Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002494.1 Hibiscus syriacus cultivar Beakdansim tig00005087_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: 90982
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:560 original size:102 final size:101
Alignment explanation
Indices: 384--573 Score: 260
Period size: 102 Copynumber: 1.9 Consensus size: 101
374 TATTCTCTAC
* *
384 ACTTTGTTGATACGTACATTTAACGTTTTAATTTAATTTAAATATTAATAATTTTAGTTATTTAT
1 ACTTTGCTGATACGTACATTTAACGTTTTAATTTAATTTAAATATTAATAATTTTA-TGATTTAT
*
449 TTAATGCATGATTATTATATTAATTAAATATCTCGAT
65 TTAATGCATGATTATTAGATTAATTAAATATCTCGAT
*
486 ACTTTGCTGATACGTAACATTTTAACGTTTTAA-TTAATTTAAATTATTATTAATATTT-TGA-T
1 ACTTTGCTGATACGT-ACA-TTTAACGTTTTAATTTAATTTAAA-TATTAATAAT-TTTATGATT
* *
548 TCTTTATTGCATGATTATTAGATTAA
62 TATTTAATGCATGATTATTAGATTAA
574 GAATTATTTT
Statistics
Matches: 78, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
102 38 0.49
103 15 0.19
104 22 0.28
105 3 0.04
ACGTcount: A:0.34, C:0.07, G:0.08, T:0.50
Consensus pattern (101 bp):
ACTTTGCTGATACGTACATTTAACGTTTTAATTTAATTTAAATATTAATAATTTTATGATTTATT
TAATGCATGATTATTAGATTAATTAAATATCTCGAT
Found at i:2081 original size:18 final size:18
Alignment explanation
Indices: 2058--2097 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
2048 CCAGCAGCCA
2058 CCGCAGCCATATATGATG
1 CCGCAGCCATATATGATG
2076 CCGCAGCCATATATGATG
1 CCGCAGCCATATATGATG
2094 CCGC
1 CCGC
2098 CATCGCCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.25, C:0.33, G:0.23, T:0.20
Consensus pattern (18 bp):
CCGCAGCCATATATGATG
Found at i:2660 original size:26 final size:24
Alignment explanation
Indices: 2588--2660 Score: 62
Period size: 25 Copynumber: 3.0 Consensus size: 24
2578 TTATATTTGT
2588 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
* *
2613 ATTT-TTTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
2636 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
2661 GTTGGACTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 13
0.69 0.07 0.24
Matches are distributed among these distances:
23 4 0.11
24 10 0.27
25 12 0.32
26 11 0.30
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.63
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:5958 original size:47 final size:49
Alignment explanation
Indices: 5839--5959 Score: 149
Period size: 51 Copynumber: 2.5 Consensus size: 49
5829 TTATACAAAA
*
5839 CGCGGTACCTGCTCCGCGCTATATAAAATTATGTCAGGAGTAAATGTATGT
1 CGCGGTACCTGCTCCGCGCTATATAAAATTATGTC--GAGTAAAAGTATGT
* *
5890 CGCGGTACCTGCCCCGAGCTATATAAAATTATG-C-AGTAAAAGTATAG-
1 CGCGGTACCTGCTCCGCGCTATATAAAATTATGTCGAGTAAAAGTAT-GT
* *
5937 CGCGGTATCTGATCCGCGCTATA
1 CGCGGTACCTGCTCCGCGCTATA
5960 CCCCTACGTG
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
47 29 0.47
48 1 0.02
50 1 0.02
51 31 0.50
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.26
Consensus pattern (49 bp):
CGCGGTACCTGCTCCGCGCTATATAAAATTATGTCGAGTAAAAGTATGT
Found at i:6055 original size:50 final size:49
Alignment explanation
Indices: 5971--6094 Score: 149
Period size: 50 Copynumber: 2.5 Consensus size: 49
5961 CCCTACGTGG
* * * **
5971 CGTATAGCGCGCTGCAAGGGCCGCACTATACCCACGTGGCACCAGCTCAC
1 CGTATAGCGCGGTGC-AGGGGCGCACTATACCCACGTGACACCAAATCAC
* * *
6021 CGTATAGCGCGGTGCAGGGGCGCGCTATACCCCACGTGACGCCAAATCAT
1 CGTATAGCGCGGTGCAGGGGCGCACTATA-CCCACGTGACACCAAATCAC
6071 CGTATAGCGCGGTGCAGGAGGCGC
1 CGTATAGCGCGGTGCAGG-GGCGC
6095 TTTACTACTA
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
49 12 0.19
50 47 0.73
51 5 0.08
ACGTcount: A:0.21, C:0.33, G:0.31, T:0.15
Consensus pattern (49 bp):
CGTATAGCGCGGTGCAGGGGCGCACTATACCCACGTGACACCAAATCAC
Found at i:9405 original size:176 final size:178
Alignment explanation
Indices: 9076--9429 Score: 676
Period size: 176 Copynumber: 2.0 Consensus size: 178
9066 TATTACCTAG
9076 AACAGAATTGCAAGAAAACAACACATATTATCCAGGAAATATTCTGTAATAATGTGAGAGTAAGG
1 AACAGAATTGCAAGAAAACAACACATATTATCCAGGAAATATTCTGTAATAATGTGAGAGTAAGG
*
9141 AAAAGATTACTCCTGACATAAAGTAGTCCACACATTCAATAATATCTAAAGATTAATATAATCAC
66 AAAAGATTACTCCTGACATAAAGTAGTCCACACATTCAATAATATCTAAAGATTAATATAACCAC
9206 AACAACAATATGCCCTCATAAAATAATGAAAGGAAGAACAAACTAGCT
131 AACAACAATATGCCCTCATAAAATAATGAAAGGAAGAACAAACTAGCT
9254 AACAGAATTGCAAGAAAACAACACATATTATCCAGGAAATATTCTGTAATAATGTGAGAGTAAGG
1 AACAGAATTGCAAGAAAACAACACATATTATCCAGGAAATATTCTGTAATAATGTGAGAGTAAGG
9319 -AAAGATTACTCCTGACAT-AAGTAGTCCACACATTCAATAATATCTAAAGATTAATATAACCAC
66 AAAAGATTACTCCTGACATAAAGTAGTCCACACATTCAATAATATCTAAAGATTAATATAACCAC
*
9382 AACAACAATATGCCCTCATAAAATAATGAAAGGAAGAACAAATTAGCT
131 AACAACAATATGCCCTCATAAAATAATGAAAGGAAGAACAAACTAGCT
9430 TTTGCAATAA
Statistics
Matches: 174, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
176 91 0.52
177 18 0.10
178 65 0.37
ACGTcount: A:0.47, C:0.16, G:0.13, T:0.23
Consensus pattern (178 bp):
AACAGAATTGCAAGAAAACAACACATATTATCCAGGAAATATTCTGTAATAATGTGAGAGTAAGG
AAAAGATTACTCCTGACATAAAGTAGTCCACACATTCAATAATATCTAAAGATTAATATAACCAC
AACAACAATATGCCCTCATAAAATAATGAAAGGAAGAACAAACTAGCT
Found at i:18558 original size:33 final size:33
Alignment explanation
Indices: 18521--18595 Score: 141
Period size: 33 Copynumber: 2.3 Consensus size: 33
18511 GCCATAGCTT
*
18521 CACTAGTCTACCACGGGGTATACCTATGGCTAC
1 CACTAGTCTACCACGGGCTATACCTATGGCTAC
18554 CACTAGTCTACCACGGGCTATACCTATGGCTAC
1 CACTAGTCTACCACGGGCTATACCTATGGCTAC
18587 CACTAGTCT
1 CACTAGTCT
18596 TGTACAAATA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (33 bp):
CACTAGTCTACCACGGGCTATACCTATGGCTAC
Found at i:19346 original size:17 final size:17
Alignment explanation
Indices: 19312--19344 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
19302 TTTGATTATA
19312 ATTATATAATTATATTT
1 ATTATATAATTATATTT
*
19329 ATTATTTAA-TATATTT
1 ATTATATAATTATATTT
19345 TACTTTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTATATAATTATATTT
Found at i:20740 original size:21 final size:20
Alignment explanation
Indices: 20717--20849 Score: 74
Period size: 20 Copynumber: 6.5 Consensus size: 20
20707 CAGTTCCCAG
20717 AATCGCAACGCGATTATGAA
1 AATCGCAACGCGATTATGAA
*
20737 GAATCGCAATGCGA-TA-GTACA
1 -AATCGCAACGCGATTATG-A-A
* ** * * *
20758 AATTAGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTAT-GAA
*
20780 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGATTATGAA
**
20800 AATCGCAACGCGAACAT-ATA
1 AATCGCAACGCGATTATGA-A
* *
20820 AATCGCAACGCGATTCTGAC
1 AATCGCAACGCGATTATGAA
*
20840 TATCGCAACG
1 AATCGCAACG
20850 AGTATCCGTA
Statistics
Matches: 85, Mismatches: 19, Indels: 17
0.70 0.16 0.14
Matches are distributed among these distances:
19 2 0.02
20 46 0.54
21 33 0.39
22 3 0.04
23 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.21
Consensus pattern (20 bp):
AATCGCAACGCGATTATGAA
Found at i:20805 original size:20 final size:20
Alignment explanation
Indices: 20780--20951 Score: 116
Period size: 20 Copynumber: 8.5 Consensus size: 20
20770 GATTTTCCAG
*
20780 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGAA
* *
20800 AATCGCAACGCGAACA-TATA
1 AATCGCAACGCGAATACGA-A
* *
20820 AATCGCAACGCG-ATTCTGAC
1 AATCGCAACGCGAATAC-GAA
* * * *
20840 TATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGAATACG-AA
* * *
20861 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
*
20881 AATCACAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* * *
20902 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
* *
20922 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
20942 AATCGCAACG
1 AATCGCAACG
20952 AGATTCTGAC
Statistics
Matches: 120, Mismatches: 24, Indels: 16
0.75 0.15 0.10
Matches are distributed among these distances:
19 2 0.02
20 82 0.68
21 36 0.30
ACGTcount: A:0.39, C:0.26, G:0.18, T:0.17
Consensus pattern (20 bp):
AATCGCAACGCGAATACGAA
Found at i:20863 original size:61 final size:61
Alignment explanation
Indices: 20798--20969 Score: 188
Period size: 61 Copynumber: 2.8 Consensus size: 61
20788 CGCGAATATG
**
20798 AAAATCGCAACGCGAACATATAAATCGCAACGCGATTCTGACTATCGCAACGAGTATCCGT
1 AAAATCGCAACGCGAACACGTAAATCGCAACGCGATTCTGACTATCGCAACGAGTATCCGT
* * * * ** *
20859 AAAATCGCAACGCGTATC-CGTAAATCACAACGACAATAC-GTAAAATCGCAACGCGTATCCGT
1 AAAATCGCAACGCG-AACACGTAAATCGCAACG-CGATTCTG-ACTATCGCAACGAGTATCCGT
* * *
20921 -AAATCGCAACGAGAATACGTAAATCGCAACGAGATTCTGACTATCGCAA
1 AAAATCGCAACGCGAACACGTAAATCGCAACGCGATTCTGACTATCGCAA
20970 TACTGAATTT
Statistics
Matches: 88, Mismatches: 18, Indels: 11
0.75 0.15 0.09
Matches are distributed among these distances:
60 12 0.14
61 52 0.59
62 24 0.27
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (61 bp):
AAAATCGCAACGCGAACACGTAAATCGCAACGCGATTCTGACTATCGCAACGAGTATCCGT
Found at i:20867 original size:21 final size:20
Alignment explanation
Indices: 20841--20953 Score: 136
Period size: 20 Copynumber: 5.5 Consensus size: 20
20831 GATTCTGACT
20841 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGAGTATCCGT-AA
*
20862 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
* ** *
20882 ATCACAACGACAATACGTAAA
1 ATCGCAACGAGTATCCGT-AA
*
20903 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
* *
20923 ATCGCAACGAGAATACGTAA
1 ATCGCAACGAGTATCCGTAA
20943 ATCGCAACGAG
1 ATCGCAACGAG
20954 ATTCTGACTA
Statistics
Matches: 77, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
20 45 0.58
21 32 0.42
ACGTcount: A:0.39, C:0.26, G:0.19, T:0.17
Consensus pattern (20 bp):
ATCGCAACGAGTATCCGTAA
Found at i:20872 original size:41 final size:41
Alignment explanation
Indices: 20841--20951 Score: 179
Period size: 41 Copynumber: 2.7 Consensus size: 41
20831 GATTCTGACT
* *
20841 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
20882 ATCACAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
20923 ATCGCAACGAGAATACGT-AAATCGCAACG
1 ATCGCAACGAGAATACGTAAAATCGCAACG
20952 AGATTCTGAC
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
40 11 0.17
41 53 0.83
ACGTcount: A:0.39, C:0.26, G:0.18, T:0.17
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:30343 original size:14 final size:14
Alignment explanation
Indices: 30317--30344 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
30307 CAATGCAAAA
30317 TGAAAATCGCAACG
1 TGAAAATCGCAACG
30331 TGAAAATCGCAACG
1 TGAAAATCGCAACG
30345 CGAATATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.21, T:0.14
Consensus pattern (14 bp):
TGAAAATCGCAACG
Found at i:32981 original size:31 final size:31
Alignment explanation
Indices: 32943--33006 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
32933 AGTCGAAGGT
*
32943 TTTACCTATGTTCTAAGGAACATATGGACAG
1 TTTACCTAGGTTCTAAGGAACATATGGACAG
** * *
32974 TTTACCTAGGTTCTTTGGGACCTATGGACAG
1 TTTACCTAGGTTCTAAGGAACATATGGACAG
33005 TT
1 TT
33007 GCCGAGGTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (31 bp):
TTTACCTAGGTTCTAAGGAACATATGGACAG
Found at i:33017 original size:30 final size:30
Alignment explanation
Indices: 32965--33060 Score: 104
Period size: 30 Copynumber: 3.2 Consensus size: 30
32955 CTAAGGAACA
* *
32965 TATGGACAGTTTACCTAGGTTCTTTGGGACC
1 TATGGACAG-TTACCGAGGTTCTTTGTGACC
* *
32996 TATGGACAGTTGCCGAGGTTCTTTATGACC
1 TATGGACAGTTACCGAGGTTCTTTGTGACC
* * *
33026 TCTGGATAGTTACCG-GGGTCTTTGTGACC
1 TATGGACAGTTACCGAGGTTCTTTGTGACC
*
33055 TCTGGA
1 TATGGA
33061 TAGGTCCTTC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
29 18 0.32
30 29 0.52
31 9 0.16
ACGTcount: A:0.18, C:0.20, G:0.28, T:0.34
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGTTCTTTGTGACC
Found at i:34135 original size:19 final size:19
Alignment explanation
Indices: 34079--34142 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
34069 AAAAATGACT
*
34079 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
34098 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
34112 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
34131 ATCGCAATGCGA
1 ATCGCAATGCGA
34143 TTATAGTTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 22 0.58
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:34173 original size:14 final size:14
Alignment explanation
Indices: 34154--34190 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
34144 TATAGTTTCG
* *
34154 CGTTGCGATTTTGT
1 CGTTGCGATTCTCT
34168 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
34182 CGTTGCGAT
1 CGTTGCGAT
34191 AGTTATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.08, C:0.22, G:0.27, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:34435 original size:17 final size:17
Alignment explanation
Indices: 34413--34445 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
34403 ATACTAACTT
34413 CACAGTGTTA-AAGAATA
1 CACAGT-TTAGAAGAATA
34430 CACAGTTTAGAAGAAT
1 CACAGTTTAGAAGAAT
34446 TGGCAGCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.24
Consensus pattern (17 bp):
CACAGTTTAGAAGAATA
Found at i:34445 original size:94 final size:94
Alignment explanation
Indices: 34278--34656 Score: 611
Period size: 94 Copynumber: 4.1 Consensus size: 94
34268 ATGGATTACA
* * * *
34278 TTAC-TTCAACCAAAAGATAAAACAAAGGCAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
34342 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
34371 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
34436 TTAGAAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
34465 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
34530 TTAGCAGAATTAGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* * *
34559 TTAC-TTCAACCAAAAGATAAAACAAAAGATAAATACTAACTTCACAGTGTTAAAGAATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* * *
34623 TTTAGCAGTATT-GTAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
34652 TTACT
1 TTACT
34657 AAGCAATCTA
Statistics
Matches: 270, Mismatches: 13, Indels: 5
0.94 0.05 0.02
Matches are distributed among these distances:
93 42 0.16
94 228 0.84
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:36360 original size:20 final size:20
Alignment explanation
Indices: 36337--36465 Score: 94
Period size: 20 Copynumber: 6.8 Consensus size: 20
36327 TGAAATGAAA
36337 ATCGCAACGAGAGAATGACT
1 ATCGCAACGAGAGAATGACT
* *
36357 ATCGTAACGCG-GAAATGACT
1 ATCGCAACGAGAG-AATGACT
*
36377 ATCACAAC--GAG-A-GA--
1 ATCGCAACGAGAGAATGACT
* * **
36391 ATCGCAACGCGA-AATTAAA
1 ATCGCAACGAGAGAATGACT
*
36410 ATCGCAATGAGAGAATGACT
1 ATCGCAACGAGAGAATGACT
* * *
36430 ATCGCAACGCGAAAATAACT
1 ATCGCAACGAGAGAATGACT
36450 ATCGCAACGAGAGAAT
1 ATCGCAACGAGAGAAT
36466 CGCAACTCAA
Statistics
Matches: 83, Mismatches: 17, Indels: 18
0.70 0.14 0.15
Matches are distributed among these distances:
14 7 0.08
16 5 0.06
17 2 0.02
18 1 0.01
19 12 0.14
20 56 0.67
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.16
Consensus pattern (20 bp):
ATCGCAACGAGAGAATGACT
Found at i:36372 original size:40 final size:40
Alignment explanation
Indices: 36328--36465 Score: 139
Period size: 40 Copynumber: 3.6 Consensus size: 40
36318 TCTTTTGGTT
*
36328 GAAATGAAAATCGCAACGAGAGAATGACTATCGTAACGCG
1 GAAATGAAAATCGCAACGAGAGAATGACTATCGCAACGCG
** *
36368 GAAATGACTATCACAAC--GAG-A-GA--ATCGCAACGC-
1 GAAATGAAAATCGCAACGAGAGAATGACTATCGCAACGCG
* *
36401 GAAATTAAAATCGCAATGAGAGAATGACTATCGCAACGCG
1 GAAATGAAAATCGCAACGAGAGAATGACTATCGCAACGCG
* *
36441 AAAAT-AACTATCGCAACGAGAGAAT
1 GAAATGAA-AATCGCAACGAGAGAAT
36466 CGCAACTCAA
Statistics
Matches: 78, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
33 12 0.15
34 9 0.12
35 3 0.04
36 3 0.04
37 3 0.04
38 3 0.04
39 12 0.15
40 33 0.42
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.15
Consensus pattern (40 bp):
GAAATGAAAATCGCAACGAGAGAATGACTATCGCAACGCG
Found at i:36451 original size:73 final size:73
Alignment explanation
Indices: 36328--36486 Score: 246
Period size: 73 Copynumber: 2.2 Consensus size: 73
36318 TCTTTTGGTT
* * * *
36328 GAAATGAAAATCGCAACGAGAGAATGACTATCGTAACGCGGAAATGACTATCACAACGAGAGAAT
1 GAAATTAAAATCGCAACGAGAGAATGACTATCGCAACGCGAAAATAACTATCACAACGAGAGAAT
36393 CGCAACGC
66 CGCAACGC
* *
36401 GAAATTAAAATCGCAATGAGAGAATGACTATCGCAACGCGAAAATAACTATCGCAACGAGAGAAT
1 GAAATTAAAATCGCAACGAGAGAATGACTATCGCAACGCGAAAATAACTATCACAACGAGAGAAT
*
36466 CGCAACTC
66 CGCAACGC
*
36474 AAAATTAAAATCG
1 GAAATTAAAATCG
36487 TTGCGATTTT
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
73 78 1.00
ACGTcount: A:0.45, C:0.19, G:0.20, T:0.16
Consensus pattern (73 bp):
GAAATTAAAATCGCAACGAGAGAATGACTATCGCAACGCGAAAATAACTATCACAACGAGAGAAT
CGCAACGC
Found at i:36468 original size:34 final size:34
Alignment explanation
Indices: 36357--36471 Score: 106
Period size: 34 Copynumber: 3.2 Consensus size: 34
36347 GAGAATGACT
* * * *
36357 ATCGTAACGCGGAAATGACTATCACAACGAGAGA
1 ATCGCAACGCGAAAATAACTATCGCAACGAGAGA
* * *
36391 ATCGCAACGCGAAATTAA-AATCGCAATGAGAGAATGA
1 ATCGCAACGCGAAAATAACTATCGCAA--CGAG-A-GA
36428 CTATCGCAACGCGAAAATAACTATCGCAACGAGAGA
1 --ATCGCAACGCGAAAATAACTATCGCAACGAGAGA
36464 ATCGCAAC
1 ATCGCAAC
36472 TCAAAATTAA
Statistics
Matches: 64, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
33 6 0.09
34 22 0.34
35 3 0.05
36 3 0.05
37 3 0.05
38 3 0.05
39 17 0.27
40 7 0.11
ACGTcount: A:0.43, C:0.22, G:0.21, T:0.15
Consensus pattern (34 bp):
ATCGCAACGCGAAAATAACTATCGCAACGAGAGA
Found at i:36532 original size:20 final size:20
Alignment explanation
Indices: 36507--36554 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
36497 TATTTCTCTG
*
36507 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCAT
**
36527 GTTGCGATTTTCATTTTCAT
1 GTTGCGATAGTCATTTTCAT
*
36547 GTTACGAT
1 GTTGCGAT
36555 TTTAAGTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.17, C:0.15, G:0.21, T:0.48
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCAT
Found at i:36555 original size:20 final size:20
Alignment explanation
Indices: 36517--36557 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
36507 GTTGCGATAG
* *
36517 TCATTTTCGTGTTGCGATTT
1 TCATTTTCATGTTACGATTT
36537 TCATTTTCATGTTACGATTT
1 TCATTTTCATGTTACGATTT
36557 T
1 T
36558 AAGTTTAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.56
Consensus pattern (20 bp):
TCATTTTCATGTTACGATTT
Found at i:37142 original size:20 final size:20
Alignment explanation
Indices: 37117--37290 Score: 181
Period size: 20 Copynumber: 8.6 Consensus size: 20
37107 CTTTAAAAAT
37117 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
37137 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* *
37157 TGTCGTTGCGATATACGGATA
1 CG-CGTTGCGATTTACGGATA
* * *
37178 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
37198 CTCGTTACGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
**
37218 CGCGTTGCGATTTTACATATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
37240 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
37259 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
37280 CTCGTTGCGAT
1 CGCGTTGCGAT
37291 AGTCAGAATC
Statistics
Matches: 124, Mismatches: 23, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
19 2 0.02
20 70 0.56
21 50 0.40
22 2 0.02
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:37176 original size:41 final size:41
Alignment explanation
Indices: 37119--37290 Score: 265
Period size: 41 Copynumber: 4.2 Consensus size: 41
37109 TTAAAAATCG
*
37119 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
37160 CGTTGCGATATACGGATACGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * *
37200 CGTTACGATTTACGGATACGCGTTGCGATTTTACATATTAT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
37241 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
37282 CGTTGCGAT
1 CGTTGCGAT
37291 AGTCAGAATC
Statistics
Matches: 117, Mismatches: 13, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
40 36 0.31
41 81 0.69
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:37259 original size:81 final size:82
Alignment explanation
Indices: 37119--37290 Score: 274
Period size: 81 Copynumber: 2.1 Consensus size: 82
37109 TTAAAAATCG
* *
37119 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATATACGGATACGCATT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACATATTATCGTTGCGATATACGGATACGCATT
* *
37184 GCGA-TTTACGTATTCT
66 GCGATTTTACGGATACT
* * *
37200 CGTTACGATTTACGGATACGCGTTGCGATTTTACATATTATCGTTGCGATTTACGGATACGCGTT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACATATTATCGTTGCGATATACGGATACGCATT
37265 GCGATTTTACGGATACT
66 GCGATTTTACGGATACT
37282 CGTTGCGAT
1 CGTTGCGAT
37291 AGTCAGAATC
Statistics
Matches: 82, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
81 64 0.78
82 18 0.22
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (82 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACATATTATCGTTGCGATATACGGATACGCATT
GCGATTTTACGGATACT
Found at i:37322 original size:20 final size:20
Alignment explanation
Indices: 37299--37351 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
37289 ATAGTCAGAA
*
37299 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
37319 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
37339 TCGCGTTGCGATT
1 TCGCGTTGCGATT
37352 CTGAAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:37326 original size:81 final size:81
Alignment explanation
Indices: 37119--37351 Score: 213
Period size: 81 Copynumber: 2.9 Consensus size: 81
37109 TTAAAAATCG
* * * * * * *
37119 CGTTGCGATTTACGGATACGCGTTGCGATTT-TACGTATTGTCGTTGCGATATACGGATACGCAT
1 CGTTACGATTCACGAATACGCGTTGCGATTTATATGT-TAG-CGTTGCGATTTACGGATACGCGT
* *
37183 TGCGA-TTTACGTATTCT
64 TGCGATTTTACGGATACT
* * * * *
37200 CGTTACGATTTACGGATACGCGTTGCGATTTTACATATTATCGTTGCGATTTACGGATACGCGTT
1 CGTTACGATTCACGAATACGCGTTGCGA-TTTATATGTTAGCGTTGCGATTTACGGATACGCGTT
37265 GCGATTTTACGGATACT
65 GCGATTTTACGGATACT
* * * ** *
37282 CGTTGCGATAGTCA-GAAT-CGCGTTGCGATTTATATGTTCGCGTTGCGATTTTCATATTCGCGT
1 CGTTACGAT--TCACGAATACGCGTTGCGATTTATATGTTAGCGTTGCGATTTACGGATACGCGT
37345 TGCGATT
64 TGCGATT
37352 CTGAAAAATC
Statistics
Matches: 126, Mismatches: 21, Indels: 10
0.80 0.13 0.06
Matches are distributed among these distances:
81 87 0.69
82 32 0.25
83 5 0.04
84 2 0.02
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (81 bp):
CGTTACGATTCACGAATACGCGTTGCGATTTATATGTTAGCGTTGCGATTTACGGATACGCGTTG
CGATTTTACGGATACT
Found at i:37450 original size:20 final size:20
Alignment explanation
Indices: 37380--37454 Score: 62
Period size: 20 Copynumber: 3.7 Consensus size: 20
37370 AATTTGTACT
* **
37380 ATCGCATTGCGATTCTTTATA
1 ATCGCGTTGCGATTCTGGA-A
* *
37401 ATCGTGTTGCGATTCTGGGA
1 ATCGCGTTGCGATTCTGGAA
**
37421 A-CTGATTTGCGATTCTGGAA
1 ATC-GCGTTGCGATTCTGGAA
37441 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
37455 TTTATTTCGC
Statistics
Matches: 42, Mismatches: 10, Indels: 5
0.74 0.18 0.09
Matches are distributed among these distances:
19 1 0.02
20 26 0.62
21 15 0.36
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.37
Consensus pattern (20 bp):
ATCGCGTTGCGATTCTGGAA
Found at i:40555 original size:17 final size:18
Alignment explanation
Indices: 40522--40555 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40512 TTTCACTAAT
*
40522 AGAGAAAATATTACAAAG
1 AGAGAAAATAGTACAAAG
40540 AGAGAAAA-AGTACAAA
1 AGAGAAAATAGTACAAA
40556 TAGCCTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.65, C:0.06, G:0.18, T:0.12
Consensus pattern (18 bp):
AGAGAAAATAGTACAAAG
Found at i:64251 original size:8 final size:8
Alignment explanation
Indices: 64238--64313 Score: 52
Period size: 8 Copynumber: 9.9 Consensus size: 8
64228 TATTAATATT
64238 TATAATAA
1 TATAATAA
*
64246 TATAATAT
1 TATAATAA
*
64254 TAT-AT-T
1 TATAATAA
* *
64260 TTTAATAT
1 TATAATAA
64268 TATAATAA
1 TATAATAA
*
64276 AATAATAA
1 TATAATAA
*
64284 AATAATCAA
1 TATAAT-AA
*
64293 T-T-ATAT
1 TATAATAA
64299 TATAATAA
1 TATAATAA
64307 TATAATA
1 TATAATA
64314 TATTATATTT
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
6 5 0.09
7 7 0.13
8 41 0.75
9 2 0.04
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (8 bp):
TATAATAA
Found at i:64256 original size:26 final size:24
Alignment explanation
Indices: 64194--64256 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
64184 CATTTTAATC
64194 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
64218 AAAATATAT-TTATTAATAT-TTAT
1 AAAATATATATTATTAAAATATT-T
64241 AATAATATAATATTAT
1 AA-AATAT-ATATTAT
64257 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 12 0.36
25 3 0.09
26 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:64267 original size:31 final size:31
Alignment explanation
Indices: 64222--64344 Score: 105
Period size: 31 Copynumber: 4.0 Consensus size: 31
64212 ATATTTAAAA
64222 TATATTTATTAATATTTATAATAATATAATAT
1 TATATTT-TTAATATTTATAATAATATAATAT
*
64254 TATATTTTTAATA-TTATAATAAAATAATA-
1 TATATTTTTAATATTTATAATAATATAATAT
* ** *
64283 -AAATAATCAATTATATTATAATAATATAATATAT
1 TATATTTTTAA-TAT-TTATAATAATAT-A-ATAT
64317 TATATTTTT-AT-TTTAATAAT-ATATAATA
1 TATATTTTTAATATTT-ATAATAATATAATA
64345 AATTATTAAT
Statistics
Matches: 73, Mismatches: 10, Indels: 19
0.72 0.10 0.19
Matches are distributed among these distances:
28 6 0.08
29 5 0.07
30 16 0.22
31 23 0.32
32 14 0.19
33 4 0.05
34 1 0.01
35 4 0.05
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.50
Consensus pattern (31 bp):
TATATTTTTAATATTTATAATAATATAATAT
Found at i:64305 original size:23 final size:23
Alignment explanation
Indices: 64277--64322 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
64267 TTATAATAAA
64277 ATAATAAAATAATCA-ATTATATT
1 ATAATAAAATAAT-ATATTATATT
*
64300 ATAATAATATAATATATTATATT
1 ATAATAAAATAATATATTATATT
64323 TTTATTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 1 0.05
23 20 0.95
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
ATAATAAAATAATATATTATATT
Found at i:64307 original size:18 final size:18
Alignment explanation
Indices: 64231--64320 Score: 58
Period size: 20 Copynumber: 4.7 Consensus size: 18
64221 ATATATTTAT
64231 TAATAT-TTATAATAATA
1 TAATATATTATAATAATA
* *
64248 TAATATTATATTTTTAATATTA
1 T-A-A-TATA-TTATAATAATA
* *
64270 TAATAAAATAATAA-AATAA
1 TAAT-ATATTATAATAAT-A
64289 TCAATTATATTATAATAATA
1 T-AA-TATATTATAATAATA
64309 TAATATATTATA
1 TAATATATTATA
64321 TTTTTATTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 19
0.67 0.10 0.23
Matches are distributed among these distances:
17 1 0.02
18 12 0.22
19 10 0.18
20 17 0.31
21 5 0.09
22 10 0.18
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (18 bp):
TAATATATTATAATAATA
Found at i:64473 original size:23 final size:23
Alignment explanation
Indices: 64447--64498 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
64437 TTAATCTAAT
*
64447 AATATTTTAATAAAGATATTTAA
1 AATATATTAATAAAGATATTTAA
* * *
64470 AATATATTAATTAATATTTTTAA
1 AATATATTAATAAAGATATTTAA
64493 AATATA
1 AATATA
64499 ATATAATACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
AATATATTAATAAAGATATTTAA
Found at i:64876 original size:15 final size:15
Alignment explanation
Indices: 64843--64899 Score: 82
Period size: 14 Copynumber: 3.9 Consensus size: 15
64833 TCAATAAATG
*
64843 TAATTCATTTTCCAA
1 TAATTCAATTTCCAA
64858 -AATTCAATTTCCAA
1 TAATTCAATTTCCAA
*
64872 TAATTCATTTTCC-A
1 TAATTCAATTTCCAA
64886 TAATTCAATTTCCA
1 TAATTCAATTTCCA
64900 GAAAACCAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
14 26 0.70
15 11 0.30
ACGTcount: A:0.35, C:0.21, G:0.00, T:0.44
Consensus pattern (15 bp):
TAATTCAATTTCCAA
Found at i:64877 original size:29 final size:29
Alignment explanation
Indices: 64843--64899 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
64833 TCAATAAATG
64843 TAATTCATTTTCCAAAATTCAATTTCCAA
1 TAATTCATTTTCCAAAATTCAATTTCCAA
*
64872 TAATTCATTTTCCATAATTCAATTTCCA
1 TAATTCATTTTCCAAAATTCAATTTCCA
64900 GAAAACCAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.35, C:0.21, G:0.00, T:0.44
Consensus pattern (29 bp):
TAATTCATTTTCCAAAATTCAATTTCCAA
Found at i:66139 original size:90 final size:90
Alignment explanation
Indices: 65975--66245 Score: 436
Period size: 90 Copynumber: 3.0 Consensus size: 90
65965 CTAGAACTGC
* * *
65975 ATCCGTAGGGCTTACCCTCAGCACACAGCAAAAGGGGAGCCAACCTAAGGATATACCTT-GGGCC
1 ATCCATAGGG-TTACCCTAAGCACACAGCAAAA-GGGAACCAACCTAAGGATATACCTTGGGGCC
* *
66039 TATAGTCCTACCCAAGGATATCCTTAG
64 TATGGGCCTACCCAAGGATATCCTTAG
* *
66066 ATCCATAGGGTTACCTTAAGCACACAACAAAAGGGAACCAACCTAAGGATATACCTTGGGGCCTA
1 ATCCATAGGGTTACCCTAAGCACACAGCAAAAGGGAACCAACCTAAGGATATACCTTGGGGCCTA
66131 TGGGCCTACCCAAGGATATCCTTAG
66 TGGGCCTACCCAAGGATATCCTTAG
*
66156 ATCCATAGGGTTACCCTAAGCACACAGCAAAAGGGAACCAACCTAAGGATATATCTTGGGGCCTA
1 ATCCATAGGGTTACCCTAAGCACACAGCAAAAGGGAACCAACCTAAGGATATACCTTGGGGCCTA
*
66221 TGGGCCTACCCAAGGGTATCCTTAG
66 TGGGCCTACCCAAGGATATCCTTAG
66246 GTCCGTAAGA
Statistics
Matches: 168, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
89 24 0.14
90 135 0.80
91 9 0.05
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.20
Consensus pattern (90 bp):
ATCCATAGGGTTACCCTAAGCACACAGCAAAAGGGAACCAACCTAAGGATATACCTTGGGGCCTA
TGGGCCTACCCAAGGATATCCTTAG
Found at i:72787 original size:9 final size:9
Alignment explanation
Indices: 72768--72818 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
72758 AACATATAAT
72768 ATAATAAAAA
1 ATAA-AAAAA
72778 ATAAAAAAA
1 ATAAAAAAA
** *
72787 ATAATTAAG
1 ATAAAAAAA
72796 ATATAAAAAA
1 ATA-AAAAAA
72806 ATAAAAAAA
1 ATAAAAAAA
72815 ATAA
1 ATAA
72819 TTAAGATATA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
9 24 0.71
10 10 0.29
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (9 bp):
ATAAAAAAA
Found at i:72800 original size:35 final size:33
Alignment explanation
Indices: 72761--72829 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 33
72751 TAAAAATAAC
72761 ATATAATATAATAAAAAATAAAAAAAATAATTAAG
1 ATATAATAT-A-AAAAAATAAAAAAAATAATTAAG
72796 -----ATATAAAAAAATAAAAAAAATAATTAAG
1 ATATAATATAAAAAAATAAAAAAAATAATTAAG
72824 ATATAA
1 ATATAA
72830 AAAATATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
28 23 0.79
29 1 0.03
30 4 0.14
33 1 0.03
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (33 bp):
ATATAATATAAAAAAATAAAAAAAATAATTAAG
Found at i:72804 original size:28 final size:28
Alignment explanation
Indices: 72773--72833 Score: 122
Period size: 28 Copynumber: 2.2 Consensus size: 28
72763 ATAATATAAT
72773 AAAAAATAAAAAAAATAATTAAGATATA
1 AAAAAATAAAAAAAATAATTAAGATATA
72801 AAAAAATAAAAAAAATAATTAAGATATA
1 AAAAAATAAAAAAAATAATTAAGATATA
72829 AAAAA
1 AAAAA
72834 TATATTTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (28 bp):
AAAAAATAAAAAAAATAATTAAGATATA
Found at i:72831 original size:20 final size:20
Alignment explanation
Indices: 72806--72848 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
72796 ATATAAAAAA
72806 ATAAAAAAAATAATTAAGAT
1 ATAAAAAAAATAATTAAGAT
* * *
72826 ATAAAAAATATATTTAATAT
1 ATAAAAAAAATAATTAAGAT
72846 ATA
1 ATA
72849 GATGAATAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
ATAAAAAAAATAATTAAGAT
Found at i:72836 original size:9 final size:9
Alignment explanation
Indices: 72771--72837 Score: 50
Period size: 8 Copynumber: 7.3 Consensus size: 9
72761 ATATAATATA
72771 ATAAAAAAT
1 ATAAAAAAT
72780 A-AAAAAA-
1 ATAAAAAAT
*
72787 ATAATTAAGAT
1 ATAA--AAAAT
72798 ATAAAAAA-
1 ATAAAAAAT
*
72806 ATAAAAAAA
1 ATAAAAAAT
*
72815 ATAATTAAGAT
1 ATAA--AAAAT
72826 ATAAAAAAT
1 ATAAAAAAT
72835 ATA
1 ATA
72838 TTTAATATAT
Statistics
Matches: 46, Mismatches: 5, Indels: 14
0.71 0.08 0.22
Matches are distributed among these distances:
7 1 0.02
8 16 0.35
9 15 0.33
10 3 0.07
11 11 0.24
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (9 bp):
ATAAAAAAT
Found at i:72845 original size:18 final size:17
Alignment explanation
Indices: 72804--72846 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
72794 AGATATAAAA
*
72804 AAATAAAAAAAATAATT
1 AAATATAAAAAATAATT
72821 AAGATATAAAAAATATATT
1 AA-ATATAAAAAATA-ATT
*
72840 TAATATA
1 AAATATA
72847 TAGATGAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 16 0.73
19 4 0.18
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (17 bp):
AAATATAAAAAATAATT
Found at i:76752 original size:3 final size:3
Alignment explanation
Indices: 76744--76777 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
76734 AACAGAGAGT
*
76744 TTA TTA TTA TTA TTA TTA TTA TGTA TTA GTA TTA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
76778 CTAGTATCTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:84046 original size:68 final size:68
Alignment explanation
Indices: 83952--84080 Score: 168
Period size: 68 Copynumber: 1.9 Consensus size: 68
83942 CCTTGTACGC
* * * * * *
83952 TATTTCAAATAAGACCCGTAAATATTTTATGATTACACGAACTACTAACCATGATAATCCTCATA
1 TATTTCAAATAAAACCCGTAAATATTTAATAATTACAAGAACCACTAACCATAATAATCCTCATA
84017 TAA
66 TAA
* * * *
84020 TATTTCAAATAAAATCTGTAAATATTTAATAATTACAAGAACCACTTACTATAATAATCCT
1 TATTTCAAATAAAACCCGTAAATATTTAATAATTACAAGAACCACTAACCATAATAATCCT
84081 TATCATTATT
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
68 51 1.00
ACGTcount: A:0.43, C:0.17, G:0.05, T:0.34
Consensus pattern (68 bp):
TATTTCAAATAAAACCCGTAAATATTTAATAATTACAAGAACCACTAACCATAATAATCCTCATA
TAA
Found at i:85324 original size:21 final size:21
Alignment explanation
Indices: 85299--85338 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
85289 CTCCATTCCA
85299 TTAAAATTATC-CACTTTAATT
1 TTAAAATTATCACA-TTTAATT
85320 TTAAAATTATCACATTTAA
1 TTAAAATTATCACATTTAA
85339 AATATATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (21 bp):
TTAAAATTATCACATTTAATT
Found at i:85721 original size:2 final size:2
Alignment explanation
Indices: 85714--85738 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
85704 ACCAGCAAAC
85714 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
85739 AATGGAGGAC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.