Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 133 of 141
Found at i:39957026 original size:44 final size:45
Alignment explanation
Indices: 39956977--39957066 Score: 112
Period size: 45 Copynumber: 2.0 Consensus size: 45
39956967 TCTCTATTCT
39956977 ATTCAACCAAACATAAT-AA-TACTATTACGCCTCTATTCCATTAC
1 ATTCAACCAAACA-AATGAATTACTATTACGCCTCTATTCCATTAC
* * ** *
39957021 ATTCAACTAAACAATTGAATTGTTATTACGCCTTTATTCCATTAC
1 ATTCAACCAAACAAATGAATTACTATTACGCCTCTATTCCATTAC
39957066 A
1 A
39957067 GCGAACCAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
43 2 0.05
44 14 0.36
45 23 0.59
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.36
Consensus pattern (45 bp):
ATTCAACCAAACAAATGAATTACTATTACGCCTCTATTCCATTAC
Found at i:39957741 original size:6 final size:6
Alignment explanation
Indices: 39957730--39957756 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
39957720 CAAAAGGTGA
39957730 AGAATC AGAATC AGAATC AGAATC AGA
1 AGAATC AGAATC AGAATC AGAATC AGA
39957757 GCAACATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.15, G:0.19, T:0.15
Consensus pattern (6 bp):
AGAATC
Found at i:39966218 original size:5 final size:5
Alignment explanation
Indices: 39966208--39966235 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
39966198 GCATAAGTTA
39966208 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
39966236 TACATAATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:39978819 original size:19 final size:18
Alignment explanation
Indices: 39978803--39978838 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
39978793 TTATAAAATT
39978803 TATTTTAAAATTAAAAAA
1 TATTTTAAAATTAAAAAA
*
39978821 TATTTTTAAATTAAAAAA
1 TATTTTAAAATTAAAAAA
39978839 GTTATGTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TATTTTAAAATTAAAAAA
Found at i:39981920 original size:6 final size:6
Alignment explanation
Indices: 39981909--39981973 Score: 58
Period size: 7 Copynumber: 9.8 Consensus size: 6
39981899 TTAGATTTAT
* *
39981909 TTAAAA TTAAAA TATTAAA TTAAAA TTAAAA TTTAAAA TGTAAAA TAAAAAA
1 TTAAAA TTAAAA T-TAAAA TTAAAA TTAAAA -TTAAAA T-TAAAA T-TAAAA
39981961 TTATAATA TTAAA
1 TTA-AA-A TTAAA
39981974 TATTTAAATA
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
6 19 0.39
7 26 0.53
8 4 0.08
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (6 bp):
TTAAAA
Found at i:39981930 original size:13 final size:12
Alignment explanation
Indices: 39981909--39981973 Score: 58
Period size: 13 Copynumber: 4.9 Consensus size: 12
39981899 TTAGATTTAT
39981909 TTAAAATTAAAA
1 TTAAAATTAAAA
*
39981921 TATTAAATTAAAA
1 T-TAAAATTAAAA
39981934 TTAAAATTTAAAA
1 TTAAAA-TTAAAA
*
39981947 TGTAAAATAAAAAA
1 T-TAAAAT-TAAAA
39981961 TTATAATATTAAA
1 TTA-AA-ATTAAA
39981974 TATTTAAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
12 5 0.12
13 21 0.49
14 15 0.35
15 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (12 bp):
TTAAAATTAAAA
Found at i:39981933 original size:19 final size:19
Alignment explanation
Indices: 39981909--39981963 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
39981899 TTAGATTTAT
39981909 TTAAAATTAAAATATTAAA
1 TTAAAATTAAAATATTAAA
39981928 TTAAAATTAAAAT-TTAAAA
1 TTAAAATTAAAATATT-AAA
*
39981947 TGTAAAA-TAAAAAATTA
1 T-TAAAATTAAAATATTA
39981964 TAATATTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
18 2 0.06
19 23 0.72
20 7 0.22
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (19 bp):
TTAAAATTAAAATATTAAA
Found at i:39981944 original size:7 final size:7
Alignment explanation
Indices: 39981907--39981981 Score: 52
Period size: 7 Copynumber: 11.0 Consensus size: 7
39981897 AGTTAGATTT
39981907 ATTTAAA
1 ATTTAAA
39981914 A-TTAAA
1 ATTTAAA
39981920 ATATT-AA
1 AT-TTAAA
39981927 A-TTAAA
1 ATTTAAA
39981933 A-TTAAA
1 ATTTAAA
39981939 ATTTAAA
1 ATTTAAA
*
39981946 ATGTAAA
1 ATTTAAA
*
39981953 A-TAAAA
1 ATTTAAA
* *
39981959 AATTATA
1 ATTTAAA
39981966 ATATTAAA
1 AT-TTAAA
39981974 TATTTAAA
1 -ATTTAAA
39981982 TAATTAAAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 13
0.73 0.09 0.18
Matches are distributed among these distances:
5 2 0.04
6 19 0.35
7 20 0.37
8 11 0.20
9 2 0.04
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (7 bp):
ATTTAAA
Found at i:39982380 original size:22 final size:21
Alignment explanation
Indices: 39982347--39982390 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
39982337 ATTTTTATAA
*
39982347 AAAAATATTTTTA-AACATTTT
1 AAAAATAGTTTTACAA-ATTTT
39982368 AAAAATAAGTTTTACAAATTTT
1 AAAAAT-AGTTTTACAAATTTT
39982390 A
1 A
39982391 CAATTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 6 0.30
22 12 0.60
23 2 0.10
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (21 bp):
AAAAATAGTTTTACAAATTTT
Found at i:39982497 original size:13 final size:14
Alignment explanation
Indices: 39982463--39982495 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
39982453 ATTTATTGTA
39982463 AATTTTATTTTTAT
1 AATTTTATTTTTAT
39982477 AATTTTATTTTTAT
1 AATTTTATTTTTAT
39982491 AATTT
1 AATTT
39982496 ATATATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
AATTTTATTTTTAT
Found at i:39987468 original size:28 final size:27
Alignment explanation
Indices: 39987424--39987477 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
39987414 TTAACAAGAA
*
39987424 GACAAAAAAAACAAGAAA-AAAGAATTT
1 GACAAAAAAAAAAAGAAACAAA-AATTT
39987451 GACAAAAAAAAAAGAGAAACAAAAATT
1 GACAAAAAAAAAA-AGAAACAAAAATT
39987478 GACGTTCAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 12 0.50
28 9 0.38
29 3 0.12
ACGTcount: A:0.72, C:0.07, G:0.11, T:0.09
Consensus pattern (27 bp):
GACAAAAAAAAAAAGAAACAAAAATTT
Found at i:39988161 original size:7 final size:7
Alignment explanation
Indices: 39988149--39988200 Score: 86
Period size: 7 Copynumber: 7.4 Consensus size: 7
39988139 GTTATTACAT
39988149 TTTATTA
1 TTTATTA
39988156 TTTATTA
1 TTTATTA
39988163 TTTATTA
1 TTTATTA
39988170 TTTATTA
1 TTTATTA
39988177 TTTATTA
1 TTTATTA
*
39988184 TATATTA
1 TTTATTA
*
39988191 TATATTA
1 TTTATTA
39988198 TTT
1 TTT
39988201 TTAAACAAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 43 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
TTTATTA
Found at i:39997313 original size:12 final size:15
Alignment explanation
Indices: 39997281--39997310 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
39997271 TATATTTTGT
39997281 ATAATTTCAAAAATA
1 ATAATTTCAAAAATA
39997296 ATAATTT-AAAAATA
1 ATAATTTCAAAAATA
39997310 A
1 A
39997311 ATTCCATGTT
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:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (15 bp):
ATAATTTCAAAAATA
Found at i:40001702 original size:24 final size:24
Alignment explanation
Indices: 40001674--40001733 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
40001664 ATTAGGTAAG
**
40001674 TTTTAAATTATTTTTGAATTTTTA
1 TTTTAAATTATTTTTGAATTAGTA
**
40001698 TTTTATTTTATTTTTGAATTAGTA
1 TTTTAAATTATTTTTGAATTAGTA
*
40001722 ATTTAAATTATT
1 TTTTAAATTATT
40001734 ATGCAACTAA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (24 bp):
TTTTAAATTATTTTTGAATTAGTA
Found at i:40004271 original size:3 final size:3
Alignment explanation
Indices: 40004263--40004309 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
40004253 ATATGTGCAG
* *
40004263 TAA TAA TAA TGA TAA TAT TAA TAA TAA TAA TAA TAA T-A TGAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
40004308 TA
1 TA
40004310 TCAAAAAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 34 0.89
4 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:40005993 original size:92 final size:89
Alignment explanation
Indices: 40005832--40006097 Score: 338
Period size: 92 Copynumber: 3.0 Consensus size: 89
40005822 AAGACTTGTA
* *
40005832 TCTTCGATCTACTTCGCCACCAGTAT-GGAACGACAAGATCTGTTATCATTGATCTACTTCACGC
1 TCTTCGATCTACTTCACCACCAGTATGGGAA-GACAAGATCTGTTATCTTTGATCTACTTCACGC
* * *
40005896 TAGTACATGAAGACAAGATTTGTTT
65 CAGTACATGAAGACAAGATCTATTT
* * * * *
40005921 TCTCAGTCGATCTGCTTCACCACCAGTATGGGAAGGCTAGATTTGTTACCTTTGATCTACTTCAC
1 TCT---TCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCAC
40005986 GCCAGTACATGAAGACAAGATCTATTT
63 GCCAGTACATGAAGACAAGATCTATTT
* * *
40006013 TCTTCGATCTACTCCACCACCAGTATGGGGAGACAAGATCTGCTT-TCTTCGATCTACTTCACGC
1 TCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTG-TTATCTTTGATCTACTTCACGC
* *
40006077 CAATACATGAGGACAAGATCT
65 CAGTACATGAAGACAAGATCT
40006098 GCTTTTTCAA
Statistics
Matches: 152, Mismatches: 20, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
89 72 0.47
90 2 0.01
92 74 0.49
93 4 0.03
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (89 bp):
TCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCC
AGTACATGAAGACAAGATCTATTT
Found at i:40006102 original size:44 final size:44
Alignment explanation
Indices: 40005863--40006102 Score: 159
Period size: 44 Copynumber: 5.3 Consensus size: 44
40005853 AGTATGGAAC
* *
40005863 GACAAGATCTG-TTATCATT-GATCTACTTCACGCTAGTACATGAA
1 GACAAGATCTGCTT-TC-TTCGATCTACTTCACGCCAGTACATGAG
* * * * ***
40005907 GACAAGATTTGTTTTCTCAGTCGATCTGCTTCACCACCAGTATGGGAAG
1 GACAAGATCTGCTTTCT---TCGATCTACTTCA-CGCCAGTACATG-AG
* * * * *
40005956 G-CTAGATTTG-TTACCTTTGATCTACTTCACGCCAGTACATGAA
1 GACAAGATCTGCTT-TCTTCGATCTACTTCACGCCAGTACATGAG
** * * *
40005999 GACAAGATCTATTTTCTTCGATCTACTCCACCACCAGT--ATGGGG
1 GACAAGATCTGCTTTCTTCGATCTACTTCA-CGCCAGTACAT-GAG
*
40006043 AGACAAGATCTGCTTTCTTCGATCTACTTCACGCCAATACATGAG
1 -GACAAGATCTGCTTTCTTCGATCTACTTCACGCCAGTACATGAG
40006088 GACAAGATCTGCTTT
1 GACAAGATCTGCTTT
40006103 TTCAATCAAT
Statistics
Matches: 149, Mismatches: 32, Indels: 30
0.71 0.15 0.14
Matches are distributed among these distances:
43 5 0.03
44 60 0.40
45 50 0.34
46 3 0.02
47 12 0.08
48 17 0.11
49 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (44 bp):
GACAAGATCTGCTTTCTTCGATCTACTTCACGCCAGTACATGAG
Found at i:40006367 original size:100 final size:100
Alignment explanation
Indices: 40006263--40006447 Score: 293
Period size: 100 Copynumber: 1.9 Consensus size: 100
40006253 AATGTCGGGG
* * *
40006263 AAACCAGATCCGTCGTCGTGGCTTCAATCTGTTCCACCGCACCG-TTAGAGAAGTAAGA-TCTGC
1 AAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACCGCACCGCTAAG-GAAGTAAGATTC-GC
40006326 CGTTGTGGCTTCAATCTTTTTAATTGCAATATCAGGA
64 CGTTGTGGCTTCAATCTTTTTAATTGCAATATCAGGA
* *
40006363 AAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATTCGCCG
1 AAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACCGCACCGCTAAGGAAGTAAGATTCGCCG
40006428 TTGTGGCTTCAATCTTTTTA
66 TTGTGGCTTCAATCTTTTTA
40006448 CTTTTCAACC
Statistics
Matches: 78, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
100 73 0.94
101 5 0.06
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (100 bp):
AAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACCGCACCGCTAAGGAAGTAAGATTCGCCG
TTGTGGCTTCAATCTTTTTAATTGCAATATCAGGA
Found at i:40018380 original size:3 final size:3
Alignment explanation
Indices: 40018372--40018421 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
40018362 ATATGTGCAG
* *
40018372 TAA TAA TAA TGA TAA TAT TAA TAA TAA TAA TAA TAA TAA T-A TGAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
40018417 TAA TA
1 TAA TA
40018422 TCAAAAAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 37 0.90
4 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:40019754 original size:20 final size:22
Alignment explanation
Indices: 40019714--40019755 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
40019704 AAATTTAATA
*
40019714 TAATAAATATAATTTATTATTT
1 TAATAAATATAATTTAATATTT
40019736 TAATAAAT-T-ATTTAATATTT
1 TAATAAATATAATTTAATATTT
40019756 AAATTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 1 0.05
22 8 0.42
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TAATAAATATAATTTAATATTT
Found at i:40019819 original size:15 final size:15
Alignment explanation
Indices: 40019799--40019855 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
40019789 ACTCAATATC
40019799 AATATTTTAATAATA
1 AATATTTTAATAATA
*
40019814 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
40019833 AATATATTAATAATA
1 AATATTTTAATAATA
*
40019848 AATGTTTT
1 AATATTTT
40019856 TAGTATAAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:40020904 original size:96 final size:96
Alignment explanation
Indices: 40020707--40020929 Score: 261
Period size: 96 Copynumber: 2.3 Consensus size: 96
40020697 TTTAAAGGTC
* * * * * * *
40020707 ATGGCCAGACTACCCAATGCCACAGCCAAACTGGAAGCCATCACACCCATGGGCAGACTGTTCAA
1 ATGGGCAGACTGCCCAATGCCATAGCCAAACGGGAACCCACCACACCCATGGGCAGACTGTCCAA
* *
40020772 TGCCATGGCCAAACAGGAACCCTCCACGCCT
66 TGCCATGGCCAAACAGGAACCCACCACCCCT
* ** *
40020803 ATGGGCAGATTGTTCAATGCCATAGCCAAACGGGAACCCACCACACTCATGGGCAGACTG-CCAA
1 ATGGGCAGACTGCCCAATGCCATAGCCAAACGGGAACCCACCACACCCATGGGCAGACTGTCC-A
* * **
40020867 ATGCCATGGTCAAACCGGAAGTCACCACACCCT
65 ATGCCATGGCCAAACAGGAACCCACCAC-CCCT
40020900 -TGGGCAGACTGCCCAATGCCATAGCCAAAC
1 ATGGGCAGACTGCCCAATGCCATAGCCAAAC
40020930 CCCAGGACAC
Statistics
Matches: 105, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
95 1 0.01
96 101 0.96
97 3 0.03
ACGTcount: A:0.30, C:0.34, G:0.21, T:0.14
Consensus pattern (96 bp):
ATGGGCAGACTGCCCAATGCCATAGCCAAACGGGAACCCACCACACCCATGGGCAGACTGTCCAA
TGCCATGGCCAAACAGGAACCCACCACCCCT
Found at i:40020930 original size:48 final size:48
Alignment explanation
Indices: 40020706--40020930 Score: 234
Period size: 48 Copynumber: 4.7 Consensus size: 48
40020696 CTTTAAAGGT
* * * * * *
40020706 CATGGCCAGACTACCCAATGCCACAGCCAAACTGGAAGCCATCACACC
1 CATGGGCAGACTGCCCAATGCCATAGCCAAACCGGAACCCACCACACC
** * * * *
40020754 CATGGGCAGACTGTTCAATGCCATGGCCAAACAGGAACCCTCCACGCC
1 CATGGGCAGACTGCCCAATGCCATAGCCAAACCGGAACCCACCACACC
* * ** * *
40020802 TATGGGCAGATTGTTCAATGCCATAGCCAAACGGGAACCCACCACACT
1 CATGGGCAGACTGCCCAATGCCATAGCCAAACCGGAACCCACCACACC
* * * **
40020850 CATGGGCAGACTGCCAAATGCCATGGTCAAACCGGAAGTCACCACACC
1 CATGGGCAGACTGCCCAATGCCATAGCCAAACCGGAACCCACCACACC
*
40020898 CTTGGGCAGACTGCCCAATGCCATAGCCAAACC
1 CATGGGCAGACTGCCCAATGCCATAGCCAAACC
40020931 CCAGGACACT
Statistics
Matches: 144, Mismatches: 33, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
48 144 1.00
ACGTcount: A:0.30, C:0.35, G:0.21, T:0.14
Consensus pattern (48 bp):
CATGGGCAGACTGCCCAATGCCATAGCCAAACCGGAACCCACCACACC
Found at i:40026555 original size:18 final size:18
Alignment explanation
Indices: 40026519--40026557 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
40026509 CAATCAATTC
40026519 AATTTTATAATTTAACAAT
1 AATTTTAT-ATTTAACAAT
40026538 AATTTTAT-TTTCAACAAT
1 AATTTTATATTT-AACAAT
40026556 AA
1 AA
40026558 ATATGAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 3 0.16
18 8 0.42
19 8 0.42
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (18 bp):
AATTTTATATTTAACAAT
Found at i:40028339 original size:13 final size:13
Alignment explanation
Indices: 40028321--40028346 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40028311 CATTGGTAGC
40028321 ATGAAAAGATGAA
1 ATGAAAAGATGAA
40028334 ATGAAAAGATGAA
1 ATGAAAAGATGAA
40028347 GAGAATTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.23, T:0.15
Consensus pattern (13 bp):
ATGAAAAGATGAA
Found at i:40029178 original size:28 final size:28
Alignment explanation
Indices: 40029128--40029192 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
40029118 AATGCATCTA
40029128 ATTTATATTACAAAGTTTGTATTTTTGC
1 ATTTATATTACAAAGTTTGTATTTTTGC
* * * *
40029156 ATTTATATTATAAATTTTTTATTTTTTC
1 ATTTATATTACAAAGTTTGTATTTTTGC
40029184 ATTTATATT
1 ATTTATATT
40029193 TTTGCATGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.62
Consensus pattern (28 bp):
ATTTATATTACAAAGTTTGTATTTTTGC
Found at i:40031524 original size:17 final size:16
Alignment explanation
Indices: 40031493--40031526 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
40031483 AATGTAATAC
*
40031493 AAATAAGTATTACAAT
1 AAATAAGTATAACAAT
40031509 AAATATAGTATAACAAT
1 AAATA-AGTATAACAAT
40031526 A
1 A
40031527 TCATTACAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.29
Consensus pattern (16 bp):
AAATAAGTATAACAAT
Found at i:40032076 original size:31 final size:31
Alignment explanation
Indices: 40032036--40032114 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
40032026 TCTTTTTTTA
*
40032036 AACCCTAAACAAAA-CTCTCTAATCCTTTTCT
1 AACCCTAAACAAAATC-CCCTAATCCTTTTCT
* *
40032067 AACCTTAAACAAAATCCCCTAATCCTTTTTTT
1 AACCCTAAACAAAATCCCCTAATCC-TTTTCT
40032099 ATACCCTAATACAAAA
1 A-ACCCTAA-ACAAAA
40032115 CTTTTAAGCT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
31 21 0.52
32 7 0.17
33 6 0.15
34 6 0.15
ACGTcount: A:0.39, C:0.29, G:0.00, T:0.32
Consensus pattern (31 bp):
AACCCTAAACAAAATCCCCTAATCCTTTTCT
Found at i:40032223 original size:19 final size:21
Alignment explanation
Indices: 40032201--40032245 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 21
40032191 ATTTTTTCGG
*
40032201 TTCTCAT-TTCTTCTT-TCTC
1 TTCTCATCTTCTCCTTATCTC
40032220 TTCT-ATCTTCTCCTTCATCTC
1 TTCTCATCTTCTCCTT-ATCTC
40032241 TTCTC
1 TTCTC
40032246 TATTCTGCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
18 2 0.10
19 11 0.52
21 8 0.38
ACGTcount: A:0.07, C:0.36, G:0.00, T:0.58
Consensus pattern (21 bp):
TTCTCATCTTCTCCTTATCTC
Found at i:40039537 original size:69 final size:69
Alignment explanation
Indices: 40039459--40039717 Score: 220
Period size: 69 Copynumber: 3.8 Consensus size: 69
40039449 AAGGGTCGGG
* * * *
40039459 AAGAGTCACATGTTGAAGCCGGAGGAAAGACCGATAGTGGAGAAGGTGATAATGTGCAAAAGGCT
1 AAGAATCACATGTTGAAGCCGGAGGAAAGACAGATAGTGGAAAAGGTGATAATGAGCAAAAGGCT
40039524 AAGC
66 AAGC
* * * * * *
40039528 AAGAATCACATTTTGATGCCGGAGGAAAGGCAGATGGTGGAAAAGGTGATAATGAGCACAAGGGT
1 AAGAATCACATGTTGAAGCCGGAGGAAAGACAGATAGTGGAAAAGGTGATAATGAGCAAAAGGCT
*
40039593 AAGG
66 AAGC
* * * ** * ** *
40039597 ACGAATCGC-GGTTTGAAGCCGGAGGAAA-AGTGGACAGTACAAAAGGTGATAACGAGCAAAAGG
1 AAGAATCACATG-TTGAAGCCGGAGGAAAGA-CAGATAGTGGAAAAGGTGATAATGAGCAAAAGG
* *
40039660 GTAAGG
64 CTAAGC
* * * *
40039666 AAGAATCGCA-GTTTGAAGCCAGG-GGAAAGGCAGATGGTGGAAAAGGCGATAA
1 AAGAATCACATG-TTGAAGCC-GGAGGAAAGACAGATAGTGGAAAAGGTGATAA
40039718 GGAGGGTCAG
Statistics
Matches: 151, Mismatches: 34, Indels: 10
0.77 0.17 0.05
Matches are distributed among these distances:
69 149 0.99
70 2 0.01
ACGTcount: A:0.38, C:0.12, G:0.35, T:0.15
Consensus pattern (69 bp):
AAGAATCACATGTTGAAGCCGGAGGAAAGACAGATAGTGGAAAAGGTGATAATGAGCAAAAGGCT
AAGC
Found at i:40041943 original size:16 final size:16
Alignment explanation
Indices: 40041912--40041945 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
40041902 AATTTAAATA
40041912 TAAAATATTTATTCTT
1 TAAAATATTTATTCTT
40041928 TAAAGATATTTA-TCTT
1 TAAA-ATATTTATTCTT
40041944 TA
1 TA
40041946 TATGACAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (16 bp):
TAAAATATTTATTCTT
Found at i:40046854 original size:19 final size:18
Alignment explanation
Indices: 40046832--40046867 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
40046822 TATAAATGCA
40046832 AAATTAAATAATCGAAATT
1 AAATTAAATAATC-AAATT
*
40046851 AAATTAGATAATCAAAT
1 AAATTAAATAATCAAAT
40046868 GTGCGAATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (18 bp):
AAATTAAATAATCAAATT
Found at i:40048454 original size:9 final size:9
Alignment explanation
Indices: 40048440--40048471 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
40048430 ACATATTTTT
40048440 TATTATATA
1 TATTATATA
40048449 TATTATATA
1 TATTATATA
*
40048458 TATTTTATA
1 TATTATATA
40048467 TATTA
1 TATTA
40048472 ACATAACATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TATTATATA
Found at i:40055117 original size:21 final size:22
Alignment explanation
Indices: 40055093--40055133 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
40055083 CCACTTCACT
40055093 TTCAAATTCTTT-ATTATTTCA
1 TTCAAATTCTTTAATTATTTCA
40055114 TTCAAATTCTTTAATTATTT
1 TTCAAATTCTTTAATTATTT
40055134 TAATATACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.59
Consensus pattern (22 bp):
TTCAAATTCTTTAATTATTTCA
Found at i:40056063 original size:26 final size:26
Alignment explanation
Indices: 40056027--40056080 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
40056017 AAAACTAAAA
*
40056027 ATTTTCAATACAGAAGTCAGATGGCC
1 ATTTTCAATACAGAAGTCAGACGGCC
* *
40056053 ATTTTCAATACAGAGGTTAGACGGCC
1 ATTTTCAATACAGAAGTCAGACGGCC
40056079 AT
1 AT
40056081 GTGTCCAGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (26 bp):
ATTTTCAATACAGAAGTCAGACGGCC
Found at i:40062143 original size:40 final size:40
Alignment explanation
Indices: 40062060--40062322 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
40062050 TTGAATGCTG
* * * * * *
40062060 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
40062100 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
40062140 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
40062180 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
40062220 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
40062260 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
40062299 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
40062323 TGAACGAGGA
Statistics
Matches: 201, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.17
40 158 0.79
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:40062342 original size:79 final size:80
Alignment explanation
Indices: 40062099--40062357 Score: 256
Period size: 80 Copynumber: 3.3 Consensus size: 80
40062089 AAGTGAATAT
* * * * * *
40062099 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** * *
40062163 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
40062179 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
** ** *
40062244 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * *
40062259 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
* *
40062323 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
40062338 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
40062358 TACGTGATTT
Statistics
Matches: 156, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
78 14 0.09
79 48 0.31
80 94 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
CGAACGAGGAGCTAA
Found at i:40073883 original size:18 final size:18
Alignment explanation
Indices: 40073857--40073891 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40073847 TATTCTTGTT
40073857 GTTTATTATCTTTTTTAC
1 GTTTATTATCTTTTTTAC
* *
40073875 GTTTTTTATGTTTTTTA
1 GTTTATTATCTTTTTTA
40073892 TAATTTTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.06, G:0.09, T:0.71
Consensus pattern (18 bp):
GTTTATTATCTTTTTTAC
Found at i:40074113 original size:18 final size:19
Alignment explanation
Indices: 40074090--40074126 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
40074080 TGGTTTAAGT
40074090 CTAAATT-TTTAATTTCTC
1 CTAAATTATTTAATTTCTC
*
40074108 CTAAATTATTTACTTTCTC
1 CTAAATTATTTAATTTCTC
40074127 TTCTACAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.27, C:0.19, G:0.00, T:0.54
Consensus pattern (19 bp):
CTAAATTATTTAATTTCTC
Found at i:40077150 original size:15 final size:15
Alignment explanation
Indices: 40077130--40077181 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
40077120 GCTGCAAAAC
40077130 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
40077145 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
40077164 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
40077179 ATT
1 ATT
40077182 AATATGTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:40077265 original size:17 final size:18
Alignment explanation
Indices: 40077217--40077267 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 18
40077207 TTATTATTTG
40077217 TAAAATTTATTAT-TAAAA
1 TAAAA-TTATTATATAAAA
* **
40077235 TAAAATCAAAATATAAAA
1 TAAAATTATTATATAAAA
40077253 T-AAATTATTATATAA
1 TAAAATTATTATATAA
40077268 CTAAATATGT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (18 bp):
TAAAATTATTATATAAAA
Found at i:40082054 original size:25 final size:24
Alignment explanation
Indices: 40082030--40082093 Score: 67
Period size: 26 Copynumber: 2.6 Consensus size: 24
40082020 TTTAGTATAT
40082030 TATTAATTATTTTAAAAAATAATA
1 TATTAATTATTTTAAAAAATAATA
* * *
40082054 TATTATTATATTTCTTAAAAATATTA
1 TATTAAT-TATTT-TAAAAAATAATA
40082080 -ATTTAATTATTTTA
1 TA-TTAATTATTTTA
40082094 GAAACAATTC
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
24 7 0.22
25 11 0.34
26 14 0.44
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
TATTAATTATTTTAAAAAATAATA
Found at i:40082056 original size:27 final size:26
Alignment explanation
Indices: 40082025--40082093 Score: 74
Period size: 25 Copynumber: 2.7 Consensus size: 26
40082015 AAATTTTTAG
40082025 TATATTATTAATTATTTTAAAAAATAA
1 TATATTATTAATTATTTTAAAAAAT-A
*
40082052 TATATTATT-A-TATTTCTTAAAAATA
1 TATATTATTAATTATTT-TAAAAAATA
*
40082077 T-TAAT-TTAATTATTTTA
1 TATATTATTAATTATTTTA
40082094 GAAACAATTC
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
23 2 0.06
24 5 0.14
25 12 0.33
26 8 0.22
27 9 0.25
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (26 bp):
TATATTATTAATTATTTTAAAAAATA
Found at i:40085884 original size:3 final size:3
Alignment explanation
Indices: 40085876--40085902 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
40085866 ACAATGTAAG
40085876 CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT
40085903 TTTAAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:40091646 original size:9 final size:9
Alignment explanation
Indices: 40091632--40091689 Score: 62
Period size: 9 Copynumber: 6.4 Consensus size: 9
40091622 TTTGGTTAAA
40091632 AATTAACCG
1 AATTAACCG
*
40091641 AATTAATCG
1 AATTAACCG
40091650 AATTAACCG
1 AATTAACCG
* * *
40091659 GATTACCCA
1 AATTAACCG
*
40091668 AATTACCCG
1 AATTAACCG
*
40091677 AATTACCCG
1 AATTAACCG
40091686 AATT
1 AATT
40091690 GAATCACTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 42 1.00
ACGTcount: A:0.40, C:0.24, G:0.10, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:40091885 original size:27 final size:27
Alignment explanation
Indices: 40091854--40091908 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
40091844 CCTAAAAACA
40091854 AAATGTGTAATTGGGTAGATACTTAAG
1 AAATGTGTAATTGGGTAGATACTTAAG
*
40091881 AAATGTGTAATTGGGTAGATATTTAAG
1 AAATGTGTAATTGGGTAGATACTTAAG
40091908 A
1 A
40091909 GTTAGACTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.35
Consensus pattern (27 bp):
AAATGTGTAATTGGGTAGATACTTAAG
Found at i:40091955 original size:38 final size:39
Alignment explanation
Indices: 40091911--40091988 Score: 140
Period size: 38 Copynumber: 2.0 Consensus size: 39
40091901 ATTTAAGAGT
*
40091911 TAGACTTTAGTTTTATTTTTATTGGGTT-GGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
40091949 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
40091988 T
1 T
40091989 TGGGTTGGAT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 27 0.71
39 11 0.29
ACGTcount: A:0.18, C:0.03, G:0.28, T:0.51
Consensus pattern (39 bp):
TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
Found at i:40091987 original size:13 final size:13
Alignment explanation
Indices: 40091969--40091993 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40091959 TTTTAGTTTT
40091969 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
40091982 ATTGGGTTGGGT
1 ATTGGGTTGGGT
40091994 TGGATAATTT
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:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:40093157 original size:32 final size:32
Alignment explanation
Indices: 40093112--40093176 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
40093102 ATCACAAGTT
* *
40093112 GGATTTTCGTTCTCAGCTACGTACATTTTTGG
1 GGATTTTCATTCTCAGCTACGCACATTTTTGG
*
40093144 GGATTTTCATTCTCAGCTATGCACATTTTTGG
1 GGATTTTCATTCTCAGCTACGCACATTTTTGG
40093176 G
1 G
40093177 ATATAGTTCC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.17, C:0.18, G:0.22, T:0.43
Consensus pattern (32 bp):
GGATTTTCATTCTCAGCTACGCACATTTTTGG
Found at i:40093549 original size:4 final size:4
Alignment explanation
Indices: 40093540--40093573 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
40093530 AAGTTTTATT
40093540 TTTA TTTA TTTA TTTA TTTA TTTTA TTTA GTTTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA -TTTA
40093574 AATTTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:40093581 original size:22 final size:22
Alignment explanation
Indices: 40093523--40093582 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
40093513 AAGTGGCCCA
*
40093523 AGTTGTAAAGTTTTATTTTTATTT
1 AGTT-TAAATTTTTA-TTTTATTT
*
40093547 A-TTT-ATTTATTTATTTTATTT
1 AGTTTAAATT-TTTATTTTATTT
40093568 AGTTTAAATTTTTAT
1 AGTTTAAATTTTTAT
40093583 ATTCAGTCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 11 0.37
22 13 0.43
23 5 0.17
24 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (22 bp):
AGTTTAAATTTTTATTTTATTT
Found at i:40099549 original size:19 final size:19
Alignment explanation
Indices: 40099521--40099584 Score: 101
Period size: 19 Copynumber: 3.3 Consensus size: 19
40099511 AATTTTCGAG
*
40099521 GATATACAATCTTAGATAT
1 GATATGCAATCTTAGATAT
40099540 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
40099559 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
40099580 GATAT
1 GATAT
40099585 ATACAATCTT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
19 23 0.55
21 19 0.45
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:40099603 original size:19 final size:21
Alignment explanation
Indices: 40099522--40099597 Score: 120
Period size: 21 Copynumber: 3.7 Consensus size: 21
40099512 ATTTTCGAGG
40099522 ATATACAATCTTAGATATG--
1 ATATACAATCTTAGATATGAT
*
40099541 ATATGCAATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
*
40099562 ATATGCAATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
40099583 ATATACAATCTTAGA
1 ATATACAATCTTAGA
40099598 AGATATGATT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
19 18 0.34
21 35 0.66
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.37
Consensus pattern (21 bp):
ATATACAATCTTAGATATGAT
Found at i:40099633 original size:21 final size:23
Alignment explanation
Indices: 40099589--40099633 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
40099579 TGATATATAC
*
40099589 AATCTTAGAAGATATGATTTTGT
1 AATCTTAGAAGATATGAATTTGT
*
40099612 AATCTTA-AAGAT-TTAATTTGT
1 AATCTTAGAAGATATGAATTTGT
40099633 A
1 A
40099634 GATACCCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
22 5 0.25
23 7 0.35
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.44
Consensus pattern (23 bp):
AATCTTAGAAGATATGAATTTGT
Found at i:40099815 original size:19 final size:21
Alignment explanation
Indices: 40099791--40099829 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
40099781 GCTTACTGTT
*
40099791 TTTTTTTCTT-TTT-CGATTA
1 TTTTTTACTTATTTACGATTA
40099810 TTTTTTACTTATTTACGATT
1 TTTTTTACTTATTTACGATT
40099830 TTAAAAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.69
Consensus pattern (21 bp):
TTTTTTACTTATTTACGATTA
Found at i:40100059 original size:3 final size:3
Alignment explanation
Indices: 40100051--40100090 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
40100041 ATTAATTTTG
*
40100051 TTA TTA TTA TTT TTA TTA TTA -TA TTA TATA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T
40100091 ACCTACATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:40100059 original size:15 final size:15
Alignment explanation
Indices: 40100035--40100089 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
40100025 GTTTTTAGTC
40100035 TATT-TTATTAATTT
1 TATTATTATTAATTT
* *
40100049 TGTTATTATTATTTT
1 TATTATTATTAATTT
40100064 TATTATTA-T-ATTAT
1 TATTATTATTAATT-T
40100078 ATATTATTATTA
1 -TATTATTATTA
40100090 TACCTACATA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
13 2 0.06
14 5 0.16
15 24 0.75
16 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
TATTATTATTAATTT
Found at i:40100066 original size:12 final size:12
Alignment explanation
Indices: 40100037--40100088 Score: 52
Period size: 12 Copynumber: 4.1 Consensus size: 12
40100027 TTTTAGTCTA
40100037 TTTTATTAATT-T
1 TTTTATT-ATTAT
*
40100049 TGTTATTATTAT
1 TTTTATTATTAT
40100061 TTTTATTATTAT
1 TTTTATTATTAT
40100073 ATTATATATTATTAT
1 -TT-T-TATTATTAT
40100088 T
1 T
40100089 ATACCTACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
11 3 0.09
12 18 0.53
13 2 0.06
14 2 0.06
15 9 0.26
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (12 bp):
TTTTATTATTAT
Found at i:40106726 original size:17 final size:17
Alignment explanation
Indices: 40106704--40106743 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
40106694 ACTTTGAGTC
**
40106704 GAAAAAAATGACGAAAT
1 GAAAAAAATGAAAAAAT
40106721 GAAAAAAATGAAAAAAT
1 GAAAAAAATGAAAAAAT
40106738 GAAAAA
1 GAAAAA
40106744 TGAAAAAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.72, C:0.03, G:0.15, T:0.10
Consensus pattern (17 bp):
GAAAAAAATGAAAAAAT
Found at i:40106734 original size:8 final size:8
Alignment explanation
Indices: 40106706--40106750 Score: 56
Period size: 8 Copynumber: 5.6 Consensus size: 8
40106696 TTTGAGTCGA
40106706 AAAAAATG
1 AAAAAATG
**
40106714 ACGAAATG
1 AAAAAATG
40106722 AAAAAAATG
1 -AAAAAATG
40106731 AAAAAATG
1 AAAAAATG
40106739 -AAAAATG
1 AAAAAATG
40106746 AAAAA
1 AAAAA
40106751 GTAAAATGGA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
7 7 0.23
8 18 0.58
9 6 0.19
ACGTcount: A:0.73, C:0.02, G:0.13, T:0.11
Consensus pattern (8 bp):
AAAAAATG
Found at i:40108230 original size:44 final size:44
Alignment explanation
Indices: 40108182--40108376 Score: 112
Period size: 44 Copynumber: 4.4 Consensus size: 44
40108172 GAGTAGGTTG
*
40108182 AAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
1 AAGATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
* * * * **
40108226 AAGATGGCAAATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAAATTT
1 AAGATTGCAGATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATCA
** * * * * * * * **
40108270 AAG-TCACCA-AGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTG
1 AAGAT-TGCAGA-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
*
40108314 AAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
1 AAGATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
** *
40108358 AAGACGGCAAATCTTATCT
1 AAGATTGCAGATCTTATCT
40108377 TTCCAAGATA
Statistics
Matches: 106, Mismatches: 35, Indels: 20
0.66 0.22 0.12
Matches are distributed among these distances:
42 4 0.04
43 8 0.08
44 84 0.79
45 8 0.08
46 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.26
Consensus pattern (44 bp):
AAGATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
Found at i:40108468 original size:132 final size:132
Alignment explanation
Indices: 40108015--40108412 Score: 647
Period size: 132 Copynumber: 3.0 Consensus size: 132
40108005 GTGATACACT
* * * *
40108015 AAGCCTTGTCTCCCTGAGCAACAGCGAAGTAGGTTGAGGATCGTAGATCTTATCTCCCT-AGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
* * * * * *
40108079 TAGTGGAGTAGATCGAGGACGACAAATTTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
66 TAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGAAGATTTAAGCCA
40108144 CC
131 CC
40108146 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
* *
40108211 TAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAA-ATTTAAGTC
66 TAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAG-AAGATTTAAGCC
40108275 ACC
130 ACC
40108278 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
*
40108343 TAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGAGAAGAAGATTTAAGCCA
66 TAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGAAGATTTAAGCCA
*
40108408 GC
131 CC
40108410 AAG
1 AAG
40108413 TCTTATCCTC
Statistics
Matches: 248, Mismatches: 16, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
131 57 0.23
132 190 0.77
133 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (132 bp):
AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
TAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGAAGATTTAAGCCA
CC
Found at i:40108723 original size:21 final size:21
Alignment explanation
Indices: 40108698--40108754 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
40108688 ATTTTCTAGG
*
40108698 ATATGCAATCTTAGGTATGAT
1 ATATGCAATCTTAGATATGAT
*
40108719 ATATGGAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
* *
40108740 ATATACAATATTAGA
1 ATATGCAATCTTAGA
40108755 AGATATGATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.37
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:40108972 original size:19 final size:21
Alignment explanation
Indices: 40108948--40108986 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
40108938 GGCTTACTAT
*
40108948 TTTTTTTCTT-TTT-CGATTA
1 TTTTTTACTTATTTACGATTA
40108967 TTTTTTACTTATTTACGATT
1 TTTTTTACTTATTTACGATT
40108987 TTAAAAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.69
Consensus pattern (21 bp):
TTTTTTACTTATTTACGATTA
Found at i:40109218 original size:3 final size:3
Alignment explanation
Indices: 40109210--40109252 Score: 70
Period size: 3 Copynumber: 14.3 Consensus size: 3
40109200 ATTAATTTTG
40109210 TTA TTA TTA TTA TTA TTA TTA -TA TTA TATA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA T
40109253 ACCTACATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:40109624 original size:51 final size:52
Alignment explanation
Indices: 40109510--40109625 Score: 132
Period size: 51 Copynumber: 2.3 Consensus size: 52
40109500 TATTTTCCAG
**
40109510 TTTT-TATAT-TATACTTATATATTTCATTTTTTTGTAAATGCATGAATATA
1 TTTTATATATATATACTTATATATTTCATTTTTTCATAAATGCATGAATATA
* * * * *
40109560 TTTTATATGTATATATTTATAT-TTTCCTTGTTTTCATAAATGCAT-TATGTA
1 TTTTATATATATATACTTATATATTTCATT-TTTTCATAAATGCATGAATATA
40109611 TTTTATATATATATA
1 TTTTATATATATATA
40109626 AGTTTTATAA
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
50 4 0.07
51 28 0.51
52 23 0.42
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (52 bp):
TTTTATATATATATACTTATATATTTCATTTTTTCATAAATGCATGAATATA
Found at i:40117854 original size:39 final size:43
Alignment explanation
Indices: 40117753--40117861 Score: 136
Period size: 45 Copynumber: 2.6 Consensus size: 43
40117743 GATTAGAGGC
40117753 GTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAAT
1 GTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT--AT
* ***
40117798 GTAATGGAATAGAGGTGTAATAG-TAATCTTGTGTTTGG-T-T
1 GTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTAT
40117838 G-AATGGAATAGAGGTGTAATAGCA
1 GTAATGGAATAGAGGTGTAATAGCA
40117862 TAATAGAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
39 21 0.36
40 2 0.03
43 1 0.02
44 11 0.19
45 23 0.40
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (43 bp):
GTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTAT
Found at i:40118035 original size:14 final size:15
Alignment explanation
Indices: 40117996--40118037 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
40117986 TTTTAACAGA
*
40117996 ATTATTATTAAATAT
1 ATTATAATTAAATAT
40118011 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
40118025 A-TATAATTTAATA
1 ATTATAATTAAATA
40118038 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:40118355 original size:24 final size:27
Alignment explanation
Indices: 40118304--40118356 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
40118294 TATATGTAAT
*
40118304 ATTATTAAAATAATATTTTTTATTTTA
1 ATTATTAAAATAATATTTTTTATATTA
*
40118331 ATTATTTAAA-AATA-TTTTTA-ATTA
1 ATTATTAAAATAATATTTTTTATATTA
40118355 AT
1 AT
40118357 GCGGTGTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 5 0.21
25 6 0.25
26 4 0.17
27 9 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
ATTATTAAAATAATATTTTTTATATTA
Found at i:40123088 original size:21 final size:21
Alignment explanation
Indices: 40123064--40123117 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
40123054 TAATACCAGA
* **
40123064 AAATGTATCGATAATTTTTTT
1 AAATTTATCGATAATTCATTT
40123085 AAATTTATCGAT-ATTCATTT
1 AAATTTATCGATAATTCATTT
40123105 AAATTTATCGATA
1 AAATTTATCGATA
40123118 CTTGGCAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 18 0.62
21 11 0.38
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.48
Consensus pattern (21 bp):
AAATTTATCGATAATTCATTT
Found at i:40124019 original size:41 final size:41
Alignment explanation
Indices: 40123974--40124148 Score: 287
Period size: 41 Copynumber: 4.3 Consensus size: 41
40123964 CAACGACACT
** * *
40123974 TAGCCTGCTAGACTTATAGCCTGATTTAGATCACCGGCACG
1 TAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACG
40124015 TAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACG
1 TAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACG
40124056 TAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACG
1 TAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACG
* **
40124097 TAGCCTGCTAGGTTTATAACCTAATTCAGATCACCGGCAAT
1 TAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACG
40124138 TAGCCTGCTAG
1 TAGCCTGCTAG
40124149 ACTTAAAGTC
Statistics
Matches: 127, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 127 1.00
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.27
Consensus pattern (41 bp):
TAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACG
Found at i:40124961 original size:12 final size:12
Alignment explanation
Indices: 40124916--40124966 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
40124906 AATAACTTTT
**
40124916 ATATATATATGT
1 ATATATATATAC
*
40124928 ATATATATTCTAGC
1 ATATATA-TATA-C
40124942 AT-TATATATAC
1 ATATATATATAC
40124953 ATATATATATAC
1 ATATATATATAC
40124965 AT
1 AT
40124967 GCTTATTCGA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
11 3 0.09
12 21 0.66
13 6 0.19
14 2 0.06
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (12 bp):
ATATATATATAC
Found at i:40127399 original size:121 final size:121
Alignment explanation
Indices: 40127185--40127422 Score: 422
Period size: 121 Copynumber: 2.0 Consensus size: 121
40127175 TCAGAAATGT
*
40127185 CTCGTTTCATACCATGCCACCAATAGTGCTGTTTCAGATCGTTATACATTTTCGTGCTACCCGGA
1 CTCGTTTCATACCATGCCACCAATAGTGCTGTTTCAGATCGTTATACATTTTCGTACTACCCGGA
*
40127250 TGAACAGAAAATCGACTATTATGAGCTTCATTCAAAATCATCTGAATTAACTCTGA
66 TGAACAGAAAATCGACTATTATGAGCTTCATTCAAAATCACCTGAATTAACTCTGA
* *
40127306 CTCGTTTCATACCATGCCACCAATAGTGCTGTTTCAGATCGTTATACATTTTTGTACTTCCCGGA
1 CTCGTTTCATACCATGCCACCAATAGTGCTGTTTCAGATCGTTATACATTTTCGTACTACCCGGA
* *
40127371 TGAACAGAAAATCGGCTATTATGAGCTTCATTCAAAATCACCTGTATTAACT
66 TGAACAGAAAATCGACTATTATGAGCTTCATTCAAAATCACCTGAATTAACT
40127423 TTGAATTTCT
Statistics
Matches: 111, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
121 111 1.00
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (121 bp):
CTCGTTTCATACCATGCCACCAATAGTGCTGTTTCAGATCGTTATACATTTTCGTACTACCCGGA
TGAACAGAAAATCGACTATTATGAGCTTCATTCAAAATCACCTGAATTAACTCTGA
Found at i:40131355 original size:41 final size:41
Alignment explanation
Indices: 40131301--40131414 Score: 138
Period size: 41 Copynumber: 2.8 Consensus size: 41
40131291 TTAATTAAAA
* * *
40131301 CAGATTCAACGGCACTTAGCTTGCTAGACTTATAGCCTGATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGACTTATAACCTGATT
* * **
40131343 TAGATCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGACTTATAACCTGATT
* *
40131384 CAGATTACCGGCAATTAGCCTGCTAGACTTA
1 CAGATCACCGGCACTTAGCCTGCTAGACTTA
40131415 AAGTCTGAAA
Statistics
Matches: 59, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
41 56 0.95
42 3 0.05
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGACTTATAACCTGATT
Found at i:40131937 original size:41 final size:41
Alignment explanation
Indices: 40131879--40131989 Score: 195
Period size: 41 Copynumber: 2.7 Consensus size: 41
40131869 ATTCGAACTC
* *
40131879 AGCGGCGTTTTTGAAGAAGCGCCGCTAAATCTCTGGTCTTT
1 AGCGGCGTTTTTTAAGAAGCGCCGCTAAAGCTCTGGTCTTT
40131920 AGCGGCGTTTTTTAAGAAGCGCCGCTAAAGCTCTGGTCTTT
1 AGCGGCGTTTTTTAAGAAGCGCCGCTAAAGCTCTGGTCTTT
*
40131961 AGGGGCGTTTTTTAAGAAGCGCCGCTAAA
1 AGCGGCGTTTTTTAAGAAGCGCCGCTAAA
40131990 AGCATTTTAT
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 67 1.00
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.30
Consensus pattern (41 bp):
AGCGGCGTTTTTTAAGAAGCGCCGCTAAAGCTCTGGTCTTT
Found at i:40132305 original size:15 final size:15
Alignment explanation
Indices: 40132282--40132320 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
40132272 GTTGAGATTT
*
40132282 AAGGTTTAGGGGTTA
1 AAGGGTTAGGGGTTA
*
40132297 AAGGGTTAGGGGTTT
1 AAGGGTTAGGGGTTA
40132312 AAGGGTTAG
1 AAGGGTTAG
40132321 ACGTGCTAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.26, C:0.00, G:0.44, T:0.31
Consensus pattern (15 bp):
AAGGGTTAGGGGTTA
Found at i:40132614 original size:14 final size:14
Alignment explanation
Indices: 40132589--40132629 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
40132579 GATTTAAGGT
*
40132589 TTAAGGGTTAGGGG
1 TTAAGAGTTAGGGG
40132603 TT-AGATGTTAGGGG
1 TTAAGA-GTTAGGGG
40132617 TTAAGAGTTAGGG
1 TTAAGAGTTAGGG
40132630 ATTTAAGGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 2 0.08
14 19 0.79
15 3 0.12
ACGTcount: A:0.24, C:0.00, G:0.44, T:0.32
Consensus pattern (14 bp):
TTAAGAGTTAGGGG
Found at i:40133384 original size:241 final size:241
Alignment explanation
Indices: 40132907--40134913 Score: 3522
Period size: 241 Copynumber: 8.3 Consensus size: 241
40132897 TTAATTTTAT
**
40132907 AAAA-AAATCAATTTAT-AAAAA-AAAATAAAAAATTTTTAGCATAGCAAAATAGCGTCATTTTG
1 AAAATAAATCAATTTATAAAAAATAAAATAAAAAA-TTTTAGCATAGCAAAACGGCGTCATTTTG
* * *
40132969 TTCAAAATGAAATAATATTTTGCGGCATTTTT-ATGAAAAACACCGCAAATAATAAATCAATTAA
65 TTCAAAATG--A-AATA----GCGGCGTTTTTGAT-AAAAACGCCGCAAAAAATAAATCAATTAA
* ****
40133033 TAAAAACCAAAATAGCAAAACGGCGTCATTTTGTTCAAAATGAAAAAAAAAATTTGTGGCGTTTT
122 TAAAAACCAAAATAGCAAAACGGCGTCATTTTGTTCAAAATG--GAAACTTTTTTGTGGCGTTTT
*
40133098 TAATAAAAACGCCGCAAAAGATAAGCAATAGCGGCGTTTTTATAAAAAGCACCACAA
185 TAATAAAAACGCCGCAAAAGATAAGCAATAGCGGCGTTTTTATAAAAAGCGCCACAA
40133155 AAAATAAATCAATTTATAAAAAATAAAATAAAAAATTTTAGCATAGCAAAACGGCGTCATTTTGT
1 AAAATAAATCAATTTATAAAAAATAAAATAAAAAATTTTAGCATAGCAAAACGGCGTCATTTTGT
40133220 TCAAAATGAAATAGCGGCGTTTTTGATAAAAACGCCGCAAAAAATAAATCAATTAATAAAAACCA
66 TCAAAATGAAATAGCGGCGTTTTTGATAAAAACGCCGCAAAAAATAAATCAATTAATAAAAACCA
*
40133285 AAATAGCAAAACGGCGTCATTTTGTTCAAGATGGAAACTTTTTTGTGGCGTTTTTAATAAAAACG
131 AAATAGCAAAACGGCGTCATTTTGTTCAAAATGGAAACTTTTTTGTGGCGTTTTTAATAAAAACG
*
40133350 CCGCAAAAGATAAGCAATAGCGGCGTTTTTATAAAAAGCGCCGCAA
196 CCGCAAAAGATAAGCAATAGCGGCGTTTTTATAAAAAGCGCCACAA
*
40133396 AAAATAAATCAATTTATAAAAACTAAAATAAAAAATTTTAGCATAGCAAAACGGCGTCATTTTGT
1 AAAATAAATCAATTTATAAAAAATAAAATAAAAAATTTTAGCATAGCAAAACGGCGTCATTTTGT
40133461 TCAAAATGAAATAGCGGCGTTTTTGATAAAAACGCCGCAAAAAATAAATCAATTAATAAAAACCA
66 TCAAAATGAAATAGCGGCGTTTTTGATAAAAACGCCGCAAAAAATAAATCAATTAATAAAAACCA
40133526 AAATAGCAAAACGGCGTCATTTTGTTCAAAATGGAAACTTTTTTGTGGCGTTTTTAATAAAAACG
131 AAATAGCAAAACGGCGTCATTTTGTTCAAAATGGAAACTTTTTTGTGGCGTTTTTAATAAAAACG
40133591 CCGCAAAAGATAAGCAATAGCGGCGTTTTTATAAAAAGCGCCACAA
196 CCGCAAAAGATAAGCAATAGCGGCGTTTTTATAAAAAGCGCCACAA
40133637 AAAATAAATCAATTTATAAAAAATAAAATAAAAAATTTTAGCATAGCAAAACGGCGTCATTTTGT
1 AAAATAAATCAATTTATAAAAAATAAAATAAAAAATTTTAGCATAGCAAAACGGCGTCATTTTGT
**
40133702 TCAAAATGAAATAGAAGCGTTTTTGATAAAAACGCCGCAAAAAATAAATCAATTAATAAAAACCA
66 TCAAAATGAAATAGCGGCGTTTTTGATAAAAACGCCGCAAAAAATAAATCAATTAATAAAAACCA
40133767 AAATAGCAAAACGGCGTCATTTTGTTCAAAATGGAAACTTTTTTGTGGCGTTTTTAATAAAAACG
131 AAATAGCAAAACGGCGTCATTTTGTTCAAAATGGAAACTTTTTTGTGGCGTTTTTAATAAAAACG
40133832 CCGCAAAAGATAAGCAATAGCGGCGTTTTTATAAAAAGCGCCACAA
196 CCGCAAAAGATAAGCAATAGCGGCGTTTTTATAAAAAGCGCCACAA
40133878 AAAATAAATCAATTTATAAAAAATAAAATAAAAAATTTTAGCATAGCAAAACGGCGTCATTTTGT
1 AAAATAAATCAATTTATAAAAAATAAAATAAAAAATTTTAGCATAGCAAAACGGCGTCATTTTGT
**
40133943 TCAAAATGAAATAGAAGCGTTTTTGATAAAAACGCCGCAAAAAATAAATCAATTAATAAAAACCA
66 TCAAAATGAAATAGCGGCGTTTTTGATAAAAACGCCGCAAAAAATAAATCAATTAATAAAAACCA
40134008 AAATAGCAAAACGGCGTCATTTTGTTCAAAATGGAAACTTTTTTGTGGCGTTTTTAATAAAAACG
131 AAATAGCAAAACGGCGTCATTTTGTTCAAAATGGAAACTTTTTTGTGGCGTTTTTAATAAAAACG
40134073 CCGCAAAAGATAAGCAATAGCGGCGTTTTTATAAAAAGCGCCACAA
196 CCGCAAAAGATAAGCAATAGCGGCGTTTTTATAAAAAGCGCCACAA
40134119 AAAATAAATCAATTTATAAAAAATAAAATAAAAAATTTTAGCATAGCAAAACGGCGTCATTTTGT
1 AAAATAAATCAATTTATAAAAAATAAAATAAAAAATTTTAGCATAGCAAAACGGCGTCATTTTGT
*
40134184 TCAAAATGAAATAGCAGCGTTTTTGATAAAAACGCCGCAAAAAATAAATCAATTAATAAAAACCA
66 TCAAAATGAAATAGCGGCGTTTTTGATAAAAACGCCGCAAAAAATAAATCAATTAATAAAAACCA
**
40134249 AAATAGCAAAACGGCGTCATTTTGTTCAAAATAAAAACTTTTTTGTGGCGTTTTTAATAAAAACG
131 AAATAGCAAAACGGCGTCATTTTGTTCAAAATGGAAACTTTTTTGTGGCGTTTTTAATAAAAACG
40134314 CCGCAAAAGATAAGCAATAGCGGCGTTTTTATAAAAAGCGCCACAA
196 CCGCAAAAGATAAGCAATAGCGGCGTTTTTATAAAAAGCGCCACAA
* *
40134360 AAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTTTAGCATAGCAAAACAGCATCATTTTG
1 AAAATAAATCAATTTAT-AAAAAATAAAATAAAAAATTTTAGCATAGCAAAACGGCGTCATTTTG
* *
40134425 TTCAAAATGAAATAGCGGCATTTTTGAT-AAAATGCCGCAAAAAATAAATCAATTAATAAAAACC
65 TTCAAAATGAAATAGCGGCGTTTTTGATAAAAACGCCGCAAAAAATAAATCAATTAATAAAAACC
*
40134489 AAAATAGCAAAACGGCGTCATTTTGTTCAAAATGAAAACTTTTTTGTGGCGTTTTTAATAAAAAC
130 AAAATAGCAAAACGGCGTCATTTTGTTCAAAATGGAAACTTTTTTGTGGCGTTTTTAATAAAAAC
40134554 GCCGCAAAAGATAAGCAATAGCGGCGTTTTTATAAAAAGCGCCACAA
195 GCCGCAAAAGATAAGCAATAGCGGCGTTTTTATAAAAAGCGCCACAA
* *
40134601 AAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTTTAGCATAGCAAAACAGCATCATTTTG
1 AAAATAAATCAATTTAT-AAAAAATAAAATAAAAAATTTTAGCATAGCAAAACGGCGTCATTTTG
* * *
40134666 TTCAAAATGAAATAGCGGCATTTTTGA-CAAAATGCCGCAAAAAATAAATCAATTAATAAAAACC
65 TTCAAAATGAAATAGCGGCGTTTTTGATAAAAACGCCGCAAAAAATAAATCAATTAATAAAAACC
* * * *
40134730 AAAATGGCAAAAGGGCGTCATGTTGTTCAAAATAGAAACTTTTTTGTGGCGTTTTTAATAAAAAC
130 AAAATAGCAAAACGGCGTCATTTTGTTCAAAATGGAAACTTTTTTGTGGCGTTTTTAATAAAAAC
40134795 GCCGCAAAAGATAAGCAATAGCGGCGTTTTTATAAAAAGCGCCACAA
195 GCCGCAAAAGATAAGCAATAGCGGCGTTTTTATAAAAAGCGCCACAA
*
40134842 AAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTTTAGCATAGCAAAATGGCGTCATTTTG
1 AAAATAAATCAATTTAT-AAAAAATAAAATAAAAAATTTTAGCATAGCAAAACGGCGTCATTTTG
40134907 TTCAAAA
65 TTCAAAA
40134914 GCAAAAAATA
Statistics
Matches: 1717, Mismatches: 36, Indels: 19
0.97 0.02 0.01
Matches are distributed among these distances:
241 1493 0.87
242 71 0.04
243 78 0.05
244 2 0.00
247 4 0.00
248 5 0.00
249 12 0.01
250 41 0.02
251 11 0.01
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.26
Consensus pattern (241 bp):
AAAATAAATCAATTTATAAAAAATAAAATAAAAAATTTTAGCATAGCAAAACGGCGTCATTTTGT
TCAAAATGAAATAGCGGCGTTTTTGATAAAAACGCCGCAAAAAATAAATCAATTAATAAAAACCA
AAATAGCAAAACGGCGTCATTTTGTTCAAAATGGAAACTTTTTTGTGGCGTTTTTAATAAAAACG
CCGCAAAAGATAAGCAATAGCGGCGTTTTTATAAAAAGCGCCACAA
Found at i:40135069 original size:212 final size:213
Alignment explanation
Indices: 40134702--40135126 Score: 762
Period size: 212 Copynumber: 2.0 Consensus size: 213
40134692 ACAAAATGCC
* *
40134702 GCAAAAAATAAATCAATTAATAAAAACCAAAATGGCAAAAGGGCGTCATGTTGTTCAAAATAGAA
1 GCAAAAAATAAATCAATTAATAAAAACCAAAATAGCAAAACGGCGTCATGTTGTTCAAAATAGAA
40134767 ACTTTTTTGTGGCGTTTTTAATAAAAACGCCGCAAAAGATAAGCAATAGCGGCGTTTTTATAAAA
66 ACTTTTTTGTGGCGTTTTTAATAAAAACGCCGCAAAAGATAAGCAATAGCGGCGTTTTTATAAAA
*
40134832 AGCGCCACAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAA-TTTTAGCATAGCAAAATG
131 AGCGCCACAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACG
*
40134896 GCGTCATTTTGTTCAAAA
196 GCGTCATTTTATTCAAAA
* *
40134914 GCAAAAAATAAATCAATTAATAAAAACCAAAATAGCAAAACGGCGTCATTTTGTTCAAAATGGAA
1 GCAAAAAATAAATCAATTAATAAAAACCAAAATAGCAAAACGGCGTCATGTTGTTCAAAATAGAA
* *
40134979 ACTTTTTTGTGGCGTTTTTAATAAAAACGCCGTAAAAGATAAGTAATAGCGGCGTTTTTATAAAA
66 ACTTTTTTGTGGCGTTTTTAATAAAAACGCCGCAAAAGATAAGCAATAGCGGCGTTTTTATAAAA
*
40135044 AGCGCCGCAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACG
131 AGCGCCACAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACG
40135109 GCGTCATTTTATTCAAAA
196 GCGTCATTTTATTCAAAA
40135127 TGATTGAATT
Statistics
Matches: 203, Mismatches: 9, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
212 169 0.83
213 34 0.17
ACGTcount: A:0.47, C:0.13, G:0.14, T:0.27
Consensus pattern (213 bp):
GCAAAAAATAAATCAATTAATAAAAACCAAAATAGCAAAACGGCGTCATGTTGTTCAAAATAGAA
ACTTTTTTGTGGCGTTTTTAATAAAAACGCCGCAAAAGATAAGCAATAGCGGCGTTTTTATAAAA
AGCGCCACAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACG
GCGTCATTTTATTCAAAA
Found at i:40135314 original size:55 final size:55
Alignment explanation
Indices: 40135230--40135341 Score: 215
Period size: 55 Copynumber: 2.0 Consensus size: 55
40135220 ATACCAAAAC
40135230 GGTGTCGTTTTCTTCCCCAAATCAAATTTGACTTAAAAAAACTTAAAACTGAGCG
1 GGTGTCGTTTTCTTCCCCAAATCAAATTTGACTTAAAAAAACTTAAAACTGAGCG
*
40135285 GGTGTCGTTTTCTTCCCCAAATCAGATTTGACTTAAAAAAACTTAAAACTGAGCG
1 GGTGTCGTTTTCTTCCCCAAATCAAATTTGACTTAAAAAAACTTAAAACTGAGCG
40135340 GG
1 GG
40135342 GTTTTGTATT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (55 bp):
GGTGTCGTTTTCTTCCCCAAATCAAATTTGACTTAAAAAAACTTAAAACTGAGCG
Found at i:40137751 original size:95 final size:94
Alignment explanation
Indices: 40137582--40137770 Score: 297
Period size: 95 Copynumber: 2.0 Consensus size: 94
40137572 TTAGCCTGAG
40137582 TGCTTCCTCTTTCATTGCCTCTACGCGCTTCCCTTTTTGTTTTTGAAGTTCTAGAGCTGGCAATA
1 TGCTTCCTCTTTCATTGCCTCTACGCGCTTCCCTTTTTGTTTTTGAAGTTCTAGAGCTGGCAATA
* *
40137647 CCATTCTTGCAGTAGGTACCTTTTTCTCA
66 CCATTCTTGCAGCACGTACCTTTTTCTCA
** * **
40137676 TGCTTCCTCTTTCATTGCCTCTGTGCGCTTCCCTTTTTTGTTTTTGAAGTTCTAGAGTTGGTGAT
1 TGCTTCCTCTTTCATTGCCTCTACGCGCTTCCC-TTTTTGTTTTTGAAGTTCTAGAGCTGGCAAT
*
40137741 ACCATTCTTGCAGCACGTACTTTTTTCTCA
65 ACCATTCTTGCAGCACGTACCTTTTTCTCA
40137771 ATTATTATAA
Statistics
Matches: 86, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
94 31 0.36
95 55 0.64
ACGTcount: A:0.14, C:0.25, G:0.16, T:0.44
Consensus pattern (94 bp):
TGCTTCCTCTTTCATTGCCTCTACGCGCTTCCCTTTTTGTTTTTGAAGTTCTAGAGCTGGCAATA
CCATTCTTGCAGCACGTACCTTTTTCTCA
Found at i:40139115 original size:43 final size:43
Alignment explanation
Indices: 40139066--40139355 Score: 245
Period size: 43 Copynumber: 6.7 Consensus size: 43
40139056 CCATAAATGA
* *
40139066 CGCTAAAGAAT-TGTACTTTTAGCGGCGTTTATGATAAAAGCGC
1 CGCTAAAGAATATGTTC-TTTAGCGGCGTTTATGATAAAAGCAC
* * * *
40139109 CGCTAAAGAGCATAT-TT-TTTAGCGGCATTTGTGATAAAAACGC
1 CGCTAAAGA--ATATGTTCTTTAGCGGCGTTTATGATAAAAGCAC
* * * *
40139152 TGCTAAAG-ATCATGTTCTTTAGCGGCATTTGTGATAAAAACAC
1 CGCTAAAGAAT-ATGTTCTTTAGCGGCGTTTATGATAAAAGCAC
* * *
40139195 TGCTAAAG-ATCATGTTCTTTAGTGGCGTTTGTGATAAAAGCAC
1 CGCTAAAGAAT-ATGTTCTTTAGCGGCGTTTATGATAAAAGCAC
* *
40139238 TGCTAAAG-ATCATGTTCTTTAGCGGCGTTTATAGGT-AAAGCAC
1 CGCTAAAGAAT-ATGTTCTTTAGCGGCGTTTAT-GATAAAAGCAC
* ** *
40139281 CGCTAAAGAACATGTTCTTTAGCGGCGTTT-TGATTTTAAGCGC
1 CGCTAAAGAATATGTTCTTTAGCGGCGTTTATGA-TAAAAGCAC
* ** *
40139324 CGCTAAAGAACATGACCTTTAGCGGAGTTTAT
1 CGCTAAAGAATATGTTCTTTAGCGGCGTTTAT
40139356 TTCTGTAAAC
Statistics
Matches: 216, Mismatches: 20, Indels: 21
0.84 0.08 0.08
Matches are distributed among these distances:
40 2 0.01
41 3 0.01
42 4 0.02
43 199 0.92
44 4 0.02
45 3 0.01
46 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (43 bp):
CGCTAAAGAATATGTTCTTTAGCGGCGTTTATGATAAAAGCAC
Found at i:40139297 original size:129 final size:128
Alignment explanation
Indices: 40139083--40139314 Score: 306
Period size: 129 Copynumber: 1.8 Consensus size: 128
40139073 GAATTGTACT
* * *
40139083 TTTAGCGGCGTTTATGATAAAAGCGCCGCTAAAGAGCATATTTTTTAGCGGCATTTGTGATAAAA
1 TTTAGCGGCGTTTATGATAAAAGCACCGCTAAAGAGCATATTCTTTAGCGGCATTTATGATAAAA
*
40139148 ACGCTGCTAAAGATCATGTTCTTTAGCGGCATTTGTGATAAAAACACTGCTAAAGATCATGTTC
66 ACGCTGCTAAAGAACATGTTCTTTAGCGGCATTT-TGATAAAAACACTGCTAAAGATCATGTTC
* * * * * * *
40139212 TTTAGTGGCGTTTGTGATAAAAGCACTGCTAAAGATCATGTTCTTTAGCGGCGTTTATAGGTAAA
1 TTTAGCGGCGTTTATGATAAAAGCACCGCTAAAGAGCATATTCTTTAGCGGCATTTAT-GATAAA
* *
40139277 GCAC-C-GCTAAAGAACATGTTCTTTAGCGGCGTTTTGAT
65 -AACGCTGCTAAAGAACATGTTCTTTAGCGGCATTTTGAT
40139315 TTTAAGCGCC
Statistics
Matches: 88, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
128 4 0.05
129 76 0.86
130 6 0.07
131 2 0.02
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (128 bp):
TTTAGCGGCGTTTATGATAAAAGCACCGCTAAAGAGCATATTCTTTAGCGGCATTTATGATAAAA
ACGCTGCTAAAGAACATGTTCTTTAGCGGCATTTTGATAAAAACACTGCTAAAGATCATGTTC
Found at i:40139329 original size:86 final size:86
Alignment explanation
Indices: 40139083--40139355 Score: 325
Period size: 86 Copynumber: 3.2 Consensus size: 86
40139073 GAATTGTACT
* * * * *
40139083 TTTAGCGGCGTTTATGATAAAAGCGCCGCTAAAGAGCATATTTTTTAGCGGCATTTGTGATAAAA
1 TTTAGCGGCGTTTATGATAAAAGCACCGCTAAAGAACATGTTCTTTAGCGGCGTTTGTGATAAAA
*
40139148 ACGCTGCTAAAGATCATGTTC
66 GCGCTGCTAAAGATCATGTTC
* * * * * *
40139169 TTTAGCGGCATTTGTGATAAAAACACTGCTAAAGATCATGTTCTTTAGTGGCGTTTGTGATAAAA
1 TTTAGCGGCGTTTATGATAAAAGCACCGCTAAAGAACATGTTCTTTAGCGGCGTTTGTGATAAAA
*
40139234 GCACTGCTAAAGATCATGTTC
66 GCGCTGCTAAAGATCATGTTC
* **
40139255 TTTAGCGGCGTTTATAGGT-AAAGCACCGCTAAAGAACATGTTCTTTAGCGGCGTTT-TGATTTT
1 TTTAGCGGCGTTTAT-GATAAAAGCACCGCTAAAGAACATGTTCTTTAGCGGCGTTTGTGA-TAA
* * **
40139318 AAGCGCCGCTAAAGAACATGACC
64 AAGCGCTGCTAAAGATCATGTTC
*
40139341 TTTAGCGGAGTTTAT
1 TTTAGCGGCGTTTAT
40139356 TTCTGTAAAC
Statistics
Matches: 158, Mismatches: 27, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
85 3 0.02
86 153 0.97
87 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.32
Consensus pattern (86 bp):
TTTAGCGGCGTTTATGATAAAAGCACCGCTAAAGAACATGTTCTTTAGCGGCGTTTGTGATAAAA
GCGCTGCTAAAGATCATGTTC
Found at i:40139329 original size:129 final size:129
Alignment explanation
Indices: 40139066--40139355 Score: 300
Period size: 129 Copynumber: 2.2 Consensus size: 129
40139056 CCATAAATGA
* * * *
40139066 CGCTAAAGAA-TTGTACTTTTAGCGGCGTTTATGATAAAAGCGCCGCTAAAGAGCATATTTTTTA
1 CGCTAAAGAACATGTTC-TTTAGCGGCGTTTATGATAAAAGCACCGCTAAAGAGCATATTCTTTA
* *
40139130 GCGGCATTTGTGATAAAAACGCTGCTAAAGATCATGTTCTTTAGCGGCATTTGTGATAAAAACAC
65 GCGGCATTTATGATAAAAACGCTGCTAAAGAACATGTTCTTTAGCGGCATTTGTGATAAAAACAC
* * * * * * *
40139195 TGCTAAAGATCATGTTCTTTAGTGGCGTTTGTGATAAAAGCACTGCTAAAGATCATGTTCTTTAG
1 CGCTAAAGAACATGTTCTTTAGCGGCGTTTATGATAAAAGCACCGCTAAAGAGCATATTCTTTAG
* * * * ** *
40139260 CGGCGTTTATAGGTAAAGCAC-C-GCTAAAGAACATGTTCTTTAGCGGCGTTT-TGATTTTAAGC
66 CGGCATTTAT-GATAAA-AACGCTGCTAAAGAACATGTTCTTTAGCGGCATTTGTGA-TAAAAAC
*
40139322 GC
128 AC
** *
40139324 CGCTAAAGAACATGACCTTTAGCGGAGTTTAT
1 CGCTAAAGAACATGTTCTTTAGCGGCGTTTAT
40139356 TTCTGTAAAC
Statistics
Matches: 129, Mismatches: 28, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
128 3 0.02
129 114 0.88
130 10 0.08
131 2 0.02
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (129 bp):
CGCTAAAGAACATGTTCTTTAGCGGCGTTTATGATAAAAGCACCGCTAAAGAGCATATTCTTTAG
CGGCATTTATGATAAAAACGCTGCTAAAGAACATGTTCTTTAGCGGCATTTGTGATAAAAACAC
Found at i:40139486 original size:22 final size:22
Alignment explanation
Indices: 40139443--40139486 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
40139433 TAGTGGCGCT
* **
40139443 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAACGCCGCTAAAAACCTA
*
40139465 AAAAAACGCCGTTAAAAACCTA
1 AAAAAACGCCGCTAAAAACCTA
40139487 TTTTGGTGTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.11
Consensus pattern (22 bp):
AAAAAACGCCGCTAAAAACCTA
Found at i:40151288 original size:17 final size:17
Alignment explanation
Indices: 40151268--40151303 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
40151258 AACTCTTAAA
40151268 ATTTTTAACATGCTTTT
1 ATTTTTAACATGCTTTT
40151285 ATTTTTAACATGCTTTT
1 ATTTTTAACATGCTTTT
40151302 AT
1 AT
40151304 AAATCTTCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.25, C:0.11, G:0.06, T:0.58
Consensus pattern (17 bp):
ATTTTTAACATGCTTTT
Found at i:40153029 original size:45 final size:45
Alignment explanation
Indices: 40152960--40153053 Score: 134
Period size: 45 Copynumber: 2.1 Consensus size: 45
40152950 AAGAGATACT
* * *
40152960 CGGTGGATTCAACACATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAACACATAGAAACCACCTTACTAATCAATGATGTC
* * *
40153005 CGGTGGAATCAGCACATAGAAACCATCTTACTAATCAATGATGTT
1 CGGTGGAATCAACACATAGAAACCACCTTACTAATCAATGATGTC
40153050 CGGT
1 CGGT
40153054 TCACATAGTA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (45 bp):
CGGTGGAATCAACACATAGAAACCACCTTACTAATCAATGATGTC
Found at i:40153117 original size:51 final size:51
Alignment explanation
Indices: 40153055--40153176 Score: 163
Period size: 51 Copynumber: 2.4 Consensus size: 51
40153045 ATGTTCGGTT
* * **
40153055 CACATAGTAGCCTACACATAGTACTACACATGTGACCATTACCATCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCAAAACCATCCGATA
* * * *
40153106 CACGTAGTAGCCTGCACATAGTACTACACACGTGATCAAAACTATCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCAAAACCATCCGATA
*
40153157 CGCATAGTAGCCTGCACATA
1 CACATAGTAGCCTGCACATA
40153177 ATCCGTGCCA
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 61 1.00
ACGTcount: A:0.34, C:0.29, G:0.16, T:0.22
Consensus pattern (51 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACCAAAACCATCCGATA
Found at i:40156677 original size:19 final size:20
Alignment explanation
Indices: 40156647--40156689 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
40156637 AACAAAAAAA
*
40156647 TTAAACGGAAAAACTAAGAC
1 TTAAACGGAAAAACTAACAC
*
40156667 TTAAA-GGAAAAATTAACAC
1 TTAAACGGAAAAACTAACAC
40156686 TTAA
1 TTAA
40156690 TCACTGAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.21
Consensus pattern (20 bp):
TTAAACGGAAAAACTAACAC
Found at i:40158823 original size:11 final size:10
Alignment explanation
Indices: 40158769--40158845 Score: 55
Period size: 11 Copynumber: 6.9 Consensus size: 10
40158759 TTTAGGTTCC
40158769 AAATTTTTTT
1 AAATTTTTTT
*
40158779 AATTTTAATTTT
1 AAATTT--TTTT
40158791 AAATTTTTTT
1 AAATTTTTTT
* *
40158801 ATATATTCTTT
1 AAAT-TTTTTT
40158812 AGAATTTTTTT
1 A-AATTTTTTT
40158823 AAAAGCTTTTTTT
1 -AAA--TTTTTTT
40158836 ATAATTTTTT
1 A-AATTTTTT
40158846 GAAAAATATA
Statistics
Matches: 53, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
10 12 0.23
11 19 0.36
12 13 0.25
13 9 0.17
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (10 bp):
AAATTTTTTT
Found at i:40158895 original size:19 final size:20
Alignment explanation
Indices: 40158857--40158903 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
40158847 AAAAATATAA
* *
40158857 ATTTTGGAATTTTTATAAA-T
1 ATTTT-GAAATTTTAAAAATT
40158877 ATTTTGAAATTTTAAAAATT
1 ATTTTGAAATTTTAAAAATT
40158897 ATTTTGA
1 ATTTTGA
40158904 TTTTTTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (20 bp):
ATTTTGAAATTTTAAAAATT
Found at i:40158909 original size:20 final size:19
Alignment explanation
Indices: 40158857--40158908 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
40158847 AAAAATATAA
*
40158857 ATTTTGGAATTTTTATAAAT
1 ATTTT-GAATTTTTAAAAAT
*
40158877 ATTTTGAAATTTTAAAAATT
1 ATTTTGAATTTTTAAAAA-T
40158897 ATTTTG-ATTTTT
1 ATTTTGAATTTTT
40158909 TTTAATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (19 bp):
ATTTTGAATTTTTAAAAAT
Found at i:40167309 original size:108 final size:107
Alignment explanation
Indices: 40167145--40167475 Score: 465
Period size: 108 Copynumber: 3.1 Consensus size: 107
40167135 ATGACATGGA
* * * *
40167145 TTGAAATTTAAG-AGGATA-TTTGGCTATTTGGTTC-AACGAGAAATCAAAACCCAGCACGTTAG
1 TTGAAATTTTAGAAGGATATTTTAGCTATTTGG-TCGAACGAAAAATCGAAACCCAGCACGTTAG
40167207 GGCACGTTTTCTCGAATTTCCAAACTCAAAATATTGCCTTATT
65 GGCACGTTTTCTCGAATTTCCAAACTCAAAATATTGCCTTATT
* *
40167250 TTGAAATTTTAGAAGGATATTTTAGCTATTTGGTCGAATGAAAAAATCGAAACCTAGCACGTTAG
1 TTGAAATTTTAGAAGGATATTTTAGCTATTTGGTCGAACG-AAAAATCGAAACCCAGCACGTTAG
* * * *
40167315 GGCGCGCTTTCTCGAACTTCTAAACGT-AAAATATTGCCTTATT
65 GGCACGTTTTCTCGAATTTCCAAAC-TCAAAATATTGCCTTATT
*
40167358 TTGAAATTTTAAAAGGATATTTTTAGCTATTTGGTCGAACGAAAAATCGAAACCCAGCACGTTAG
1 TTGAAATTTTAGAAGGATA-TTTTAGCTATTTGGTCGAACGAAAAATCGAAACCCAGCACGTTAG
* *
40167423 GGCACGTTTTCTCAAACTTT-CAAACGCAAAATATTGCCTTATT
65 GGCACGTTTTCTCGAA-TTTCCAAACTCAAAATATTGCCTTATT
40167466 TTGAAATTTT
1 TTGAAATTTT
40167476 TATTTGGATA
Statistics
Matches: 199, Mismatches: 19, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
105 11 0.06
106 8 0.04
107 15 0.08
108 142 0.71
109 23 0.12
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Consensus pattern (107 bp):
TTGAAATTTTAGAAGGATATTTTAGCTATTTGGTCGAACGAAAAATCGAAACCCAGCACGTTAGG
GCACGTTTTCTCGAATTTCCAAACTCAAAATATTGCCTTATT
Found at i:40167726 original size:15 final size:15
Alignment explanation
Indices: 40167696--40167729 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
40167686 GATTAATGAT
40167696 ATAAATAACAATATA
1 ATAAATAACAATATA
40167711 ATAAA-AACAATAATA
1 ATAAATAACAAT-ATA
40167726 ATAA
1 ATAA
40167730 TCAACGATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (15 bp):
ATAAATAACAATATA
Found at i:40169002 original size:16 final size:15
Alignment explanation
Indices: 40168969--40169001 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
40168959 TTGTTTCGAC
40168969 TTTCTTTTTTTGTCT
1 TTTCTTTTTTTGTCT
40168984 TTTCTTTTTGTTGT-T
1 TTTCTTTTT-TTGTCT
40168999 TTT
1 TTT
40169002 TGTTTGCGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.82
Consensus pattern (15 bp):
TTTCTTTTTTTGTCT
Found at i:40171730 original size:17 final size:17
Alignment explanation
Indices: 40171708--40171751 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
40171698 CTATGTGGGG
40171708 TGGCCGTGTGCCACACA
1 TGGCCGTGTGCCACACA
40171725 TGGCCGTGTGCCACACA
1 TGGCCGTGTGCCACACA
*
40171742 TGGCCATGTG
1 TGGCCGTGTG
40171752 ACAGCCCGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.16, C:0.32, G:0.32, T:0.20
Consensus pattern (17 bp):
TGGCCGTGTGCCACACA
Found at i:40177770 original size:13 final size:13
Alignment explanation
Indices: 40177754--40177793 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
40177744 TTTAAACTAA
40177754 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* *
40177767 ACTTTTCCATAGC
1 ACTTTTCAAAAGC
40177780 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
40177793 A
1 A
40177794 TTGCCAAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.35, C:0.25, G:0.07, T:0.33
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:40178892 original size:26 final size:26
Alignment explanation
Indices: 40178863--40178914 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
40178853 GTAATAGGCG
40178863 TAAGTGAAGGAGCAAGACTGAGTACT
1 TAAGTGAAGGAGCAAGACTGAGTACT
40178889 TAAGTGAAGGAGCAAGACTGAGTACT
1 TAAGTGAAGGAGCAAGACTGAGTACT
40178915 CTAGAATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.12, G:0.31, T:0.19
Consensus pattern (26 bp):
TAAGTGAAGGAGCAAGACTGAGTACT
Found at i:40182219 original size:16 final size:17
Alignment explanation
Indices: 40182192--40182229 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
40182182 CTAAAAATAG
*
40182192 ATTGAGAAAATTATTTA
1 ATTGAGAAAATTAATTA
40182209 ATTGA-AAAATTAATTA
1 ATTGAGAAAATTAATTA
40182225 ATTGA
1 ATTGA
40182230 TTAAATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (17 bp):
ATTGAGAAAATTAATTA
Found at i:40189093 original size:4 final size:4
Alignment explanation
Indices: 40189077--40189110 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
40189067 TGTGGTGAGG
40189077 TTTA TTT- TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
40189111 TAATACTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (4 bp):
TTTA
Found at i:40189733 original size:6 final size:6
Alignment explanation
Indices: 40189715--40189752 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
40189705 GAAAAAAATT
*
40189715 AAAA-G AAAA-G AAAAGG AAAAGG AAAAGG AAAAAG AAAA
1 AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AAAA
40189753 AGAGAAAAGC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
5 9 0.29
6 22 0.71
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (6 bp):
AAAAGG
Found at i:40189753 original size:6 final size:6
Alignment explanation
Indices: 40189715--40189761 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
40189705 GAAAAAAATT
* * *
40189715 AAAAG- AAAAGA AAAGGA AAAGGA AAAGGA AAAAGA AAAAGA GAAAAG
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA -AAAAG
40189762 CGAGAGAGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
5 5 0.13
6 28 0.74
7 5 0.13
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:40189828 original size:33 final size:32
Alignment explanation
Indices: 40189791--40189911 Score: 147
Period size: 33 Copynumber: 3.7 Consensus size: 32
40189781 AATATGAATG
40189791 AAACGAGTGCAAAAGAAAGAGAGCTTGAAAAGA
1 AAACGAGTG-AAAAGAAAGAGAGCTTGAAAAGA
40189824 AAACGAGTGAAAAAGAAAGAGAGCTTGAAAAGA
1 AAACGAGTG-AAAAGAAAGAGAGCTTGAAAAGA
** *
40189857 AAATAAGTGAAAGAGAGAGAGAGCTTGAAAA-A
1 AAACGAGTGAAA-AGAAAGAGAGCTTGAAAAGA
*
40189889 GAAACGTGTGAAGAAG-AAGAGAG
1 -AAACGAGTGAA-AAGAAAGAGAG
40189912 TGCTCAAACA
Statistics
Matches: 77, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
32 10 0.13
33 66 0.86
34 1 0.01
ACGTcount: A:0.55, C:0.06, G:0.30, T:0.10
Consensus pattern (32 bp):
AAACGAGTGAAAAGAAAGAGAGCTTGAAAAGA
Found at i:40189839 original size:16 final size:15
Alignment explanation
Indices: 40189791--40189859 Score: 52
Period size: 17 Copynumber: 4.2 Consensus size: 15
40189781 AATATGAATG
40189791 AAACGAGTGCAAAAGA
1 AAACGAGTG-AAAAGA
40189807 AAGA-GAGCTTGAAAAGA
1 AA-ACGAG--TGAAAAGA
40189824 AAACGAGTGAAAAAGA
1 AAACGAGTG-AAAAGA
40189840 AAGA-GAGCTTGAAAAGA
1 AA-ACGAG--TGAAAAGA
40189857 AAA
1 AAA
40189860 TAAGTGAAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 16
0.74 0.00 0.26
Matches are distributed among these distances:
15 2 0.04
16 18 0.40
17 21 0.47
18 4 0.09
ACGTcount: A:0.58, C:0.07, G:0.26, T:0.09
Consensus pattern (15 bp):
AAACGAGTGAAAAGA
Found at i:40195413 original size:2 final size:2
Alignment explanation
Indices: 40195406--40195430 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40195396 ACATATTAAT
40195406 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
40195431 GTGTGTGTTC
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:40201213 original size:30 final size:30
Alignment explanation
Indices: 40201177--40201236 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
40201167 CGAAATATCG
*
40201177 GTCATAAGCCCAATCCTATCTGCCCCATCA
1 GTCATAAACCCAATCCTATCTGCCCCATCA
* *
40201207 GTCATAAACTCAATCTTATCTGCCCCATCA
1 GTCATAAACCCAATCCTATCTGCCCCATCA
40201237 TTATCTGTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.28, C:0.37, G:0.08, T:0.27
Consensus pattern (30 bp):
GTCATAAACCCAATCCTATCTGCCCCATCA
Found at i:40206872 original size:27 final size:27
Alignment explanation
Indices: 40206842--40206893 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
40206832 TATTGAAGGA
40206842 GTTAGTACTGATTTATTTATTTATTGG
1 GTTAGTACTGATTTATTTATTTATTGG
40206869 GTTAGTACTGATTTATTTATTTATT
1 GTTAGTACTGATTTATTTATTTATT
40206894 TATTTTTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.23, C:0.04, G:0.15, T:0.58
Consensus pattern (27 bp):
GTTAGTACTGATTTATTTATTTATTGG
Found at i:40210069 original size:16 final size:18
Alignment explanation
Indices: 40210039--40210090 Score: 65
Period size: 16 Copynumber: 3.0 Consensus size: 18
40210029 TTAAATATCC
40210039 TTTATAACTTTTTTTAGAA
1 TTTATAA-TTTTTTTAGAA
*
40210058 TTT-TTATTTTTTTA-AA
1 TTTATAATTTTTTTAGAA
40210074 TTTATAA-TTTTTTAGAA
1 TTTATAATTTTTTTAGAA
40210091 AATATAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 12 0.41
17 12 0.41
18 2 0.07
19 3 0.10
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (18 bp):
TTTATAATTTTTTTAGAA
Found at i:40211124 original size:26 final size:27
Alignment explanation
Indices: 40211072--40211125 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
40211062 AAGTAAAAAC
* **
40211072 AGAAACGTTAAAAGAAATTTTTTTTAT
1 AGAAACATTAAAAGAAATTTTAATTAT
40211099 AGAAACATTAAAAG-AATTTTAATTAT
1 AGAAACATTAAAAGAAATTTTAATTAT
40211125 A
1 A
40211126 TATGATCTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 11 0.46
27 13 0.54
ACGTcount: A:0.50, C:0.04, G:0.09, T:0.37
Consensus pattern (27 bp):
AGAAACATTAAAAGAAATTTTAATTAT
Found at i:40215689 original size:21 final size:21
Alignment explanation
Indices: 40215657--40215697 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
40215647 GAACATTTGG
40215657 TGTATAGGCTAAGAA-AGGCCT
1 TGTATAGGCTAA-AACAGGCCT
40215678 TGTAT-GGCCTAAAACAGGCC
1 TGTATAGG-CTAAAACAGGCC
40215698 CCTCGAGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.22
Consensus pattern (21 bp):
TGTATAGGCTAAAACAGGCCT
Found at i:40231554 original size:17 final size:16
Alignment explanation
Indices: 40231527--40231558 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
40231517 AATTTTTATA
40231527 TTAATTATATATAATT
1 TTAATTATATATAATT
40231543 TTAATATATATATAAT
1 TTAAT-TATATATAAT
40231559 ACATCAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAATTATATATAATT
Found at i:40231694 original size:21 final size:21
Alignment explanation
Indices: 40231668--40231713 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
40231658 ACTTAACAAG
*
40231668 CAAATGTCTCTAAAATGATAA
1 CAAATGTCTCTAAAATAATAA
*
40231689 CAAATGTCTTTAAAATAATAA
1 CAAATGTCTCTAAAATAATAA
40231710 CAAA
1 CAAA
40231714 ATTAACAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.52, C:0.13, G:0.07, T:0.28
Consensus pattern (21 bp):
CAAATGTCTCTAAAATAATAA
Found at i:40237110 original size:10 final size:10
Alignment explanation
Indices: 40237095--40237119 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
40237085 AGTAGTTATT
40237095 TTTCTGTTAC
1 TTTCTGTTAC
40237105 TTTCTGTTAC
1 TTTCTGTTAC
40237115 TTTCT
1 TTTCT
40237120 TTCCTTGCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.20, G:0.08, T:0.64
Consensus pattern (10 bp):
TTTCTGTTAC
Found at i:40244684 original size:14 final size:14
Alignment explanation
Indices: 40244665--40244700 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
40244655 CTTAATTACA
40244665 AAAGAAAATTAAAT
1 AAAGAAAATTAAAT
40244679 AAAGAAAATTAAAT
1 AAAGAAAATTAAAT
*
40244693 AGAGAAAA
1 AAAGAAAA
40244701 AAAGCCTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.11, T:0.17
Consensus pattern (14 bp):
AAAGAAAATTAAAT
Found at i:40245066 original size:17 final size:17
Alignment explanation
Indices: 40245044--40245076 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40245034 TGAGTTTGTT
40245044 TAAAT-ATTATTAAATAA
1 TAAATAATTA-TAAATAA
40245061 TAAATAATTATAAATA
1 TAAATAATTATAAATA
40245077 CATACTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAATAATTATAAATAA
Found at i:40245644 original size:13 final size:12
Alignment explanation
Indices: 40245624--40245663 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
40245614 TTAATGTATA
40245624 ATTTTAATATTT
1 ATTTTAATATTT
40245636 ATTTCTAATATTT
1 ATTT-TAATATTT
*
40245649 ATTTATAATAATT
1 ATTT-TAATATTT
40245662 AT
1 AT
40245664 AATTAAGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 4 0.16
13 21 0.84
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (12 bp):
ATTTTAATATTT
Found at i:40246459 original size:16 final size:16
Alignment explanation
Indices: 40246438--40246468 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
40246428 ATATTTAATA
40246438 TATATTTGATTAAAAG
1 TATATTTGATTAAAAG
40246454 TATATTTGATTAAAA
1 TATATTTGATTAAAA
40246469 ATAAAACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (16 bp):
TATATTTGATTAAAAG
Found at i:40251839 original size:20 final size:20
Alignment explanation
Indices: 40251816--40251866 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
40251806 AATCAAGTGC
40251816 AAATGATTTTAACCAAGTCA
1 AAATGATTTTAACCAAGTCA
* * *
40251836 AAATGA-TTCAATCAAGTTA
1 AAATGATTTTAACCAAGTCA
*
40251855 AAATCATTTTAA
1 AAATGATTTTAA
40251867 AATGATTTTC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.33
Consensus pattern (20 bp):
AAATGATTTTAACCAAGTCA
Found at i:40251851 original size:19 final size:20
Alignment explanation
Indices: 40251806--40251863 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 20
40251796 ACAATTTTAA
*
40251806 AATCAAGTGC-AAATGATTTT
1 AATCAAGT-CAAAATGATTTC
*
40251826 AACCAAGTCAAAATGA-TTC
1 AATCAAGTCAAAATGATTTC
* *
40251845 AATCAAGTTAAAATCATTT
1 AATCAAGTCAAAATGATTT
40251864 TAAAATGATT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.31
Consensus pattern (20 bp):
AATCAAGTCAAAATGATTTC
Done.