (27 bp):
ATTTTACGTACTCATTTTAACAAAAAA
Found at i:15382 original size:43 final size:43
Alignment explanation
Indices: 15304--15385 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 43
15294 AAAGTATGGC
* *** *
15304 CGAGGCAAGAAAAATTGTAAAGTGAAGTGAGTAAAAGTTTTGT
1 CGAGGCAAGAAAAATTGCAAAGTGAAACAAATAAAAGTTTTGT
15347 CGAGGCAAGAAAAATATGCAAAGT-AAACAAATAAAAGTT
1 CGAGGCAAGAAAAAT-TGCAAAGTGAAACAAATAAAAGTT
15386 GTTAAGGCTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
43 26 0.79
44 7 0.21
ACGTcount: A:0.49, C:0.07, G:0.23, T:0.21
Consensus pattern (43 bp):
CGAGGCAAGAAAAATTGCAAAGTGAAACAAATAAAAGTTTTGT
Found at i:16891 original size:18 final size:18
Alignment explanation
Indices: 16868--16902 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
16858 TCGTTGTTAT
16868 TGCATTTTTAGATTTTGA
1 TGCATTTTTAGATTTTGA
16886 TGCATTTTTAGATTTTG
1 TGCATTTTTAGATTTTG
16903 CTACATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.20, C:0.06, G:0.17, T:0.57
Consensus pattern (18 bp):
TGCATTTTTAGATTTTGA
Found at i:16909 original size:18 final size:18
Alignment explanation
Indices: 16870--16910 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
16860 GTTGTTATTG
*
16870 CATTTTTAGATTTTGATG
1 CATTTTTAGATTTTGATA
*
16888 CATTTTTAGATTTTGCTA
1 CATTTTTAGATTTTGATA
16906 CATTT
1 CATTT
16911 ATGTTATTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.22, C:0.10, G:0.12, T:0.56
Consensus pattern (18 bp):
CATTTTTAGATTTTGATA
Found at i:16966 original size:20 final size:19
Alignment explanation
Indices: 16941--16980 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
16931 GTTTATTTGG
16941 TATTTGGTACTTGAATGTTT
1 TATTTGGTACTTGAAT-TTT
*
16961 TATTTGGTATTTGAATTTT
1 TATTTGGTACTTGAATTTT
16980 T
1 T
16981 GTTATTACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.20, C:0.03, G:0.17, T:0.60
Consensus pattern (19 bp):
TATTTGGTACTTGAATTTT
Found at i:17569 original size:19 final size:19
Alignment explanation
Indices: 17520--17573 Score: 81
Period size: 20 Copynumber: 2.8 Consensus size: 19
17510 ATTTTTGGCT
*
17520 CAAAGGATCGATCCCCTAG
1 CAAATGATCGATCCCCTAG
*
17539 CAAAATGTTCGATCCCCTAG
1 C-AAATGATCGATCCCCTAG
17559 CAAATGATCGATCCC
1 CAAATGATCGATCCC
17574 TTATACCAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.20
Consensus pattern (19 bp):
CAAATGATCGATCCCCTAG
Found at i:19111 original size:10 final size:10
Alignment explanation
Indices: 19083--19125 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
19073 ACCGAACCGA
*
19083 ATAAATTATT
1 ATAAATTTTT
*
19093 AAAAATTTTT
1 ATAAATTTTT
19103 -TAAATTTTT
1 ATAAATTTTT
*
19112 ATAAATATTT
1 ATAAATTTTT
19122 ATAA
1 ATAA
19126 TAATTTAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 8 0.29
10 20 0.71
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (10 bp):
ATAAATTTTT
Found at i:25336 original size:29 final size:29
Alignment explanation
Indices: 25300--25369 Score: 133
Period size: 29 Copynumber: 2.4 Consensus size: 29
25290 GATTCGTAGG
25300 TTTT-CCTTTTCTTTGTGATTTTCAATAT
1 TTTTACCTTTTCTTTGTGATTTTCAATAT
25328 TTTTACCTTTTCTTTGTGATTTTCAATAT
1 TTTTACCTTTTCTTTGTGATTTTCAATAT
25357 TTTTACCTTTTCT
1 TTTTACCTTTTCT
25370 GCATAATATT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 4 0.10
29 37 0.90
ACGTcount: A:0.14, C:0.16, G:0.06, T:0.64
Consensus pattern (29 bp):
TTTTACCTTTTCTTTGTGATTTTCAATAT
Found at i:25460 original size:6 final size:6
Alignment explanation
Indices: 25449--25498 Score: 86
Period size: 6 Copynumber: 8.7 Consensus size: 6
25439 ATCGTCATGC
25449 CCATTT CCATTT CCATTT CCATTT CCATTT CCA-TT CCATTT CCA-TT
1 CCATTT CCATTT CCATTT CCATTT CCATTT CCATTT CCATTT CCATTT
25495 CCAT
1 CCAT
25499 GCGAGATTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
5 10 0.24
6 32 0.76
ACGTcount: A:0.18, C:0.36, G:0.00, T:0.46
Consensus pattern (6 bp):
CCATTT
Done.