Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000763.1 Hibiscus syriacus cultivar Beakdansim tig00001480_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: 47117
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:122 original size:19 final size:21
Alignment explanation
Indices: 99--151 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 21
89 ACGCGATTTA
*
99 AAAAATGTATTGCGATAG-TT
1 AAAAATGTATTGCGAGAGTTT
*
119 -AAAATGTGTTGCGAGAGTTT
1 AAAAATGTATTGCGAGAGTTT
139 GAAAAATGTATTG
1 -AAAAATGTATTG
152 TTACGATAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 15 0.56
20 2 0.07
22 10 0.37
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.34
Consensus pattern (21 bp):
AAAAATGTATTGCGAGAGTTT
Found at i:1976 original size:25 final size:27
Alignment explanation
Indices: 1920--1983 Score: 105
Period size: 25 Copynumber: 2.4 Consensus size: 27
1910 GATAATGGCT
1920 CTGAATCATTCAGAATGTACTTCTGTG
1 CTGAATCATTCAGAATGTACTTCTGTG
1947 CTGAATCATTCAGAA-GT-CTTCTGTG
1 CTGAATCATTCAGAATGTACTTCTGTG
*
1972 TTGAATCATTCA
1 CTGAATCATTCA
1984 TCACTATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
25 19 0.53
26 2 0.06
27 15 0.42
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.38
Consensus pattern (27 bp):
CTGAATCATTCAGAATGTACTTCTGTG
Found at i:6173 original size:2 final size:2
Alignment explanation
Indices: 6166--6198 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
6156 CCTCTTGAGA
*
6166 AT AT AT AT AT A- AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6199 TAAATTAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:6854 original size:2 final size:2
Alignment explanation
Indices: 6847--6893 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
6837 ATCACATCAC
*
6847 AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6887 AT AT AT A
1 AT AT AT A
6894 AACTTACATG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:12865 original size:20 final size:21
Alignment explanation
Indices: 12840--12891 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
12830 TTTTCCCAAT
*
12840 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
12860 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
12881 TCGCAATGCGA
1 TCGCAATGCGA
12892 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:13578 original size:19 final size:19
Alignment explanation
Indices: 13531--13572 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
13521 ACGAGATAAT
*
13531 CGCAACGCGAAATAAAAAA
1 CGCAACGCGAAACAAAAAA
*
13550 CGCAACGCGAAACAAAAAT
1 CGCAACGCGAAACAAAAAA
13569 CGCA
1 CGCA
13573 TTGCGATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.52, C:0.26, G:0.17, T:0.05
Consensus pattern (19 bp):
CGCAACGCGAAACAAAAAA
Found at i:13614 original size:20 final size:19
Alignment explanation
Indices: 13568--13638 Score: 115
Period size: 19 Copynumber: 3.7 Consensus size: 19
13558 GAAACAAAAA
*
13568 TCGCATTGCGATTTTTATT
1 TCGCGTTGCGATTTTTATT
13587 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTTATT
*
13606 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTTATT
13626 TCGCGTTGCGATT
1 TCGCGTTGCGATT
13639 GTCTGGTCGC
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
19 31 0.63
20 18 0.37
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (19 bp):
TCGCGTTGCGATTTTTATT
Found at i:13649 original size:39 final size:39
Alignment explanation
Indices: 13573--13649 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
13563 AAAAATCGCA
* * **
13573 TTGCGATTTTTATTTCGCGTTGCGATTTTTATTTCGCGG
1 TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
13612 TTGCGATTTTCATTTCGCGTTGCGATTGTCT-GGTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATT-TCTAGGTCGCG
13650 ATAGTCATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 31 0.94
40 2 0.06
ACGTcount: A:0.09, C:0.18, G:0.26, T:0.47
Consensus pattern (39 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
Found at i:13658 original size:33 final size:33
Alignment explanation
Indices: 13621--13705 Score: 125
Period size: 33 Copynumber: 2.5 Consensus size: 33
13611 GTTGCGATTT
* *
13621 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
* *
13654 TCATTTCGCATTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
13687 TCATTTCCGCGTTGCGATT
1 TCATTT-CGCGTTGCGATT
13706 TTCATTTCAA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 35 0.76
34 11 0.24
ACGTcount: A:0.13, C:0.24, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:14885 original size:18 final size:19
Alignment explanation
Indices: 14861--14945 Score: 102
Period size: 19 Copynumber: 4.5 Consensus size: 19
14851 ACGAAACTTA
14861 AATCGCAACGCG-AATGAC
1 AATCGCAACGCGAAATGAC
* *
14879 TATCGCAACGCGGAAATGGC
1 AATCGCAACGC-GAAATGAC
* * *
14899 TATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAC
14918 AATCGCAACGCGAAATGA-
1 AATCGCAACGCGAAATGAC
14936 AATCGCAACG
1 AATCGCAACG
14946 ACAAAATCGC
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
18 20 0.34
19 23 0.40
20 15 0.26
ACGTcount: A:0.39, C:0.24, G:0.24, T:0.14
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAC
Found at i:15012 original size:14 final size:14
Alignment explanation
Indices: 14993--15050 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
14983 TTTCATTTCG
14993 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
15007 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
*
15023 CGCATTGCAATTTTGT
1 CG--TTGCGATTTTGT
15039 CGTTGCGATTTT
1 CGTTGCGATTTT
15051 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 8 0.22
18 8 0.22
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:15021 original size:32 final size:33
Alignment explanation
Indices: 14979--15066 Score: 151
Period size: 32 Copynumber: 2.7 Consensus size: 33
14969 AATCGCATTA
*
14979 CGATTTTCATTTCGCGTTGCGATTTTGTCGTTG
1 CGATTTTCATTTCGCATTGCGATTTTGTCGTTG
*
15012 CGA-TTTCATTTCGCATTGCAATTTTGTCGTTG
1 CGATTTTCATTTCGCATTGCGATTTTGTCGTTG
15044 CGATTTTCATTTCGCATTGCGAT
1 CGATTTTCATTTCGCATTGCGAT
15067 AGCCATTTCC
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
32 30 0.59
33 21 0.41
ACGTcount: A:0.14, C:0.19, G:0.20, T:0.47
Consensus pattern (33 bp):
CGATTTTCATTTCGCATTGCGATTTTGTCGTTG
Found at i:15085 original size:20 final size:19
Alignment explanation
Indices: 15051--15105 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
15041 TTGCGATTTT
*
15051 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
15070 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
15090 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
15106 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:15613 original size:18 final size:18
Alignment explanation
Indices: 15587--15631 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
15577 GTCGATCAGA
*
15587 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
15605 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
15623 TGATGGCTC
1 TGATGGCTC
15632 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:16967 original size:20 final size:20
Alignment explanation
Indices: 16942--16984 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
16932 AATAGTTTCT
16942 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
*
16962 GAAAATGAAAATCGCAACGC
1 GAAAATGAAAATCGCAACAC
16982 GAA
1 GAA
16985 TTCGACTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.53, C:0.19, G:0.19, T:0.09
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:17556 original size:20 final size:20
Alignment explanation
Indices: 17495--17608 Score: 111
Period size: 20 Copynumber: 5.7 Consensus size: 20
17485 GATTATGTAT
17495 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
17515 AATAGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
17535 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
17555 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
17576 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
17596 TATCGCATTGCGA
1 TATCGCGTTGCGA
17609 TTTTCCCAAT
Statistics
Matches: 76, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
20 63 0.83
21 13 0.17
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:17586 original size:21 final size:21
Alignment explanation
Indices: 17553--17653 Score: 59
Period size: 20 Copynumber: 4.9 Consensus size: 21
17543 TGCGAAAGTA
* * *
17553 AGTATCTCGTTGCGATTTTTT
1 AGTATCGCATTGCGATTTTTC
* **
17574 ATTATCGCATTGCGA-TAGTC
1 AGTATCGCATTGCGATTTTTC
*
17594 AGTATCGCATTGCGATTTTCCC
1 AGTATCGCATTGCGATTTT-TC
* *
17616 AAT-TCACATTGCGATTTACTT-
1 AGTATCGCATTGCGATTT--TTC
17637 A-T-TCGCATTGCGATTTT
1 AGTATCGCATTGCGATTTT
17654 CCCAATTCGC
Statistics
Matches: 62, Mismatches: 14, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
18 1 0.02
20 30 0.48
21 27 0.44
22 3 0.05
23 1 0.02
ACGTcount: A:0.21, C:0.20, G:0.17, T:0.43
Consensus pattern (21 bp):
AGTATCGCATTGCGATTTTTC
Found at i:17598 original size:41 final size:41
Alignment explanation
Indices: 17475--17612 Score: 116
Period size: 41 Copynumber: 3.4 Consensus size: 41
17465 CGCTTTGAAA
* * * * *
17475 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTTTTTATTATCGCATTGCGAAAGTAAGT
* * *** * * *
17516 ATAGCGTTGCGA-AAGTCAGTATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATTTTTTATTATCGCATTGCGAAAGTAAGT
* * * *
17556 ATCTCGTTGCGATTTTTTATTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTTTATTATCGCATTGCGAAAGTAAGT
17597 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
17613 CCCAATTCAC
Statistics
Matches: 75, Mismatches: 21, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
40 31 0.41
41 44 0.59
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.35
Consensus pattern (41 bp):
ATCGCATTGCGATTTTTTATTATCGCATTGCGAAAGTAAGT
Found at i:17626 original size:41 final size:41
Alignment explanation
Indices: 17581--17690 Score: 134
Period size: 41 Copynumber: 2.7 Consensus size: 41
17571 TTTATTATCG
17581 CATTGCGATAGTCA-GTA-TCGCATTGCGATTTTCCCAATTCA
1 CATTGCGAT--TCACGTATTCGCATTGCGATTTTCCCAATTCA
* * *
17622 CATTGCGATTTACTTATTCGCATTGCGATTTTCCCAATTCG
1 CATTGCGATTCACGTATTCGCATTGCGATTTTCCCAATTCA
* * *
17663 CGTTGCGATTTACTTATTCGCATTGCGA
1 CATTGCGATTCACGTATTCGCATTGCGA
17691 ATTGGGAAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
39 2 0.03
40 2 0.03
41 59 0.94
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.38
Consensus pattern (41 bp):
CATTGCGATTCACGTATTCGCATTGCGATTTTCCCAATTCA
Found at i:17645 original size:20 final size:21
Alignment explanation
Indices: 17598--17690 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
17588 ATAGTCAGTA
*
17598 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTACCAAT
* **
17619 TCACATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACCAAT
*
17639 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTACCAAT
* **
17660 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACCAAT
17680 TCGCATTGCGA
1 TCGCATTGCGA
17691 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.19, C:0.25, G:0.16, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTACCAAT
Found at i:18676 original size:18 final size:18
Alignment explanation
Indices: 18630--18678 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
18620 TAATTAAGTC
**
18630 TAAATTAAA-TAATCGGT
1 TAAATTAAATTAATCGAA
* *
18647 TAAATCATATTAATCGAA
1 TAAATTAAATTAATCGAA
18665 TAAATTAAATTAAT
1 TAAATTAAATTAAT
18679 TTTAAAATTT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
17 7 0.28
18 18 0.72
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (18 bp):
TAAATTAAATTAATCGAA
Found at i:19351 original size:25 final size:25
Alignment explanation
Indices: 19299--19347 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
19289 TACAAATATA
* *
19299 ATTTCAAATTTAATAAAAAAGTAAT
1 ATTTAAAATTTAATAAAAAAGAAAT
*
19324 ATTTAAAATTTAAT-AACAAGAAAT
1 ATTTAAAATTTAATAAAAAAGAAAT
19348 TATTGTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (25 bp):
ATTTAAAATTTAATAAAAAAGAAAT
Found at i:24059 original size:2 final size:2
Alignment explanation
Indices: 24054--24078 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
24044 AATTAAGTTT
24054 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 T
24079 CTTTGGGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27456 original size:22 final size:23
Alignment explanation
Indices: 27431--27478 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 23
27421 ATATTTGGAT
27431 AAATTATG-CGTTTAATACCTAA
1 AAATTATGCCGTTTAATACCTAA
*
27453 AAATTTTGACCCGTTTAATACCTAA
1 AAATTATG--CCGTTTAATACCTAA
27478 A
1 A
27479 CTTTTAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
25 15 0.68
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (23 bp):
AAATTATGCCGTTTAATACCTAA
Found at i:32279 original size:54 final size:54
Alignment explanation
Indices: 32197--32618 Score: 695
Period size: 54 Copynumber: 7.8 Consensus size: 54
32187 TACCGAATGA
* * * *
32197 GCACTATGTGTACAACCTAATAAATTCATAATAAGTTTATGGATTTTCGTATTG
1 GCACTATGTGTGCAGCCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTG
32251 GCACTATGTGTGCAGCCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTG
1 GCACTATGTGTGCAGCCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTG
32305 GCACTATGTGTGCAGCCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTG
1 GCACTATGTGTGCAGCCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTG
*
32359 ACACTATGTGTGCAGCCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTG
1 GCACTATGTGTGCAGCCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTG
32413 GCACTATGTGTGCAGCCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTG
1 GCACTATGTGTGCAGCCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTG
*
32467 ACACTATGTGTGCAGCCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTG
1 GCACTATGTGTGCAGCCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTG
* *
32521 GCATTATGTGTGCAGCCTAAGAAATTCATAATAAGTTTATGAA-TTTC-CATTG
1 GCACTATGTGTGCAGCCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTG
* * * * * *
32573 GCACTATGTGTGCAATCCCACGTAATTCATAATGAGTTTGTGAATT
1 GCACTATGTGTGC-AGCCTAAGAAATTCATAATAAGTTTATGAATT
32619 ACCGTATCGA
Statistics
Matches: 349, Mismatches: 17, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
52 16 0.05
53 28 0.08
54 305 0.87
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.37
Consensus pattern (54 bp):
GCACTATGTGTGCAGCCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTG
Found at i:34005 original size:31 final size:33
Alignment explanation
Indices: 33970--34042 Score: 91
Period size: 31 Copynumber: 2.3 Consensus size: 33
33960 GGTAAGAAAT
* *
33970 TTATTTTTATGTTAGTAT-TT-T-TAAATAGTTA
1 TTATTTTTATATTAATATATTATGTAAATA-TTA
34001 TTATTTTTATATTAATATATTATGTAAATATTA
1 TTATTTTTATATTAATATATTATGTAAATATTA
34034 -TATTTTTAT
1 TTATTTTTAT
34043 TAAAATAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
31 16 0.43
32 11 0.30
33 4 0.11
34 6 0.16
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (33 bp):
TTATTTTTATATTAATATATTATGTAAATATTA
Found at i:34238 original size:17 final size:17
Alignment explanation
Indices: 34216--34269 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
34206 AATGTTAATA
34216 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * *
34233 TTTAAATTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
34250 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
34267 TTT
1 TTT
34270 TTATAATCCA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:40046 original size:31 final size:31
Alignment explanation
Indices: 39986--40064 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
39976 ATTCAACGTC
* * *
39986 CAAGTGATCAAAACTTAATAAAACGATAACG
1 CAAGTGACCAAAACTTAATAAAACAATAACA
* * **
40017 CAAGTGACTATAACTTAATAAAGTAATAACA
1 CAAGTGACCAAAACTTAATAAAACAATAACA
*
40048 TAAGTGACCAAAACTTA
1 CAAGTGACCAAAACTTA
40065 TGTTTTTTGA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.51, C:0.15, G:0.11, T:0.23
Consensus pattern (31 bp):
CAAGTGACCAAAACTTAATAAAACAATAACA
Found at i:42193 original size:2 final size:2
Alignment explanation
Indices: 42186--42223 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
42176 CTTTTCTGCC
42186 AT AT AT AT AT 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 AT AT AT AT AT
42224 TTAAGTGTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42386 original size:29 final size:29
Alignment explanation
Indices: 42353--42410 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
42343 ATGAACCGGC
42353 AAGGATTAATCACGAATTTAAGGAAAGGT
1 AAGGATTAATCACGAATTTAAGGAAAGGT
42382 AAGGATTAATCACGAATTTAAGGAAAGGT
1 AAGGATTAATCACGAATTTAAGGAAAGGT
42411 CCCCCAAGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.45, C:0.07, G:0.24, T:0.24
Consensus pattern (29 bp):
AAGGATTAATCACGAATTTAAGGAAAGGT
Done.