Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007711.1 Hibiscus syriacus cultivar Beakdansim tig00109926_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: 1768490
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 8 of 8
Found at i:1729609 original size:33 final size:34
Alignment explanation
Indices: 1729572--1729636 Score: 105
Period size: 33 Copynumber: 1.9 Consensus size: 34
1729562 ATCGGATTGG
*
1729572 GTTTTTTAAAGTTTGATATTCGGGTCG-GGTCGA
1 GTTTTTTAAAGTATGATATTCGGGTCGAGGTCGA
*
1729605 GTTTTTTTAAGTATGATATTCGGGTCGAGGTC
1 GTTTTTTAAAGTATGATATTCGGGTCGAGGTC
1729637 TGGCTTAGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 25 0.86
34 4 0.14
ACGTcount: A:0.18, C:0.09, G:0.29, T:0.43
Consensus pattern (34 bp):
GTTTTTTAAAGTATGATATTCGGGTCGAGGTCGA
Found at i:1730230 original size:16 final size:16
Alignment explanation
Indices: 1730209--1730239 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1730199 GTTTTAGATT
1730209 CAGATTCCAATTCCTA
1 CAGATTCCAATTCCTA
1730225 CAGATTCCAATTCCT
1 CAGATTCCAATTCCT
1730240 TCACAAATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.32, G:0.06, T:0.32
Consensus pattern (16 bp):
CAGATTCCAATTCCTA
Found at i:1732921 original size:2 final size:2
Alignment explanation
Indices: 1732914--1732947 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1732904 TCCGCAGGTT
1732914 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1732948 CATTTCCTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1734041 original size:2 final size:2
Alignment explanation
Indices: 1734034--1734067 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1734024 AGGTAGGAAT
1734034 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1734068 GGTTTTAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1735619 original size:34 final size:34
Alignment explanation
Indices: 1735581--1735673 Score: 132
Period size: 34 Copynumber: 2.7 Consensus size: 34
1735571 CCTGACCTTA
* * *
1735581 CTTAAGAGACCTAGTGCCTCATCCCCTAACATTG
1 CTTAAGGGACCTAATGACTCATCCCCTAACATTG
*
1735615 CTTAAGGGACCTAATGACTCATCCCCTGACATTG
1 CTTAAGGGACCTAATGACTCATCCCCTAACATTG
* *
1735649 CTTAAGGGACCTATTGTCTCATCCC
1 CTTAAGGGACCTAATGACTCATCCC
1735674 ACTTTCTCTA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 53 1.00
ACGTcount: A:0.25, C:0.31, G:0.16, T:0.28
Consensus pattern (34 bp):
CTTAAGGGACCTAATGACTCATCCCCTAACATTG
Found at i:1736814 original size:19 final size:19
Alignment explanation
Indices: 1736790--1736828 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1736780 TCGAATGCAT
1736790 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
1736809 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
1736828 T
1 T
1736829 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:1736845 original size:65 final size:63
Alignment explanation
Indices: 1736727--1736935 Score: 217
Period size: 65 Copynumber: 3.2 Consensus size: 63
1736717 TATTCAAAGG
* *
1736727 CATGCACCGATGCA-TCAGTCCATGCATCGATGCATCGATGAAT-TAATT-GAACATCGAATGCA
1 CATGCACCGATGCACTC--TCCATGCATCGATGCATC--TGAATAT-TTTCAAACATCGAATGCA
*
1736789 TTC
61 TTT
1736792 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCA-TCTGAATATTTTC-AAACATCGAATGCATTT
* * *** * **
1736857 GATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTCTCAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCATCTGAATATTT-TCAAACATCGAATGCATTT
*
1736921 CATGCATCGATGCAC
1 CATGCACCGATGCAC
1736936 ACTTGGTGCA
Statistics
Matches: 126, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
63 7 0.06
64 56 0.44
65 61 0.48
66 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (63 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCATCTGAATATTTTCAAACATCGAATGCATTT
Found at i:1736927 original size:64 final size:65
Alignment explanation
Indices: 1736776--1736936 Score: 218
Period size: 65 Copynumber: 2.5 Consensus size: 65
1736766 GAATTAATTG
* * *** *
1736776 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
* **
1736841 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCA-TCAGGCTATTTCTC-
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTT-TCA
1736904 A
65 A
1736905 AACATCGAATGCATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
1736937 CTTGGTGCAC
Statistics
Matches: 85, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
64 40 0.47
65 45 0.53
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:1736951 original size:64 final size:64
Alignment explanation
Indices: 1736727--1736956 Score: 225
Period size: 64 Copynumber: 3.6 Consensus size: 64
1736717 TATTCAAAGG
* * * *
1736727 CATGCACCGATGCATCAGTCCATGCATCGATGCATCGATGAAT-TAATT--GAACATCGAATGCA
1 CATGCATCGATGCA-CACTCCATGCATCGATGCATC-A-GAATAT-TTTCAAAACATCGAATGCA
*
1736789 TTC
62 TTT
* * *
1736792 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCATCGATGCACACTCCATGCATCGATGCA-TCAGAATATTTTCAAAACATCGAATGCATTT
* ** **
1736857 GATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTCTC-AAACATCGAATGCATTT
1 CATGCATCGATGCACACTCCATGCATCGATGCATCAGAATATTT-TCAAAACATCGAATGCATTT
*** *
1736921 CATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 CATGCATCGATGCACACTCCATGCATCGATGCATCA
1736957 AGTGTTCCAA
Statistics
Matches: 139, Mismatches: 21, Indels: 11
0.81 0.12 0.06
Matches are distributed among these distances:
63 6 0.04
64 72 0.52
65 61 0.44
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.27
Consensus pattern (64 bp):
CATGCATCGATGCACACTCCATGCATCGATGCATCAGAATATTTTCAAAACATCGAATGCATTT
Found at i:1742761 original size:20 final size:21
Alignment explanation
Indices: 1742732--1742787 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
1742722 TTTGTGCTTC
*
1742732 ATGCACCGATGCAT-TT-AACA
1 ATGCATCGATGCATCTTGAA-A
*
1742752 ATGCATCGATGCATCCTTGAAT
1 ATGCATCGATGCAT-CTTGAAA
1742774 ATGCATCGATGCAT
1 ATGCATCGATGCAT
1742788 AAGACCATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.42
22 16 0.52
23 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGCATCGATGCATCTTGAAA
Found at i:1744360 original size:21 final size:21
Alignment explanation
Indices: 1744318--1744361 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1744308 ACCCCGGGAG
* *
1744318 CTAGTTCTTCACGAGTTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
1744339 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
1744360 CT
1 CT
1744362 CCTCCTCCAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.34, G:0.16, T:0.41
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:1745415 original size:19 final size:19
Alignment explanation
Indices: 1745391--1745429 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1745381 TCGAATGCAT
1745391 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
1745410 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
1745429 T
1 T
1745430 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:1745528 original size:64 final size:65
Alignment explanation
Indices: 1745377--1745537 Score: 218
Period size: 65 Copynumber: 2.5 Consensus size: 65
1745367 GAATTAATTG
* * *** *
1745377 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
* **
1745442 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCA-TCAGGCTATTTCTC-
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTT-TCA
1745505 A
65 A
1745506 AACATCGAATGCATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
1745538 CTTGGTGCAC
Statistics
Matches: 85, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
64 40 0.47
65 45 0.53
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:1745552 original size:64 final size:64
Alignment explanation
Indices: 1745329--1745557 Score: 223
Period size: 64 Copynumber: 3.5 Consensus size: 64
1745319 ATTCAAAGGT
* * * *
1745329 ATGCACCGATGCATCAGTCCATGCATCGATGCATCGATGAAT-TAATT--GAACATCGAATGCAT
1 ATGCATCGATGCA-CACTCCATGCATCGATGCATC-A-GAATAT-TTTCAAAACATCGAATGCAT
*
1745391 TCC
62 TTC
* * * *
1745394 ATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTTG
1 ATGCATCGATGCACACTCCATGCATCGATGCA-TCAGAATATTTTCAAAACATCGAATGCATTTC
** **
1745459 ATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTCTC-AAACATCGAATGCATTTC
1 ATGCATCGATGCACACTCCATGCATCGATGCATCAGAATATTT-TCAAAACATCGAATGCATTTC
*** *
1745523 ATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 ATGCATCGATGCACACTCCATGCATCGATGCATCA
1745558 AGTGTTCCAA
Statistics
Matches: 138, Mismatches: 21, Indels: 11
0.81 0.12 0.06
Matches are distributed among these distances:
63 6 0.04
64 72 0.52
65 60 0.43
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (64 bp):
ATGCATCGATGCACACTCCATGCATCGATGCATCAGAATATTTTCAAAACATCGAATGCATTTC
Found at i:1746388 original size:17 final size:16
Alignment explanation
Indices: 1746348--1746389 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
1746338 TCGATAAAAG
1746348 CTCGACTCG-AGTTGA
1 CTCGACTCGAAGTTGA
* *
1746363 CTCGGCTCGAATTTGAA
1 CTCGACTCGAAGTTG-A
1746380 CTCGACTCGA
1 CTCGACTCGA
1746390 GACCTTAACA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 8 0.36
16 4 0.18
17 10 0.45
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (16 bp):
CTCGACTCGAAGTTGA
Found at i:1765341 original size:86 final size:86
Alignment explanation
Indices: 1765182--1765343 Score: 193
Period size: 86 Copynumber: 1.9 Consensus size: 86
1765172 AATTTAATAT
* * * *
1765182 CTAAACTATCAGTTTTAGTATATTTTACTACTTAAACTTTTAAAATTTTCAAAACCATAAATAAC
1 CTAAACTATCAATTTTAGTATATTTTAATACTTAAACTTTTAAAATTTTCAAAACAAAAAATAAC
1765247 ATTTAATTTTTGTTTTAGTAC
66 ATTTAATTTTTGTTTTAGTAC
* * * *** *
1765268 CTAAACTATTAATTTTGGTATGTTTTAATACTTAAACTTTTACTTTTTTTAAAA-AAAAAATTAA
1 CTAAACTATCAATTTTAGTATATTTTAATACTTAAACTTTTAAAATTTTCAAAACAAAAAA-TAA
*
1765332 C-TTTAAATTTTG
65 CATTTAATTTTTG
1765344 AACAAGATAC
Statistics
Matches: 63, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
85 14 0.22
86 49 0.78
ACGTcount: A:0.38, C:0.10, G:0.05, T:0.47
Consensus pattern (86 bp):
CTAAACTATCAATTTTAGTATATTTTAATACTTAAACTTTTAAAATTTTCAAAACAAAAAATAAC
ATTTAATTTTTGTTTTAGTAC
Found at i:1766650 original size:3 final size:3
Alignment explanation
Indices: 1766642--1766679 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
1766632 CAACGAAAAT
1766642 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTAA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA T
1766680 GTTGTTTCAC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Done.