Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr12
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: 39383930
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.32
Warning! 780790 characters in sequence are not A, C, G, or T
File 41 of 126
Found at i:11919769 original size:18 final size:18
Alignment explanation
Indices: 11919733--11919768 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
11919723 CCGATACAAC
11919733 ATCAATACCCAACATAAA
1 ATCAATACCCAACATAAA
*
11919751 ATCAATA-CCAACTTAAA
1 ATCAATACCCAACATAAA
11919768 A
1 A
11919769 ACTTTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.56, C:0.25, G:0.00, T:0.19
Consensus pattern (18 bp):
ATCAATACCCAACATAAA
Found at i:11923066 original size:18 final size:18
Alignment explanation
Indices: 11923032--11923091 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
11923022 TCTAGTTTAT
*
11923032 TTTTTATTT-ATTAAATTA
1 TTTTTCTTTAATT-AATTA
11923050 TTTTTCTTTAATTAATT-
1 TTTTTCTTTAATTAATTA
*
11923067 TTTATT-TTTAAATTTATTA
1 TTT-TTCTTT-AATTAATTA
11923086 TTTTTC
1 TTTTTC
11923092 ATTATCTTGG
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
17 6 0.17
18 23 0.66
19 6 0.17
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTTCTTTAATTAATTA
Found at i:11933290 original size:15 final size:16
Alignment explanation
Indices: 11933265--11933294 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
11933255 GTATAATATG
11933265 AAATAGAAAAAAATTA
1 AAATAGAAAAAAATTA
11933281 AAAT-GAAAAAAATT
1 AAATAGAAAAAAATT
11933295 CACTATTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (16 bp):
AAATAGAAAAAAATTA
Found at i:11933680 original size:20 final size:20
Alignment explanation
Indices: 11933645--11933690 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
11933635 GTATCAATCC
* *
11933645 GGTATCGATACTTTTCTTAG
1 GGTATCGATACTTTTCCTAA
11933665 GGTATCGATA-TATTTCCTAA
1 GGTATCGATACT-TTTCCTAA
11933685 GGTATC
1 GGTATC
11933691 TATTGAGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (20 bp):
GGTATCGATACTTTTCCTAA
Found at i:11935979 original size:20 final size:21
Alignment explanation
Indices: 11935949--11935999 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
11935939 AATTTAATTT
11935949 AGTTCAGCTCACTCAAGCTCA
1 AGTTCAGCTCACTCAAGCTCA
* *
11935970 AGTT-AGCTCATTCGAGCTCA
1 AGTTCAGCTCACTCAAGCTCA
11935990 A-TTCAGCTCA
1 AGTTCAGCTCA
11936000 ATCTTAACCC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 21 0.78
21 4 0.15
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.27
Consensus pattern (21 bp):
AGTTCAGCTCACTCAAGCTCA
Found at i:11936461 original size:22 final size:21
Alignment explanation
Indices: 11936432--11936479 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
11936422 AAGCATGAAC
*
11936432 TGAA-ATTTTAATGATTTAGTG
1 TGAACATTTTAATGAATT-GTG
* *
11936453 TGAACATTTTTATTAATTGTG
1 TGAACATTTTAATGAATTGTG
11936474 TGAACA
1 TGAACA
11936480 CATAGATGCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (21 bp):
TGAACATTTTAATGAATTGTG
Found at i:11940938 original size:22 final size:21
Alignment explanation
Indices: 11940909--11940956 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
11940899 AAGCATGAAC
*
11940909 TGAA-ATTTTAATGATTTAGTG
1 TGAACATTTTAATGAATT-GTG
* *
11940930 TGAACATTTTTATTAATTGTG
1 TGAACATTTTAATGAATTGTG
11940951 TGAACA
1 TGAACA
11940957 CATAGATGCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (21 bp):
TGAACATTTTAATGAATTGTG
Found at i:11943815 original size:23 final size:23
Alignment explanation
Indices: 11943789--11943861 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 23
11943779 GACTTGCTTG
* *
11943789 GTAAAGCCTGTGTGGCATATTCT
1 GTAAAGCCTATGTGGCGTATTCT
*
11943812 GTAAAGCCTTTGTGGCGTATTCT
1 GTAAAGCCTATGTGGCGTATTCT
* * * *
11943835 ATGATGCCTATGTGGCGTGTTCT
1 GTAAAGCCTATGTGGCGTATTCT
11943858 GTAA
1 GTAA
11943862 CGCCCTTGAG
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.19, C:0.16, G:0.27, T:0.37
Consensus pattern (23 bp):
GTAAAGCCTATGTGGCGTATTCT
Found at i:11950922 original size:23 final size:23
Alignment explanation
Indices: 11950896--11951005 Score: 105
Period size: 23 Copynumber: 4.7 Consensus size: 23
11950886 TAATGTTCAA
* *
11950896 GAACATGTTCATTTAAC-TTAATC
1 GAACATGTTCA-TGAACATTAAAC
11950919 GAACATGTTCATGAACATTAAAC
1 GAACATGTTCATGAACATTAAAC
* * * *
11950942 GAATATGTTCACGAACACTAAAT
1 GAACATGTTCATGAACATTAAAC
***
11950965 GAACATGTTCATGAACATATAGTT
1 GAACATGTTCATGAACAT-TAAAC
*
11950989 GAACATGTTCACGAACA
1 GAACATGTTCATGAACA
11951006 ATGTTAATAA
Statistics
Matches: 73, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
22 4 0.05
23 50 0.68
24 19 0.26
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (23 bp):
GAACATGTTCATGAACATTAAAC
Found at i:11951317 original size:22 final size:22
Alignment explanation
Indices: 11951292--11951336 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
11951282 CTGAAAACCT
*
11951292 GAAAATAAAAAATCCTCAAAAC
1 GAAAACAAAAAATCCTCAAAAC
* * *
11951314 GAAAACACAAAATTCTCTAAAC
1 GAAAACAAAAAATCCTCAAAAC
11951336 G
1 G
11951337 TGTTATGAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.58, C:0.20, G:0.07, T:0.16
Consensus pattern (22 bp):
GAAAACAAAAAATCCTCAAAAC
Found at i:11953238 original size:11 final size:11
Alignment explanation
Indices: 11953222--11953267 Score: 76
Period size: 11 Copynumber: 4.2 Consensus size: 11
11953212 TAGTAGCATC
11953222 TTCAAAAAAAA
1 TTCAAAAAAAA
11953233 TTCAAAAAAAA
1 TTCAAAAAAAA
11953244 -TCGAAAAAAAA
1 TTC-AAAAAAAA
11953255 TTCAAAAAAAA
1 TTCAAAAAAAA
11953266 TT
1 TT
11953268 TAGTTTCTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 2 0.06
11 29 0.88
12 2 0.06
ACGTcount: A:0.70, C:0.09, G:0.02, T:0.20
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:11953241 original size:10 final size:10
Alignment explanation
Indices: 11953226--11953264 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
11953216 AGCATCTTCA
11953226 AAAAAAATTC
1 AAAAAAATTC
*
11953236 AAAAAAAATC
1 AAAAAAATTC
11953246 GAAAAAAAATTC
1 --AAAAAAATTC
11953258 AAAAAAA
1 AAAAAAA
11953265 ATTTAGTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 16 0.64
12 9 0.36
ACGTcount: A:0.77, C:0.08, G:0.03, T:0.13
Consensus pattern (10 bp):
AAAAAAATTC
Found at i:11953253 original size:22 final size:22
Alignment explanation
Indices: 11953225--11953266 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
11953215 TAGCATCTTC
11953225 AAAAAAAATTCAAAAAAAATCG
1 AAAAAAAATTCAAAAAAAATCG
11953247 AAAAAAAATTCAAAAAAAAT
1 AAAAAAAATTCAAAAAAAAT
11953267 TTAGTTTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.14
Consensus pattern (22 bp):
AAAAAAAATTCAAAAAAAATCG
Found at i:11959106 original size:24 final size:24
Alignment explanation
Indices: 11959079--11959157 Score: 133
Period size: 24 Copynumber: 3.3 Consensus size: 24
11959069 TCATTAATAA
11959079 ATAAACGAGTCAATAAATGAGTTT
1 ATAAACGAGTCAATAAATGAGTTT
11959103 ATAAACGAGTCAATAAATGAGTTT
1 ATAAACGAGTCAATAAATGAGTTT
* *
11959127 ATAAACGAGCCAATAAATGAGCTT
1 ATAAACGAGTCAATAAATGAGTTT
11959151 A-AAACGA
1 ATAAACGA
11959158 ACCGAACACA
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
23 6 0.11
24 47 0.89
ACGTcount: A:0.48, C:0.11, G:0.16, T:0.24
Consensus pattern (24 bp):
ATAAACGAGTCAATAAATGAGTTT
Found at i:11959148 original size:12 final size:12
Alignment explanation
Indices: 11959078--11959143 Score: 69
Period size: 12 Copynumber: 5.5 Consensus size: 12
11959068 ATCATTAATA
11959078 AATAAACGAGTC
1 AATAAACGAGTC
* *
11959090 AATAAATGAGTT
1 AATAAACGAGTC
*
11959102 TATAAACGAGTC
1 AATAAACGAGTC
* *
11959114 AATAAATGAGTT
1 AATAAACGAGTC
* *
11959126 TATAAACGAGCC
1 AATAAACGAGTC
11959138 AATAAA
1 AATAAA
11959144 TGAGCTTAAA
Statistics
Matches: 41, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
12 41 1.00
ACGTcount: A:0.50, C:0.11, G:0.15, T:0.24
Consensus pattern (12 bp):
AATAAACGAGTC
Found at i:11960894 original size:2 final size:2
Alignment explanation
Indices: 11960849--11960874 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11960839 TCTCTCTCTA
11960849 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
11960875 CGCGCGCGCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:11966811 original size:24 final size:25
Alignment explanation
Indices: 11966779--11966834 Score: 62
Period size: 24 Copynumber: 2.2 Consensus size: 25
11966769 TAAAGTAAAA
11966779 AAAATAAAA-AATAATCAAAATTTAT
1 AAAATAAAATAATAAT-AAAATTTAT
* *
11966804 AAAA-AAAATATTAATAAAATTTCT
1 AAAATAAAATAATAATAAAATTTAT
11966828 AGAAATA
1 A-AAATA
11966835 TTATAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 13 0.50
25 12 0.46
26 1 0.04
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.29
Consensus pattern (25 bp):
AAAATAAAATAATAATAAAATTTAT
Found at i:11966854 original size:21 final size:22
Alignment explanation
Indices: 11966806--11966854 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
11966796 AAATTTATAA
* *
11966806 AAAAAATATTAATAAAATTTCT
1 AAAAAATATTAATAAAAATTAT
*
11966828 -AGAAATATT-ATAAAAATTAT
1 AAAAAATATTAATAAAAATTAT
11966848 AAAAAAT
1 AAAAAAT
11966855 TTCCAATAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAAAATATTAATAAAAATTAT
Found at i:11971725 original size:70 final size:70
Alignment explanation
Indices: 11971612--11971751 Score: 280
Period size: 70 Copynumber: 2.0 Consensus size: 70
11971602 CATTTGAATA
11971612 ATATTATTTATATTATCTTGAATAATAGATTTACCACTAAGCAATTTGCTTAGCGTATGATTTTG
1 ATATTATTTATATTATCTTGAATAATAGATTTACCACTAAGCAATTTGCTTAGCGTATGATTTTG
11971677 TTTTC
66 TTTTC
11971682 ATATTATTTATATTATCTTGAATAATAGATTTACCACTAAGCAATTTGCTTAGCGTATGATTTTG
1 ATATTATTTATATTATCTTGAATAATAGATTTACCACTAAGCAATTTGCTTAGCGTATGATTTTG
11971747 TTTTC
66 TTTTC
11971752 TTCGTGCATA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.47
Consensus pattern (70 bp):
ATATTATTTATATTATCTTGAATAATAGATTTACCACTAAGCAATTTGCTTAGCGTATGATTTTG
TTTTC
Found at i:11975441 original size:17 final size:17
Alignment explanation
Indices: 11975415--11975447 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
11975405 CACTAACATT
*
11975415 AAAATGCAATGACAATA
1 AAAATACAATGACAATA
11975432 AAAATACAATGACAAT
1 AAAATACAATGACAAT
11975448 TTTCACTAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.12, G:0.09, T:0.18
Consensus pattern (17 bp):
AAAATACAATGACAATA
Found at i:11975590 original size:21 final size:20
Alignment explanation
Indices: 11975560--11975604 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
11975550 GCACGATGTT
*
11975560 TCTTCTTCTTCCTCTTTTTC
1 TCTTCTTCTTCATCTTTTTC
* *
11975580 TCTTCCTTCTTGATCTTTTTG
1 TCTT-CTTCTTCATCTTTTTC
11975601 TCTT
1 TCTT
11975605 TGAAGCGCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.02, C:0.29, G:0.04, T:0.64
Consensus pattern (20 bp):
TCTTCTTCTTCATCTTTTTC
Found at i:11984034 original size:16 final size:17
Alignment explanation
Indices: 11984013--11984045 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
11984003 AAATATTATG
11984013 AAATAAA-ATCAAACAA
1 AAATAAACATCAAACAA
11984029 AAATAAACATCAAACAA
1 AAATAAACATCAAACAA
11984046 TGCCATCCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.73, C:0.15, G:0.00, T:0.12
Consensus pattern (17 bp):
AAATAAACATCAAACAA
Found at i:11986243 original size:14 final size:14
Alignment explanation
Indices: 11986224--11986250 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11986214 TAGCTTTAGT
11986224 TTTAATTAGTTTAA
1 TTTAATTAGTTTAA
11986238 TTTAATTAGTTTA
1 TTTAATTAGTTTA
11986251 TCATTATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
TTTAATTAGTTTAA
Found at i:11986331 original size:25 final size:25
Alignment explanation
Indices: 11986303--11986352 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
11986293 TTCTAGTAGA
* *
11986303 CTAATAATTATTTTCTACAAGTAAC
1 CTAATAATAATTTTCTACAAATAAC
*
11986328 CTAATAATAATTTTCTCCAAATAAC
1 CTAATAATAATTTTCTACAAATAAC
11986353 AATCCATTCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.42, C:0.18, G:0.02, T:0.38
Consensus pattern (25 bp):
CTAATAATAATTTTCTACAAATAAC
Found at i:11992900 original size:25 final size:25
Alignment explanation
Indices: 11992871--11992920 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
11992861 AAAATGAAAC
* *
11992871 ATTAAGTGCACAAGATAGTGAAAGT
1 ATTAAGTGAACAAAATAGTGAAAGT
11992896 ATTAAGTGAACAAAATAGTGAAAGT
1 ATTAAGTGAACAAAATAGTGAAAGT
11992921 GAAAGGTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.48, C:0.06, G:0.22, T:0.24
Consensus pattern (25 bp):
ATTAAGTGAACAAAATAGTGAAAGT
Found at i:11996233 original size:14 final size:14
Alignment explanation
Indices: 11996216--11996245 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
11996206 AATACGAAGA
11996216 AAGAAATGTTTGAT
1 AAGAAATGTTTGAT
11996230 AAGAAATGTTTGAT
1 AAGAAATGTTTGAT
11996244 AA
1 AA
11996246 TCACAATGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (14 bp):
AAGAAATGTTTGAT
Found at i:11998014 original size:28 final size:28
Alignment explanation
Indices: 11997943--11998024 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 28
11997933 AGTGGTGGAT
*
11997943 AATCCAAAGTACAAGCCAAAGTGACGAAC
1 AATCC-AAGTACAAGCCAAAGTGGCGAAC
* *
11997972 AGTCCAAGTATAAGCCAAAGTGGCGAAC
1 AATCCAAGTACAAGCCAAAGTGGCGAAC
* * *
11998000 AATCCCAGTGCAAGCCAATGTGGCG
1 AATCCAAGTACAAGCCAAAGTGGCG
11998025 GATAGTCCGA
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 41 0.91
29 4 0.09
ACGTcount: A:0.39, C:0.24, G:0.23, T:0.13
Consensus pattern (28 bp):
AATCCAAGTACAAGCCAAAGTGGCGAAC
Found at i:12000554 original size:43 final size:43
Alignment explanation
Indices: 12000490--12000607 Score: 132
Period size: 43 Copynumber: 2.7 Consensus size: 43
12000480 CTGATAAGTG
* *
12000490 TTTTCGTGTAATAGCACGTCTGGGACATTGGCATCGACTTGT-A
1 TTTTCGTGTAAGA-CCCGTCTGGGACATTGGCATCGACTTGTGA
* *
12000533 TTTTCGTGTAAGACCCTGTCTGGGACAATGGCATCGATTTGTGA
1 TTTTCGTGTAAGACCC-GTCTGGGACATTGGCATCGACTTGTGA
* * *
12000577 -TTACATGTAAGACCACGTCTGGGACGTTGGC
1 TTTTCGTGTAAGACC-CGTCTGGGACATTGGC
12000608 GTTGTACGAG
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
42 2 0.03
43 60 0.94
44 2 0.03
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.32
Consensus pattern (43 bp):
TTTTCGTGTAAGACCCGTCTGGGACATTGGCATCGACTTGTGA
Found at i:12003497 original size:29 final size:29
Alignment explanation
Indices: 12003446--12003543 Score: 92
Period size: 29 Copynumber: 3.4 Consensus size: 29
12003436 AACAGTGGTG
*
12003446 GACAAGCCAAAAGTACAAGCCAAAGTGGCA
1 GACAATCC-AAAGTACAAGCCAAAGTGGCA
* *
12003476 GACAATCCAAAGTACAAGCCAAAATGG-T
1 GACAATCCAAAGTACAAGCCAAAGTGGCA
* * *
12003504 GAACAATCC-TAGTGCAAGCCAATGTGGCA
1 G-ACAATCCAAAGTACAAGCCAAAGTGGCA
* *
12003533 GATAGTCCAAA
1 GACAATCCAAA
12003544 TGTGGCGAAC
Statistics
Matches: 54, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
28 20 0.37
29 27 0.50
30 7 0.13
ACGTcount: A:0.43, C:0.22, G:0.21, T:0.13
Consensus pattern (29 bp):
GACAATCCAAAGTACAAGCCAAAGTGGCA
Found at i:12003547 original size:18 final size:18
Alignment explanation
Indices: 12003524--12003584 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
12003514 AGTGCAAGCC
12003524 AATGTGGCAGATAGTCCA
1 AATGTGGCAGATAGTCCA
* *
12003542 AATGTGGC-GAACAATCCA
1 AATGTGGCAG-ATAGTCCA
*
12003560 AATGTGGCAAATAGTCCA
1 AATGTGGCAGATAGTCCA
12003578 AATGTGG
1 AATGTGG
12003585 TGAACAATCT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 1 0.03
18 35 0.97
ACGTcount: A:0.36, C:0.16, G:0.26, T:0.21
Consensus pattern (18 bp):
AATGTGGCAGATAGTCCA
Found at i:12003603 original size:36 final size:36
Alignment explanation
Indices: 12003524--12003593 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
12003514 AGTGCAAGCC
*
12003524 AATGTGGCAGATAGTCCAAATGTGGCGAACAATCCA
1 AATGTGGCAAATAGTCCAAATGTGGCGAACAATCCA
*
12003560 AATGTGGCAAATAGTCCAAATGTGGTGAACAATC
1 AATGTGGCAAATAGTCCAAATGTGGCGAACAATC
12003594 TAAGAGTGGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.21
Consensus pattern (36 bp):
AATGTGGCAAATAGTCCAAATGTGGCGAACAATCCA
Found at i:12006880 original size:22 final size:20
Alignment explanation
Indices: 12006832--12006870 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
12006822 TCATATAGTG
12006832 AAATATTTTATTTTATATAT
1 AAATATTTTATTTTATATAT
12006852 AAATATTTTATTTTATATA
1 AAATATTTTATTTTATATA
12006871 ATTAAGTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
AAATATTTTATTTTATATAT
Found at i:12020808 original size:38 final size:38
Alignment explanation
Indices: 12020754--12020828 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 38
12020744 GGTGAAATTC
* * *
12020754 AGGCTTAGTGATTAGCAGGCTTTGTGCTGATGTTATTT
1 AGGCTTAGTGACTAGCAGGCTTGGTGCCGATGTTATTT
* *
12020792 AGGCTTAGTGCCTAGCAGGCTTGGTGCCGGTGTTATT
1 AGGCTTAGTGACTAGCAGGCTTGGTGCCGATGTTATT
12020829 AGTGCCGGTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.16, C:0.15, G:0.32, T:0.37
Consensus pattern (38 bp):
AGGCTTAGTGACTAGCAGGCTTGGTGCCGATGTTATTT
Found at i:12020835 original size:15 final size:15
Alignment explanation
Indices: 12020815--12020843 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
12020805 AGCAGGCTTG
12020815 GTGCCGGTGTTATTA
1 GTGCCGGTGTTATTA
12020830 GTGCCGGTGTTATT
1 GTGCCGGTGTTATT
12020844 CAGGCTTAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.14, G:0.34, T:0.41
Consensus pattern (15 bp):
GTGCCGGTGTTATTA
Found at i:12021128 original size:12 final size:12
Alignment explanation
Indices: 12021113--12021145 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
12021103 AACAGAACCG
12021113 TAAATATTTTTA
1 TAAATATTTTTA
12021125 TAAATATTTTTA
1 TAAATATTTTTA
12021137 TAAATATTT
1 TAAATATTT
12021146 ACGGAGTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TAAATATTTTTA
Found at i:12021993 original size:287 final size:287
Alignment explanation
Indices: 12021477--12022055 Score: 1095
Period size: 287 Copynumber: 2.0 Consensus size: 287
12021467 CATTGTTAAA
12021477 GACTTTGAAGCTTCGGCCAAGCTTCAATGTATTCATGTAAGTCCATTTTGAACCCGTTTCTCGTA
1 GACTTTGAAGCTTCGGCCAAGCTTCAATGTATTCATGTAAGTCCATTTTGAACCCGTTTCTCGTA
* *
12021542 ATTTTTATGTTTTTGAGATCGTTGCAACTAGGTCCAGCTAGCCCGTACCTTCGTTTTTGAATTTG
66 ATTTTTATGTTTTTGAGATCGTTGCAACTAGGTCCAGCTAGCCCGTACCTTCATTTTTAAATTTG
*
12021607 TTAAAGATTTTAAATGTTGCCATTGATGAATCTTTGTGATTTTAGATTTTAAGTGATGAATTTGA
131 TTAAAGATTTTAAATGTTGCCATTGATGAATCTTTGTGATTTTAGATGTTAAGTGATGAATTTGA
*
12021672 AGTATTAGTTGTTATTTATAAGTATTTTGTTAAGTGATTTTTAATGATTTAAATGTTTAGGGATT
196 AGTATTAGTTGTTATTTATAAGTATTTTGTTAAGTAATTTTTAATGATTTAAATGTTTAGGGATT
*
12021737 AAATTGCTAAAGGAATAATAATTCAAG
261 AAATTGCTAAAGGAATAATAAGTCAAG
*
12021764 GACTTTGAAGCTTCGGCCAAGCTTTAATGTATTCATGTAAGTCCATTTTGAACCCGTTTCTCGTA
1 GACTTTGAAGCTTCGGCCAAGCTTCAATGTATTCATGTAAGTCCATTTTGAACCCGTTTCTCGTA
12021829 ATTTTTATGTTTTTGAGATCGTTGCAACTAGGTCCAGCTAGCCCGTACCTTCATTTTTAAATTTG
66 ATTTTTATGTTTTTGAGATCGTTGCAACTAGGTCCAGCTAGCCCGTACCTTCATTTTTAAATTTG
12021894 TTAAAGATTTTAAATGTTGCCATTGATGAATCTTTGTGATTTTAGATGTTAAGTGATGAATTTGA
131 TTAAAGATTTTAAATGTTGCCATTGATGAATCTTTGTGATTTTAGATGTTAAGTGATGAATTTGA
*
12021959 AGTATTTGTTGTTATTTATAAGTATTTTGTTAAGTAATTTTTAATGATTTAAATGTTTAGGGATT
196 AGTATTAGTTGTTATTTATAAGTATTTTGTTAAGTAATTTTTAATGATTTAAATGTTTAGGGATT
12022024 AAATTGCTAAAGGAATAATAAGTCAAG
261 AAATTGCTAAAGGAATAATAAGTCAAG
12022051 GACTT
1 GACTT
12022056 GATGTGAAAT
Statistics
Matches: 285, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
287 285 1.00
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.42
Consensus pattern (287 bp):
GACTTTGAAGCTTCGGCCAAGCTTCAATGTATTCATGTAAGTCCATTTTGAACCCGTTTCTCGTA
ATTTTTATGTTTTTGAGATCGTTGCAACTAGGTCCAGCTAGCCCGTACCTTCATTTTTAAATTTG
TTAAAGATTTTAAATGTTGCCATTGATGAATCTTTGTGATTTTAGATGTTAAGTGATGAATTTGA
AGTATTAGTTGTTATTTATAAGTATTTTGTTAAGTAATTTTTAATGATTTAAATGTTTAGGGATT
AAATTGCTAAAGGAATAATAAGTCAAG
Found at i:12030312 original size:38 final size:37
Alignment explanation
Indices: 12030260--12030490 Score: 219
Period size: 38 Copynumber: 6.1 Consensus size: 37
12030250 ATGAGGTCAA
* * * *
12030260 ATTCAAGCTTAGTGCCTAGTAAGCTTAGTCCCAGTGTT
1 ATTCAGGCTTAGTGCCTAGCAGGCTTAGTGCC-GTGTT
* ** *
12030298 ATTCAGGCTCAGTGCCTAATAGGCTTAGTGTCGGTGTT
1 ATTCAGGCTTAGTGCCTAGCAGGCTTAGTG-CCGTGTT
* * *
12030336 ATTCAGACTTAGAGCTTAGCAGGCTTAGTGCCGATGTT
1 ATTCAGGCTTAGTGCCTAGCAGGCTTAGTGCCG-TGTT
* * **
12030374 ATCCAGGCTTACTGCCTAATAGGCTTAGTGCCTGTGTT
1 ATTCAGGCTTAGTGCCTAGCAGGCTTAGTGCC-GTGTT
* * *
12030412 ATTCATGCTTAGTGTCTAGCAGGCTTAGTGTCGATGTT
1 ATTCAGGCTTAGTGCCTAGCAGGCTTAGTGCCG-TGTT
* * *
12030450 ATTCTGGCTTAATGCCTAGCAGGTTTAGTGCCAGTGTT
1 ATTCAGGCTTAGTGCCTAGCAGGCTTAGTGCC-GTGTT
12030488 ATT
1 ATT
12030491 TAGACTTATT
Statistics
Matches: 155, Mismatches: 33, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
37 3 0.02
38 149 0.96
39 3 0.02
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.35
Consensus pattern (37 bp):
ATTCAGGCTTAGTGCCTAGCAGGCTTAGTGCCGTGTT
Found at i:12030390 original size:76 final size:76
Alignment explanation
Indices: 12030294--12030498 Score: 252
Period size: 76 Copynumber: 2.7 Consensus size: 76
12030284 TTAGTCCCAG
* * * *
12030294 TGTTATTCAGGCTCAGTGCCTAATAGGCTTAGTGTCGGTGTTATTCAGACTTAGAG-CTTAGCAG
1 TGTTATTCAGGCTTAATGCCTAATAGGCTTAGTGCCAGTGTTATTCAGACTTAGAGTC-TAGCAG
12030358 GCTTAGTGCCGA
65 GCTTAGTGCCGA
* * * *
12030370 TGTTATCCAGGCTTACTGCCTAATAGGCTTAGTGCCTGTGTTATTCATG-CTTAGTGTCTAGCAG
1 TGTTATTCAGGCTTAATGCCTAATAGGCTTAGTGCCAGTGTTATTCA-GACTTAGAGTCTAGCAG
*
12030434 GCTTAGTGTCGA
65 GCTTAGTGCCGA
* ** * *
12030446 TGTTATTCTGGCTTAATGCCTAGCAGGTTTAGTGCCAGTGTTATTTAGACTTA
1 TGTTATTCAGGCTTAATGCCTAATAGGCTTAGTGCCAGTGTTATTCAGACTTA
12030499 TTGCCACTGT
Statistics
Matches: 111, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
75 1 0.01
76 108 0.97
77 2 0.02
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (76 bp):
TGTTATTCAGGCTTAATGCCTAATAGGCTTAGTGCCAGTGTTATTCAGACTTAGAGTCTAGCAGG
CTTAGTGCCGA
Found at i:12030470 original size:114 final size:114
Alignment explanation
Indices: 12030266--12030489 Score: 281
Period size: 114 Copynumber: 2.0 Consensus size: 114
12030256 TCAAATTCAA
* * *
12030266 GCTTAGTGCCTAGTAAGCTTAGTCCCAGTGTTATTCAGGCTCAGTGCCTAATAGGCTTAGTGTCG
1 GCTTACTGCCTAATAAGCTTAGTCCCAGTGTTATTCAGGCTCAGTGCCTAACAGGCTTAGTGTCG
* *
12030331 GTGTTATTCAGACTTAGAGCTTAGCAGGCTTAGTGCC-GATGTTATCCAG
66 ATGTTATTCAGACTTAGAGCCTAGCAGGCTTAGTGCCAG-TGTTATCCAG
* * * * * * *
12030380 GCTTACTGCCTAATAGGCTTAGTGCCTGTGTTATTCATGCTTAGTGTCTAGCAGGCTTAGTGTCG
1 GCTTACTGCCTAATAAGCTTAGTCCCAGTGTTATTCAGGCTCAGTGCCTAACAGGCTTAGTGTCG
* * *
12030445 ATGTTATTCTGGCTTA-ATGCCTAGCAGGTTTAGTGCCAGTGTTAT
66 ATGTTATTCAGACTTAGA-GCCTAGCAGGCTTAGTGCCAGTGTTAT
12030490 TTAGACTTAT
Statistics
Matches: 93, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
113 1 0.01
114 91 0.98
115 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (114 bp):
GCTTACTGCCTAATAAGCTTAGTCCCAGTGTTATTCAGGCTCAGTGCCTAACAGGCTTAGTGTCG
ATGTTATTCAGACTTAGAGCCTAGCAGGCTTAGTGCCAGTGTTATCCAG
Found at i:12032844 original size:50 final size:50
Alignment explanation
Indices: 12032738--12032957 Score: 260
Period size: 50 Copynumber: 4.3 Consensus size: 50
12032728 GAAGATGTGA
*
12032738 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAGG
* *
12032794 TCCCATGTAAGACCATGTCTGAGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* **
12032844 TCTCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
** * * * **
12032894 TCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAAAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
*
12032944 TCCGATGTAAGACC
1 TCCCATGTAAGACC
12032958 GTATCTAGGA
Statistics
Matches: 145, Mismatches: 19, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
50 106 0.73
53 3 0.02
55 1 0.01
56 35 0.24
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.22
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:12032979 original size:100 final size:100
Alignment explanation
Indices: 12032786--12032980 Score: 230
Period size: 100 Copynumber: 1.9 Consensus size: 100
12032776 CATTGAGATT
* * * * **
12032786 ATGAGAGGTCCCATGTAAGACCATGTCTGAGACATGGCGTTGGCACCGAGATGAGAGGTCTCATG
1 ATGAGAGGTCCCACGTAAGACCATGTCTGAGACATGGCATGGGCACCGAGATGAAAACTCTCATG
* * ***
12032851 TAAGACCATGTCTGGGACATGGTGTTGGCACCGAG
66 TAAGACCATATCTAGGACATGAAATTGGCACCGAG
* * *
12032886 ATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAAAACTC-CGAT
1 ATGAGAGGTCCCACGTAAGACCATGTCTGAGACATGGCATGGGCACCGAGATGAAAACTCTC-AT
* *
12032950 GTAAGACCGTATCTAGGATATGAAATTGGCA
65 GTAAGACCATATCTAGGACATGAAATTGGCA
12032981 GTAAAGGAAA
Statistics
Matches: 78, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
99 1 0.01
100 77 0.99
ACGTcount: A:0.28, C:0.21, G:0.30, T:0.22
Consensus pattern (100 bp):
ATGAGAGGTCCCACGTAAGACCATGTCTGAGACATGGCATGGGCACCGAGATGAAAACTCTCATG
TAAGACCATATCTAGGACATGAAATTGGCACCGAG
Found at i:12037095 original size:50 final size:50
Alignment explanation
Indices: 12037020--12037190 Score: 243
Period size: 50 Copynumber: 3.4 Consensus size: 50
12037010 TGATTTTCAG
*
12037020 ATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAAGACC
1 ATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACC
* **
12037070 ATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCGTAAGACC
1 ATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACC
* * **
12037120 ATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCCCATGTAAGACC
1 ATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACC
* * *
12037170 ATATCTAGGATATGGCATTGG
1 ATGTCTGGGACATGGCATTGG
12037191 TAGTAAACGA
Statistics
Matches: 108, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 108 1.00
ACGTcount: A:0.25, C:0.22, G:0.32, T:0.21
Consensus pattern (50 bp):
ATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACC
Found at i:12040104 original size:23 final size:22
Alignment explanation
Indices: 12040077--12040132 Score: 78
Period size: 21 Copynumber: 2.5 Consensus size: 22
12040067 TAAATCTAAT
*
12040077 AAATTATAAAAAAATATTATATA
1 AAATTATAAAAAAA-ATTATAAA
12040100 AAATTAT-AAAAAAATTATAAA
1 AAATTATAAAAAAAATTATAAA
*
12040121 AAATCATAAAAA
1 AAATTATAAAAA
12040133 TGGAAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 13 0.43
22 10 0.33
23 7 0.23
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.29
Consensus pattern (22 bp):
AAATTATAAAAAAAATTATAAA
Found at i:12040120 original size:19 final size:19
Alignment explanation
Indices: 12040077--12040318 Score: 80
Period size: 17 Copynumber: 12.7 Consensus size: 19
12040067 TAAATCTAAT
12040077 AAATTATAAAAAAATATTATATA
1 AAATTAT-AAAAAA-A-T-TATA
12040100 AAATTATAAAAAAATTATA
1 AAATTATAAAAAAATTATA
* * *
12040119 AAA-AATCATAAAAATGGA-A
1 AAATTAT-AAAAAAAT-TATA
* *
12040138 AAA-TAT-TAAAAA-TAGGA
1 AAATTATAAAAAAATTA-TA
* *
12040155 AAATTATTAAAAAATCATA
1 AAATTATAAAAAAATTATA
* *
12040174 AAATTAT--TAAAATTAAA
1 AAATTATAAAAAAATTATA
**
12040191 AAATTA-AAATTAA-TATA
1 AAATTATAAAAAAATTATA
*
12040208 AACTTAT-AAAAAATTATAA
1 AAATTATAAAAAAATTAT-A
**
12040227 TAAAAAATAATAAAAACTTATA
1 -AAATTATAA-AAAAA-TTATA
* *
12040249 AATATTATAAAAATATAAT-
1 AA-ATTATAAAAAAATTATA
12040268 AAA-TAT-AAAAAATTATA
1 AAATTATAAAAAAATTATA
* **
12040285 AAA-AATAATATAAACGTATAA
1 AAATTATAA-A-AAAATTAT-A
12040306 AAATTATAAAAAA
1 AAATTATAAAAAA
12040319 TAAAAAATAA
Statistics
Matches: 165, Mismatches: 31, Indels: 49
0.67 0.13 0.20
Matches are distributed among these distances:
15 1 0.01
16 8 0.05
17 43 0.26
18 12 0.07
19 37 0.22
20 19 0.12
21 13 0.08
22 21 0.13
23 11 0.07
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (19 bp):
AAATTATAAAAAAATTATA
Found at i:12040121 original size:9 final size:9
Alignment explanation
Indices: 12040039--12040326 Score: 99
Period size: 9 Copynumber: 31.7 Consensus size: 9
12040029 AAAAGTAATA
12040039 AAAAATTAT
1 AAAAATTAT
* *
12040048 AAATATTTT
1 AAAAATTAT
12040057 AAAAATCTA-
1 AAAAAT-TAT
*
12040066 ATAAATCTA-
1 AAAAAT-TAT
*
12040075 ATAAATTAT
1 AAAAATTAT
12040084 AAAAAAATATTAT
1 ---AAAA-ATTAT
12040097 ATAAAATTAT
1 A-AAAATTAT
12040107 AAAAAAATTAT
1 --AAAAATTAT
*
12040118 AAAAAATCAT
1 -AAAAATTAT
**
12040128 AAAAA-TGG
1 AAAAATTAT
12040136 AAAAA-TATT
1 AAAAATTA-T
*
12040145 AAAAA-TAG
1 AAAAATTAT
*
12040153 GAAAATTATT
1 AAAAATTA-T
*
12040163 AAAAAATCAT
1 -AAAAATTAT
12040173 -AAAATTAT
1 AAAAATTAT
*
12040181 TAAAATTA-
1 AAAAATTAT
12040189 AAAAA-T-T
1 AAAAATTAT
12040196 -AAAATTAAT
1 AAAAATT-AT
*
12040205 ATAAACTTAT
1 A-AAAATTAT
12040215 AAAAAATTAT
1 -AAAAATTAT
12040225 ---AA-TA-
1 AAAAATTAT
*
12040229 AAAAATAAT
1 AAAAATTAT
12040238 AAAAACTTAT
1 AAAAA-TTAT
*
12040248 AAATATTAT
1 AAAAATTAT
12040257 AAAAA-TAT
1 AAAAATTAT
12040265 AATAAA-TAT
1 AA-AAATTAT
12040274 AAAAAATTAT
1 -AAAAATTAT
*
12040284 AAAAAATAAT
1 -AAAAATTAT
**
12040294 ATAAACGTAT
1 A-AAAATTAT
12040304 AAAAATTAT
1 AAAAATTAT
*
12040313 AAAAAATA-
1 AAAAATTAT
12040321 AAAAAT
1 AAAAAT
12040327 AAACTTGAAC
Statistics
Matches: 215, Mismatches: 33, Indels: 63
0.69 0.11 0.20
Matches are distributed among these distances:
5 2 0.01
6 6 0.03
7 4 0.02
8 34 0.16
9 84 0.39
10 53 0.25
11 23 0.11
12 4 0.02
13 5 0.02
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:12040185 original size:18 final size:18
Alignment explanation
Indices: 12040127--12040185 Score: 68
Period size: 19 Copynumber: 3.3 Consensus size: 18
12040117 TAAAAAATCA
*
12040127 TAAAAAT-GGAAAAATAT
1 TAAAAATAGGAAAATTAT
12040144 TAAAAATAGGAAAATTAT
1 TAAAAATAGGAAAATTAT
*
12040162 TAAAAAATCA-TAAAATTAT
1 T-AAAAAT-AGGAAAATTAT
12040181 TAAAA
1 TAAAA
12040186 TTAAAAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
17 7 0.19
18 14 0.38
19 15 0.41
20 1 0.03
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.27
Consensus pattern (18 bp):
TAAAAATAGGAAAATTAT
Found at i:12040218 original size:33 final size:33
Alignment explanation
Indices: 12040171--12040276 Score: 101
Period size: 34 Copynumber: 3.2 Consensus size: 33
12040161 TTAAAAAATC
*
12040171 ATAAAATTATTAAAATTA-AAAAATTAAAATTAAT
1 ATAAACTTA-TAAAATTATAAAAA-TAAAATTAAT
*
12040205 ATAAACTTATAAAAAATTATAATAA-AAAA-TAAT
1 ATAAACTTAT--AAAATTATAAAAATAAAATTAAT
* * *
12040238 AAAAACTTATAAATATTATAAAAATATAATAAAT
1 ATAAACTTATAAA-ATTATAAAAATAAAATTAAT
12040272 ATAAA
1 ATAAA
12040277 AAATTATAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
31 3 0.05
32 9 0.15
33 17 0.29
34 19 0.32
35 7 0.12
36 4 0.07
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (33 bp):
ATAAACTTATAAAATTATAAAAATAAAATTAAT
Found at i:12040231 original size:13 final size:13
Alignment explanation
Indices: 12040213--12040298 Score: 52
Period size: 13 Copynumber: 6.4 Consensus size: 13
12040203 ATATAAACTT
*
12040213 ATAAAAAATTATA
1 ATAAAAAATAATA
12040226 ATAAAAAATAATA
1 ATAAAAAATAATA
* *
12040239 AAAACTTATAAAT-ATT
1 ATAA---A-AAATAATA
12040255 ATAAAAATATAATAA
1 ATAAAAA-ATAAT-A
* *
12040270 ATATAAAA-AATT
1 ATAAAAAATAATA
12040282 ATAAAAAATAAT-
1 ATAAAAAATAATA
12040294 ATAAA
1 ATAAA
12040299 CGTATAAAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 17
0.70 0.10 0.21
Matches are distributed among these distances:
12 14 0.25
13 24 0.42
14 3 0.05
15 6 0.11
16 6 0.11
17 4 0.07
ACGTcount: A:0.70, C:0.01, G:0.00, T:0.29
Consensus pattern (13 bp):
ATAAAAAATAATA
Found at i:12040288 original size:56 final size:58
Alignment explanation
Indices: 12040212--12040327 Score: 166
Period size: 56 Copynumber: 2.0 Consensus size: 58
12040202 AATATAAACT
* * *
12040212 TATAAAAAATTATAATAAAAAATAATAAAAACTTATAAATATTATAAAAATATAATAAA
1 TATAAAAAATTATAATAAAAAATAATAAAAACGTATAAAAATTATAAAAA-ATAAAAAA
*
12040271 TATAAAAAA-T-T-ATAAAAAATAATATAAACGTATAAAAATTATAAAAAATAAAAAA
1 TATAAAAAATTATAATAAAAAATAATAAAAACGTATAAAAATTATAAAAAATAAAAAA
12040326 TA
1 TA
12040328 AACTTGAACT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
55 9 0.17
56 33 0.62
57 1 0.02
58 1 0.02
59 9 0.17
ACGTcount: A:0.69, C:0.02, G:0.01, T:0.28
Consensus pattern (58 bp):
TATAAAAAATTATAATAAAAAATAATAAAAACGTATAAAAATTATAAAAAATAAAAAA
Found at i:12041035 original size:31 final size:31
Alignment explanation
Indices: 12040987--12041047 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
12040977 TTATAAGTTT
*
12040987 TTTTATAAATTTTTAAATATTTTA-AATATA
1 TTTTATAAATTTATAAATATTTTATAATATA
*
12041017 TTTTATTAACTTTATAAATATTTTATAATAT
1 TTTTA-TAAATTTATAAATATTTTATAATAT
12041048 CTTATATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 5 0.19
31 17 0.63
32 5 0.19
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (31 bp):
TTTTATAAATTTATAAATATTTTATAATATA
Found at i:12041052 original size:10 final size:10
Alignment explanation
Indices: 12040987--12041066 Score: 62
Period size: 10 Copynumber: 8.2 Consensus size: 10
12040977 TTATAAGTTT
12040987 TTTTATAA-A
1 TTTTATAATA
12040996 TTTT-TAAATA
1 TTTTAT-AATA
*
12041006 TTTTAAATATA
1 TTTTATA-ATA
*
12041017 TTTTATTA-A
1 TTTTATAATA
*
12041026 CTTTATAAATA
1 TTTTAT-AATA
12041037 TTTTATAATA
1 TTTTATAATA
*
12041047 TCTTAT-AT-
1 TTTTATAATA
12041055 TTTTATAATA
1 TTTTATAATA
12041065 TT
1 TT
12041067 CATAAGTTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
8 6 0.11
9 16 0.29
10 19 0.35
11 14 0.25
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.59
Consensus pattern (10 bp):
TTTTATAATA
Found at i:12041078 original size:19 final size:18
Alignment explanation
Indices: 12041037--12041079 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
12041027 TTTATAAATA
*
12041037 TTTTATAATATCTTATAT
1 TTTTATAATATCATATAT
12041055 TTTTATAATATTCATA-AGT
1 TTTTATAATA-TCATATA-T
12041074 TTTTAT
1 TTTTAT
12041080 TATTTATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (18 bp):
TTTTATAATATCATATAT
Found at i:12041300 original size:20 final size:20
Alignment explanation
Indices: 12041277--12041315 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
12041267 AGATTTTTTA
12041277 TATTTTTATAAATTTTATAT
1 TATTTTTATAAATTTTATAT
*
12041297 TATTTTTATAATTTTTATA
1 TATTTTTATAAATTTTATA
12041316 AGTTTATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TATTTTTATAAATTTTATAT
Found at i:12041924 original size:18 final size:18
Alignment explanation
Indices: 12041877--12041931 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 18
12041867 TATATGTCAC
*
12041877 ATTAATAAATA-ATTAAAA
1 ATTAA-AAATATATTTAAA
*
12041895 ATTATAAA-ATATTTAAA
1 ATTAAAAATATATTTAAA
*
12041912 ATTAAAAATATATATAAA
1 ATTAAAAATATATTTAAA
12041930 AT
1 AT
12041932 GTTGATAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
16 1 0.03
17 16 0.52
18 14 0.45
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
ATTAAAAATATATTTAAA
Found at i:12044334 original size:18 final size:18
Alignment explanation
Indices: 12044311--12044345 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12044301 ATAACAGTAA
* *
12044311 ATTTTAGAATTTTTTTAT
1 ATTTTAAAATATTTTTAT
12044329 ATTTTAAAATATTTTTA
1 ATTTTAAAATATTTTTA
12044346 AAAGAATCTT
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:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (18 bp):
ATTTTAAAATATTTTTAT
Found at i:12047393 original size:74 final size:74
Alignment explanation
Indices: 12047305--12047455 Score: 293
Period size: 74 Copynumber: 2.0 Consensus size: 74
12047295 AGTTAATTAA
12047305 AGATTAAGCATAATATATATCAACTTAGTGGAAGGAAAGATGATAATCTTCATCTTCCTCCACCA
1 AGATTAAGCATAATATATATCAACTTAGTGGAAGGAAAGATGATAATCTTCATCTTCCTCCACCA
*
12047370 TCCATGTTG
66 TCCATCTTG
12047379 AGATTAAGCATAATATATATCAACTTAGTGGAAGGAAAGATGATAATCTTCATCTTCCTCCACCA
1 AGATTAAGCATAATATATATCAACTTAGTGGAAGGAAAGATGATAATCTTCATCTTCCTCCACCA
12047444 TCCATCTTG
66 TCCATCTTG
12047453 AGA
1 AGA
12047456 AAAAAAAGAA
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 76 1.00
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (74 bp):
AGATTAAGCATAATATATATCAACTTAGTGGAAGGAAAGATGATAATCTTCATCTTCCTCCACCA
TCCATCTTG
Found at i:12048139 original size:97 final size:97
Alignment explanation
Indices: 12047966--12048183 Score: 312
Period size: 97 Copynumber: 2.2 Consensus size: 97
12047956 ATAATGTTTA
** * **
12047966 GAAACCATCGCTGTCGGGCAACCCGAGGTGGTAGAATGTACATATTTTAGTATTCATTGTTGTTA
1 GAAACCATCATTGTCGGGCAACCCGAGGTGGTAGAATGTACATATTTTAGTAGTCATCATTGTTA
* *
12048031 GGTATTCCGGGATGACAGTGTAATCAGATAGT
66 AGTATTCCGGGATGACAGAGTAATCAGATAGT
*
12048063 GAAACCATCATTGTCGGGTAACCCGAGGTGGTAGAATGTACATATTTTAGTAGTCATCATTGTTA
1 GAAACCATCATTGTCGGGCAACCCGAGGTGGTAGAATGTACATATTTTAGTAGTCATCATTGTTA
*
12048128 AGTA-TCTCGGGATGACAGAGTAATTAGATAGT
66 AGTATTC-CGGGATGACAGAGTAATCAGATAGT
* *
12048160 GAAAATCATCATTATCGGGCAACC
1 G-AAACCATCATTGTCGGGCAACC
12048184 AAAGATGGTA
Statistics
Matches: 107, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
96 2 0.02
97 86 0.80
98 19 0.18
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (97 bp):
GAAACCATCATTGTCGGGCAACCCGAGGTGGTAGAATGTACATATTTTAGTAGTCATCATTGTTA
AGTATTCCGGGATGACAGAGTAATCAGATAGT
Found at i:12050840 original size:6 final size:6
Alignment explanation
Indices: 12050829--12050858 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
12050819 ATGGTACAAG
12050829 TTTGAA TTTGAA TTTGAA TTTGAA TTTGAA
1 TTTGAA TTTGAA TTTGAA TTTGAA TTTGAA
12050859 CTGCTGCGCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
TTTGAA
Found at i:12073659 original size:38 final size:37
Alignment explanation
Indices: 12073590--12073662 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 37
12073580 TTTTCATAAT
* *
12073590 TTCACTTTTTCACTTTTAATCACTATTCAATTCAAAA
1 TTCACTTTTCCACTTTTAATCAATATTCAATTCAAAA
12073627 TTCACTTTTCCA-TTTTCAAGTCAATATTCAATTCAA
1 TTCACTTTTCCACTTTT-AA-TCAATATTCAATTCAA
12073663 TTCCACACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
36 4 0.12
37 13 0.41
38 15 0.47
ACGTcount: A:0.32, C:0.22, G:0.01, T:0.45
Consensus pattern (37 bp):
TTCACTTTTCCACTTTTAATCAATATTCAATTCAAAA
Found at i:12073693 original size:23 final size:22
Alignment explanation
Indices: 12073650--12073693 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
12073640 TTTCAAGTCA
12073650 ATATTCAATTCAATTCCACACAT
1 ATATTCAATTCAATT-CACACAT
12073673 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
12073694 TTAATCGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACAT
Found at i:12073818 original size:23 final size:23
Alignment explanation
Indices: 12073792--12073844 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
12073782 ATAAGTGCCA
*
12073792 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGACGAAGCTAC
*
12073815 CACTGAAATGTAGACGAAGCTAC
1 CACTGATATGTAGACGAAGCTAC
12073838 CACTGAT
1 CACTGAT
12073845 CAATAACACT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGACGAAGCTAC
Found at i:12078380 original size:42 final size:42
Alignment explanation
Indices: 12078321--12078425 Score: 174
Period size: 42 Copynumber: 2.5 Consensus size: 42
12078311 CACGGCCAAG
12078321 CCACACGCCCGTGTGCTAGGCCGTGTACCCTTCGAAATAGCC
1 CCACACGCCCGTGTGCTAGGCCGTGTACCCTTCGAAATAGCC
12078363 CCACACGCCCGTGTGCTAGGCCGTGTACCCTTCGAAATAGCC
1 CCACACGCCCGTGTGCTAGGCCGTGTACCCTTCGAAATAGCC
* * * *
12078405 TCACATGCCCGTCTGCCAGGC
1 CCACACGCCCGTGTGCTAGGC
12078426 TGTCTACCAC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.18, C:0.39, G:0.24, T:0.19
Consensus pattern (42 bp):
CCACACGCCCGTGTGCTAGGCCGTGTACCCTTCGAAATAGCC
Found at i:12078893 original size:20 final size:20
Alignment explanation
Indices: 12078868--12078906 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
12078858 AACATTCAAA
12078868 ATACCATAATCACAA-CCAAG
1 ATACCATAA-CACAAGCCAAG
12078888 ATACCATAACACAAGCCAA
1 ATACCATAACACAAGCCAA
12078907 ACCATACGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.51, C:0.31, G:0.05, T:0.13
Consensus pattern (20 bp):
ATACCATAACACAAGCCAAG
Found at i:12080071 original size:24 final size:25
Alignment explanation
Indices: 12079994--12080115 Score: 156
Period size: 25 Copynumber: 4.9 Consensus size: 25
12079984 TCCTGTACAT
* * *
12079994 GTATGCTTAGACGAGTTGTAAATTG
1 GTATGCTCACACGAGCTGTAAATTG
12080019 GTATGCTCACACGAGCTGTAAATTG
1 GTATGCTCACACGAGCTGTAAATTG
* * *
12080044 GTATGATCTCACGAGCTG-AAATTA
1 GTATGCTCACACGAGCTGTAAATTG
* * *
12080068 GTATGCTCACACGAGCTATATATCG
1 GTATGCTCACACGAGCTGTAAATTG
12080093 GTATGCTCACACGAGCTGTAAAT
1 GTATGCTCACACGAGCTGTAAAT
12080116 CAGCATGCTC
Statistics
Matches: 82, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
24 20 0.24
25 62 0.76
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Consensus pattern (25 bp):
GTATGCTCACACGAGCTGTAAATTG
Found at i:12080072 original size:49 final size:50
Alignment explanation
Indices: 12080004--12080132 Score: 161
Period size: 49 Copynumber: 2.6 Consensus size: 50
12079994 GTATGCTTAG
* * * * *
12080004 ACGAGTTGTAAATTGGTATGCTCACACGAGCTGTAAATTGGTATGATCTC
1 ACGAGCTGTAAATTAGTATGCTCACACGAGCTATAAATCGGTATGATCAC
* *
12080054 ACGAGCTG-AAATTAGTATGCTCACACGAGCTATATATCGGTATGCTCAC
1 ACGAGCTGTAAATTAGTATGCTCACACGAGCTATAAATCGGTATGATCAC
* * *
12080103 ACGAGCTGTAAATCAGCATGCTCATACGAG
1 ACGAGCTGTAAATTAGTATGCTCACACGAG
12080133 TTGTGGGTCG
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
49 43 0.63
50 25 0.37
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.27
Consensus pattern (50 bp):
ACGAGCTGTAAATTAGTATGCTCACACGAGCTATAAATCGGTATGATCAC
Found at i:12080123 original size:25 final size:25
Alignment explanation
Indices: 12079994--12080132 Score: 136
Period size: 25 Copynumber: 5.6 Consensus size: 25
12079984 TCCTGTACAT
* * * **
12079994 GTATGCTTAGACGAGTTGTAAATTG
1 GTATGCTCACACGAGCTGTAAATCA
**
12080019 GTATGCTCACACGAGCTGTAAATTG
1 GTATGCTCACACGAGCTGTAAATCA
* * *
12080044 GTATGATCTCACGAGCTG-AAATTA
1 GTATGCTCACACGAGCTGTAAATCA
* * *
12080068 GTATGCTCACACGAGCTATATATCG
1 GTATGCTCACACGAGCTGTAAATCA
12080093 GTATGCTCACACGAGCTGTAAATCA
1 GTATGCTCACACGAGCTGTAAATCA
* *
12080118 GCATGCTCATACGAG
1 GTATGCTCACACGAG
12080133 TTGTGGGTCG
Statistics
Matches: 96, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
24 20 0.21
25 76 0.79
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.28
Consensus pattern (25 bp):
GTATGCTCACACGAGCTGTAAATCA
Found at i:12094804 original size:27 final size:29
Alignment explanation
Indices: 12094756--12094809 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
12094746 TGAATTGTGA
* *
12094756 AAATTAATCAATTTT-TATTTTGTTTTAG
1 AAATTAATCAATTTTCAATTTGGTTTTAG
12094784 AAATTAA-CAATTTTCAATTTGGTTTT
1 AAATTAATCAATTTTCAATTTGGTTTT
12094810 TGGTTTAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.33, C:0.06, G:0.07, T:0.54
Consensus pattern (29 bp):
AAATTAATCAATTTTCAATTTGGTTTTAG
Found at i:12095908 original size:14 final size:14
Alignment explanation
Indices: 12095889--12095917 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
12095879 ATCAAGTTCG
12095889 AATATAACTACGAA
1 AATATAACTACGAA
12095903 AATATAACTACGAA
1 AATATAACTACGAA
12095917 A
1 A
12095918 CTGGACTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.14, G:0.07, T:0.21
Consensus pattern (14 bp):
AATATAACTACGAA
Found at i:12097585 original size:33 final size:34
Alignment explanation
Indices: 12097514--12097593 Score: 117
Period size: 33 Copynumber: 2.4 Consensus size: 34
12097504 TTATTGAAAG
* *
12097514 TGTTGAAGACACCAACGAAGTAATAAGAGTACTG
1 TGTTGAAGACACTAACGAAGTAATAAGAGTACTC
* *
12097548 TGTTGAAGACACTAATGAAGT-ATTAGAGTACTC
1 TGTTGAAGACACTAACGAAGTAATAAGAGTACTC
12097581 TGTTGAAGACACT
1 TGTTGAAGACACT
12097594 TTCAACTAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 23 0.55
34 19 0.45
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.26
Consensus pattern (34 bp):
TGTTGAAGACACTAACGAAGTAATAAGAGTACTC
Found at i:12098337 original size:18 final size:18
Alignment explanation
Indices: 12098314--12098348 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12098304 AGGCGCTCTC
* *
12098314 CACCAAGTTATTCTCGAT
1 CACCAAGATATGCTCGAT
12098332 CACCAAGATATGCTCGA
1 CACCAAGATATGCTCGA
12098349 AGTTACTCCC
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:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (18 bp):
CACCAAGATATGCTCGAT
Found at i:12104917 original size:23 final size:23
Alignment explanation
Indices: 12104891--12104982 Score: 71
Period size: 23 Copynumber: 3.9 Consensus size: 23
12104881 GGACTCAGCA
*
12104891 CAGCTTGTATGAGCTTACTGTTT
1 CAGCTTGTATGAGCTTACCGTTT
* *
12104914 CAGC-TCTACGGAGCTTACCGTTT
1 CAGCTTGTA-TGAGCTTACCGTTT
*
12104937 CAGCTCG-ATAGAGCTTACCGTTTAT
1 CAGCTTGTAT-GAGCTTACCG-TT-T
* *
12104962 CAGCTCGAAATGAGCTTACCG
1 CAGCTTG-TATGAGCTTACCG
12104983 ATCATGGCTC
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
22 3 0.05
23 31 0.55
24 2 0.04
25 8 0.14
26 10 0.18
27 2 0.04
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.32
Consensus pattern (23 bp):
CAGCTTGTATGAGCTTACCGTTT
Found at i:12104982 original size:26 final size:23
Alignment explanation
Indices: 12104901--12105000 Score: 94
Period size: 23 Copynumber: 4.2 Consensus size: 23
12104891 CAGCTTGTAT
* * **
12104901 GAGCTTACTGTTTCAGCTCTACG
1 GAGCTTACCGTTTCAGCTCGAAA
*
12104924 GAGCTTACCGTTTCAGCTCGATA
1 GAGCTTACCGTTTCAGCTCGAAA
12104947 GAGCTTACCGTTTATCAGCTCGAAA
1 GAGCTTACCG-TT-TCAGCTCGAAA
*
12104972 TGAGCTTACCG-ATCATGGCTCGAAA
1 -GAGCTTACCGTTTCA--GCTCGAAA
12104997 GAGC
1 GAGC
12105001 GAAAATGACA
Statistics
Matches: 66, Mismatches: 6, Indels: 9
0.81 0.07 0.11
Matches are distributed among these distances:
23 32 0.48
24 6 0.09
25 18 0.27
26 10 0.15
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.28
Consensus pattern (23 bp):
GAGCTTACCGTTTCAGCTCGAAA
Found at i:12108181 original size:23 final size:23
Alignment explanation
Indices: 12108155--12108223 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
12108145 AGACTCACCA
12108155 CAGCTTGTATGAGCTTACCGTTT
1 CAGCTTGTATGAGCTTACCGTTT
* * *
12108178 CAGC-TCTACGGAGCTTACCATTT
1 CAGCTTGTA-TGAGCTTACCGTTT
*
12108201 CAGCTCG-ATAGAGCTTACCGTTT
1 CAGCTTGTAT-GAGCTTACCGTTT
12108224 ATCAACTCAG
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
22 3 0.08
23 33 0.92
ACGTcount: A:0.20, C:0.26, G:0.20, T:0.33
Consensus pattern (23 bp):
CAGCTTGTATGAGCTTACCGTTT
Found at i:12110185 original size:23 final size:23
Alignment explanation
Indices: 12110159--12110250 Score: 71
Period size: 23 Copynumber: 3.9 Consensus size: 23
12110149 GGACTCAGCA
*
12110159 CAGCTTGTATGAGCTTACTGTTT
1 CAGCTTGTATGAGCTTACCGTTT
* *
12110182 CAGC-TCTACGGAGCTTACCGTTT
1 CAGCTTGTA-TGAGCTTACCGTTT
*
12110205 CAGCTCG-ATAGAGCTTACCGTTTAT
1 CAGCTTGTAT-GAGCTTACCG-TT-T
* *
12110230 CAGCTCGAAATGAGCTTACCG
1 CAGCTTG-TATGAGCTTACCG
12110251 ATCATGGCTC
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
22 3 0.05
23 31 0.55
24 2 0.04
25 8 0.14
26 10 0.18
27 2 0.04
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.32
Consensus pattern (23 bp):
CAGCTTGTATGAGCTTACCGTTT
Found at i:12110250 original size:26 final size:23
Alignment explanation
Indices: 12110169--12110250 Score: 92
Period size: 23 Copynumber: 3.4 Consensus size: 23
12110159 CAGCTTGTAT
* * **
12110169 GAGCTTACTGTTTCAGCTCTACG
1 GAGCTTACCGTTTCAGCTCGAAA
*
12110192 GAGCTTACCGTTTCAGCTCGATA
1 GAGCTTACCGTTTCAGCTCGAAA
12110215 GAGCTTACCGTTTATCAGCTCGAAA
1 GAGCTTACCG-TT-TCAGCTCGAAA
12110240 TGAGCTTACCG
1 -GAGCTTACCG
12110251 ATCATGGCTC
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
23 29 0.57
24 2 0.04
25 10 0.20
26 10 0.20
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (23 bp):
GAGCTTACCGTTTCAGCTCGAAA
Found at i:12118676 original size:29 final size:29
Alignment explanation
Indices: 12118635--12118751 Score: 146
Period size: 29 Copynumber: 4.1 Consensus size: 29
12118625 GAAACATAAA
* *
12118635 TATGAAAATTAATTATGGTGAATTTATAT
1 TATGTAAACTAATTATGGTGAATTTATAT
* *
12118664 CATTTAAACTAATTATGGTGAATTTATAT
1 TATGTAAACTAATTATGGTGAATTTATAT
*
12118693 TATGTAAACTAATTATGGT-AAATTATAT
1 TATGTAAACTAATTATGGTGAATTTATAT
* * * *
12118721 TATGTAAATTAATTATGATAAATATATAT
1 TATGTAAACTAATTATGGTGAATTTATAT
12118750 TA
1 TA
12118752 ACTAATTATG
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
28 25 0.33
29 51 0.67
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (29 bp):
TATGTAAACTAATTATGGTGAATTTATAT
Found at i:12118727 original size:14 final size:14
Alignment explanation
Indices: 12118687--12118751 Score: 80
Period size: 14 Copynumber: 4.6 Consensus size: 14
12118677 TATGGTGAAT
12118687 TTATATTATGTAAA
1 TTATATTATGTAAA
*
12118701 CTA-ATTATGGTAAA
1 TTATATTAT-GTAAA
12118715 TTATATTATGTAAA
1 TTATATTATGTAAA
12118729 TTA-ATTATGATAAA
1 TTATATTATG-TAAA
12118743 TATATATTA
1 T-TATATTA
12118752 ACTAATTATG
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
13 11 0.25
14 22 0.50
15 7 0.16
16 4 0.09
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.46
Consensus pattern (14 bp):
TTATATTATGTAAA
Found at i:12118736 original size:57 final size:58
Alignment explanation
Indices: 12118635--12118751 Score: 146
Period size: 57 Copynumber: 2.0 Consensus size: 58
12118625 GAAACATAAA
* * * * * *
12118635 TATGAAAATTAATTATGGTGAATTTATATCATTTAAACTAATTATGGTGAATTTATAT
1 TATGAAAACTAATTATGGTGAAATTATATCATGTAAACTAATTATGATAAATATATAT
* * *
12118693 TATGTAAACTAATTATGGT-AAATTATATTATGTAAATTAATTATGATAAATATATAT
1 TATGAAAACTAATTATGGTGAAATTATATCATGTAAACTAATTATGATAAATATATAT
12118750 TA
1 TA
12118752 ACTAATTATG
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
57 33 0.66
58 17 0.34
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (58 bp):
TATGAAAACTAATTATGGTGAAATTATATCATGTAAACTAATTATGATAAATATATAT
Found at i:12128931 original size:20 final size:21
Alignment explanation
Indices: 12128906--12128947 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
12128896 AAATAAAAGA
* *
12128906 TGGAAACGAGCT-CATTGAGC
1 TGGAAACAAGCTGAATTGAGC
12128926 TGGAAACAAGCTGAATTGAGC
1 TGGAAACAAGCTGAATTGAGC
12128947 T
1 T
12128948 CAACAAGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (21 bp):
TGGAAACAAGCTGAATTGAGC
Found at i:12130968 original size:20 final size:20
Alignment explanation
Indices: 12130930--12130966 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
12130920 TTTTTGGAGG
*
12130930 TATCGATATTTTAGTAAATT
1 TATCGATATCTTAGTAAATT
12130950 TATCGATA-CTTAGTAAA
1 TATCGATATCTTAGTAAA
12130967 ATACCGATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (20 bp):
TATCGATATCTTAGTAAATT
Found at i:12133942 original size:18 final size:18
Alignment explanation
Indices: 12133916--12133952 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
12133906 ATTAAGACTA
*
12133916 ATATTTAGTTGATTGATG
1 ATATGTAGTTGATTGATG
12133934 ATATGTAGTTGATTGATG
1 ATATGTAGTTGATTGATG
12133952 A
1 A
12133953 CAAAGTGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.46
Consensus pattern (18 bp):
ATATGTAGTTGATTGATG
Found at i:12133962 original size:18 final size:18
Alignment explanation
Indices: 12133921--12133962 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
12133911 GACTAATATT
* *
12133921 TAGTTGATTGATGATATG
1 TAGTTGATTGATGAAAAG
12133939 TAGTTGATTGATGACAAAG
1 TAGTTGATTGATGA-AAAG
12133958 T-GTTG
1 TAGTTG
12133963 TCATTGACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.29, C:0.02, G:0.29, T:0.40
Consensus pattern (18 bp):
TAGTTGATTGATGAAAAG
Found at i:12146742 original size:40 final size:40
Alignment explanation
Indices: 12146698--12146961 Score: 360
Period size: 40 Copynumber: 6.7 Consensus size: 40
12146688 GCTCCTCGTT
* *
12146698 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
12146738 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
12146778 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
12146818 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
12146858 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
12146897 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAT-TTAGTAAC-TCGCA
12146938 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
12146962 CATCATTCAA
Statistics
Matches: 206, Mismatches: 12, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
38 2 0.01
39 49 0.24
40 146 0.71
41 9 0.04
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:12155786 original size:40 final size:40
Alignment explanation
Indices: 12155742--12156003 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
12155732 GCTCCTCGTT
* *
12155742 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
12155782 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
12155822 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
12155861 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
12155900 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
12155939 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
12155980 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
12156004 CATCATTCAA
Statistics
Matches: 205, Mismatches: 9, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
38 2 0.01
39 128 0.62
40 64 0.31
41 11 0.05
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:12159869 original size:28 final size:27
Alignment explanation
Indices: 12159847--12159934 Score: 149
Period size: 27 Copynumber: 3.2 Consensus size: 27
12159837 TTTTACATAC
12159847 TTTTTTAATTTTTTTTAATTTTAAAATA
1 TTTTTTAA-TTTTTTTAATTTTAAAATA
12159875 TTTTTTTAATTTTTTTAATTTTAAAATA
1 -TTTTTTAATTTTTTTAATTTTAAAATA
*
12159903 TTTTTTTATTTTTTTAATTTTAAAATA
1 TTTTTTAATTTTTTTAATTTTAAAATA
12159930 TTTTT
1 TTTTT
12159935 AAAATACTTT
Statistics
Matches: 58, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
27 31 0.53
28 19 0.33
29 8 0.14
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (27 bp):
TTTTTTAATTTTTTTAATTTTAAAATA
Found at i:12159869 original size:40 final size:38
Alignment explanation
Indices: 12159816--12159896 Score: 128
Period size: 40 Copynumber: 2.1 Consensus size: 38
12159806 AATATATTTA
12159816 TTTTTTTAATTTTAAAATA-TTTTTTACATACTTTTTTAAT
1 TTTTTTTAATTTTAAAATATTTTTTTA-AT--TTTTTTAAT
12159856 TTTTTTTAATTTTAAAATATTTTTTTAATTTTTTTAAT
1 TTTTTTTAATTTTAAAATATTTTTTTAATTTTTTTAAT
12159894 TTT
1 TTT
12159897 AAAATATTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
38 12 0.30
40 21 0.52
41 7 0.17
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.69
Consensus pattern (38 bp):
TTTTTTTAATTTTAAAATATTTTTTTAATTTTTTTAAT
Found at i:12159887 original size:8 final size:9
Alignment explanation
Indices: 12159815--12159923 Score: 69
Period size: 9 Copynumber: 11.6 Consensus size: 9
12159805 AAATATATTT
12159815 ATTTTTTTA
1 ATTTTTTTA
**
12159824 A-TTTTAAA
1 ATTTTTTTA
12159832 ATATTTTTTA
1 AT-TTTTTTA
12159842 CATACTTTTTTA
1 -AT--TTTTTTA
12159854 ATTTTTTTTA
1 A-TTTTTTTA
***
12159864 ATTTTAAAA
1 ATTTTTTTA
12159873 TATTTTTTTA
1 -ATTTTTTTA
12159883 ATTTTTTTA
1 ATTTTTTTA
**
12159892 A-TTTTAAA
1 ATTTTTTTA
*
12159900 ATATTTTTTT
1 AT-TTTTTTA
12159910 ATTTTTTTA
1 ATTTTTTTA
12159919 ATTTT
1 ATTTT
12159924 AAAATATTTT
Statistics
Matches: 75, Mismatches: 17, Indels: 16
0.69 0.16 0.15
Matches are distributed among these distances:
8 12 0.16
9 27 0.36
10 25 0.33
11 3 0.04
12 8 0.11
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (9 bp):
ATTTTTTTA
Found at i:12159887 original size:27 final size:28
Alignment explanation
Indices: 12159847--12159934 Score: 160
Period size: 28 Copynumber: 3.1 Consensus size: 28
12159837 TTTTACATAC
12159847 TTTTTTAATTTTTTTTAATTTTAAAATAT
1 TTTTTTAA-TTTTTTTAATTTTAAAATAT
12159876 TTTTTTAATTTTTTTAATTTTAAAATAT
1 TTTTTTAATTTTTTTAATTTTAAAATAT
12159904 TTTTTT-ATTTTTTTAATTTTAAAATAT
1 TTTTTTAATTTTTTTAATTTTAAAATAT
12159931 TTTT
1 TTTT
12159935 AAAATACTTT
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
27 25 0.42
28 26 0.44
29 8 0.14
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (28 bp):
TTTTTTAATTTTTTTAATTTTAAAATAT
Found at i:12159895 original size:68 final size:67
Alignment explanation
Indices: 12159815--12159971 Score: 201
Period size: 68 Copynumber: 2.3 Consensus size: 67
12159805 AAATATATTT
***
12159815 ATTTTTTTAATTTTAAAATATTTTTTACATACTTTTTTAATTTT-TTTTAATTTTAAAATA-TTT
1 ATTTTTTTAATTTTAAAATATTTTTT---TACTTTTTTAATTTTAAAATAATTTTAAAATACTTT
12159878 TTTTA
63 TTTTA
* *
12159883 ATTTTTTTAATTTTAAAATATTTTTTTATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTT
1 ATTTTTTTAATTTTAAAATATTTTTTTACTTTTTTAATTTTAAAATAATTTTAAAATACTTTTTT
12159948 TA
66 TA
*
12159950 ATTTTTTAAAATTTTTAAAATA
1 ATTTTTT-TAA-TTTTAAAATA
12159972 AAAATGGGCC
Statistics
Matches: 79, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
65 14 0.18
66 12 0.15
67 15 0.19
68 28 0.35
69 10 0.13
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (67 bp):
ATTTTTTTAATTTTAAAATATTTTTTTACTTTTTTAATTTTAAAATAATTTTAAAATACTTTTTT
TA
Found at i:12159908 original size:19 final size:19
Alignment explanation
Indices: 12159814--12159887 Score: 87
Period size: 19 Copynumber: 3.8 Consensus size: 19
12159804 TAAATATATT
12159814 TATTTTTTTAATTTTAAAA
1 TATTTTTTTAATTTTAAAA
* **
12159833 TATTTTTTACATACTTTTTTAA
1 TATTTTTT---TAATTTTAAAA
12159855 T-TTTTTTTAATTTTAAAA
1 TATTTTTTTAATTTTAAAA
12159873 TATTTTTTTAATTTT
1 TATTTTTTTAATTTT
12159888 TTTAATTTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
18 9 0.20
19 21 0.47
21 6 0.13
22 9 0.20
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (19 bp):
TATTTTTTTAATTTTAAAA
Found at i:12164017 original size:45 final size:45
Alignment explanation
Indices: 12163950--12164124 Score: 237
Period size: 45 Copynumber: 3.9 Consensus size: 45
12163940 GTGTACTGAG
* **
12163950 TATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACTAGG
1 TATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCAAA
* * *
12163995 TACCATTGATTATAAAAGTGGTTGCTATGTGCTGACTCCACCAAA
1 TATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCAAA
* **
12164040 AATCATTGAAAATAAAGGTGGTTGCTATGTGCTGATTCCACCAAA
1 TATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCAAA
* *
12164085 TATAATTGATTATAAGGGTGG-TGCTATGTGCTGA-TCCACC
1 TATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACC
12164125 GTGTAACGGT
Statistics
Matches: 113, Mismatches: 17, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
43 6 0.05
44 13 0.12
45 94 0.83
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (45 bp):
TATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCAAA
Found at i:12172040 original size:27 final size:27
Alignment explanation
Indices: 12172010--12172105 Score: 68
Period size: 27 Copynumber: 3.5 Consensus size: 27
12172000 AAATATATAA
*
12172010 ACTAAATAAATTAGTATATTGAAATAT
1 ACTAAATAAATTAGTATATTAAAATAT
* * * ** *
12172037 ACTAAACAAA-TATTTATGTTTAATTTAA
1 ACTAAATAAATTA-GTAT-ATTAAAATAT
*
12172065 ACTATAATAAATTAGTAAATTAAAATAT
1 ACTA-AATAAATTAGTATATTAAAATAT
* *
12172093 ATTAAAAAAATTA
1 ACTAAATAAATTA
12172106 TTAGAGAAGT
Statistics
Matches: 49, Mismatches: 16, Indels: 8
0.67 0.22 0.11
Matches are distributed among these distances:
26 2 0.04
27 20 0.41
28 18 0.37
29 7 0.14
30 2 0.04
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (27 bp):
ACTAAATAAATTAGTATATTAAAATAT
Found at i:12175186 original size:23 final size:23
Alignment explanation
Indices: 12175154--12175205 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
12175144 GAGTTGACAT
* **
12175154 TAATGATTAAACCGTTAATCTTC
1 TAATGCTTAAACAATTAATCTTC
*
12175177 TAATGCTTAAACAATTAATTTTC
1 TAATGCTTAAACAATTAATCTTC
12175200 TAATGC
1 TAATGC
12175206 AGTGAAAACC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.40
Consensus pattern (23 bp):
TAATGCTTAAACAATTAATCTTC
Found at i:12178925 original size:20 final size:20
Alignment explanation
Indices: 12178797--12178956 Score: 92
Period size: 20 Copynumber: 7.8 Consensus size: 20
12178787 ATTTTGTATA
* *
12178797 TTACCAAAATTTATAAGGAAA
1 TTACCAAAATTTCTAA-GAAT
* * *
12178818 TT-CCAAATTTTTTAAGGAT
1 TTACCAAAATTTCTAAGAAT
* * * *
12178837 TTACAAAAAGTTCTAAGTAG
1 TTACCAAAATTTCTAAGAAT
* *
12178857 TTACCAAAATTTCTAATAAA
1 TTACCAAAATTTCTAAGAAT
*** *
12178877 TTATTGAAATTTCT-A-AAG
1 TTACCAAAATTTCTAAGAAT
*
12178895 TTACACAAAAATTTCTAAGACT
1 TTAC-C-AAAATTTCTAAGAAT
12178917 TTACCAAAATTAGTATCTAAGAAT
1 TTACCAAAA-T--T-TCTAAGAAT
12178941 TTACCAAAATTTCTAA
1 TTACCAAAATTTCTAA
12178957 TATGCCATAT
Statistics
Matches: 105, Mismatches: 25, Indels: 19
0.70 0.17 0.13
Matches are distributed among these distances:
18 5 0.05
19 5 0.05
20 65 0.62
21 6 0.06
22 5 0.05
23 2 0.02
24 17 0.16
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.36
Consensus pattern (20 bp):
TTACCAAAATTTCTAAGAAT
Found at i:12182619 original size:17 final size:19
Alignment explanation
Indices: 12182587--12182621 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
12182577 TTATATATTT
12182587 AAGAATAGATTAAGTGAAG
1 AAGAATAGATTAAGTGAAG
12182606 AAGAATA-A-TAAGTGAA
1 AAGAATAGATTAAGTGAA
12182622 TTAGAAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 1 0.06
19 7 0.44
ACGTcount: A:0.57, C:0.00, G:0.23, T:0.20
Consensus pattern (19 bp):
AAGAATAGATTAAGTGAAG
Found at i:12185375 original size:22 final size:22
Alignment explanation
Indices: 12185345--12185387 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
12185335 CAGAATGATT
12185345 TGTTAATTATTAAAATATATTA
1 TGTTAATTATTAAAATATATTA
* **
12185367 TGTTGATTATTATGATATATT
1 TGTTAATTATTAAAATATATT
12185388 CAGGAATTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.53
Consensus pattern (22 bp):
TGTTAATTATTAAAATATATTA
Found at i:12185571 original size:24 final size:24
Alignment explanation
Indices: 12185541--12185587 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
12185531 TTCAGGTTGA
12185541 GATTTCAATGCATCTCATCTCATT
1 GATTTCAATGCATCTCATCTCATT
12185565 GATTTCAATGCATCTCATCTCAT
1 GATTTCAATGCATCTCATCTCAT
12185588 CACATCACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.09, T:0.40
Consensus pattern (24 bp):
GATTTCAATGCATCTCATCTCATT
Found at i:12193626 original size:9 final size:9
Alignment explanation
Indices: 12193612--12193642 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
12193602 GATAAAGGAA
12193612 AATTAAATT
1 AATTAAATT
12193621 AATTAAATT
1 AATTAAATT
12193630 AATTAAAATT
1 AATT-AAATT
12193640 AAT
1 AAT
12193643 ATGATATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 13 0.62
10 8 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
AATTAAATT
Found at i:12194106 original size:37 final size:37
Alignment explanation
Indices: 12194060--12194130 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
12194050 AAAAATAGTA
*
12194060 TTATTTTAATAGT-TTAATATTAAATTTAAT-TTAATAC
1 TTATCTTAATAGTATT-ATATT-AATTTAATATTAATAC
*
12194097 TTATCTTAATAGTATTTTATTAATTTAATATTAA
1 TTATCTTAATAGTATTATATTAATTTAATATTAA
12194131 AATTATTATC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 8 0.27
37 20 0.67
38 2 0.07
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (37 bp):
TTATCTTAATAGTATTATATTAATTTAATATTAATAC
Found at i:12199403 original size:6 final size:6
Alignment explanation
Indices: 12199346--12199421 Score: 53
Period size: 6 Copynumber: 12.3 Consensus size: 6
12199336 TAAACAAATT
* * * * * *
12199346 AAATTA AAATAA AAATTAA ATACAA AAACAA AGATAA AGATAA AAATGAA
1 AAATAA AAATAA AAA-TAA AAATAA AAATAA AAATAA AAATAA AAAT-AA
* * *
12199396 AAATAA AACTAA AACTTA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AA
12199422 TTTTTAAAAT
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
6 46 0.81
7 11 0.19
ACGTcount: A:0.72, C:0.05, G:0.04, T:0.18
Consensus pattern (6 bp):
AAATAA
Found at i:12211360 original size:12 final size:12
Alignment explanation
Indices: 12211343--12211367 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12211333 ACATATGAAG
12211343 ACCAATAATTAA
1 ACCAATAATTAA
12211355 ACCAATAATTAA
1 ACCAATAATTAA
12211367 A
1 A
12211368 ATGACTCAAA
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:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (12 bp):
ACCAATAATTAA
Found at i:12213460 original size:6 final size:6
Alignment explanation
Indices: 12213415--12213441 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
12213405 CAATTTGGTT
12213415 TTTTTA TTTTTA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTT
12213442 AATTAATTTT
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:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:12222328 original size:26 final size:25
Alignment explanation
Indices: 12222297--12222360 Score: 69
Period size: 26 Copynumber: 2.6 Consensus size: 25
12222287 TATTTTCTCG
12222297 AAATTTTATTAAGGGCAAAATCATC
1 AAATTTTATTAAGGGCAAAATCATC
* **
12222322 AAAATTTTACT-AGAGGCAAAATTGTC
1 -AAATTTTATTAAG-GGCAAAATCATC
12222348 -AATTTTATTAAGG
1 AAATTTTATTAAGG
12222361 ATAAAATTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
24 9 0.28
25 4 0.12
26 19 0.59
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.34
Consensus pattern (25 bp):
AAATTTTATTAAGGGCAAAATCATC
Found at i:12226305 original size:23 final size:23
Alignment explanation
Indices: 12226252--12226301 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
12226242 AATCACAACT
**
12226252 TGAAACATTTTTCAGTTATGTTG
1 TGAAACATTTTTCAGTTATGAAG
12226275 TGAAACATTTTTCAGTTAT-AAG
1 TGAAACATTTTTCAGTTATGAAG
12226297 TGAAA
1 TGAAA
12226302 ACATGAGTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 6 0.24
23 19 0.76
ACGTcount: A:0.34, C:0.08, G:0.16, T:0.42
Consensus pattern (23 bp):
TGAAACATTTTTCAGTTATGAAG
Found at i:12228620 original size:5 final size:5
Alignment explanation
Indices: 12228610--12228663 Score: 81
Period size: 5 Copynumber: 10.6 Consensus size: 5
12228600 AATCAAAGCT
**
12228610 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTCC TTGCC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT-C TTTTC TTTTC
12228661 TTT
1 TTT
12228664 GGGTTTTGCT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
5 41 0.93
6 3 0.07
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (5 bp):
TTTTC
Found at i:12244682 original size:40 final size:39
Alignment explanation
Indices: 12244645--12244736 Score: 132
Period size: 39 Copynumber: 2.3 Consensus size: 39
12244635 GCTACTCGTT
*
12244645 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGG-CATAGCCCGGAAT-TAGTAACTCGCA
* *
12244685 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCATAGCCCGGAATTAGTAACTCGCA
12244724 CAAATGCCTTCGG
1 CAAATGCCTTCGG
12244737 ATCTTAGTCC
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
39 33 0.69
40 15 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGCATAGCCCGGAATTAGTAACTCGCA
Found at i:12244716 original size:39 final size:40
Alignment explanation
Indices: 12244626--12244789 Score: 176
Period size: 40 Copynumber: 4.1 Consensus size: 40
12244616 CGGAATTTAA
** *
12244626 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
*
12244666 CCGGTTATAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
12244705 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
12244745 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
12244785 CCGGA
1 CCGGA
12244790 CATCATTCAA
Statistics
Matches: 105, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
38 3 0.03
39 32 0.30
40 58 0.55
41 12 0.11
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:12264454 original size:18 final size:18
Alignment explanation
Indices: 12264431--12264468 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
12264421 TGAAAGGTTG
12264431 TTGATAGATAAACAACTT
1 TTGATAGATAAACAACTT
12264449 TTGATAGATAAACAACTT
1 TTGATAGATAAACAACTT
12264467 TT
1 TT
12264469 ATGAAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (18 bp):
TTGATAGATAAACAACTT
Found at i:12288773 original size:10 final size:10
Alignment explanation
Indices: 12288758--12288847 Score: 62
Period size: 10 Copynumber: 9.0 Consensus size: 10
12288748 TTCAAATAAT
*
12288758 TATAAAAAAA
1 TATAAAAATA
12288768 TATAAAAATA
1 TATAAAAATA
*
12288778 TTTAAAAATA
1 TATAAAAATA
12288788 TATATAAAGA-A
1 TATA-AAA-ATA
* *
12288799 TTATAAGAATT
1 -TATAAAAATA
*
12288810 TATAAAATTA
1 TATAAAAATA
*
12288820 T-TAAAATTA
1 TATAAAAATA
12288829 T-TAAAAAT-
1 TATAAAAATA
12288837 TCATAAAAATA
1 T-ATAAAAATA
12288848 AAAATAGTAA
Statistics
Matches: 64, Mismatches: 9, Indels: 13
0.74 0.10 0.15
Matches are distributed among these distances:
8 1 0.02
9 15 0.23
10 37 0.58
11 6 0.09
12 5 0.08
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.34
Consensus pattern (10 bp):
TATAAAAATA
Found at i:12288776 original size:22 final size:22
Alignment explanation
Indices: 12288751--12288804 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 22
12288741 ATGATTTTTC
12288751 AAATAATTATAAAAAAATATAA
1 AAATAATTATAAAAAAATATAA
* *
12288773 AAAT-ATT-TAAAAATATATAT
1 AAATAATTATAAAAAAATATAA
*
12288793 AAAGAATTATAA
1 AAATAATTATAA
12288805 GAATTTATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 14 0.52
21 6 0.22
22 7 0.26
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (22 bp):
AAATAATTATAAAAAAATATAA
Found at i:12293399 original size:17 final size:16
Alignment explanation
Indices: 12293377--12293411 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
12293367 TTTATGTATT
12293377 AAGTTGATTGTTTCGAA
1 AAGTTGATTGTTTC-AA
12293394 AAGTTGATTGTTTCAA
1 AAGTTGATTGTTTCAA
12293410 AA
1 AA
12293412 TTCTCTGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.34, C:0.06, G:0.20, T:0.40
Consensus pattern (16 bp):
AAGTTGATTGTTTCAA
Found at i:12302743 original size:17 final size:15
Alignment explanation
Indices: 12302721--12302762 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 15
12302711 ATTCCCTAAT
12302721 TTATTTTTATAATTAA
1 TTATTTTTATAA-TAA
12302737 TTAATTTTT-TAAT-A
1 TT-ATTTTTATAATAA
12302751 TTATTTTTATAA
1 TTATTTTTATAA
12302763 AAAAACCGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 6 0.25
14 6 0.25
15 1 0.04
16 5 0.21
17 6 0.25
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTATTTTTATAATAA
Found at i:12303703 original size:61 final size:61
Alignment explanation
Indices: 12303645--12303765 Score: 165
Period size: 61 Copynumber: 2.0 Consensus size: 61
12303635 ATATAAAATA
** *
12303645 TTCAACAAATTTAG-CACTCAATGTTTACAAAACTTGTCATTTTAGTT-TGAATTCTAAAAAG
1 TTCAACAAATTTAGTC-CTCAAAATTTACAAAACTTGTCAATTTAGTTCT-AATTCTAAAAAG
* *
12303706 TTCAATAAATTTAGTCCTCAAAATTTACAAAATTTGTCAATTTAGTTCTAATTCTAAAAA
1 TTCAACAAATTTAGTCCTCAAAATTTACAAAACTTGTCAATTTAGTTCTAATTCTAAAAA
12303766 ATTAATAAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
61 51 0.96
62 2 0.04
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.39
Consensus pattern (61 bp):
TTCAACAAATTTAGTCCTCAAAATTTACAAAACTTGTCAATTTAGTTCTAATTCTAAAAAG
Found at i:12306954 original size:189 final size:189
Alignment explanation
Indices: 12306623--12306990 Score: 619
Period size: 189 Copynumber: 1.9 Consensus size: 189
12306613 TCGAGCTACC
* *
12306623 GGAGAGAAGGTTTCTTTGAAATCAACACCATATTGTTATGCATAACCTTTCGCCACAAGACAAGC
1 GGAGAGAAGGTTTCTTCGAAATCAACACCATATTGCTATGCATAACCTTTCGCCACAAGACAAGC
* *
12306688 TTTGTGCTTTTGGATGCTTCCATCTACACCAAATTTTTTCTTGAACACCCACTTCAAACCAATTG
66 TTTGTGCTTTTGGATGCTTCCATCTACACCAAATTTTGTCTTAAACACCCACTTCAAACCAATTG
* * *
12306753 CATTTTTGTCTTTCGACAAGTCGACCATGTCCCAAGTTCCATTCTTTTCAATAGAAACA
131 CAATTCTGTCTTTCGACAAGTCGACCATCTCCCAAGTTCCATTCTTTTCAATAGAAACA
*
12306812 GGAGAGAAGGTTTCTTCGAAATCAACACCATATTGCTATGCATAACCTTTCGCCACAAGACGAGC
1 GGAGAGAAGGTTTCTTCGAAATCAACACCATATTGCTATGCATAACCTTTCGCCACAAGACAAGC
**
12306877 TTTGTGCTTTTGGATGCTTCCATCTGTACCAAATTTTGTCTTAAACACCCACTTCAAACCAATTG
66 TTTGTGCTTTTGGATGCTTCCATCTACACCAAATTTTGTCTTAAACACCCACTTCAAACCAATTG
* * *
12306942 TAATTCTGTCTTTCGGCAAGTCGACCATCTCCCAATTTCCATTCTTTTC
131 CAATTCTGTCTTTCGACAAGTCGACCATCTCCCAAGTTCCATTCTTTTC
12306991 GATGGATTTC
Statistics
Matches: 166, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
189 166 1.00
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.33
Consensus pattern (189 bp):
GGAGAGAAGGTTTCTTCGAAATCAACACCATATTGCTATGCATAACCTTTCGCCACAAGACAAGC
TTTGTGCTTTTGGATGCTTCCATCTACACCAAATTTTGTCTTAAACACCCACTTCAAACCAATTG
CAATTCTGTCTTTCGACAAGTCGACCATCTCCCAAGTTCCATTCTTTTCAATAGAAACA
Found at i:12308392 original size:17 final size:17
Alignment explanation
Indices: 12308351--12308384 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
12308341 TTAAATCAGG
12308351 AACAAATTGAACATTGT
1 AACAAATTGAACATTGT
12308368 AACAAATTGAACATTGT
1 AACAAATTGAACATTGT
12308385 CCAAAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (17 bp):
AACAAATTGAACATTGT
Found at i:12319377 original size:20 final size:20
Alignment explanation
Indices: 12319338--12319377 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
12319328 TCTGACGAGA
*
12319338 AAATTCATTTTTAGTGTATT
1 AAATTCATTTTTAGTCTATT
* *
12319358 AAATTTATTTTTGGTCTATT
1 AAATTCATTTTTAGTCTATT
12319378 GGGAAGTTCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.05, G:0.10, T:0.57
Consensus pattern (20 bp):
AAATTCATTTTTAGTCTATT
Found at i:12324737 original size:52 final size:52
Alignment explanation
Indices: 12324656--12324760 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
12324646 GCAGCCAGTG
12324656 TAGGGAACTCGAGATTTGTTAAACATGAGTGCCAGCGGTGTGGTAGAAATCA
1 TAGGGAACTCGAGATTTGTTAAACATGAGTGCCAGCGGTGTGGTAGAAATCA
*
12324708 TAGGGAACTCGAGATTTGTTAAACCTGAGTGCCAGCGGTGTGGTAGAAATCA
1 TAGGGAACTCGAGATTTGTTAAACATGAGTGCCAGCGGTGTGGTAGAAATCA
12324760 T
1 T
12324761 TTTGGTCCGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.30, C:0.14, G:0.30, T:0.26
Consensus pattern (52 bp):
TAGGGAACTCGAGATTTGTTAAACATGAGTGCCAGCGGTGTGGTAGAAATCA
Found at i:12329745 original size:46 final size:46
Alignment explanation
Indices: 12329695--12329869 Score: 314
Period size: 46 Copynumber: 3.8 Consensus size: 46
12329685 TGGTTGAGCA
12329695 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
12329741 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
*
12329787 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
12329833 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
12329870 GCGGGTTACA
Statistics
Matches: 125, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 125 1.00
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:12334190 original size:28 final size:27
Alignment explanation
Indices: 12334128--12334279 Score: 232
Period size: 27 Copynumber: 5.6 Consensus size: 27
12334118 TAAATTGTGC
* *
12334128 AGCACTAAGTGTGCGAATTGAATATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
12334155 AGCACTAAGTGTGCGAGTTAGACTATGT
1 AGCACTAAGTGTGCGAGTT-GACTATGT
12334183 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
12334210 AGCACTAAGTGTGCGAGTATGATTATGT
1 AGCACTAAGTGTGCGAGT-TGACTATGT
* *
12334238 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
12334265 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
12334280 GACTTAATAA
Statistics
Matches: 118, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
27 66 0.56
28 52 0.44
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:12334193 original size:55 final size:55
Alignment explanation
Indices: 12334128--12334279 Score: 234
Period size: 55 Copynumber: 2.8 Consensus size: 55
12334118 TAAATTGTGC
*
12334128 AGCACTAAGTGTGCGAATTGAATATGTAGCACTAAGTGTGCGAGT-TAGACTATGT
1 AGCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCGAGTAT-GACTATGT
* *
12334183 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTATGATTATGT
1 AGCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCGAGTATGACTATGT
* * *
12334238 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCG
12334280 GACTTAATAA
Statistics
Matches: 90, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
55 89 0.99
56 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.30
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCGAGTATGACTATGT
Done.