Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001014.1 Hibiscus syriacus cultivar Beakdansim tig00002021_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: 67693
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:6094 original size:20 final size:20
Alignment explanation
Indices: 6051--6258 Score: 222
Period size: 20 Copynumber: 10.2 Consensus size: 20
6041 CTGACTATAA
*
6051 CAACGAGTATCCGTAAAATCG
1 CAACGCGTATCCGT-AAATCG
*
6072 CAACGCGTATCCGTAAATTG
1 CAACGCGTATCCGTAAATCG
* *
6092 CAACGAC-AATACGTAAAATCG
1 CAACG-CGTATCCGT-AAATCG
*
6113 CAACGCGTATCCGTAAATCA
1 CAACGCGTATCCGTAAATCG
* * *
6133 CAACGAGAATACGTAAATCG
1 CAACGCGTATCCGTAAATCG
*
6153 CAACGCGTATCTGTAAATCG
1 CAACGCGTATCCGTAAATCG
* * *
6173 CAACGAGAATACGTAAATCG
1 CAACGCGTATCCGTAAATCG
*
6193 CAATGCGTATCCGTAAATCG
1 CAACGCGTATCCGTAAATCG
* *
6213 CAACGAC-AATACGTAAAATCG
1 CAACG-CGTATCCGT-AAATCG
6234 CAACGCGTATCCGTAAATCG
1 CAACGCGTATCCGTAAATCG
6254 CAACG
1 CAACG
6259 TGATTTTTAA
Statistics
Matches: 152, Mismatches: 29, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
20 106 0.70
21 46 0.30
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
CAACGCGTATCCGTAAATCG
Found at i:6162 original size:40 final size:41
Alignment explanation
Indices: 6051--6258 Score: 330
Period size: 41 Copynumber: 5.1 Consensus size: 41
6041 CTGACTATAA
* * *
6051 CAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAAATTG
1 CAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCG
* *
6092 CAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCA
1 CAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCG
*
6133 CAACGAGAATACGT-AAATCGCAACGCGTATCTGTAAATCG
1 CAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCG
*
6173 CAACGAGAATACGT-AAATCGCAATGCGTATCCGTAAATCG
1 CAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCG
*
6213 CAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCG
1 CAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCG
6254 CAACG
1 CAACG
6259 TGATTTTTAA
Statistics
Matches: 154, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
40 75 0.49
41 79 0.51
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (41 bp):
CAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCG
Found at i:8548 original size:24 final size:24
Alignment explanation
Indices: 8514--8567 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
8504 CTGAAAAATC
8514 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
8538 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
8562 ATCAAA
1 ATCAAA
8568 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:8581 original size:24 final size:24
Alignment explanation
Indices: 8514--8581 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
8504 CTGAAAAATC
* * *
8514 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
8538 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
8562 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
8582 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:9445 original size:19 final size:19
Alignment explanation
Indices: 9421--9472 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
9411 CGATACCGGA
9421 GATCGCGTTGCGAATTATC
1 GATCGCGTTGCGAATTATC
* *
9440 GATCGCGTTGCGATTTATG
1 GATCGCGTTGCGAATTATC
9459 GATACGCGTTGCGA
1 GAT-CGCGTTGCGA
9473 TTTTACGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 20 0.67
20 10 0.33
ACGTcount: A:0.19, C:0.19, G:0.31, T:0.31
Consensus pattern (19 bp):
GATCGCGTTGCGAATTATC
Found at i:9468 original size:20 final size:20
Alignment explanation
Indices: 9424--9657 Score: 206
Period size: 20 Copynumber: 11.6 Consensus size: 20
9414 TACCGGAGAT
*
9424 CGCGTTGCGAATTATC-GAT-
1 CGCGTTGCGATTTA-CGGATA
*
9443 CGCGTTGCGATTTATGGATA
1 CGCGTTGCGATTTACGGATA
*
9463 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
9483 TGTCGTTTGCGATTTACGGATA
1 CG-CG-TTGCGATTTACGGATA
* * *
9505 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* **
9525 CTCGTTGCGATTTACATATA
1 CGCGTTGCGATTTACGGATA
* *
9545 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
9565 CTCGTTGCAATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
9585 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
9605 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* *
9626 CGCATTGCAATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
9647 CTCGTTGCGAT
1 CGCGTTGCGAT
9658 AGTCAGAATC
Statistics
Matches: 173, Mismatches: 32, Indels: 19
0.77 0.14 0.08
Matches are distributed among these distances:
19 16 0.09
20 98 0.57
21 52 0.30
22 7 0.04
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.38
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:9612 original size:41 final size:41
Alignment explanation
Indices: 9445--9657 Score: 304
Period size: 41 Copynumber: 5.2 Consensus size: 41
9435 TTATCGATCG
* *
9445 CGTTGCGATTTATGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
9486 CGTTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCT
1 CG-TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
**
9527 CGTTGCGATTTACATATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
9567 CGTTGCAATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * * *
9608 CGTTGCGATTTACGGATACGCATTGCAATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
9649 CGTTGCGAT
1 CGTTGCGAT
9658 AGTCAGAATC
Statistics
Matches: 154, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
40 60 0.39
41 70 0.45
42 24 0.16
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.38
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:9671 original size:122 final size:120
Alignment explanation
Indices: 9422--9699 Score: 364
Period size: 122 Copynumber: 2.3 Consensus size: 120
9412 GATACCGGAG
* * *
9422 ATCGCGTTGCGAATTATCGATCGCGTTGCGATTTATGGATACGCGTTGCGATTTTACGTATTGTC
1 ATCGCGTTGCGATTTATCGATCGCGTTGCAATTTACGGATACGCGTTGCGATTTTACGTATTGTC
* * * * *
9487 GTTTGCGATTTACGGATACGCATTGCGATTTACGTATTCTCGTTGCGATTTACAT
66 GTTTGCGATTTACGGATACGCATTGCAATTTACGGATACTCGTTGCGATGTACAA
*
9542 ATACGCGTTGCGATTTA-CGTATTCTCGTTGCAATTTACGGATACGCGTTGCGATTTTACGTATT
1 AT-CGCGTTGCGATTTATCG-A-TCGCGTTGCAATTTACGGATACGCGTTGCGATTTTACGTATT
9606 GTCG-TTGCGATTTACGGATACGCATTGCAATTTTACGGATACTCGTTGCGATAGT-CAGA
63 GTCGTTTGCGATTTACGGATACGCATTGCAA-TTTACGGATACTCGTTGCGAT-GTACA-A
* * *
9665 ATCGCGTTGCGATTTATATGTTCGCGTTGCGATTT
1 ATCGCGTTGCGATTTAT-CGATCGCGTTGCAATTT
9700 TCATATTCGC
Statistics
Matches: 137, Mismatches: 13, Indels: 14
0.84 0.08 0.09
Matches are distributed among these distances:
120 4 0.03
121 39 0.28
122 90 0.66
123 3 0.02
124 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (120 bp):
ATCGCGTTGCGATTTATCGATCGCGTTGCAATTTACGGATACGCGTTGCGATTTTACGTATTGTC
GTTTGCGATTTACGGATACGCATTGCAATTTACGGATACTCGTTGCGATGTACAA
Found at i:9689 original size:20 final size:20
Alignment explanation
Indices: 9666--9714 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
9656 ATAGTCAGAA
*
9666 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
9686 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
9706 TCGCGTTGC
1 TCGCGTTGC
9715 AATTCTGGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.12, C:0.20, G:0.24, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:9817 original size:20 final size:20
Alignment explanation
Indices: 9747--9821 Score: 64
Period size: 20 Copynumber: 3.7 Consensus size: 20
9737 AATTTGTACT
** *
9747 ATCGCATTGCGATTCTTCATA
1 ATCGCATTGCGATTCTGGA-G
*
9768 ATCGCGTTGCGATTCTGG-G
1 ATCGCATTGCGATTCTGGAG
*
9787 AACTG-ATTTGCGATTCTGGAG
1 ATC-GCA-TTGCGATTCTGGAG
9808 ATCGCATTGCGATT
1 ATCGCATTGCGATT
9822 TTTATTTCGC
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
19 2 0.05
20 22 0.51
21 19 0.44
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (20 bp):
ATCGCATTGCGATTCTGGAG
Found at i:17340 original size:2 final size:2
Alignment explanation
Indices: 17333--17371 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
17323 ATCAGTGAAT
17333 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
17372 ATATATATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:25211 original size:23 final size:23
Alignment explanation
Indices: 25185--25234 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
25175 AATTCTCCAA
**
25185 TTTCTCTACGTTTTTCAATTTAT
1 TTTCTCTACCCTTTTCAATTTAT
*
25208 TTTCTCTTCCCTTTTCAATTTAT
1 TTTCTCTACCCTTTTCAATTTAT
25231 TTTC
1 TTTC
25235 ATTTGGATTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.14, C:0.22, G:0.02, T:0.62
Consensus pattern (23 bp):
TTTCTCTACCCTTTTCAATTTAT
Found at i:27930 original size:18 final size:19
Alignment explanation
Indices: 27895--27930 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
27885 TTTCTTTAGA
*
27895 TTAATATAATATTTTCATT
1 TTAATATAATATTGTCATT
27914 TTAATAT-ATATTGTCAT
1 TTAATATAATATTGTCAT
27931 ATTATGGTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.56
Consensus pattern (19 bp):
TTAATATAATATTGTCATT
Found at i:30219 original size:15 final size:16
Alignment explanation
Indices: 30199--30228 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
30189 TTATGCTAAT
30199 TTATAAG-TTTGGTTA
1 TTATAAGTTTTGGTTA
30214 TTATAAGTTTTGGTT
1 TTATAAGTTTTGGTT
30229 CATAAGAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.23, C:0.00, G:0.20, T:0.57
Consensus pattern (16 bp):
TTATAAGTTTTGGTTA
Found at i:39868 original size:21 final size:19
Alignment explanation
Indices: 39832--39872 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 19
39822 ATAAATTTGA
39832 TTTTTTAAAAATAATTTAAT
1 TTTTTTAAAAA-AATTTAAT
39852 TTTTTTAAAGTAAAATTTAAT
1 TTTTTTAAA--AAAATTTAAT
39873 ATATAAACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 9 0.47
21 8 0.42
22 2 0.11
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
TTTTTTAAAAAAATTTAAT
Found at i:40217 original size:2 final size:2
Alignment explanation
Indices: 40212--40237 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40202 TACCCCCCTC
40212 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
40238 TCCTTATTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:45912 original size:2 final size:2
Alignment explanation
Indices: 45905--45932 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
45895 TTTGAAAAGA
45905 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
45933 TAATAATCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47299 original size:26 final size:26
Alignment explanation
Indices: 47270--47319 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
47260 TTATATAAGT
47270 AATCTCTACAAAGTAATTATCATAGC
1 AATCTCTACAAAGTAATTATCATAGC
*
47296 AATCTCTACAAATTAATTATCATA
1 AATCTCTACAAAGTAATTATCATA
47320 AACTTAAGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.44, C:0.18, G:0.04, T:0.34
Consensus pattern (26 bp):
AATCTCTACAAAGTAATTATCATAGC
Found at i:52629 original size:162 final size:160
Alignment explanation
Indices: 52362--52684 Score: 619
Period size: 162 Copynumber: 2.0 Consensus size: 160
52352 TGCAAGGCGT
*
52362 ACTCTAGGTGCTTCAACCCGTACATTGCCTCAGGCGCTCGGCACAAAAAAGCTCTAGCCTGAGTA
1 ACTCTAGGTGCTTCAACCCGTACATTGCCTCAGGCGCTCGACACAAAAAAGCTCTAGCCTGAGTA
52427 AAGCATAGAAAATGAAAGAAAAAAGGTGAACAATGAAAGAAACTAAAAATAAATTTAATCCGGGG
66 AAGCATAGAAAATGAAAGAAAAAAGGTGAACAATGAAAGAAACTAAAAATAAATTTAATCC-GGG
52492 TGGGGGGAGGTTTATGCCTACCGCCTTAGAGA
130 -GGGGGGAGGTTTATGCCTACCGCCTTAGAGA
52524 ACTCTAGGTGCTTCAACCCGTACATTGCCTCAGGCGCTCGACACAAAAAAGCTCTAGCCTGAGTA
1 ACTCTAGGTGCTTCAACCCGTACATTGCCTCAGGCGCTCGACACAAAAAAGCTCTAGCCTGAGTA
52589 AAGCATAGAAAATGAAAGAAAAAAGGTGAACAATGAAAGAAACTAAAAATAAATTTAATCCGGGG
66 AAGCATAGAAAATGAAAGAAAAAAGGTGAACAATGAAAGAAACTAAAAATAAATTTAATCCGGGG
52654 GGGGGAGGTTTATGCCTACCGCCTTAGAGA
131 GGGGGAGGTTTATGCCTACCGCCTTAGAGA
52684 A
1 A
52685 AAGTGTGCCT
Statistics
Matches: 160, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
160 32 0.20
161 3 0.02
162 125 0.78
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.20
Consensus pattern (160 bp):
ACTCTAGGTGCTTCAACCCGTACATTGCCTCAGGCGCTCGACACAAAAAAGCTCTAGCCTGAGTA
AAGCATAGAAAATGAAAGAAAAAAGGTGAACAATGAAAGAAACTAAAAATAAATTTAATCCGGGG
GGGGGAGGTTTATGCCTACCGCCTTAGAGA
Done.