Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005681.1 Hibiscus syriacus cultivar Beakdansim tig00013287_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: 165246
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:2184 original size:82 final size:82
Alignment explanation
Indices: 2082--2729 Score: 824
Period size: 82 Copynumber: 7.9 Consensus size: 82
2072 TACATCGGTG
* *
2082 AAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCCATTTTCTAAAAAATTGTTTAAATTAT
1 AAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCCGTTTTCTGAAAAATTGTTTAAATTAT
2147 GCATTGAATGACCTCTA
66 GCATTGAATGACCTCTA
* * * * *
2164 AAAAGTGGCAGAAAATGATAATGCATCATTATTTCACACGTTTTTCTG-AAAATTGTTTAAATTA
1 AAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCCG-TTTTCTGAAAAATTGTTTAAATTA
2228 TGCATTGAATGACCTCTGA
65 TGCATTGAATGACCTCT-A
* * * * * * *
2247 AAAA-TTGTAGAAGATGATAATGCATCACTAATTAACCCGTTTTTTGAAAAGTTATTTAAATTAT
1 AAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCCGTTTTCTGAAAAATTGTTTAAATTAT
* *
2311 GCATTAAATGACCTCTG
66 GCATTGAATGACCTCTA
* * * * * *
2328 AAAAGTTGCAGAAGATGATAATGCACTACTATTTCACTCGTTGTCTGAAAAATTATTTAAATCAC
1 AAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCCGTTTTCTGAAAAATTGTTTAAATTAT
* *
2393 GCATTGAATAACCTCTG
66 GCATTGAATGACCTCTA
* * * *
2410 AAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCCATTTTTTGAAAAGTTTTTTAAATTAT
1 AAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCCGTTTTCTGAAAAATTGTTTAAATTAT
*
2475 GCATTGAATGACTTCTGA
66 GCATTGAATGACCTCT-A
* * * * * *
2493 AAAAGTTGCAGAAAATGAGAATACACCATTATTTCACCTGTTTTCTGAAAAGTTGTTTAAATTAT
1 AAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCCGTTTTCTGAAAAATTGTTTAAATTAT
* *
2558 GAATT-AGATGACCTTTA
66 GCATTGA-ATGACCTCTA
*
2575 AAAAGTTGCAG-A-ATGAT-ATGC-CCACTATTTCACCTGTTTTCTGAAAAATTGTTTAAATTAT
1 AAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCCGTTTTCTGAAAAATTGTTTAAATTAT
* *
2636 GCATTAAATGACCTCTG
66 GCATTGAATGACCTCTA
* * *
2653 AAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCTGTTGTCTGAAAAGTTGTTTAAATTAT
1 AAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCCGTTTTCTGAAAAATTGTTTAAATTAT
2718 GCATTGAATGAC
66 GCATTGAATGAC
2730 ATTGTCTGAA
Statistics
Matches: 490, Mismatches: 65, Indels: 22
0.85 0.11 0.04
Matches are distributed among these distances:
78 61 0.12
79 5 0.01
80 9 0.02
81 15 0.03
82 321 0.66
83 79 0.16
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (82 bp):
AAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCCGTTTTCTGAAAAATTGTTTAAATTAT
GCATTGAATGACCTCTA
Found at i:2744 original size:38 final size:38
Alignment explanation
Indices: 2693--2767 Score: 150
Period size: 38 Copynumber: 2.0 Consensus size: 38
2683 ATTTCACCTG
2693 TTGTCTGAAAAGTTGTTTAAATTATGCATTGAATGACA
1 TTGTCTGAAAAGTTGTTTAAATTATGCATTGAATGACA
2731 TTGTCTGAAAAGTTGTTTAAATTATGCATTGAATGAC
1 TTGTCTGAAAAGTTGTTTAAATTATGCATTGAATGAC
2768 CTTTGGAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.40
Consensus pattern (38 bp):
TTGTCTGAAAAGTTGTTTAAATTATGCATTGAATGACA
Found at i:2829 original size:120 final size:120
Alignment explanation
Indices: 2614--2849 Score: 375
Period size: 120 Copynumber: 2.0 Consensus size: 120
2604 TCACCTGTTT
*
2614 TCTGAAAAATTGTTTAAATTATGCATTAAATGACCTCTGAAAAGTTGCAGAAGATGATAATGCAC
1 TCTGAAAAATTGTTTAAATTATGCATTAAATGACCTCTGAAAAGTTGCAGAACATGATAATGCAC
*
2679 CACTATTTCACCTGTTGTCTGAAAAGTTGTTTAAATTATGCATTGAATGACATTG
66 CACTATTTCACCTGTTGTCTGAAAAATTGTTTAAATTATGCATTGAATGACATTG
* * * *
2734 TCTGAAAAGTTGTTTAAATTATGCATTGAATGACCTTTGGAAAGTTGCAGAACATGATAATGCAC
1 TCTGAAAAATTGTTTAAATTATGCATTAAATGACCTCTGAAAAGTTGCAGAACATGATAATGCAC
* * *
2799 TACTATTTCACAC-GTTTTCTGAAAAATTGTTTAAATTGTGCATTGAATGAC
66 CACTATTTCAC-CTGTTGTCTGAAAAATTGTTTAAATTATGCATTGAATGAC
2850 CTTTGAAAAG
Statistics
Matches: 106, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
120 105 0.99
121 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (120 bp):
TCTGAAAAATTGTTTAAATTATGCATTAAATGACCTCTGAAAAGTTGCAGAACATGATAATGCAC
CACTATTTCACCTGTTGTCTGAAAAATTGTTTAAATTATGCATTGAATGACATTG
Found at i:14696 original size:14 final size:14
Alignment explanation
Indices: 14676--14714 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
14666 TTCTATAATC
14676 CGTTCGTTTATGTT
1 CGTTCGTTTATGTT
*
14690 TGTTCGTTTATGTT
1 CGTTCGTTTATGTT
14704 CGTTCGTTTAT
1 CGTTCGTTTAT
14715 ATTCAGCCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.08, C:0.13, G:0.21, T:0.59
Consensus pattern (14 bp):
CGTTCGTTTATGTT
Found at i:15855 original size:24 final size:24
Alignment explanation
Indices: 15827--15874 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
15817 TTGATAATCC
*
15827 GTTCGTTTATATTTGTTCATTTAT
1 GTTCGTTTATATTCGTTCATTTAT
*
15851 GTTCGTTTATGTTCGTTCATTTAT
1 GTTCGTTTATATTCGTTCATTTAT
15875 ATTCAGCCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.15, C:0.10, G:0.15, T:0.60
Consensus pattern (24 bp):
GTTCGTTTATATTCGTTCATTTAT
Found at i:18589 original size:55 final size:55
Alignment explanation
Indices: 18505--18613 Score: 155
Period size: 55 Copynumber: 2.0 Consensus size: 55
18495 CAAATCCTGA
* * * *
18505 CGATTGTGAATTGAGTAAACTATGTTGGGAGGGTGACTCTTACCTCTGCAGTATC
1 CGATTGTGAATGGAGTAAACTAGGTTGGGAGGGTAACTCTTACCTCTACAGTATC
* * *
18560 CGATTGTTAATGGAGTAAACTGGGTTGGGAGGGTAACTCTTACTTCTACAGTAT
1 CGATTGTGAATGGAGTAAACTAGGTTGGGAGGGTAACTCTTACCTCTACAGTAT
18614 ATGATCTGGA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
55 47 1.00
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.33
Consensus pattern (55 bp):
CGATTGTGAATGGAGTAAACTAGGTTGGGAGGGTAACTCTTACCTCTACAGTATC
Found at i:19658 original size:18 final size:18
Alignment explanation
Indices: 19635--19680 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
19625 TATATATAAC
*
19635 TTATTTTATTTTTAAAAT
1 TTATTTCATTTTTAAAAT
19653 TTATTTCATTTTTAAAAT
1 TTATTTCATTTTTAAAAT
19671 TTATTTCATT
1 TTATTTCATT
19681 ATGGGGTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.65
Consensus pattern (18 bp):
TTATTTCATTTTTAAAAT
Found at i:21137 original size:2 final size:2
Alignment explanation
Indices: 21130--21174 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
21120 TCTATTTACA
21130 AT AT 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 AT AT
21172 AT A
1 AT A
21175 GGATGGGAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:22187 original size:14 final size:14
Alignment explanation
Indices: 22170--22203 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
22160 TCGTTTTTAT
22170 TCATTCATTTTTGG
1 TCATTCATTTTTGG
22184 TCATTCATTTTTGG
1 TCATTCATTTTTGG
22198 TCATTC
1 TCATTC
22204 GTTTATGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.15, C:0.18, G:0.12, T:0.56
Consensus pattern (14 bp):
TCATTCATTTTTGG
Found at i:28887 original size:88 final size:88
Alignment explanation
Indices: 28725--28889 Score: 222
Period size: 88 Copynumber: 1.9 Consensus size: 88
28715 TTCAAGTTAT
* * * *
28725 CTTTAATATTCTGAATTCAACGATTCACATAAGACAACTCCGTCAATTTTGCCTCAGACATCCTC
1 CTTTAATATTCTGAAATCAACGATTCACACAAGACAAATCCGTCAATTTTGCCTCAGACATCCCC
* * *
28790 TCTCTCTCTCTCGGGATGTCTCC
66 CCCCCCTCTCTCGGGATGTCTCC
*** * *
28813 CTTTAATATTCTGAAATCAATTTTTCAGACAAGACAAATCCGTCATTTTTGCCTCAGACATCCCC
1 CTTTAATATTCTGAAATCAACGATTCACACAAGACAAATCCGTCAATTTTGCCTCAGACATCCCC
28878 CCCCCCTCTCTC
66 CCCCCCTCTCTC
28890 TCTGTCTGGC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
88 65 1.00
ACGTcount: A:0.25, C:0.32, G:0.10, T:0.33
Consensus pattern (88 bp):
CTTTAATATTCTGAAATCAACGATTCACACAAGACAAATCCGTCAATTTTGCCTCAGACATCCCC
CCCCCCTCTCTCGGGATGTCTCC
Found at i:31120 original size:26 final size:26
Alignment explanation
Indices: 31084--31136 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
31074 GCTTGACCAT
31084 TGGCACTTGGCAGATACCAGTTTACC
1 TGGCACTTGGCAGATACCAGTTTACC
*
31110 TGGCGCTTGGCAGATACCAGTTTACC
1 TGGCACTTGGCAGATACCAGTTTACC
31136 T
1 T
31137 ATTGCTTACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.21, C:0.26, G:0.25, T:0.28
Consensus pattern (26 bp):
TGGCACTTGGCAGATACCAGTTTACC
Found at i:31813 original size:10 final size:10
Alignment explanation
Indices: 31798--31824 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
31788 GAATACGGTT
31798 GGAAGTGCAG
1 GGAAGTGCAG
31808 GGAAGTGCAG
1 GGAAGTGCAG
31818 GGAAGTG
1 GGAAGTG
31825 AGGTGGCTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.52, T:0.11
Consensus pattern (10 bp):
GGAAGTGCAG
Found at i:37306 original size:48 final size:46
Alignment explanation
Indices: 37254--37355 Score: 107
Period size: 48 Copynumber: 2.1 Consensus size: 46
37244 ATGTCACTTG
* **
37254 AAAATTT-CTAAATGAAGTATCCAGAACTAAACAGGTGAGAAATTATAA
1 AAAATTTACTAAATGAAGTA---ACAACTAAACAGGTGAGAAAAAATAA
* *
37302 AAAATTGTTACTAAATGATGTAACAAGTAAACAGGTGAGAAAAAATAA
1 AAAA-T-TTACTAAATGAAGTAACAACTAAACAGGTGAGAAAAAATAA
37350 AAAATT
1 AAAATT
37356 ACCTCCAGTA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
46 1 0.02
47 1 0.02
48 30 0.65
49 1 0.02
50 2 0.04
51 11 0.24
ACGTcount: A:0.53, C:0.08, G:0.15, T:0.25
Consensus pattern (46 bp):
AAAATTTACTAAATGAAGTAACAACTAAACAGGTGAGAAAAAATAA
Found at i:43648 original size:35 final size:34
Alignment explanation
Indices: 43563--43649 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 34
43553 ATTTGATATT
* *
43563 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGA
* *
43597 TAAATGATAACCAAATTACAATAACTGATATTAAATGA
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGA
43635 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
43650 ACTAAAACAT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.55
36 1 0.02
37 5 0.11
38 9 0.20
ACGTcount: A:0.56, C:0.10, G:0.07, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGA
Found at i:43887 original size:12 final size:12
Alignment explanation
Indices: 43870--43895 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
43860 GCTGTCACCA
43870 TCATCGTCGTCG
1 TCATCGTCGTCG
43882 TCATCGTCGTCG
1 TCATCGTCGTCG
43894 TC
1 TC
43896 CTGAGCAGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.35, G:0.23, T:0.35
Consensus pattern (12 bp):
TCATCGTCGTCG
Found at i:45932 original size:111 final size:111
Alignment explanation
Indices: 45793--46014 Score: 372
Period size: 111 Copynumber: 2.0 Consensus size: 111
45783 ATTACAAAAA
* * *
45793 TTAATTCTTTATATAATAATCATGCATTAAATGAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATATAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
45858 AATTAAAACATTAAAATGTTACCGTATCAACAAAATGTCGAGATAT
66 AATTAAAACATTAAAATGTTACCGTATCAACAAAATGTAGAGATAT
* *
45904 TTAATTCTTAATCTAATAATCATTCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATATAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
* *
45969 AATTAAAACATTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACATTAAAATGTTACCGTATCAACAAAATGTAGAGATAT
46015 ATGATTTCTA
Statistics
Matches: 103, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
111 103 1.00
ACGTcount: A:0.46, C:0.11, G:0.06, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATATAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACATTAAAATGTTACCGTATCAACAAAATGTAGAGATAT
Found at i:46152 original size:12 final size:10
Alignment explanation
Indices: 46138--46179 Score: 59
Period size: 10 Copynumber: 4.2 Consensus size: 10
46128 ACCTTAAAAA
*
46138 GAGAGTATTT
1 GAGAGAATTT
46148 GAGAGAAATTT
1 GAGAG-AATTT
46159 -AGAGAATTT
1 GAGAGAATTT
46168 GAGAGAATTT
1 GAGAGAATTT
46178 GA
1 GA
46180 TGTGATAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 5 0.17
10 20 0.69
11 4 0.14
ACGTcount: A:0.40, C:0.00, G:0.29, T:0.31
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:52082 original size:18 final size:18
Alignment explanation
Indices: 52056--52099 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
52046 ACTATCAGTT
*
52056 GGAAAATCAATTTTCGAC
1 GGAATATCAATTTTCGAC
*
52074 GGAATATCAATTTTTGAC
1 GGAATATCAATTTTCGAC
*
52092 AGAATATC
1 GGAATATC
52100 TATGCTCGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (18 bp):
GGAATATCAATTTTCGAC
Found at i:52772 original size:25 final size:24
Alignment explanation
Indices: 52744--52793 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 24
52734 ATTCTACTGC
52744 TTCTGAAATACCTGACGATTGCCTT
1 TTCTG-AATACCTGACGATTGCCTT
*
52769 TTCTGATTACCTGACGATTGCCTT
1 TTCTGAATACCTGACGATTGCCTT
52793 T
1 T
52794 CCTGCGCAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.40
Consensus pattern (24 bp):
TTCTGAATACCTGACGATTGCCTT
Found at i:53300 original size:18 final size:18
Alignment explanation
Indices: 53277--53311 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
53267 CAATTTGTTT
*
53277 TGTCTTGATTGCAGAAGC
1 TGTCTTGATTGAAGAAGC
*
53295 TGTCTTGCTTGAAGAAG
1 TGTCTTGATTGAAGAAG
53312 AAAGCATTGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.14, G:0.29, T:0.34
Consensus pattern (18 bp):
TGTCTTGATTGAAGAAGC
Found at i:54000 original size:27 final size:27
Alignment explanation
Indices: 53964--54015 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
53954 CTTCTCAGAT
* * *
53964 TGTTTGTGTGAATTTTGGCTCGAAAGA
1 TGTTTATGTGAATTCTGACTCGAAAGA
53991 TGTTTATGTGAATTCTGACTCGAAA
1 TGTTTATGTGAATTCTGACTCGAAA
54016 AATATAGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.40
Consensus pattern (27 bp):
TGTTTATGTGAATTCTGACTCGAAAGA
Found at i:61785 original size:23 final size:23
Alignment explanation
Indices: 61758--61822 Score: 103
Period size: 23 Copynumber: 2.8 Consensus size: 23
61748 CTCGAGACTC
*
61758 GAACTTGATTCAAGCTCGATTTT
1 GAACTCGATTCAAGCTCGATTTT
61781 GAACTCGATTCAAGCTCGATTTT
1 GAACTCGATTCAAGCTCGATTTT
* *
61804 GAAATCGATTCAAACTCGA
1 GAACTCGATTCAAGCTCGA
61823 GCTAAGCTCG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (23 bp):
GAACTCGATTCAAGCTCGATTTT
Found at i:63414 original size:21 final size:21
Alignment explanation
Indices: 63352--63418 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
63342 CATAATCGAA
* * *
63352 TTTAGAGTTTATGATTTAAGG
1 TTTATAGTTTAGGATTTAGGG
* * *
63373 TTTATAATTTAGTATTAAGGG
1 TTTATAGTTTAGGATTTAGGG
*
63394 TTTATAGTTTAGGGTTTAGGG
1 TTTATAGTTTAGGATTTAGGG
63415 TTTA
1 TTTA
63419 CGATTCATTA
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (21 bp):
TTTATAGTTTAGGATTTAGGG
Found at i:63598 original size:12 final size:11
Alignment explanation
Indices: 63531--63594 Score: 53
Period size: 11 Copynumber: 5.9 Consensus size: 11
63521 GTATTATAGA
63531 ATTTTTAATAT
1 ATTTTTAATAT
63542 ATTTTTTAA-A-
1 A-TTTTTAATAT
63552 ATTTTATAAT-T
1 ATTTT-TAATAT
*** *
63563 ATCAATAATGT
1 ATTTTTAATAT
63574 ATTTTTAATAT
1 ATTTTTAATAT
63585 ATTTTTAATA
1 ATTTTTAATA
63595 ATATAATTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
9 4 0.10
10 8 0.20
11 22 0.54
12 7 0.17
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:74380 original size:15 final size:15
Alignment explanation
Indices: 74360--74393 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
74350 ATAGAGGGAA
74360 GTTCTGTATACGACT
1 GTTCTGTATACGACT
74375 GTTCTGTATACGACT
1 GTTCTGTATACGACT
74390 GTTC
1 GTTC
74394 GACAACTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.41
Consensus pattern (15 bp):
GTTCTGTATACGACT
Found at i:76929 original size:16 final size:16
Alignment explanation
Indices: 76908--76941 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
76898 CTGAAAAAAA
76908 GGGAACTCGGAGTCTT
1 GGGAACTCGGAGTCTT
76924 GGGAACTCGGAGTCTT
1 GGGAACTCGGAGTCTT
76940 GG
1 GG
76942 ACAACCATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.18, G:0.41, T:0.24
Consensus pattern (16 bp):
GGGAACTCGGAGTCTT
Found at i:84811 original size:12 final size:12
Alignment explanation
Indices: 84779--84818 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
84769 TGCGGAAAAA
84779 TTAAAATC-A-T
1 TTAAAATCTATT
84789 TT-AAATCTATT
1 TTAAAATCTATT
*
84800 TTAAAATTTATT
1 TTAAAATCTATT
84812 TTAAAAT
1 TTAAAAT
84819 ATAGATTGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
9 5 0.19
10 3 0.12
11 3 0.12
12 15 0.58
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (12 bp):
TTAAAATCTATT
Found at i:84830 original size:22 final size:22
Alignment explanation
Indices: 84805--85146 Score: 490
Period size: 22 Copynumber: 15.6 Consensus size: 22
84795 CTATTTTAAA
*
84805 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
84827 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* * ***
84849 ATTTCTTTTAAAATATGAAAAA
1 ATTTATTTTAAAATATGGATTG
*
84871 AGTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
84893 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
84915 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
* **
84937 ATTTATTTTAAAATGTAAATTG
1 ATTTATTTTAAAATATGGATTG
84959 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
84981 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
85003 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
***
85025 ATTTATTTTAAAATAT-GAAAA
1 ATTTATTTTAAAATATGGATTG
85046 ATTTTATTTTAAAATATGGATTG
1 A-TTTATTTTAAAATATGGATTG
* *
85069 ATTTATTTTAAAATATAGATCG
1 ATTTATTTTAAAATATGGATTG
*
85091 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
*
85113 ATTTATTTT-AAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
85134 ATTTATTTTAAAA
1 ATTTATTTTAAAA
85147 AATTTATTAT
Statistics
Matches: 286, Mismatches: 31, Indels: 6
0.89 0.10 0.02
Matches are distributed among these distances:
21 22 0.08
22 261 0.91
23 3 0.01
ACGTcount: A:0.40, C:0.01, G:0.10, T:0.49
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:85227 original size:31 final size:31
Alignment explanation
Indices: 85169--85228 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
85159 TAGTTGTATG
* *
85169 AATTATTTAAATTTCAGTTTTATAAAACTAA
1 AATTATTTAAATTTCAGTATTACAAAACTAA
*
85200 AATTATTTAAATTTCAGTATTGCAAAACT
1 AATTATTTAAATTTCAGTATTACAAAACT
85229 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.43
Consensus pattern (31 bp):
AATTATTTAAATTTCAGTATTACAAAACTAA
Found at i:85840 original size:2 final size:2
Alignment explanation
Indices: 85833--85877 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
85823 ATATGAAGAA
* *
85833 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT -T GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
85874 AT AT
1 AT AT
85878 GGGTGAGAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
AT
Found at i:86291 original size:18 final size:19
Alignment explanation
Indices: 86268--86313 Score: 78
Period size: 18 Copynumber: 2.5 Consensus size: 19
86258 TTTAAACACA
86268 AACTCGAAAATTTGACTC-
1 AACTCGAAAATTTGACTCG
86286 AACTCGAAAATTTGACTCG
1 AACTCGAAAATTTGACTCG
86305 AA-TCGAAAA
1 AACTCGAAAA
86314 AATTTCAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 25 0.93
19 2 0.07
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.24
Consensus pattern (19 bp):
AACTCGAAAATTTGACTCG
Found at i:92729 original size:19 final size:19
Alignment explanation
Indices: 92705--92743 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
92695 TCGAATGCAT
92705 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
92724 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
92743 T
1 T
92744 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:98662 original size:20 final size:21
Alignment explanation
Indices: 98633--98688 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
98623 TTTGTGCTTC
*
98633 ATGCACCGATGCAT-TT-AACA
1 ATGCATCGATGCATCTTGAA-A
*
98653 ATGCATCGATGCATCCTTGAAT
1 ATGCATCGATGCAT-CTTGAAA
98675 ATGCATCGATGCAT
1 ATGCATCGATGCAT
98689 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:100260 original size:21 final size:21
Alignment explanation
Indices: 100218--100261 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
100208 ACCCCGAGAG
*
100218 CTAGTTCTTCATGAGCTGCTC
1 CTAGTTCTTCATGAGCTCCTC
*
100239 CTAGTTCTTC-TCGTGCTCCTC
1 CTAGTTCTTCAT-GAGCTCCTC
100260 CT
1 CT
100262 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.09, C:0.34, G:0.16, T:0.41
Consensus pattern (21 bp):
CTAGTTCTTCATGAGCTCCTC
Found at i:101315 original size:19 final size:19
Alignment explanation
Indices: 101291--101329 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
101281 TCGAATGCAT
101291 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
101310 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
101329 T
1 T
101330 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:101428 original size:64 final size:65
Alignment explanation
Indices: 101277--101437 Score: 200
Period size: 65 Copynumber: 2.5 Consensus size: 65
101267 AAATTAATTG
* * *** *
101277 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
* * * **
101342 AACATCGAATGCATTTGATGCATCGATGTACAAGCCATGCATTGATGCA-TCAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATA-TTTTCA
101405 A
65 A
101406 AACATCGAATGCATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
101438 CTTGGTGCAC
Statistics
Matches: 82, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
64 36 0.44
65 46 0.56
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:101453 original size:64 final size:64
Alignment explanation
Indices: 101277--101457 Score: 202
Period size: 64 Copynumber: 2.8 Consensus size: 64
101267 AAATTAATTG
* * * *
101277 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCA-TCAGAATATTTTCAA
* * ** * **
101342 AACATCGAATGCATTTGATGCATCGATGTACAAGCCATGCATTGATGCATCAGGCTATTTTTC-A
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCAGAATA-TTTTCAA
*** *
101406 AACATCGAATGCATTTCATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCA
101458 AGTGTTCCAA
Statistics
Matches: 95, Mismatches: 20, Indels: 3
0.81 0.17 0.03
Matches are distributed among these distances:
64 49 0.52
65 46 0.48
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCAGAATATTTTCAA
Found at i:106116 original size:79 final size:79
Alignment explanation
Indices: 105960--106122 Score: 173
Period size: 79 Copynumber: 2.1 Consensus size: 79
105950 TACGACGCAT
* * * * *
105960 GAATCCAGCAGTGAAGCATGAACGCACGAGCCACCTTAATGGCTGGAATCAAGGCATTAACCTAG
1 GAATCCAACAGTGAAGCATGAACACACGAGCCACATTAATGGATGGAATCAAGACATTAACCTAG
* *
106025 GTTGAATGATGCAG
66 GTTCAATAATGCAG
** * * * ** *
106039 GAATCCAACAGTGAAGTGTGAATACACGAGCCACATTAATGGATGGATTTAAGACATTATTCTGG
1 GAATCCAACAGTGAAGCATGAACACACGAGCCACATTAATGGATGGAATCAAGACATTAACCTAG
* *
106104 GTTCTATAATGCAT
66 GTTCAATAATGCAG
106118 GAATC
1 GAATC
106123 TAAGTGTATA
Statistics
Matches: 67, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
79 67 1.00
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (79 bp):
GAATCCAACAGTGAAGCATGAACACACGAGCCACATTAATGGATGGAATCAAGACATTAACCTAG
GTTCAATAATGCAG
Found at i:118049 original size:21 final size:20
Alignment explanation
Indices: 118023--118064 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
118013 AGGTACAAAA
*
118023 ACATACCAAAACTGATAATTT
1 ACATA-CAAAACTCATAATTT
*
118044 ACATACTAAACTCATAATTT
1 ACATACAAAACTCATAATTT
118064 A
1 A
118065 TCCAGAAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.48, C:0.19, G:0.02, T:0.31
Consensus pattern (20 bp):
ACATACAAAACTCATAATTT
Found at i:119106 original size:10 final size:10
Alignment explanation
Indices: 119091--119122 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
119081 AAGTTTAGAT
119091 ATTAAAACTG
1 ATTAAAACTG
119101 ATTAAAACTG
1 ATTAAAACTG
119111 ATTAAAACTG
1 ATTAAAACTG
119121 AT
1 AT
119123 GTTCAGGTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.31
Consensus pattern (10 bp):
ATTAAAACTG
Found at i:120779 original size:21 final size:21
Alignment explanation
Indices: 120753--120795 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
120743 TGTTATGTCG
120753 TTTTTTTAATAATATAACATA
1 TTTTTTTAATAATATAACATA
120774 TTTTTTTAATAATATAACATA
1 TTTTTTTAATAATATAACATA
120795 T
1 T
120796 ATCATGTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTTTTTAATAATATAACATA
Found at i:120797 original size:23 final size:23
Alignment explanation
Indices: 120753--120819 Score: 77
Period size: 21 Copynumber: 3.0 Consensus size: 23
120743 TGTTATGTCG
120753 TTTTTTTAATAATATAAC--ATA
1 TTTTTTTAATAATATAACATATA
120774 TTTTTTTAATAATATAACATATA
1 TTTTTTTAATAATATAACATATA
** * *
120797 TCATGTTAATAAT-TAAAATATA
1 TTTTTTTAATAATATAACATATA
120819 T
1 T
120820 AAAAATATCA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
21 18 0.45
22 9 0.22
23 13 0.32
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.49
Consensus pattern (23 bp):
TTTTTTTAATAATATAACATATA
Found at i:122030 original size:20 final size:21
Alignment explanation
Indices: 121994--122039 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
121984 CGTTAATTTT
121994 GCGAA-AGTCAAATTCGCAAC
1 GCGAATAGTCAAATTCGCAAC
*
122014 GCGAATAGTTAAA-TCGCAAC
1 GCGAATAGTCAAATTCGCAAC
*
122034 GTGAAT
1 GCGAAT
122040 TTCATTTTCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.20
Consensus pattern (21 bp):
GCGAATAGTCAAATTCGCAAC
Found at i:122133 original size:20 final size:20
Alignment explanation
Indices: 122108--122180 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
122098 TATTTAGAGA
122108 ATTCGCGTTGCGATTTACCT
1 ATTCGCGTTGCGATTTACCT
** * *
122128 ATTCGCGTTGAAAATTACAT
1 ATTCGCGTTGCGATTTACCT
** *
122148 ATTATCGTTGCGATTTAACT
1 ATTCGCGTTGCGATTTACCT
122168 ATTCGCGTTGCGA
1 ATTCGCGTTGCGA
122181 ATTTGGAAAA
Statistics
Matches: 40, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (20 bp):
ATTCGCGTTGCGATTTACCT
Found at i:122272 original size:20 final size:19
Alignment explanation
Indices: 122249--122287 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
122239 TTAACTATTC
122249 GCGTTGCGAATTTGACTTTT
1 GCGTTGCGAATTTGA-TTTT
122269 GCGTTGCGAATTTGATTTT
1 GCGTTGCGAATTTGATTTT
122288 CGCAATGCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (19 bp):
GCGTTGCGAATTTGATTTT
Found at i:122296 original size:20 final size:20
Alignment explanation
Indices: 122253--122298 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
122243 CTATTCGCGT
**
122253 TGCGAATTTGACTTTTGCGT
1 TGCGAATTTGACTTTTGCAA
122273 TGCGAATTTGA-TTTTCGCAA
1 TGCGAATTTGACTTTT-GCAA
122293 TGCGAA
1 TGCGAA
122299 ATTCGAATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (20 bp):
TGCGAATTTGACTTTTGCAA
Found at i:122467 original size:20 final size:20
Alignment explanation
Indices: 122429--122477 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
122419 TGGAGAATTC
122429 GCGTTGCGATTTACATATTA
1 GCGTTGCGATTTACATATTA
* *
122449 TCGTTGCGATTTA-ACTATTC
1 GCGTTGCGATTTACA-TATTA
122469 GCGTTGCGA
1 GCGTTGCGA
122478 ATTTGACTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.39
Consensus pattern (20 bp):
GCGTTGCGATTTACATATTA
Found at i:122489 original size:20 final size:20
Alignment explanation
Indices: 122450--122542 Score: 77
Period size: 20 Copynumber: 4.7 Consensus size: 20
122440 TACATATTAT
*
122450 CGTTGCG-ATTTAACTATTCG
1 CGTTGCGAATTTGACT-TTCG
122470 CGTTGCGAATTTGACTTTCG
1 CGTTGCGAATTTGACTTTCG
** *
122490 CGTTGCGCTTTTGGAAC-CT-G
1 CGTTGCGAATTT-G-ACTTTCG
*
122510 CGTTGCGAAATTTGA-GTTCG
1 CGTTGCG-AATTTGACTTTCG
122530 CGTTGCGAATTTG
1 CGTTGCGAATTTG
122543 TTGGTCATTT
Statistics
Matches: 60, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
19 8 0.13
20 38 0.63
21 12 0.20
22 2 0.03
ACGTcount: A:0.16, C:0.19, G:0.27, T:0.38
Consensus pattern (20 bp):
CGTTGCGAATTTGACTTTCG
Found at i:126386 original size:39 final size:38
Alignment explanation
Indices: 126294--126572 Score: 157
Period size: 39 Copynumber: 7.6 Consensus size: 38
126284 TATATAAGTC
* * * *
126294 TATATATTATATA-ATTTGTAAATGTTTTTAAATATATA
1 TATATATTATATAGTTTTGAAAATATTTTGAAA-ATATA
* *
126332 TATATAATATATAGTTTTGAAAATATATTTGAAAATATT
1 TATATATTATATAGTTTTGAAAATAT-TTTGAAAATATA
* * * *
126371 TATATATTATATAGTTTTTTTAAAACATTTTAAAAATAAA
1 TATATATTATATAG--TTTTGAAAATATTTTGAAAATATA
** *
126411 TATA-ATATATAATTTTTTTAAAAATATTTTTG-AAA-ATA
1 TATATAT-TAT-ATAGTTTTGAAAATA-TTTTGAAAATATA
* * * *
126449 TATATATTATACATTTTTTAAAACATTTTGAAAA-ATA
1 TATATATTATATAGTTTTGAAAATATTTTGAAAATATA
*
126486 TATAGT-TT-T-TA------AAAATATTTTGAAAACATA
1 TATA-TATTATATAGTTTTGAAAATATTTTGAAAATATA
126516 TATAT-T-ATATAGTTTTG-AAATCATTTTGAAAACT-TA
1 TATATATTATATAGTTTTGAAAAT-ATTTTGAAAA-TATA
*
126552 TATA-A-TATATAGTTTTAAAAA
1 TATATATTATATAGTTTTGAAAA
126573 ACTATTTTTT
Statistics
Matches: 191, Mismatches: 26, Indels: 49
0.72 0.10 0.18
Matches are distributed among these distances:
29 17 0.09
30 9 0.05
35 5 0.03
36 32 0.17
37 26 0.14
38 22 0.12
39 42 0.22
40 26 0.14
41 12 0.06
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (38 bp):
TATATATTATATAGTTTTGAAAATATTTTGAAAATATA
Found at i:126421 original size:38 final size:38
Alignment explanation
Indices: 126319--126489 Score: 152
Period size: 38 Copynumber: 4.4 Consensus size: 38
126309 TTGTAAATGT
* *
126319 TTTTAAATATATATATATAATATATAG--TTTTGAAAATA
1 TTTTAAA-A-ATATATATAATATATAGTTTTTTTAAAACA
* *
126357 TATTTGAAAATATTTATATATTATATAGTTTTTTTAAAACA
1 T-TTT-AAAA-ATATATATAATATATAGTTTTTTTAAAACA
* * *
126398 TTTTAAAAATAAATATAATATATAATTTTTTTAAAAATA
1 TTTTAAAAATATATATAATATATAGTTTTTTT-AAAACA
* **
126437 TTTTTGAAAATATATAT-AT-TATACATTTTTTAAAACA
1 -TTTTAAAAATATATATAATATATAGTTTTTTTAAAACA
126474 TTTTGAAAAATATATA
1 TTTT-AAAAATATATA
126490 GTTTTTAAAA
Statistics
Matches: 111, Mismatches: 15, Indels: 15
0.79 0.11 0.11
Matches are distributed among these distances:
36 4 0.04
37 15 0.14
38 31 0.28
39 31 0.28
40 20 0.18
41 10 0.09
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.48
Consensus pattern (38 bp):
TTTTAAAAATATATATAATATATAGTTTTTTTAAAACA
Found at i:126494 original size:28 final size:30
Alignment explanation
Indices: 126462--126519 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
126452 ATATTATACA
*
126462 TTTTTTAAAACATTTTGAAAA-ATATATAG
1 TTTTTAAAAACATTTTGAAAACATATATAG
*
126491 TTTTTAAAAATATTTTGAAAACATATATA
1 TTTTTAAAAACATTTTGAAAACATATATA
126520 TTATATAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 19 0.73
30 7 0.27
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (30 bp):
TTTTTAAAAACATTTTGAAAACATATATAG
Found at i:126541 original size:65 final size:66
Alignment explanation
Indices: 126425--126547 Score: 194
Period size: 65 Copynumber: 1.9 Consensus size: 66
126415 ATATATAATT
* * *
126425 TTTTTAAAAATATTTTTGAAAATATATATATTATACATTTTTTAAAACATTTTGAAAAATATATA
1 TTTTTAAAAATATTTTTGAAAACATATATATTATACAGTTTTGAAAACATTTTGAAAAATATATA
126490 G
66 G
* *
126491 TTTTTAAAAATA-TTTTGAAAACATATATATTATATAGTTTTGAAATCATTTTGAAAA
1 TTTTTAAAAATATTTTTGAAAACATATATATTATACAGTTTTGAAAACATTTTGAAAA
126548 CTTATATAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
65 40 0.77
66 12 0.23
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (66 bp):
TTTTTAAAAATATTTTTGAAAACATATATATTATACAGTTTTGAAAACATTTTGAAAAATATATA
G
Found at i:126580 original size:38 final size:36
Alignment explanation
Indices: 126482--126595 Score: 133
Period size: 36 Copynumber: 3.1 Consensus size: 36
126472 CATTTTGAAA
126482 AATATATAGTTTTTAAAAA-TATTTTGAAAACATATAT
1 AATATATAG-TTTTAAAAACTATTTTGAAAAC-TATAT
* * *
126519 ATTATATAGTTTTGAAATC-ATTTTGAAAACTTATAT
1 AATATATAGTTTTAAAAACTATTTTGAAAAC-TATAT
*
126555 AATATATAGTTTTAAAAAACTATTTTTTAAAACTATAT
1 AATATATAGTTTT-AAAAACTA-TTTTGAAAACTATAT
126593 AAT
1 AAT
126596 TTTGAAAACA
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
36 35 0.54
37 12 0.18
38 9 0.14
39 9 0.14
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (36 bp):
AATATATAGTTTTAAAAACTATTTTGAAAACTATAT
Found at i:126609 original size:103 final size:103
Alignment explanation
Indices: 126378--126669 Score: 267
Period size: 103 Copynumber: 2.8 Consensus size: 103
126368 ATTTATATAT
* * * ** *
126378 TATATAGTTTTTTTAAAACATTTTAAAAATAAATATAATATATAATTTTTTTAAAAATATTTTTG
1 TATATAG-ATTTTAAAAACATTTT-AAAA-AATTATAATATAT-ATAATTTT-AAAATACTTTTG
* **
126443 AAAATATAT-ATATTATACATTTTTTAAAAC-A-TTTTGAAAAA
61 AAAATATATAATA-TATAGATTTTAAAAAACTATTTTTGAAAAA
* * * * *
126484 TATATAGTTTTTAAAAATATTTTGAAAACA-TAT-ATATTATATAGTTTTGAAAT-CATTTTGAA
1 TATATAGATTTTAAAAACATTTT-AAAAAATTATAATA-TATATAATTTTAAAATAC-TTTTGAA
* *
126546 AACTTATATAATATATAG-TTTTAAAAAACTATTTTTTAAAAC
63 AA--TATATAATATATAGATTTTAAAAAACTATTTTTGAAAAA
*
126588 TATATA-ATTTTGAAAACATTTTAAAAAATTATAATATATATAATTTTAAAATACTTTTGAAAAT
1 TATATAGATTTTAAAAACATTTTAAAAAATTATAATATATATAATTTTAAAATACTTTTGAAAAT
*
126652 ATATATTATATAGATTTT
66 ATATAATATATAGATTTT
126670 TGGAAAATAA
Statistics
Matches: 155, Mismatches: 20, Indels: 26
0.77 0.10 0.13
Matches are distributed among these distances:
101 26 0.17
102 27 0.17
103 55 0.35
104 22 0.14
105 18 0.12
106 7 0.05
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (103 bp):
TATATAGATTTTAAAAACATTTTAAAAAATTATAATATATATAATTTTAAAATACTTTTGAAAAT
ATATAATATATAGATTTTAAAAAACTATTTTTGAAAAA
Found at i:126662 original size:36 final size:35
Alignment explanation
Indices: 126588--126706 Score: 98
Period size: 36 Copynumber: 3.3 Consensus size: 35
126578 TTTTTAAAAC
* * *
126588 TATATAATTTTGAAA-ACATTTTAAAAAATTATAATA
1 TATATAATTTTAAAATAC-TTTTAAAATA-TATATTA
126624 TATATAATTTTAAAATACTTTTGAAAATATATATTA
1 TATATAATTTTAAAATACTTTT-AAAATATATATTA
* * * * *
126660 TATAGATTTTTGGAAAATAATTAT-ATATATATATATA
1 TATATAATTTT--AAAATACTTTTAAAATATATAT-TA
126697 TATATAATTT
1 TATATAATTT
126707 ATTTATTTGT
Statistics
Matches: 68, Mismatches: 10, Indels: 9
0.78 0.11 0.10
Matches are distributed among these distances:
36 42 0.62
37 17 0.25
38 9 0.13
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (35 bp):
TATATAATTTTAAAATACTTTTAAAATATATATTA
Found at i:126695 original size:103 final size:101
Alignment explanation
Indices: 126359--126697 Score: 248
Period size: 103 Copynumber: 3.3 Consensus size: 101
126349 TGAAAATATA
* * *
126359 TTTGAAAATATTTATATAT-TATATAGT-TTTTTTAAAACATTTTAAAAATAAATATAATATATA
1 TTTGAAAATAATTATATATAAATATA-TATTTTTAAAAACATTTT-AAAA-AAATATAATATAT-
** * *
126422 ATTTTTTTAAAAATATTTTTGAAAATATATATATTATACATT
62 ATAATTTT-AAAATACTTTTGAAAATATATATA-TATAGATT
* * * * * *
126464 TTTTAAAA-CATT-T-TGAAAAATATATAGTTTTTAAAAATATTTTGAAAACATAT-ATATTATA
1 TTTGAAAATAATTATAT-ATAAATATATA-TTTTTAAAAACATTTTAAAAAAATATAATA-TATA
* *
126525 TAGTTTTGAAAT-CATTTTGAAAACTTATATAATATATAG-TT
63 TAATTTTAAAATAC-TTTTGAAAA--TATAT-ATATATAGATT
** * * * * *
126566 TTAAAAAACT-ATTTTTTA-AAACTATATAATTTTGAAAACATTTTAAAAAATTATAATATATAT
1 TTTGAAAA-TAATTATATATAAA-TATATATTTTTAAAAACATTTTAAAAAAATATAATATATAT
126629 AATTTTAAAATACTTTTGAAAATATATATTATATAGATT
64 AATTTTAAAATACTTTTGAAAATATATA-TATATAGATT
*
126668 TTTGGAAAATAATTATATATATATATATAT
1 TTT-GAAAATAATTATATATAAATATATAT
126698 ATATAATTTA
Statistics
Matches: 183, Mismatches: 30, Indels: 44
0.71 0.12 0.17
Matches are distributed among these distances:
100 1 0.01
101 25 0.14
102 23 0.13
103 85 0.46
104 27 0.15
105 22 0.12
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (101 bp):
TTTGAAAATAATTATATATAAATATATATTTTTAAAAACATTTTAAAAAAATATAATATATATAA
TTTTAAAATACTTTTGAAAATATATATATATAGATT
Found at i:127840 original size:6 final size:6
Alignment explanation
Indices: 127829--127935 Score: 107
Period size: 6 Copynumber: 18.5 Consensus size: 6
127819 CTTTTATTCC
* *
127829 TTTTAT TTTTAT TTTTAT TTTTAT TTTTGT TTTTAT TTTTAT TTTCAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
* * * *
127877 TTTCAT TTTCA- TTTTA- TTTTA- TTTTAT TTGTTAT TTTT-T ATATAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TT-TTAT TTTTAT TTTTAT
*
127922 CTTTA- TTTTAT TTT
1 TTTTAT TTTTAT TTT
127936 AGTCCTTTAA
Statistics
Matches: 88, Mismatches: 9, Indels: 8
0.84 0.09 0.08
Matches are distributed among these distances:
5 21 0.24
6 61 0.69
7 6 0.07
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTTAT
Found at i:128018 original size:2 final size:2
Alignment explanation
Indices: 128011--128047 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
128001 ATACGTATTT
128011 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
128048 TATATATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:128052 original size:2 final size:2
Alignment explanation
Indices: 128047--128078 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
128037 ACACACACAC
128047 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
128079 TATTTATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:128112 original size:3 final size:3
Alignment explanation
Indices: 128076--128139 Score: 83
Period size: 3 Copynumber: 20.7 Consensus size: 3
128066 TATATATATA
* * *
128076 TAT TATT TATT TAT TTT TAT TTT TAT TAT AAT TAT TAT TAT TAT TAT
1 TAT TA-T TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
128123 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
128140 ACGCATATAT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
3 47 0.87
4 7 0.13
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:132867 original size:12 final size:12
Alignment explanation
Indices: 132850--132959 Score: 148
Period size: 12 Copynumber: 9.2 Consensus size: 12
132840 CGGACCTGCT
132850 AAGGAAGAGAAG
1 AAGGAAGAGAAG
132862 AAGGAAGAGAAG
1 AAGGAAGAGAAG
*
132874 AAGGAAGAAAAG
1 AAGGAAGAGAAG
* *
132886 AAAGAGGAGAAG
1 AAGGAAGAGAAG
*
132898 AAAGAAGAGAAG
1 AAGGAAGAGAAG
* *
132910 AAAGAGGAGAAG
1 AAGGAAGAGAAG
132922 AAGGAAGAGAAG
1 AAGGAAGAGAAG
* *
132934 AAAGAGGAGAAG
1 AAGGAAGAGAAG
132946 AAGGAAGAGAAG
1 AAGGAAGAGAAG
132958 AA
1 AA
132960 ATAGCTAAAC
Statistics
Matches: 86, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 86 1.00
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (12 bp):
AAGGAAGAGAAG
Found at i:132886 original size:24 final size:24
Alignment explanation
Indices: 132850--132960 Score: 186
Period size: 24 Copynumber: 4.6 Consensus size: 24
132840 CGGACCTGCT
* *
132850 AAGGAAGAGAAGAAGGAAGAGAAG
1 AAGGAAGAGAAGAAAGAGGAGAAG
*
132874 AAGGAAGAAAAGAAAGAGGAGAAG
1 AAGGAAGAGAAGAAAGAGGAGAAG
*
132898 AAAGAAGAGAAGAAAGAGGAGAAG
1 AAGGAAGAGAAGAAAGAGGAGAAG
132922 AAGGAAGAGAAGAAAGAGGAGAAG
1 AAGGAAGAGAAGAAAGAGGAGAAG
132946 AAGGAAGAGAAGAAA
1 AAGGAAGAGAAGAAA
132961 TAGCTAAACG
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 81 1.00
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (24 bp):
AAGGAAGAGAAGAAAGAGGAGAAG
Found at i:132928 original size:4 final size:5
Alignment explanation
Indices: 132853--132958 Score: 71
Period size: 5 Copynumber: 21.0 Consensus size: 5
132843 ACCTGCTAAG
* *
132853 GAAGA GAAGAA GGAAGA GAAGAA GGAAGA AAAGA -AAGA GGAGAA GAA-A
1 GAAGA GAAG-A -GAAGA GAAG-A -GAAGA GAAGA GAAGA GAAG-A GAAGA
* *
132901 GAAGA GAAGA -AAGA GGAGAA GAAG- GAAGA GAAGA -AAGA GGAGAA GAAG-
1 GAAGA GAAGA GAAGA GAAG-A GAAGA GAAGA GAAGA GAAGA GAAG-A GAAGA
132949 GAAGA GAAGA
1 GAAGA GAAGA
132959 AATAGCTAAA
Statistics
Matches: 81, Mismatches: 7, Indels: 26
0.71 0.06 0.23
Matches are distributed among these distances:
4 24 0.30
5 34 0.42
6 15 0.19
7 8 0.10
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (5 bp):
GAAGA
Found at i:133788 original size:21 final size:22
Alignment explanation
Indices: 133762--133805 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
133752 AATATGTGCA
133762 TTGCGA-TAGTCCAAGTTCGCG
1 TTGCGATTAGTCCAAGTTCGCG
*
133783 TTGCGATTTATTCCAAGTTCGCG
1 TTGCGA-TTAGTCCAAGTTCGCG
133806 CTACGATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 6 0.30
23 14 0.70
ACGTcount: A:0.18, C:0.23, G:0.25, T:0.34
Consensus pattern (22 bp):
TTGCGATTAGTCCAAGTTCGCG
Found at i:133800 original size:23 final size:23
Alignment explanation
Indices: 133771--133841 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
133761 ATTGCGATAG
133771 TCCAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGCGTTGCGATTTAT
* *
133794 TCCAAGTTCGCGCTACGATTTAT
1 TCCAAGTTCGCGTTGCGATTTAT
*
133817 TCCAAATT--CGTTGCGATTTAT
1 TCCAAGTTCGCGTTGCGATTTAT
133838 TCCA
1 TCCA
133842 CGACCACGAC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
21 15 0.35
23 28 0.65
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.38
Consensus pattern (23 bp):
TCCAAGTTCGCGTTGCGATTTAT
Found at i:134360 original size:6 final size:6
Alignment explanation
Indices: 134351--134381 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
134341 CGCCGTCATC
134351 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
134382 AATACGTGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:136563 original size:12 final size:12
Alignment explanation
Indices: 136546--136570 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
136536 TCCTTTCTAG
136546 TTGCTTGACATC
1 TTGCTTGACATC
136558 TTGCTTGACATC
1 TTGCTTGACATC
136570 T
1 T
136571 ATTACAAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.16, T:0.44
Consensus pattern (12 bp):
TTGCTTGACATC
Found at i:144731 original size:31 final size:31
Alignment explanation
Indices: 144658--144717 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
144648 AGTTACGTCG
144658 GGGACCATATTGCAAACGGACTAAATGTTGA
1 GGGACCATATTGCAAACGGACTAAATGTTGA
144689 GGGACCATATTGCAAACGGACTAAATGTT
1 GGGACCATATTGCAAACGGACTAAATGTT
144718 AGGAGATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (31 bp):
GGGACCATATTGCAAACGGACTAAATGTTGA
Found at i:145413 original size:31 final size:30
Alignment explanation
Indices: 145350--145426 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 30
145340 CTTTTAAAAC
** *
145350 TTGCAATATAATCCCCAACATTTAGTCCAT
1 TTGCAATATGGTCCCCAACATTCAGTCCAT
*
145380 TTGCAATATGGTCCCTCAACATTCAGTCTAT
1 TTGCAATATGGTCCC-CAACATTCAGTCCAT
145411 TTGCAATATGGTCCCC
1 TTGCAATATGGTCCCC
145427 GATGTAACCG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
30 14 0.33
31 28 0.67
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.34
Consensus pattern (30 bp):
TTGCAATATGGTCCCCAACATTCAGTCCAT
Found at i:148234 original size:2 final size:2
Alignment explanation
Indices: 148171--148215 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
148161 TTAATTAAAA
148171 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
148211 AT AT A
1 AT AT A
148216 CCAATTTTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:148417 original size:19 final size:19
Alignment explanation
Indices: 148388--148449 Score: 59
Period size: 19 Copynumber: 3.6 Consensus size: 19
148378 TTGGGGTAAT
148388 ATTTGATAAATTTTATTATA
1 ATTT-ATAAATTTTATTATA
148408 ATTTATAAA-TTTA--ATA
1 ATTTATAAATTTTATTATA
148424 A--T-T--ATTTTATTATA
1 ATTTATAAATTTTATTATA
148438 ATTTATAAATTT
1 ATTTATAAATTT
148450 AATAATCATT
Statistics
Matches: 34, Mismatches: 0, Indels: 17
0.67 0.00 0.33
Matches are distributed among these distances:
11 1 0.03
12 4 0.12
13 1 0.03
14 5 0.15
16 5 0.15
17 1 0.03
18 4 0.12
19 9 0.26
20 4 0.12
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
ATTTATAAATTTTATTATA
Found at i:148433 original size:30 final size:30
Alignment explanation
Indices: 148397--148493 Score: 169
Period size: 30 Copynumber: 3.2 Consensus size: 30
148387 TATTTGATAA
148397 ATTTTATTATAATTTATAAATTTAATAATT
1 ATTTTATTATAATTTATAAATTTAATAATT
*
148427 ATTTTATTATAATTTATAAATTTAATAATC
1 ATTTTATTATAATTTATAAATTTAATAATT
148457 ATTTTATTATAATTTA-AAACTTTAATAATT
1 ATTTTATTATAATTTATAAA-TTTAATAATT
148487 ATTTTAT
1 ATTTTAT
148494 AGTTTTGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
29 3 0.05
30 61 0.95
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (30 bp):
ATTTTATTATAATTTATAAATTTAATAATT
Found at i:148953 original size:3 final size:3
Alignment explanation
Indices: 148945--148976 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
148935 TATTCAACAA
148945 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
148977 GTTCTCAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:163110 original size:23 final size:24
Alignment explanation
Indices: 163078--163122 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
163068 TCTATTCCTC
* *
163078 AAAATAATATGTATGATTAAATTA
1 AAAATAATATATATGATAAAATTA
163102 AAAAT-ATATATATGATAAAAT
1 AAAATAATATATATGATAAAAT
163123 ATACGTTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.36
Consensus pattern (24 bp):
AAAATAATATATATGATAAAATTA
Done.