Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 129 of 313
Found at i:41735209 original size:16 final size:17
Alignment explanation
Indices: 41735177--41735209 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
41735167 CAATTCAGAG
*
41735177 AAAATAAAAAACTAACC
1 AAAAAAAAAAACTAACC
41735194 AAAAAAAAAAAC-AACC
1 AAAAAAAAAAACTAACC
41735210 CACAAACGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.76, C:0.18, G:0.00, T:0.06
Consensus pattern (17 bp):
AAAAAAAAAAACTAACC
Found at i:41741492 original size:13 final size:13
Alignment explanation
Indices: 41741474--41741501 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
41741464 AACTCAATCC
41741474 AAAAATTTAAATT
1 AAAAATTTAAATT
41741487 AAAAATTTAAATT
1 AAAAATTTAAATT
41741500 AA
1 AA
41741502 TTTAAACTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAAAATTTAAATT
Found at i:41743373 original size:13 final size:13
Alignment explanation
Indices: 41743355--41743382 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
41743345 AACTCAATCC
41743355 AAAAATTTAAATT
1 AAAAATTTAAATT
41743368 AAAAATTTAAATT
1 AAAAATTTAAATT
41743381 AA
1 AA
41743383 TTTAAACTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAAAATTTAAATT
Found at i:41744638 original size:22 final size:23
Alignment explanation
Indices: 41744608--41744650 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
41744598 ATATTAAATA
*
41744608 ATAATTAAACTTATATATTTATG
1 ATAATTAAACTTATAAATTTATG
*
41744631 ATAA-TAAATTTATAAATTTA
1 ATAATTAAACTTATAAATTTA
41744651 ATATATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
ATAATTAAACTTATAAATTTATG
Found at i:41746104 original size:3 final size:3
Alignment explanation
Indices: 41746098--41746122 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
41746088 TTCCTGTTCG
41746098 TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA T
41746123 TAGGGACTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:41749868 original size:9 final size:10
Alignment explanation
Indices: 41749843--41749883 Score: 57
Period size: 10 Copynumber: 4.0 Consensus size: 10
41749833 TTTTTGGACA
41749843 TTAAAAATAT
1 TTAAAAATAT
41749853 TTAAAAATAT
1 TTAAAAATAT
41749863 TTAAAAA-AT
1 TTAAAAATAT
41749872 CATTAAAAATAT
1 --TTAAAAATAT
41749884 AAAAAAATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 2 0.07
10 17 0.61
11 7 0.25
12 2 0.07
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (10 bp):
TTAAAAATAT
Found at i:41749871 original size:21 final size:20
Alignment explanation
Indices: 41749853--41749899 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
41749843 TTAAAAATAT
*
41749853 TTAAAAATATTTAAAAAATCA
1 TTAAAAATA-TAAAAAAATCA
41749874 TTAAAAATATAAAAAAATCA
1 TTAAAAATATAAAAAAATCA
41749894 -TAAAAA
1 TTAAAAA
41749900 AATATGGACC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 6 0.24
20 10 0.40
21 9 0.36
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (20 bp):
TTAAAAATATAAAAAAATCA
Found at i:41749889 original size:10 final size:10
Alignment explanation
Indices: 41749845--41749904 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
41749835 TTTGGACATT
**
41749845 AAAAATATTT
1 AAAAATATAA
*
41749855 AAAAATATTTA
1 AAAAATA-TAA
*
41749866 AAAAATCAT-T
1 AAAAAT-ATAA
41749876 AAAAATATAA
1 AAAAATATAA
41749886 AAAAATCATAA
1 AAAAAT-ATAA
41749897 AAAAATAT
1 AAAAATAT
41749905 GGACCCAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
9 2 0.05
10 21 0.49
11 19 0.44
12 1 0.02
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.28
Consensus pattern (10 bp):
AAAAATATAA
Found at i:41749890 original size:11 final size:11
Alignment explanation
Indices: 41749865--41749902 Score: 53
Period size: 10 Copynumber: 3.6 Consensus size: 11
41749855 AAAAATATTT
41749865 AAAAAATCAT-
1 AAAAAATCATA
*
41749875 TAAAAAT-ATA
1 AAAAAATCATA
41749885 AAAAAATCATA
1 AAAAAATCATA
41749896 AAAAAAT
1 AAAAAAT
41749903 ATGGACCCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 2 0.08
10 12 0.50
11 10 0.42
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (11 bp):
AAAAAATCATA
Found at i:41764811 original size:73 final size:74
Alignment explanation
Indices: 41764734--41764880 Score: 278
Period size: 73 Copynumber: 2.0 Consensus size: 74
41764724 TGGCCGGAAC
*
41764734 CCAGTACACAGTACAAAGAAAAAAAATTTATTTTTTTTTCGCGTCAGAATCAGAT-AAAAAATAG
1 CCAGTACACAGTACAAAGAAAAAAAAATTATTTTTTTTTCGCGTCAGAATCAGATAAAAAAATAG
41764798 GAAAAAATT
66 GAAAAAATT
41764807 CCAGTACACAGTACAAAGAAAAAAAAATTATTTTTTTTTCGCGTCAGAATCAGATAAAAAAATAG
1 CCAGTACACAGTACAAAGAAAAAAAAATTATTTTTTTTTCGCGTCAGAATCAGATAAAAAAATAG
41764872 GAAAAAATT
66 GAAAAAATT
41764881 TAGAAAAAAA
Statistics
Matches: 72, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
73 54 0.75
74 18 0.25
ACGTcount: A:0.49, C:0.12, G:0.12, T:0.27
Consensus pattern (74 bp):
CCAGTACACAGTACAAAGAAAAAAAAATTATTTTTTTTTCGCGTCAGAATCAGATAAAAAAATAG
GAAAAAATT
Found at i:41764953 original size:118 final size:118
Alignment explanation
Indices: 41764807--41765214 Score: 541
Period size: 118 Copynumber: 3.6 Consensus size: 118
41764797 GGAAAAAATT
41764807 CCAGTACACAGTACAAAGAAAAAAAAATTATTTTTTTTTCGCGTCAGAATCAGATAAAAAAATA-
1 CCAGTACACAGTACAAAGAAAAAAAAATTATTTTTTTTTCGCGTCAGAATCAGATAAAAAAATAC
* *
41764871 GGAAAAAATTTAGAAAAAAAAAATTTTGGGGGCTGGCCTGTCAATGGCCGGCAC
66 GAAAAAAATTTA-AAAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCAC
* * *
41764925 CCAGTACGCAGTACAAAGAAAAAAAAATTATTTTCTTTTCGTGTCAGAATCAGATAAAAAAATAC
1 CCAGTACACAGTACAAAGAAAAAAAAATTATTTTTTTTTCGCGTCAGAATCAGATAAAAAAATAC
41764990 GAAAAAAATTT----AAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCAC
66 GAAAAAAATTTAAAAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCAC
* *
41765039 CCAGTACATAGTAC------------A--ATTTTTTTTTCGTGTCAGAATCAGATAAAAAAATAC
1 CCAGTACACAGTACAAAGAAAAAAAAATTATTTTTTTTTCGCGTCAGAATCAGATAAAAAAATAC
* ** *
41765090 GAAAAAAAATTAAAAAAAAATTTTTTTGGGTGCTGGCCTGTCAATGGCCGGAAC
66 GAAAAAAATTTAAAAAAAAA-AATTTTGGGTGCTGGCCTGTCAATGGCCGGCAC
* *
41765144 CCAGTACACAGTACAAAGAAAAAAAATTTATTTTTTTTTCGCGTCAGAATCAGAT-AAAAAATAG
1 CCAGTACACAGTACAAAGAAAAAAAAATTATTTTTTTTTCGCGTCAGAATCAGATAAAAAAATAC
41765208 GAAAAAA
66 GAAAAAA
41765215 TTCCAGTACA
Statistics
Matches: 254, Mismatches: 16, Indels: 40
0.82 0.05 0.13
Matches are distributed among these distances:
100 45 0.18
102 1 0.00
104 5 0.02
105 43 0.17
114 49 0.19
118 76 0.30
119 35 0.14
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (118 bp):
CCAGTACACAGTACAAAGAAAAAAAAATTATTTTTTTTTCGCGTCAGAATCAGATAAAAAAATAC
GAAAAAAATTTAAAAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCAC
Found at i:41764973 original size:191 final size:193
Alignment explanation
Indices: 41764644--41765287 Score: 589
Period size: 191 Copynumber: 3.2 Consensus size: 193
41764634 ACATAGTACA
* **
41764644 ATTTTTTTTTCGTGTCAGAATCAGATAAAAAAATACGAAAAAAAATTAAAAAAAAATTTTTTTGG
1 ATTTTTTTTTCGCGTCAGAATCAGATAAAAAAATACGAAAAAAAATTAAAAAAAAATAATTTTGG
* * *
41764709 GTGCTGGCCTGTCAATGGCCGGAACCCAGTACACAGTACAAAGAAAAAAAATTTATTTTTTTTTC
66 GGGCTGGCCTGTCAATGGCCGGAACCCAGTACACAGTACAAAGAAAAAAAAATTATTTTCTTTTC
*
41764774 GCGTCAGAATCAGAT-AAAAAATAGGAAAAAATTCCAGTACACAGTACAAAGAAAAAAAAATT
131 GCGTCAGAATCAGATAAAAAAATACGAAAAAATTCCAGTACACAGTACAAAGAAAAAAAAATT
* *
41764836 ATTTTTTTTTCGCGTCAGAATCAGATAAAAAAATA-GGAAAAAATTTAGAAAAAAAA-AATTTTG
1 ATTTTTTTTTCGCGTCAGAATCAGATAAAAAAATACGAAAAAAAATTA-AAAAAAAATAATTTTG
* *
41764899 GGGGCTGGCCTGTCAATGGCCGGCACCCAGTACGCAGTACAAAGAAAAAAAAATTATTTTCTTTT
65 GGGGCTGGCCTGTCAATGGCCGGAACCCAGTACACAGTACAAAGAAAAAAAAATTATTTTCTTTT
* ** * * *
41764964 CGTGTCAGAATCAGATAAAAAAATACGAAAAAAATTTAAAAAAATTTTGGGTGCTGGCCTGT-CA
130 CGCGTCAGAATCAGATAAAAAAATACG-AAAAAA-TT----CCA------GTAC---ACAGTACA
* *** ** **
41765028 ATGGCCGGCACCCAGTACAT
180 A-----AG-AAAAAAAAATT
* **** **** ** ** **
41765048 AGTACAATTTTTTTTTCGTGTCAGAATCAGATAAAAAAATACGAAAAAAAATTAAAAAAAAATTT
1 ATTTTTTTTTCGCGTCAGAATCAG------ATAAAAAAATACGAAAAAAAATTAAAAAAAAATAA
* *
41765113 TTTTGGGTGCTGGCCTGTCAATGGCCGGAACCCAGTACACAGTACAAAGAAAAAAAATTTATTTT
60 TTTTGGGGGCTGGCCTGTCAATGGCCGGAACCCAGTACACAGTACAAAGAAAAAAAAATTATTTT
* *
41765178 TTTTTCGCGTCAGAATCAGAT-AAAAAATAGGAAAAAATTCCAGTACACAGTACAAAGAAAAAAA
125 CTTTTCGCGTCAGAATCAGATAAAAAAATACGAAAAAATTCCAGTACACAGTACAAAGAAAAAAA
41765242 AATT
190 AATT
*
41765246 ATTTTTTTTTCGCGTCAGAATCAGAT-AAAAAATAGGAAAAAA
1 ATTTTTTTTTCGCGTCAGAATCAGATAAAAAAATACGAAAAAA
41765288 TTCCAGTACT
Statistics
Matches: 344, Mismatches: 76, Indels: 65
0.71 0.16 0.13
Matches are distributed among these distances:
191 105 0.31
192 53 0.15
193 6 0.02
194 2 0.01
198 16 0.05
199 1 0.00
203 3 0.01
204 6 0.02
206 6 0.02
207 3 0.01
211 1 0.00
212 16 0.05
216 2 0.01
217 6 0.02
218 28 0.08
219 90 0.26
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (193 bp):
ATTTTTTTTTCGCGTCAGAATCAGATAAAAAAATACGAAAAAAAATTAAAAAAAAATAATTTTGG
GGGCTGGCCTGTCAATGGCCGGAACCCAGTACACAGTACAAAGAAAAAAAAATTATTTTCTTTTC
GCGTCAGAATCAGATAAAAAAATACGAAAAAATTCCAGTACACAGTACAAAGAAAAAAAAATT
Found at i:41765149 original size:105 final size:101
Alignment explanation
Indices: 41764836--41765159 Score: 371
Period size: 105 Copynumber: 3.0 Consensus size: 101
41764826 AAAAAAAATT
* * *
41764836 ATTTTTTTTTCGCGTCAGAATCAGATAAAAAAATAGGAAAAAATTTAGAAAAAAAAAATTTTGGG
1 ATTTTTTTTTCGTGTCAGAATCAGATAAAAAAATACGAAAAAAATT---AAAAAAAAATTTTGGG
* * *
41764901 GGCTGGCCTGTCAATGGCCGGCACCCAGTACGCAGTACAAAGAAAAAAAA
63 TGCTGGCCTGTCAATGGCCGGCACCCAGTA--CA-T----AG----TACA
*
41764951 ATTATTTTCTTTTCGTGTCAGAATCAGATAAAAAAATACGAAAAAAATT-TAAAAAAATTTTGGG
1 A-T-TTTT-TTTTCGTGTCAGAATCAGATAAAAAAATACGAAAAAAATTAAAAAAAAATTTTGGG
41765015 TGCTGGCCTGTCAATGGCCGGCACCCAGTACATAGTACA
63 TGCTGGCCTGTCAATGGCCGGCACCCAGTACATAGTACA
41765054 ATTTTTTTTTCGTGTCAGAATCAGATAAAAAAATACGAAAAAAAATTAAAAAAAAATTTTTTTGG
1 ATTTTTTTTTCGTGTCAGAATCAGATAAAAAAATACG-AAAAAAATTAAAAAAAAA---TTTTGG
* *
41765119 GTGCTGGCCTGTCAATGGCCGGAACCCAGTACACAGTACA
62 GTGCTGGCCTGTCAATGGCCGGCACCCAGTACATAGTACA
41765159 A
1 A
41765160 AGAAAAAAAA
Statistics
Matches: 191, Mismatches: 10, Indels: 26
0.84 0.04 0.11
Matches are distributed among these distances:
100 31 0.16
101 13 0.07
102 8 0.04
103 3 0.02
105 45 0.24
107 2 0.01
111 1 0.01
112 2 0.01
114 43 0.23
115 1 0.01
116 1 0.01
117 4 0.02
118 37 0.19
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (101 bp):
ATTTTTTTTTCGTGTCAGAATCAGATAAAAAAATACGAAAAAAATTAAAAAAAAATTTTGGGTGC
TGGCCTGTCAATGGCCGGCACCCAGTACATAGTACA
Found at i:41765221 original size:73 final size:73
Alignment explanation
Indices: 41765144--41765296 Score: 297
Period size: 73 Copynumber: 2.1 Consensus size: 73
41765134 TGGCCGGAAC
*
41765144 CCAGTACACAGTACAAAGAAAAAAAATTTATTTTTTTTTCGCGTCAGAATCAGATAAAAAATAGG
1 CCAGTACACAGTACAAAGAAAAAAAAATTATTTTTTTTTCGCGTCAGAATCAGATAAAAAATAGG
41765209 AAAAAATT
66 AAAAAATT
41765217 CCAGTACACAGTACAAAGAAAAAAAAATTATTTTTTTTTCGCGTCAGAATCAGATAAAAAATAGG
1 CCAGTACACAGTACAAAGAAAAAAAAATTATTTTTTTTTCGCGTCAGAATCAGATAAAAAATAGG
41765282 AAAAAATT
66 AAAAAATT
41765290 CCAGTAC
1 CCAGTAC
41765297 TACTGTGTAC
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 79 1.00
ACGTcount: A:0.48, C:0.14, G:0.12, T:0.26
Consensus pattern (73 bp):
CCAGTACACAGTACAAAGAAAAAAAAATTATTTTTTTTTCGCGTCAGAATCAGATAAAAAATAGG
AAAAAATT
Found at i:41767377 original size:46 final size:46
Alignment explanation
Indices: 41767307--41767445 Score: 235
Period size: 46 Copynumber: 3.0 Consensus size: 46
41767297 CATGGCAAAG
* *
41767307 TGTGAAACGTATGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
*
41767353 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
41767399 TGTGAAAAGTAGGTATGGTATTTTC-GTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTA-TTTCAGTGAAGAAAACCATACTGAGT
41767445 T
1 T
41767446 ATAGCAATGT
Statistics
Matches: 88, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
46 84 0.95
47 4 0.05
ACGTcount: A:0.35, C:0.09, G:0.26, T:0.30
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
Found at i:41768661 original size:28 final size:28
Alignment explanation
Indices: 41768629--41768722 Score: 134
Period size: 28 Copynumber: 3.4 Consensus size: 28
41768619 AAGTTCACAC
* * *
41768629 ACTTAGTGCTTAATAATCAAACTCGCAT
1 ACTTAGTGCTTTACAATTAAACTCGCAT
* *
41768657 ACTTAGTGCTTTACCATTAAACTCGCAC
1 ACTTAGTGCTTTACAATTAAACTCGCAT
*
41768685 ACTTAGTGCTTTACAATTAAACTCACAT
1 ACTTAGTGCTTTACAATTAAACTCGCAT
41768713 ACTTAGTGCT
1 ACTTAGTGCT
41768723 AATCTCATTA
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 58 1.00
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.34
Consensus pattern (28 bp):
ACTTAGTGCTTTACAATTAAACTCGCAT
Found at i:41772055 original size:17 final size:17
Alignment explanation
Indices: 41772021--41772062 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 17
41772011 TTATACTTTT
*
41772021 AATATGAATTATAGTTTAA
1 AATAT-AATAATAGTTT-A
41772040 AATATAATAATA-TTTA
1 AATATAATAATAGTTTA
41772056 AATATAA
1 AATATAA
41772063 ATTATTGGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 8 0.36
17 3 0.14
18 6 0.27
19 5 0.23
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (17 bp):
AATATAATAATAGTTTA
Found at i:41782535 original size:23 final size:23
Alignment explanation
Indices: 41782508--41782580 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
41782498 ACCTACTTCC
41782508 TTACTGTAGTAATTTTCGGGGTA
1 TTACTGTAGTAATTTTCGGGGTA
*
41782531 TTACTGTAGTAATTTTTGGGGTA
1 TTACTGTAGTAATTTTCGGGGTA
* *
41782554 TTACAGTAGTAATTTTCGGGATA
1 TTACTGTAGTAATTTTCGGGGTA
41782577 TTAC
1 TTAC
41782581 ACTGTTGATG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.25, C:0.08, G:0.23, T:0.44
Consensus pattern (23 bp):
TTACTGTAGTAATTTTCGGGGTA
Found at i:41783430 original size:30 final size:29
Alignment explanation
Indices: 41783396--41783463 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 29
41783386 ATGTGTCTAC
* *
41783396 ATTTGTATCTGAATT-TGAATATGCATCTG
1 ATTTGTATCTG-ATTATGAAAATACATCTG
41783425 TATTTGTATCTGATTATGAAAATACATCTG
1 -ATTTGTATCTGATTATGAAAATACATCTG
41783455 ATTTTGTAT
1 A-TTTGTAT
41783464 ACGAGAATGT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 4 0.12
30 30 0.88
ACGTcount: A:0.29, C:0.09, G:0.15, T:0.47
Consensus pattern (29 bp):
ATTTGTATCTGATTATGAAAATACATCTG
Found at i:41785664 original size:38 final size:38
Alignment explanation
Indices: 41785622--41785745 Score: 131
Period size: 38 Copynumber: 3.0 Consensus size: 38
41785612 GTGTCTTGAC
41785622 TTTCTAAGTGTGATCCTTTATGAGTCGTTTTTCATGAT
1 TTTCTAAGTGTGATCCTTTATGAGTCGTTTTTCATGAT
* * *
41785660 TTTCTAAGTGTGATCCTTTATGGGTGTGATCCTTTTATGTGTCTTGAT
1 TTTCTAAGTGTGATCCTTTA----TGAG-T-C-GTT-T-T-TCATGAT
41785708 TTTCTAAGTGTGATCCTTTATGAGTCGTTTTTCATGAT
1 TTTCTAAGTGTGATCCTTTATGAGTCGTTTTTCATGAT
41785746 ATATTTAAGT
Statistics
Matches: 70, Mismatches: 6, Indels: 20
0.73 0.06 0.21
Matches are distributed among these distances:
38 26 0.37
39 1 0.01
40 1 0.01
41 2 0.03
42 4 0.06
43 2 0.03
44 4 0.06
45 2 0.03
46 1 0.01
47 1 0.01
48 26 0.37
ACGTcount: A:0.17, C:0.13, G:0.20, T:0.50
Consensus pattern (38 bp):
TTTCTAAGTGTGATCCTTTATGAGTCGTTTTTCATGAT
Found at i:41802799 original size:4 final size:4
Alignment explanation
Indices: 41802741--41802853 Score: 63
Period size: 4 Copynumber: 27.8 Consensus size: 4
41802731 AAGGAATAAC
* * * *
41802741 AAAT AAAT GAAT AAAGG AATT AGAAT AAA- AAAGT AAAT AAAT GAAT -AAT
1 AAAT AAAT AAAT AAA-T AAAT A-AAT AAAT AAA-T AAAT AAAT AAAT AAAT
* * * * *
41802790 ATAT AAAT AAAT AAGT AAGT AAGT AAAT GAAT AAAAT AAA- AGGAAT -AAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT A--AAT AAAT
41802839 AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAA
41802854 AGGAAACCGT
Statistics
Matches: 86, Mismatches: 13, Indels: 20
0.72 0.11 0.17
Matches are distributed among these distances:
3 10 0.12
4 63 0.73
5 13 0.15
ACGTcount: A:0.66, C:0.00, G:0.11, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:41807120 original size:20 final size:19
Alignment explanation
Indices: 41807097--41807157 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 19
41807087 ATTATTCATA
41807097 TATATATTTTTATATTTGTT
1 TATATATTTTTATATTT-TT
*
41807117 TATA-ATTTATTA-GTTTTT
1 TATATATTT-TTATATTTTT
41807135 TATATAAGTTTTTATAATTTTT
1 TATAT-A-TTTTTAT-ATTTTT
41807157 T
1 T
41807158 TAAAAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
18 6 0.18
19 7 0.21
20 11 0.33
21 3 0.09
22 6 0.18
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (19 bp):
TATATATTTTTATATTTTT
Found at i:41814105 original size:22 final size:23
Alignment explanation
Indices: 41814073--41814115 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
41814063 AGTATAAAAT
41814073 ATAATAATTATATATTTATATAA
1 ATAATAATTATATATTTATATAA
* *
41814096 ATAA-AATTATGTGTTTATAT
1 ATAATAATTATATATTTATAT
41814116 TTGATTATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (23 bp):
ATAATAATTATATATTTATATAA
Found at i:41820360 original size:27 final size:28
Alignment explanation
Indices: 41820322--41820385 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 28
41820312 AGTTTTAAAA
*
41820322 ATTATA-TT-TAATACAATAAAATATTT
1 ATTATATTTATAATACAATAAAACATTT
*
41820348 ATT-TATTTATAATATAATAAAACATTT
1 ATTATATTTATAATACAATAAAACATTT
41820375 ATTATATTTAT
1 ATTATATTTAT
41820386 GATAATGTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 2 0.06
26 5 0.15
27 19 0.58
28 7 0.21
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (28 bp):
ATTATATTTATAATACAATAAAACATTT
Found at i:41821241 original size:22 final size:23
Alignment explanation
Indices: 41821211--41821255 Score: 56
Period size: 25 Copynumber: 1.9 Consensus size: 23
41821201 AAGAACCTAA
41821211 AAAAATAC-ATATAATATTATGG
1 AAAAATACAATATAATATTATGG
*
41821233 AAAAGTACAAAATATAATATTAT
1 AAAAATAC--AATATAATATTAT
41821256 TTTTTTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 7 0.37
25 12 0.63
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.31
Consensus pattern (23 bp):
AAAAATACAATATAATATTATGG
Found at i:41825598 original size:19 final size:19
Alignment explanation
Indices: 41825561--41825599 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
41825551 AACTCTAGTA
*
41825561 AATAATAAATAATATTTTT
1 AATAATAAATAATAATTTT
*
41825580 AATAATAAATATTAATTTT
1 AATAATAAATAATAATTTT
41825599 A
1 A
41825600 TTACAATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AATAATAAATAATAATTTT
Found at i:41825901 original size:5 final size:5
Alignment explanation
Indices: 41825891--41825917 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
41825881 ATATTATTTT
41825891 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
41825918 AAATTAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:41829649 original size:28 final size:29
Alignment explanation
Indices: 41829609--41829666 Score: 109
Period size: 28 Copynumber: 2.0 Consensus size: 29
41829599 TTGACACCCT
41829609 GCGCGACAGTTGTTCATCTTCATCTACTC
1 GCGCGACAGTTGTTCATCTTCATCTACTC
41829638 GCGC-ACAGTTGTTCATCTTCATCTACTC
1 GCGCGACAGTTGTTCATCTTCATCTACTC
41829666 G
1 G
41829667 TGAGCGAGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 25 0.86
29 4 0.14
ACGTcount: A:0.17, C:0.31, G:0.17, T:0.34
Consensus pattern (29 bp):
GCGCGACAGTTGTTCATCTTCATCTACTC
Found at i:41831922 original size:27 final size:27
Alignment explanation
Indices: 41831892--41831949 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
41831882 TTTAGTCCCT
41831892 ATTTCAAAAAAACTCAAAATATTCAAA
1 ATTTCAAAAAAACTCAAAATATTCAAA
* * *
41831919 ATTTTAACACAACTCAAAATATTCAAA
1 ATTTCAAAAAAACTCAAAATATTCAAA
41831946 ATTT
1 ATTT
41831950 TAACATACTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (27 bp):
ATTTCAAAAAAACTCAAAATATTCAAA
Found at i:41831950 original size:27 final size:27
Alignment explanation
Indices: 41831902--41831954 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
41831892 ATTTCAAAAA
41831902 AACTCAAAATATTCAAAATTTTAACAC
1 AACTCAAAATATTCAAAATTTTAACAC
41831929 AACTCAAAATATTCAAAATTTTAACA
1 AACTCAAAATATTCAAAATTTTAACA
41831955 TACTCTAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (27 bp):
AACTCAAAATATTCAAAATTTTAACAC
Found at i:41841506 original size:29 final size:29
Alignment explanation
Indices: 41841468--41841599 Score: 110
Period size: 31 Copynumber: 4.4 Consensus size: 29
41841458 AAAATTAACT
**
41841468 AATTACATTTTGGTCTCCAACTTTCCTAA
1 AATTACATTTTGAACTCCAACTTTCCTAA
*
41841497 AATTACATTTT-AAC-CCTAAATTATCCTAA
1 AATTACATTTTGAACTCC-AACTT-TCCTAA
*
41841526 AATTACA-TTTGACCCTCCAACTTTTCCTAA
1 AATTACATTTTGA-ACTCCAAC-TTTCCTAA
* * *
41841556 AATTACATTTT-AACCCTCTAAATTTTTCTAA
1 AATTACATTTTGAA--CTC-CAACTTTCCTAA
41841587 AATTACATTTTGA
1 AATTACATTTTGA
41841600 CCCTGAAAGT
Statistics
Matches: 83, Mismatches: 9, Indels: 19
0.75 0.08 0.17
Matches are distributed among these distances:
27 2 0.02
28 8 0.10
29 25 0.30
30 17 0.20
31 28 0.34
32 3 0.04
ACGTcount: A:0.34, C:0.22, G:0.03, T:0.41
Consensus pattern (29 bp):
AATTACATTTTGAACTCCAACTTTCCTAA
Found at i:41841567 original size:59 final size:61
Alignment explanation
Indices: 41841468--41841603 Score: 199
Period size: 59 Copynumber: 2.3 Consensus size: 61
41841458 AAAATTAACT
**
41841468 AATTACATTTTG-GTCTCCAACTTTCCTAAAATTACATTTTAA-CC-CTAAATTATCCTAA
1 AATTACATTTTGACCCTCCAACTTTCCTAAAATTACATTTTAACCCTCTAAATTATCCTAA
* *
41841526 AATTACA-TTTGACCCTCCAACTTTTCCTAAAATTACATTTTAACCCTCTAAATTTTTCTAA
1 AATTACATTTTGACCCTCCAAC-TTTCCTAAAATTACATTTTAACCCTCTAAATTATCCTAA
41841587 AATTACATTTTGACCCT
1 AATTACATTTTGACCCT
41841604 GAAAGTTTTG
Statistics
Matches: 69, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
57 4 0.06
58 14 0.20
59 21 0.30
60 2 0.03
61 19 0.28
62 9 0.13
ACGTcount: A:0.33, C:0.24, G:0.03, T:0.40
Consensus pattern (61 bp):
AATTACATTTTGACCCTCCAACTTTCCTAAAATTACATTTTAACCCTCTAAATTATCCTAA
Found at i:41841587 original size:31 final size:31
Alignment explanation
Indices: 41841489--41841603 Score: 155
Period size: 31 Copynumber: 3.8 Consensus size: 31
41841479 GGTCTCCAAC
41841489 TTTCCTAAAATTACATTTTAA-CC-CTAAAT
1 TTTCCTAAAATTACATTTTAACCCTCTAAAT
* * * *
41841518 TATCCTAAAATTACA-TTTGACCCTCCAACT
1 TTTCCTAAAATTACATTTTAACCCTCTAAAT
41841548 TTTCCTAAAATTACATTTTAACCCTCTAAAT
1 TTTCCTAAAATTACATTTTAACCCTCTAAAT
* *
41841579 TTTTCTAAAATTACATTTTGACCCT
1 TTTCCTAAAATTACATTTTAACCCT
41841604 GAAAGTTTTG
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
28 4 0.05
29 16 0.22
30 18 0.25
31 35 0.48
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.41
Consensus pattern (31 bp):
TTTCCTAAAATTACATTTTAACCCTCTAAAT
Found at i:41842146 original size:11 final size:10
Alignment explanation
Indices: 41842123--41842195 Score: 57
Period size: 11 Copynumber: 7.4 Consensus size: 10
41842113 GCAAAACAAG
41842123 AAGAGAA-AA
1 AAGAGAAGAA
41842132 AAGAGGAAGAA
1 AAGA-GAAGAA
41842143 AAGAGAA-AA
1 AAGAGAAGAA
41842152 GAA-A-AA-AA
1 -AAGAGAAGAA
41842160 AAGAGAAAGAA
1 AAGAG-AAGAA
*
41842171 GAGAGAAGAGA
1 AAGAGAAGA-A
*
41842182 AAGAGGAGAA
1 AAGAGAAGAA
41842192 AAGA
1 AAGA
41842196 TATGAAGGGC
Statistics
Matches: 53, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
7 2 0.04
8 5 0.09
9 7 0.13
10 19 0.36
11 20 0.38
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (10 bp):
AAGAGAAGAA
Found at i:41842169 original size:28 final size:28
Alignment explanation
Indices: 41842128--41842183 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
41842118 ACAAGAAGAG
*
41842128 AAAAAAGAGGAAGAAAAGAGAAAAGAAA
1 AAAAAAGAGAAAGAAAAGAGAAAAGAAA
* *
41842156 AAAAAAGAGAAAGAAGAGAGAAGAGAAA
1 AAAAAAGAGAAAGAAAAGAGAAAAGAAA
41842184 GAGGAGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (28 bp):
AAAAAAGAGAAAGAAAAGAGAAAAGAAA
Found at i:41842190 original size:16 final size:16
Alignment explanation
Indices: 41842139--41842195 Score: 69
Period size: 16 Copynumber: 3.5 Consensus size: 16
41842129 AAAAAGAGGA
*
41842139 AGAAAAGAGAAAAGAAA
1 AGAAAAGAG-AAAGAAG
*
41842156 AAAAAAGAGAAAGAAG
1 AGAAAAGAGAAAGAAG
* *
41842172 AGAGAAGAGAAAGAGG
1 AGAAAAGAGAAAGAAG
41842188 AGAAAAGA
1 AGAAAAGA
41842196 TATGAAGGGC
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
16 26 0.76
17 8 0.24
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (16 bp):
AGAAAAGAGAAAGAAG
Found at i:41842302 original size:17 final size:16
Alignment explanation
Indices: 41842280--41842315 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
41842270 GGTTTGAGTT
*
41842280 GAAAGAAGAAGGAAAAA
1 GAAAGAA-AAAGAAAAA
41842297 GAAAGAAAAAGAAAAA
1 GAAAGAAAAAGAAAAA
41842313 GAA
1 GAA
41842316 CAGTCGGTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (16 bp):
GAAAGAAAAAGAAAAA
Found at i:41846750 original size:23 final size:23
Alignment explanation
Indices: 41846704--41846757 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 23
41846694 GAATAATAAG
41846704 AATAAAAACAAAAATAAGATAAAT
1 AATAAAAACAAAAAT-AGATAAAT
*
41846728 AATAAAAGCAAAAAT-GATGAAAT
1 AATAAAAACAAAAATAGAT-AAAT
41846751 AATAAAA
1 AATAAAA
41846758 TAGTAAGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 3 0.11
23 11 0.39
24 14 0.50
ACGTcount: A:0.72, C:0.04, G:0.07, T:0.17
Consensus pattern (23 bp):
AATAAAAACAAAAATAGATAAAT
Found at i:41846899 original size:3 final size:3
Alignment explanation
Indices: 41846891--41847040 Score: 81
Period size: 3 Copynumber: 50.0 Consensus size: 3
41846881 ATAACAATGT
* * * * * * *
41846891 ATA ATA ATA ACA ATA GTA GTA AAA ATA AAA ATA ATA ATA TTA GTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
41846939 ATA A-A A-A ATA ATG ATA ATG ATA ATA ATA A-A GTA AGTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA
* * ** * * * *
41846982 ATA ATA GCACA ATG ATA ATA ATA GCA ATA TTA AAA ATA ATA GTA ACA
1 ATA ATA --ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
41847029 ATA ATG ATA ATA
1 ATA ATA ATA ATA
41847041 CTATCGAAAT
Statistics
Matches: 107, Mismatches: 35, Indels: 10
0.70 0.23 0.07
Matches are distributed among these distances:
2 5 0.05
3 97 0.91
4 3 0.03
5 2 0.02
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:41846901 original size:16 final size:18
Alignment explanation
Indices: 41846876--41846923 Score: 64
Period size: 16 Copynumber: 2.8 Consensus size: 18
41846866 CAAAACAGTT
41846876 TAAAAATAACAAT-GTA-
1 TAAAAATAACAATAGTAG
*
41846892 TAATAATAACAATAGTAG
1 TAAAAATAACAATAGTAG
*
41846910 TAAAAATAAAAATA
1 TAAAAATAACAATA
41846924 ATAATATTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 12 0.44
17 3 0.11
18 12 0.44
ACGTcount: A:0.65, C:0.04, G:0.06, T:0.25
Consensus pattern (18 bp):
TAAAAATAACAATAGTAG
Found at i:41846962 original size:25 final size:25
Alignment explanation
Indices: 41846908--41846968 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
41846898 TAACAATAGT
* *
41846908 AGTAAAAAT-AAAAATAATAATATT
1 AGTAATAATAAAAAATAATAATATG
*
41846932 AGTAATAATAAAAAATAATGATAATG
1 AGTAATAATAAAAAATAATAAT-ATG
41846958 A-TAATAATAAA
1 AGTAATAATAAA
41846969 GTAAGTAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 8 0.25
25 21 0.66
26 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.28
Consensus pattern (25 bp):
AGTAATAATAAAAAATAATAATATG
Found at i:41848988 original size:20 final size:20
Alignment explanation
Indices: 41848961--41849010 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
41848951 TGAAAGTAAT
*
41848961 ACATGAAAGAATTATTTAAA
1 ACATGAAAGAATTACTTAAA
* *
41848981 AGATGAAAGAGTTACTTAAA
1 ACATGAAAGAATTACTTAAA
41849001 ACAT-AAAGAA
1 ACATGAAAGAA
41849011 AAAATTAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.56, C:0.06, G:0.14, T:0.24
Consensus pattern (20 bp):
ACATGAAAGAATTACTTAAA
Found at i:41851261 original size:27 final size:28
Alignment explanation
Indices: 41851192--41851262 Score: 81
Period size: 27 Copynumber: 2.5 Consensus size: 28
41851182 ACCCATTTTT
41851192 TAATAAACATTAAAAAATTATTTTAAAAA
1 TAATAAA-ATTAAAAAATTATTTTAAAAA
* * *
41851221 TAA-AAAAATAAAAAAATATTTTAAAAG
1 TAATAAAATTAAAAAATTATTTTAAAAA
**
41851248 TTTTAAAATTAAAAA
1 TAATAAAATTAAAAA
41851263 TAAAAATAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
27 19 0.54
28 13 0.37
29 3 0.09
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (28 bp):
TAATAAAATTAAAAAATTATTTTAAAAA
Found at i:41852180 original size:17 final size:20
Alignment explanation
Indices: 41852158--41852204 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 20
41852148 AGTTATTGTG
41852158 TATTATTATT-C-T-AAAGT
1 TATTATTATTACTTAAAAGT
41852175 TATTATTATTACTTAAAAGT
1 TATTATTATTACTTAAAAGT
41852195 TA-TATTATTA
1 TATTATTATTA
41852205 TTTTTAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 10 0.37
18 1 0.04
19 9 0.33
20 7 0.26
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.53
Consensus pattern (20 bp):
TATTATTATTACTTAAAAGT
Found at i:41852183 original size:20 final size:18
Alignment explanation
Indices: 41852158--41852206 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
41852148 AGTTATTGTG
*
41852158 TATTATTATTCTAAAGTTA
1 TATTATTATT-AAAAGTTA
41852177 TTATTATTACTTAAAAGTTA
1 -TATTATTA-TTAAAAGTTA
41852197 TATTATTATT
1 TATTATTATT
41852207 TTTAATTTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 2 0.07
19 8 0.30
20 15 0.56
21 2 0.07
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (18 bp):
TATTATTATTAAAAGTTA
Found at i:41859484 original size:26 final size:25
Alignment explanation
Indices: 41859436--41859484 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
41859426 ATCAATCATC
* **
41859436 TAGTAAAGATTTAATAATTTATTTT
1 TAGTAAAAATTTAATAACATATTTT
41859461 TAGTAATAAATTTAATAACATATT
1 TAGTAA-AAATTTAATAACATATT
41859485 AATAACTTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 6 0.30
26 14 0.70
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (25 bp):
TAGTAAAAATTTAATAACATATTTT
Found at i:41863670 original size:19 final size:20
Alignment explanation
Indices: 41863648--41863692 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
41863638 AAGAATTTCC
* *
41863648 AAAATAT-TAAAAATTTCAT
1 AAAATATCTAAAAATTTAAA
41863667 AAAA-ATCTAAAAATTTAAA
1 AAAATATCTAAAAATTTAAA
41863686 AAAATAT
1 AAAATAT
41863693 ATGAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 18 0.82
20 2 0.09
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAATATCTAAAAATTTAAA
Found at i:41863828 original size:19 final size:19
Alignment explanation
Indices: 41863799--41863837 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
41863789 TGAAATTTTT
41863799 AATATAAAATTTGAGAAAAA
1 AATATAAAATTTGA-AAAAA
41863819 AATA-AAAATTTGAAAAAA
1 AATATAAAATTTGAAAAAA
41863837 A
1 A
41863838 TTGTTGTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.32
19 9 0.47
20 4 0.21
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (19 bp):
AATATAAAATTTGAAAAAA
Found at i:41866775 original size:109 final size:107
Alignment explanation
Indices: 41866584--41866791 Score: 317
Period size: 109 Copynumber: 1.9 Consensus size: 107
41866574 AAGTTTTAAG
* **
41866584 AGGATATTTGGCTATTTAGTCGAACGAGAAAACGAAACCCAGCACGTTAGGGCATGTTTTCTCGA
1 AGGATATTTGGCTATTTAGTCGAACGAGAAAACGAAACCCAACACGTTAGGGCACATTTTCTCGA
** *
41866649 TTTTCCAAACGCAAAACATTGTCCCTCTTTTTGAAATTATTGAA
66 TTTTCCAAAAACAAAACATTG--CCTCGTTTTGAAATTATTGAA
* *
41866693 AGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACGTTAGGGCACATTTTCTCGA
1 AGGATATTTGGCTATTTAGTCGAACGAGAAAACGAAACCCAACACGTTAGGGCACATTTTCTCGA
*
41866758 TTTTCTAAAAACAAAACATTGCCTCGTTTTGAAA
66 TTTTCCAAAAACAAAACATTGCCTCGTTTTGAAA
41866792 AAATTTTCCT
Statistics
Matches: 90, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
107 12 0.13
109 78 0.87
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Consensus pattern (107 bp):
AGGATATTTGGCTATTTAGTCGAACGAGAAAACGAAACCCAACACGTTAGGGCACATTTTCTCGA
TTTTCCAAAAACAAAACATTGCCTCGTTTTGAAATTATTGAA
Found at i:41867541 original size:197 final size:198
Alignment explanation
Indices: 41867316--41867712 Score: 760
Period size: 197 Copynumber: 2.0 Consensus size: 198
41867306 TATATTTATG
41867316 TATATCTATGTATATAAAGATATGAAATATAAAATATAAAAAATATATATTTATAATAAATGAAA
1 TATATCTATGTATATAAAGATATGAAATATAAAATATAAAAAATATATATTTATAATAAATGAAA
41867381 AGTATGTACGTAAATATATATTATAAAAATGTATGAACAATTTGAAATTATGAATATTAAAATAT
66 AGTATGTACGTAAATATATATTATAAAAATGTATGAACAATTTGAAATTATGAATATTAAAATAT
41867446 TTAATATAGATAATAATACATAAGATGATAATATATGAATTTAAACCAAATAAATAAACA-AAAA
131 TTAATATAGATAATAATACATAAGATGATAATATATGAATTTAAACCAAATAAATAAACAGAAAA
41867510 AAA
196 AAA
*
41867513 TATATCTATGTATATAAAGATATGAAATATAAAATATAAAAAGTATATATTTATAATAAATGAAA
1 TATATCTATGTATATAAAGATATGAAATATAAAATATAAAAAATATATATTTATAATAAATGAAA
41867578 AGTATGTACGTAAATATATATTATAAAAATGTATGAACAATTTGAAATTATGAATATTAAAATAT
66 AGTATGTACGTAAATATATATTATAAAAATGTATGAACAATTTGAAATTATGAATATTAAAATAT
* *
41867643 TTAATATAGATAATAATATATAAGATGATAATATATGAATTTAAACCAAATAAATAAACAGAATA
131 TTAATATAGATAATAATACATAAGATGATAATATATGAATTTAAACCAAATAAATAAACAGAAAA
41867708 AAA
196 AAA
41867711 TA
1 TA
41867713 AAAACTTGAG
Statistics
Matches: 196, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
197 188 0.96
198 8 0.04
ACGTcount: A:0.55, C:0.03, G:0.08, T:0.34
Consensus pattern (198 bp):
TATATCTATGTATATAAAGATATGAAATATAAAATATAAAAAATATATATTTATAATAAATGAAA
AGTATGTACGTAAATATATATTATAAAAATGTATGAACAATTTGAAATTATGAATATTAAAATAT
TTAATATAGATAATAATACATAAGATGATAATATATGAATTTAAACCAAATAAATAAACAGAAAA
AAA
Found at i:41870421 original size:98 final size:94
Alignment explanation
Indices: 41870250--41870431 Score: 258
Period size: 98 Copynumber: 1.9 Consensus size: 94
41870240 AATAGGGATT
* *
41870250 TTTTATATAAAATAATTAAAATGCTCATTGTATGTAAATTTATTATATAATATGCATATGAATTG
1 TTTTATATAAAATAATTAAAATACTCATTGGATGTAAATTTATTATATAATATGCATATGAATTG
41870315 ATGAAAATATATTTTATTCATTAGAGTTC
66 ATGAAAATATATTTTATTCATTAGAGTTC
* * *
41870344 TTTTATATAAAATAATTGAAGTACTTATTGGATGTAAAATTTATTATTATATGATATGCATATGA
1 TTTTATATAAAATAATTAAAATACTCATTGGATGT-AAATTTATTA-TATA--ATATGCATATGA
*
41870409 ATTGAT-AGAAATATCTTTTATTC
62 ATTGATGA-AAATATATTTTATTC
41870432 TTTATTATTA
Statistics
Matches: 77, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
94 30 0.39
95 10 0.13
96 4 0.05
97 1 0.01
98 32 0.42
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (94 bp):
TTTTATATAAAATAATTAAAATACTCATTGGATGTAAATTTATTATATAATATGCATATGAATTG
ATGAAAATATATTTTATTCATTAGAGTTC
Found at i:41872194 original size:13 final size:13
Alignment explanation
Indices: 41872178--41872230 Score: 54
Period size: 13 Copynumber: 4.1 Consensus size: 13
41872168 TTTAAACCAA
*
41872178 ACTTTTTAAAAGC
1 ACTTTTCAAAAGC
*
41872191 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
* *
41872204 ATTTTTTC-ATAGC
1 A-CTTTTCAAAAGC
41872217 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
41872230 A
1 A
41872231 ATGAGAACTG
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
12 5 0.16
13 22 0.71
14 4 0.13
ACGTcount: A:0.36, C:0.21, G:0.08, T:0.36
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:41872210 original size:26 final size:26
Alignment explanation
Indices: 41872180--41872230 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
41872170 TAAACCAAAC
41872180 TTTTTAAAAGCACTTCTCAAAAGCAT
1 TTTTTAAAAGCACTTCTCAAAAGCAT
* * *
41872206 TTTTTCATAGCACTTTTCAAAAGCA
1 TTTTTAAAAGCACTTCTCAAAAGCA
41872231 ATGAGAACTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.37
Consensus pattern (26 bp):
TTTTTAAAAGCACTTCTCAAAAGCAT
Found at i:41873711 original size:9 final size:9
Alignment explanation
Indices: 41873691--41873724 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
41873681 AATGCCCCTT
41873691 TTTTAAAA-
1 TTTTAAAAG
*
41873699 TTTTACAAG
1 TTTTAAAAG
41873708 TTTTAAAAG
1 TTTTAAAAG
41873717 TTTTAAAA
1 TTTTAAAA
41873725 ATGTGAGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (9 bp):
TTTTAAAAG
Found at i:41876675 original size:20 final size:19
Alignment explanation
Indices: 41876601--41876678 Score: 84
Period size: 19 Copynumber: 4.1 Consensus size: 19
41876591 TTTGTTTCCA
*
41876601 ACCATTTCTGACAAAATTT
1 ACCATTTCTGACAAAAATT
* * *
41876620 ACCGTTTTTGACAAAAACTA
1 ACCATTTCTGACAAAAA-TT
* *
41876640 ATCATTTCTCACAAAAATT
1 ACCATTTCTGACAAAAATT
*
41876659 ACCATTTCTGACGAAAATT
1 ACCATTTCTGACAAAAATT
41876678 A
1 A
41876679 GTTTGGGAAT
Statistics
Matches: 46, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
19 32 0.70
20 14 0.30
ACGTcount: A:0.40, C:0.21, G:0.06, T:0.33
Consensus pattern (19 bp):
ACCATTTCTGACAAAAATT
Found at i:41877322 original size:10 final size:10
Alignment explanation
Indices: 41877307--41877407 Score: 66
Period size: 10 Copynumber: 10.4 Consensus size: 10
41877297 TTTTTCAAAT
*
41877307 AATTATAAAA
1 AATTATTAAA
*
41877317 AATTATTGAA
1 AATTATTAAA
**
41877327 AA-TATGGAA
1 AATTATTAAA
*
41877336 AATTATTTAAG
1 AATTA-TTAAA
*
41877347 AA-TATTAAT
1 AATTATTAAA
*
41877356 AATTATAAAA
1 AATTATTAAA
* *
41877366 AATTACT-GA
1 AATTATTAAA
41877375 AATTATTAAA
1 AATTATTAAA
* *
41877385 AGTTAATAAA
1 AATTATTAAA
41877395 AA-TATTAAA
1 AATTATTAAA
41877404 AATT
1 AATT
41877408 TAATTAATTA
Statistics
Matches: 68, Mismatches: 18, Indels: 10
0.71 0.19 0.10
Matches are distributed among these distances:
9 29 0.43
10 35 0.51
11 4 0.06
ACGTcount: A:0.57, C:0.01, G:0.06, T:0.36
Consensus pattern (10 bp):
AATTATTAAA
Found at i:41877819 original size:21 final size:18
Alignment explanation
Indices: 41877795--41877835 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 18
41877785 TGTCTAATGT
41877795 AATTTTAAATAACTTTTATTA
1 AATTTT-AAT-ACTTTT-TTA
41877816 AATTTTAATACTTTTTTA
1 AATTTTAATACTTTTTTA
41877834 AA
1 AA
41877836 AAATTATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 5 0.25
19 6 0.30
20 3 0.15
21 6 0.30
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (18 bp):
AATTTTAATACTTTTTTA
Found at i:41877864 original size:30 final size:30
Alignment explanation
Indices: 41877828--41877892 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
41877818 TTTTAATACT
41877828 TTTTTAAAAAATTAT-TATA-ATTCTTGATAA
1 TTTTTAAAAAATTATCTATATATT-TT-ATAA
* *
41877858 TTTTTAAATAATTTTCTATATATTTTATAA
1 TTTTTAAAAAATTATCTATATATTTTATAA
41877888 TTTTT
1 TTTTT
41877893 TTTAAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 22 0.71
31 6 0.19
32 3 0.10
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (30 bp):
TTTTTAAAAAATTATCTATATATTTTATAA
Found at i:41884408 original size:30 final size:31
Alignment explanation
Indices: 41884369--41884428 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
41884359 GGAGGTGGGA
*
41884369 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
41884400 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
41884429 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:41884661 original size:9 final size:9
Alignment explanation
Indices: 41884647--41884683 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
41884637 TATAGTTTGA
41884647 TATTCGAAT
1 TATTCGAAT
41884656 TATTCGAAT
1 TATTCGAAT
*
41884665 TATTCGAGT
1 TATTCGAAT
*
41884674 TATTCAAAT
1 TATTCGAAT
41884683 T
1 T
41884684 CGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:41885119 original size:15 final size:15
Alignment explanation
Indices: 41885093--41885135 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
41885083 AAAATTAGGT
41885093 TAAAATATTTTAAACA
1 TAAAA-ATTTTAAACA
*
41885109 TAAAAATTTTAAATA
1 TAAAAATTTTAAACA
*
41885124 -AAAAATTCTAAA
1 TAAAAATTTTAAA
41885136 AATTCAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 11 0.44
15 9 0.36
16 5 0.20
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (15 bp):
TAAAAATTTTAAACA
Found at i:41885387 original size:20 final size:20
Alignment explanation
Indices: 41885374--41885446 Score: 60
Period size: 20 Copynumber: 3.5 Consensus size: 20
41885364 TTTTAACGTA
41885374 ATTTTTAATTTTTTAAATAT
1 ATTTTTAATTTTTTAAATAT
*
41885394 ATTTTTAATAATTTT-AATA-
1 ATTTTTAAT-TTTTTAAATAT
* * *
41885413 ATTTGTATTTATTTTTAAGATTT
1 ATTTTTA-AT-TTTTTAA-ATAT
41885436 ATTTTTAATTT
1 ATTTTTAATTT
41885447 CTTTTTTAGA
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
19 6 0.15
20 19 0.46
21 7 0.17
22 3 0.07
23 6 0.15
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (20 bp):
ATTTTTAATTTTTTAAATAT
Found at i:41885437 original size:13 final size:13
Alignment explanation
Indices: 41885419--41885469 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
41885409 AATAATTTGT
41885419 ATTTATTTTTAAG
1 ATTTATTTTTAAG
41885432 ATTTATTTTT-A-
1 ATTTATTTTTAAG
* *
41885443 ATTTCTTTTTTAG
1 ATTTATTTTTAAG
* *
41885456 AATTATTGTTAAG
1 ATTTATTTTTAAG
41885469 A
1 A
41885470 AAACTTTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
11 9 0.29
12 2 0.06
13 20 0.65
ACGTcount: A:0.29, C:0.02, G:0.08, T:0.61
Consensus pattern (13 bp):
ATTTATTTTTAAG
Found at i:41885451 original size:24 final size:24
Alignment explanation
Indices: 41885419--41885467 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
41885409 AATAATTTGT
* *
41885419 ATTTATTTTTAAGATTTATTTTTA
1 ATTTATTTTTAAGAATTATTGTTA
* *
41885443 ATTTCTTTTTTAGAATTATTGTTA
1 ATTTATTTTTAAGAATTATTGTTA
41885467 A
1 A
41885468 GAAAACTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.63
Consensus pattern (24 bp):
ATTTATTTTTAAGAATTATTGTTA
Found at i:41893265 original size:3 final size:3
Alignment explanation
Indices: 41893247--41893297 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
41893237 TTAAATATCC
* * * * *
41893247 TTA TTA TTT TTA -TA TTA TTA GTA TTA TTA ATA TTA CTA TTA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
41893294 TTA T
1 TTA T
41893298 GTACTAGTGT
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:41893430 original size:3 final size:3
Alignment explanation
Indices: 41893422--41893448 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
41893412 TATTCCAATG
41893422 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
41893449 NNNNNNNNNN
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:41907837 original size:16 final size:15
Alignment explanation
Indices: 41907814--41907850 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
41907804 TAAATTAAAC
*
41907814 AAAAAAGAAAAGGCA
1 AAAAAAGAAAAGCCA
41907829 AAGAAAAGAAAAGCCA
1 AA-AAAAGAAAAGCCA
41907845 AAAAAA
1 AAAAAA
41907851 TTGATACCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.76, C:0.08, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAGCCA
Found at i:41913651 original size:11 final size:9
Alignment explanation
Indices: 41913612--41913654 Score: 50
Period size: 10 Copynumber: 4.4 Consensus size: 9
41913602 TCATTTTAAC
*
41913612 TAAACAAAA
1 TAAATAAAA
41913621 GTAAATAAAA
1 -TAAATAAAA
41913631 TAAATAAAA
1 TAAATAAAA
41913640 TGAAAGTAAAA
1 T-AAA-TAAAA
41913651 TAAA
1 TAAA
41913655 ATAATGAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 10 0.33
10 14 0.47
11 6 0.20
ACGTcount: A:0.72, C:0.02, G:0.07, T:0.19
Consensus pattern (9 bp):
TAAATAAAA
Found at i:41913666 original size:20 final size:20
Alignment explanation
Indices: 41913626--41913663 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
41913616 CAAAAGTAAA
41913626 TAAAATAAATAAAATGAAAG
1 TAAAATAAATAAAATGAAAG
*
41913646 TAAAATAAA-ATAATGAAA
1 TAAAATAAATAAAATGAAA
41913664 AGTTTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (20 bp):
TAAAATAAATAAAATGAAAG
Found at i:41915732 original size:120 final size:120
Alignment explanation
Indices: 41915519--41915878 Score: 630
Period size: 120 Copynumber: 3.0 Consensus size: 120
41915509 GCACGTATAC
* * *
41915519 AACAAGCATAAAACTTAGACTGAACTTTCAAAGGTTCCCAAAATTCTTGTCAAAGTTTCTTGTAA
1 AACAAGCATAAAACATAGACTGAACTTTCAAAAGTTCCCAAAATTCTTGTCAAAGTTTCTTGTGA
*
41915584 CTGTTGATTCAGCCAAAAATTAATAATTAAAAAAGCAAAGGAACCACCACTTTGA
66 CTGTTGATACAGCCAAAAATTAATAATTAAAAAAGCAAAGGAACCACCACTTTGA
41915639 AACAAGCATAAAACATAGACTGAACTTTCAAAAGTTCCCAAAATTCTTGTCAAAGTTTCTTGTGA
1 AACAAGCATAAAACATAGACTGAACTTTCAAAAGTTCCCAAAATTCTTGTCAAAGTTTCTTGTGA
* *
41915704 CTGTTGATACAGCCAAAATTTAATAATTAAAAAAGAAAAGGAACCACCACTTTGA
66 CTGTTGATACAGCCAAAAATTAATAATTAAAAAAGCAAAGGAACCACCACTTTGA
* * *
41915759 AACAAGCATAAAACATAGACTGAACTTTCAAAAGCTCCCAAAATTCTTGTCAAAGGTTCTTGGGA
1 AACAAGCATAAAACATAGACTGAACTTTCAAAAGTTCCCAAAATTCTTGTCAAAGTTTCTTGTGA
*
41915824 CTGTTGGTACAGCCAAAAATTAATAATTAAAAAAGCAAAGGAACCACCACTTTGA
66 CTGTTGATACAGCCAAAAATTAATAATTAAAAAAGCAAAGGAACCACCACTTTGA
41915879 CTCATAAAAC
Statistics
Matches: 228, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
120 228 1.00
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.26
Consensus pattern (120 bp):
AACAAGCATAAAACATAGACTGAACTTTCAAAAGTTCCCAAAATTCTTGTCAAAGTTTCTTGTGA
CTGTTGATACAGCCAAAAATTAATAATTAAAAAAGCAAAGGAACCACCACTTTGA
Found at i:41934821 original size:6 final size:6
Alignment explanation
Indices: 41934779--41934812 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
41934769 ATAAAAATAT
*
41934779 ATACTA ATACATA ATAGTA ATACTA ATACTA ATA
1 ATACTA ATAC-TA ATACTA ATACTA ATACTA ATA
41934813 ATACTAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.32
Consensus pattern (6 bp):
ATACTA
Found at i:41935327 original size:11 final size:12
Alignment explanation
Indices: 41935294--41935328 Score: 54
Period size: 11 Copynumber: 2.9 Consensus size: 12
41935284 AGAAAAAAAA
41935294 GAAGAGAGAGAGG
1 GAAGAGAGA-AGG
41935307 GAAGAGAGAAGG
1 GAAGAGAGAAGG
41935319 G-AGAGAGAAG
1 GAAGAGAGAAG
41935329 AGAGGGGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 9 0.41
12 4 0.18
13 9 0.41
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (12 bp):
GAAGAGAGAAGG
Found at i:41940737 original size:111 final size:111
Alignment explanation
Indices: 41940540--41940762 Score: 374
Period size: 111 Copynumber: 2.0 Consensus size: 111
41940530 GAATGGACCT
* * * *
41940540 AACTGTTGGAAATATTAGTTTATAAAATAGTATTTTTAAGCACGGTAAAAGTTTAAAAAGTTTCT
1 AACTGTTGGAAAAATCAGTTTACAAAATAGTATTTTTAAGCACAGTAAAAGTTTAAAAAGTTTCT
*
41940605 TAAAATCGAGCATTGTGATATTTATAACAATAAACTCTTAACCAAA
66 TAAAATCGAGCATTGTAATATTTATAACAATAAACTCTTAACCAAA
* *
41940651 AACTGTTGGAAAAATCGGTTTACAAAATAGTATTTTTAAGCACAGTGAAAGTTTAAAAAGTTTCT
1 AACTGTTGGAAAAATCAGTTTACAAAATAGTATTTTTAAGCACAGTAAAAGTTTAAAAAGTTTCT
*
41940716 TAAAATCGAGCTTTGTAATATTTATAACAATAAACTCTTAACCAAA
66 TAAAATCGAGCATTGTAATATTTATAACAATAAACTCTTAACCAAA
41940762 A
1 A
41940763 TCATGCATGT
Statistics
Matches: 104, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
111 104 1.00
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.34
Consensus pattern (111 bp):
AACTGTTGGAAAAATCAGTTTACAAAATAGTATTTTTAAGCACAGTAAAAGTTTAAAAAGTTTCT
TAAAATCGAGCATTGTAATATTTATAACAATAAACTCTTAACCAAA
Found at i:41940996 original size:11 final size:11
Alignment explanation
Indices: 41940980--41941007 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
41940970 CACTAGTTAT
41940980 CTAATATTTAA
1 CTAATATTTAA
41940991 CTAATATTTAA
1 CTAATATTTAA
41941002 CTAATA
1 CTAATA
41941008 CTAAACAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (11 bp):
CTAATATTTAA
Found at i:41942143 original size:16 final size:17
Alignment explanation
Indices: 41942122--41942154 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
41942112 TTGAGTTTAG
41942122 AAAATT-ATTTAGTTAA
1 AAAATTAATTTAGTTAA
41942138 AAAATTAATTTAGTTAA
1 AAAATTAATTTAGTTAA
41942155 TTTAATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (17 bp):
AAAATTAATTTAGTTAA
Found at i:41944314 original size:28 final size:28
Alignment explanation
Indices: 41944255--41944314 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
41944245 ATGTAAAATT
*
41944255 TAAATATTATTCTTAATATTTTATTGAA
1 TAAATATTATTCTTAATATTTTAATGAA
41944283 -AAATATT-TTACATTAATATTTTAAT-AA
1 TAAATATTATT-C-TTAATATTTTAATGAA
41944310 TAAAT
1 TAAAT
41944315 GTATATTACA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
26 2 0.07
27 10 0.36
28 16 0.57
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (28 bp):
TAAATATTATTCTTAATATTTTAATGAA
Found at i:41944337 original size:35 final size:36
Alignment explanation
Indices: 41944297--41944386 Score: 94
Period size: 37 Copynumber: 2.5 Consensus size: 36
41944287 ATTTTACATT
* **
41944297 AATATTTTAATAATAAATG-TATATTACAATTTATA
1 AATATTTTAATAATAAATGTTATAGTACAAAATATA
* * *
41944332 AATA-TTTAGTAATAAATGTTTTATAGTATAAAATATG
1 AATATTTTAATAATAAATG--TTATAGTACAAAATATA
41944369 AATATTTTAATAATAAAT
1 AATATTTTAATAATAAAT
41944387 ATGCTTATTT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
34 13 0.30
35 4 0.09
37 15 0.34
38 12 0.27
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (36 bp):
AATATTTTAATAATAAATGTTATAGTACAAAATATA
Found at i:41948702 original size:13 final size:13
Alignment explanation
Indices: 41948684--41948710 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
41948674 TTTCGGTTTA
41948684 ATTTAAACAATAT
1 ATTTAAACAATAT
41948697 ATTTAAACAATAT
1 ATTTAAACAATAT
41948710 A
1 A
41948711 GTTGTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (13 bp):
ATTTAAACAATAT
Found at i:41948949 original size:97 final size:97
Alignment explanation
Indices: 41948814--41949143 Score: 624
Period size: 97 Copynumber: 3.4 Consensus size: 97
41948804 TTAAAGACTC
* * *
41948814 AAACAATAAATCAAGTTCCAATTTCGATTCTTATATAATGTCCAAATTTAAGATTAAATCTACAT
1 AAACAATCAATCAAGTTCCAATTTCGATGCTTATATAATGTCCAAATTTAAGATTAAATCTGCAT
*
41948879 ATTTTAATGAAAATATAATTCGGTACTTATAT
66 ATTTTAATTAAAATATAATTCGGTACTTATAT
41948911 AAACAATCAATCAAGTTCCAATTTCGATGCTTATATAATGTCCAAATTTAAGATTAAATCTGCAT
1 AAACAATCAATCAAGTTCCAATTTCGATGCTTATATAATGTCCAAATTTAAGATTAAATCTGCAT
41948976 ATTTTAATTAAAATATAATTCGGTACTTATAT
66 ATTTTAATTAAAATATAATTCGGTACTTATAT
41949008 AAACAATCAATCAAGTTCCAATTTCGATGCTTATATAATGTCCAAATTTAAGATTAAATCTGCAT
1 AAACAATCAATCAAGTTCCAATTTCGATGCTTATATAATGTCCAAATTTAAGATTAAATCTGCAT
41949073 ATTTTAATTAAAATATAATTCGGTACTTATAT
66 ATTTTAATTAAAATATAATTCGGTACTTATAT
41949105 AAACAATCAATCAAGTTCCAATTTCGATGCTTATATAAT
1 AAACAATCAATCAAGTTCCAATTTCGATGCTTATATAAT
41949144 TGTTATTAAA
Statistics
Matches: 229, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
97 229 1.00
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.38
Consensus pattern (97 bp):
AAACAATCAATCAAGTTCCAATTTCGATGCTTATATAATGTCCAAATTTAAGATTAAATCTGCAT
ATTTTAATTAAAATATAATTCGGTACTTATAT
Found at i:41949216 original size:23 final size:23
Alignment explanation
Indices: 41949181--41949225 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
41949171 CCTTATTTAA
**
41949181 TTCAAATTGATTAT-AATATTATT
1 TTCAAATAAATTATCAA-ATTATT
41949204 TTCAAATAAATTATCAAATTAT
1 TTCAAATAAATTATCAAATTAT
41949226 AAAATGACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (23 bp):
TTCAAATAAATTATCAAATTATT
Found at i:41952553 original size:15 final size:15
Alignment explanation
Indices: 41952518--41952569 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
41952508 TTAAGAATTT
*
41952518 TATTAAATTAT-ATA
1 TATTTAATTATAATA
41952532 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
41952546 TATTTAATAATAAT-
1 TATTTAATTATAATA
41952560 TATGTTAATT
1 TAT-TTAATT
41952570 TATCTTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:41952598 original size:120 final size:120
Alignment explanation
Indices: 41952393--41952805 Score: 722
Period size: 120 Copynumber: 3.4 Consensus size: 120
41952383 AATTATTTTA
* * *
41952393 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTGAAATTT-TCTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT--AATTTATCTT
* * *
41952456 TTATAGTATCATATATTATGATTTGAGTAAATTCATAGAAGAATTTTATTTATTAAG
64 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
41952513 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATCTTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATCTTTT
41952578 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
41952633 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATCTTTT
*
41952698 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
41952753 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
41952806 TAAATATGAT
Statistics
Matches: 283, Mismatches: 8, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
119 5 0.02
120 276 0.98
121 2 0.01
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATCTTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:41952673 original size:15 final size:15
Alignment explanation
Indices: 41952638--41952689 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
41952628 TTAAGAATTT
*
41952638 TATTAAATTAT-ATA
1 TATTTAATTATAATA
41952652 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
41952666 TATTTAATAATAAT-
1 TATTTAATTATAATA
41952680 TATGTTAATT
1 TAT-TTAATT
41952690 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:41952788 original size:16 final size:16
Alignment explanation
Indices: 41952767--41952808 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
41952757 TTATTAAATT
*
41952767 ATATATTTTAATTATA
1 ATATATTTTAATAATA
41952783 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
41952798 AT-TATGTTTAA
1 ATATAT-TTTAA
41952809 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:41952793 original size:15 final size:15
Alignment explanation
Indices: 41952758--41952799 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
41952748 TTAAGAATTT
*
41952758 TATTAAATTAT-ATA
1 TATTTAATTATAATA
41952772 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
41952786 TATTTAATAATAAT
1 TATTTAATTATAAT
41952800 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:41952920 original size:157 final size:159
Alignment explanation
Indices: 41952742--41953064 Score: 551
Period size: 157 Copynumber: 2.0 Consensus size: 159
41952732 ATAAGAATAT
*
41952742 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
* *
41952807 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAAT-AAT-AATAAC
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAAATAAATAAC
*
41952870 AATAATAATTTACCAAAACAAATTTCTGC
131 AATAATAATTTACCAAAACAAATTTATGC
41952899 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
41952964 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAAT-A-AAT-A-AA
*
41953029 TAACAATAATCATTTACCAAAACAAATTTATGC
127 TAACAATAATAATTTACCAAAACAAATTTATGC
41953062 TAA
1 TAA
41953065 GGGTATTCTA
Statistics
Matches: 155, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
157 116 0.75
160 3 0.02
163 36 0.23
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (159 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAAATAAATAAC
AATAATAATTTACCAAAACAAATTTATGC
Found at i:41952939 original size:18 final size:17
Alignment explanation
Indices: 41952911--41952945 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
41952901 ATTATTAAGA
*
41952911 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
41952928 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
41952946 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:41954106 original size:30 final size:28
Alignment explanation
Indices: 41954071--41954144 Score: 102
Period size: 24 Copynumber: 2.7 Consensus size: 28
41954061 TTTGTAGGAA
41954071 AATATAATAAAACATTTATTTATGTTTTTT
1 AATATAATAAAACATTTATTTA--TTTTTT
41954101 AATATAATAAAAC----ATTTATTTTTT
1 AATATAATAAAACATTTATTTATTTTTT
41954125 AATATAATAAAACATTTATT
1 AATATAATAAAACATTTATT
41954145 ATGGTAGTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
24 19 0.47
26 5 0.12
28 3 0.08
30 13 0.32
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.49
Consensus pattern (28 bp):
AATATAATAAAACATTTATTTATTTTTT
Found at i:41968644 original size:17 final size:19
Alignment explanation
Indices: 41968622--41968671 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
41968612 TTTATAAATG
*
41968622 AAAAAAA-AAAAGAGCTCA
1 AAAAAAAGAAAAGAACTCA
41968640 AAAAAAAGAAAAGAACTCA
1 AAAAAAAGAAAAGAACTCA
41968659 AATACAAAAGAAA
1 AA-A-AAAAGAAA
41968672 TAATTTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 7 0.25
19 12 0.43
20 1 0.04
21 8 0.29
ACGTcount: A:0.74, C:0.10, G:0.10, T:0.06
Consensus pattern (19 bp):
AAAAAAAGAAAAGAACTCA
Found at i:41971531 original size:15 final size:15
Alignment explanation
Indices: 41971511--41971550 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
41971501 AAATCACAAA
41971511 TGCTTTGCACCCAGG
1 TGCTTTGCACCCAGG
41971526 TGCTTTGCACCCAGG
1 TGCTTTGCACCCAGG
41971541 TGCTTTGCAC
1 TGCTTTGCAC
41971551 GTGCCCAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.12, C:0.33, G:0.25, T:0.30
Consensus pattern (15 bp):
TGCTTTGCACCCAGG
Found at i:41977520 original size:30 final size:30
Alignment explanation
Indices: 41977486--41977548 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
41977476 ACTTAACAAG
41977486 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
*
41977516 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
41977546 CAA
1 CAA
41977549 TAAAATAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.57, C:0.16, G:0.03, T:0.24
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:41978997 original size:15 final size:15
Alignment explanation
Indices: 41978977--41979018 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 15
41978967 ATTACACATA
41978977 TAAAAATTATATTTAT
1 TAAAAATTATATTT-T
41978993 TAAAAAATTATATTTT
1 T-AAAAATTATATTTT
*
41979009 TAATAATTAT
1 TAAAAATTAT
41979019 TTGATTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 8 0.33
16 3 0.12
17 13 0.54
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAAAAATTATATTTT
Found at i:41979000 original size:17 final size:16
Alignment explanation
Indices: 41978978--41979011 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
41978968 TTACACATAT
41978978 AAAAATTATATTTATTA
1 AAAAATTATATTT-TTA
41978995 AAAAATTATATTTTTA
1 AAAAATTATATTTTTA
41979011 A
1 A
41979012 TAATTATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAAAATTATATTTTTA
Found at i:41979094 original size:22 final size:23
Alignment explanation
Indices: 41979051--41979094 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
41979041 TATTAATTAA
*
41979051 AAATAAAAAATTGAAATAGTATG
1 AAATAAAAAATTCAAATAGTATG
41979074 AAAT-AAAAATTACAAAT-GTAT
1 AAATAAAAAATT-CAAATAGTAT
41979095 TTGAAAGAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.61, C:0.02, G:0.09, T:0.27
Consensus pattern (23 bp):
AAATAAAAAATTCAAATAGTATG
Found at i:41989527 original size:17 final size:16
Alignment explanation
Indices: 41989507--41989552 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
41989497 TATATATGTA
41989507 TAATAAATATATAAAAC
1 TAATAAATAT-TAAAAC
*
41989524 TAATAACTATTAAAAGC
1 TAATAAATATTAAAA-C
41989541 T-ATAAA-ATTAAA
1 TAATAAATATTAAA
41989553 TTTTAATAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 6 0.23
16 9 0.35
17 11 0.42
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (16 bp):
TAATAAATATTAAAAC
Found at i:41994737 original size:3 final size:3
Alignment explanation
Indices: 41994694--41994721 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
41994684 GCCCTTTCAC
41994694 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
41994722 GGCTTAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:42002375 original size:22 final size:22
Alignment explanation
Indices: 42002350--42002395 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
42002340 TTTTGATTAA
* *
42002350 TCGATCGTTCACGGTATCTAAT
1 TCGATCGGTCACCGTATCTAAT
*
42002372 TCGATCGGTCACCGTATTTAAT
1 TCGATCGGTCACCGTATCTAAT
42002394 TC
1 TC
42002396 AGCTGGAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (22 bp):
TCGATCGGTCACCGTATCTAAT
Found at i:42003459 original size:13 final size:13
Alignment explanation
Indices: 42003443--42003469 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
42003433 AATGTGAATA
42003443 AATATTAATAATT
1 AATATTAATAATT
42003456 AATATTAATAATT
1 AATATTAATAATT
42003469 A
1 A
42003470 TAAAAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AATATTAATAATT
Found at i:42004208 original size:17 final size:17
Alignment explanation
Indices: 42004186--42004223 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
42004176 CAATAGGTTG
*
42004186 AATTTTTTTAACGGCTA
1 AATTTTTTTAAAGGCTA
*
42004203 AATTTTTTTAAAGGCTT
1 AATTTTTTTAAAGGCTA
42004220 AATT
1 AATT
42004224 AATTTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.08, G:0.11, T:0.50
Consensus pattern (17 bp):
AATTTTTTTAAAGGCTA
Found at i:42016764 original size:53 final size:53
Alignment explanation
Indices: 42016701--42016805 Score: 192
Period size: 53 Copynumber: 2.0 Consensus size: 53
42016691 ATAGAACACT
*
42016701 TTGGGGTGGTAGATATGAGAATACTTAATTTCAATAGGAAGCTCGGTTGGATG
1 TTGGGGTGGTAGATATGAGAATACTTAATTTCAATAGGAAACTCGGTTGGATG
*
42016754 TTGGGGTGGTAGATATGAGAATACTTAGTTTCAATAGGAAACTCGGTTGGAT
1 TTGGGGTGGTAGATATGAGAATACTTAATTTCAATAGGAAACTCGGTTGGAT
42016806 TAAGCATAGA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.29, C:0.08, G:0.31, T:0.32
Consensus pattern (53 bp):
TTGGGGTGGTAGATATGAGAATACTTAATTTCAATAGGAAACTCGGTTGGATG
Found at i:42026677 original size:22 final size:22
Alignment explanation
Indices: 42026652--42026693 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
42026642 CAAATTTATT
*
42026652 TAAAAACTATTAAGAATTATAA
1 TAAAAACTATTAAAAATTATAA
*
42026674 TAAAAATTATTAAAAATTAT
1 TAAAAACTATTAAAAATTAT
42026694 TAAAATTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (22 bp):
TAAAAACTATTAAAAATTATAA
Found at i:42026687 original size:32 final size:33
Alignment explanation
Indices: 42026651--42026717 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 33
42026641 ACAAATTTAT
*
42026651 TTAAAAACTATTAAGAATT-AT-AATAAAAATTA
1 TTAAAAACTATTAA-AATTAATAAATAAAAAGTA
*
42026683 TTAAAAATTATTAAAATTAATAAATAAAAAGTA
1 TTAAAAACTATTAAAATTAATAAATAAAAAGTA
42026716 TT
1 TT
42026718 GAACGAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
31 4 0.13
32 15 0.48
33 12 0.39
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (33 bp):
TTAAAAACTATTAAAATTAATAAATAAAAAGTA
Found at i:42026689 original size:10 final size:10
Alignment explanation
Indices: 42026651--42026698 Score: 60
Period size: 10 Copynumber: 4.6 Consensus size: 10
42026641 ACAAATTTAT
*
42026651 TTAAAAACTA
1 TTAAAAATTA
*
42026661 TTAAGAATTA
1 TTAAAAATTA
42026671 TAATAAAAATTA
1 T--TAAAAATTA
42026683 TTAAAAATTA
1 TTAAAAATTA
42026693 TTAAAA
1 TTAAAA
42026699 TTAATAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
10 24 0.73
12 9 0.27
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (10 bp):
TTAAAAATTA
Found at i:42026881 original size:52 final size:53
Alignment explanation
Indices: 42026801--42026905 Score: 194
Period size: 52 Copynumber: 2.0 Consensus size: 53
42026791 AACTGTTTCT
*
42026801 TAAATAGTTATTAAAAGTTAAACGAAATTAT-AAAAAATATTAGGAATTATAA
1 TAAATAGTTATTAAAAGTTAAACAAAATTATAAAAAAATATTAGGAATTATAA
42026853 TAAATAGTTATTAAAAGTTAAACAAAATTATAAAAAAATATTAGGAATTATAA
1 TAAATAGTTATTAAAAGTTAAACAAAATTATAAAAAAATATTAGGAATTATAA
42026906 GAATTTGTAA
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
52 30 0.59
53 21 0.41
ACGTcount: A:0.57, C:0.02, G:0.09, T:0.32
Consensus pattern (53 bp):
TAAATAGTTATTAAAAGTTAAACAAAATTATAAAAAAATATTAGGAATTATAA
Found at i:42027551 original size:11 final size:10
Alignment explanation
Indices: 42027525--42027549 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
42027515 AACTTCATTT
42027525 AAAAATATAA
1 AAAAATATAA
42027535 AAAAATATAA
1 AAAAATATAA
42027545 AAAAA
1 AAAAA
42027550 ATCCTTATAA
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (10 bp):
AAAAATATAA
Found at i:42041508 original size:21 final size:22
Alignment explanation
Indices: 42041479--42041525 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
42041469 CAGAAGGAGT
*
42041479 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
42041501 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
42041522 GAGT
1 GAGT
42041526 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:42043923 original size:29 final size:32
Alignment explanation
Indices: 42043872--42043933 Score: 94
Period size: 30 Copynumber: 2.0 Consensus size: 32
42043862 AATCTATATC
42043872 TTTATAATTTTTAAAAGATT-AAAT-TAATTT
1 TTTATAATTTTTAAAAGATTAAAATATAATTT
*
42043902 TTTATTATTTTTAAAAG-TTAAAATATAATTT
1 TTTATAATTTTTAAAAGATTAAAATATAATTT
42043933 T
1 T
42043934 ACCATTATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 2 0.07
30 20 0.69
31 7 0.24
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (32 bp):
TTTATAATTTTTAAAAGATTAAAATATAATTT
Found at i:42056583 original size:512 final size:512
Alignment explanation
Indices: 42055619--42056597 Score: 1949
Period size: 512 Copynumber: 1.9 Consensus size: 512
42055609 GTATCCAATA
42055619 GGTTAATTAATGTGAATTGTTGTTACTTTTATATATGAATGGAATACAGAAGGTATTGTAATTTG
1 GGTTAATTAATGTGAATTGTTGTTACTTTTATATATGAATGGAATACAGAAGGTATTGTAATTTG
42055684 TGAATTTATTGTGCGAGTTCAATGACTTGAAAATTATAGGGAGAGAGACGAGAATATAAAGTATT
66 TGAATTTATTGTGCGAGTTCAATGACTTGAAAATTATAGGGAGAGAGACGAGAATATAAAGTATT
42055749 TATTTTAAAAAAGAAGTGTGAAAGAGAGATTACAAATTTTGTGTGGATGGGAAAAGTGGAGGAAT
131 TATTTTAAAAAAGAAGTGTGAAAGAGAGATTACAAATTTTGTGTGGATGGGAAAAGTGGAGGAAT
42055814 TACGAGCCATGGTAGGAGAATCCAAGTGAGCCCTCTTCTTCTTTGGTTCTTCAAATTCAAAGCTT
196 TACGAGCCATGGTAGGAGAATCCAAGTGAGCCCTCTTCTTCTTTGGTTCTTCAAATTCAAAGCTT
42055879 TTCATTTACTATAGTTAGTATTGTGATTTGGGTTGAGGGAGGCCAACCGCCAGCTGCGACAGAGG
261 TTCATTTACTATAGTTAGTATTGTGATTTGGGTTGAGGGAGGCCAACCGCCAGCTGCGACAGAGG
42055944 CAGCAAATTGGGTTGGGTTGAGTATTCTACAACTGTTCGATAGATAGTTACCAAAACATGCTTTA
326 CAGCAAATTGGGTTGGGTTGAGTATTCTACAACTGTTCGATAGATAGTTACCAAAACATGCTTTA
42056009 CGTTTTCAGCAAACGCCAATTCTTCTTGGATTGCACCATCTCTGAAACAATCAATTTCATATTTG
391 CGTTTTCAGCAAACGCCAATTCTTCTTGGATTGCACCATCTCTGAAACAATCAATTTCATATTTG
42056074 GAGATGCAACGAAAATTTCGAATTTTAAGACTAAAAAATTACACAAAAAAGGCAAAG
456 GAGATGCAACGAAAATTTCGAATTTTAAGACTAAAAAATTACACAAAAAAGGCAAAG
*
42056131 GGTTAATTAATGTGAATTGTTGTTGCTTTTATATATGAATGGAATACAGAAGGTATTGTAATTTG
1 GGTTAATTAATGTGAATTGTTGTTACTTTTATATATGAATGGAATACAGAAGGTATTGTAATTTG
42056196 TGAATTTATTGTGCGAGTTCAATGACTTGAAAATTATAGGGAGAGAGACGAGAATATAAAGTATT
66 TGAATTTATTGTGCGAGTTCAATGACTTGAAAATTATAGGGAGAGAGACGAGAATATAAAGTATT
42056261 TATTTTAAAAAAGAAGTGTGAAAGAGAGATTACAAATTTTGTGTGGATGGGAAAAGTGGAGGAAT
131 TATTTTAAAAAAGAAGTGTGAAAGAGAGATTACAAATTTTGTGTGGATGGGAAAAGTGGAGGAAT
42056326 TACGAGCCATGGTAGGAGAATCCAAGTGAGCCCTCTTCTTCTTTGGTTCTTCAAATTCAAAGCTT
196 TACGAGCCATGGTAGGAGAATCCAAGTGAGCCCTCTTCTTCTTTGGTTCTTCAAATTCAAAGCTT
42056391 TTCATTTACTATAGTTAGTATTGTGATTTGGGTTGAGGGAGGCCAACCGCCAGCTGCGACAGAGG
261 TTCATTTACTATAGTTAGTATTGTGATTTGGGTTGAGGGAGGCCAACCGCCAGCTGCGACAGAGG
42056456 CAGCAAATTGGGTTGGGTTGAGTATTCTACAACTGTTCGATAGATAGTTACCAAAACATGCTTTA
326 CAGCAAATTGGGTTGGGTTGAGTATTCTACAACTGTTCGATAGATAGTTACCAAAACATGCTTTA
42056521 CGTTTTCAGCAAACGCCAATTCTTCTTGGATTGCACCATCTCTGAAACAATCAATTTCATATTTG
391 CGTTTTCAGCAAACGCCAATTCTTCTTGGATTGCACCATCTCTGAAACAATCAATTTCATATTTG
42056586 GAGATGCAACGA
456 GAGATGCAACGA
42056598 CAGCCTCCCA
Statistics
Matches: 466, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
512 466 1.00
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (512 bp):
GGTTAATTAATGTGAATTGTTGTTACTTTTATATATGAATGGAATACAGAAGGTATTGTAATTTG
TGAATTTATTGTGCGAGTTCAATGACTTGAAAATTATAGGGAGAGAGACGAGAATATAAAGTATT
TATTTTAAAAAAGAAGTGTGAAAGAGAGATTACAAATTTTGTGTGGATGGGAAAAGTGGAGGAAT
TACGAGCCATGGTAGGAGAATCCAAGTGAGCCCTCTTCTTCTTTGGTTCTTCAAATTCAAAGCTT
TTCATTTACTATAGTTAGTATTGTGATTTGGGTTGAGGGAGGCCAACCGCCAGCTGCGACAGAGG
CAGCAAATTGGGTTGGGTTGAGTATTCTACAACTGTTCGATAGATAGTTACCAAAACATGCTTTA
CGTTTTCAGCAAACGCCAATTCTTCTTGGATTGCACCATCTCTGAAACAATCAATTTCATATTTG
GAGATGCAACGAAAATTTCGAATTTTAAGACTAAAAAATTACACAAAAAAGGCAAAG
Found at i:42057364 original size:17 final size:18
Alignment explanation
Indices: 42057342--42057377 Score: 56
Period size: 17 Copynumber: 2.0 Consensus size: 18
42057332 CATTAAATTA
42057342 AATATTTAC-TTTAATAT
1 AATATTTACATTTAATAT
42057359 AATATTTACATTTTAATAT
1 AATATTTACA-TTTAATAT
42057378 TATTATGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
19 8 0.47
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.53
Consensus pattern (18 bp):
AATATTTACATTTAATAT
Found at i:42064034 original size:13 final size:13
Alignment explanation
Indices: 42064016--42064042 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
42064006 AAACCAGCAT
42064016 TTATTTATAAATA
1 TTATTTATAAATA
42064029 TTATTTATAAATA
1 TTATTTATAAATA
42064042 T
1 T
42064043 AGACAACATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTATTTATAAATA
Found at i:42076838 original size:44 final size:44
Alignment explanation
Indices: 42076790--42076876 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 44
42076780 TTTTACTTTT
* * *
42076790 AGTTTTTTACTTAAACTCTGATTAGTGTATGTTATTTTAATATC
1 AGTTTCTTACTTAAACTCTGATTAATGTAAGTTATTTTAATATC
42076834 AGTTTCTTACTTAAACTCTGATTAATGTAAGTTATTTTAATAT
1 AGTTTCTTACTTAAACTCTGATTAATGTAAGTTATTTTAATAT
42076877 TATTTGACCT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.30, C:0.09, G:0.10, T:0.51
Consensus pattern (44 bp):
AGTTTCTTACTTAAACTCTGATTAATGTAAGTTATTTTAATATC
Found at i:42077718 original size:6 final size:6
Alignment explanation
Indices: 42077707--42077737 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
42077697 GTGAATGAAT
42077707 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA A
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA A
42077738 GTCCGTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
ATTTTA
Found at i:42084250 original size:43 final size:42
Alignment explanation
Indices: 42084112--42084253 Score: 117
Period size: 43 Copynumber: 3.2 Consensus size: 42
42084102 GAAATTTATG
* * *
42084112 AAATTATATATCATTATTAAATTAAATTTAATATTAATTATTTT
1 AAATTATATATTATTATTAAATTATA-TT-ATAATAATTATTTT
* ** *
42084156 AAATTGTATAAATTCATATAAGAAAATT-TATTATCAATAATT-TTATG
1 AAA-T-TATATATT-AT-T-ATTAAATTATATTAT-AATAATTATT-TT
42084203 AAATTATATATTATTATTAAATTATATGTATAATAATTATTTT
1 AAATTATATATTATTATTAAATTATAT-TATAATAATTATTTT
42084246 AAATTATA
1 AAATTATA
42084254 CAAATTCATA
Statistics
Matches: 77, Mismatches: 11, Indels: 21
0.71 0.10 0.19
Matches are distributed among these distances:
42 6 0.08
43 20 0.26
44 10 0.13
45 8 0.10
46 11 0.14
47 14 0.18
48 2 0.03
49 6 0.08
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (42 bp):
AAATTATATATTATTATTAAATTATATTATAATAATTATTTT
Found at i:42084286 original size:90 final size:89
Alignment explanation
Indices: 42084073--42084287 Score: 279
Period size: 90 Copynumber: 2.3 Consensus size: 89
42084063 TGATTTTAGT
* *
42084073 AAATTCATATAAGAACATTTTATTATTAAGAAATTTATGAAATTATATATCATTATTAAATTAAA
1 AAATTCATATAAGAA-A-TTTATTATT-ATAATTTTATGAAATTATATATCATTATTAAATTAAA
* * * *
42084138 TTTAATATTAATTATTTTAAATTGTAT
63 TGTAATAATAATTATTTTAAATTATAC
* * *
42084165 AAATTCATATAAGAAAATTTATTATCAATAATTTTATGAAATTATATATTATTATTAAATTATAT
1 AAATTCATATAAG-AAATTTATTAT-TATAATTTTATGAAATTATATATCATTATTAAATTAAAT
42084230 GT-ATAATAATTATTTTAAATTATAC
64 GTAATAATAATTATTTTAAATTATAC
42084255 AAATTCATATAAGATAATTTATTAGTTATAATT
1 AAATTCATATAAGA-AATTTATTA-TTATAATT
42084288 ATTTTAAATT
Statistics
Matches: 109, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
89 1 0.01
90 48 0.44
91 44 0.40
92 14 0.13
93 2 0.02
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (89 bp):
AAATTCATATAAGAAATTTATTATTATAATTTTATGAAATTATATATCATTATTAAATTAAATGT
AATAATAATTATTTTAAATTATAC
Found at i:42084297 original size:90 final size:91
Alignment explanation
Indices: 42084073--42084278 Score: 297
Period size: 91 Copynumber: 2.3 Consensus size: 91
42084063 TGATTTTAGT
* * * *
42084073 AAATTCATATAAGAACATTTTATTATTAAGAAATTTATGAAATTATATATCATTATTAAATTAAA
1 AAATTCATATAAGAA-AATTTATTATCAATAATTTTATGAAATTATATATCATTATTAAATTAAA
* * * *
42084138 TTTAATATTAATTATTTTAAATTGTAT
65 TGTAATAATAATTATTTTAAATTATAC
* *
42084165 AAATTCATATAAGAAAATTTATTATCAATAATTTTATGAAATTATATATTATTATTAAATTATAT
1 AAATTCATATAAGAAAATTTATTATCAATAATTTTATGAAATTATATATCATTATTAAATTAAAT
42084230 GT-ATAATAATTATTTTAAATTATAC
66 GTAATAATAATTATTTTAAATTATAC
*
42084255 AAATTCATATAAGATAATTTATTA
1 AAATTCATATAAGAAAATTTATTA
42084279 GTTATAATTA
Statistics
Matches: 103, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
90 43 0.42
91 45 0.44
92 15 0.15
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (91 bp):
AAATTCATATAAGAAAATTTATTATCAATAATTTTATGAAATTATATATCATTATTAAATTAAAT
GTAATAATAATTATTTTAAATTATAC
Found at i:42084352 original size:14 final size:14
Alignment explanation
Indices: 42084310--42084352 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
42084300 ATTAACTCAT
*
42084310 ATATTTTAAATAAA
1 ATATTTTAAATTAA
42084324 ATATATTTAATATTAA
1 ATAT-TTTAA-ATTAA
*
42084340 TTATTTTAAATTA
1 ATATTTTAAATTA
42084353 TATTTTATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 8 0.32
15 10 0.40
16 7 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
ATATTTTAAATTAA
Found at i:42084402 original size:66 final size:62
Alignment explanation
Indices: 42084332--42084650 Score: 224
Period size: 59 Copynumber: 5.2 Consensus size: 62
42084322 AAATATATTT
42084332 AATATTAATTATTTTAAATTATATTTTATAGTATCATATATTATGATTTCAGTAAATTCATATAA
1 AATATTAATTA-TTT-AA-TATATTTTATAGTATCATATATTATGATTT-AGTAAATTCATATAA
42084397 G
62 G
* * * * * **
42084398 AATATTAATTA-TTAAGA-ATTTTATTA-AATTATATATT-TTAATTA-T-AA-T-ATAT-TT
1 AATATTAATTATTTAATATATTTTA-TAGTATCATATATTATGATTTAGTAAATTCATATAAG
*
42084452 AATAATAATTATGTTAATTTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTAT-TTAA--TATATTTTATAGTATCATATATTATGATTT-AGTAAATTCATATAA
42084517 G
62 G
* * * * * **
42084518 AATATTAATTA-TTAAGA-ATTTTATTA-AATTATATATT-TTAATTA-T-AA-T-ATAT-TT
1 AATATTAATTATTTAATATATTTTA-TAGTATCATATATTATGATTTAGTAAATTCATATAAG
* *
42084572 AATAATAATTATGTTAATTTATATTTTATAGTATCATATATTATGATTTGAGTAAATTTATATAA
1 AATATTAATTAT-TTAA--TATATTTTATAGTATCATATATTATGATTT-AGTAAATTCATATAA
42084637 G
62 G
*
42084638 AATATTGATTATT
1 AATATTAATTATT
42084651 AAGAATTTTA
Statistics
Matches: 192, Mismatches: 33, Indels: 57
0.68 0.12 0.20
Matches are distributed among these distances:
54 20 0.10
55 8 0.04
56 10 0.05
57 4 0.02
58 8 0.04
59 32 0.17
60 16 0.08
61 32 0.17
62 8 0.04
63 6 0.03
64 8 0.04
65 9 0.05
66 31 0.16
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (62 bp):
AATATTAATTATTTAATATATTTTATAGTATCATATATTATGATTTAGTAAATTCATATAAG
Found at i:42084418 original size:120 final size:120
Alignment explanation
Indices: 42084294--42084711 Score: 703
Period size: 120 Copynumber: 3.5 Consensus size: 120
42084284 AATTATTTTA
* * * * *
42084294 AATTTTATTAACTCATATATTTTAAATAAAATATATTTAATATTAATTATTTTAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAAATATAATATATTTAATAATAATTATGTTAAATTATATTTT
*
42084359 ATAGTATCATATATTATGATTTCAGTAAATTCATATAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
42084414 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAAATATAATATATTTAATAATAATTATGTTAAATTATATTTT
42084479 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
42084534 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAAATATAATATATTTAATAATAATTATGTTAAATTATATTTT
* *
42084599 ATAGTATCATATATTATGATTTGAGTAAATTTATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
42084654 AATTTTATTAAATTATATA-TTTAAATTATAATATATTTAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAAA-TATAATATATTTAATAATAATTATG-TTAAAT
42084712 ATGATTAAAT
Statistics
Matches: 284, Mismatches: 12, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
119 5 0.02
120 274 0.96
121 5 0.02
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAAATATAATATATTTAATAATAATTATGTTAAATTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:42084454 original size:15 final size:15
Alignment explanation
Indices: 42084419--42084470 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
42084409 TTAAGAATTT
*
42084419 TATTAAATTAT-ATA
1 TATTTAATTATAATA
42084433 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
42084447 TATTTAATAATAAT-
1 TATTTAATTATAATA
42084461 TATGTTAATT
1 TAT-TTAATT
42084471 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:42084574 original size:15 final size:15
Alignment explanation
Indices: 42084539--42084590 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
42084529 TTAAGAATTT
*
42084539 TATTAAATTAT-ATA
1 TATTTAATTATAATA
42084553 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
42084567 TATTTAATAATAAT-
1 TATTTAATTATAATA
42084581 TATGTTAATT
1 TAT-TTAATT
42084591 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Done.