Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
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: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 115 of 444
Found at i:29292514 original size:25 final size:25
Alignment explanation
Indices: 29292486--29292559 Score: 130
Period size: 25 Copynumber: 3.0 Consensus size: 25
29292476 GGTTTTTTTG
*
29292486 GCGAATATGAGTAAACAAATTAAAT
1 GCGAAGATGAGTAAACAAATTAAAT
*
29292511 GCGAAGATGCGTAAACAAATTAAAT
1 GCGAAGATGAGTAAACAAATTAAAT
29292536 GCGAAGATGAGTAAACAAATTAAA
1 GCGAAGATGAGTAAACAAATTAAA
29292560 GTCATTATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 46 1.00
ACGTcount: A:0.51, C:0.09, G:0.19, T:0.20
Consensus pattern (25 bp):
GCGAAGATGAGTAAACAAATTAAAT
Found at i:29294085 original size:42 final size:42
Alignment explanation
Indices: 29294029--29294119 Score: 175
Period size: 42 Copynumber: 2.2 Consensus size: 42
29294019 ACATAATTTC
29294029 ATTA-TATTAAGCAGTACTATGAAAATGTGTCATTTTAACTA
1 ATTATTATTAAGCAGTACTATGAAAATGTGTCATTTTAACTA
29294070 ATTATTATTAAGCAGTACTATGAAAATGTGTCATTTTAACTA
1 ATTATTATTAAGCAGTACTATGAAAATGTGTCATTTTAACTA
29294112 ATTATTAT
1 ATTATTAT
29294120 GCTAAACACA
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 4 0.08
42 45 0.92
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (42 bp):
ATTATTATTAAGCAGTACTATGAAAATGTGTCATTTTAACTA
Found at i:29295806 original size:12 final size:11
Alignment explanation
Indices: 29295789--29295822 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
29295779 ACCATGTGTG
29295789 TGTTCTTTCTGT
1 TGTTCTTT-TGT
29295801 TGTTCTTTTGT
1 TGTTCTTTTGT
29295812 TGCTTCTTTTG
1 TG-TTCTTTTG
29295823 GCATAAATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.24
12 16 0.76
ACGTcount: A:0.00, C:0.15, G:0.18, T:0.68
Consensus pattern (11 bp):
TGTTCTTTTGT
Found at i:29300446 original size:23 final size:23
Alignment explanation
Indices: 29300416--29300459 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
29300406 CAATTCTCGT
29300416 ATCAAAGTATGACATCTTTTCGG
1 ATCAAAGTATGACATCTTTTCGG
29300439 ATCAAAGTATGACATCTTTTC
1 ATCAAAGTATGACATCTTTTC
29300460 AAACTGCAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (23 bp):
ATCAAAGTATGACATCTTTTCGG
Found at i:29301781 original size:16 final size:14
Alignment explanation
Indices: 29301751--29301791 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
29301741 ACTGTTAGAT
29301751 AGAAAATTTAGAGA
1 AGAAAATTTAGAGA
29301765 AGAAGAATTT-GAG-
1 AGAA-AATTTAGAGA
*
29301778 AGAAAATTGAGAGA
1 AGAAAATTTAGAGA
29301792 TTAGGATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
12 4 0.17
13 7 0.30
14 7 0.30
15 5 0.22
ACGTcount: A:0.54, C:0.00, G:0.27, T:0.20
Consensus pattern (14 bp):
AGAAAATTTAGAGA
Found at i:29303925 original size:19 final size:19
Alignment explanation
Indices: 29303903--29303942 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
29303893 GCCGGTATTG
* *
29303903 ACCAAACTGGCCGAAATAC
1 ACCAAAATGACCGAAATAC
*
29303922 ACCAAAATGACCTAAATAC
1 ACCAAAATGACCGAAATAC
29303941 AC
1 AC
29303943 TGGAATTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.30, G:0.10, T:0.12
Consensus pattern (19 bp):
ACCAAAATGACCGAAATAC
Found at i:29309313 original size:40 final size:40
Alignment explanation
Indices: 29309236--29309313 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
29309226 TGTAAACATT
* * **
29309236 AAAAAGTATTAAGATAATTATATATAAAATTTTAATAAAC
1 AAAAAGTATTAAAATAATTAAATATAAAATTAAAATAAAC
*
29309276 AAAAA-TATATAAAATAATTAAATATTAAATTAAAATAA
1 AAAAAGTAT-TAAAATAATTAAATATAAAATTAAAATAA
29309314 TATATATTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
39 3 0.09
40 29 0.91
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (40 bp):
AAAAAGTATTAAAATAATTAAATATAAAATTAAAATAAAC
Found at i:29314012 original size:4 final size:4
Alignment explanation
Indices: 29314005--29314040 Score: 63
Period size: 4 Copynumber: 8.8 Consensus size: 4
29313995 TACATACACA
29314005 AAAT AAAT AAAT AAAT AAAT AAAT AAAGT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA-T AAAT AAA
29314041 AATGTTATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 27 0.87
5 4 0.13
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:29315174 original size:12 final size:12
Alignment explanation
Indices: 29315159--29315211 Score: 79
Period size: 12 Copynumber: 4.4 Consensus size: 12
29315149 GGTTATTTCT
* *
29315159 ATTTCAATTTTA
1 ATTTCGATTTTG
*
29315171 ATTTCGATTCTG
1 ATTTCGATTTTG
29315183 ATTTCGATTTTG
1 ATTTCGATTTTG
29315195 ATTTCGATTTTG
1 ATTTCGATTTTG
29315207 ATTTC
1 ATTTC
29315212 AATTCTAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.21, C:0.11, G:0.11, T:0.57
Consensus pattern (12 bp):
ATTTCGATTTTG
Found at i:29315192 original size:24 final size:24
Alignment explanation
Indices: 29315155--29315215 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
29315145 TTAGGGTTAT
29315155 TTCT-ATTTCAATTTTAATTTCGA
1 TTCTGATTTCAATTTTAATTTCGA
* *
29315178 TTCTGATTTCGATTTTGATTTCGA
1 TTCTGATTTCAATTTTAATTTCGA
*
29315202 TTTTGATTTCAATT
1 TTCTGATTTCAATT
29315216 CTAAAACACT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
23 4 0.12
24 29 0.88
ACGTcount: A:0.21, C:0.11, G:0.10, T:0.57
Consensus pattern (24 bp):
TTCTGATTTCAATTTTAATTTCGA
Found at i:29315293 original size:24 final size:24
Alignment explanation
Indices: 29315231--29315299 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
29315221 ACACTCACTG
* *
29315231 ATTTTGATTTTGATTTTGATTCCA
1 ATTTTGATTTTGATTTAGATTACA
* * *
29315255 ATTTTGATCTCGATTTAGACTTAGA
1 ATTTTGATTTTGATTTAGA-TTACA
*
29315280 A-TTTGATTTTGATTTCGATT
1 ATTTTGATTTTGATTTAGATT
29315300 TGGATTTCGA
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
23 2 0.06
24 30 0.83
25 4 0.11
ACGTcount: A:0.23, C:0.09, G:0.14, T:0.54
Consensus pattern (24 bp):
ATTTTGATTTTGATTTAGATTACA
Found at i:29315328 original size:6 final size:6
Alignment explanation
Indices: 29315229--29315312 Score: 60
Period size: 6 Copynumber: 14.0 Consensus size: 6
29315219 AAACACTCAC
* ** * * * *
29315229 TGATTT TGATTT TGATTT TGATTC CAATTT TGATCT CGATTT AGACTT
1 TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT
* * * * *
29315277 AGAATT TGATTT TGATTT CGATTT GGATTT CGATTT
1 TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT
29315313 AGGGTTATTT
Statistics
Matches: 61, Mismatches: 17, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 61 1.00
ACGTcount: A:0.21, C:0.08, G:0.17, T:0.54
Consensus pattern (6 bp):
TGATTT
Found at i:29315461 original size:47 final size:48
Alignment explanation
Indices: 29315349--29315469 Score: 154
Period size: 47 Copynumber: 2.5 Consensus size: 48
29315339 GCCATATGCA
* * * * *
29315349 TGATGTTTATTGTTTGTTTCTTCCATTGTATGAATGCCATTATCAAAT
1 TGATGTTTATTGTGTATATCTGCCATTGTATGAATGCCATTATCAAAC
* ** *
29315397 TGATGTGTATTACGTATATCTGCCATTGTATGAATG-CATTATCAAGC
1 TGATGTTTATTGTGTATATCTGCCATTGTATGAATGCCATTATCAAAC
29315444 TGATGTTTATTGTGTATATCTGCCAT
1 TGATGTTTATTGTGTATATCTGCCAT
29315470 GATGTTTATT
Statistics
Matches: 61, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
47 32 0.52
48 29 0.48
ACGTcount: A:0.24, C:0.13, G:0.17, T:0.45
Consensus pattern (48 bp):
TGATGTTTATTGTGTATATCTGCCATTGTATGAATGCCATTATCAAAC
Found at i:29315794 original size:15 final size:15
Alignment explanation
Indices: 29315774--29315817 Score: 88
Period size: 15 Copynumber: 2.9 Consensus size: 15
29315764 GAAGAAAACA
29315774 TGTCTGGTAGTGATG
1 TGTCTGGTAGTGATG
29315789 TGTCTGGTAGTGATG
1 TGTCTGGTAGTGATG
29315804 TGTCTGGTAGTGAT
1 TGTCTGGTAGTGAT
29315818 AGTGATGCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.14, C:0.07, G:0.39, T:0.41
Consensus pattern (15 bp):
TGTCTGGTAGTGATG
Found at i:29316804 original size:2 final size:2
Alignment explanation
Indices: 29316797--29316827 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
29316787 AAACTCTATT
29316797 TA TA TA 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 TA TA TA T
29316828 TTATGTTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29317569 original size:43 final size:43
Alignment explanation
Indices: 29317475--29317654 Score: 269
Period size: 43 Copynumber: 4.3 Consensus size: 43
29317465 TTGCTGATCA
* * *
29317475 CATGCATTGATTGTTTGAAAGCTATTGACT-TTTTTTAATATG
1 CATGCAATGATTGTTGGAAAGCTGTTGACTATTTTTTAATATG
*
29317517 TATGCAATGATTGTTGGAAAGCTGTTGACTATTTTTTAATATG
1 CATGCAATGATTGTTGGAAAGCTGTTGACTATTTTTTAATATG
*
29317560 CATGTAATGATTGTTGGAAAGCTGTTGACTATTTTTTAATATG
1 CATGCAATGATTGTTGGAAAGCTGTTGACTATTTTTTAATATG
* *
29317603 CATGCAATGATTGTTGG--TG-TGTTGCCTATTTTTTAATATG
1 CATGCAATGATTGTTGGAAAGCTGTTGACTATTTTTTAATATG
29317643 CATGCAATGATT
1 CATGCAATGATT
29317655 TTTTTTATAA
Statistics
Matches: 128, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
40 32 0.25
41 1 0.01
42 26 0.20
43 69 0.54
ACGTcount: A:0.26, C:0.09, G:0.20, T:0.45
Consensus pattern (43 bp):
CATGCAATGATTGTTGGAAAGCTGTTGACTATTTTTTAATATG
Found at i:29317652 original size:83 final size:84
Alignment explanation
Indices: 29317475--29317654 Score: 265
Period size: 83 Copynumber: 2.1 Consensus size: 84
29317465 TTGCTGATCA
* * *
29317475 CATGCATTGATTGTTTGAAAGCTATTGACTTTTTTTAATATGTATGCAATGATTGTTGGAAAGCT
1 CATGCAATGATTGTTGGAAAGCTATTGACTTTTTTTAATATGCATGCAATGATTGTTGG-AAGCT
29317540 GTTGACTATTTTTTAATATG
65 GTTGACTATTTTTTAATATG
* * *
29317560 CATGTAATGATTGTTGGAAAGCTGTTGACTATTTTTTAATATGCATGCAATGATTGTTGG-TG-T
1 CATGCAATGATTGTTGGAAAGCTATTGACT-TTTTTTAATATGCATGCAATGATTGTTGGAAGCT
*
29317623 GTTGCCTATTTTTTAATATG
65 GTTGACTATTTTTTAATATG
29317643 CATGCAATGATT
1 CATGCAATGATT
29317655 TTTTTTATAA
Statistics
Matches: 86, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
83 31 0.36
84 1 0.01
85 26 0.30
86 28 0.33
ACGTcount: A:0.26, C:0.09, G:0.20, T:0.45
Consensus pattern (84 bp):
CATGCAATGATTGTTGGAAAGCTATTGACTTTTTTTAATATGCATGCAATGATTGTTGGAAGCTG
TTGACTATTTTTTAATATG
Found at i:29318388 original size:21 final size:21
Alignment explanation
Indices: 29318355--29318408 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
29318345 CTCAACAAGG
* *
29318355 TGCCCCAATTCAGTTA-CTCAC
1 TGCCCCAACTCAGATACCT-AC
*
29318376 TGCCTCAACTCAGATACCTAC
1 TGCCCCAACTCAGATACCTAC
29318397 TGCCCCAACTCA
1 TGCCCCAACTCA
29318409 TCAAGAAGCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 26 0.93
22 2 0.07
ACGTcount: A:0.26, C:0.41, G:0.09, T:0.24
Consensus pattern (21 bp):
TGCCCCAACTCAGATACCTAC
Found at i:29318892 original size:59 final size:59
Alignment explanation
Indices: 29318800--29318936 Score: 238
Period size: 59 Copynumber: 2.3 Consensus size: 59
29318790 TTTGTTATCT
*
29318800 AACTGTTAAACAATTTGTATACCAACTGTTATCTTTTCTAACTAGCAGCCATGTATACC
1 AACTGTTAAGCAATTTGTATACCAACTGTTATCTTTTCTAACTAGCAGCCATGTATACC
* *
29318859 AACTGTTAAGCAATTTGTATATCAATTGTTATCTTTTCTAACTAGCAGCCATGTATACC
1 AACTGTTAAGCAATTTGTATACCAACTGTTATCTTTTCTAACTAGCAGCCATGTATACC
*
29318918 AAGTGTTAAGCAATTTGTA
1 AACTGTTAAGCAATTTGTA
29318937 AACAACAACA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 74 1.00
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.37
Consensus pattern (59 bp):
AACTGTTAAGCAATTTGTATACCAACTGTTATCTTTTCTAACTAGCAGCCATGTATACC
Found at i:29319015 original size:28 final size:30
Alignment explanation
Indices: 29318983--29319041 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
29318973 AGGCATTTTT
29318983 AACAC-ATGT-TAAGCAACAAAAATATTCC
1 AACACAATGTGTAAGCAACAAAAATATTCC
* * *
29319011 AACACAATTTGTAATCAACAAAAATTTTCC
1 AACACAATGTGTAAGCAACAAAAATATTCC
29319041 A
1 A
29319042 TTTCATTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 5 0.19
29 3 0.12
30 18 0.69
ACGTcount: A:0.49, C:0.20, G:0.05, T:0.25
Consensus pattern (30 bp):
AACACAATGTGTAAGCAACAAAAATATTCC
Found at i:29319508 original size:20 final size:20
Alignment explanation
Indices: 29319479--29319526 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
29319469 GGCATATCCA
29319479 TTTT-TTCTCTT-CTCCTTCT
1 TTTTCTTCTCTTCCTCC-TCT
29319498 TTTTCTTCTCTTCCTCCTCT
1 TTTTCTTCTCTTCCTCCTCT
29319518 TTTTCTTCT
1 TTTTCTTCT
29319527 TCTTTTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.15
20 19 0.70
21 4 0.15
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTCTTCTCTTCCTCCTCT
Found at i:29319512 original size:18 final size:19
Alignment explanation
Indices: 29319480--29319541 Score: 69
Period size: 18 Copynumber: 3.4 Consensus size: 19
29319470 GCATATCCAT
29319480 TTTTTC-TCTTC-TCCTTC
1 TTTTTCTTCTTCTTCCTTC
29319497 TTTTTCTTC-TCTTCCTCCTC
1 TTTTTCTTCTTCTTCCT--TC
*
29319517 TTTTTCTTCTTCTT-TTTC
1 TTTTTCTTCTTCTTCCTTC
29319535 TTTTTCT
1 TTTTTCT
29319542 CAAACCCTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
17 8 0.21
18 15 0.38
20 12 0.31
21 4 0.10
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTTCTTCTTCTTCCTTC
Found at i:29328417 original size:21 final size:21
Alignment explanation
Indices: 29328391--29328432 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
29328381 TTCAATCTTT
* *
29328391 CTTCCTTGTACAACTCCTTGC
1 CTTCCTTCTACAACTACTTGC
*
29328412 CTTCCTTCTTCAACTACTTGC
1 CTTCCTTCTACAACTACTTGC
29328433 TTATTCAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.14, C:0.38, G:0.07, T:0.40
Consensus pattern (21 bp):
CTTCCTTCTACAACTACTTGC
Found at i:29339893 original size:11 final size:11
Alignment explanation
Indices: 29339875--29339919 Score: 74
Period size: 11 Copynumber: 4.2 Consensus size: 11
29339865 TTAATAAGAT
29339875 ATTTTATTATA
1 ATTTTATTATA
*
29339886 AGTTTATTATA
1 ATTTTATTATA
29339897 ATTTTATTATA
1 ATTTTATTATA
29339908 ATTTTATT-TA
1 ATTTTATTATA
29339918 AT
1 AT
29339920 ATATAAGGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
10 4 0.12
11 28 0.88
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (11 bp):
ATTTTATTATA
Found at i:29342069 original size:99 final size:100
Alignment explanation
Indices: 29341898--29342129 Score: 306
Period size: 99 Copynumber: 2.3 Consensus size: 100
29341888 AATATATGTG
* * ** *
29341898 TATACGTGTAAAACCATAGCTGGGTTATGGCATCCTAATGATAAGACTGTAACTGGGTTATCACA
1 TATACGTGTAAAACCATAGTTGGGCTATGGCATCCTAATGATAAGACAATAACTAGGTTATCACA
*
29341963 TTACGAGTGCAAGACCATGGCAGGGCCATGACA-A
66 CTACGAGTGCAAGACCATGGCAGGGCCATGACAGA
* * **
29341997 TATACGTGTAAAACCATAGTTGGGCTATGTCATCCTGATGATAAGACAATAACTAGGTTATGGCA
1 TATACGTGTAAAACCATAGTTGGGCTATGGCATCCTAATGATAAGACAATAACTAGGTTATCACA
* * **
29342062 CTACGAGTGTAAGACCATGGTAGGGCCATGGTAGA
66 CTACGAGTGCAAGACCATGGCAGGGCCATGACAGA
* *
29342097 -ATACGTGTAAGACCATAGTTGGACTATGGCATC
1 TATACGTGTAAAACCATAGTTGGGCTATGGCATC
29342130 AAGTAAACGA
Statistics
Matches: 115, Mismatches: 17, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
99 114 0.99
100 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (100 bp):
TATACGTGTAAAACCATAGTTGGGCTATGGCATCCTAATGATAAGACAATAACTAGGTTATCACA
CTACGAGTGCAAGACCATGGCAGGGCCATGACAGA
Found at i:29342847 original size:63 final size:63
Alignment explanation
Indices: 29342748--29342875 Score: 211
Period size: 63 Copynumber: 2.0 Consensus size: 63
29342738 GGATACCGTA
* * *
29342748 GATTTATTCACTTAGTGAGTTGTTAAATATAACTTCATGAGTATTGTGGTCTCTATTTCAAAT
1 GATTTATTCACTTAGTAAGCTATTAAATATAACTTCATGAGTATTGTGGTCTCTATTTCAAAT
* *
29342811 GATTTATTCACTTAGTAAGCTATTAAATATAGCTTCATGAGTATTGTGGTCTTTATTTCAAAT
1 GATTTATTCACTTAGTAAGCTATTAAATATAACTTCATGAGTATTGTGGTCTCTATTTCAAAT
29342874 GA
1 GA
29342876 CCACAGAGCG
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.44
Consensus pattern (63 bp):
GATTTATTCACTTAGTAAGCTATTAAATATAACTTCATGAGTATTGTGGTCTCTATTTCAAAT
Found at i:29345393 original size:24 final size:24
Alignment explanation
Indices: 29345365--29345413 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
29345355 TTAAATCATC
29345365 TCTCTCAAAT-TTCTCTCTTTTCTT
1 TCTCTC-AATCTTCTCTCTTTTCTT
* *
29345389 TCTCTCATTCTTCTCTGTTTTCTT
1 TCTCTCAATCTTCTCTCTTTTCTT
29345413 T
1 T
29345414 GATTTCTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 2 0.09
24 20 0.91
ACGTcount: A:0.08, C:0.29, G:0.02, T:0.61
Consensus pattern (24 bp):
TCTCTCAATCTTCTCTCTTTTCTT
Found at i:29347206 original size:24 final size:24
Alignment explanation
Indices: 29347174--29347228 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
29347164 ATATGTTCAA
29347174 TCTGATAACCGACTAGACCGTAGC
1 TCTGATAACCGACTAGACCGTAGC
29347198 TCTGATAACCGACTAGACCGTAGC
1 TCTGATAACCGACTAGACCGTAGC
29347222 TCTGATA
1 TCTGATA
29347229 TCAATAAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (24 bp):
TCTGATAACCGACTAGACCGTAGC
Found at i:29348910 original size:10 final size:8
Alignment explanation
Indices: 29348874--29348912 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
29348864 TCGTATACAT
29348874 ATATCATCA
1 ATAT-ATCA
29348883 AT-T-TCA
1 ATATATCA
29348889 ATATATCA
1 ATATATCA
29348897 ATATATCA
1 ATATATCA
29348905 ATATATCA
1 ATATATCA
29348913 TGTGCCATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
6 5 0.18
7 1 0.04
8 20 0.71
9 2 0.07
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATATCA
Found at i:29357948 original size:32 final size:32
Alignment explanation
Indices: 29357907--29357971 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
29357897 TGAGTAGGAA
29357907 ACTGATATGTATGTCTGATTGTACTGTTAAGT
1 ACTGATATGTATGTCTGATTGTACTGTTAAGT
29357939 ACTGATATGTATGTCTGATTGTACTGTTAAGT
1 ACTGATATGTATGTCTGATTGTACTGTTAAGT
29357971 A
1 A
29357972 TGCATTTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.26, C:0.09, G:0.22, T:0.43
Consensus pattern (32 bp):
ACTGATATGTATGTCTGATTGTACTGTTAAGT
Found at i:29358203 original size:55 final size:55
Alignment explanation
Indices: 29358119--29358232 Score: 219
Period size: 55 Copynumber: 2.1 Consensus size: 55
29358109 CCAGAACAGG
29358119 ATTACGGAGCATTACCGATCACTACAGTTCAAACACTAATAATACAAGAATATTT
1 ATTACGGAGCATTACCGATCACTACAGTTCAAACACTAATAATACAAGAATATTT
*
29358174 ATTACGGAGGATTACCGATCACTACAGTTCAAACACTAATAATACAAGAATATTT
1 ATTACGGAGCATTACCGATCACTACAGTTCAAACACTAATAATACAAGAATATTT
29358229 ATTA
1 ATTA
29358233 TGTAGTTCAG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 58 1.00
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.28
Consensus pattern (55 bp):
ATTACGGAGCATTACCGATCACTACAGTTCAAACACTAATAATACAAGAATATTT
Found at i:29364657 original size:34 final size:34
Alignment explanation
Indices: 29364609--29364689 Score: 117
Period size: 34 Copynumber: 2.4 Consensus size: 34
29364599 ATAAGTGTTA
* * *
29364609 TTATAGTTGATGTATTTATGGTGGTTTGATACTT
1 TTATGGTTGATGTATTTATGGTAGTTTGATACCT
*
29364643 TTATGGTTGATGTATTTATGGTAGTTTGATGCCT
1 TTATGGTTGATGTATTTATGGTAGTTTGATACCT
*
29364677 TGATGGTTGATGT
1 TTATGGTTGATGT
29364690 TAGTATGACT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.19, C:0.04, G:0.27, T:0.51
Consensus pattern (34 bp):
TTATGGTTGATGTATTTATGGTAGTTTGATACCT
Found at i:29364673 original size:19 final size:18
Alignment explanation
Indices: 29364615--29364673 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 18
29364605 GTTATTATAG
29364615 TTGATGTATTTATGGTGGT
1 TTGATGTATTTATGGT-GT
*
29364634 TTGATACT-TTTAT-G-G-
1 TTGAT-GTATTTATGGTGT
29364649 TTGATGTATTTATGGTAGT
1 TTGATGTATTTATGGT-GT
29364668 TTGATG
1 TTGATG
29364674 CCTTGATGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
14 1 0.03
15 10 0.31
16 2 0.06
18 2 0.06
19 16 0.50
20 1 0.03
ACGTcount: A:0.19, C:0.02, G:0.27, T:0.53
Consensus pattern (18 bp):
TTGATGTATTTATGGTGT
Found at i:29367304 original size:93 final size:93
Alignment explanation
Indices: 29367186--29367358 Score: 251
Period size: 93 Copynumber: 1.9 Consensus size: 93
29367176 CGCCCATAAG
* * * *
29367186 CGAACTCGGACTCAACTCAATGAGCTTAGG-CGTTCGCATCCATAAGTGAGCTCGGACTCAACTC
1 CGAACTAGGACTCAACTCAACGAGCTT-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
29367250 AACGAG-TTCAGATGCCTAGTTACATTTCA
65 AACGAGCTT-AGATGCCTAGTTACATTTCA
* **
29367279 CGAACTAGGACTCAACTCAACGAGCTTGGACATTTGCATCCATAAGTGAACTCGGACTTGACTCA
1 CGAACTAGGACTCAACTCAACGAGCTTGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
29367344 ACGAGCTTAGATGCC
66 ACGAGCTTAGATGCC
29367359 CAAATATCCT
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
92 2 0.03
93 67 0.94
94 2 0.03
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.24
Consensus pattern (93 bp):
CGAACTAGGACTCAACTCAACGAGCTTGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGCTTAGATGCCTAGTTACATTTCA
Found at i:29372350 original size:21 final size:23
Alignment explanation
Indices: 29372324--29372366 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
29372314 AATGATGCTC
29372324 GTTTAT-CAC-ATTGAGAATGAT
1 GTTTATCCACAATTGAGAATGAT
*
29372345 GTTTATCCACAATTTAGAATGA
1 GTTTATCCACAATTGAGAATGA
29372367 CGTATCCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 3 0.16
23 10 0.53
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (23 bp):
GTTTATCCACAATTGAGAATGAT
Found at i:29372605 original size:23 final size:23
Alignment explanation
Indices: 29372556--29372605 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
29372546 AAAGTGCCAG
* *
29372556 AATGAATTGCACTATAATGGCAA
1 AATGAATTGCACTAAAATGACAA
*
29372579 AATGAATTGCACTAAAATGACAT
1 AATGAATTGCACTAAAATGACAA
29372602 AATG
1 AATG
29372606 CTTCCTCCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.46, C:0.12, G:0.16, T:0.26
Consensus pattern (23 bp):
AATGAATTGCACTAAAATGACAA
Found at i:29374914 original size:15 final size:14
Alignment explanation
Indices: 29374878--29374922 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
29374868 AAATACGCCT
29374878 ATAATATAATATAC
1 ATAATATAATATAC
* *
29374892 ACACTATAATATTAC
1 ATAATATAATA-TAC
29374907 ATAATATAATAATAC
1 ATAATATAAT-ATAC
29374922 A
1 A
29374923 AATTAATTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
14 9 0.36
15 15 0.60
16 1 0.04
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAATATAATATAC
Found at i:29375201 original size:10 final size:10
Alignment explanation
Indices: 29375186--29375214 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
29375176 CCTGGACGCT
29375186 CCCACCCCCC
1 CCCACCCCCC
29375196 CCCACCCCCC
1 CCCACCCCCC
29375206 CCC-CCCCCC
1 CCCACCCCCC
29375215 AATTAAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.32
10 13 0.68
ACGTcount: A:0.07, C:0.93, G:0.00, T:0.00
Consensus pattern (10 bp):
CCCACCCCCC
Found at i:29380555 original size:6 final size:6
Alignment explanation
Indices: 29380547--29380593 Score: 85
Period size: 6 Copynumber: 7.8 Consensus size: 6
29380537 AATCACCGAA
*
29380547 GAAGAA GAAGAC GAAGAC GAAGAC GAAGAC GAAGAC GAAGAC GAAGA
1 GAAGAC GAAGAC GAAGAC GAAGAC GAAGAC GAAGAC GAAGAC GAAGA
29380594 AAGCGATGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.53, C:0.13, G:0.34, T:0.00
Consensus pattern (6 bp):
GAAGAC
Found at i:29381412 original size:17 final size:17
Alignment explanation
Indices: 29381390--29381422 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
29381380 ATTCATTTTC
29381390 AACATTTAAAAAAAATT
1 AACATTTAAAAAAAATT
*
29381407 AACATTTAAACAAAAT
1 AACATTTAAAAAAAAT
29381423 AGAATTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (17 bp):
AACATTTAAAAAAAATT
Found at i:29384413 original size:43 final size:44
Alignment explanation
Indices: 29384364--29384514 Score: 182
Period size: 43 Copynumber: 3.5 Consensus size: 44
29384354 AATTACCGAG
*
29384364 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT
* *
29384408 -TGTGATTACGTGTAAGACCATGTCTGGGACATTAGCATCGT-T
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT
* * * * * *
29384450 ATATGATTTCGTGTAAGACCCTGTCTAGGACAATGGCATCG-AT
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT
* *
29384493 ATGTAATAACATGTAAGACCAT
1 ATGTGATTACATGTAAGACCAT
29384515 ATCTAAGATG
Statistics
Matches: 90, Mismatches: 15, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
42 1 0.01
43 89 0.99
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (44 bp):
ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT
Found at i:29386520 original size:38 final size:38
Alignment explanation
Indices: 29386477--29387212 Score: 685
Period size: 38 Copynumber: 20.1 Consensus size: 38
29386467 CTTATTGAAG
* * *
29386477 GGTTGGGAAAGACCTAGTC-AAGGCCAACCTTTGAAAAA
1 GGTTGGGATAGACCTTGTCTAAGG-CAACCTTTAAAAAA
*
29386515 GGTTGGGATAGA-CTCGTCTAAGGCAACC-TT-AAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAAA
* * **
29386550 GGTAGGGATAGACC-AGTCTAAGATAACCTTTTAAAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACC-TTTAAAAAA
* * *
29386588 AGTTGGGATAGAACTTGTCTAAGGAAACCTTTAAAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAAA
* * * *
29386626 AGTTGGGATAGATCTTGTCTAAGGAAACCTTTAAAAGA
1 GGTTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAAA
* * * *
29386664 GATTAGGATAGA-ATCGTCTAAGGCAACC-TT-AAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAAA
* * *
29386699 GGTTGGTATAGACCTTGTCTAAGGAAACCTCTAAAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAAA
*
29386737 GGTTGGGATAGACC-AGTCTAAGGCAACCTTTTAAAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACC-TTTAAAAAA
*
29386775 -ATTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAAA
* *
29386812 GGTTGGGATAGA-CTTGTCTAAGGCAACCTTTTAAAAT
1 GGTTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAAA
* *
29386849 TGTTGGGATAGA-CTAGTCTAAGGCAACCTTCT-AAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACCTT-TAAAAAA
* * *
29386886 TGTTGGGATAGACCTTGTTTAAGGCAACCTTAAAAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAAA
*
29386924 GGTTGGGATAGA-CTTGTCTATGGCAACC-TT-AAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAAA
* * **
29386959 TGTGGGGATA-AATTTGTCTAAGGCAACC-TT-AAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAAA
* *
29386994 GGTTGGGATAGA-TTTGTCTAAGGTAACC-TT-AAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAAA
* * * *
29387029 GGTTGGGATAGGCCTTGTCCAAGGAAACTTTTAAAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAAA
* * *
29387067 GGTTGGGATTGA-CATGTCTAAGACAACC-TT-AAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAAA
* * * *
29387102 TGTTGGGATAGA-CTCGTTTAAAGCAA-CTTT-AAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAAA
* * *
29387137 GGTTGGGATAGACTTTTTTCCAAGGCAA-C-TTAAAACAA
1 GGTTGGGATAGAC-CTTGTCTAAGGCAACCTTTAAAA-AA
* * *
29387175 -GTTGGGATA-AACTCGTCTAAGGTAACC-TT-AAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAAA
29387209 GGTT
1 GGTT
29387213 AGGGGGTAAA
Statistics
Matches: 585, Mismatches: 86, Indels: 57
0.80 0.12 0.08
Matches are distributed among these distances:
34 4 0.01
35 172 0.29
36 40 0.07
37 174 0.30
38 184 0.31
39 11 0.02
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (38 bp):
GGTTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAAA
Found at i:29386692 original size:37 final size:36
Alignment explanation
Indices: 29386477--29387257 Score: 713
Period size: 37 Copynumber: 21.3 Consensus size: 36
29386467 CTTATTGAAG
* *
29386477 GGTTGGGAAAGACCTAGTC-AAGGCCAACCTTTGAAAAA
1 GGTTGGGATAGA-CTTGTCTAAGG-CAACCTTT-AAAAA
*
29386515 GGTTGGGATAGACTCGTCTAAGGCAACC-TTAAAAA
1 GGTTGGGATAGACTTGTCTAAGGCAACCTTTAAAAA
* ** **
29386550 GGTAGGGATAGACCAGTCTAAGATAACCTTTTAAAAAA
1 GGTTGGGATAGACTTGTCTAAGGCAACC-TTT-AAAAA
* *
29386588 AGTTGGGATAGAACTTGTCTAAGGAAACCTTTAAAAAA
1 GGTTGGGATAG-ACTTGTCTAAGGCAACCTTT-AAAAA
* *
29386626 AGTTGGGATAGATCTTGTCTAAGGAAACCTTTAAAAGA
1 GGTTGGGATAGA-CTTGTCTAAGGCAACCTTTAAAA-A
* * * *
29386664 GATTAGGATAGAATCGTCTAAGGCAACC-TTAAAAA
1 GGTTGGGATAGACTTGTCTAAGGCAACCTTTAAAAA
* * *
29386699 GGTTGGTATAGACCTTGTCTAAGGAAACCTCTAAAAAA
1 GGTTGGGATAGA-CTTGTCTAAGGCAACCT-TTAAAAA
**
29386737 GGTTGGGATAGACCAGTCTAAGGCAACCTTTTAAAAA
1 GGTTGGGATAGACTTGTCTAAGGCAACC-TTTAAAAA
**
29386774 AATTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAAA
1 GGTTGGGATAGA-CTTGTCTAAGGCAACCTTT-AAAAA
*
29386812 GGTTGGGATAGACTTGTCTAAGGCAACCTTTTAAAAT
1 GGTTGGGATAGACTTGTCTAAGGCAACC-TTTAAAAA
* *
29386849 TGTTGGGATAGACTAGTCTAAGGCAACCTTCTAAAAA
1 GGTTGGGATAGACTTGTCTAAGGCAACCTT-TAAAAA
* * *
29386886 TGTTGGGATAGACCTTGTTTAAGGCAACCTTAAAAAAA
1 GGTTGGGATAGA-CTTGTCTAAGGCAACCTT-TAAAAA
*
29386924 GGTTGGGATAGACTTGTCTATGGCAACC-TTAAAAA
1 GGTTGGGATAGACTTGTCTAAGGCAACCTTTAAAAA
* * * *
29386959 TGTGGGGATAAATTTGTCTAAGGCAACC-TTAAAAA
1 GGTTGGGATAGACTTGTCTAAGGCAACCTTTAAAAA
* *
29386994 GGTTGGGATAGATTTGTCTAAGGTAACC-TTAAAAA
1 GGTTGGGATAGACTTGTCTAAGGCAACCTTTAAAAA
* * * *
29387029 GGTTGGGATAGGCCTTGTCCAAGGAAACTTTTAAAAAA
1 GGTTGGGATA-GACTTGTCTAAGGCAACCTTT-AAAAA
* * *
29387067 GGTTGGGATTGACATGTCTAAGACAACC-TTAAAAA
1 GGTTGGGATAGACTTGTCTAAGGCAACCTTTAAAAA
* * * *
29387102 TGTTGGGATAGACTCGTTTAAAGCAA-CTTTAAAAA
1 GGTTGGGATAGACTTGTCTAAGGCAACCTTTAAAAA
* *
29387137 GGTTGGGATAGACTTTTTTCCAAGGCAA-C-TTAAAACA
1 GGTTGGGATAGAC--TTGTCTAAGGCAACCTTTAAAA-A
* * * *
29387174 AGTTGGGATAAACTCGTCTAAGGTAACC-TTAAAAA
1 GGTTGGGATAGACTTGTCTAAGGCAACCTTTAAAAA
* * *** * *
29387209 GGTTAGGGGGTAAACCCATCTAAGGCAAAC-TTAGAAA
1 GGTT--GGGATAGACTTGTCTAAGGCAACCTTTAAAAA
29387246 GGTTGGGATAGA
1 GGTTGGGATAGA
29387258 TCTTTTATCT
Statistics
Matches: 619, Mismatches: 98, Indels: 55
0.80 0.13 0.07
Matches are distributed among these distances:
34 1 0.00
35 176 0.28
36 52 0.08
37 203 0.33
38 174 0.28
39 13 0.02
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.26
Consensus pattern (36 bp):
GGTTGGGATAGACTTGTCTAAGGCAACCTTTAAAAA
Found at i:29386794 original size:75 final size:73
Alignment explanation
Indices: 29386478--29387208 Score: 606
Period size: 73 Copynumber: 10.0 Consensus size: 73
29386468 TTATTGAAGG
* * *
29386478 GTTGGGAAAGACCTAGTC-AAGGCCAACCTTTGAAAAAGGTTGGGATAGA-CTCGTCTAAGGCAA
1 GTTGGGATAGACCTTGTCTAAGG-AAACCTTT-AAAAAGGTTGGGATAGACCT-GTCTAAGGCAA
*
29386541 CC-TTAAAAAG
63 CCTTTAAAAAA
* * * * *
29386551 GTAGGGATAGACC-AGTCTAA-GATAACCTTTTAAAAAAAGTTGGGATAGAACTTGTCTAAGGAA
1 GTTGGGATAGACCTTGTCTAAGGA-AACC-TTT-AAAAAGGTTGGGATAG-ACCTGTCTAAGGCA
29386614 ACCTTTAAAAAAA
62 ACCTTT-AAAAAA
* * * *
29386627 GTTGGGATAGATCTTGTCTAAGGAAACCTTTAAAAGAGATTAGGATAGA-ATCGTCTAAGGCAAC
1 GTTGGGATAGACCTTGTCTAAGGAAACCTTTAAAA-AGGTTGGGATAGACCT-GTCTAAGGCAAC
*
29386691 C-TTAAAAAG
64 CTTTAAAAAA
* * *
29386700 GTTGGTATAGACCTTGTCTAAGGAAACCTCTAAAAAAGGTTGGGATAGACCAGTCTAAGGCAACC
1 GTTGGGATAGACCTTGTCTAAGGAAACCT-TTAAAAAGGTTGGGATAGACCTGTCTAAGGCAACC
29386765 TTTTAAAAAA
65 -TTTAAAAAA
* * *
29386775 ATTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAAAGGTTGGGATAGACTTGTCTAAGGCAACC
1 GTTGGGATAGACCTTGTCTAAGGAAACCTTT-AAAAAGGTTGGGATAGACCTGTCTAAGGCAACC
**
29386840 TTTTAAAATT
65 -TTTAAAAAA
* * * *
29386850 GTTGGGATAGA-CTAGTCTAAGGCAACCTTCTAAAAATGTTGGGATAGACCTTGTTTAAGGCAAC
1 GTTGGGATAGACCTTGTCTAAGGAAACCTT-TAAAAAGGTTGGGATAGACC-TGTCTAAGGCAAC
*
29386914 CTTAAAAAAA
64 CTTTAAAAAA
* * * * * **
29386924 GGTTGGGATAGA-CTTGTCTATGGCAACC-TTAAAAATGTGGGGATAAATTTGTCTAAGGCAACC
1 -GTTGGGATAGACCTTGTCTAAGGAAACCTTTAAAAAGGTTGGGATAGACCTGTCTAAGGCAACC
*
29386987 -TTAAAAAG
65 TTTAAAAAA
* * * * * *
29386995 GTTGGGATAGA-TTTGTCTAAGGTAACC-TTAAAAAGGTTGGGATAGGCCTTGTCCAAGGAAACT
1 GTTGGGATAGACCTTGTCTAAGGAAACCTTTAAAAAGGTTGGGATAGACC-TGTCTAAGGCAACC
29387058 TTTAAAAAA
65 TTTAAAAAA
* * * * *
29387067 GGTTGGGATTGA-CATGTCTAA-GACAACC-TTAAAAATGTTGGGATAGA-CTCGTTTAAAGCAA
1 -GTTGGGATAGACCTTGTCTAAGGA-AACCTTTAAAAAGGTTGGGATAGACCT-GTCTAAGGCAA
*
29387128 -CTTTAAAAAG
63 CCTTTAAAAAA
* * * * * * *
29387138 GTTGGGATAGACTTTTTTCCAAGGCAA-C-TTAAAACAAGTTGGGATA-AACTCGTCTAAGGTAA
1 GTTGGGATAGAC-CTTGTCTAAGGAAACCTTTAAAA-AGGTTGGGATAGACCT-GTCTAAGGCAA
29387200 CC-TTAAAAA
63 CCTTTAAAAA
29387209 GGTTAGGGGG
Statistics
Matches: 543, Mismatches: 85, Indels: 61
0.79 0.12 0.09
Matches are distributed among these distances:
70 49 0.09
71 34 0.06
72 73 0.13
73 143 0.26
74 63 0.12
75 141 0.26
76 28 0.05
77 10 0.02
78 2 0.00
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.27
Consensus pattern (73 bp):
GTTGGGATAGACCTTGTCTAAGGAAACCTTTAAAAAGGTTGGGATAGACCTGTCTAAGGCAACCT
TTAAAAAA
Found at i:29396580 original size:36 final size:36
Alignment explanation
Indices: 29396533--29396604 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
29396523 AGCTTCAAAA
29396533 TATGGTAAGGTCCAATAAATCTAGGGCTCAATTTGC
1 TATGGTAAGGTCCAATAAATCTAGGGCTCAATTTGC
*
29396569 TATGGTAAGGTCCAATAAATCTAGGGCTTAATTTGC
1 TATGGTAAGGTCCAATAAATCTAGGGCTCAATTTGC
29396605 CTTACGACCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (36 bp):
TATGGTAAGGTCCAATAAATCTAGGGCTCAATTTGC
Found at i:29401247 original size:37 final size:36
Alignment explanation
Indices: 29401197--29401283 Score: 147
Period size: 37 Copynumber: 2.3 Consensus size: 36
29401187 TACGAAGTCT
29401197 TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
1 TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
29401233 GTACCCGGACATAATCTCCACACGTAGTCATCGGGTC
1 -TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
29401270 TCACCCGGAACATA
1 T-ACCCGG-ACATA
29401284 TTTCCAAGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
36 1 0.02
37 42 0.88
38 5 0.10
ACGTcount: A:0.26, C:0.33, G:0.20, T:0.21
Consensus pattern (36 bp):
TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
Found at i:29401419 original size:49 final size:49
Alignment explanation
Indices: 29401352--29401663 Score: 516
Period size: 49 Copynumber: 6.4 Consensus size: 49
29401342 TTTACCTCAT
*
29401352 ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 ATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
*
29401401 ATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCTTATCAC
1 ATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
* * *
29401450 ATATACATATACTTTCACATTCACCACATCGGCCGTTAGGCCTTATCAC
1 ATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
29401499 ATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 ATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
* *
29401548 ATATACATACATTTTCACATTCATCACATCGGCCATTAGGCCTCATCAC
1 ATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
* * *
29401597 ATATAAATACATTTTCACATTCATCACATCGGCCATTAGGCCTCATCAC
1 ATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
* *
29401646 ATATAAATACATTTTCAC
1 ATATACATACACTTTCAC
29401664 GAATCTTGAT
Statistics
Matches: 253, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 253 1.00
ACGTcount: A:0.31, C:0.29, G:0.08, T:0.31
Consensus pattern (49 bp):
ATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
Found at i:29406565 original size:18 final size:18
Alignment explanation
Indices: 29406527--29406565 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
29406517 ATGTGGCCTG
*
29406527 CCCGTGTGGGCCCATACA
1 CCCGTGTGGGCCCACACA
29406545 CCCGTGT-GGCCCACACGA
1 CCCGTGTGGGCCCACAC-A
29406563 CCC
1 CCC
29406566 AAATTGGCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.15, C:0.46, G:0.26, T:0.13
Consensus pattern (18 bp):
CCCGTGTGGGCCCACACA
Found at i:29407742 original size:21 final size:22
Alignment explanation
Indices: 29407718--29407763 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
29407708 GGGGTGTTAC
*
29407718 AAATCT-ATTTAAAAAAAAAGT
1 AAATCTGATGTAAAAAAAAAGT
* *
29407739 AAATCTGATGTAAAAATAAATT
1 AAATCTGATGTAAAAAAAAAGT
29407761 AAA
1 AAA
29407764 ATAAATAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.28
Consensus pattern (22 bp):
AAATCTGATGTAAAAAAAAAGT
Found at i:29415457 original size:125 final size:125
Alignment explanation
Indices: 29415305--29415557 Score: 506
Period size: 125 Copynumber: 2.0 Consensus size: 125
29415295 GAATCAAATT
29415305 AGACAAAAGGAAGTCAAACCTAAATAGAAACTAGTTGAAGACCTAACCTTGTAGCATAAACCAAA
1 AGACAAAAGGAAGTCAAACCTAAATAGAAACTAGTTGAAGACCTAACCTTGTAGCATAAACCAAA
29415370 ATCTATCTCCCATTCAAGCACAAATTGTTATAAACCCTTATATGCAACACAAATCTTTCA
66 ATCTATCTCCCATTCAAGCACAAATTGTTATAAACCCTTATATGCAACACAAATCTTTCA
29415430 AGACAAAAGGAAGTCAAACCTAAATAGAAACTAGTTGAAGACCTAACCTTGTAGCATAAACCAAA
1 AGACAAAAGGAAGTCAAACCTAAATAGAAACTAGTTGAAGACCTAACCTTGTAGCATAAACCAAA
29415495 ATCTATCTCCCATTCAAGCACAAATTGTTATAAACCCTTATATGCAACACAAATCTTTCA
66 ATCTATCTCCCATTCAAGCACAAATTGTTATAAACCCTTATATGCAACACAAATCTTTCA
29415555 AGA
1 AGA
29415558 AACTTAATTG
Statistics
Matches: 128, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
125 128 1.00
ACGTcount: A:0.43, C:0.22, G:0.11, T:0.24
Consensus pattern (125 bp):
AGACAAAAGGAAGTCAAACCTAAATAGAAACTAGTTGAAGACCTAACCTTGTAGCATAAACCAAA
ATCTATCTCCCATTCAAGCACAAATTGTTATAAACCCTTATATGCAACACAAATCTTTCA
Found at i:29425932 original size:2 final size:2
Alignment explanation
Indices: 29425925--29425968 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
29425915 GCTTCGCCAC
*
29425925 AT AT AT AT AT AT AT AT AT AT AC 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
29425967 AT
1 AT
29425969 CTGTTCTGGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29433215 original size:8 final size:8
Alignment explanation
Indices: 29433202--29433226 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
29433192 TTACAAATAA
29433202 AATGATCC
1 AATGATCC
29433210 AATGATCC
1 AATGATCC
29433218 AATGATCC
1 AATGATCC
29433226 A
1 A
29433227 TATTTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.24, G:0.12, T:0.24
Consensus pattern (8 bp):
AATGATCC
Found at i:29436699 original size:36 final size:36
Alignment explanation
Indices: 29436652--29436755 Score: 181
Period size: 36 Copynumber: 2.9 Consensus size: 36
29436642 AAAGAGTCTG
*
29436652 AGTGTTTCTTTTGTAAAAAGAAAGGACACTCGTCCA
1 AGTGTTTCTTTTGTAAAAAGAAAGGACACTCATCCA
*
29436688 AGTGTTTCTTTTGTAAAAAGAAAGGACACCCATCCA
1 AGTGTTTCTTTTGTAAAAAGAAAGGACACTCATCCA
*
29436724 AGTGTTTCTTTTGTAAAAAGAAAGAACACTCA
1 AGTGTTTCTTTTGTAAAAAGAAAGGACACTCA
29436756 AAGAAGGACT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 64 1.00
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (36 bp):
AGTGTTTCTTTTGTAAAAAGAAAGGACACTCATCCA
Found at i:29440154 original size:40 final size:41
Alignment explanation
Indices: 29440110--29440192 Score: 141
Period size: 40 Copynumber: 2.0 Consensus size: 41
29440100 GAATAAAAGC
*
29440110 ATAATGTATATTAATCATAGAAGACTGTAAAATATG-AAAA
1 ATAATGTATATTAATCATAGAAGACTATAAAATATGCAAAA
*
29440150 ATAATGTATATTAATCATAGAAGATTATAAAATATGCAAAA
1 ATAATGTATATTAATCATAGAAGACTATAAAATATGCAAAA
29440191 AT
1 AT
29440193 TGAACATTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
40 34 0.85
41 6 0.15
ACGTcount: A:0.53, C:0.05, G:0.11, T:0.31
Consensus pattern (41 bp):
ATAATGTATATTAATCATAGAAGACTATAAAATATGCAAAA
Found at i:29440208 original size:41 final size:39
Alignment explanation
Indices: 29440119--29440209 Score: 103
Period size: 40 Copynumber: 2.3 Consensus size: 39
29440109 CATAATGTAT
* * *
29440119 ATTAATCATAGAAGACTGTAAAATATGAAAAATAATGTAT
1 ATTAATCATAGAAGACTATAAAATATGAAAAAT-ATGAAC
*
29440159 ATTAATCATAGAAGATTATAAAATATGCAAAAAT-TGAAC
1 ATTAATCATAGAAGACTATAAAATATG-AAAAATATGAAC
29440198 ATTTACATCATA
1 A-TTA-ATCATA
29440210 TAAAGTATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
39 4 0.09
40 28 0.64
41 12 0.27
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.31
Consensus pattern (39 bp):
ATTAATCATAGAAGACTATAAAATATGAAAAATATGAAC
Found at i:29442156 original size:46 final size:46
Alignment explanation
Indices: 29442106--29442278 Score: 199
Period size: 46 Copynumber: 3.7 Consensus size: 46
29442096 TGGTTGAGCA
* *
29442106 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
29442152 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
29442199 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
29442245 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
29442279 GGGGTGGGTT
Statistics
Matches: 106, Mismatches: 14, Indels: 14
0.79 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 60 0.57
47 29 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:29442262 original size:93 final size:93
Alignment explanation
Indices: 29442103--29442273 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
29442093 GGATGGTTGA
* * *
29442103 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
29442168 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
29442196 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
29442261 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
29442274 ACTTAGGGGT
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:29442539 original size:19 final size:20
Alignment explanation
Indices: 29442502--29442539 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
29442492 ATAAGGTGGT
29442502 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
29442522 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
29442540 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:29449736 original size:46 final size:46
Alignment explanation
Indices: 29449686--29449857 Score: 208
Period size: 45 Copynumber: 3.7 Consensus size: 46
29449676 TGGTTGAGCA
*
29449686 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
29449732 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
29449779 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
*
29449825 -CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
29449858 GGGGCGGGTT
Statistics
Matches: 107, Mismatches: 12, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
43 6 0.06
45 34 0.32
46 30 0.28
47 29 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:29450119 original size:19 final size:20
Alignment explanation
Indices: 29450082--29450119 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
29450072 ATAAGGTGGT
29450082 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
29450102 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
29450120 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:29462742 original size:41 final size:41
Alignment explanation
Indices: 29462697--29462814 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
29462687 TGAAAGATAA
29462697 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
29462738 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
29462768 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
29462809 ATGTAG
1 ATGTAG
29462815 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:29462753 original size:71 final size:71
Alignment explanation
Indices: 29462665--29462828 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
29462655 GAGATGTATC
29462665 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
29462730 AGGACA
66 AGGACA
29462736 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
29462801 AGGACA
66 AGGACA
29462807 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
29462829 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:29470319 original size:41 final size:41
Alignment explanation
Indices: 29470274--29470391 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
29470264 TGAAAGATAA
29470274 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
29470315 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
29470345 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
29470386 ATGTAG
1 ATGTAG
29470392 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:29470330 original size:71 final size:71
Alignment explanation
Indices: 29470242--29470405 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
29470232 GAGATGTATC
29470242 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
29470307 AGGACA
66 AGGACA
29470313 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
29470378 AGGACA
66 AGGACA
29470384 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
29470406 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:29471894 original size:238 final size:239
Alignment explanation
Indices: 29471476--29471953 Score: 924
Period size: 238 Copynumber: 2.0 Consensus size: 239
29471466 CATGTATAGT
29471476 AGGCTTAATTATTTTGTTACGTGTCATATTTGTCTAGGTTTAAAATATTAGTTACAGTACTCGAC
1 AGGCTTAATTATTTTGTTACGTGTCATATTTGTCTAGGTTTAAAATATTAGTTACAGTACTCGAC
29471541 CAGCTATTTGTACAAGCCATTAAAGTTGGCTAATATTGTTCAAGACATATATTATACGATGCACT
66 CAGCTATTTGTACAAGCCATTAAAGTTGGCTAATATTGTTCAAGACATATATTATACGATGCACT
*
29471606 ATCAAATTGGATGACATATTTATATTTCGGTTATGTTTAATGGTATGTGTTATGTTCTGGTAATA
131 ATCAAATTGGATGACATATTTATATCTCGGTTATGTTTAATGGTATGTGTTATGTTCTGGTAATA
29471671 CCTTGTATCCTGTT-CGGCGACGGTAACGGGTAAGGGGTGTTAC
196 CCTTGTATCCTGTTCCGGCGACGGTAACGGGTAAGGGGTGTTAC
29471714 AGGCTTAATTATTTTGTTACGTGTCATATTTGTCTAGGTTTAAAATATTAGTTACAGTACTCGAC
1 AGGCTTAATTATTTTGTTACGTGTCATATTTGTCTAGGTTTAAAATATTAGTTACAGTACTCGAC
29471779 CAGCTACTTTGTACAAGCCATTAAAGTTGGCTAATATTGTTCAAGACATAT-TTATACGATGCAC
66 CAGCTA-TTTGTACAAGCCATTAAAGTTGGCTAATATTGTTCAAGACATATATTATACGATGCAC
29471843 TATCAAATTGGATGACATATTTATATCTCGGTTATGTTTAATGGTATGTGTTATGTTCTGGTAAT
130 TATCAAATTGGATGACATATTTATATCTCGGTTATGTTTAATGGTATGTGTTATGTTCTGGTAAT
29471908 ACCTTGTATCCTGTTCCGGCGACGGTAACGGGTAAGGGGTGTTAC
195 ACCTTGTATCCTGTTCCGGCGACGGTAACGGGTAAGGGGTGTTAC
29471953 A
1 A
29471954 TTTAGTGGTA
Statistics
Matches: 237, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
238 163 0.69
239 74 0.31
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (239 bp):
AGGCTTAATTATTTTGTTACGTGTCATATTTGTCTAGGTTTAAAATATTAGTTACAGTACTCGAC
CAGCTATTTGTACAAGCCATTAAAGTTGGCTAATATTGTTCAAGACATATATTATACGATGCACT
ATCAAATTGGATGACATATTTATATCTCGGTTATGTTTAATGGTATGTGTTATGTTCTGGTAATA
CCTTGTATCCTGTTCCGGCGACGGTAACGGGTAAGGGGTGTTAC
Found at i:29477205 original size:236 final size:235
Alignment explanation
Indices: 29476790--29477260 Score: 908
Period size: 236 Copynumber: 2.0 Consensus size: 235
29476780 GGCCTAATCG
29476790 GAATAGTGGTTTCGTGACCACAAATCCGAGATAGAAATAATTGTTTTATAATTATTTTGGGGTTT
1 GAATAGTGGTTTCGTGACCACAAATCCGAGATAGAAATAATTGTTTTATAATTATTTTGGGGTTT
29476855 ATGATATGATTGCATGATTGTGTGAAAATTTCGTGATGAAATTCTATGCCTAAAGTGCTTAAATT
66 ATGATATGATTGCATGATTGTGTGAAAATTTCGTGATGAAATTCTATGCCTAAAGTGCTTAAATT
*
29476920 GAAAGTAGGGACTAAATCGAATAAGTTGCAAAATTTGCATCCCGAAGTTTTTAGTATGAAATTGT
131 GAAAGTAGGGACTAAATCGAATAAGTTGCAAAATTTGCATCCAGAAGTTTTTAGTATGAAATTGT
29476985 TTTGGAATATTAATTAGGAGGTCTTAAATAGCAATTTGAC
196 TTTGGAATATTAATTAGGAGGTCTTAAATAGCAATTTGAC
29477025 GAATAGTGGTTTCGTGACCACAAAT-CGAGATAGAAATAATTGTTTTATAATTATTTTTGGGGTT
1 GAATAGTGGTTTCGTGACCACAAATCCGAGATAGAAATAATTGTTTTATAATTA-TTTTGGGGTT
29477089 TATGATTATGATTGCATGATTGTGTGAAAATTTCGTGATGAAATTCTATGCCTAAAGTGCTTAAA
65 TATGA-TATGATTGCATGATTGTGTGAAAATTTCGTGATGAAATTCTATGCCTAAAGTGCTTAAA
29477154 TTGAAAGTAGGGACTAAATCGAATAAGTTGCAAAATTTGCATCCAGAAGTTTTTAGTATGAAATT
129 TTGAAAGTAGGGACTAAATCGAATAAGTTGCAAAATTTGCATCCAGAAGTTTTTAGTATGAAATT
29477219 GTTTTGGAATATTAATTAGGAGGTCTTAAATAGCAATTTGAC
194 GTTTTGGAATATTAATTAGGAGGTCTTAAATAGCAATTTGAC
29477261 CAATTTTAAG
Statistics
Matches: 233, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
234 28 0.12
235 40 0.17
236 165 0.71
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.37
Consensus pattern (235 bp):
GAATAGTGGTTTCGTGACCACAAATCCGAGATAGAAATAATTGTTTTATAATTATTTTGGGGTTT
ATGATATGATTGCATGATTGTGTGAAAATTTCGTGATGAAATTCTATGCCTAAAGTGCTTAAATT
GAAAGTAGGGACTAAATCGAATAAGTTGCAAAATTTGCATCCAGAAGTTTTTAGTATGAAATTGT
TTTGGAATATTAATTAGGAGGTCTTAAATAGCAATTTGAC
Found at i:29478364 original size:41 final size:41
Alignment explanation
Indices: 29478319--29478436 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
29478309 TGAAAGATAA
29478319 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
29478360 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
29478390 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
29478431 ATGTAG
1 ATGTAG
29478437 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:29478375 original size:71 final size:71
Alignment explanation
Indices: 29478287--29478450 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
29478277 GAGATGTATC
29478287 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
29478352 AGGACA
66 AGGACA
29478358 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
29478423 AGGACA
66 AGGACA
29478429 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
29478451 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:29485942 original size:41 final size:41
Alignment explanation
Indices: 29485897--29486014 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
29485887 TGAAAGATAA
29485897 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
29485938 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
29485968 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
29486009 ATGTAG
1 ATGTAG
29486015 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:29485953 original size:71 final size:71
Alignment explanation
Indices: 29485865--29486028 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
29485855 GAGATGTATC
29485865 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
29485930 AGGACA
66 AGGACA
29485936 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
29486001 AGGACA
66 AGGACA
29486007 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
29486029 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:29490983 original size:40 final size:40
Alignment explanation
Indices: 29490939--29491026 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 40
29490929 TCGCTCGAAA
* * * *
29490939 GCCTTCGGGACATAGCCCGG-TTATAATAGCTCGTACAAAT
1 GCCTTCGGGACATAACCCGGATT-TAAGAACTCGCACAAAT
* * *
29490979 GCCTTTGGGACTTAACCCGGATTTAGGAACTCGCACAAAT
1 GCCTTCGGGACATAACCCGGATTTAAGAACTCGCACAAAT
29491019 GCCTTCGG
1 GCCTTCGG
29491027 ATCTTAGTCC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
40 37 0.95
41 2 0.05
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (40 bp):
GCCTTCGGGACATAACCCGGATTTAAGAACTCGCACAAAT
Found at i:29495474 original size:26 final size:26
Alignment explanation
Indices: 29495440--29495528 Score: 160
Period size: 26 Copynumber: 3.4 Consensus size: 26
29495430 AATTGATAAT
*
29495440 TGTTCCATGATAATGTGTTAGGTAAA
1 TGTTCCATGATAATGGGTTAGGTAAA
*
29495466 TGTTTCATGATAATGGGTTAGGTAAA
1 TGTTCCATGATAATGGGTTAGGTAAA
29495492 TGTTCCATGATAATGGGTTAGGTAAA
1 TGTTCCATGATAATGGGTTAGGTAAA
29495518 TGTTCCATGAT
1 TGTTCCATGAT
29495529 GGGAATTTCA
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 60 1.00
ACGTcount: A:0.29, C:0.08, G:0.25, T:0.38
Consensus pattern (26 bp):
TGTTCCATGATAATGGGTTAGGTAAA
Found at i:29499391 original size:25 final size:25
Alignment explanation
Indices: 29499359--29499406 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
29499349 CTATAACATG
* * *
29499359 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
29499384 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
29499407 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:29499490 original size:11 final size:11
Alignment explanation
Indices: 29499454--29499509 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
29499444 CATGGTATGT
29499454 ATGATATGCAC
1 ATGATATGCAC
* *
29499465 ATGACATG--T
1 ATGATATGCAC
29499474 ATGATATGCAC
1 ATGATATGCAC
*
29499485 ATGATATG--T
1 ATGATATGCAC
29499494 ATGATATGCAC
1 ATGATATGCAC
29499505 ATGAT
1 ATGAT
29499510 GTAATCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:29499509 original size:20 final size:20
Alignment explanation
Indices: 29499443--29499509 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
29499433 ATTTTGATAA
*
29499443 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
29499463 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
29499483 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
29499503 ACATGAT
1 ACATGAT
29499510 GTAATCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:29499614 original size:24 final size:23
Alignment explanation
Indices: 29499558--29499709 Score: 205
Period size: 24 Copynumber: 6.4 Consensus size: 23
29499548 GAGGAAGTGA
29499558 AAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
29499581 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
* *
29499604 CAAAAGGGCTTATGCCCTAGTTACC
1 -AAAAGGGCTTATGCCCCAGTTA-T
*
29499629 GAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
29499652 TAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTA-T
*
29499676 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTA-T
29499700 AAAAGAGGCT
1 AAAAG-GGCT
29499710 AGGCCTCCAG
Statistics
Matches: 115, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
23 43 0.37
24 68 0.59
25 4 0.03
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (23 bp):
AAAAGGGCTTATGCCCCAGTTAT
Found at i:29499657 original size:47 final size:46
Alignment explanation
Indices: 29499559--29499702 Score: 207
Period size: 47 Copynumber: 3.1 Consensus size: 46
29499549 AGGAAGTGAA
* *
29499559 AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTAT-T
* **
29499606 AAAGGGCTTATGCCCTAGTTACCGAAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTA-TAAAAGGGCTTATGCCCCAGTTATT
*
29499653 AAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTTTGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTA-TAAAAGGGCTTATGCCCCAGTTATT
29499700 AAA
1 AAA
29499703 AGAGGCTAGG
Statistics
Matches: 87, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
47 65 0.75
48 22 0.25
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (46 bp):
AAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
Found at i:29499680 original size:71 final size:71
Alignment explanation
Indices: 29499559--29499697 Score: 251
Period size: 71 Copynumber: 2.0 Consensus size: 71
29499549 AGGAAGTGAA
*
29499559 AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCTAG
1 AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAG
29499624 TTACCG
66 TTACCG
* *
29499630 AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTTTGCCCCAG
1 AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAG
29499695 TTA
66 TTA
29499698 TTAAAAGAGG
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 65 1.00
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (71 bp):
AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAG
TTACCG
Found at i:29499951 original size:31 final size:31
Alignment explanation
Indices: 29499916--29499976 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
29499906 CGTTTATAGT
29499916 AAAGGCTTCGGCCCAGTAATATGAAATATGG
1 AAAGGCTTCGGCCCAGTAATATGAAATATGG
**
29499947 AAAGGCTTCGGCCCAGTGTTATGAAATATG
1 AAAGGCTTCGGCCCAGTAATATGAAATATG
29499977 AAATATGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGG
Found at i:29501751 original size:30 final size:31
Alignment explanation
Indices: 29501695--29501757 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
29501685 CCTTTTCATA
*
29501695 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
**
29501726 TTTCAAATTTCATATTACT-GGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
29501756 TT
1 TT
29501758 ACGGTAAACG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 13 0.45
31 16 0.55
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTGGGCCGAAGCCT
Found at i:29502003 original size:24 final size:24
Alignment explanation
Indices: 29501951--29502138 Score: 251
Period size: 24 Copynumber: 8.0 Consensus size: 24
29501941 GCTTTATCAT
*
29501951 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
29501976 ATAACTGGGGCAAAAGCCCTTTTT
1 ATAACTGGGGCATAAGCCCTTTTA
29502000 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
* *
29502023 ATAACTGGGGCGTAA-CCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
29502046 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
29502070 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
29502094 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
29502117 ATAATTGGGG-ATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
29502139 TCACTTCCTC
Statistics
Matches: 149, Mismatches: 10, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
22 11 0.07
23 49 0.33
24 77 0.52
25 12 0.08
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.30
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:29502066 original size:70 final size:71
Alignment explanation
Indices: 29501951--29502139 Score: 258
Period size: 70 Copynumber: 2.7 Consensus size: 71
29501941 GCTTTATCAT
* * *
29501951 ATAACTGGAGGCCTAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTTTATAACTGGGGCATAAG
1 ATAACTGG-GGCATAACC-CTTTTAATAACTGGGGCATAAGCCCTTTTTATAACTGGGGCATAAG
29502016 CCC-TTTA
64 CCCTTTTA
* * *
29502023 ATAACTGGGGCGTAACCCTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCC
1 ATAACTGGGGCATAACCCTTTTAATAACTGGGGCATAAGCCCTTTTTATAACTGGGGCATAAGCC
*
29502088 CTTTTG
66 CTTTTA
*
29502094 ATAACTGGGGCATAAGCCC-TTTAATAATTGGGG-ATAAGCCCTTTTT
1 ATAACTGGGGCATAA-CCCTTTTAATAACTGGGGCATAAGCCCTTTTT
29502140 CACTTCCTCC
Statistics
Matches: 105, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
70 58 0.55
71 36 0.34
72 11 0.10
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (71 bp):
ATAACTGGGGCATAACCCTTTTAATAACTGGGGCATAAGCCCTTTTTATAACTGGGGCATAAGCC
CTTTTA
Found at i:29502087 original size:94 final size:95
Alignment explanation
Indices: 29501951--29502126 Score: 284
Period size: 94 Copynumber: 1.9 Consensus size: 95
29501941 GCTTTATCAT
* *
29501951 ATAACTGGAGGCCTAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTTTATAACTGGGGCATAAG
1 ATAACTGGAGGCATAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGCATAAG
29502016 CCCTTTAATAACTGGGGCGTAACCCTTTTG
66 CCCTTTAATAACTGGGGCGTAACCCTTTTG
* *
29502046 ATAACTGG-GGCATAAGCC-CTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAA
1 ATAACTGGAGGCAT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGCATAA
*
29502109 GCCCTTTAATAATTGGGG
65 GCCCTTTAATAACTGGGG
29502127 ATAAGCCCTT
Statistics
Matches: 75, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
94 63 0.84
95 12 0.16
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (95 bp):
ATAACTGGAGGCATAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGCATAAG
CCCTTTAATAACTGGGGCGTAACCCTTTTG
Found at i:29502210 original size:9 final size:9
Alignment explanation
Indices: 29502196--29502272 Score: 64
Period size: 9 Copynumber: 7.9 Consensus size: 9
29502186 ATCTCGTGTG
29502196 CATATCATA
1 CATATCATA
*
29502205 CATATCATGTG
1 CATATCA--TA
29502216 CATATCATA
1 CATATCATA
* *
29502225 CATGTCATGTG
1 CATATCA--TA
29502236 CATATCATA
1 CATATCATA
*
29502245 CATATCATGTG
1 CATATCA--TA
29502256 CATATCATA
1 CATATCATA
29502265 CATATCAT
1 CATATCAT
29502273 GTTTATCAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
9 31 0.57
11 23 0.43
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:29502215 original size:20 final size:20
Alignment explanation
Indices: 29502192--29502274 Score: 157
Period size: 20 Copynumber: 4.2 Consensus size: 20
29502182 GAACATCTCG
29502192 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
*
29502212 TGTGCATATCATACATGTCA
1 TGTGCATATCATACATATCA
29502232 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
29502252 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
29502272 TGT
1 TGT
29502275 TTATCAAAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:29502221 original size:11 final size:11
Alignment explanation
Indices: 29502192--29502263 Score: 66
Period size: 11 Copynumber: 7.1 Consensus size: 11
29502182 GAACATCTCG
29502192 TGTGCATATCA
1 TGTGCATATCA
*
29502203 --TACATATCA
1 TGTGCATATCA
29502212 TGTGCATATCA
1 TGTGCATATCA
* *
29502223 --TACATGTCA
1 TGTGCATATCA
29502232 TGTGCATATCA
1 TGTGCATATCA
*
29502243 --TACATATCA
1 TGTGCATATCA
29502252 TGTGCATATCA
1 TGTGCATATCA
29502263 T
1 T
29502264 ACATATCATG
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
9 23 0.49
11 24 0.51
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.36
Consensus pattern (11 bp):
TGTGCATATCA
Found at i:29502357 original size:25 final size:25
Alignment explanation
Indices: 29502311--29502358 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
29502301 ATATATAAAC
* * * *
29502311 CCTAGGGGTATAATGGTTATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
29502336 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
29502359 CATATTATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:29503617 original size:27 final size:27
Alignment explanation
Indices: 29503597--29504097 Score: 501
Period size: 27 Copynumber: 18.6 Consensus size: 27
29503587 AGGGTATTTT
* *
29503597 AGTAATTTTGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCAAGGGTAAAAC
29503624 AGTAATTCTGTAAATCAAGGGTAAAAC
1 AGTAATTCTGTAAATCAAGGGTAAAAC
* ** *
29503651 AGTAATTCTATAAATTGAGGGTAAAAT
1 AGTAATTCTGTAAATCAAGGGTAAAAC
* **
29503678 GGTAATTCTGTAAATTGAGGGTAAAAC
1 AGTAATTCTGTAAATCAAGGGTAAAAC
* *
29503705 GGTAATTCTGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCAAGGGTAAAAC
* ** *
29503732 -GATAATTATGTAAATCGGGGGTAAAAT
1 AG-TAATTCTGTAAATCAAGGGTAAAAC
* * * *
29503759 GGTAATTATGTAAATTAGGGGTAAAAC
1 AGTAATTCTGTAAATCAAGGGTAAAAC
* * * *
29503786 GGTAATTCTATAAATCGAGGGTAAAAT
1 AGTAATTCTGTAAATCAAGGGTAAAAC
*
29503813 AGTAATTCTGTAAA-CTGAGGGTAAAAC
1 AGTAATTCTGTAAATC-AAGGGTAAAAC
* *
29503840 GGTAATTCTGTAAATCGA-GGTAAAAC
1 AGTAATTCTGTAAATCAAGGGTAAAAC
* * ** *
29503866 GGTAATTTTACAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCAAGGGTAAAAC
* * *
29503893 GGTAATTCTATAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCAAGGGTAAAAC
*
29503920 AATAATTCTGTAAATCAAGGGTAAAAC
1 AGTAATTCTGTAAATCAAGGGTAAAAC
* *
29503947 AATAATTCTGTAAA-CTGAGGGTAAAAC
1 AGTAATTCTGTAAATC-AAGGGTAAAAC
* * *
29503974 GGTAATTCTGTAAATCGAGGGTAAAAT
1 AGTAATTCTGTAAATCAAGGGTAAAAC
*
29504001 AGTAATTCTGTAAA-CTGAGGGTAAAAC
1 AGTAATTCTGTAAATC-AAGGGTAAAAC
* *
29504028 GGTAATTCTGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCAAGGGTAAAAC
* *
29504055 AGTAATTCTATAAA-CTGAGGGTAAAAC
1 AGTAATTCTGTAAATC-AAGGGTAAAAC
*
29504082 GGTAATTCTGTAAATC
1 AGTAATTCTGTAAATC
29504098 GGGAGTACTT
Statistics
Matches: 417, Mismatches: 46, Indels: 21
0.86 0.10 0.04
Matches are distributed among these distances:
26 28 0.07
27 384 0.92
28 5 0.01
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28
Consensus pattern (27 bp):
AGTAATTCTGTAAATCAAGGGTAAAAC
Found at i:29503683 original size:81 final size:81
Alignment explanation
Indices: 29503598--29504098 Score: 647
Period size: 81 Copynumber: 6.2 Consensus size: 81
29503588 GGGTATTTTA
* * *
29503598 GTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAACAGTAATTCTATA
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTATA
* *
29503663 AATTGAGGGTAAAATG
66 AATCGAGGGTAAAACG
* * *
29503679 GTAATTCTGTAAATTGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAAC-GATAATTATGT
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACAG-TAATTCTAT
* *
29503743 AAATCGGGGGTAAAATG
65 AAATCGAGGGTAAAACG
* * * * *
29503760 GTAATTATGTAAAT-TAGGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAATAGTAATTCTGT
1 GTAATTCTGTAAATCGA-GGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTAT
29503824 AAA-CTGAGGGTAAAACG
65 AAATC-GAGGGTAAAACG
* ** *
29503841 GTAATTCTGTAAATCGA-GGTAAAACGGTAATTTTACAAATCGAGGGTAAAACGGTAATTCTATA
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTATA
*
29503905 AATCGAGGGTAAAACA
66 AATCGAGGGTAAAACG
* * ** * *
29503921 ATAATTCTGTAAATCAAGGGTAAAACAATAATTCTGTAAA-CTGAGGGTAAAACGGTAATTCTGT
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATC-GAGGGTAAAACAGTAATTCTAT
**
29503985 AAATCGAGGGTAAAATA
65 AAATCGAGGGTAAAACG
29504002 GTAATTCTGTAAA-CTGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTAT
1 GTAATTCTGTAAATC-GAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTAT
29504066 AAA-CTGAGGGTAAAACG
65 AAATC-GAGGGTAAAACG
29504083 GTAATTCTGTAAATCG
1 GTAATTCTGTAAATCG
29504099 GGAGTACTTT
Statistics
Matches: 368, Mismatches: 40, Indels: 24
0.85 0.09 0.06
Matches are distributed among these distances:
80 76 0.21
81 288 0.78
82 4 0.01
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28
Consensus pattern (81 bp):
GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTATA
AATCGAGGGTAAAACG
Found at i:29504115 original size:54 final size:54
Alignment explanation
Indices: 29503598--29504098 Score: 645
Period size: 54 Copynumber: 9.3 Consensus size: 54
29503588 GGGTATTTTA
* * * *
29503598 GTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACG
* * * *
29503652 GTAATTCTATAAATTGAGGGTAAAATGGTAATTCTGTAAATTGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACG
* * * *
29503706 GTAATTCTGTAAATCGAGGGTAAAACGATAATTATGTAAATCGGGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACG
* * * **
29503760 GTAATTATGTAAAT-TAGGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAATA
1 GTAATTCTGTAAATCGA-GGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACG
29503814 GTAATTCTGTAAA-CTGAGGGTAAAACGGTAATTCTGTAAATCGA-GGTAAAACG
1 GTAATTCTGTAAATC-GAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACG
* ** * *
29503867 GTAATTTTACAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACG
* * **
29503921 ATAATTCTGTAAATCAAGGGTAAAACAATAATTCTGTAAA-CTGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATC-GAGGGTAAAACG
**
29503975 GTAATTCTGTAAATCGAGGGTAAAATAGTAATTCTGTAAA-CTGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATC-GAGGGTAAAACG
* *
29504029 GTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTATAAA-CTGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATC-GAGGGTAAAACG
29504083 GTAATTCTGTAAATCG
1 GTAATTCTGTAAATCG
29504099 GGAGTACTTT
Statistics
Matches: 393, Mismatches: 48, Indels: 12
0.87 0.11 0.03
Matches are distributed among these distances:
53 47 0.12
54 345 0.88
55 1 0.00
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28
Consensus pattern (54 bp):
GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACG
Found at i:29506815 original size:31 final size:31
Alignment explanation
Indices: 29506780--29506843 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
29506770 CCTTTTCATA
*
29506780 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
**
29506811 TTTCAAATTTCATATTACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
29506842 TT
1 TT
29506844 ACGGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTGGGCCGAAGCCT
Found at i:29509226 original size:27 final size:27
Alignment explanation
Indices: 29509196--29509281 Score: 91
Period size: 27 Copynumber: 3.2 Consensus size: 27
29509186 TACCATACAG
* *
29509196 GGGTATTTTGGTAGTTTTACAAATTGA
1 GGGTATTTTGGTAATTTTACAAATCGA
** * * *
29509223 GGGTATTGCGGTAATTTCACAAACCAA
1 GGGTATTTTGGTAATTTTACAAATCGA
* *
29509250 GGGTATTTTAGTAATTTTATAAATCGA
1 GGGTATTTTGGTAATTTTACAAATCGA
29509277 GGGTA
1 GGGTA
29509282 AAACAGTAAT
Statistics
Matches: 45, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.30, C:0.08, G:0.24, T:0.37
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAATCGA
Found at i:29509289 original size:27 final size:27
Alignment explanation
Indices: 29509260--29509761 Score: 611
Period size: 27 Copynumber: 18.6 Consensus size: 27
29509250 GGGTATTTTA
* * *
29509260 GTAATTTTATAAATCGAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
29509287 GTAATTCTATAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
29509314 GTAATTCTGTAAATTGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
29509341 GTAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* * *
29509368 ATAATTATGTAAATCG-GGGATAAAATG
1 GTAATTCTGTAAATCGAGGG-TAAAACG
* *
29509395 GTAATTATGTAAAT-TAGGGGTAAAACG
1 GTAATTCTGTAAATCGA-GGGTAAAACG
* * **
29509422 GTAATTTTATAAATCGAGGGTAAAATA
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
29509449 GTAATTCTGTAAA-CTGAGGGTAAAACT
1 GTAATTCTGTAAATC-GAGGGTAAAACG
*
29509476 GTAATTCTGTAAATCAAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* **
29509503 GTAATTTTACAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* **
29509530 GTAATTCTATAAATCGAGGGTAAAATA
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
29509557 GTAATTCTGTAAATCAAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
29509584 ATAATTCTGTAAA-CTGAGGGTAAAACG
1 GTAATTCTGTAAATC-GAGGGTAAAACG
**
29509611 GTAATTCTGTAAATCGAGGGTAAAATA
1 GTAATTCTGTAAATCGAGGGTAAAACG
29509638 GTAATTCTGTAAA-CTGAGGGTAAAACG
1 GTAATTCTGTAAATC-GAGGGTAAAACG
29509665 GTAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* ** *
29509692 GTAATTTTACAAATCGAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
29509719 GTAATTCTATAAA-CTGAGGGTAAAACG
1 GTAATTCTGTAAATC-GAGGGTAAAACG
29509746 GTAATTCTGTAAATCG
1 GTAATTCTGTAAATCG
29509762 GGAGTACTTT
Statistics
Matches: 412, Mismatches: 51, Indels: 24
0.85 0.10 0.05
Matches are distributed among these distances:
26 7 0.02
27 397 0.96
28 8 0.02
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28
Consensus pattern (27 bp):
GTAATTCTGTAAATCGAGGGTAAAACG
Found at i:29515261 original size:26 final size:26
Alignment explanation
Indices: 29515227--29515367 Score: 264
Period size: 26 Copynumber: 5.4 Consensus size: 26
29515217 AATTGATAAT
29515227 TGTTCCATGATAATGGGTTAGGTAAA
1 TGTTCCATGATAATGGGTTAGGTAAA
*
29515253 TGTTTCATGATAATGGGTTAGGTAAA
1 TGTTCCATGATAATGGGTTAGGTAAA
29515279 TGTTCCATGATAATGGGTTAGGTAAA
1 TGTTCCATGATAATGGGTTAGGTAAA
*
29515305 TGTTTCATGATAATGGGTTAGGTAAA
1 TGTTCCATGATAATGGGTTAGGTAAA
29515331 TGTTCCATGATAATGGGTTAGGTAAA
1 TGTTCCATGATAATGGGTTAGGTAAA
29515357 TGTTCCATGAT
1 TGTTCCATGAT
29515368 GGGAATTTCA
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 111 1.00
ACGTcount: A:0.30, C:0.07, G:0.26, T:0.37
Consensus pattern (26 bp):
TGTTCCATGATAATGGGTTAGGTAAA
Found at i:29516931 original size:21 final size:21
Alignment explanation
Indices: 29516905--29516944 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
29516895 CATGTTTGAC
29516905 TGTTGTTATTA-CTGCATGCCA
1 TGTTGTTATTATCTG-ATGCCA
29516926 TGTTGTTATTATCTGATGC
1 TGTTGTTATTATCTGATGC
29516945 ATGGGATTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.17, C:0.15, G:0.20, T:0.47
Consensus pattern (21 bp):
TGTTGTTATTATCTGATGCCA
Found at i:29529055 original size:16 final size:16
Alignment explanation
Indices: 29529031--29529067 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
29529021 TTTAAAAAGG
*
29529031 AAAACAAATGAATCTT
1 AAAAAAAATGAATCTT
*
29529047 AAAAAAAATGAGTCTT
1 AAAAAAAATGAATCTT
29529063 AAAAA
1 AAAAA
29529068 CTTAATGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.22
Consensus pattern (16 bp):
AAAAAAAATGAATCTT
Found at i:29535953 original size:16 final size:16
Alignment explanation
Indices: 29535932--29535974 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
29535922 TCTCAGAATA
*
29535932 ATAAAGAATACAAAAC
1 ATAAAGAAAACAAAAC
29535948 ATAAAGAAAACAAAAC
1 ATAAAGAAAACAAAAC
29535964 ATAAAGAAAAC
1 ATAAAGAAAAC
29535975 TCAAAACTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.72, C:0.12, G:0.07, T:0.09
Consensus pattern (16 bp):
ATAAAGAAAACAAAAC
Found at i:29538949 original size:21 final size:21
Alignment explanation
Indices: 29538925--29538965 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
29538915 GATACCTAGT
* *
29538925 AAAAGGTGTCCATACTTTTTG
1 AAAAGGTATCAATACTTTTTG
29538946 AAAAGGTATCAATACTTTTT
1 AAAAGGTATCAATACTTTTT
29538966 ATGATTGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (21 bp):
AAAAGGTATCAATACTTTTTG
Found at i:29542176 original size:31 final size:31
Alignment explanation
Indices: 29542141--29542202 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
29542131 AACTAGAAAG
29542141 TAAACTTACCGATAATTAACATACAACCATA
1 TAAACTTACCGATAATTAACATACAACCATA
*
29542172 TAAACTTACTGATAATTAACATACAACCATA
1 TAAACTTACCGATAATTAACATACAACCATA
29542203 ATAAGCAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.48, C:0.21, G:0.03, T:0.27
Consensus pattern (31 bp):
TAAACTTACCGATAATTAACATACAACCATA
Found at i:29543629 original size:16 final size:16
Alignment explanation
Indices: 29543608--29543661 Score: 99
Period size: 16 Copynumber: 3.4 Consensus size: 16
29543598 TTATTTCATT
29543608 AAAATGCCAAATGACC
1 AAAATGCCAAATGACC
29543624 AAAATGCCAAATGACC
1 AAAATGCCAAATGACC
*
29543640 AAAATGCTAAATGACC
1 AAAATGCCAAATGACC
29543656 AAAATG
1 AAAATG
29543662 GCCTTAAGTC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.52, C:0.20, G:0.13, T:0.15
Consensus pattern (16 bp):
AAAATGCCAAATGACC
Found at i:29543633 original size:8 final size:9
Alignment explanation
Indices: 29543608--29543661 Score: 57
Period size: 7 Copynumber: 6.7 Consensus size: 9
29543598 TTATTTCATT
29543608 AAAATG-CC
1 AAAATGACC
29543616 -AAATGACC
1 AAAATGACC
29543624 AAAATG-CC
1 AAAATGACC
29543632 -AAATGACC
1 AAAATGACC
29543640 AAAATG--C
1 AAAATGACC
*
29543647 TAAATGACC
1 AAAATGACC
29543656 AAAATG
1 AAAATG
29543662 GCCTTAAGTC
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
7 16 0.42
8 6 0.16
9 16 0.42
ACGTcount: A:0.52, C:0.20, G:0.13, T:0.15
Consensus pattern (9 bp):
AAAATGACC
Found at i:29561896 original size:5 final size:5
Alignment explanation
Indices: 29561886--29561916 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
29561876 ATAATAATAA
29561886 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT T
1 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT T
29561917 GAAAGAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TAAAT
Found at i:29576481 original size:32 final size:30
Alignment explanation
Indices: 29576438--29576496 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
29576428 AGAGAAAAAA
29576438 AGTAAATTACACCTAAGGTCACTCAACTATT
1 AGTAAATTACA-CTAAGGTCACTCAACTATT
**
29576469 AGTAAACTTACACTTTGGTCACTCAACT
1 AGTAAA-TTACACTAAGGTCACTCAACT
29576497 TTAAAAAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 20 0.80
32 5 0.20
ACGTcount: A:0.36, C:0.24, G:0.10, T:0.31
Consensus pattern (30 bp):
AGTAAATTACACTAAGGTCACTCAACTATT
Found at i:29582188 original size:155 final size:147
Alignment explanation
Indices: 29581913--29582214 Score: 478
Period size: 155 Copynumber: 2.0 Consensus size: 147
29581903 GTAAGATAGA
* * *
29581913 TTGATTTCACTGATTTTAGGCTTGAATTTTTCGAATAAAAAGTTTGCTTCCTTCATCAACTGTCA
1 TTGATTTCACTGATTTTAGGCTTGAATTTTTCAAAGAAAAAATTTGCTTCCTTCATCAACTGTCA
29581978 TTTTATATAGTAGCAGACATTGATACCTTTGATAGCATTCTGTGTTGTATAGTTTTTATTTTATT
66 TTTTATATAGTAGCAGACATTGATACCTTTGATAGCATTCTGTGTTGTATAGTTTTTATTTTA-T
*
29582043 TTTATATTCTGCAGAATG
130 CTTATATTCTGCAGAATG
29582061 TTGATTTCACTGATTTTAGGCTTGAATTTTACGTTCTTTAAAGAAAAAATTTGCTTCCTTCATCA
1 TTGATTTCACTGATTTTAGGCTTGAA-TTT---TTC---AAAGAAAAAATTTGCTTCCTTCATCA
* *
29582126 ACTGTCATTTTATATGGTAGCAGACATTGATACCTTTGATTGCATTCTGTGTTGTATAGTTTTTA
59 ACTGTCATTTTATATAGTAGCAGACATTGATACCTTTGATAGCATTCTGTGTTGTATAGTTTTTA
29582191 TTTTATCTTATATTCTGCAGAATG
124 TTTTATCTTATATTCTGCAGAATG
29582215 GGGATGATTC
Statistics
Matches: 141, Mismatches: 6, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
148 26 0.18
149 3 0.02
152 3 0.02
154 18 0.13
155 91 0.65
ACGTcount: A:0.25, C:0.13, G:0.15, T:0.46
Consensus pattern (147 bp):
TTGATTTCACTGATTTTAGGCTTGAATTTTTCAAAGAAAAAATTTGCTTCCTTCATCAACTGTCA
TTTTATATAGTAGCAGACATTGATACCTTTGATAGCATTCTGTGTTGTATAGTTTTTATTTTATC
TTATATTCTGCAGAATG
Found at i:29586025 original size:2 final size:2
Alignment explanation
Indices: 29586018--29586042 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29586008 AGACCTCCAC
29586018 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
29586043 CCCTCGACAA
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:29588305 original size:21 final size:21
Alignment explanation
Indices: 29588279--29588322 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
29588269 TAATTATTAC
29588279 TTTAAATAT-TTATTTTTTATT
1 TTTAAATATCTTATTTTTT-TT
*
29588300 TTTAAATTTCTTATTTTTTTT
1 TTTAAATATCTTATTTTTTTT
29588321 TT
1 TT
29588323 GTTATCCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTAAATATCTTATTTTTTTT
Found at i:29588878 original size:12 final size:12
Alignment explanation
Indices: 29588861--29588885 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29588851 TTGTGTGTTC
29588861 TTTATTTTATTT
1 TTTATTTTATTT
29588873 TTTATTTTATTT
1 TTTATTTTATTT
29588885 T
1 T
29588886 ATTTTCACAA
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:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTATTTTATTT
Found at i:29599787 original size:40 final size:40
Alignment explanation
Indices: 29599687--29599893 Score: 285
Period size: 40 Copynumber: 5.2 Consensus size: 40
29599677 TGAATGATAC
* * *
29599687 CCGGGCTAAGCCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATAT
29599727 -CGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
*
29599766 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* *
29599806 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAC
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* * ** *
29599846 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
29599886 CC-GGCTAA
1 CCGGGCTAA
29599894 ATTCCGAAGA
Statistics
Matches: 150, Mismatches: 15, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
39 38 0.25
40 112 0.75
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
Found at i:29607843 original size:40 final size:40
Alignment explanation
Indices: 29607762--29608007 Score: 347
Period size: 40 Copynumber: 6.2 Consensus size: 40
29607752 TGAATGATAC
* * *
29607762 CCGGGCTAAG-CCCCAAGGCA-TTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATAT
29607800 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
*
29607840 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
*
29607880 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* *
29607920 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAC
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* * ** *
29607960 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
29608000 CC-GGCTAA
1 CCGGGCTAA
29608008 ATTCCAAAGA
Statistics
Matches: 190, Mismatches: 15, Indels: 5
0.90 0.07 0.02
Matches are distributed among these distances:
38 10 0.05
39 14 0.07
40 164 0.86
41 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
Found at i:29615369 original size:29 final size:29
Alignment explanation
Indices: 29615288--29615374 Score: 129
Period size: 29 Copynumber: 3.0 Consensus size: 29
29615278 GAAGAGGTGG
* * * * *
29615288 AGAACTTGTTCGTTGAGAGTTCGCGACGA
1 AGAACTTGTTCATTGAGAATTCGTGTCAA
29615317 AGAACTTGTTCATTGAGAATTCGTGTCAA
1 AGAACTTGTTCATTGAGAATTCGTGTCAA
29615346 AGAACTTGTTCATTGAGAATTCGTGTCAA
1 AGAACTTGTTCATTGAGAATTCGTGTCAA
29615375 GGTGGAGACT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (29 bp):
AGAACTTGTTCATTGAGAATTCGTGTCAA
Found at i:29617355 original size:40 final size:40
Alignment explanation
Indices: 29617263--29617481 Score: 303
Period size: 40 Copynumber: 5.5 Consensus size: 40
29617253 CGAATGATGT
* * *
29617263 CCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAAA
* *
29617304 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAA
* *
29617344 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAA
* *
29617384 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAA
* * * *
29617424 CCGGGCTAATTCCCGAAGGCAATTGTGCGAATTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAA
*
29617464 CCGGGCTATGTCCCGAAG
1 CCGGGCTAAGTCCCGAAG
29617482 ACAATCGAGC
Statistics
Matches: 163, Mismatches: 15, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
40 137 0.84
41 26 0.16
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAA
Found at i:29617506 original size:80 final size:80
Alignment explanation
Indices: 29617262--29617506 Score: 220
Period size: 80 Copynumber: 3.0 Consensus size: 80
29617252 TCGAATGATG
** * * * * * *
29617262 TCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAAACCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCAATTGTGCGAA-TTACCAAAACCGGGCTAAGTCCCGAAGACAAT
* * * *
29617327 TGTGCGAGTTACCAAA
65 CGAGCGAGTCACTAAA
* * * * * * * *
29617343 ACCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAACCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCAATTGTGCGAATTACCAAAACCGGGCTAAGTCCCGAAGACAATC
* *
29617408 GTGCGAGTTACTAAA
66 GAGCGAGTCACTAAA
* * * *
29617423 TCCGGGCTAATTCCCGAAGGCAATTGTGCGAATTACTATAACCGGGCTATGTCCCGAAGACAATC
1 TCCGGGCTAAGTCCCGAAGGCAATTGTGCGAATTACCAAAACCGGGCTAAGTCCCGAAGACAATC
* * *
29617488 GAGCTAGTCGCTACA
66 GAGCGAGTCACTAAA
29617503 TCCG
1 TCCG
29617507 ATTAAATTCC
Statistics
Matches: 139, Mismatches: 25, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
80 112 0.81
81 27 0.19
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.24
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCAATTGTGCGAATTACCAAAACCGGGCTAAGTCCCGAAGACAATC
GAGCGAGTCACTAAA
Found at i:29625377 original size:15 final size:16
Alignment explanation
Indices: 29625357--29625387 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
29625347 TTTATAAGTA
29625357 ATATAAT-AAAAATAT
1 ATATAATGAAAAATAT
29625372 ATATAATGAAAAATAT
1 ATATAATGAAAAATAT
29625388 TTTTATCGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
ATATAATGAAAAATAT
Found at i:29629008 original size:23 final size:23
Alignment explanation
Indices: 29628953--29629020 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
29628943 CTAAGGATTG
* **
29628953 AAACGGTAAACTCCGAAGAGCT-
1 AAACGGTAAGCTCATAAGAGCTA
* *
29628975 GAATGGTAAGCTCATAAGAGCTA
1 AAACGGTAAGCTCATAAGAGCTA
*
29628998 AAACGGTAAGCTCATATGAGCTA
1 AAACGGTAAGCTCATAAGAGCTA
29629021 TAGTGAGTTT
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
22 17 0.46
23 20 0.54
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (23 bp):
AAACGGTAAGCTCATAAGAGCTA
Found at i:29640126 original size:2 final size:2
Alignment explanation
Indices: 29640119--29640152 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
29640109 AACACTTAAC
29640119 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
29640153 GTCAGCTTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29641453 original size:48 final size:48
Alignment explanation
Indices: 29641311--29641435 Score: 232
Period size: 48 Copynumber: 2.6 Consensus size: 48
29641301 TCATGTCAGT
*
29641311 GCCAATGCCATGTCCCAGACATGGTCTTATACTAGCACACATATCATC
1 GCCAATGCCATGTCCCAAACATGGTCTTATACTAGCACACATATCATC
*
29641359 GCCGATGCCATGTCCCAAACATGGTCTTATACTAGCACACATATCATC
1 GCCAATGCCATGTCCCAAACATGGTCTTATACTAGCACACATATCATC
29641407 GCCAATGCCATGTCCCAAACATGGTCTTA
1 GCCAATGCCATGTCCCAAACATGGTCTTA
29641436 CATAGGCACA
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 74 1.00
ACGTcount: A:0.29, C:0.31, G:0.15, T:0.25
Consensus pattern (48 bp):
GCCAATGCCATGTCCCAAACATGGTCTTATACTAGCACACATATCATC
Found at i:29644298 original size:40 final size:40
Alignment explanation
Indices: 29644221--29644446 Score: 257
Period size: 40 Copynumber: 5.7 Consensus size: 40
29644211 ATTTGATGTG
* *
29644221 TGTATCCGGGCTTAAAGA-CCGCAGGCT-T-CGTACTGGAAT
1 TGTATCCGGGTTTAAAGACCCGCAGGCTATATGT--TGGAAT
*
29644260 GGTATCCGGGTTTAAAGACCCGCAGGCTATATGTTGGAAT
1 TGTATCCGGGTTTAAAGACCCGCAGGCTATATGTTGGAAT
* *
29644300 TGTATCCGGGTTTAAAGACCCGCAGGCTATATGCTGGAGT
1 TGTATCCGGGTTTAAAGACCCGCAGGCTATATGTTGGAAT
* * *
29644340 TGTATCCGGGTTTAAAGACCCGCAGACTAGATGCTGGAAT
1 TGTATCCGGGTTTAAAGACCCGCAGGCTATATGTTGGAAT
* *
29644380 TGTATCTGGGTTTAAAGACCCGCAGGCT-T-CGTACTGGAAT
1 TGTATCCGGGTTTAAAGACCCGCAGGCTATATGT--TGGAAT
* * *
29644420 GGAATCCGGG-TTAAAGACCCGTAGGCT
1 TGTATCCGGGTTTAAAGACCCGCAGGCT
29644447 CGTGTTAGAA
Statistics
Matches: 164, Mismatches: 18, Indels: 10
0.85 0.09 0.05
Matches are distributed among these distances:
38 1 0.01
39 32 0.20
40 128 0.78
41 1 0.01
42 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.26
Consensus pattern (40 bp):
TGTATCCGGGTTTAAAGACCCGCAGGCTATATGTTGGAAT
Found at i:29644353 original size:80 final size:80
Alignment explanation
Indices: 29644221--29644446 Score: 323
Period size: 80 Copynumber: 2.9 Consensus size: 80
29644211 ATTTGATGTG
*
29644221 TGTATCCGGGCTTAAAGA-CCGCAGGCTTCGTACTGGAATGGTATCCGGGTTTAAAGACCCGCAG
1 TGTATCCGGGTTTAAAGACCCGCAGGCTTCGTACTGGAATGGTATCCGGGTTTAAAGACCCGCAG
* *
29644285 GCTATATGTTGGAAT
66 GCTAGATGCTGGAAT
* * * *
29644300 TGTATCCGGGTTTAAAGACCCGCAGGCTAT-ATGCTGGAGTTGTATCCGGGTTTAAAGACCCGCA
1 TGTATCCGGGTTTAAAGACCCGCAGGCT-TCGTACTGGAATGGTATCCGGGTTTAAAGACCCGCA
*
29644364 GACTAGATGCTGGAAT
65 GGCTAGATGCTGGAAT
* * *
29644380 TGTATCTGGGTTTAAAGACCCGCAGGCTTCGTACTGGAATGGAATCCGGG-TTAAAGACCCGTAG
1 TGTATCCGGGTTTAAAGACCCGCAGGCTTCGTACTGGAATGGTATCCGGGTTTAAAGACCCGCAG
29644444 GCT
66 GCT
29644447 CGTGTTAGAA
Statistics
Matches: 128, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
79 33 0.26
80 94 0.73
81 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.26
Consensus pattern (80 bp):
TGTATCCGGGTTTAAAGACCCGCAGGCTTCGTACTGGAATGGTATCCGGGTTTAAAGACCCGCAG
GCTAGATGCTGGAAT
Found at i:29644638 original size:2 final size:2
Alignment explanation
Indices: 29644631--29644660 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
29644621 TTAAATAACG
29644631 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
29644661 GTGTGGATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29649708 original size:2 final size:2
Alignment explanation
Indices: 29649697--29649728 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
29649687 GTATAGTAAA
29649697 AT AT -T AT 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 AT AT AT AT A
29649729 AAAGGAAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.