Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 140 of 171
Found at i:42994298 original size:85 final size:84
Alignment explanation
Indices: 42994163--42994476 Score: 393
Period size: 85 Copynumber: 3.7 Consensus size: 84
42994153 CGTTTATTAG
* * * *
42994163 AAAAAGCGCCGCTATAGAACATGGTTTTTAGCGGTGC-TTTTCACAAAAACGCCGCTAAAGAACA
1 AAAAA-CGCAGCTAAAGAACATGGTCTTTAGCGGCGCTTTTTCAC--AAACGCCGCTAAAGAACA
42994227 TGGTCTTTAGCGGCGCTTTCTC
63 TGGTCTTTAGCGGCGCTTTCTC
*
42994249 AAAAACGCAGCTAAAGAACATGGTCTTTAGCGGTGCTTTTTCGACAAACGCCGCTAAAGAACATG
1 AAAAACGCAGCTAAAGAACATGGTCTTTAGCGGCGCTTTTTC-ACAAACGCCGCTAAAGAACATG
*
42994314 GTCTTCAGCGGCGCTTT-TC
65 GTCTTTAGCGGCGCTTTCTC
* * * **
42994333 ACACAAATGCCA-CTAAAGAACATTG-CTTTTAACGGCGCTTTACCCACAAACGCCGCTAAAGAA
1 A-A-AAACG-CAGCTAAAGAACATGGTC-TTTAGCGGCGCTTT-TTCACAAACGCCGCTAAAGAA
*
42994396 CATGCTCTTTAGCGGCGCTTTCTC
61 CATGGTCTTTAGCGGCGCTTTCTC
*
42994420 AAAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTTTCACAAACGCCGCTAA
1 AAAAACGCAGCTAAAGAACATGGTCTTTAGCGGCGC-TTTTTCACAAACGCCGCTAA
42994477 CATTAATAAA
Statistics
Matches: 199, Mismatches: 18, Indels: 23
0.83 0.08 0.10
Matches are distributed among these distances:
84 4 0.02
85 107 0.54
86 80 0.40
87 8 0.04
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (84 bp):
AAAAACGCAGCTAAAGAACATGGTCTTTAGCGGCGCTTTTTCACAAACGCCGCTAAAGAACATGG
TCTTTAGCGGCGCTTTCTC
Found at i:42995863 original size:2 final size:2
Alignment explanation
Indices: 42995856--42995883 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
42995846 CACAGGATGT
42995856 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
42995884 ATGAGCAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:42998631 original size:41 final size:41
Alignment explanation
Indices: 42998568--42999095 Score: 724
Period size: 41 Copynumber: 12.9 Consensus size: 41
42998558 AAACTCAACT
* *
42998568 TTTAGTGGCGCTTT-TCTATAAGCGCCGCTATTGCTTTGACC
1 TTTAGCGGCGCTTTCTC-ATAAGCGCCGCTATTGCTCTGACC
* * * * *
42998609 TTTAACGGCGCTTTTTTATAAGCGCCGCTATTGCTTTAACC
1 TTTAGCGGCGCTTTCTCATAAGCGCCGCTATTGCTCTGACC
*
42998650 TTTAGCGGCGCTTTATCATAAGCGCCGCTATTGCTCTGACC
1 TTTAGCGGCGCTTTCTCATAAGCGCCGCTATTGCTCTGACC
* * *
42998691 TTTAGCGGCG-TTTTTCTATAAGCGCCGCTATTGCTTTAACC
1 TTTAGCGGCGCTTTCTC-ATAAGCGCCGCTATTGCTCTGACC
* *
42998732 TTTAGCGACGCTTGCTCATAAGCGCCGCTATTGCTCTGACC
1 TTTAGCGGCGCTTTCTCATAAGCGCCGCTATTGCTCTGACC
*
42998773 TTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACC
1 TTTAGCGGCGCTTTCTCATAAGCGCCGCTATTGCTCTGACC
* * *
42998814 TTTAGCGGCG-TTTTTCTATAAGCGCCGCTATTGCTTTAACC
1 TTTAGCGGCGCTTTCTC-ATAAGCGCCGCTATTGCTCTGACC
* *
42998855 TTTAGCGACGCTTGCTCATAAGCGCCGCTATTGCTCTGACC
1 TTTAGCGGCGCTTTCTCATAAGCGCCGCTATTGCTCTGACC
* * *
42998896 TTTAGCGGCGTTTTCCCATAAGCGCCGCTATTGGTCTGACC
1 TTTAGCGGCGCTTTCTCATAAGCGCCGCTATTGCTCTGACC
* *
42998937 TTTAGCGGTGCTTTCTCATAAGCGCCGCTATTGCTTTGACC
1 TTTAGCGGCGCTTTCTCATAAGCGCCGCTATTGCTCTGACC
* *
42998978 TTTAGCGGCGCTTGCTCATAAGTGCCGCTATTGCTCTGACC
1 TTTAGCGGCGCTTTCTCATAAGCGCCGCTATTGCTCTGACC
* * *
42999019 TTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTC-CACT
1 TTTAGCGGCGCTTTCTCATAAGCGCCGCTATTGCTCTGACC
42999059 TTTAGCGGCGCTTT-TCTATAAGCGCCGCTATTGCTCT
1 TTTAGCGGCGCTTTCTC-ATAAGCGCCGCTATTGCTCT
42999096 AGTTTTTGTG
Statistics
Matches: 431, Mismatches: 49, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
39 1 0.00
40 44 0.10
41 377 0.87
42 9 0.02
ACGTcount: A:0.16, C:0.29, G:0.21, T:0.34
Consensus pattern (41 bp):
TTTAGCGGCGCTTTCTCATAAGCGCCGCTATTGCTCTGACC
Found at i:42998784 original size:24 final size:24
Alignment explanation
Indices: 42998752--42999030 Score: 66
Period size: 24 Copynumber: 13.4 Consensus size: 24
42998742 CTTGCTCATA
42998752 AGCGCCGCTATTGCTCTGACCTTT
1 AGCGCCGCTATTGCTCTGACCTTT
* * *
42998776 AGCGGCGC--TT--TC---CCATA
1 AGCGCCGCTATTGCTCTGACCTTT
42998793 AGCGCCGCTATTGCTCTGACCTTT
1 AGCGCCGCTATTGCTCTGACCTTT
* * *
42998817 AGCGGCG-T-TT-TTCT-A---TA
1 AGCGCCGCTATTGCTCTGACCTTT
* *
42998834 AGCGCCGCTATTGCTTTAACCTTT
1 AGCGCCGCTATTGCTCTGACCTTT
* *
42998858 AGCGACGC--TTGCTC--A---TA
1 AGCGCCGCTATTGCTCTGACCTTT
42998875 AGCGCCGCTATTGCTCTGACCTTT
1 AGCGCCGCTATTGCTCTGACCTTT
* * *
42998899 AGCGGCG-T-TT--TC---CCATA
1 AGCGCCGCTATTGCTCTGACCTTT
*
42998916 AGCGCCGCTATTGGTCTGACCTTT
1 AGCGCCGCTATTGCTCTGACCTTT
** *
42998940 AGCGGTGCT-TT-CTC--A---TA
1 AGCGCCGCTATTGCTCTGACCTTT
*
42998957 AGCGCCGCTATTGCTTTGACCTTT
1 AGCGCCGCTATTGCTCTGACCTTT
* *
42998981 AGCGGCGC--TTGCTC--A---TA
1 AGCGCCGCTATTGCTCTGACCTTT
*
42998998 AGTGCCGCTATTGCTCTGACCTTT
1 AGCGCCGCTATTGCTCTGACCTTT
*
42999022 AGCGGCGCT
1 AGCGCCGCT
42999031 TTCCCATAAG
Statistics
Matches: 173, Mismatches: 40, Indels: 84
0.58 0.13 0.28
Matches are distributed among these distances:
17 49 0.28
18 4 0.02
19 20 0.12
20 10 0.06
21 11 0.06
22 18 0.10
23 4 0.02
24 57 0.33
ACGTcount: A:0.15, C:0.30, G:0.23, T:0.32
Consensus pattern (24 bp):
AGCGCCGCTATTGCTCTGACCTTT
Found at i:42998793 original size:123 final size:123
Alignment explanation
Indices: 42998568--42999093 Score: 840
Period size: 123 Copynumber: 4.3 Consensus size: 123
42998558 AAACTCAACT
* * * * ** *
42998568 TTTAGTGGCGCTTTTCTATAAGCGCCGCTATTGCTTTGACCTTTAACGGCGCTTTTTTATAAGCG
1 TTTAGCGGCGCTTTTCTATAAGCGCCGCTATTGCTTTAACCTTTAGCGACGCTTGCTCATAAGCG
* * **
42998633 CCGCTATTGCTTTAACCTTTAGCGGCGCTTTATCATAAGCGCCGCTATTGCTCTGACC
66 CCGCTATTGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACC
*
42998691 TTTAGCGGCGTTTTTCTATAAGCGCCGCTATTGCTTTAACCTTTAGCGACGCTTGCTCATAAGCG
1 TTTAGCGGCGCTTTTCTATAAGCGCCGCTATTGCTTTAACCTTTAGCGACGCTTGCTCATAAGCG
42998756 CCGCTATTGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACC
66 CCGCTATTGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACC
*
42998814 TTTAGCGGCGTTTTTCTATAAGCGCCGCTATTGCTTTAACCTTTAGCGACGCTTGCTCATAAGCG
1 TTTAGCGGCGCTTTTCTATAAGCGCCGCTATTGCTTTAACCTTTAGCGACGCTTGCTCATAAGCG
* *
42998879 CCGCTATTGCTCTGACCTTTAGCGGCGTTTTCCCATAAGCGCCGCTATTGGTCTGACC
66 CCGCTATTGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACC
* * * *
42998937 TTTAGCGGTGC-TTTCTCATAAGCGCCGCTATTGCTTTGACCTTTAGCGGCGCTTGCTCATAAGT
1 TTTAGCGGCGCTTTTCT-ATAAGCGCCGCTATTGCTTTAACCTTTAGCGACGCTTGCTCATAAGC
* *
42999001 GCCGCTATTGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTC-CACT
65 GCCGCTATTGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACC
42999059 TTTAGCGGCGCTTTTCTATAAGCGCCGCTATTGCT
1 TTTAGCGGCGCTTTTCTATAAGCGCCGCTATTGCT
42999094 CTAGTTTTTG
Statistics
Matches: 377, Mismatches: 24, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
122 35 0.09
123 342 0.91
ACGTcount: A:0.16, C:0.29, G:0.21, T:0.34
Consensus pattern (123 bp):
TTTAGCGGCGCTTTTCTATAAGCGCCGCTATTGCTTTAACCTTTAGCGACGCTTGCTCATAAGCG
CCGCTATTGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACC
Found at i:42999908 original size:43 final size:43
Alignment explanation
Indices: 42999813--43000038 Score: 215
Period size: 43 Copynumber: 5.3 Consensus size: 43
42999803 TTTGTTAATA
* * * **
42999813 TTAGTGGCGTTTGTGGG-AAAGTGCTGCTAAAGCCCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGAACATGTTCT
* * * * * *
42999855 TTAGTGGCGTTTGTGGAAAAAGCACCGCTGAAGACCGTGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGAACATGTTCT
* * * *
42999898 TTAGCGGCGTTTGTAGTAAAAGCGCCGTTAAAGACCATTGTT-T
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGAACA-TGTTCT
* * * *
42999941 TTAGCGGCATTTATGGGGAAAA-CGCCGCTAAAAAACATGGTCT
1 TTAGCGGCGTTTGT-GGGAAAAGCGCCGCTAAAGAACATGTTCT
* *
42999984 TTAGCGGCGTTTGTGGGGAAAGTGCCGCTAAAGAACATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGAACATGTTCT
*
43000027 ATAGCGGCGTTT
1 TTAGCGGCGTTT
43000039 TCCATCATAA
Statistics
Matches: 150, Mismatches: 29, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
42 25 0.17
43 116 0.77
44 9 0.06
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.29
Consensus pattern (43 bp):
TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGAACATGTTCT
Found at i:43005204 original size:21 final size:22
Alignment explanation
Indices: 43005180--43005231 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
43005170 TGTCAAAAAA
*
43005180 TTATA-CTTTTTAAAAATTAAT
1 TTATATCTTTTTAAAAAATAAT
*
43005201 TTATATTTTTTTTAAAAAATAAT
1 TTATA-TCTTTTTAAAAAATAAT
*
43005224 TTACATCT
1 TTATATCT
43005232 GTCATGTACC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
21 5 0.20
22 2 0.08
23 18 0.72
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (22 bp):
TTATATCTTTTTAAAAAATAAT
Found at i:43008570 original size:321 final size:322
Alignment explanation
Indices: 43007984--43008629 Score: 1195
Period size: 321 Copynumber: 2.0 Consensus size: 322
43007974 GGGTATTCGT
43007984 ATTTAATACTGATATTTAAAAAATTATACCCGTAAATGATACGAATATCAGTATTAAATACGAAT
1 ATTTAATACTGATATTTAAAAAATTATACCCGTAAATGATACGAATATCAGTATTAAATACGAAT
* *
43008049 ATGTTAACCTATATTATGTAAGTGAATGTTCAATATGAATTTATTAACATGTAAATATATGAGAT
66 ATGTTAACCTATATTATGTAAGTGAATATTCAATACGAATTTATTAACATGTAAATATATGAGAT
* *
43008114 ATTTAATACTATATGTTAAGTATTTTTAGAATTGATATGAATTTATCTAAAAATACTTAATTTAT
131 ATTTAATACTATATGTTAAGTATTTTTAGAACTGATACGAATTTATCTAAAAATACTTAATTTAT
* * *
43008179 TTTTAGCTGTTAAAATTCGTATAAGTTCTTAAATGAGATATTCACTTACATAATATAGGTTTAGG
196 TTTCAGCTATTAAAATTCGTATAAGTTCTTAAATGAGATATTCACTTACATAATATAGGTTTAAG
43008244 TATTGAATATCTCATATATTAACATGTAAATATAATAAACCCGTTTAAAATCATATTAATAA
261 TATTGAATATCTCATATATTAACATGTAAATATAATAAACCCGTTTAAAATCATATTAATAA
43008306 ATTTAATACTGATATTTAAAAAATTATACCCGTAAATGATACGAATATCAGTATTAAATAC-AAT
1 ATTTAATACTGATATTTAAAAAATTATACCCGTAAATGATACGAATATCAGTATTAAATACGAAT
43008370 ATGTTAACCTATATTATGTAAGTGAATATTCAATACGAATTTATTAACATGTAAATATATGAGAT
66 ATGTTAACCTATATTATGTAAGTGAATATTCAATACGAATTTATTAACATGTAAATATATGAGAT
*
43008435 ATTTAATACTATATGTTAAGTATTTTTAGAACTGATGCGAATTTATCTAAAAATACTTAATTTAT
131 ATTTAATACTATATGTTAAGTATTTTTAGAACTGATACGAATTTATCTAAAAATACTTAATTTAT
* *
43008500 TTTCCGCTATTAAAATTCGTATCAGTTCTTAAATGAGATATTCACTTACATAATATAGGTTTAAG
196 TTTCAGCTATTAAAATTCGTATAAGTTCTTAAATGAGATATTCACTTACATAATATAGGTTTAAG
43008565 TATTGAATATCTCATATATTAACATGTAAATATAATAAACCCGTTTAAAATCATATTAATAA
261 TATTGAATATCTCATATATTAACATGTAAATATAATAAACCCGTTTAAAATCATATTAATAA
43008627 ATT
1 ATT
43008630 AAAACAAAAA
Statistics
Matches: 314, Mismatches: 10, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
321 253 0.81
322 61 0.19
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.40
Consensus pattern (322 bp):
ATTTAATACTGATATTTAAAAAATTATACCCGTAAATGATACGAATATCAGTATTAAATACGAAT
ATGTTAACCTATATTATGTAAGTGAATATTCAATACGAATTTATTAACATGTAAATATATGAGAT
ATTTAATACTATATGTTAAGTATTTTTAGAACTGATACGAATTTATCTAAAAATACTTAATTTAT
TTTCAGCTATTAAAATTCGTATAAGTTCTTAAATGAGATATTCACTTACATAATATAGGTTTAAG
TATTGAATATCTCATATATTAACATGTAAATATAATAAACCCGTTTAAAATCATATTAATAA
Found at i:43012973 original size:24 final size:24
Alignment explanation
Indices: 43012940--43012990 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
43012930 AGAAATAATC
* *
43012940 TTTCAGTTAAACTTTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
43012964 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
43012988 TTT
1 TTT
43012991 GAGTCAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.10, G:0.10, T:0.59
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:43012999 original size:24 final size:24
Alignment explanation
Indices: 43012948--43013002 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
43012938 TCTTTCAGTT
* *
43012948 AAACTTTGTTTATTTGTTTCAATT
1 AAACTCTGTTTATTTGTTTCAATC
* *
43012972 AAACTCTGTTTATTTGTTTGAGTC
1 AAACTCTGTTTATTTGTTTCAATC
43012996 AAACTCT
1 AAACTCT
43013003 TATTACTCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.25, C:0.13, G:0.11, T:0.51
Consensus pattern (24 bp):
AAACTCTGTTTATTTGTTTCAATC
Found at i:43013396 original size:20 final size:20
Alignment explanation
Indices: 43013371--43013410 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
43013361 ATATAACCAA
43013371 TTTAACGAAAGATTCATACT
1 TTTAACGAAAGATTCATACT
43013391 TTTAACGAAAGATTCATACT
1 TTTAACGAAAGATTCATACT
43013411 AACACGCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (20 bp):
TTTAACGAAAGATTCATACT
Found at i:43013795 original size:13 final size:14
Alignment explanation
Indices: 43013761--43013810 Score: 59
Period size: 13 Copynumber: 3.6 Consensus size: 14
43013751 GAATGAAAGT
43013761 AAAAGACAAGAAACG-
1 AAAAGA-AAG-AACGA
43013776 AAAAGAAAGAAC-A
1 AAAAGAAAGAACGA
*
43013789 GAAAGAAAGAACGA
1 AAAAGAAAGAACGA
43013803 AAAAGAAA
1 AAAAGAAA
43013811 CGTTCAAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 14 0.45
14 11 0.35
15 6 0.19
ACGTcount: A:0.72, C:0.08, G:0.20, T:0.00
Consensus pattern (14 bp):
AAAAGAAAGAACGA
Found at i:43018917 original size:38 final size:38
Alignment explanation
Indices: 43018866--43018942 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
43018856 TCGATGTTAC
43018866 CTACCAAATAAAAAGCCTGATCAGAAAGAACCCTTAAG
1 CTACCAAATAAAAAGCCTGATCAGAAAGAACCCTTAAG
*
43018904 CTACCAAATAAAAAGCCTGTTCAGAAAGAACCCTTAAG
1 CTACCAAATAAAAAGCCTGATCAGAAAGAACCCTTAAG
43018942 C
1 C
43018943 AGCTAAGTCT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.45, C:0.25, G:0.13, T:0.17
Consensus pattern (38 bp):
CTACCAAATAAAAAGCCTGATCAGAAAGAACCCTTAAG
Found at i:43021840 original size:10 final size:9
Alignment explanation
Indices: 43021814--43021904 Score: 51
Period size: 9 Copynumber: 9.8 Consensus size: 9
43021804 CAATAAAGGA
*
43021814 TATAAATAT
1 TATAAAAAT
*
43021823 TAT-TAAAT
1 TATAAAAAT
43021831 TAATAAAAAT
1 T-ATAAAAAT
* *
43021841 TAGAAAAAAA
1 TA-TAAAAAT
43021851 TATAAAAAT
1 TATAAAAAT
*
43021860 CGTA-AAAAAA
1 --TATAAAAAT
43021870 TATAAAAAT
1 TATAAAAAT
* *
43021879 TGTAAAATTT
1 TATAAAA-AT
43021889 TATAAAAAT
1 TATAAAAAT
*
43021898 CATAAAA
1 TATAAAA
43021905 GAATTATAAT
Statistics
Matches: 61, Mismatches: 14, Indels: 14
0.69 0.16 0.16
Matches are distributed among these distances:
8 6 0.10
9 29 0.48
10 24 0.39
11 2 0.03
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (9 bp):
TATAAAAAT
Found at i:43021857 original size:19 final size:20
Alignment explanation
Indices: 43021833--43021885 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
43021823 TATTAAATTA
43021833 ATAAAAATTAG-AAAAAAAT
1 ATAAAAATTAGTAAAAAAAT
*
43021852 ATAAAAA-TCGTAAAAAAAT
1 ATAAAAATTAGTAAAAAAAT
43021871 ATAAAAATT-GTAAAA
1 ATAAAAATTAGTAAAA
43021886 TTTTATAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 2 0.06
19 28 0.90
20 1 0.03
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.23
Consensus pattern (20 bp):
ATAAAAATTAGTAAAAAAAT
Found at i:43021892 original size:19 final size:19
Alignment explanation
Indices: 43021844--43021904 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 19
43021834 TAAAAATTAG
43021844 AAAAAAATATAAAAATCGT
1 AAAAAAATATAAAAATCGT
*
43021863 AAAAAAATATAAAAATTGT
1 AAAAAAATATAAAAATCGT
*** *
43021882 AAAATTTTATAAAAATCAT
1 AAAAAAATATAAAAATCGT
43021901 AAAA
1 AAAA
43021905 GAATTATAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.26
Consensus pattern (19 bp):
AAAAAAATATAAAAATCGT
Found at i:43022048 original size:12 final size:12
Alignment explanation
Indices: 43022031--43022055 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43022021 AAAAGAAGCA
43022031 TTTTATAATTTT
1 TTTTATAATTTT
43022043 TTTTATAATTTT
1 TTTTATAATTTT
43022055 T
1 T
43022056 ATTGATTTTT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTATAATTTT
Found at i:43022250 original size:17 final size:18
Alignment explanation
Indices: 43022224--43022274 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
43022214 TTCTACAAAA
*
43022224 TTTTATAATTTATTTA-T
1 TTTTAAAATTTATTTATT
* *
43022241 TTTTAAAATTTAATAATT
1 TTTTAAAATTTATTTATT
43022259 TTTCTAAAATTTATTT
1 TTT-TAAAATTTATTT
43022275 TTTATAACTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
17 13 0.48
18 4 0.15
19 10 0.37
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTAAAATTTATTTATT
Found at i:43022277 original size:17 final size:16
Alignment explanation
Indices: 43022224--43022277 Score: 54
Period size: 19 Copynumber: 3.1 Consensus size: 16
43022214 TTCTACAAAA
*
43022224 TTTTATAATTTATTTAT
1 TTTTAAAATTTATTT-T
43022241 TTTTAAAATTTAATAATTT
1 TTTTAAAATTT-AT--TTT
*
43022260 TTCTAAAATTTATTTT
1 TTTTAAAATTTATTTT
43022276 TT
1 TT
43022278 ATAACTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
16 5 0.16
17 10 0.31
18 4 0.12
19 11 0.34
20 2 0.06
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTAAAATTTATTTT
Found at i:43022467 original size:88 final size:87
Alignment explanation
Indices: 43022313--43022512 Score: 226
Period size: 88 Copynumber: 2.3 Consensus size: 87
43022303 GAGCAAGGGT
* * * *
43022313 TTAATTGCTTTTTTGAAAAATTTTGATGGTCTTTTTTATACATTTTGAAAGTTCAAATATCTAAT
1 TTAATTACTTTTTTGAAAAAGTTTGAAGGCCTTTTTTATACATTTTGAAAGTTCAAATATCTAAT
*
43022378 TGAGTGGAGAAAAAAACAGAGGC
66 TGAGTGCA-AAAAAAACAGAGGC
* * * * *
43022401 TTAATTACTTTTTTTAATAAGTTTGAAGGCCTTTTTTATGCATTTTGAAAGTTCAAGT-GCTCAA
1 TTAATTACTTTTTTGAAAAAGTTTGAAGGCCTTTTTTATACATTTTGAAAGTTCAAATATCT-AA
* *
43022465 TTGAGTGC-AAAAAAA-AGTGAC
65 TTGAGTGCAAAAAAAACAGAGGC
* *
43022486 TTAATTGCTTTTTTTGAGAAAGTTTGA
1 TTAATTAC-TTTTTTGAAAAAGTTTGA
43022513 GAGCTTTTAC
Statistics
Matches: 94, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
85 11 0.12
86 22 0.23
87 2 0.02
88 59 0.63
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.41
Consensus pattern (87 bp):
TTAATTACTTTTTTGAAAAAGTTTGAAGGCCTTTTTTATACATTTTGAAAGTTCAAATATCTAAT
TGAGTGCAAAAAAAACAGAGGC
Found at i:43027788 original size:21 final size:22
Alignment explanation
Indices: 43027752--43027798 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
43027742 TGTCAAAAAA
43027752 TTATACTTTTT-AAAAATTAAT
1 TTATACTTTTTAAAAAATTAAT
43027773 TTATA-TTTTTAAAAAAAATTAAT
1 TTATACTTTTT--AAAAAATTAAT
43027796 TTA
1 TTA
43027799 CATCTGTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.22
21 5 0.22
23 13 0.57
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
TTATACTTTTTAAAAAATTAAT
Found at i:43028795 original size:15 final size:16
Alignment explanation
Indices: 43028759--43028796 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
43028749 TAATAAAAAT
*
43028759 ATAATTTATTATTTTA
1 ATAATTTATTATCTTA
*
43028775 ATAATTTA-TATCTTC
1 ATAATTTATTATCTTA
43028790 ATAATTT
1 ATAATTT
43028797 TTAAGGGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (16 bp):
ATAATTTATTATCTTA
Found at i:43037903 original size:27 final size:27
Alignment explanation
Indices: 43037873--43037986 Score: 99
Period size: 28 Copynumber: 4.1 Consensus size: 27
43037863 TAAAAATAAT
* *
43037873 AAATTTGGGCCCTTAAAAACTTAAAAA
1 AAATTTGGACCCTTAAAAATTTAAAAA
* *
43037900 AAATTT-AAGCCCTTAAAAGTTTATAAAA
1 AAATTTGGA-CCCTTAAAAATTTA-AAAA
* * *
43037928 AAATTT-TAACCTATAAAAGTTTAAAAAA
1 AAATTTGGACCCT-TAAAAATTT-AAAAA
43037956 AAATTTGGACCCATTAAAAA-TTAAAAA
1 AAATTTGGACCC-TTAAAAATTTAAAAA
43037983 AAAT
1 AAAT
43037987 AAAAATTTAA
Statistics
Matches: 72, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
27 30 0.42
28 32 0.44
29 9 0.12
30 1 0.01
ACGTcount: A:0.54, C:0.11, G:0.07, T:0.29
Consensus pattern (27 bp):
AAATTTGGACCCTTAAAAATTTAAAAA
Found at i:43049804 original size:58 final size:58
Alignment explanation
Indices: 43049716--43049861 Score: 174
Period size: 58 Copynumber: 2.5 Consensus size: 58
43049706 ATATATTATA
* *
43049716 ATTTTTACT-AATTCATATTTTAATAATAATTATATTAAAA-AT-ATT-ATTAAATTACAT
1 ATTTTTATTAAATT-ATA-TTTAATAATAATTATATTAAAATATAATTAAATAAATTA-AT
* *
43049773 ATTATTTTATTAAATTGTATTTAATAATAATTATGTTAAAATATAATTAAATAAATTAAT
1 A-T-TTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATAAATTAAT
*
43049833 ATTTTTATTCAATTATATTTAATAATAAT
1 ATTTTTATTAAATTATATTTAATAATAAT
43049862 CATTAAAATT
Statistics
Matches: 77, Mismatches: 6, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
57 1 0.01
58 47 0.61
59 11 0.14
60 10 0.13
61 8 0.10
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (58 bp):
ATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATAAATTAAT
Found at i:43050000 original size:39 final size:44
Alignment explanation
Indices: 43049944--43050049 Score: 116
Period size: 46 Copynumber: 2.5 Consensus size: 44
43049934 TTTTCTTATG
*
43049944 TTATTACAGCATC-ATTCCATT-CAACCAA-ACACAA-GAA-TA-
1 TTATTACAGC-TCTATTCCATTCCAACCAACAAACAATGAATTAC
*
43049983 TTATTACAGCTCTATTCCATTCCAATCAACCAAACAATTGAATTAC
1 TTATTACAGCTCTATTCCATTCCAACCAA-CAAACAA-TGAATTAC
*
43050029 TGATTACAGCTCTATTCCATT
1 TTATTACAGCTCTATTCCATT
43050050 ACAGCTATAT
Statistics
Matches: 56, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
38 2 0.04
39 18 0.32
40 6 0.11
42 5 0.09
44 3 0.05
45 2 0.04
46 20 0.36
ACGTcount: A:0.37, C:0.25, G:0.06, T:0.32
Consensus pattern (44 bp):
TTATTACAGCTCTATTCCATTCCAACCAACAAACAATGAATTAC
Found at i:43050048 original size:46 final size:44
Alignment explanation
Indices: 43049956--43050049 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
43049946 ATTACAGCAT
* *
43049956 CATTCCATTCAACCAAACACAAGAATATTATTACAGCTCTATTC
1 CATTCCAATCAACCAAACACAAGAATATGATTACAGCTCTATTC
*
43050000 CATTCCAATCAACCAAACA-ATTGAATTACTGATTACAGCTCTATTC
1 CATTCCAATCAACCAAACACA-AGAA-TA-TGATTACAGCTCTATTC
43050046 CATT
1 CATT
43050050 ACAGCTATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 1 0.02
44 21 0.48
45 2 0.05
46 20 0.45
ACGTcount: A:0.37, C:0.27, G:0.05, T:0.31
Consensus pattern (44 bp):
CATTCCAATCAACCAAACACAAGAATATGATTACAGCTCTATTC
Found at i:43050052 original size:16 final size:16
Alignment explanation
Indices: 43050031--43050086 Score: 94
Period size: 16 Copynumber: 3.5 Consensus size: 16
43050021 TGAATTACTG
43050031 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
43050047 ATTACAGCTATATTCC
1 ATTACAGCTCTATTCC
*
43050063 ATTACACCTCTATTCC
1 ATTACAGCTCTATTCC
43050079 ATTACAGC
1 ATTACAGC
43050087 GAACCAAACG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.29, C:0.30, G:0.05, T:0.36
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:43050284 original size:24 final size:24
Alignment explanation
Indices: 43050257--43050319 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 24
43050247 TATATTATTT
*
43050257 TTTTTTAAAATTTATAAT-GA-TA
1 TTTTTTAAAATTTATAATACATTA
* *
43050279 TATTTTATAATTTTATAATACATTA
1 TTTTTTA-AAATTTATAATACATTA
*
43050304 TTTTTAAAAATTTATA
1 TTTTTTAAAATTTATA
43050320 TATTATCAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
22 6 0.19
23 10 0.31
24 9 0.28
25 7 0.22
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (24 bp):
TTTTTTAAAATTTATAATACATTA
Found at i:43051458 original size:14 final size:13
Alignment explanation
Indices: 43051439--43051480 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
43051429 TTTAAAAGTT
43051439 TTTTTCAAAATCAC
1 TTTTTCAAAA-CAC
43051453 TTTTTCAAAACAC
1 TTTTTCAAAACAC
43051466 TTTTT-AAAAGCAC
1 TTTTTCAAAA-CAC
43051479 TT
1 TT
43051481 CTCAAAAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 4 0.15
13 13 0.48
14 10 0.37
ACGTcount: A:0.36, C:0.19, G:0.02, T:0.43
Consensus pattern (13 bp):
TTTTTCAAAACAC
Found at i:43051488 original size:13 final size:13
Alignment explanation
Indices: 43051440--43051488 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
43051430 TTAAAAGTTT
*
43051440 TTTTCAAAATCAC
1 TTTTCAAAAGCAC
43051453 TTTTTCAAAA-CAC
1 -TTTTCAAAAGCAC
*
43051466 TTTTTAAAAGCAC
1 TTTTCAAAAGCAC
*
43051479 TTCTCAAAAG
1 TTTTCAAAAG
43051489 TAATATTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
12 8 0.26
13 14 0.45
14 9 0.29
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.37
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:43052991 original size:220 final size:220
Alignment explanation
Indices: 43052609--43053036 Score: 802
Period size: 220 Copynumber: 1.9 Consensus size: 220
43052599 AAAATCGTAC
43052609 GTGACAAACGATCGTGTGGTAGACTGTGTAACTAACTGTTTTCTGATTAGAGACACACGGGCATG
1 GTGACAAACGATCGTGTGGTAGACTGTGTAACTAACTGTTTTCTGATTAGAGACACACGGGCATG
**
43052674 TGCTAAATCGTGTGTGGAAAAAATAAGGTGCAATGGTCACACGGGCCTGTGTCCAGGCCGTATAA
66 TGCTAAATCGTGTGTGGAAAAAATAAGGTGCAATGGTCACACGAACCTGTGTCCAGGCCGTATAA
* *
43052739 CTCATTGTTTTGAATATTTGGACATACGGACACTCACACGACCGTGTATCAAACCGTGTGGAGCC
131 CTCACTGTTTTGAATATTTGGACATACGGACACTCACACGACCATGTATCAAACCGTGTGGAGCC
43052804 ACACGGATGTGTGTGCAATCCATGT
196 ACACGGATGTGTGTGCAATCCATGT
*
43052829 GTGACAAACGATCGTGTGGTAGACTGTGTAACTAACTGTTTTCTGATTAGAGACACACGGGCGTG
1 GTGACAAACGATCGTGTGGTAGACTGTGTAACTAACTGTTTTCTGATTAGAGACACACGGGCATG
*
43052894 TGCTAAATCGTGTGTGGAAAAAATAAGGTGCAATGGTCACACGAACCTGTGTCCAGGCCGTGTAA
66 TGCTAAATCGTGTGTGGAAAAAATAAGGTGCAATGGTCACACGAACCTGTGTCCAGGCCGTATAA
43052959 CTCACTGTTTTGAATATTTGGACATACGGACACTCACACGACCATGTATCAAACCGTGTGGAGCC
131 CTCACTGTTTTGAATATTTGGACATACGGACACTCACACGACCATGTATCAAACCGTGTGGAGCC
43053024 ACACGGATGTGTG
196 ACACGGATGTGTG
43053037 AGCCTGAAAA
Statistics
Matches: 202, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
220 202 1.00
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (220 bp):
GTGACAAACGATCGTGTGGTAGACTGTGTAACTAACTGTTTTCTGATTAGAGACACACGGGCATG
TGCTAAATCGTGTGTGGAAAAAATAAGGTGCAATGGTCACACGAACCTGTGTCCAGGCCGTATAA
CTCACTGTTTTGAATATTTGGACATACGGACACTCACACGACCATGTATCAAACCGTGTGGAGCC
ACACGGATGTGTGTGCAATCCATGT
Found at i:43054531 original size:18 final size:20
Alignment explanation
Indices: 43054500--43054538 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
43054490 AATAAAACAT
*
43054500 ATTTTATGATAATT-TTAAA
1 ATTTAATGATAATTATTAAA
43054519 ATTTAATGA-AATTATTAAA
1 ATTTAATGATAATTATTAAA
43054538 A
1 A
43054539 AATTAATCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (20 bp):
ATTTAATGATAATTATTAAA
Found at i:43054591 original size:21 final size:21
Alignment explanation
Indices: 43054567--43054629 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
43054557 GAAAATTTAA
43054567 TTATAATGATAATTTTTATAT
1 TTATAATGATAATTTTTATAT
* *
43054588 TTATAATAAT-ATTATT-TAT
1 TTATAATGATAATTTTTATAT
* *
43054607 CTCT-ATGATAATTTTATATAT
1 TTATAATGATAATTTT-TATAT
43054628 TT
1 TT
43054630 GTATTTTTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
18 4 0.12
19 9 0.28
20 6 0.19
21 13 0.41
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (21 bp):
TTATAATGATAATTTTTATAT
Found at i:43057114 original size:43 final size:43
Alignment explanation
Indices: 43057031--43057135 Score: 111
Period size: 43 Copynumber: 2.4 Consensus size: 43
43057021 TACATATCTG
** * ** * * *
43057031 AACTTAAACTAAAATAAATTTGGACAGAGTCTACACATGGTTA
1 AACTTAAACTAAAATAAATTTAAACAAAACCCACAAATGGTGA
*
43057074 AACTTAAACTAGAATAAATTTAAACAAAACCCACAAATGGTGA
1 AACTTAAACTAAAATAAATTTAAACAAAACCCACAAATGGTGA
* *
43057117 AACTTGAACCAAAATAAAT
1 AACTTAAACTAAAATAAAT
43057136 ATGGAGAGAA
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.50, C:0.15, G:0.10, T:0.24
Consensus pattern (43 bp):
AACTTAAACTAAAATAAATTTAAACAAAACCCACAAATGGTGA
Found at i:43059639 original size:21 final size:22
Alignment explanation
Indices: 43059615--43059659 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
43059605 AAGGCAAAGT
43059615 AAAATCATT-TAAAAAAAAAAA
1 AAAATCATTGTAAAAAAAAAAA
* * *
43059636 AAAATCTTTGTAAGAAAAATAA
1 AAAATCATTGTAAAAAAAAAAA
43059658 AA
1 AA
43059660 CACAAAGTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.22
Consensus pattern (22 bp):
AAAATCATTGTAAAAAAAAAAA
Found at i:43060733 original size:70 final size:67
Alignment explanation
Indices: 43060640--43060772 Score: 185
Period size: 70 Copynumber: 1.9 Consensus size: 67
43060630 TCCGAATAAG
* ** *
43060640 AAAAGGTAAAACTACGTCGTTTTGATAAATGTTTACTCTTTCTAAAGTTAAAAGTCAAAACCATT
1 AAAAGGTAAAACTACGTCATTTTGATAAATGTTTA-TCCAT-T-AAGTTAAAAGGCAAAACCATT
43060705 AAGTT
63 AAGTT
* *
43060710 AAAAGGTAAAATTATGTCATTTTGATAAATGTTTATCCATTAAGTTAAAAGGCAAAACCATTA
1 AAAAGGTAAAACTACGTCATTTTGATAAATGTTTATCCATTAAGTTAAAAGGCAAAACCATTA
43060773 TATTATTTAT
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
67 21 0.37
68 1 0.02
69 3 0.05
70 32 0.56
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (67 bp):
AAAAGGTAAAACTACGTCATTTTGATAAATGTTTATCCATTAAGTTAAAAGGCAAAACCATTAAG
TT
Found at i:43062909 original size:23 final size:23
Alignment explanation
Indices: 43062835--43063025 Score: 123
Period size: 23 Copynumber: 8.5 Consensus size: 23
43062825 TAAACGGAAC
* * *
43062835 AAACAGAGAGTAC-CGAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* *
43062857 GAACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
43062879 GGGCAACAGAGAGCACACAAAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
*
43062905 AAACAGAGAGTACACAAA--G-T
1 AAACAGAGAGCACACAAAGTGCT
* *
43062925 --AC--TGAGCACACAAAGTGTT
1 AAACAGAGAGCACACAAAGTGCT
* *
43062944 AATCAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
43062967 AATAACAGAGAGCACGA-GACGTGCT
1 -A-AACAGAGAGCAC-ACAAAGTGCT
*
43062992 AAACAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
43063015 AATCAGAGAGC
1 AAACAGAGAGC
43063026 GCGCTAGTGT
Statistics
Matches: 131, Mismatches: 22, Indels: 31
0.71 0.12 0.17
Matches are distributed among these distances:
16 10 0.08
18 3 0.02
19 1 0.01
20 1 0.01
21 2 0.02
22 18 0.14
23 57 0.44
24 2 0.02
25 29 0.22
26 8 0.06
ACGTcount: A:0.42, C:0.21, G:0.25, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:43062975 original size:25 final size:23
Alignment explanation
Indices: 43062928--43063025 Score: 126
Period size: 23 Copynumber: 4.2 Consensus size: 23
43062918 ACAAAGTACT
* *
43062928 GAGCACACAAAGTGTTAATCAGA
1 GAGCACACACAGTGCTAATCAGA
43062951 GAGCACACACAGTGCTAATAACAGA
1 GAGCACACACAGTGCTAAT--CAGA
* *
43062976 GAGCACGAGAC-GTGCTAAACAGA
1 GAGCAC-ACACAGTGCTAATCAGA
43062999 GAGCACACACAGTGCTAATCAGA
1 GAGCACACACAGTGCTAATCAGA
43063022 GAGC
1 GAGC
43063026 GCGCTAGTGT
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
22 3 0.05
23 42 0.65
25 17 0.26
26 3 0.05
ACGTcount: A:0.41, C:0.22, G:0.24, T:0.12
Consensus pattern (23 bp):
GAGCACACACAGTGCTAATCAGA
Found at i:43070144 original size:23 final size:23
Alignment explanation
Indices: 43070110--43070199 Score: 78
Period size: 23 Copynumber: 3.8 Consensus size: 23
43070100 GGAATACTTG
*
43070110 CGTGCCTACTGTTTAGCAC-GTTT
1 CGTGCCT-CTGTTTAGCACTGTGT
*
43070133 CGTGCCATCTGTTCAGCACTGTGT
1 CGTGCC-TCTGTTTAGCACTGTGT
* *
43070157 -GTGCTTCTGTTTAGCACTTTGT
1 CGTGCCTCTGTTTAGCACTGTGT
43070179 -GTGCCTACTGTTGTCAGCACT
1 CGTGCCT-CTGTT-T-AGCACT
43070200 TATATACCCT
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
22 20 0.36
23 25 0.45
24 5 0.09
25 6 0.11
ACGTcount: A:0.12, C:0.26, G:0.23, T:0.39
Consensus pattern (23 bp):
CGTGCCTCTGTTTAGCACTGTGT
Found at i:43070172 original size:22 final size:22
Alignment explanation
Indices: 43070118--43070182 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
43070108 TGCGTGCCTA
*
43070118 CTGTTTAGCAC-GTTTCGTGCCAT
1 CTGTTTAGCACTGTGT-GTG-CAT
* *
43070141 CTGTTCAGCACTGTGTGTGCTT
1 CTGTTTAGCACTGTGTGTGCAT
*
43070163 CTGTTTAGCACTTTGTGTGC
1 CTGTTTAGCACTGTGTGTGC
43070183 CTACTGTTGT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
22 20 0.56
23 13 0.36
24 3 0.08
ACGTcount: A:0.11, C:0.23, G:0.25, T:0.42
Consensus pattern (22 bp):
CTGTTTAGCACTGTGTGTGCAT
Found at i:43071439 original size:90 final size:90
Alignment explanation
Indices: 43071286--43071465 Score: 261
Period size: 90 Copynumber: 2.0 Consensus size: 90
43071276 TGCGTAGCAT
* * * *
43071286 TAGTTAATTAAACTGACAAACAATAAGTGAGCTCAACTCTAATTAGATTAACCAACGGTTTTGCG
1 TAGTTAATTAAACTGACAAACAATAAGTAAGCCCAACTCTAATTAGATTAACCAACGATTTTGCA
* * **
43071351 TCCAACTCTAGTCGGATAAATCGAC
66 CCCAACGCTAGTCAAATAAATCGAC
* * *
43071376 TAGTTAATTAAACTGACAAACAATAAGTAAGCCCAACTCTAGTTGGATTAACTAACGATTTTGCA
1 TAGTTAATTAAACTGACAAACAATAAGTAAGCCCAACTCTAATTAGATTAACCAACGATTTTGCA
43071441 CCCAACGCTAGTCAAATAAATCGAC
66 CCCAACGCTAGTCAAATAAATCGAC
43071466 GATATGTGCC
Statistics
Matches: 79, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
90 79 1.00
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (90 bp):
TAGTTAATTAAACTGACAAACAATAAGTAAGCCCAACTCTAATTAGATTAACCAACGATTTTGCA
CCCAACGCTAGTCAAATAAATCGAC
Found at i:43076099 original size:18 final size:19
Alignment explanation
Indices: 43076058--43076095 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
43076048 TATTAATGAA
43076058 TATTTTATATAATTGATAAT
1 TATTTTATAT-ATTGATAAT
43076078 TATTTTATAT-TTGA-AAT
1 TATTTTATATATTGATAAT
43076095 T
1 T
43076096 TATTCAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.22
18 4 0.22
20 10 0.56
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (19 bp):
TATTTTATATATTGATAAT
Found at i:43077559 original size:41 final size:41
Alignment explanation
Indices: 43077485--43077715 Score: 291
Period size: 41 Copynumber: 5.6 Consensus size: 41
43077475 TATAGATTAA
* * * * *
43077485 CTAATGCTTTGACCTTGAGCGACACTTCTTCATAAGCGCCG
1 CTAATGCTCTGACCTTTAGCGGCGCTTCCTCATAAGCGCCG
*
43077526 CTAATGCTCTGACCTTTAGCGGCGCCTCCTCATAAGCGCCG
1 CTAATGCTCTGACCTTTAGCGGCGCTTCCTCATAAGCGCCG
* * * *
43077567 TTAATGCTCTGACCTTTAGCGGCGTTTCCTCATTAGAGCCG
1 CTAATGCTCTGACCTTTAGCGGCGCTTCCTCATAAGCGCCG
* * * **
43077608 CTAATGCTCTGACTTTTAGCGGTGCTTTCTCATAAGCGTAG
1 CTAATGCTCTGACCTTTAGCGGCGCTTCCTCATAAGCGCCG
* * *
43077649 CTAATGCTCTAACCTTTAGCGGCGTTTCCTCATAAGCGTCG
1 CTAATGCTCTGACCTTTAGCGGCGCTTCCTCATAAGCGCCG
*
43077690 CCAATGCTCTGACCTTTAGCGGCGCT
1 CTAATGCTCTGACCTTTAGCGGCGCT
43077716 AACGCTCTGA
Statistics
Matches: 161, Mismatches: 29, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 161 1.00
ACGTcount: A:0.19, C:0.29, G:0.21, T:0.31
Consensus pattern (41 bp):
CTAATGCTCTGACCTTTAGCGGCGCTTCCTCATAAGCGCCG
Found at i:43077764 original size:65 final size:65
Alignment explanation
Indices: 43077648--43077772 Score: 169
Period size: 65 Copynumber: 1.9 Consensus size: 65
43077638 CATAAGCGTA
* * * * * *
43077648 GCTAATGCTCTAACCTTTAGCGGCGTTTCCTCATAAGCGTCGCCAATGCTCTGACCTTTAGCGGC
1 GCTAACGCTCTAACCTTTAGCGGCGCTTCCTCATAAACGCCGCCAACGCTCTAACCTTTAGCGGC
* * *
43077713 GCTAACGCTCTGACCTTTAGTGGCGCTTCCTCATAAACGCCGCTAACGCTCTAACCTTTA
1 GCTAACGCTCTAACCTTTAGCGGCGCTTCCTCATAAACGCCGCCAACGCTCTAACCTTTA
43077773 ACGACACTTC
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
65 51 1.00
ACGTcount: A:0.20, C:0.32, G:0.19, T:0.29
Consensus pattern (65 bp):
GCTAACGCTCTAACCTTTAGCGGCGCTTCCTCATAAACGCCGCCAACGCTCTAACCTTTAGCGGC
Found at i:43077770 original size:41 final size:41
Alignment explanation
Indices: 43077712--43077816 Score: 138
Period size: 41 Copynumber: 2.6 Consensus size: 41
43077702 CCTTTAGCGG
* * *
43077712 CGCTAACGCTCTGACCTTTAGTGGCGCTTCCTCATAAACGC
1 CGCTAACGCTCTGACCTTTAGCGACACTTCCTCATAAACGC
* * *
43077753 CGCTAACGCTCTAACCTTTAACGACACTTCCTTATAAACGC
1 CGCTAACGCTCTGACCTTTAGCGACACTTCCTCATAAACGC
* *
43077794 TGCTAATGCTCTGACCTTTAGCG
1 CGCTAACGCTCTGACCTTTAGCG
43077817 GTGTTTTTCC
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.23, C:0.32, G:0.16, T:0.29
Consensus pattern (41 bp):
CGCTAACGCTCTGACCTTTAGCGACACTTCCTCATAAACGC
Found at i:43077802 original size:106 final size:106
Alignment explanation
Indices: 43077606--43077817 Score: 264
Period size: 106 Copynumber: 2.0 Consensus size: 106
43077596 TCATTAGAGC
* * * * * * * * *
43077606 CGCTAATGCTCTGACTTTTAGCGGTGCTTTCTCATAAGCGTAGCTAATGCTCTAACCTTTAGCGG
1 CGCTAACGCTCTGACCTTTAGCGGCGCTTCCTCATAAACGCAGCTAACGCTCTAACCTTTAACGA
** *
43077671 CGTTTCCTCATAAGCGTCGCCAATGCTCTGACCTTTAGCGG
66 CACTTCCTCATAAACGTCGCCAATGCTCTGACCTTTAGCGG
* *
43077712 CGCTAACGCTCTGACCTTTAGTGGCGCTTCCTCATAAACGCCGCTAACGCTCTAACCTTTAACGA
1 CGCTAACGCTCTGACCTTTAGCGGCGCTTCCTCATAAACGCAGCTAACGCTCTAACCTTTAACGA
* *
43077777 CACTTCCTTATAAACG-CTGCTAATGCTCTGACCTTTAGCGG
66 CACTTCCTCATAAACGTC-GCCAATGCTCTGACCTTTAGCGG
43077818 TGTTTTTCCT
Statistics
Matches: 89, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
105 1 0.01
106 88 0.99
ACGTcount: A:0.21, C:0.30, G:0.19, T:0.30
Consensus pattern (106 bp):
CGCTAACGCTCTGACCTTTAGCGGCGCTTCCTCATAAACGCAGCTAACGCTCTAACCTTTAACGA
CACTTCCTCATAAACGTCGCCAATGCTCTGACCTTTAGCGG
Found at i:43077853 original size:147 final size:147
Alignment explanation
Indices: 43077572--43077838 Score: 333
Period size: 147 Copynumber: 1.8 Consensus size: 147
43077562 CGCCGTTAAT
* * * * * * *** *
43077572 GCTCTGACCTTTAGCGGCGTTTCCTCATTAGAGCCGCTAATGCTCTGACTTTTAGCGGTGCTTTC
1 GCTCTGACCTTTAGCGGCGCTTCCTCATTAAAGCCGCTAACGCTCTAACCTTTAACGACACTTCC
* *
43077637 TCATAAGCGTAGCTAATGCTCTAACCTTTAGCGGCGTTTCCTCATAAGCGTCGCCAATGCTCTGA
66 TCATAAACGTAGCTAATGCTCTAACCTTTAGCGGCGTTTCCTCATAAACGTCGCCAATGCTCTGA
43077702 CCTTTAGCGGCGCTAAC
131 CCTTTAGCGGCGCTAAC
*
43077719 GCTCTGACCTTTAGTGGCGCTTCCTCA-TAAACGCCGCTAACGCTCTAACCTTTAACGACACTTC
1 GCTCTGACCTTTAGCGGCGCTTCCTCATTAAA-GCCGCTAACGCTCTAACCTTTAACGACACTTC
* * *
43077783 CTTATAAACGCT-GCTAATGCTCTGACCTTTAGCGGTGTTTTTCCT-ATAAACGTCGC
65 CTCATAAACG-TAGCTAATGCTCTAACCTTTAGCGGCG--TTTCCTCATAAACGTCGC
43077839 TATTGCTTTA
Statistics
Matches: 100, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
146 3 0.03
147 80 0.80
148 11 0.11
149 6 0.06
ACGTcount: A:0.20, C:0.29, G:0.19, T:0.31
Consensus pattern (147 bp):
GCTCTGACCTTTAGCGGCGCTTCCTCATTAAAGCCGCTAACGCTCTAACCTTTAACGACACTTCC
TCATAAACGTAGCTAATGCTCTAACCTTTAGCGGCGTTTCCTCATAAACGTCGCCAATGCTCTGA
CCTTTAGCGGCGCTAAC
Found at i:43077863 original size:188 final size:188
Alignment explanation
Indices: 43077519--43077863 Score: 435
Period size: 188 Copynumber: 1.8 Consensus size: 188
43077509 CTTCTTCATA
* * * * *
43077519 AGCGCCGCTAATGCTCTGACCTTTAGCGGCGCCTCCTCATAAGCGCCGTTAATGCTCTGACCTTT
1 AGCGCCGCTAACGCTCTGACCTTTAGCGGCGCCTCCTCATAAACGCCGCTAACGCTCTAACCTTT
* * ** * * *
43077584 AGCGGCGTTTCCTCATTAGAGCCGCTAATGCTCTGACTTTTAGCGGTGCTTTCTCATAAGCGTAG
66 AACGACACTTCCTCATTAAAGCCGCTAATGCTCTGACCTTTAGCGGTGCTTTCTCATAAACGTAG
43077649 CTAATGCTCTAACCTTTAGCGGCGTTTCCTCATAAGCGTCGCCAATGCTCTGACCTTT
131 CTAATGCTCTAACCTTTAGCGGCGTTTCCTCATAAGCGTCGCCAATGCTCTGACCTTT
* * *
43077707 AGCGGCGCTAACGCTCTGACCTTTAGTGGCGCTTCCTCATAAACGCCGCTAACGCTCTAACCTTT
1 AGCGCCGCTAACGCTCTGACCTTTAGCGGCGCCTCCTCATAAACGCCGCTAACGCTCTAACCTTT
* * *
43077772 AACGACACTTCCTTA-TAAACGCTGCTAATGCTCTGACCTTTAGCGGTG-TTTTTCCTATAAACG
66 AACGACACTTCCTCATTAAA-GCCGCTAATGCTCTGACCTTTAGCGGTGCTTTCT-C-ATAAACG
* * * * *
43077835 TCGCTATTGCT-TTACCTTTTGTGGCGTTT
128 TAGCTAATGCTCTAACCTTTAGCGGCGTTT
43077864 TTCCATAAAC
Statistics
Matches: 131, Mismatches: 23, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
187 7 0.05
188 109 0.83
189 15 0.11
ACGTcount: A:0.19, C:0.29, G:0.20, T:0.32
Consensus pattern (188 bp):
AGCGCCGCTAACGCTCTGACCTTTAGCGGCGCCTCCTCATAAACGCCGCTAACGCTCTAACCTTT
AACGACACTTCCTCATTAAAGCCGCTAATGCTCTGACCTTTAGCGGTGCTTTCTCATAAACGTAG
CTAATGCTCTAACCTTTAGCGGCGTTTCCTCATAAGCGTCGCCAATGCTCTGACCTTT
Found at i:43077882 original size:40 final size:41
Alignment explanation
Indices: 43077780--43077896 Score: 137
Period size: 40 Copynumber: 2.8 Consensus size: 41
43077770 TTAACGACAC
* * * * *
43077780 TTCCTTATAAACGCTGCTAATGCTCTGACCTTTAGCGGTGTTT
1 TTCC-TATAAACGCCGCTATTGCT-TTACCTTTTGCGGCGTTT
* *
43077823 TTCCTATAAACGTCGCTATTGCTTTACCTTTTGTGGCGTTT
1 TTCCTATAAACGCCGCTATTGCTTTACCTTTTGCGGCGTTT
*
43077864 TTCC-ATAAACGCCGCTATTGCTTTACTTTTTGC
1 TTCCTATAAACGCCGCTATTGCTTTACCTTTTGC
43077897 TACCTTTTAC
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
40 26 0.41
41 18 0.28
42 16 0.25
43 4 0.06
ACGTcount: A:0.17, C:0.24, G:0.16, T:0.43
Consensus pattern (41 bp):
TTCCTATAAACGCCGCTATTGCTTTACCTTTTGCGGCGTTT
Found at i:43083953 original size:13 final size:13
Alignment explanation
Indices: 43083935--43083959 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43083925 ACCTATATTT
43083935 CTTACAAAAATAC
1 CTTACAAAAATAC
43083948 CTTACAAAAATA
1 CTTACAAAAATA
43083960 ATTTAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.20, G:0.00, T:0.24
Consensus pattern (13 bp):
CTTACAAAAATAC
Found at i:43086830 original size:22 final size:23
Alignment explanation
Indices: 43086805--43086858 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
43086795 TAATTGTTTA
*
43086805 ATAAATATTTATATTAATA-AAT
1 ATAAATATTTAAATTAATATAAT
*
43086827 AT-AATATTTTAAATTGATATAAT
1 ATAAATA-TTTAAATTAATATAAT
*
43086850 AGAAATATT
1 ATAAATATT
43086859 AAAACGGTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 4 0.15
22 12 0.46
23 6 0.23
24 4 0.15
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (23 bp):
ATAAATATTTAAATTAATATAAT
Found at i:43098560 original size:14 final size:15
Alignment explanation
Indices: 43098541--43098570 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
43098531 ATTGTCTGAC
43098541 TTAAAAAT-TAATTT
1 TTAAAAATATAATTT
43098555 TTAAAAATATAATTT
1 TTAAAAATATAATTT
43098570 T
1 T
43098571 AATTTTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTAAAAATATAATTT
Found at i:43098572 original size:21 final size:20
Alignment explanation
Indices: 43098548--43098611 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
43098538 GACTTAAAAA
43098548 TTAATTTTTAAAAATATAATT
1 TTAATTTTTAAAAAT-TAATT
*
43098569 TTAA-TTTTAATTAATTTAATT
1 TTAATTTTTAA--AAATTAATT
* * *
43098590 TTACTTTATCAAAATTAATT
1 TTAATTTTTAAAAATTAATT
43098610 TT
1 TT
43098612 CGCAAAAATC
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
20 16 0.46
21 12 0.34
22 7 0.20
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (20 bp):
TTAATTTTTAAAAATTAATT
Found at i:43099120 original size:6 final size:6
Alignment explanation
Indices: 43099100--43099158 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
43099090 TTAAATGGGT
* * * *
43099100 TTTAAA TTT-AT TTTAAA TTTAAA TTTACTTA TTTAAG TTT-AC TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA
43099148 TTTAAA TTTAA
1 TTTAAA TTTAA
43099159 TCAAATTTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
5 8 0.19
6 29 0.69
8 5 0.12
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:43099120 original size:17 final size:16
Alignment explanation
Indices: 43099100--43099169 Score: 72
Period size: 17 Copynumber: 4.4 Consensus size: 16
43099090 TTAAATGGGT
43099100 TTTAAATTTATTTTAAA
1 TTTAAATTTA-TTTAAA
*
43099117 TTTAAATTTACTT--A
1 TTTAAATTTATTTAAA
*
43099131 TTTAAGTTTACTTTAAA
1 TTTAAATTTA-TTTAAA
* *
43099148 TTTAAATTTAATCAAA
1 TTTAAATTTATTTAAA
43099164 TTTAAA
1 TTTAAA
43099170 ATAATATTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
14 10 0.23
15 2 0.05
16 12 0.27
17 20 0.45
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.53
Consensus pattern (16 bp):
TTTAAATTTATTTAAA
Found at i:43099905 original size:9 final size:9
Alignment explanation
Indices: 43099891--43099918 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
43099881 ATCAATAGCC
43099891 ATTAATAAT
1 ATTAATAAT
43099900 ATTAATAAT
1 ATTAATAAT
43099909 ATTAATAAT
1 ATTAATAAT
43099918 A
1 A
43099919 AATGGTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
ATTAATAAT
Found at i:43101160 original size:30 final size:29
Alignment explanation
Indices: 43101096--43101231 Score: 88
Period size: 29 Copynumber: 4.7 Consensus size: 29
43101086 GGACCGTCCG
* *
43101096 AAAATTACCATTTTACCCTCGAACTTT-CC-
1 AAAATTACCATTTAACCC-CG-ATTTTACCA
43101125 AAAATT-CCATCTCTAACCCCGATTTTACCA
1 AAAATTACCAT-T-TAACCCCGATTTTACCA
* * * *
43101155 AAAATTACCATTTTACCCCTAAACTCT-CC-
1 AAAATTACCATTTAACCCC--GATTTTACCA
*
43101184 AAAATT-CCATTTTTAACCTCGATTTTACCA
1 AAAATTACCA--TTTAACCCCGATTTTACCA
43101214 AAAATTACCATTT-ACCCC
1 AAAATTACCATTTAACCCC
43101232 TAAACTCTCT
Statistics
Matches: 83, Mismatches: 12, Indels: 25
0.69 0.10 0.21
Matches are distributed among these distances:
28 18 0.22
29 28 0.34
30 27 0.33
31 10 0.12
ACGTcount: A:0.34, C:0.31, G:0.02, T:0.33
Consensus pattern (29 bp):
AAAATTACCATTTAACCCCGATTTTACCA
Found at i:43101253 original size:58 final size:59
Alignment explanation
Indices: 43101096--43101333 Score: 311
Period size: 59 Copynumber: 4.0 Consensus size: 59
43101086 GGACCGTCCG
* * * *
43101096 AAAATTACCATTTTA-CCCTCGAACTTTCCAAAATTCCATCTCTAACCCCGATTTTACCA
1 AAAATTACCATTTTACCCCT-AAACTCTCCAAAATTCCATTTTTAACCCCGATTTTACCA
*
43101155 AAAATTACCATTTTACCCCTAAACTCTCCAAAATTCCATTTTTAACCTCGATTTTACCA
1 AAAATTACCATTTTACCCCTAAACTCTCCAAAATTCCATTTTTAACCCCGATTTTACCA
* *
43101214 AAAATTACCA-TTTACCCCTAAACTCTCTAAAATTCCATTTTTGACCCC-AGTTTTACCA
1 AAAATTACCATTTTACCCCTAAACTCTCCAAAATTCCATTTTTAACCCCGA-TTTTACCA
* ** * * *
43101272 ACAATTACCATTTTACCCCCCGAACTTTCCAAAATTCCATTTTTAGCCCCGATTTCACCA
1 AAAATTACCATTTTA-CCCCTAAACTCTCCAAAATTCCATTTTTAACCCCGATTTTACCA
43101332 AA
1 AA
43101334 GTTTCCAAAA
Statistics
Matches: 157, Mismatches: 17, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
57 1 0.01
58 52 0.33
59 63 0.40
60 40 0.25
61 1 0.01
ACGTcount: A:0.32, C:0.31, G:0.03, T:0.33
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCTAAACTCTCCAAAATTCCATTTTTAACCCCGATTTTACCA
Found at i:43101332 original size:29 final size:28
Alignment explanation
Indices: 43101123--43101333 Score: 85
Period size: 29 Copynumber: 7.2 Consensus size: 28
43101113 CTCGAACTTT
* * *
43101123 CCAAAATTCCATCTCTAACCCCGATTTTA
1 CCAAAATTCCAT-TTTTACCCCGATTTCA
* ** *
43101152 CCAAAAATTACCA-TTTTACCCCTAAACTCT
1 CC-AAAATT-CCATTTTTACCCC-GATTTCA
* *
43101182 CCAAAATTCCATTTTTAACCTCGATTTTA
1 CCAAAATTCCATTTTT-ACCCCGATTTCA
* ** *
43101211 CCAAAAATTACCA--TTTACCCCTAAACTCT
1 CC-AAAATT-CCATTTTTACCCC-GATTTCA
* *
43101240 CTAAAATTCCATTTTTGACCCC-AGTTTTA
1 CCAAAATTCCATTTTT-ACCCCGA-TTTCA
43101269 CCAACAATTACCA-TTTTACCCCCCGAACTTT--
1 CCAA-AATT-CCATTTTTA--CCCCG-A-TTTCA
43101300 CCAAAATTCCATTTTTAGCCCCGATTTCA
1 CCAAAATTCCATTTTTA-CCCCGATTTCA
43101329 CCAAA
1 CCAAA
43101334 GTTTCCAAAA
Statistics
Matches: 134, Mismatches: 27, Indels: 42
0.66 0.13 0.21
Matches are distributed among these distances:
27 6 0.04
28 15 0.11
29 50 0.37
30 42 0.31
31 17 0.13
33 4 0.03
ACGTcount: A:0.32, C:0.32, G:0.03, T:0.33
Consensus pattern (28 bp):
CCAAAATTCCATTTTTACCCCGATTTCA
Found at i:43101348 original size:38 final size:38
Alignment explanation
Indices: 43101297--43101371 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
43101287 CCCCCCGAAC
*
43101297 TTTCCAAAATTCCATTTTTAGCCCCGATTTCACCAAAG
1 TTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAG
*
43101335 TTTCCAAAATTCCATTTTTAACCCCGGTTTCACCAAA
1 TTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAA
43101372 AATTACCATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.29, C:0.29, G:0.07, T:0.35
Consensus pattern (38 bp):
TTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAG
Found at i:43106022 original size:25 final size:24
Alignment explanation
Indices: 43105994--43106048 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 24
43105984 ACACTAGCGC
* *
43105994 GCTCTCTATTATTAGCATTGTGTGT
1 GCTCTCT-TGATTAGCACTGTGTGT
43106019 GCTCTC-TGATTAGCACTGTGTGT
1 GCTCTCTTGATTAGCACTGTGTGT
43106042 GCTCTCT
1 GCTCTCT
43106049 GTTACCCAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 21 0.78
25 6 0.22
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.44
Consensus pattern (24 bp):
GCTCTCTTGATTAGCACTGTGTGT
Found at i:43106030 original size:23 final size:23
Alignment explanation
Indices: 43106004--43106049 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
43105994 GCTCTCTATT
*
43106004 ATTAGCATTGTGTGTGCTCTCTG
1 ATTAGCACTGTGTGTGCTCTCTG
43106027 ATTAGCACTGTGTGTGCTCTCTG
1 ATTAGCACTGTGTGTGCTCTCTG
43106050 TTACCCAGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.13, C:0.20, G:0.26, T:0.41
Consensus pattern (23 bp):
ATTAGCACTGTGTGTGCTCTCTG
Found at i:43109820 original size:31 final size:32
Alignment explanation
Indices: 43109782--43109851 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
43109772 TCTAAATTTC
* *
43109782 TAATCAATCCTAATTTC-TCCAAGGTTTGTAT
1 TAATCAATCCTAATTTCTTCAAAGATTTGTAT
*
43109813 TAATCAATCCTAATTTCTTTAAAGATTTGTAT
1 TAATCAATCCTAATTTCTTCAAAGATTTGTAT
43109845 TAATCAA
1 TAATCAA
43109852 CGTCTAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
31 17 0.49
32 18 0.51
ACGTcount: A:0.34, C:0.16, G:0.07, T:0.43
Consensus pattern (32 bp):
TAATCAATCCTAATTTCTTCAAAGATTTGTAT
Found at i:43113472 original size:5 final size:5
Alignment explanation
Indices: 43113462--43113493 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
43113452 AAGAAGTGAT
43113462 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TT
43113494 AATCAACCTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:43117371 original size:30 final size:30
Alignment explanation
Indices: 43117312--43117373 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
43117302 TATTTTATTG
* * **
43117312 TTAATTTTGTTATTATTTTAGATGCATTTA
1 TTAATTTTGTTACTATTTTAAAAACATTTA
*
43117342 TTAATTTTGTTACTATTTTAAAAATATTTA
1 TTAATTTTGTTACTATTTTAAAAACATTTA
43117372 TT
1 TT
43117374 TGTTAAGTTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.60
Consensus pattern (30 bp):
TTAATTTTGTTACTATTTTAAAAACATTTA
Found at i:43117526 original size:13 final size:12
Alignment explanation
Indices: 43117490--43117526 Score: 58
Period size: 11 Copynumber: 3.1 Consensus size: 12
43117480 TTATATATAT
43117490 TTAAAAATAATA
1 TTAAAAATAATA
43117502 TT-AAAATAATA
1 TTAAAAATAATA
43117513 TTAAAAATTAATA
1 TTAAAAA-TAATA
43117526 T
1 T
43117527 GGGCAGGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.48
12 6 0.26
13 6 0.26
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TTAAAAATAATA
Found at i:43117997 original size:11 final size:12
Alignment explanation
Indices: 43117979--43118007 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
43117969 TTTACAATTC
43117979 ATATATTAATAA
1 ATATATTAATAA
43117991 A-ATATTAATAA
1 ATATATTAATAA
43118002 ATATAT
1 ATATAT
43118008 ATTTATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATATTAATAA
Found at i:43118023 original size:26 final size:27
Alignment explanation
Indices: 43117979--43118065 Score: 76
Period size: 26 Copynumber: 3.3 Consensus size: 27
43117969 TTTACAATTC
*
43117979 ATATATTAATAA--AATATTAATAAAT
1 ATATATTTATAATTAATATTAATAAAT
**
43118004 ATATATTTAT-ATTAATATTAATATTT
1 ATATATTTATAATTAATATTAATAAAT
*
43118030 ACATATTTTATAATTAA-ATTTAAATAAA-
1 ATATA-TTTATAATTAATA-TT-AATAAAT
43118058 ATATATTT
1 ATATATTT
43118066 TTCTACTATT
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
24 1 0.02
25 9 0.18
26 15 0.31
27 9 0.18
28 11 0.22
29 4 0.08
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (27 bp):
ATATATTTATAATTAATATTAATAAAT
Found at i:43119460 original size:27 final size:27
Alignment explanation
Indices: 43119419--43119479 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
43119409 AAATTCTAAG
**
43119419 TGGTGCCTATGGGGTAGGCGGCACCAA
1 TGGTGCCTATGGGGTAGGCAACACCAA
* *
43119446 TGGTGTCTATTGGGTAGGCAACACCAA
1 TGGTGCCTATGGGGTAGGCAACACCAA
43119473 TGGTGCC
1 TGGTGCC
43119480 ATACATGTAG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.20, C:0.21, G:0.36, T:0.23
Consensus pattern (27 bp):
TGGTGCCTATGGGGTAGGCAACACCAA
Found at i:43128743 original size:23 final size:23
Alignment explanation
Indices: 43128594--43128731 Score: 122
Period size: 23 Copynumber: 5.9 Consensus size: 23
43128584 CGAAGTACTT
43128594 AACAGTAAGCACACA-AGTGCTGGGGA
1 AACAGTAAGCACACACAGTGC----GA
43128620 AACAGTAAGCACACACAGTGC-A
1 AACAGTAAGCACACACAGTGCGA
* * * * *
43128642 ATCAGTAGGCGCACATAGCGC-A
1 AACAGTAAGCACACACAGTGCGA
*
43128664 AATCAGTAGGCACACGA-AGTGCGA
1 AA-CAGTAAGCACAC-ACAGTGCGA
*
43128688 AACAGTAAGCACACAGAGTGCGA
1 AACAGTAAGCACACACAGTGCGA
*
43128711 AACAGTAAGCACAGACAGTGC
1 AACAGTAAGCACACACAGTGC
43128732 TGAACGGTAA
Statistics
Matches: 96, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
22 20 0.21
23 52 0.54
24 4 0.04
26 15 0.16
27 5 0.05
ACGTcount: A:0.40, C:0.23, G:0.26, T:0.11
Consensus pattern (23 bp):
AACAGTAAGCACACACAGTGCGA
Found at i:43131403 original size:16 final size:15
Alignment explanation
Indices: 43131368--43131409 Score: 66
Period size: 16 Copynumber: 2.7 Consensus size: 15
43131358 GGGTTTATGG
43131368 TTTAAGGTTTTGAGT
1 TTTAAGGTTTTGAGT
*
43131383 TTTAAGGTTTATGATT
1 TTTAAGGTTT-TGAGT
43131399 TTTAAGGTTTT
1 TTTAAGGTTTT
43131410 AGGGTTAAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 11 0.44
16 14 0.56
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.57
Consensus pattern (15 bp):
TTTAAGGTTTTGAGT
Found at i:43131521 original size:8 final size:8
Alignment explanation
Indices: 43131510--43131560 Score: 54
Period size: 7 Copynumber: 6.6 Consensus size: 8
43131500 GTATTTAGGT
43131510 TTTTAAGG
1 TTTTAAGG
*
43131518 TTTTAGGG
1 TTTTAAGG
43131526 ATTTTAAGG
1 -TTTTAAGG
43131535 -TTTAAGG
1 TTTTAAGG
*
43131542 -TTTAAAG
1 TTTTAAGG
43131549 -TTTAAGG
1 TTTTAAGG
43131556 TTTTA
1 TTTTA
43131561 GTGATATATG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
7 19 0.51
8 11 0.30
9 7 0.19
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (8 bp):
TTTTAAGG
Found at i:43131639 original size:12 final size:12
Alignment explanation
Indices: 43131608--43131641 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
43131598 CTAACTCCAT
* *
43131608 TAATTAAATACT
1 TAATTAAGTACA
43131620 TAATTAAGTACA
1 TAATTAAGTACA
43131632 TAATTAAGTA
1 TAATTAAGTA
43131642 GTTAAGTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (12 bp):
TAATTAAGTACA
Found at i:43131721 original size:14 final size:14
Alignment explanation
Indices: 43131654--43131721 Score: 52
Period size: 14 Copynumber: 4.9 Consensus size: 14
43131644 TAAGTTGACC
43131654 TAAACCCTAAACCT
1 TAAACCCTAAACCT
*
43131668 TACACCC-AAATCCT
1 TAAACCCTAAA-CCT
* *
43131682 TTAACCCTACA-CT
1 TAAACCCTAAACCT
*
43131695 CGAAA-CCTAAAACCT
1 -TAAACCCT-AAACCT
43131710 TAAACCCTAAAC
1 TAAACCCTAAAC
43131722 ATAAACATAA
Statistics
Matches: 40, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
13 8 0.20
14 25 0.62
15 7 0.17
ACGTcount: A:0.41, C:0.37, G:0.01, T:0.21
Consensus pattern (14 bp):
TAAACCCTAAACCT
Found at i:43131728 original size:6 final size:6
Alignment explanation
Indices: 43131717--43131775 Score: 66
Period size: 6 Copynumber: 9.5 Consensus size: 6
43131707 CCTTAAACCC
* *
43131717 TAAACA TAAACA TAATTA-A TTAAATA CAAACA TAAACA TAAACA TAAACA
1 TAAACA TAAACA TAA--ACA -TAAACA TAAACA TAAACA TAAACA TAAACA
43131767 TAAACA TAA
1 TAAACA TAA
43131776 TTAATTCTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
6 40 0.87
7 2 0.04
8 4 0.09
ACGTcount: A:0.64, C:0.14, G:0.00, T:0.22
Consensus pattern (6 bp):
TAAACA
Found at i:43132236 original size:27 final size:27
Alignment explanation
Indices: 43132184--43132241 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
43132174 TTCTGGCTTG
*
43132184 ACCAACCCGTATTATATCCATGGTCTA
1 ACCAACCCGTATTATATCCATCGTCTA
* *
43132211 ACCAACCCG-ATTGATATCTATCGTCTG
1 ACCAACCCGTATT-ATATCCATCGTCTA
43132238 ACCA
1 ACCA
43132242 CCCCAGAACG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 3 0.11
27 24 0.89
ACGTcount: A:0.29, C:0.31, G:0.12, T:0.28
Consensus pattern (27 bp):
ACCAACCCGTATTATATCCATCGTCTA
Found at i:43133551 original size:20 final size:19
Alignment explanation
Indices: 43133526--43133563 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
43133516 TTATAAAGTT
*
43133526 AAAAATAATTAATTTTATTA
1 AAAAATAA-CAATTTTATTA
43133546 AAAAATAACAATTTTATT
1 AAAAATAACAATTTTATT
43133564 TATTAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAAATAACAATTTTATTA
Found at i:43133857 original size:18 final size:17
Alignment explanation
Indices: 43133836--43133871 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
43133826 AAAATAAATC
43133836 AAAAACAAAAAAAAGTAT
1 AAAAACAAAAAAAA-TAT
*
43133854 AAAAACATAAAAAATAT
1 AAAAACAAAAAAAATAT
43133871 A
1 A
43133872 TATATAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.78, C:0.06, G:0.03, T:0.14
Consensus pattern (17 bp):
AAAAACAAAAAAAATAT
Found at i:43133873 original size:19 final size:18
Alignment explanation
Indices: 43133826--43133873 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
43133816 AAATTTTTAT
*
43133826 AAAATAAATCAAAAACAAA
1 AAAATATAT-AAAAACAAA
43133845 AAAA-AGTATAAAAACATAA
1 AAAATA-TATAAAAACA-AA
43133864 AAAATATATA
1 AAAATATATA
43133874 TATAAACACT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 8 0.32
19 16 0.64
20 1 0.04
ACGTcount: A:0.75, C:0.06, G:0.02, T:0.17
Consensus pattern (18 bp):
AAAATATATAAAAACAAA
Found at i:43134025 original size:26 final size:28
Alignment explanation
Indices: 43133966--43134026 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 28
43133956 ATCCACTATA
*
43133966 AACAAACACACTTAACTAATATTATTTT
1 AACAAACACACTTAACTAATATTATATT
*
43133994 AAACAACCACACTTAACTAATATT-TATT
1 -AACAAACACACTTAACTAATATTATATT
43134022 -ACAAA
1 AACAAA
43134027 GTTAAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 4 0.14
28 3 0.10
29 22 0.76
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (28 bp):
AACAAACACACTTAACTAATATTATATT
Found at i:43143693 original size:24 final size:23
Alignment explanation
Indices: 43143634--43143693 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 23
43143624 TACTTCTAGT
* *
43143634 TATTCACTTCAAATCATTCATCAA
1 TATTCACTTCATA-CAATCATCAA
*
43143658 -ATT-AC-TCCTACAATCATCCAA
1 TATTCACTTCATACAATCAT-CAA
43143679 TATTCACTTCATACA
1 TATTCACTTCATACA
43143694 TAAACATAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
20 6 0.21
21 6 0.21
22 5 0.18
23 5 0.18
24 6 0.21
ACGTcount: A:0.37, C:0.28, G:0.00, T:0.35
Consensus pattern (23 bp):
TATTCACTTCATACAATCATCAA
Found at i:43151784 original size:24 final size:24
Alignment explanation
Indices: 43151757--43151802 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
43151747 TAAAATATCC
43151757 AAAA-ATAATCAAAGTTTAACTGGA
1 AAAATATAAT-AAAGTTTAACTGGA
* *
43151781 AAAATATAGTAGAGTTTAACTG
1 AAAATATAATAAAGTTTAACTG
43151803 TGAGAAGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.50, C:0.07, G:0.15, T:0.28
Consensus pattern (24 bp):
AAAATATAATAAAGTTTAACTGGA
Found at i:43153801 original size:15 final size:15
Alignment explanation
Indices: 43153781--43153818 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
43153771 ATATAATGAT
43153781 ATATATGTGAGAAAA
1 ATATATGTGAGAAAA
* *
43153796 ATATATGTGTGAAAT
1 ATATATGTGAGAAAA
43153811 AT-TATGTG
1 ATATATGTG
43153819 GTTAATTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.37
Consensus pattern (15 bp):
ATATATGTGAGAAAA
Found at i:43154116 original size:41 final size:40
Alignment explanation
Indices: 43154070--43154170 Score: 100
Period size: 38 Copynumber: 2.6 Consensus size: 40
43154060 TCGACCTTGA
**
43154070 GTCGATGAGACACTGGGTGTCATTACTTTACTTAGGATAG
1 GTCGATGAGACACTGGGTGTCACCACTTTACTTAGGATAG
* ** * *
43154110 ATTCGATGAGGTACT-GG-GT-ACCACTTTACTTCGGTTAG
1 -GTCGATGAGACACTGGGTGTCACCACTTTACTTAGGATAG
*
43154148 GCCGATGAGACACTGGGTGTCAC
1 GTCGATGAGACACTGGGTGTCAC
43154171 TTTATTGCTT
Statistics
Matches: 46, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
37 10 0.22
38 17 0.37
39 4 0.09
40 4 0.09
41 11 0.24
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.30
Consensus pattern (40 bp):
GTCGATGAGACACTGGGTGTCACCACTTTACTTAGGATAG
Found at i:43159321 original size:65 final size:65
Alignment explanation
Indices: 43159240--43159389 Score: 187
Period size: 65 Copynumber: 2.3 Consensus size: 65
43159230 TATGGTTGTA
* ** * *
43159240 TATAAATGTA-AT-TGAAATATATTTGCATGTATATATAATTTATTAAGAAATTAAAAATTAGAC
1 TATAAATATATATGTGAAATATATTTAAATGTATATATAATTTATCAAGAAACTAAAAATTAGAC
* * * *
43159303 TATAAATATATATGTGAAAAATATTTAAATGTGTATATAATTTATCAAGAAACTGAAAATTAGAT
1 TATAAATATATATGTGAAATATATTTAAATGTATATATAATTTATCAAGAAACTAAAAATTAGAC
* *
43159368 TGTAAATATATATGAGAAATAT
1 TATAAATATATATGTGAAATAT
43159390 TTAAAAACAT
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
63 9 0.12
64 2 0.03
65 62 0.85
ACGTcount: A:0.49, C:0.03, G:0.11, T:0.38
Consensus pattern (65 bp):
TATAAATATATATGTGAAATATATTTAAATGTATATATAATTTATCAAGAAACTAAAAATTAGAC
Found at i:43161206 original size:18 final size:19
Alignment explanation
Indices: 43161164--43161199 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
43161154 GTAAAATATT
*
43161164 ATTATATTAAGAATAAAAA
1 ATTAAATTAAGAATAAAAA
43161183 ATTAAATTAA-AATAAAA
1 ATTAAATTAAGAATAAAA
43161200 TTTTAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (19 bp):
ATTAAATTAAGAATAAAAA
Found at i:43161309 original size:19 final size:20
Alignment explanation
Indices: 43161281--43161319 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
43161271 AATTATATTA
*
43161281 ATATTTCAA-TAATAAATAT
1 ATATTACAATTAATAAATAT
*
43161300 ATATTACAATTTATAAATAT
1 ATATTACAATTAATAAATAT
43161320 TCAGTAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (20 bp):
ATATTACAATTAATAAATAT
Found at i:43166024 original size:21 final size:21
Alignment explanation
Indices: 43165985--43166025 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
43165975 GAGTAATATA
*
43165985 GTGTTTCTAGAGAATAAAATT
1 GTGTTTCTAGAGAACAAAATT
*
43166006 GTGTTTCTAGAGGACAAAAT
1 GTGTTTCTAGAGAACAAAAT
43166026 GAGGTTTTGT
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:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (21 bp):
GTGTTTCTAGAGAACAAAATT
Found at i:43167695 original size:23 final size:23
Alignment explanation
Indices: 43167669--43167716 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
43167659 AATAATATTC
* *
43167669 TCAATTAGATTATATAAATGAAT
1 TCAATAAGATGATATAAATGAAT
*
43167692 TCAATAAGGTGATATAAATGAAT
1 TCAATAAGATGATATAAATGAAT
43167715 TC
1 TC
43167717 CTAGGAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.35
Consensus pattern (23 bp):
TCAATAAGATGATATAAATGAAT
Found at i:43169154 original size:39 final size:38
Alignment explanation
Indices: 43169076--43169346 Score: 142
Period size: 39 Copynumber: 6.9 Consensus size: 38
43169066 CTGTGATAAC
* * *
43169076 TCAGGGCAAA-AGAAAAATTCAGAATG-CTCTTTTGCTATT
1 TCAGGGCAAAGAG-AAAA-TCAGAA-GATTCTTATGATATT
43169115 TCAGGGCCAAAGAGGAAAAT-AGAAGATTCTTATGATATT
1 TCAGGG-CAAAGA-GAAAATCAGAAGATTCTTATGATATT
* * * *
43169154 TCAGGGGCAAAGCGAAAATCAGAAGATTCTTGTGATGTC
1 TCA-GGGCAAAGAGAAAATCAGAAGATTCTTATGATATT
* ** * * *
43169193 TCTTGGGCAAAGAGAAAATCAGAAGATAATTGTGATGTC
1 TC-AGGGCAAAGAGAAAATCAGAAGATTCTTATGATATT
* * * *
43169232 TCTGGGGTAAAGAGAAAATCTGAAGATTCCTCTA-G-T-TCC
1 TC-AGGGCAAAGAGAAAATCAGAAGATT-CT-TATGATAT-T
* * * * *
43169271 TCAGGACCAAAGAGAAAATCTGAAGATTCCTGTAAT-TT
1 TCAGG-GCAAAGAGAAAATCAGAAGATTCTTATGATATT
* * *
43169309 ATCAGGGCCAAAGAGAAAATCAGAGGACTCTTCTGATA
1 -TCAGGG-CAAAGAGAAAATCAGAAGATTCTTATGATA
43169347 ACTCAGTTCC
Statistics
Matches: 185, Mismatches: 31, Indels: 31
0.75 0.13 0.13
Matches are distributed among these distances:
37 1 0.01
38 11 0.06
39 156 0.84
40 10 0.05
41 6 0.03
42 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (38 bp):
TCAGGGCAAAGAGAAAATCAGAAGATTCTTATGATATT
Found at i:43173672 original size:59 final size:59
Alignment explanation
Indices: 43173550--43173672 Score: 142
Period size: 59 Copynumber: 2.1 Consensus size: 59
43173540 TTATGTTTTC
* * **
43173550 TTTTTGTATTCCCTTAGAATTTTTAGTATTCTTTCATATTTTTTGATACATCCTCAGTT
1 TTTTTATATTCCCTCAGAATTTTTAGTATTCTTTCATATTTTTTGATACATCCTCAGAA
* * * *
43173609 TTTTTATATTCCCTCATAATTTTTCGTATATC-TTCATAATTTTTTGATACTTTCTCA-AA
1 TTTTTATATTCCCTCAGAATTTTTAGTAT-TCTTTCAT-ATTTTTTGATACATCCTCAGAA
43173668 TTTTT
1 TTTTT
43173673 TGGTATGCCC
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
59 35 0.65
60 19 0.35
ACGTcount: A:0.22, C:0.15, G:0.06, T:0.57
Consensus pattern (59 bp):
TTTTTATATTCCCTCAGAATTTTTAGTATTCTTTCATATTTTTTGATACATCCTCAGAA
Found at i:43174893 original size:21 final size:22
Alignment explanation
Indices: 43174846--43174894 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
43174836 ATTTAATTTA
**
43174846 ATTTAAATTTTGAGTTTTTTAT
1 ATTTAAATTTTGAGTTTTGAAT
*
43174868 A-TTAAGTTTTGA-TTTTGAAT
1 ATTTAAATTTTGAGTTTTGAAT
43174888 ATTTAAA
1 ATTTAAA
43174895 CTCATTTTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 7 0.32
21 14 0.64
22 1 0.05
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (22 bp):
ATTTAAATTTTGAGTTTTGAAT
Found at i:43189897 original size:7 final size:8
Alignment explanation
Indices: 43189867--43189897 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
43189857 TAGGAAGATA
43189867 TGATGTTT
1 TGATGTTT
43189875 TGATGTTT
1 TGATGTTT
43189883 TGATGTTT
1 TGATGTTT
43189891 T-ATGTTT
1 TGATGTTT
43189898 GAATCCAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 6 0.26
8 17 0.74
ACGTcount: A:0.13, C:0.00, G:0.23, T:0.65
Consensus pattern (8 bp):
TGATGTTT
Found at i:43194424 original size:11 final size:12
Alignment explanation
Indices: 43194402--43194437 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 12
43194392 ATGTACTAGG
43194402 TGTAATTTTTTT
1 TGTAATTTTTTT
43194414 TGTAATTTTTTTTT
1 TGTAA--TTTTTTT
43194428 TGTAATTTTT
1 TGTAATTTTT
43194438 GGTGTCGGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 10 0.45
14 12 0.55
ACGTcount: A:0.17, C:0.00, G:0.08, T:0.75
Consensus pattern (12 bp):
TGTAATTTTTTT
Found at i:43194426 original size:14 final size:14
Alignment explanation
Indices: 43194407--43194437 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
43194397 CTAGGTGTAA
43194407 TTTTTTTTGTAATT
1 TTTTTTTTGTAATT
43194421 TTTTTTTTGTAATT
1 TTTTTTTTGTAATT
43194435 TTT
1 TTT
43194438 GGTGTCGGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.13, C:0.00, G:0.06, T:0.81
Consensus pattern (14 bp):
TTTTTTTTGTAATT
Found at i:43197002 original size:21 final size:21
Alignment explanation
Indices: 43196978--43197024 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
43196968 TTGTTTCAGC
* *
43196978 AGAAGAGTCTCTTGTATCGGT
1 AGAAGAGTCACTTGTATCGCT
**
43196999 AGAACTGTCACTTGTATCGCT
1 AGAAGAGTCACTTGTATCGCT
43197020 AGAAG
1 AGAAG
43197025 TCTGCATTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.30
Consensus pattern (21 bp):
AGAAGAGTCACTTGTATCGCT
Found at i:43200823 original size:36 final size:36
Alignment explanation
Indices: 43200778--43200876 Score: 162
Period size: 36 Copynumber: 2.8 Consensus size: 36
43200768 AGTAACAGGC
*
43200778 ATGACCTTTGGATCAATAGGAAGTAAATTGAGCATT
1 ATGACCTTTGGGTCAATAGGAAGTAAATTGAGCATT
* *
43200814 ATGATCTTTGGGTCAATAGGAAGTAAATTGAGTATT
1 ATGACCTTTGGGTCAATAGGAAGTAAATTGAGCATT
*
43200850 ATGACCTTTGGGTCAACAGGAAGTAAA
1 ATGACCTTTGGGTCAATAGGAAGTAAA
43200877 GTGAATAACG
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 58 1.00
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.30
Consensus pattern (36 bp):
ATGACCTTTGGGTCAATAGGAAGTAAATTGAGCATT
Found at i:43208189 original size:42 final size:42
Alignment explanation
Indices: 43208074--43208198 Score: 146
Period size: 42 Copynumber: 3.0 Consensus size: 42
43208064 CTATTGCTTA
* * * *
43208074 ACCTTTAGCAGCGTTTTTCTCATAAGCGCCGCTGATGCTCTG
1 ACCTTTAGCGGCGTTTTTCCCATAAACGCCGCTAATGCTCTG
* * *
43208116 ACCATTAGCGGCG--TTTCCCCTAGAAGTGCCGCTAATGCTCTG
1 ACCTTTAGCGGCGTTTTTCCCATA-AA-CGCCGCTAATGCTCTG
*
43208158 ACCTTTAACGGCGTTTTTCCCATAAACGCCGCTAATGCTCT
1 ACCTTTAGCGGCGTTTTTCCCATAAACGCCGCTAATGCTCT
43208199 TTCCTATATT
Statistics
Matches: 68, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
40 7 0.10
41 1 0.01
42 50 0.74
43 2 0.03
44 8 0.12
ACGTcount: A:0.19, C:0.30, G:0.20, T:0.30
Consensus pattern (42 bp):
ACCTTTAGCGGCGTTTTTCCCATAAACGCCGCTAATGCTCTG
Found at i:43210171 original size:41 final size:41
Alignment explanation
Indices: 43210090--43210390 Score: 341
Period size: 41 Copynumber: 7.3 Consensus size: 41
43210080 TTTAAATAAA
* * * * *
43210090 TTAGTGGCGTTTTCCCCATAAACGCCGCTAGTGTTATGACCT
1 TTAGCGGCGCTTT-CCCATAAACGCCGCTAATGCTCTGACCT
* *
43210132 TTAGCGGCGCTTTCCCATAAACGCCGTTAATGGTCTGACCT
1 TTAGCGGCGCTTTCCCATAAACGCCGCTAATGCTCTGACCT
* * * *
43210173 TTAGCGGCACTTTCTCATAAATGCCGCTAATGGTCTGACCT
1 TTAGCGGCGCTTTCCCATAAACGCCGCTAATGCTCTGACCT
** * *
43210214 TTAGCGATGCTTTCCCATAAACGCCGCTAATGCTATAACCT
1 TTAGCGGCGCTTTCCCATAAACGCCGCTAATGCTCTGACCT
* * *
43210255 TTAGCGGTGCTTTGCCAGAAACGCCGCTAATGCTCTGACCT
1 TTAGCGGCGCTTTCCCATAAACGCCGCTAATGCTCTGACCT
** * *
43210296 TTAGCAACGCTTTACCGTAAACGCCGCTAATGCTCTGACCT
1 TTAGCGGCGCTTTCCCATAAACGCCGCTAATGCTCTGACCT
** * * *
43210337 TTAGCAACGCTTCCCCATAAGCGCCGCTAATGCTTTGACCT
1 TTAGCGGCGCTTTCCCATAAACGCCGCTAATGCTCTGACCT
*
43210378 TTAGCGGTGCTTT
1 TTAGCGGCGCTTT
43210391 TTCACAAGCA
Statistics
Matches: 221, Mismatches: 38, Indels: 1
0.85 0.15 0.00
Matches are distributed among these distances:
41 210 0.95
42 11 0.05
ACGTcount: A:0.21, C:0.29, G:0.20, T:0.30
Consensus pattern (41 bp):
TTAGCGGCGCTTTCCCATAAACGCCGCTAATGCTCTGACCT
Found at i:43210323 original size:123 final size:123
Alignment explanation
Indices: 43210101--43210461 Score: 393
Period size: 123 Copynumber: 2.9 Consensus size: 123
43210091 TAGTGGCGTT
* * * * * *
43210101 TTCCCCATAAACGCCGCTAGTGTTATGACCTTTAGCGGCGCTTTCCCATAAACGCCGTTAATGGT
1 TTCCCCATAAACGCCGCTAATGCTATGACCTTTAGCGGTGCTTTCCCAGAAACGCCGCTAATGCT
** * * * *
43210166 CTGACCTTTAGCGGCACTTTCTCATAAATGCCGCTAATGGTCTGACCTTTAGCGATGC
66 CTGACCTTTAGCAACACTTTCTCATAAACGCCGCTAATGCTCTGACCTTTAGCAACGC
* * *
43210224 TTTCCCATAAACGCCGCTAATGCTATAACCTTTAGCGGTGCTTTGCCAGAAACGCCGCTAATGCT
1 TTCCCCATAAACGCCGCTAATGCTATGACCTTTAGCGGTGCTTTCCCAGAAACGCCGCTAATGCT
* *
43210289 CTGACCTTTAGCAACGCTTTAC-CGTAAACGCCGCTAATGCTCTGACCTTTAGCAACGC
66 CTGACCTTTAGCAACACTTT-CTCATAAACGCCGCTAATGCTCTGACCTTTAGCAACGC
* * ** * * * *
43210347 TTCCCCATAAGCGCCGCTAATGCTTTGACCTTTAGCGGTGCTTTTTCACAAGCACCACTAATGCT
1 TTCCCCATAAACGCCGCTAATGCTATGACCTTTAGCGGTGCTTTCCCAGAAACGCCGCTAATGCT
* * * ** * * *
43210412 TTGACTTTTAGCTACGTTTTTTCTATAAACGCCGCTATTGCT-TTACCTTT
66 CTGACCTTTAGCAACACTTTCTC-ATAAACGCCGCTAATGCTCTGACCTTT
43210462 TGCGGTGTTT
Statistics
Matches: 200, Mismatches: 35, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
123 183 0.92
124 17 0.09
ACGTcount: A:0.22, C:0.29, G:0.18, T:0.32
Consensus pattern (123 bp):
TTCCCCATAAACGCCGCTAATGCTATGACCTTTAGCGGTGCTTTCCCAGAAACGCCGCTAATGCT
CTGACCTTTAGCAACACTTTCTCATAAACGCCGCTAATGCTCTGACCTTTAGCAACGC
Found at i:43210408 original size:82 final size:82
Alignment explanation
Indices: 43210104--43210492 Score: 343
Period size: 82 Copynumber: 4.8 Consensus size: 82
43210094 TGGCGTTTTC
* * * *
43210104 CCCATAAACGCCGCTAGTG-TTATGACCTTTAGCGGCGCTTTCCCATAAACGCCGTTAATGGTCT
1 CCCATAAACGCCGCTAATGCTT-TGACCTTTAGCGGTGCTTTCCCATAAACGCCGCTAATGCTCT
* *
43210168 GACCTTTAGCGGCACTTT
65 GACCTTTAGCGACGCTTT
* * * * * * *
43210186 CTCATAAATGCCGCTAATGGTCTGACCTTTAGCGATGCTTTCCCATAAACGCCGCTAATGCTATA
1 CCCATAAACGCCGCTAATGCTTTGACCTTTAGCGGTGCTTTCCCATAAACGCCGCTAATGCTCTG
**
43210251 ACCTTTAGCGGTGCTTT
66 ACCTTTAGCGACGCTTT
* * * *** * *
43210268 GCCAGAAACGCCGCTAATGCTCTGACCTTTAGCAACGCTTTACCGTAAACGCCGCTAATGCTCTG
1 CCCATAAACGCCGCTAATGCTTTGACCTTTAGCGGTGCTTTCCCATAAACGCCGCTAATGCTCTG
* *
43210333 ACCTTTAGCAACGCTTC
66 ACCTTTAGCGACGCTTT
* ** * * * * *
43210350 CCCATAAGCGCCGCTAATGCTTTGACCTTTAGCGGTGCTTTTTCACAAGCACCACTAATGCTTTG
1 CCCATAAACGCCGCTAATGCTTTGACCTTTAGCGGTGCTTTCCCATAAACGCCGCTAATGCTCTG
* * *
43210415 ACTTTTAGCTACGTTTTT
66 ACCTTTAGCGACG-CTTT
* * * * * * * *
43210433 TCTATAAACGCCGCTATTGCTTT-ACCTTTTGCGGTG-TTTACGAAAAACGCCGCTATTGCT
1 CCCATAAACGCCGCTAATGCTTTGACCTTTAGCGGTGCTTTCCCATAAACGCCGCTAATGCT
43210493 TTATCTTTTG
Statistics
Matches: 246, Mismatches: 59, Indels: 5
0.79 0.19 0.02
Matches are distributed among these distances:
81 16 0.07
82 208 0.85
83 22 0.09
ACGTcount: A:0.22, C:0.28, G:0.19, T:0.31
Consensus pattern (82 bp):
CCCATAAACGCCGCTAATGCTTTGACCTTTAGCGGTGCTTTCCCATAAACGCCGCTAATGCTCTG
ACCTTTAGCGACGCTTT
Found at i:43210487 original size:39 final size:40
Alignment explanation
Indices: 43210438--43210543 Score: 178
Period size: 39 Copynumber: 2.7 Consensus size: 40
43210428 TTTTTTCTAT
*
43210438 AAACGCCGCTATTGCTTTACCTTTTGCGGTGTTTACG-AA
1 AAACGCCGCTATTGCTTTATCTTTTGCGGTGTTTACGAAA
*
43210477 AAACGCCGCTATTGCTTTATCTTTTGCGGTGTTTATGAAA
1 AAACGCCGCTATTGCTTTATCTTTTGCGGTGTTTACGAAA
*
43210517 AAACACCGCTATTGCTTTATCTTTTGC
1 AAACGCCGCTATTGCTTTATCTTTTGC
43210544 TGCATTTTCT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
39 35 0.56
40 28 0.44
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.39
Consensus pattern (40 bp):
AAACGCCGCTATTGCTTTATCTTTTGCGGTGTTTACGAAA
Found at i:43211319 original size:22 final size:22
Alignment explanation
Indices: 43211294--43211335 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
43211284 TTTTCATGTA
* *
43211294 TTATTTTTTTGTCCCTATAATT
1 TTATTTTTTAGCCCCTATAATT
43211316 TTATTTTTTAGCCCCTATAA
1 TTATTTTTTAGCCCCTATAA
43211336 ATCTAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.17, G:0.05, T:0.57
Consensus pattern (22 bp):
TTATTTTTTAGCCCCTATAATT
Found at i:43211344 original size:23 final size:22
Alignment explanation
Indices: 43211296--43211347 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
43211286 TTCATGTATT
* * * *
43211296 ATTTTTTTGTCCCTATAATTTT
1 ATTTTTTAGCCCCTATAATCTA
43211318 ATTTTTTAGCCCCTATAAATCTA
1 ATTTTTTAGCCCCTAT-AATCTA
43211341 ATTTTTT
1 ATTTTTT
43211348 CTTCATGTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 14 0.56
23 11 0.44
ACGTcount: A:0.23, C:0.15, G:0.04, T:0.58
Consensus pattern (22 bp):
ATTTTTTAGCCCCTATAATCTA
Found at i:43211412 original size:24 final size:22
Alignment explanation
Indices: 43211342--43211425 Score: 71
Period size: 22 Copynumber: 3.7 Consensus size: 22
43211332 ATAAATCTAA
* *
43211342 TTTTTTCTTCATGT-AGTTCATT
1 TTTTTTCTCCCTGTAAG-TCATT
* *
43211364 TTTTTCCTCCCTGTAAGTCAAT
1 TTTTTTCTCCCTGTAAGTCATT
*
43211386 TTTTTTCTCCCTGTAATTCGACTT
1 TTTTTTCTCCCTGTAAGTC-A-TT
* *
43211410 TTTTTTGTCTCTGTAA
1 TTTTTTCTCCCTGTAA
43211426 ATTGAATTTT
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
22 32 0.64
23 3 0.06
24 15 0.30
ACGTcount: A:0.14, C:0.20, G:0.10, T:0.56
Consensus pattern (22 bp):
TTTTTTCTCCCTGTAAGTCATT
Found at i:43211435 original size:24 final size:24
Alignment explanation
Indices: 43211361--43211437 Score: 79
Period size: 24 Copynumber: 3.3 Consensus size: 24
43211351 CATGTAGTTC
* *
43211361 ATTTTTTTCCTCCCTGTAAGTC-A
1 ATTTTTTTTCTCCCTGTAATTCGA
43211384 A-TTTTTTTCTCCCTGTAATTCGA
1 ATTTTTTTTCTCCCTGTAATTCGA
* * *
43211407 CTTTTTTTTGTCTCTGTAAATT-GA
1 ATTTTTTTTCTCCCTGT-AATTCGA
43211431 ATTTTTT
1 ATTTTTT
43211438 GTCCTTATAA
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
22 18 0.40
23 2 0.04
24 21 0.47
25 4 0.09
ACGTcount: A:0.17, C:0.18, G:0.09, T:0.56
Consensus pattern (24 bp):
ATTTTTTTTCTCCCTGTAATTCGA
Found at i:43211449 original size:21 final size:23
Alignment explanation
Indices: 43211410--43211459 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
43211400 AATTCGACTT
*
43211410 TTTTTTGTCTCTGTAAATT-GAA
1 TTTTTTGTCTCTGTAAATTCAAA
43211432 TTTTTTGTC-CT-TATAATTCAAA
1 TTTTTTGTCTCTGTA-AATTCAAA
43211454 TTTTTT
1 TTTTTT
43211460 AGTTCATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 2 0.08
21 6 0.24
22 17 0.68
ACGTcount: A:0.22, C:0.10, G:0.08, T:0.60
Consensus pattern (23 bp):
TTTTTTGTCTCTGTAAATTCAAA
Found at i:43214763 original size:15 final size:15
Alignment explanation
Indices: 43214740--43214794 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 15
43214730 TGTTTCACTA
*
43214740 TCACTTATTGCATCT
1 TCACCTATTGCATCT
43214755 TCACCTATTGCATCT
1 TCACCTATTGCATCT
** ** *
43214770 TCGTCTGCTGCACCT
1 TCACCTATTGCATCT
43214785 TCACCTATTG
1 TCACCTATTG
43214795 TTAATCATAG
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.16, C:0.33, G:0.11, T:0.40
Consensus pattern (15 bp):
TCACCTATTGCATCT
Found at i:43217667 original size:26 final size:26
Alignment explanation
Indices: 43217638--43217688 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
43217628 TTTAAATAAA
*
43217638 CAGTTAATATAATCAGTTGATCAAAT
1 CAGTTAATAGAATCAGTTGATCAAAT
*
43217664 CAGTTAATAGAATCATTTGATCAAA
1 CAGTTAATAGAATCAGTTGATCAAA
43217689 CCAATCATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (26 bp):
CAGTTAATAGAATCAGTTGATCAAAT
Found at i:43219608 original size:158 final size:158
Alignment explanation
Indices: 43219320--43219610 Score: 422
Period size: 158 Copynumber: 1.8 Consensus size: 158
43219310 AATACTGGGA
* * * * *
43219320 ATTACATGGTATATGGGTGTTGGTCTTAGATGTCCTATCAATGGCTGAGATCCAGCATAAGTTTC
1 ATTACATGGTATATGGGTGCTGGTCTTAGATGGCATACCAATGGCTGAGATCCAGCATAAGTTGC
* * *
43219385 AGATTCTCCACAGCTCGTGTGAGTAGCATCGTGTGGCCTATCATCTTGACCCACAACTCATGTGA
66 AGATTCTCCACAGCTCGTGTGAGTAGCATCGTGTAGCCTAACATCTCGACCCACAACTCATGTGA
43219450 GCAAGCCTACTCCATAGCTCGTGTGAGC
131 GCAAGCCTACTCCATAGCTCGTGTGAGC
* * * *
43219478 ATTACATGGTATATGGGTGCTGGTCTTAGATGGCATACCGATGGTTGAGAT-CTGACATATGTTG
1 ATTACATGGTATATGGGTGCTGGTCTTAGATGGCATACCAATGGCTGAGATCCAG-CATAAGTTG
* * * *
43219542 CGGATTCTCCATAGCTCGTGTGAGTAGCATCGTGTAGCTTAACATCTCGACCCACAGCTCATGTG
65 CAGATTCTCCACAGCTCGTGTGAGTAGCATCGTGTAGCCTAACATCTCGACCCACAACTCATGTG
43219607 AGCA
130 AGCA
43219611 GACCCATTTC
Statistics
Matches: 116, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
157 2 0.02
158 114 0.98
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (158 bp):
ATTACATGGTATATGGGTGCTGGTCTTAGATGGCATACCAATGGCTGAGATCCAGCATAAGTTGC
AGATTCTCCACAGCTCGTGTGAGTAGCATCGTGTAGCCTAACATCTCGACCCACAACTCATGTGA
GCAAGCCTACTCCATAGCTCGTGTGAGC
Found at i:43228807 original size:20 final size:20
Alignment explanation
Indices: 43228784--43228824 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
43228774 CTATTCAAAC
* *
43228784 AATATTACTTGAATAGTTAT
1 AATATTACATGAATAATTAT
*
43228804 AATATTAGATGAATAATTAT
1 AATATTACATGAATAATTAT
43228824 A
1 A
43228825 TGTTTTTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.02, G:0.10, T:0.41
Consensus pattern (20 bp):
AATATTACATGAATAATTAT
Found at i:43230395 original size:9 final size:9
Alignment explanation
Indices: 43230381--43230413 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
43230371 TACTTTCTCT
43230381 CAAAGAATA
1 CAAAGAATA
43230390 CAAAGAATA
1 CAAAGAATA
43230399 CAAAGAATA
1 CAAAGAATA
*
43230408 TAAAGA
1 CAAAGA
43230414 GTGGAGTGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.67, C:0.09, G:0.12, T:0.12
Consensus pattern (9 bp):
CAAAGAATA
Found at i:43236323 original size:51 final size:51
Alignment explanation
Indices: 43236263--43236393 Score: 190
Period size: 51 Copynumber: 2.6 Consensus size: 51
43236253 TGACATATTA
* * *
43236263 TCATCGGACCTTTAATTCGTCATGGATTCATTTACTCACGATGACACTTAG
1 TCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCACGATGACACTTAG
* * *
43236314 TCGTTGGACCTTTAATCCGTAAAGGATTCATTTACTCACGATGACACTTGG
1 TCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCACGATGACACTTAG
* *
43236365 TCATCGGACCTTTCATCTGTAAAGGATTC
1 TCATCGGACCTTTAATCCGTAAAGGATTC
43236394 TAAGGACTGG
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 70 1.00
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (51 bp):
TCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCACGATGACACTTAG
Found at i:43241185 original size:17 final size:17
Alignment explanation
Indices: 43241163--43241197 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
43241153 AAGTTAAAGT
*
43241163 AGCAAAAAAGCAATTTA
1 AGCAAAAAAGCAACTTA
*
43241180 AGCAAACAAGCAACTTA
1 AGCAAAAAAGCAACTTA
43241197 A
1 A
43241198 AGTAGAAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.57, C:0.17, G:0.11, T:0.14
Consensus pattern (17 bp):
AGCAAAAAAGCAACTTA
Found at i:43241485 original size:25 final size:24
Alignment explanation
Indices: 43241456--43241516 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
43241446 ACTATTTTAT
*
43241456 ATTTATTTATTGCATACAAAAATAA
1 ATTTATTTATTAC-TACAAAAATAA
* *
43241481 TTTTATTTATCTACTATAAAAATAA
1 ATTTATTTAT-TACTACAAAAATAA
*
43241506 ATTAATTTATT
1 ATTTATTTATT
43241517 TATTTCTTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 1 0.03
25 27 0.90
26 2 0.07
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.48
Consensus pattern (24 bp):
ATTTATTTATTACTACAAAAATAA
Found at i:43242320 original size:4 final size:4
Alignment explanation
Indices: 43242295--43242345 Score: 57
Period size: 4 Copynumber: 12.2 Consensus size: 4
43242285 GGAGAAGAAG
* * *
43242295 AAGA AGGA AAGGA AATA AAGA AAGA AAGA GAAAA AAGA AAGA AAGA AAGA
1 AAGA AAGA AA-GA AAGA AAGA AAGA AAGA -AAGA AAGA AAGA AAGA AAGA
43242345 A
1 A
43242346 GAAGAACATG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
4 32 0.82
5 7 0.18
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (4 bp):
AAGA
Found at i:43242321 original size:17 final size:17
Alignment explanation
Indices: 43242295--43242340 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
43242285 GGAGAAGAAG
*
43242295 AAGAAGGAAAG-GAAATA
1 AAGAAAGAAAGAGAAA-A
43242312 AAGAAAGAAAGAGAAAA
1 AAGAAAGAAAGAGAAAA
43242329 AAGAAAGAAAGA
1 AAGAAAGAAAGA
43242341 AAGAAGAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 23 0.85
18 4 0.15
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (17 bp):
AAGAAAGAAAGAGAAAA
Found at i:43242351 original size:25 final size:26
Alignment explanation
Indices: 43242289--43242351 Score: 76
Period size: 25 Copynumber: 2.4 Consensus size: 26
43242279 GCTACAGGAG
* *
43242289 AAGAAGAAGAAGGAAAGGAAATAAAGA
1 AAGAAGAAGAA-GAAAAGAAAGAAAGA
43242316 AAGAA-AGAGAA-AAAAGAAAGAAAGA
1 AAGAAGA-AGAAGAAAAGAAAGAAAGA
43242341 AAGAAGAAGAA
1 AAGAAGAAGAA
43242352 CATGAAGGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 21 0.66
26 2 0.06
27 9 0.28
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (26 bp):
AAGAAGAAGAAGAAAAGAAAGAAAGA
Found at i:43242724 original size:5 final size:5
Alignment explanation
Indices: 43242691--43242723 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
43242681 TTTTGTTATT
*
43242691 TTTAA TTTAA TTTAA TTTAA TTTAA TTTTA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTT
43242724 TGTTAGTAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (5 bp):
TTTAA
Found at i:43242761 original size:24 final size:21
Alignment explanation
Indices: 43242713--43242756 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
43242703 TAATTTAATT
43242713 TAATTTTATTTTGTTAGTAAG
1 TAATTTTATTTTGTTAGTAAG
*
43242734 TAATTTTATTTTGTAAGT-AG
1 TAATTTTATTTTGTTAGTAAG
43242754 TAA
1 TAA
43242757 GTAATATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.55
Consensus pattern (21 bp):
TAATTTTATTTTGTTAGTAAG
Done.