Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014077.1 Kokia drynarioides strain JFW-HI SEQ_129108, whole genome shotgun sequence
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: 234618
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 254 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:58 original size:9 final size:9
Alignment explanation
Indices: 44--68 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
34 AAGAATAAAG
44 AAAAGAAAC
1 AAAAGAAAC
53 AAAAGAAAC
1 AAAAGAAAC
62 AAAAGAA
1 AAAAGAA
69 GAACAAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.08, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAAGAAAC
Found at i:12102 original size:27 final size:27
Alignment explanation
Indices: 12072--12138 Score: 64
Period size: 27 Copynumber: 2.5 Consensus size: 27
12062 TTAACAAAAC
12072 TAAAAATATGAAATATGAAATATAATA
1 TAAAAATATGAAATATGAAATATAATA
* * * * * *
12099 T-AAATTTTAAATATATTAAATTTTATA
1 TAAAAATATGAA-ATATGAAATATAATA
12126 TAAAAATATGAAA
1 TAAAAATATGAAA
12139 ATAACAAACC
Statistics
Matches: 29, Mismatches: 9, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
26 7 0.24
27 15 0.52
28 7 0.24
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.37
Consensus pattern (27 bp):
TAAAAATATGAAATATGAAATATAATA
Found at i:12120 original size:16 final size:18
Alignment explanation
Indices: 12089--12123 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
12079 ATGAAATATG
12089 AAATATAATATAAATTTT
1 AAATATAATATAAATTTT
12107 AAATAT-AT-TAAATTTT
1 AAATATAATATAAATTTT
12123 A
1 A
12124 TATAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 2 0.12
18 6 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AAATATAATATAAATTTT
Found at i:15831 original size:18 final size:18
Alignment explanation
Indices: 15792--15842 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
15782 CTTATATTTT
* *
15792 ATATTATTAATAA-TAAA
1 ATATTATTATTAATTATA
*
15809 ATATTATTATTTATTATA
1 ATATTATTATTAATTATA
15827 ATATTATTATTAATTA
1 ATATTATTATTAATTA
15843 ATATATCTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 11 0.38
18 18 0.62
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATTATTATTAATTATA
Found at i:15847 original size:21 final size:19
Alignment explanation
Indices: 15792--15847 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 19
15782 CTTATATTTT
15792 ATATTATTAA-TAATA-AA
1 ATATTATTAATTAATATAA
* *
15809 ATATTATTATTTATTATAA
1 ATATTATTAATTAATATAA
15828 TATTATTATTAATTAATATA
1 -A-TATTATTAATTAATATA
15848 TCTTTTGATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
17 9 0.29
18 4 0.13
19 2 0.06
20 1 0.03
21 15 0.48
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATATTATTAATTAATATAA
Found at i:15848 original size:18 final size:18
Alignment explanation
Indices: 15791--15848 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
15781 TCTTATATTT
*
15791 TATATTATTAATAA-TAA
1 TATATTATTATTAATTAA
* *
15808 AATATTATTATTTATT-A
1 TATATTATTATTAATTAA
15825 TAATATTATTATTAATTAA
1 T-ATATTATTATTAATTAA
15844 TATAT
1 TATAT
15849 CTTTTGATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
17 12 0.36
18 19 0.58
19 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TATATTATTATTAATTAA
Found at i:31484 original size:156 final size:155
Alignment explanation
Indices: 30965--32734 Score: 2677
Period size: 156 Copynumber: 11.5 Consensus size: 155
30955 AAAATGTATT
* * * *
30965 GGCCTATTAGCTCAGTTGGTTAGAGCGTCGTGCTAATAACGCGAAGATTGCAGGTCTTGA-ACCT
1 GGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGT-TCGAGACCT
* * *
31029 GCAAGGGCCATTAATAC-A-TTCTTATTTGTCTTTTGCGAGAACGGCAAAACG--TTA-TT-TTT
65 GCATGGGCCATTAATACAATTTCTT-TTT-TCTTTTGTGAAAACGGC--AACGTTTTACTTATTT
* *** *
31088 ATGAAT-TTTTATTTTGTGCAATAAATCAAC
126 -TTAATAAAGTATTTAGTGCAATAAATCAAC
*
31118 GGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAAACCTG
1 GGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTG
* * **
31183 CATGGGCCATTAATACAATTTCTTTTTTCTTTCGTGAAAACGGCAATGTTTT-CTTATTTTCGAT
66 CATGGGCCATTAATACAATTTCTTTTTTCTTTTGTGAAAACGGCAACGTTTTACTTATTTTTAAT
31247 AAAGTATTTAGTGCAATAAATCAAC
131 AAAGTATTTAGTGCAATAAATCAAC
31272 GGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTG
1 GGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTG
31337 CATGGGCCATTAATACAATTTCTTTTTTCTTTTGTGAAAACGGCAACGTTTTACATTATTTTTAA
66 CATGGGCCATTAATACAATTTCTTTTTTCTTTTGTGAAAACGGCAACGTTTTAC-TTATTTTTAA
* * * *
31402 TTAAGTATTTACTGCAATAAACCAAT
130 TAAAGTATTTAGTGCAATAAATCAAC
*
31428 GGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCAAAGGTCGCAGGTTCGAGACCTG
1 GGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTG
**
31493 CATGGGCCATTAATACAAATTT-TTTTTTCTTTTGTGAAAACGGCAACGTTTT-CTTATTTTCGA
66 CATGGGCCATTAATAC-AATTTCTTTTTTCTTTTGTGAAAACGGCAACGTTTTACTTATTTTTAA
*
31556 TAAAGTATTTAGTGCGATAAATCAAC
130 TAAAGTATTTAGTGCAATAAATCAAC
* *
31582 GGCCTATAAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAAACCTG
1 GGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTG
31647 CATGGGCCATTAATACAATTTCTTTTTTCTTTTGTGAAAACGGCAACGTTTTACATTATTTTTAA
66 CATGGGCCATTAATACAATTTCTTTTTTCTTTTGTGAAAACGGCAACGTTTTAC-TTATTTTTAA
* * * *
31712 TTAAGTATTTACTGCAATAAACCAAT
130 TAAAGTATTTAGTGCAATAAATCAAC
*
31738 GGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCAAAGGTCGCAGGTTCGAGACCTG
1 GGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTG
* **
31803 CATGGGCCATTAATACAATTTCTTTTTTCTTTTGTGAAAACGGAAACGTTTT-CTTATTTTCGAT
66 CATGGGCCATTAATACAATTTCTTTTTTCTTTTGTGAAAACGGCAACGTTTTACTTATTTTTAAT
31867 AAAGTATTTAGTGCAATAAATCAAC
131 AAAGTATTTAGTGCAATAAATCAAC
*
31892 GGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAAACCTG
1 GGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTG
*
31957 CATGGGCCATTAATACAATTTCTTTTTTCTTTTGTGAAAACGGCAACGTTTTACTTATTTTTGAT
66 CATGGGCCATTAATACAATTTCTTTTTTCTTTTGTGAAAACGGCAACGTTTTACTTATTTTTAAT
*
32022 AAAGTATTTAGCGCAATAAATCAAC
131 AAAGTATTTAGTGCAATAAATCAAC
32047 GGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTG
1 GGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTG
* *
32112 CATGGGCCATTAATACAATTTCATTTGTCTTTTGT-ATAAACGGCAACGTTTTACATTATTTTTA
66 CATGGGCCATTAATACAATTTCTTTTTTCTTTTGTGA-AAACGGCAACGTTTTAC-TTATTTTTA
* * *
32176 ATCAAGTATTTAGTGCAATAAACCAAT
129 ATAAAGTATTTAGTGCAATAAATCAAC
32203 GGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTG
1 GGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTG
* *
32268 CATGGGCCATTAATACAATTTCTTTTTTCTTTTGT----------ATGTTTTACTTATTTTTGAT
66 CATGGGCCATTAATACAATTTCTTTTTTCTTTTGTGAAAACGGCAACGTTTTACTTATTTTTAAT
32323 AAAGTATTTAGTGCAATAAATCAAC
131 AAAGTATTTAGTGCAATAAATCAAC
*
32348 GGCCTATTAGCTCAGCCGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTG
1 GGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTG
* * *
32413 CATGGGCCATTAATACAATTTCATTTGTCTTTTGTGTAAACGGCAACGTTTTACATTATTTTTAA
66 CATGGGCCATTAATACAATTTCTTTTTTCTTTTGTGAAAACGGCAACGTTTTAC-TTATTTTTAA
* * * *
32478 TCAAGTATTTAGTGCAAAAAACCAAT
130 TAAAGTATTTAGTGCAATAAATCAAC
*
32504 GGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAATGCGAAGGTCGCAGGTTCGAGACCTG
1 GGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTG
* *
32569 CGTGGGCCATTAATACAATTTCTTTTTCTCTTTTGTGAAAACGGCAGCGTTTTACTTATTTTTAA
66 CATGGGCCATTAATACAATTTCTTTTT-TCTTTTGTGAAAACGGCAACGTTTTACTTATTTTTAA
*
32634 TAAAGTATTTAGCGCAATAAATCAAC
130 TAAAGTATTTAGTGCAATAAATCAAC
* ** *** **
32660 GGCATATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACAAGAAGGTTATAGGTTCGAGACCCA
1 GGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTG
32725 CATGGGCCAT
66 CATGGGCCAT
32735 ATTTTTGTCT
Statistics
Matches: 1485, Mismatches: 103, Indels: 55
0.90 0.06 0.03
Matches are distributed among these distances:
145 129 0.09
146 8 0.01
151 3 0.00
152 3 0.00
153 98 0.07
154 423 0.28
155 166 0.11
156 625 0.42
157 30 0.02
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (155 bp):
GGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTG
CATGGGCCATTAATACAATTTCTTTTTTCTTTTGTGAAAACGGCAACGTTTTACTTATTTTTAAT
AAAGTATTTAGTGCAATAAATCAAC
Found at i:31524 original size:310 final size:309
Alignment explanation
Indices: 30965--32734 Score: 2668
Period size: 310 Copynumber: 5.7 Consensus size: 309
30955 AAAATGTATT
* * * *
30965 GGCCTATTAGCTCAGTTGGTTAGAGCGTCGTGCTAATAACGCGAAGATTGCAGGTCTTGA-ACCT
1 GGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGT-TCGAGACCT
* * *
31029 GCAAGGGCCATTAATAC-A-TTCTTATTTGTCTTTTGCGAGAACGGCAAAACG--TTA-TT-TTT
65 GCATGGGCCATTAATACAATTTCTT-TTT-TCTTTTGTGAAAACGGC--AACGTTTTACTTATTT
* *** **
31088 ATGAAT-TTTTATTTTGTGCAATAAATCAACGGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCT
126 -TTAATAAAGTATTTACTGCAATAAATCAACGGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCT
* * *
31152 AATAACGCGAAGGTCGCAGGTTCGAAACCTGCATGGGCCATTAATACAATTTCTTTTTTCTTTCG
190 AATAACGCAAAGGTCGCAGGTTCGAGACCTGCATGGGCCATTAATACAATTTCTTTTTTCTTTTG
*
31217 TGAAAACGGCAATGTTTTCTTATTTTCGATAAAGTATTTAGTGCAATAAATCAAC
255 TGAAAACGGCAACGTTTTCTTATTTTCGATAAAGTATTTAGTGCAATAAATCAAC
31272 GGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTG
1 GGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTG
31337 CATGGGCCATTAATACAATTTCTTTTTTCTTTTGTGAAAACGGCAACGTTTTACATTATTTTTAA
66 CATGGGCCATTAATACAATTTCTTTTTTCTTTTGTGAAAACGGCAACGTTTTAC-TTATTTTTAA
* * *
31402 TTAAGTATTTACTGCAATAAACCAATGGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAA
130 TAAAGTATTTACTGCAATAAATCAACGGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAA
31467 CGCAAAGGTCGCAGGTTCGAGACCTGCATGGGCCATTAATACAAATTT-TTTTTTCTTTTGTGAA
195 CGCAAAGGTCGCAGGTTCGAGACCTGCATGGGCCATTAATAC-AATTTCTTTTTTCTTTTGTGAA
*
31531 AACGGCAACGTTTTCTTATTTTCGATAAAGTATTTAGTGCGATAAATCAAC
259 AACGGCAACGTTTTCTTATTTTCGATAAAGTATTTAGTGCAATAAATCAAC
* *
31582 GGCCTATAAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAAACCTG
1 GGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTG
31647 CATGGGCCATTAATACAATTTCTTTTTTCTTTTGTGAAAACGGCAACGTTTTACATTATTTTTAA
66 CATGGGCCATTAATACAATTTCTTTTTTCTTTTGTGAAAACGGCAACGTTTTAC-TTATTTTTAA
* * *
31712 TTAAGTATTTACTGCAATAAACCAATGGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAA
130 TAAAGTATTTACTGCAATAAATCAACGGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAA
31777 CGCAAAGGTCGCAGGTTCGAGACCTGCATGGGCCATTAATACAATTTCTTTTTTCTTTTGTGAAA
195 CGCAAAGGTCGCAGGTTCGAGACCTGCATGGGCCATTAATACAATTTCTTTTTTCTTTTGTGAAA
*
31842 ACGGAAACGTTTTCTTATTTTCGATAAAGTATTTAGTGCAATAAATCAAC
260 ACGGCAACGTTTTCTTATTTTCGATAAAGTATTTAGTGCAATAAATCAAC
*
31892 GGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAAACCTG
1 GGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTG
*
31957 CATGGGCCATTAATACAATTTCTTTTTTCTTTTGTGAAAACGGCAACGTTTTACTTATTTTTGAT
66 CATGGGCCATTAATACAATTTCTTTTTTCTTTTGTGAAAACGGCAACGTTTTACTTATTTTTAAT
32022 AAAGTATTTAGC-GCAATAAATCAACGGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAA
131 AAAGTATTTA-CTGCAATAAATCAACGGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAA
* * *
32086 CGCGAAGGTCGCAGGTTCGAGACCTGCATGGGCCATTAATACAATTTCATTTGTCTTTTGT-ATA
195 CGCAAAGGTCGCAGGTTCGAGACCTGCATGGGCCATTAATACAATTTCTTTTTTCTTTTGTGA-A
** * * *
32150 AACGGCAACGTTTTACATTATTTTTAATCAAGTATTTAGTGCAATAAACCAAT
259 AACGGCAACGTTTT-C-TTATTTTCGATAAAGTATTTAGTGCAATAAATCAAC
32203 GGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTG
1 GGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTG
* *
32268 CATGGGCCATTAATACAATTTCTTTTTTCTTTTGT----------ATGTTTTACTTATTTTTGAT
66 CATGGGCCATTAATACAATTTCTTTTTTCTTTTGTGAAAACGGCAACGTTTTACTTATTTTTAAT
* *
32323 AAAGTATTTAGTGCAATAAATCAACGGCCTATTAGCTCAGCCGGTTAGAGCGTCGTGCTAATAAC
131 AAAGTATTTACTGCAATAAATCAACGGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAAC
* * * *
32388 GCGAAGGTCGCAGGTTCGAGACCTGCATGGGCCATTAATACAATTTCATTTGTCTTTTGTGTAAA
196 GCAAAGGTCGCAGGTTCGAGACCTGCATGGGCCATTAATACAATTTCTTTTTTCTTTTGTGAAAA
** * * * *
32453 CGGCAACGTTTTACATTATTTTTAATCAAGTATTTAGTGCAAAAAACCAAT
261 CGGCAACGTTTT-C-TTATTTTCGATAAAGTATTTAGTGCAATAAATCAAC
*
32504 GGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAATGCGAAGGTCGCAGGTTCGAGACCTG
1 GGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTG
* *
32569 CGTGGGCCATTAATACAATTTCTTTTTCTCTTTTGTGAAAACGGCAGCGTTTTACTTATTTTTAA
66 CATGGGCCATTAATACAATTTCTTTTT-TCTTTTGTGAAAACGGCAACGTTTTACTTATTTTTAA
*
32634 TAAAGTATTTAGC-GCAATAAATCAACGGCATATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATA
130 TAAAGTATTTA-CTGCAATAAATCAACGGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATA
* *** **
32698 AC-AAGAAGGTTATAGGTTCGAGACCCACATGGGCCAT
194 ACGCA-AAGGTCGCAGGTTCGAGACCTGCATGGGCCAT
32735 ATTTTTGTCT
Statistics
Matches: 1374, Mismatches: 59, Indels: 55
0.92 0.04 0.04
Matches are distributed among these distances:
301 284 0.21
302 8 0.01
305 4 0.00
306 3 0.00
307 90 0.07
308 5 0.00
309 157 0.11
310 583 0.42
311 135 0.10
312 105 0.08
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (309 bp):
GGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTG
CATGGGCCATTAATACAATTTCTTTTTTCTTTTGTGAAAACGGCAACGTTTTACTTATTTTTAAT
AAAGTATTTACTGCAATAAATCAACGGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAAC
GCAAAGGTCGCAGGTTCGAGACCTGCATGGGCCATTAATACAATTTCTTTTTTCTTTTGTGAAAA
CGGCAACGTTTTCTTATTTTCGATAAAGTATTTAGTGCAATAAATCAAC
Found at i:34390 original size:6 final size:6
Alignment explanation
Indices: 34357--34402 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
34347 TCCTCCGCCC
* * * *
34357 CCTCCG CTTCCA CCTCCG CTTCCG CCTCCC CCTCCG CCTCCG CCTC
1 CCTCCG CCTCCG CCTCCG CCTCCG CCTCCG CCTCCG CCTCCG CCTC
34403 TGCCATCATT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.02, C:0.65, G:0.11, T:0.22
Consensus pattern (6 bp):
CCTCCG
Found at i:34390 original size:18 final size:18
Alignment explanation
Indices: 34357--34402 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
34347 TCCTCCGCCC
*
34357 CCTCCGCTTCCACCTCCG
1 CCTCCGCCTCCACCTCCG
* *
34375 CTTCCGCCTCCCCCTCCG
1 CCTCCGCCTCCACCTCCG
34393 CCTCCGCCTC
1 CCTCCGCCTC
34403 TGCCATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.02, C:0.65, G:0.11, T:0.22
Consensus pattern (18 bp):
CCTCCGCCTCCACCTCCG
Found at i:37666 original size:6 final size:6
Alignment explanation
Indices: 37655--37688 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
37645 AAACCAATCC
37655 CCAAAA CCAAAA CCAAAA CCAAAA CCAAAA CCAA
1 CCAAAA CCAAAA CCAAAA CCAAAA CCAAAA CCAA
37689 CCAACAATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.65, C:0.35, G:0.00, T:0.00
Consensus pattern (6 bp):
CCAAAA
Found at i:39321 original size:12 final size:12
Alignment explanation
Indices: 39306--39331 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
39296 ATACACTTAA
39306 AAATATTAAAAC
1 AAATATTAAAAC
39318 AAATATTAAAAC
1 AAATATTAAAAC
39330 AA
1 AA
39332 CAAACAAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (12 bp):
AAATATTAAAAC
Found at i:48462 original size:6 final size:6
Alignment explanation
Indices: 48451--48476 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
48441 TTATTACTAT
48451 AATTAC AATTAC AATTAC AATTAC AA
1 AATTAC AATTAC AATTAC AATTAC AA
48477 ATATACATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (6 bp):
AATTAC
Found at i:49101 original size:33 final size:33
Alignment explanation
Indices: 49039--49101 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
49029 ATAATAATAA
* *
49039 TAATATTTATGTCTAATCTTTTGCGTTACACTT
1 TAATATTTAAGTCTAATCTTATGCGTTACACTT
*
49072 TAATATTTAAGTCCTAAT-TTATGCTTTACA
1 TAATATTTAAGT-CTAATCTTATGCGTTACA
49102 GGGTGAGCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 21 0.81
34 5 0.19
ACGTcount: A:0.29, C:0.14, G:0.08, T:0.49
Consensus pattern (33 bp):
TAATATTTAAGTCTAATCTTATGCGTTACACTT
Found at i:49954 original size:4 final size:4
Alignment explanation
Indices: 49928--49970 Score: 52
Period size: 4 Copynumber: 10.8 Consensus size: 4
49918 AAAATTGAAG
* *
49928 GAAA -AAA GAAA AAAA AAAGA GAAA GAAA GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAA
49971 GGAGAAGAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 3 0.09
4 29 0.83
5 3 0.09
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:49980 original size:9 final size:9
Alignment explanation
Indices: 49966--49995 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
49956 GAAAGAAAGA
49966 AAGAAGGAG
1 AAGAAGGAG
*
49975 AAGAAGGGG
1 AAGAAGGAG
49984 AAGAAGGAG
1 AAGAAGGAG
49993 AAG
1 AAG
49996 GAAAAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (9 bp):
AAGAAGGAG
Found at i:50188 original size:12 final size:12
Alignment explanation
Indices: 50171--50195 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
50161 TTAAGTATGG
50171 TTAATTTTAAAA
1 TTAATTTTAAAA
50183 TTAATTTTAAAA
1 TTAATTTTAAAA
50195 T
1 T
50196 ATTTTAATTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAATTTTAAAA
Found at i:50394 original size:20 final size:21
Alignment explanation
Indices: 50355--50395 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
50345 ATTTACTTTT
50355 ATTTAATTTTGCTAGTTAGTA
1 ATTTAATTTTGCTAGTTAGTA
* *
50376 ATTTTATTTTG-TTGTTAGTA
1 ATTTAATTTTGCTAGTTAGTA
50396 GTAGTAAGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.24, C:0.02, G:0.15, T:0.59
Consensus pattern (21 bp):
ATTTAATTTTGCTAGTTAGTA
Found at i:51805 original size:43 final size:43
Alignment explanation
Indices: 51723--51807 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
51713 ATTAACATGT
* * *
51723 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTTAC
1 TAAATTATATTACTTGACGCGTATTAATATGCTTGCATGTTAC
* *
51766 TAAATTATATTACTTTACGCTTATTAATAT-CTTGACATGTTA
1 TAAATTATATTACTTGACGCGTATTAATATGCTTG-CATGTTA
51808 TTAATTGTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 3 0.08
43 33 0.92
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.46
Consensus pattern (43 bp):
TAAATTATATTACTTGACGCGTATTAATATGCTTGCATGTTAC
Found at i:52509 original size:45 final size:45
Alignment explanation
Indices: 52380--52510 Score: 181
Period size: 45 Copynumber: 2.9 Consensus size: 45
52370 CTCATTAAGT
*
52380 CAAGGATATCAGCCTCAGTTTGACGAGCCACCACAATACTCAAGC
1 CAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATACTCAAGC
* * *
52425 CAAGGATATCAGCCTCAATTTGACGACCCACCGCAATACTCAAGG
1 CAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATACTCAAGC
* * * * *
52470 GAAGGATATCAGGCTGAGTTTGACGAGCCATCGCGATACTC
1 CAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATACTC
52511 TATTCCTCCT
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 75 1.00
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.19
Consensus pattern (45 bp):
CAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATACTCAAGC
Found at i:55713 original size:4 final size:4
Alignment explanation
Indices: 55698--55733 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
55688 TCCTTCTCCC
*
55698 TTCT TCCT TTCT TTCT TTCTT TTCT TTCT TTCT TTC
1 TTCT TTCT TTCT TTCT TTC-T TTCT TTCT TTCT TTC
55734 CCATTTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 25 0.86
5 4 0.14
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (4 bp):
TTCT
Found at i:55723 original size:13 final size:13
Alignment explanation
Indices: 55705--55732 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
55695 CCCTTCTTCC
55705 TTTCTTTCTTTCT
1 TTTCTTTCTTTCT
55718 TTTCTTTCTTTCT
1 TTTCTTTCTTTCT
55731 TT
1 TT
55733 CCCATTTATT
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:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTCTTTCTTTCT
Found at i:56490 original size:24 final size:24
Alignment explanation
Indices: 56456--56501 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
56446 AATCGTTTAA
56456 TTTAAGCTTTCTTTTCTCTATTTT
1 TTTAAGCTTTCTTTTCTCTATTTT
*
56480 TTTAAGGTTTCTTTTCTCTATT
1 TTTAAGCTTTCTTTTCTCTATT
56502 AATTAAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.13, C:0.15, G:0.07, T:0.65
Consensus pattern (24 bp):
TTTAAGCTTTCTTTTCTCTATTTT
Found at i:56862 original size:21 final size:21
Alignment explanation
Indices: 56836--56878 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
56826 TTTCAAGCTC
56836 ACTTAATTTTTTTGTAAAAAG
1 ACTTAATTTTTTTGTAAAAAG
56857 ACTTAATTTTTTTGTAAAAAG
1 ACTTAATTTTTTTGTAAAAAG
56878 A
1 A
56879 AAAACCAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.47
Consensus pattern (21 bp):
ACTTAATTTTTTTGTAAAAAG
Found at i:58404 original size:27 final size:27
Alignment explanation
Indices: 58360--58415 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
58350 TATATTATTT
* * *
58360 TTAAATGTGTTATCATCATAATTTTTA
1 TTAAATGTATAATCATCATAACTTTTA
* *
58387 TTAAATGTATAATTATCATCACTTTTA
1 TTAAATGTATAATCATCATAACTTTTA
58414 TT
1 TT
58416 TTACATCAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.34, C:0.09, G:0.05, T:0.52
Consensus pattern (27 bp):
TTAAATGTATAATCATCATAACTTTTA
Found at i:59254 original size:15 final size:15
Alignment explanation
Indices: 59234--59262 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
59224 TTCCCTTTCC
59234 CCTTCTTCTTATTTT
1 CCTTCTTCTTATTTT
59249 CCTTCTTCTTATTT
1 CCTTCTTCTTATTT
59263 GTCTTTTTTG
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:0.07, C:0.28, G:0.00, T:0.66
Consensus pattern (15 bp):
CCTTCTTCTTATTTT
Found at i:61071 original size:30 final size:28
Alignment explanation
Indices: 61028--61351 Score: 155
Period size: 29 Copynumber: 11.1 Consensus size: 28
61018 ATTTGGATAA
*
61028 AAAATGGAATTTTTTGGACATTCGAGGGT
1 AAAATGGAA-TTTTTGGAAATTCGAGGGT
* *
61057 AAAATGGTAATTTTTAGGAAAATCG-GGAT
1 AAAATGG-AATTTTT-GGAAATTCGAGGGT
*
61086 AAAAATGGAATTTTTGGACATTCGAGGGT
1 -AAAATGGAATTTTTGGAAATTCGAGGGT
*
61115 -AAAGGGTAATTTTT-GAAAGTTTCG-GGGTT
1 AAAATGG-AATTTTTGGAAA--TTCGAGGG-T
* *
61144 AAAAATAGAATTTTTGGATATTCGAGGGT
1 -AAAATGGAATTTTTGGAAATTCGAGGGT
** *
61173 AAAATGGTAATTTTTAGGAGTTTC-AAGGT
1 AAAATGG-AATTTTT-GGAAATTCGAGGGT
* *
61202 CAAAATTGGGATTTTT-GAAAGTTCG-GAGAT
1 -AAAA-TGGAATTTTTGGAAA-TTCGAG-GGT
* * ** *
61232 AAAAATGTAATTTTTGGAAGTTTTAAGGTT
1 -AAAATGGAATTTTTGGAA-ATTCGAGGGT
* *
61262 AAAAATGGAA-TTTTGGAAGTT-TAGGGGT
1 -AAAATGGAATTTTTGGAAATTCGA-GGGT
* * * ** *
61290 GAAAATGTAATTTTTAGAAGTTTTAAGGT
1 -AAAATGGAATTTTTGGAAATTCGAGGGT
61319 CAAAATGGAA-TTTTGGAAAGTTCGAGGGT
1 -AAAATGGAATTTTTGGAAA-TTCGAGGGT
61348 AAAA
1 AAAA
61352 ATATAATTTT
Statistics
Matches: 227, Mismatches: 42, Indels: 53
0.70 0.13 0.16
Matches are distributed among these distances:
27 9 0.04
28 49 0.22
29 92 0.41
30 66 0.29
31 11 0.05
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.35
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAAATTCGAGGGT
Found at i:61090 original size:59 final size:59
Alignment explanation
Indices: 60938--61191 Score: 259
Period size: 58 Copynumber: 4.3 Consensus size: 59
60928 CTTTAGGGGC
* ** * * *
60938 AAAATGGTAATTTTGAGGAAGTTCAGGGTTAAAAATGGAA-TTTTAGACACTCGAGGGT
1 AAAATGGTAATTTTTAGGAAAATCAGGGATAAAAATGGAATTTTTGGACATTCGAGGGT
** ** **
60996 AAAATGGTAACTTTCAAAAAAAAT-TTGGATAAAAAATGGAATTTTTTGGACATTCGAGGGT
1 AAAATGGTAA-TTTTTAGGAAAATCAGGGAT-AAAAATGGAA-TTTTTGGACATTCGAGGGT
61057 AAAATGGTAATTTTTAGGAAAATC-GGGATAAAAATGGAATTTTTGGACATTCGAGGGT
1 AAAATGGTAATTTTTAGGAAAATCAGGGATAAAAATGGAATTTTTGGACATTCGAGGGT
* * * * * *
61115 -AAAGGGTAATTTTT--GAAAGTTTCGGGGTTAAAAATAGAATTTTTGGATATTCGAGGGT
1 AAAATGGTAATTTTTAGGAAA--ATCAGGGATAAAAATGGAATTTTTGGACATTCGAGGGT
61173 AAAATGGTAATTTTTAGGA
1 AAAATGGTAATTTTTAGGA
61192 GTTTCAAGGT
Statistics
Matches: 163, Mismatches: 22, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
55 4 0.02
57 15 0.09
58 63 0.39
59 40 0.25
60 13 0.08
61 28 0.17
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.32
Consensus pattern (59 bp):
AAAATGGTAATTTTTAGGAAAATCAGGGATAAAAATGGAATTTTTGGACATTCGAGGGT
Found at i:61207 original size:58 final size:60
Alignment explanation
Indices: 61027--61351 Score: 277
Period size: 58 Copynumber: 5.6 Consensus size: 60
61017 AATTTGGATA
* *** * *
61027 AAAAATGGAATTTTTTGGACA-TTCGAGGGTAAAATGGTAATTTTTAGGAAAATC-GGGAT
1 AAAAATGGAA-TTTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTAGGAGTTTCAAGGTT
* * * **
61086 AAAAATGGAATTTTTGGACA-TTCGAGGGT-AAAGGGTAATTTTT-GAAAGTTTCGGGGTT
1 AAAAATGGAATTTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTAG-GAGTTTCAAGGTT
* * *
61144 AAAAATAGAATTTTTGGATA-TTCGAGGGTAAAATGGTAATTTTTAGGAGTTTCAAGGTC
1 AAAAATGGAATTTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTAGGAGTTTCAAGGTT
* * * *
61203 AAAATTGGGATTTTT-GAAAGTTCG-GAGATAAAAAT-GTAATTTTT-GGAAGTTTTAAGGTT
1 AAAAATGGAATTTTTGGAAAGTTCGAG-GGT-AAAATGGTAATTTTTAGG-AGTTTCAAGGTT
* * *
61262 AAAAATGGAA-TTTTGG-AAGTT-TAGGGGTGAAAAT-GTAATTTTTAGAAGTTTTAAGG-T
1 AAAAATGGAATTTTTGGAAAGTTCGA-GGGT-AAAATGGTAATTTTTAGGAGTTTCAAGGTT
*
61319 CAAAATGGAA-TTTTGGAAAGTTCGAGGGTAAAA
1 AAAAATGGAATTTTTGGAAAGTTCGAGGGTAAAA
61352 ATATAATTTT
Statistics
Matches: 224, Mismatches: 28, Indels: 30
0.79 0.10 0.11
Matches are distributed among these distances:
56 1 0.00
57 36 0.16
58 100 0.45
59 81 0.36
60 6 0.03
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (60 bp):
AAAAATGGAATTTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTAGGAGTTTCAAGGTT
Found at i:61339 original size:29 final size:29
Alignment explanation
Indices: 61231--61370 Score: 108
Period size: 29 Copynumber: 4.8 Consensus size: 29
61221 AGTTCGGAGA
*
61231 TAAAAATGTAATTTTTGG-AAGTTTTAAGG
1 TAAAAATGGAA-TTTTGGAAAGTTTTAAGG
*
61260 TTAAAAATGGAATTTTGG-AAG-TTTAGGGG
1 -TAAAAATGGAATTTTGGAAAGTTTTA-AGG
* * *
61289 TGAAAATGTAATTTT-TAGAAGTTTTAAGG
1 TAAAAATGGAATTTTGGA-AAGTTTTAAGG
* ** *
61318 TCAAAATGGAATTTTGGAAAGTTCGAGGG
1 TAAAAATGGAATTTTGGAAAGTTTTAAGG
** *
61347 TAAAAATATAATTTTGGACAGTTT
1 TAAAAATGGAATTTTGGAAAGTTT
61371 AGGGACCTCC
Statistics
Matches: 88, Mismatches: 17, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
28 17 0.19
29 56 0.64
30 15 0.17
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.37
Consensus pattern (29 bp):
TAAAAATGGAATTTTGGAAAGTTTTAAGG
Found at i:63152 original size:17 final size:17
Alignment explanation
Indices: 63126--63221 Score: 77
Period size: 17 Copynumber: 5.6 Consensus size: 17
63116 CTTCTTAATT
* *
63126 AATTTTAATTTACAGTA
1 AATTTAAATTTAAAGTA
63143 AATTTAAATTTAAAGTA
1 AATTTAAATTTAAAGTA
** * *
63160 AATTTAAACTCAAAAATG
1 AATTTAAA-TTTAAAGTA
*
63178 AATTTAAATTTAGAA-CA
1 AATTTAAATTTA-AAGTA
* *
63195 AATTCAAACTTAAAGTA
1 AATTTAAATTTAAAGTA
*
63212 AATTAAAATT
1 AATTTAAATT
63222 AAAAATTGGA
Statistics
Matches: 61, Mismatches: 15, Indels: 6
0.74 0.18 0.07
Matches are distributed among these distances:
16 2 0.03
17 44 0.72
18 15 0.25
ACGTcount: A:0.52, C:0.06, G:0.05, T:0.36
Consensus pattern (17 bp):
AATTTAAATTTAAAGTA
Found at i:63309 original size:13 final size:13
Alignment explanation
Indices: 63291--63328 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
63281 TAATTTTATA
63291 TTTAAAAAATAAT
1 TTTAAAAAATAAT
*
63304 TTT--AAATTAAT
1 TTTAAAAAATAAT
63315 TTTAAAAAATAAT
1 TTTAAAAAATAAT
63328 T
1 T
63329 AATTTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
11 10 0.48
13 11 0.52
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TTTAAAAAATAAT
Found at i:65048 original size:3 final size:3
Alignment explanation
Indices: 65040--65065 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
65030 ATCAACATTA
65040 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
65066 AACTATAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:66482 original size:21 final size:19
Alignment explanation
Indices: 66439--66482 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
66429 GAAAAATGAT
* *
66439 TTTTGGAAAATAATTTATT
1 TTTTGGAAAATAATATATA
66458 TTTTGGAAAATTTAATATATA
1 TTTTGGAAAA--TAATATATA
66479 TTTT
1 TTTT
66483 TTTGTTTGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 10 0.48
21 11 0.52
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (19 bp):
TTTTGGAAAATAATATATA
Found at i:72082 original size:31 final size:31
Alignment explanation
Indices: 72044--72103 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
72034 AAGTGGACAT
72044 TGAACTATTCGAAAGTTTTTATTTAAGTTGC
1 TGAACTATTCGAAAGTTTTTATTTAAGTTGC
*
72075 TGAACTATTTGAAAGTTTTTATTTAAGTT
1 TGAACTATTCGAAAGTTTTTATTTAAGTT
72104 ATCGAGTTGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (31 bp):
TGAACTATTCGAAAGTTTTTATTTAAGTTGC
Found at i:74027 original size:33 final size:30
Alignment explanation
Indices: 73985--74052 Score: 84
Period size: 33 Copynumber: 2.2 Consensus size: 30
73975 GCGTCATTTA
73985 ATTAATAAATCAAAAATTAAACTAATATA-TAAT
1 ATTAATAAAT--AAAATTAAA--AATATATTAAT
*
74018 ATTAATAAATAAAATTAAAAATATATTTAT
1 ATTAATAAATAAAATTAAAAATATATTAAT
74048 ATTAA
1 ATTAA
74053 AGATTCGTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
29 6 0.18
30 8 0.24
31 9 0.27
33 10 0.30
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (30 bp):
ATTAATAAATAAAATTAAAAATATATTAAT
Found at i:74495 original size:21 final size:22
Alignment explanation
Indices: 74471--74511 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
74461 TATATAATTT
74471 ATATAAAAATAATTT-TATTAA
1 ATATAAAAATAATTTATATTAA
* *
74492 ATATATATATAATTTATATT
1 ATATAAAAATAATTTATATT
74512 TTTATATAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATATAAAAATAATTTATATTAA
Found at i:75148 original size:18 final size:19
Alignment explanation
Indices: 75127--75165 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
75117 ATTAAAATTT
75127 ATTAAAAATCA-TAAAAAA
1 ATTAAAAATCATTAAAAAA
* *
75145 ATTATAAATTATTAAAAAA
1 ATTAAAAATCATTAAAAAA
75164 AT
1 AT
75166 AACAATATCG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (19 bp):
ATTAAAAATCATTAAAAAA
Found at i:76404 original size:2 final size:2
Alignment explanation
Indices: 76397--76424 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
76387 GTATCAACAA
76397 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
76425 CAGAAGCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:77559 original size:7 final size:7
Alignment explanation
Indices: 77547--77571 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
77537 AAATAGATGC
77547 TTTTTCT
1 TTTTTCT
77554 TTTTTCT
1 TTTTTCT
77561 TTTTTCT
1 TTTTTCT
77568 TTTT
1 TTTT
77572 ATACATATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTCT
Found at i:85052 original size:2 final size:2
Alignment explanation
Indices: 85045--85070 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
85035 ACTTTAAAGG
85045 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
85071 CAATAATAAT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:93841 original size:15 final size:15
Alignment explanation
Indices: 93821--93859 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
93811 TTAATATTAT
*
93821 TAGATTATTTTATAA
1 TAGATTATTCTATAA
93836 TAGATTATTCTATAA
1 TAGATTATTCTATAA
93851 -AGAATTATT
1 TAG-ATTATT
93860 GCAGAAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 2 0.09
15 20 0.91
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.49
Consensus pattern (15 bp):
TAGATTATTCTATAA
Found at i:95373 original size:19 final size:19
Alignment explanation
Indices: 95340--95384 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
95330 AAATTTTAAA
*
95340 ATAATTTTATTTTATTTTT
1 ATAAATTTATTTTATTTTT
95359 -TAAATTTATTATTATTTTT
1 ATAAATTTATT-TTATTTTT
95378 ATAAATT
1 ATAAATT
95385 AAATAACTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 9 0.39
19 8 0.35
20 6 0.26
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
ATAAATTTATTTTATTTTT
Found at i:101569 original size:18 final size:19
Alignment explanation
Indices: 101548--101589 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
101538 ATTAGTGTTA
*
101548 TTATTAATATTAA-AACAG
1 TTATTAATATTAATAAAAG
101566 TTATTAATATTAATAAAAG
1 TTATTAATATTAATAAAAG
101585 TTATT
1 TTATT
101590 GAAAAGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (19 bp):
TTATTAATATTAATAAAAG
Found at i:101582 original size:21 final size:21
Alignment explanation
Indices: 101544--101583 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
101534 GGTCATTAGT
* *
101544 GTTATTATTAATATTAAAACA
1 GTTATTAATAATAATAAAACA
*
101565 GTTATTAATATTAATAAAA
1 GTTATTAATAATAATAAAA
101584 GTTATTGAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (21 bp):
GTTATTAATAATAATAAAACA
Found at i:102270 original size:35 final size:35
Alignment explanation
Indices: 102225--102324 Score: 114
Period size: 35 Copynumber: 2.8 Consensus size: 35
102215 TTTATTTATT
*
102225 TTAAACTTTAAATTTGAAAATAATTTTAAA-CTTAAA
1 TTAAA-TTTAAATTT-AAAATAAATTTAAATCTTAAA
*
102261 TTAAATTTAAAATTTAAAATAAATTTAAATTTTTAAA
1 TTAAATTT-AAATTTAAAATAAATTTAAA-TCTTAAA
* *
102298 -CAAATTTAATTTTAAAATAAATTTAAA
1 TTAAATTTAAATTTAAAATAAATTTAAA
102325 GGGAGTATGG
Statistics
Matches: 57, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
35 35 0.61
36 17 0.30
37 5 0.09
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (35 bp):
TTAAATTTAAATTTAAAATAAATTTAAATCTTAAA
Found at i:102290 original size:17 final size:17
Alignment explanation
Indices: 102226--102324 Score: 108
Period size: 18 Copynumber: 5.6 Consensus size: 17
102216 TTATTTATTT
102226 TAAACTTTAAATTTGAAAA
1 TAAA-TTTAAATTT-AAAA
* * *
102245 TAATTTTAAACTTAAAT
1 TAAATTTAAATTTAAAA
102262 TAAATTTAAAATTTAAAA
1 TAAATTT-AAATTTAAAA
*
102280 TAAATTTAAATTTTTAAA
1 TAAATTTAAA-TTTAAAA
* *
102298 CAAATTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
102315 TAAATTTAAA
1 TAAATTTAAA
102325 GGGAGTATGG
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
17 26 0.39
18 37 0.56
19 3 0.05
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:102324 original size:6 final size:6
Alignment explanation
Indices: 102224--102292 Score: 54
Period size: 6 Copynumber: 11.5 Consensus size: 6
102214 TTTTATTTAT
* * *
102224 TTTAAA CTTTAAA TTTGAAA -ATAAT TTTAAA CTTAAA -TTAAA TTTAAAA
1 TTTAAA -TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA
*
102273 TTTAAA -ATAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTT
102293 TTAAACAAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
5 11 0.22
6 24 0.48
7 15 0.30
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:102469 original size:49 final size:47
Alignment explanation
Indices: 102404--102498 Score: 120
Period size: 49 Copynumber: 2.0 Consensus size: 47
102394 TATCTTAATA
* * *
102404 TAATTTTTTAAGGTATTTTAAAT-TTGTTTATTTTTTAATATTTGTTT
1 TAATTTTTTAAGGTATTTGAAATATTATATATTTTTTAA-ATTTGTTT
*
102451 TAATATTTTTAAGTGTATTTGATATATTATATATTTTTTAAATTTGTT
1 TAAT-TTTTTAAG-GTATTTGAAATATTATATATTTTTTAAATTTGTT
102499 GTATGTAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
47 4 0.10
48 8 0.20
49 16 0.39
50 13 0.32
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.63
Consensus pattern (47 bp):
TAATTTTTTAAGGTATTTGAAATATTATATATTTTTTAAATTTGTTT
Found at i:103136 original size:23 final size:23
Alignment explanation
Indices: 103093--103143 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
103083 TAAACCTCAT
* *
103093 TTTAAATTTTAATTTATTTTGAG
1 TTTAAATTTTAATTTAATTTGAA
*
103116 TTTAAA-TTTATTTTAAATTTGAA
1 TTTAAATTTTAATTT-AATTTGAA
103139 TTTAA
1 TTTAA
103144 TTAAAAAGTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (23 bp):
TTTAAATTTTAATTTAATTTGAA
Found at i:103140 original size:17 final size:17
Alignment explanation
Indices: 103091--103142 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 17
103081 CTTAAACCTC
*
103091 ATTTTAAATTTTAATTT
1 ATTTTAAATTTAAATTT
* *
103108 ATTTTGAGTTTAAATTT
1 ATTTTAAATTTAAATTT
*
103125 ATTTTAAATTTGAATTT
1 ATTTTAAATTTAAATTT
103142 A
1 A
103143 ATTAAAAAGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.60
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:103145 original size:11 final size:12
Alignment explanation
Indices: 103093--103143 Score: 52
Period size: 11 Copynumber: 4.4 Consensus size: 12
103083 TAAACCTCAT
*
103093 TTTAAATTTTAA
1 TTTAAATTTGAA
* *
103105 TTT-ATTTTGAG
1 TTTAAATTTGAA
*
103116 TTTAAATTT-AT
1 TTTAAATTTGAA
103127 TTTAAATTTGAA
1 TTTAAATTTGAA
103139 TTTAA
1 TTTAA
103144 TTAAAAAGTC
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
11 18 0.58
12 13 0.42
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (12 bp):
TTTAAATTTGAA
Found at i:104911 original size:17 final size:17
Alignment explanation
Indices: 104822--104916 Score: 84
Period size: 17 Copynumber: 5.5 Consensus size: 17
104812 AAAATTTTAG
*
104822 ATTTTAAATCTT-AATTC
1 ATTTTAAAT-TTAAATTT
* *
104839 ATTTTCATTTTAAATTT
1 ATTTTAAATTTAAATTT
* **
104856 ATTGTAAATTTAAGCTT
1 ATTTTAAATTTAAATTT
** *
104873 ATTTGGAGTTTAAATTT
1 ATTTTAAATTTAAATTT
104890 ATTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
104907 ATTTTGAAAT
1 ATTTT-AAAT
104917 AAAAATTTAA
Statistics
Matches: 59, Mismatches: 17, Indels: 3
0.75 0.22 0.04
Matches are distributed among these distances:
16 2 0.03
17 53 0.90
18 4 0.07
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.55
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:104922 original size:18 final size:17
Alignment explanation
Indices: 104884--104925 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
104874 TTTGGAGTTT
**
104884 AAATTTATTTTAAATTT
1 AAATTTATTTTAAATAA
104901 AAATTTATTTTGAAATAA
1 AAATTTATTTT-AAATAA
104919 AAATTTA
1 AAATTTA
104926 AATTTAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
AAATTTATTTTAAATAA
Found at i:106701 original size:29 final size:27
Alignment explanation
Indices: 106668--106770 Score: 82
Period size: 29 Copynumber: 3.6 Consensus size: 27
106658 CATAATTCTC
106668 CAAAAATTACATTTTTATCCCAAATTTT
1 CAAAAATTACATTTTTA-CCCAAATTTT
* * *
106696 CTAAAATT-CTATTTTTGACCTCGAACTTT
1 CAAAAATTAC-ATTTTT-ACC-CAAATTTT
* * *
106725 CCAAAATTTCATTTTCAACCCTAAATTTT
1 CAAAAATTACATTTT-TACCC-AAATTTT
106754 CAAAAAATTACATTTTT
1 C-AAAAATTACATTTTT
106771 GCCCCCGAAC
Statistics
Matches: 58, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
27 1 0.02
28 16 0.28
29 28 0.48
30 13 0.22
ACGTcount: A:0.36, C:0.19, G:0.02, T:0.43
Consensus pattern (27 bp):
CAAAAATTACATTTTTACCCAAATTTT
Found at i:106728 original size:58 final size:59
Alignment explanation
Indices: 106666--106799 Score: 159
Period size: 59 Copynumber: 2.3 Consensus size: 59
106656 CCCATAATTC
* * * *
106666 TCCAAAAATTACATTTTTATCCC-AAATTTTC-TAAAATT-CTATTTTTGACCTCGAACTT
1 TCCAAAAATTACATTTTCAACCCTAAATTTTCAAAAAATTAC-ATTTTTGACCCCGAAC-T
* *
106724 TCC-AAAATTTCATTTTCAACCCTAAATTTTCAAAAAATTACATTTTTGCCCCCGAACT
1 TCCAAAAATTACATTTTCAACCCTAAATTTTCAAAAAATTACATTTTTGACCCCGAACT
106782 TCCAAAAATTACCATTTT
1 TCCAAAAATTA-CATTTT
106800 ACCCTCGAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
57 16 0.25
58 15 0.23
59 26 0.41
60 7 0.11
ACGTcount: A:0.34, C:0.23, G:0.03, T:0.40
Consensus pattern (59 bp):
TCCAAAAATTACATTTTCAACCCTAAATTTTCAAAAAATTACATTTTTGACCCCGAACT
Found at i:106799 original size:29 final size:29
Alignment explanation
Indices: 106756--106887 Score: 85
Period size: 29 Copynumber: 4.6 Consensus size: 29
106746 TAAATTTTCA
*
106756 AAAAATTA-CATTTTTGCCCCCGAACT-TCC
1 AAAAATTACCA-TTTTACCCCCGAA-TGTCC
* *
106785 AAAAATTACCATTTTACCCTCGAATGTCT
1 AAAAATTACCATTTTACCCCCGAATGTCC
* ** * *
106814 AAAAA-TACCATTTTTTA-TCCTTAGTCTTCC
1 AAAAATTACCA--TTTTACCCCCGAAT-GTCC
* *
106844 AAAAATTACCATTTTACCCTCGAATGTCT
1 AAAAATTACCATTTTACCCCCGAATGTCC
*
106873 AAAAATT-CCCTTTTA
1 AAAAATTACCATTTTA
106888 AACTTCGAAC
Statistics
Matches: 78, Mismatches: 18, Indels: 15
0.70 0.16 0.14
Matches are distributed among these distances:
28 13 0.17
29 43 0.55
30 17 0.22
31 5 0.06
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.36
Consensus pattern (29 bp):
AAAAATTACCATTTTACCCCCGAATGTCC
Found at i:106818 original size:59 final size:60
Alignment explanation
Indices: 106755--106877 Score: 162
Period size: 59 Copynumber: 2.1 Consensus size: 60
106745 CTAAATTTTC
*
106755 AAAAAATTA-CATTTTTGCCCCCGA-ACTTCCAAAAATTACCATTTTACCCTCGAATGTCT
1 AAAAAA-TACCATTTTTGACCCCGAGACTTCCAAAAATTACCATTTTACCCTCGAATGTCT
* * ** *
106814 -AAAAATACCATTTTTTATCCTTAGTCTTCCAAAAATTACCATTTTACCCTCGAATGTCT
1 AAAAAATACCATTTTTGACCCCGAGACTTCCAAAAATTACCATTTTACCCTCGAATGTCT
106873 AAAAA
1 AAAAA
106878 TTCCCTTTTA
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
57 2 0.04
58 15 0.27
59 34 0.62
60 4 0.07
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.34
Consensus pattern (60 bp):
AAAAAATACCATTTTTGACCCCGAGACTTCCAAAAATTACCATTTTACCCTCGAATGTCT
Found at i:106826 original size:28 final size:29
Alignment explanation
Indices: 106785--106887 Score: 104
Period size: 29 Copynumber: 3.6 Consensus size: 29
106775 CCGAACTTCC
106785 AAAAATTACCATTTTACCCTCGAATGTCT
1 AAAAATTACCATTTTACCCTCGAATGTCT
* * * * *
106814 AAAAA-TACCATTTTTTATCCT-TAGTCTTCC
1 AAAAATTACCA--TTTTACCCTCGAAT-GTCT
106844 AAAAATTACCATTTTACCCTCGAATGTCT
1 AAAAATTACCATTTTACCCTCGAATGTCT
*
106873 AAAAATT-CCCTTTTA
1 AAAAATTACCATTTTA
106888 AACTTCGAAC
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
28 12 0.21
29 24 0.41
30 17 0.29
31 5 0.09
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (29 bp):
AAAAATTACCATTTTACCCTCGAATGTCT
Found at i:106908 original size:59 final size:58
Alignment explanation
Indices: 106780--106917 Score: 170
Period size: 59 Copynumber: 2.3 Consensus size: 58
106770 TGCCCCCGAA
* ** **
106780 CTTCCAAAAATTACCATTTTACCCTCGAATGTCTAAAAATACCATTTTTTATCCTTAGT
1 CTTCCAAAAATTACCATTTTACCCTCGAATGTCTAAAAATACCA-CTTTTAAACTTAAC
*
106839 CTTCCAAAAATTACCATTTTACCCTCGAATGTCTAAAAATTCC-CTTTTAAACTTCGAAC
1 CTTCCAAAAATTACCATTTTACCCTCGAATGTCTAAAAATACCACTTTTAAACTT--AAC
* *
106898 CTTTCGAAAATTACCATTTT
1 CTTCCAAAAATTACCATTTT
106918 GTTCCCGAAG
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
57 8 0.12
59 61 0.88
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.38
Consensus pattern (58 bp):
CTTCCAAAAATTACCATTTTACCCTCGAATGTCTAAAAATACCACTTTTAAACTTAAC
Found at i:110963 original size:16 final size:17
Alignment explanation
Indices: 110942--110975 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
110932 CAATTAACCA
110942 TTCTTTG-ATTCAATTT
1 TTCTTTGAATTCAATTT
*
110958 TTCTTTGAATTCCATTT
1 TTCTTTGAATTCAATTT
110975 T
1 T
110976 ATTTCTATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.18, C:0.15, G:0.06, T:0.62
Consensus pattern (17 bp):
TTCTTTGAATTCAATTT
Found at i:111452 original size:13 final size:12
Alignment explanation
Indices: 111425--111459 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 12
111415 TGAAACCTAA
111425 AAAAAT-AAAAT
1 AAAAATGAAAAT
111436 AAAAATGAAAAT
1 AAAAATGAAAAT
111448 GAAAAATGAAAA
1 -AAAAATGAAAA
111460 ATCAATCCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 6 0.27
12 5 0.23
13 11 0.50
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (12 bp):
AAAAATGAAAAT
Found at i:112285 original size:7 final size:7
Alignment explanation
Indices: 112269--112323 Score: 51
Period size: 7 Copynumber: 7.7 Consensus size: 7
112259 GATTTTACCC
112269 AAAAAA-
1 AAAAAAG
112275 AAAAAAG
1 AAAAAAG
112282 AAAAATGAGG
1 AAAAA--A-G
*
112292 AAAAAAT
1 AAAAAAG
112299 AAAAAA-
1 AAAAAAG
*
112305 TAAAAAG
1 AAAAAAG
112312 AAAAAAG
1 AAAAAAG
112319 AAAAA
1 AAAAA
112324 GGAGAGGTCG
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
6 11 0.27
7 22 0.54
8 1 0.02
9 1 0.02
10 6 0.15
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.05
Consensus pattern (7 bp):
AAAAAAG
Found at i:113477 original size:49 final size:49
Alignment explanation
Indices: 113416--113863 Score: 246
Period size: 49 Copynumber: 9.1 Consensus size: 49
113406 CAAATATTAT
* *
113416 GGGAAAGATTTAAGCCGTAACGGCGAATCCAATACCACGAAGATTTGAA
1 GGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATTTGAA
* * * * *
113465 GGGAAAGGTTTAAGTCGCAATGGCGAA-CCTTGTACCTCAGAAGCA--TGAA
1 GGGAAAGATTTAAGCCGCAACGGCGAATCC-AGTACCAC-GAAG-ATTTGAA
113514 GGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATTT-AGA
1 GGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATTTGA-A
* * * * * * * *
113563 GAGAAAGGTTTAAGTCGCAACGAC-AAACCTTGTACCTCAAAAGCA--TGAA
1 GGGAAAGATTTAAGCCGCAACGGCGAATCC-AGTACCAC-GAAG-ATTTGAA
* * *
113612 GGGAGAGATTTAAGCCGCAACAGCAAATCCAGTACCAC-AAGGATATTG-A
1 GGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAA-GAT-TTGAA
* * * * * ** **
113661 GAGAAAGGTTTAAGTCACAATGGCGAATCTTGTACCTTGAAAGCA--TGAA
1 GGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACG-AAG-ATTTGAA
* * * * * **
113710 AGCAAATATTTAAGCCGCAACAGCGAATCTAGTACCAC-AAGGATATAAAA
1 GGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAA-GAT-TTGAA
* * * * *
113760 GGGAAAGGTTTAAGTCGAAACGGCGAA-CCTTGTACCTCGAAAGCA--TGAA
1 GGGAAAGATTTAAGCCGCAACGGCGAATCC-AGTACCACG-AAG-ATTTGAA
* * *
113809 -GGAAAGATTTAAGCTGCAACGGCGAATCTAGTACCATGAAGATATTG-A
1 GGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGAT-TTGAA
113857 GGGAAAG
1 GGGAAAG
113864 GTTACAACAG
Statistics
Matches: 291, Mismatches: 75, Indels: 66
0.67 0.17 0.15
Matches are distributed among these distances:
46 1 0.00
47 10 0.03
48 44 0.15
49 182 0.63
50 45 0.15
51 6 0.02
52 3 0.01
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.19
Consensus pattern (49 bp):
GGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATTTGAA
Found at i:113539 original size:98 final size:100
Alignment explanation
Indices: 113416--113904 Score: 576
Period size: 98 Copynumber: 5.0 Consensus size: 100
113406 CAAATATTAT
* *
113416 GGGAAAGATTTAAGCCGTAACGGCGAATCCAATACCACGAAGAT-TTGAAGGGAAAGGTTTAAGT
1 GGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATTGAAGGGAAAGGTTTAAGT
*
113480 CGCAATGGCGAACCTTGTACCTCAG-AAGCATGAA
66 CGCAACGGCGAACCTTGTACCTCAGAAAGCATGAA
*
113514 GGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGAT-TT-AGAGAGAAAGGTTTAAG
1 GGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATTGA-AGGGAAAGGTTTAAG
* *
113577 TCGCAACGACAAACCTTGTACCTCA-AAAGCATGAA
65 TCGCAACGGCGAACCTTGTACCTCAGAAAGCATGAA
* * * *
113612 GGGAGAGATTTAAGCCGCAACAGCAAATCCAGTACCAC-AAGGATATTG-AGAGAAAGGTTTAAG
1 GGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAA-GATATTGAAGGGAAAGGTTTAAG
* * * *
113675 TCACAATGGCGAATCTTGTACCT-TGAAAGCATGAA
65 TCGCAACGGCGAACCTTGTACCTCAGAAAGCATGAA
* * * * * **
113710 AGCAAATATTTAAGCCGCAACAGCGAATCTAGTACCAC-AAGGATATAAAAGGGAAAGGTTTAAG
1 GGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAA-GATATTGAAGGGAAAGGTTTAAG
*
113774 TCGAAACGGCGAACCTTGTACCTC-GAAAGCATGAA
65 TCGCAACGGCGAACCTTGTACCTCAGAAAGCATGAA
* * *
113809 -GGAAAGATTTAAGCTGCAACGGCGAATCTAGTACCATGAAGATATTG-AGGGAAAGG-TTACA-
1 GGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATTGAAGGGAAAGGTTTA-AG
* * *
113870 ACAGCAACGGCGAAACTTGTACCTTAGAAA-CATGA
65 TC-GCAACGGCGAACCTTGTACCTCAGAAAGCATGA
113905 CCAGAAAGAT
Statistics
Matches: 340, Mismatches: 39, Indels: 25
0.84 0.10 0.06
Matches are distributed among these distances:
96 4 0.01
97 37 0.11
98 251 0.74
99 48 0.14
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.19
Consensus pattern (100 bp):
GGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATTGAAGGGAAAGGTTTAAGT
CGCAACGGCGAACCTTGTACCTCAGAAAGCATGAA
Found at i:114318 original size:39 final size:39
Alignment explanation
Indices: 114180--114323 Score: 144
Period size: 39 Copynumber: 3.7 Consensus size: 39
114170 TCATTAGCTA
* * * * *
114180 ATCTCCTACCCTGAGCCTGGGGTAGATTGCAACCATTCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATTACAATCATTCG
* * * * * * * *
114219 ATCTCTTATCTCAAGCCTGAGGCAGATCACTATCAGTCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTACAATCATTCG
* *
114258 ATCTCTTACCCCGAGCTTGGGGAAGATTACAATCATTCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATTACAATCATTCG
*
114297 ATCTTTTACCCCGAGCCTGGGGCAGAT
1 ATCTCTTACCCCGAGCCTGGGGCAGAT
114324 CATCATTAAC
Statistics
Matches: 79, Mismatches: 26, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
39 79 1.00
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATTACAATCATTCG
Found at i:114346 original size:39 final size:38
Alignment explanation
Indices: 114137--114362 Score: 129
Period size: 39 Copynumber: 5.8 Consensus size: 38
114127 ATCACCATCA
* * *
114137 ACCAATCTCTTACCACAAGCCTGGGGCAGAGCATCATT
1 ACCAATCTCTTACCCCGAGCCTGGGGCAGATCATCATT
* * * * *
114175 AGCTAATCTCCTACCCTGAGCCTGGGGTAGATTGCAACCATT
1 A-CCAATCTCTTACCCCGAGCCTGGGGCAGA-T-C-ATCATT
* * * * * *
114217 --CGATCTCTTATCTCAAGCCTGAGGCAGATCA-CTATC
1 ACCAATCTCTTACCCCGAGCCTGGGGCAGATCATC-ATT
* * *
114253 AGTCAATCTCTTACCCCGAGCTTGGGGAAGATTACAATCATT
1 A-CCAATCTCTTACCCCGAGCCTGGGGCAGA-T-C-ATCATT
* *
114295 --CGATCTTTTACCCCGAGCCTGGGGCAGATCATCATT
1 ACCAATCTCTTACCCCGAGCCTGGGGCAGATCATCATT
* * *
114331 AACCAATCTCCTACCCCGAGTCTGGGACAGAT
1 -ACCAATCTCTTACCCCGAGCCTGGGGCAGAT
114363 TGCACTTATC
Statistics
Matches: 138, Mismatches: 35, Indels: 29
0.68 0.17 0.14
Matches are distributed among these distances:
35 1 0.01
36 9 0.07
37 2 0.01
38 3 0.02
39 111 0.80
40 1 0.01
41 2 0.01
42 8 0.06
43 1 0.01
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.25
Consensus pattern (38 bp):
ACCAATCTCTTACCCCGAGCCTGGGGCAGATCATCATT
Found at i:114363 original size:78 final size:76
Alignment explanation
Indices: 114141--114363 Score: 232
Period size: 78 Copynumber: 2.9 Consensus size: 76
114131 CCATCAACCA
* * * * *
114141 ATCTCTTACCACAAGCCTGGGGCAGAGCATCATTAGCTAATCTCCTACCCTGAGCCTGGGGTAGA
1 ATCTCTTACCCCAAGCCTGGGGCAGATCATCATTAGCCAATCTCCTACCCCGAG-CT-GGGAAGA
*
114206 TTGCAACCATTCG
64 TTACAACCATTCG
* * * * * *
114219 ATCTCTTATCTCAAGCCTGAGGCAGATCA-CTATCAGTCAATCTCTTACCCCGAGCTTGGGGAAG
1 ATCTCTTACCCCAAGCCTGGGGCAGATCATC-ATTAGCCAATCTCCTACCCCGAGC-T-GGGAAG
*
114283 ATTACAATCATTCG
63 ATTACAACCATTCG
* * *
114297 ATCTTTTACCCCGAGCCTGGGGCAGATCATCATTAACCAATCTCCTACCCCGAGTCTGGGACAGA
1 ATCTCTTACCCCAAGCCTGGGGCAGATCATCATTAGCCAATCTCCTACCCCGAG-CTGGGA-AGA
114362 TT
64 TT
114364 GCACTTATCC
Statistics
Matches: 119, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
77 6 0.05
78 111 0.93
79 2 0.02
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (76 bp):
ATCTCTTACCCCAAGCCTGGGGCAGATCATCATTAGCCAATCTCCTACCCCGAGCTGGGAAGATT
ACAACCATTCG
Found at i:115025 original size:17 final size:17
Alignment explanation
Indices: 114946--115039 Score: 84
Period size: 17 Copynumber: 5.5 Consensus size: 17
114936 AAAATTTTAG
*
114946 ATTTTAAATCTT-AATTC
1 ATTTTAAAT-TTAAATTT
*
114963 ATTTTAATTTTAAATTT
1 ATTTTAAATTTAAATTT
* **
114980 ATTGTAAATTTAAGCTT
1 ATTTTAAATTTAAATTT
* **
114997 ATTTGATGTTTAAATTT
1 ATTTTAAATTTAAATTT
115014 ATTTTAAATTT-AATTT
1 ATTTTAAATTTAAATTT
115030 ATTTTGAAAT
1 ATTTT-AAAT
115040 AAAAATTTAA
Statistics
Matches: 60, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
16 12 0.20
17 48 0.80
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.56
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:115036 original size:34 final size:33
Alignment explanation
Indices: 114946--115036 Score: 112
Period size: 34 Copynumber: 2.7 Consensus size: 33
114936 AAAATTTTAG
* *
114946 ATTTTAAATCTTAATTCATTTTAATTTTAAATTT
1 ATTTTAAAT-TTAATTTATTTTGATTTTAAATTT
* *
114980 ATTGTAAATTTAAGCTTA-TTTGATGTTTAAATTT
1 ATTTTAAATTTAA-TTTATTTTGAT-TTTAAATTT
115014 ATTTTAAATTTAATTTATTTTGA
1 ATTTTAAATTTAATTTATTTTGA
115037 AATAAAAATT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
33 12 0.25
34 36 0.75
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.57
Consensus pattern (33 bp):
ATTTTAAATTTAATTTATTTTGATTTTAAATTT
Found at i:115046 original size:34 final size:34
Alignment explanation
Indices: 114946--115048 Score: 102
Period size: 34 Copynumber: 3.0 Consensus size: 34
114936 AAAATTTTAG
* *
114946 ATTTTAAATCTTAATTCATTTT-AATTTTAAATTT
1 ATTTTAAAT-TTAATTTATTTTGAAATTTAAATTT
* * **
114980 ATTGTAAATTTAAGCTTA-TTTGATGTTTAAATTT
1 ATTTTAAATTTAA-TTTATTTTGAAATTTAAATTT
**
115014 ATTTTAAATTTAATTTATTTTGAAATAAAAATTT
1 ATTTTAAATTTAATTTATTTTGAAATTTAAATTT
115048 A
1 A
115049 AATTTAAAAG
Statistics
Matches: 55, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
33 10 0.18
34 45 0.82
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (34 bp):
ATTTTAAATTTAATTTATTTTGAAATTTAAATTT
Found at i:116758 original size:29 final size:29
Alignment explanation
Indices: 116664--116777 Score: 99
Period size: 29 Copynumber: 3.9 Consensus size: 29
116654 CCCATAATTC
* * *
116664 TCCAAAAATTATATTTTTACTCCCAAATTT
1 TCCAAAAATTATATTTTTGCCCCCAAA-CT
** *
116694 TCC-AAAATT-TCATTTTTGATCCCTAACT
1 TCCAAAAATTAT-ATTTTTGCCCCCAAACT
*
116722 TTCAAAAATTATATTTTTGCCCCCAAACT
1 TCCAAAAATTATATTTTTGCCCCCAAACT
* *
116751 TCCAAAAAATACCA-TTTTGCCCCCAAA
1 TCCAAAAATTA-TATTTTTGCCCCCAAA
116778 TGTCTAAAAA
Statistics
Matches: 69, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
28 4 0.06
29 60 0.87
30 5 0.07
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.37
Consensus pattern (29 bp):
TCCAAAAATTATATTTTTGCCCCCAAACT
Found at i:116875 original size:29 final size:28
Alignment explanation
Indices: 116810--116884 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 28
116800 CTTTGAACCT
*
116810 TCCAAAAATTACCATTTTGTTCCCCAAGCA
1 TCCAAAAATTACCA-TTT-TACCCCAAGCA
**
116840 TCC-AAAATTACCATTTTACCCCTGGGCA
1 TCCAAAAATTACCATTTTACCCC-AAGCA
*
116868 TCCAAAAATCA-CATTTT
1 TCCAAAAATTACCATTTT
116885 TGACTCTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 5 0.13
28 15 0.38
29 16 0.41
30 3 0.08
ACGTcount: A:0.33, C:0.29, G:0.07, T:0.31
Consensus pattern (28 bp):
TCCAAAAATTACCATTTTACCCCAAGCA
Found at i:118801 original size:15 final size:16
Alignment explanation
Indices: 118771--118811 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
118761 CCTTTGTTTT
*
118771 TAATATCATTTTTTATA
1 TAATAT-ATTTGTTATA
118788 -AATATATTTGTTATA
1 TAATATATTTGTTATA
118803 TAA-ATATTT
1 TAATATATTT
118812 CATTCACATC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 15 0.68
16 7 0.32
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (16 bp):
TAATATATTTGTTATA
Found at i:118806 original size:17 final size:16
Alignment explanation
Indices: 118772--118809 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
118762 CTTTGTTTTT
118772 AATATCATTTTTTATA
1 AATATCATTTTTTATA
118788 AATAT-ATTTGTTATATA
1 AATATCATTT-TT-TATA
118805 AATAT
1 AATAT
118810 TTCATTCACA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 4 0.20
16 7 0.35
17 9 0.45
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (16 bp):
AATATCATTTTTTATA
Found at i:120887 original size:16 final size:16
Alignment explanation
Indices: 120868--120899 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
120858 TAAATGTGAA
120868 AAATAATAAAATAAAT
1 AAATAATAAAATAAAT
*
120884 AAATAATAAATTAAAT
1 AAATAATAAAATAAAT
120900 TAAAAAGATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
AAATAATAAAATAAAT
Found at i:121297 original size:19 final size:19
Alignment explanation
Indices: 121262--121300 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
121252 CACGTTTCTC
**
121262 TCATTTTTCTTTTTCTTTT
1 TCATTTTTCTTCATCTTTT
121281 TCATTTTTCTTCATCTTTT
1 TCATTTTTCTTCATCTTTT
121300 T
1 T
121301 TTCCCAGAAT
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:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (19 bp):
TCATTTTTCTTCATCTTTT
Found at i:122401 original size:6 final size:6
Alignment explanation
Indices: 122374--122449 Score: 52
Period size: 6 Copynumber: 12.8 Consensus size: 6
122364 TAAACCCAAT
* * *
122374 TTTAAA TTTTAAA TTT-AT TTTAAA TTTAAA CTT--A TTCTGAA TTTAAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA TTTAAA
* *
122421 TTT-AT TTTGAA TTTAAA TTTAAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTT-AAA TTTAA
122450 TCAAAAGTCC
Statistics
Matches: 55, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
4 2 0.04
5 9 0.16
6 29 0.53
7 15 0.27
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:122403 original size:17 final size:17
Alignment explanation
Indices: 122372--122441 Score: 95
Period size: 17 Copynumber: 4.1 Consensus size: 17
122362 AATAAACCCA
122372 ATTTTAAATTTTAAATTT
1 ATTTTAAA-TTTAAATTT
*
122390 ATTTTAAATTTAAACTT
1 ATTTTAAATTTAAATTT
* *
122407 ATTCTGAATTTAAATTT
1 ATTTTAAATTTAAATTT
*
122424 ATTTTGAATTTAAATTT
1 ATTTTAAATTTAAATTT
122441 A
1 A
122442 AAATTTAATC
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
17 39 0.83
18 8 0.17
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:123196 original size:18 final size:18
Alignment explanation
Indices: 123155--123201 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
123145 GATATCAATT
123155 TAATAAATAAAATTACTTA
1 TAAT-AATAAAATTACTTA
*
123174 AAATAATAATAATTA-TTA
1 TAATAATAA-AATTACTTA
123192 TAATAATAAA
1 TAATAATAAA
123202 CCGAATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 1 0.04
18 16 0.64
19 8 0.32
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
TAATAATAAAATTACTTA
Found at i:129460 original size:18 final size:17
Alignment explanation
Indices: 129429--129465 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
129419 TGAGTTTTAT
129429 TAAAATATAAAATAAAA
1 TAAAATATAAAATAAAA
*
129446 TAAAATATGAAAATACAA
1 TAAAATAT-AAAATAAAA
129464 TA
1 TA
129466 GGAATACACG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.24
Consensus pattern (17 bp):
TAAAATATAAAATAAAA
Found at i:130269 original size:17 final size:17
Alignment explanation
Indices: 130226--130269 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
130216 TTTTATATTC
*
130226 AGTTCTTATTTTTTTAT
1 AGTTTTTATTTTTTTAT
* *
130243 A-TTTTGATTTTTTTCT
1 AGTTTTTATTTTTTTAT
130259 AGTTTTTATTT
1 AGTTTTTATTT
130270 ACCTTTGTGG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.16, C:0.05, G:0.07, T:0.73
Consensus pattern (17 bp):
AGTTTTTATTTTTTTAT
Found at i:131726 original size:21 final size:21
Alignment explanation
Indices: 131702--131741 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
131692 TCTAATACCC
*
131702 ATAAGTAGAAATTTAAAAAAA
1 ATAAGGAGAAATTTAAAAAAA
*
131723 ATAAGGATAAATTTAAAAA
1 ATAAGGAGAAATTTAAAAA
131742 GAGGTGTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.25
Consensus pattern (21 bp):
ATAAGGAGAAATTTAAAAAAA
Found at i:134194 original size:24 final size:24
Alignment explanation
Indices: 134167--134234 Score: 93
Period size: 24 Copynumber: 2.8 Consensus size: 24
134157 TTTATAAACA
*
134167 ATAAAAATTAA-ATTAATATAATAT
1 ATAAATATTAAGA-TAATATAATAT
*
134191 ATAAATATTAAGATATTATAATAT
1 ATAAATATTAAGATAATATAATAT
*
134215 ATAAATATTAAGATATTATA
1 ATAAATATTAAGATAATATA
134235 TTAACTGATA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
24 40 0.98
25 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (24 bp):
ATAAATATTAAGATAATATAATAT
Found at i:134878 original size:14 final size:15
Alignment explanation
Indices: 134861--134894 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
134851 AAACTAAAAG
134861 AAAAAAAT-ATATAA
1 AAAAAAATAATATAA
134875 AAAAAAATGAATATAA
1 AAAAAAAT-AATATAA
134891 AAAA
1 AAAA
134895 TTAAAGGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
16 10 0.56
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (15 bp):
AAAAAAATAATATAA
Found at i:144945 original size:32 final size:31
Alignment explanation
Indices: 144883--144941 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
144873 TATTAGATAG
**
144883 AAATAATTAATAGGTAATGCAAATGCAATAA
1 AAATAATTAATAGGTAATGCAAATAAAATAA
*
144914 AAATATTTAATATGGTAATGC-AATAAAA
1 AAATAATTAATA-GGTAATGCAAATAAAA
144942 ATAACTTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 16 0.67
32 8 0.33
ACGTcount: A:0.54, C:0.05, G:0.12, T:0.29
Consensus pattern (31 bp):
AAATAATTAATAGGTAATGCAAATAAAATAA
Found at i:157424 original size:22 final size:22
Alignment explanation
Indices: 157382--157424 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
157372 TTGTAAAAGT
*
157382 TAATTAATTAAAATATTTAAAA
1 TAATTAATTAAAATATATAAAA
*
157404 TAATTAAGTTCAAAT-TATAAA
1 TAATTAA-TTAAAATATATAAA
157425 TGCAATGCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (22 bp):
TAATTAATTAAAATATATAAAA
Found at i:160237 original size:324 final size:327
Alignment explanation
Indices: 159564--160249 Score: 936
Period size: 325 Copynumber: 2.1 Consensus size: 327
159554 TTTTCTCGTG
* * * * *
159564 AAATCAATTTTATTTCTAATTTTAATTTTATTTATTGTTTCGACATTGCTTTTTCTCTTTTATTT
1 AAATCAATTTTATTTCTAATTTTAACTTTCTTTATTATTTCGACATTGCTCTCTCTCTTTTATTT
* * * * *
159629 TTAATATTATTTTTTGGCCATTTTTTACCATTAATTTTGCAAGTATAGCAATTCCTTCTTTTCTA
66 TTAATATTATTTTTTGGACATATTTCACCATTAATTTTGCAAGTATAGCAATTCCTCCTTCTCTA
* * * *
159694 GGTTTATAGGCAAAGTAGGAAGGCAAACATCATTGTAGGAACCTATAATGGTCGAGTAGACACAG
131 GGTTTACAAGCAAAGTAGGAAGGCAAACATCATAGTAGGAACCTATAATGGTCGAGTAGACACAA
* * ** *
159759 AAGAATGATGTGACATTAGTATTTATAGCCCATCTTGACCACACAATATTCATCGTTGATGTTGG
196 AAGAATGATGTGACATTAGTATTGATAACCCATCTCCACCACACAATATTCATCGTTAATGTTGG
*
159824 TCTATTCTATAGACCTTACCTTCACAACTACTTGTTATTAGTATGTCGATTCACAATCCTTCTAG
261 TCTATTCTATAGACCTTACCTTCACAACTACTTGTTATTAGCATGTCGATTCACAATCCTTCTAG
*
159889 CG
326 CA
* * * *
159891 AAATCAATTTTATTTTTAATTTTAACTTTCTTTTTTATTTTGACGTTGCTCTCTCTCTTTTATTT
1 AAATCAATTTTATTTCTAATTTTAACTTTCTTTATTATTTCGACATTGCTCTCTCTCTTTTATTT
* * * *
159956 TTAATATTATTTTTT-GAC-TATTTCCCCCTTTATTTTGCAAGTATAGCAGTTCCTCCTTCTCTA
66 TTAATATTATTTTTTGGACATATTTCACCATTAATTTTGCAAGTATAGCAATTCCTCCTTCTCTA
* *
160019 GTTTTACAAGCAAAGTAGGAAGGCAAACATTATAGTAGGAACCTATAATGGTC-AGGTAGACACA
131 GGTTTACAAGCAAAGTAGGAAGGCAAACATCATAGTAGGAACCTATAATGGTCGA-GTAGACACA
* *
160083 AAAGAATGATGTGACATTATTATTGATAACCCATCTCCA-CACACAATATTCA-CTTTCAATGTT
195 AAAGAATGATGTGACATTAGTATTGATAACCCATCTCCACCACACAATATTCATCGTT-AATGTT
* * * * *
160146 GGTTTATTCTATAGGCCTTACCTTCATAAGTACTTGTTATTGGCATGTCGA-TCTACAATCCTTC
259 GGTCTATTCTATAGACCTTACCTTCACAACTACTTGTTATTAGCATGTCGATTC-ACAATCCTTC
160210 TA-CAA
323 TAGC-A
*
160215 AAATCAAATTTATTTCTAATTTTAACTTTCTTTAT
1 AAATCAATTTTATTTCTAATTTTAACTTTCTTTAT
160250 CGTTTTGCAT
Statistics
Matches: 314, Mismatches: 41, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
323 6 0.02
324 108 0.34
325 127 0.40
326 2 0.01
327 71 0.23
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (327 bp):
AAATCAATTTTATTTCTAATTTTAACTTTCTTTATTATTTCGACATTGCTCTCTCTCTTTTATTT
TTAATATTATTTTTTGGACATATTTCACCATTAATTTTGCAAGTATAGCAATTCCTCCTTCTCTA
GGTTTACAAGCAAAGTAGGAAGGCAAACATCATAGTAGGAACCTATAATGGTCGAGTAGACACAA
AAGAATGATGTGACATTAGTATTGATAACCCATCTCCACCACACAATATTCATCGTTAATGTTGG
TCTATTCTATAGACCTTACCTTCACAACTACTTGTTATTAGCATGTCGATTCACAATCCTTCTAG
CA
Found at i:165415 original size:3 final size:3
Alignment explanation
Indices: 165407--165431 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
165397 GGGTAAATGT
165407 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
165432 GACTTGTAGA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:166237 original size:3 final size:3
Alignment explanation
Indices: 166229--166257 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
166219 GCTGCATTTA
166229 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
166258 AAAGAAGCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:166729 original size:41 final size:41
Alignment explanation
Indices: 166635--166918 Score: 296
Period size: 41 Copynumber: 7.1 Consensus size: 41
166625 GTTTATGTCA
*
166635 AAGCGCCGCTAAAGGTCAGG-CATTAGCGACGC-TTCCCAT
1 AAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTTCCCAT
** * * *
166674 AAGCGATGCCAAAGGTCAGGTCATTAACGACGCTTTCCCAT
1 AAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTTCCCAT
* * * *
166715 AAGCGTCGCTAAAGGTCAGGTAATTAGTGGCGCTTCCCCAT
1 AAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTTCCCAT
* * * *
166756 AAACACCGTTAAAGGT----T-ATTAGCGGCGCTTTTCCAT
1 AAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTTCCCAT
** * *
166792 AAGCGTTGCTAAAGGTCAGGTCATTAGCGGTGCTTCCCCAT
1 AAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTTCCCAT
* * * *
166833 AAGCGCCGCTAAAGGCCAGGTCATTAGCGGCTCTTTCTCAA
1 AAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTTCCCAT
* *
166874 AAGCGCCGCTAAAGGTCAAG-AATTAGCGGCGCTTTCCCAT
1 AAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTTCCCAT
166914 AAGCG
1 AAGCG
166919 TCACTAATAC
Statistics
Matches: 197, Mismatches: 41, Indels: 13
0.78 0.16 0.05
Matches are distributed among these distances:
36 27 0.14
37 1 0.01
39 17 0.09
40 33 0.17
41 119 0.60
ACGTcount: A:0.26, C:0.26, G:0.25, T:0.23
Consensus pattern (41 bp):
AAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTTCCCAT
Found at i:166846 original size:77 final size:79
Alignment explanation
Indices: 166635--166918 Score: 254
Period size: 77 Copynumber: 3.6 Consensus size: 79
166625 GTTTATGTCA
* * ** *
166635 AAGCGCCGCTAAAGGTCAGG-CATTAGCGACGCTT-CCCATAAGCGATGCCAAAGGTCAGGTCAT
1 AAGCGTCGCTAAAGGTCAGGTCATTAGCGGCGCTTCCCCATAAGCGCCGCTAAAGGT---GTCAT
166698 TAACGACGCTTTCCCAT
63 TAACGACGCTTTCCCAT
* * * * * *
166715 AAGCGTCGCTAAAGGTCAGGTAATTAGTGGCGCTTCCCCATAAACACCGTTAAAGGT-T-ATTAG
1 AAGCGTCGCTAAAGGTCAGGTCATTAGCGGCGCTTCCCCATAAGCGCCGCTAAAGGTGTCATTAA
* *
166778 CGGCGCTTTTCCAT
66 CGACGCTTTCCCAT
* * *
166792 AAGCGTTGCTAAAGGTCAGGTCATTAGCGGTGCTTCCCCATAAGCGCCGCTAAAGGCCAGGTCAT
1 AAGCGTCGCTAAAGGTCAGGTCATTAGCGGCGCTTCCCCATAAGCGCCGCTAAAGG---TGTCAT
* * * * *
166857 TAGCGGCTCTTTCTCAA
63 TAACGACGCTTTCCCAT
* * * *
166874 AAGCGCCGCTAAAGGTCAAG-AATTAGCGGCGCTTTCCCATAAGCG
1 AAGCGTCGCTAAAGGTCAGGTCATTAGCGGCGCTTCCCCATAAGCG
166919 TCACTAATAC
Statistics
Matches: 166, Mismatches: 31, Indels: 13
0.79 0.15 0.06
Matches are distributed among these distances:
77 65 0.39
78 1 0.01
80 19 0.11
81 34 0.20
82 47 0.28
ACGTcount: A:0.26, C:0.26, G:0.25, T:0.23
Consensus pattern (79 bp):
AAGCGTCGCTAAAGGTCAGGTCATTAGCGGCGCTTCCCCATAAGCGCCGCTAAAGGTGTCATTAA
CGACGCTTTCCCAT
Found at i:166887 original size:118 final size:119
Alignment explanation
Indices: 166656--166919 Score: 309
Period size: 118 Copynumber: 2.2 Consensus size: 119
166646 AAGGTCAGGC
* * *
166656 ATTAGCGACGC-TTCCCATAAGCGATGCCAAAGGTCAGGTCATTAACGACGCTTTCCCATAAGCG
1 ATTAGCGGCGCTTTCCCATAAGCGTTGCCAAAGGTCAGGTCATTAACGACGCTTCCCCATAAGCG
* * * * *
166720 TCGCTAAAGGTCAGGTAATTAGTGGCGCTTCCCCATAAACACCGTTAAAGGT-T
66 CCGCTAAAGGCCAGGTAATTAGCGGCGCTTCCCCATAAACACCGCTAAAGGTAA
* * * **
166773 ATTAGCGGCGCTTTTCCATAAGCGTTGCTAAAGGTCAGGTCATTAGCGGTGCTTCCCCATAAGCG
1 ATTAGCGGCGCTTTCCCATAAGCGTTGCCAAAGGTCAGGTCATTAACGACGCTTCCCCATAAGCG
* * * * *
166838 CCGCTAAAGGCCAGGTCATTAGCGGCTCTTTCTCA-AAAGCGCCGCTAAAGGTCAAGA
66 CCGCTAAAGGCCAGGTAATTAGCGGCGCTTCCCCATAAA-CACCGCTAAAGGT--A-A
166895 ATTAGCGGCGCTTTCCCATAAGCGT
1 ATTAGCGGCGCTTTCCCATAAGCGT
166920 CACTAATACA
Statistics
Matches: 122, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
117 13 0.11
118 85 0.70
122 24 0.20
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (119 bp):
ATTAGCGGCGCTTTCCCATAAGCGTTGCCAAAGGTCAGGTCATTAACGACGCTTCCCCATAAGCG
CCGCTAAAGGCCAGGTAATTAGCGGCGCTTCCCCATAAACACCGCTAAAGGTAA
Found at i:167587 original size:19 final size:20
Alignment explanation
Indices: 167559--167599 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
167549 TAAATTTTAT
*
167559 AATATAATTTT-ATTTATTA
1 AATATAATTTTCATTTAATA
*
167578 AATATTATTTTCATTTAATA
1 AATATAATTTTCATTTAATA
167598 AA
1 AA
167600 ATATCATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
AATATAATTTTCATTTAATA
Found at i:168629 original size:10 final size:10
Alignment explanation
Indices: 168616--168663 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
168606 GTTTTATATT
168616 TTTTAATCTG
1 TTTTAATCTG
*
168626 TTTTAATTTG
1 TTTTAATCTG
168636 TTTTATAT-T-
1 TTTTA-ATCTG
168645 TTTTAATCTG
1 TTTTAATCTG
168655 TTTTTAATC
1 -TTTTAATC
168664 CAGCTTGTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
8 2 0.06
9 6 0.18
10 15 0.45
11 10 0.30
ACGTcount: A:0.21, C:0.06, G:0.06, T:0.67
Consensus pattern (10 bp):
TTTTAATCTG
Found at i:168629 original size:29 final size:29
Alignment explanation
Indices: 168597--168658 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
168587 TGAAGCTTGT
168597 TTTTAATTCGTTTTATATTTTTTAATCTG
1 TTTTAATTCGTTTTATATTTTTTAATCTG
*
168626 TTTTAATTTGTTTTATATTTTTTAATCTG
1 TTTTAATTCGTTTTATATTTTTTAATCTG
168655 TTTT
1 TTTT
168659 TAATCCAGCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.19, C:0.05, G:0.06, T:0.69
Consensus pattern (29 bp):
TTTTAATTCGTTTTATATTTTTTAATCTG
Found at i:168634 original size:18 final size:19
Alignment explanation
Indices: 168596--168634 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
168586 ATGAAGCTTG
168596 TTTTTAATTCGTTTTATAT
1 TTTTTAATTCGTTTTATAT
168615 TTTTTAA-TCTGTTTTA-AT
1 TTTTTAATTC-GTTTTATAT
168633 TT
1 TT
168635 GTTTTATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.69
Consensus pattern (19 bp):
TTTTTAATTCGTTTTATAT
Found at i:173166 original size:43 final size:43
Alignment explanation
Indices: 173101--173225 Score: 178
Period size: 43 Copynumber: 2.9 Consensus size: 43
173091 AGACCATGGT
* * * *
173101 GTTTGAGGTAAAAGCGCTGCTAAAGATCATATTTTTTAGCGGC
1 GTTTGGGGTAGAAGCGCCGCTAAAGATCATATTCTTTAGCGGC
*
173144 GTTTGGGGTAGAAGCGCCGCTAAAGATCATGTTCTTTAGCGGC
1 GTTTGGGGTAGAAGCGCCGCTAAAGATCATATTCTTTAGCGGC
* * *
173187 GTTTGGGGTAGAAGCGCCGCTAAAAACCATGTTCTTTAG
1 GTTTGGGGTAGAAGCGCCGCTAAAGATCATATTCTTTAG
173226 TGGTGTTTTT
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 75 1.00
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.30
Consensus pattern (43 bp):
GTTTGGGGTAGAAGCGCCGCTAAAGATCATATTCTTTAGCGGC
Found at i:175178 original size:2 final size:2
Alignment explanation
Indices: 175171--175198 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
175161 TCAATGTTTA
175171 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
175199 TAAAATTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:181732 original size:17 final size:19
Alignment explanation
Indices: 181697--181735 Score: 64
Period size: 17 Copynumber: 2.2 Consensus size: 19
181687 AAGTAAATTG
181697 TATTATTTTGATAATATTT
1 TATTATTTTGATAATATTT
181716 TATTA-TTTGAT-ATATTT
1 TATTATTTTGATAATATTT
181733 TAT
1 TAT
181736 GTAAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 9 0.45
18 6 0.30
19 5 0.25
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (19 bp):
TATTATTTTGATAATATTT
Found at i:187004 original size:51 final size:51
Alignment explanation
Indices: 186923--187114 Score: 278
Period size: 51 Copynumber: 3.8 Consensus size: 51
186913 TCGTATAGGA
* * * * *
186923 ATTCATATACTCACGATGACACTGAATCATCGGACCTTTAATTCGTCATGG
1 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAATGG
* *
186974 ATTCATTTACTCACGATGACACTTAGTCATCAGACCTTTAATCCGTAAAGG
1 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAATGG
*
187025 ATTCA-TTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAGGG
1 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAATGG
* *
187075 ATTCAATTACTCACGATGACACTTAGTTATCGGACTCTTT
1 ATTCATTTACTCACGATGACACTTAGTCATCGGAC-CTTT
187115 CGTTTATAGC
Statistics
Matches: 129, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
50 48 0.37
51 77 0.60
52 4 0.03
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.32
Consensus pattern (51 bp):
ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAATGG
Found at i:187053 original size:50 final size:50
Alignment explanation
Indices: 186874--187114 Score: 277
Period size: 51 Copynumber: 4.6 Consensus size: 50
186864 TTTCATTTAA
** * *
186874 TACTCACGATGACA-TATAGTCATCGGACCCCTTTTTGTTTCGTATAGGAATTCAT
1 TACTCACGATGACACT-TAGTCATCGGA--CC--TTTAATCCGTAAAGG-ATTCAT
* * * * *
186929 ATACTCACGATGACACTGAATCATCGGACCTTTAATTCGTCATGGATTCATT
1 -TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCA-T
*
186981 TACTCACGATGACACTTAGTCATCAGACCTTTAATCCGTAAAGGATTCAT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCAT
*
187031 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAGGGATTCAAT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTC-AT
*
187082 TACTCACGATGACACTTAGTTATCGGACTCTTT
1 TACTCACGATGACACTTAGTCATCGGAC-CTTT
187115 CGTTTATAGC
Statistics
Matches: 165, Mismatches: 16, Indels: 12
0.85 0.08 0.06
Matches are distributed among these distances:
50 47 0.28
51 77 0.47
52 15 0.09
54 2 0.01
56 23 0.14
57 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (50 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCAT
Found at i:187055 original size:101 final size:103
Alignment explanation
Indices: 186914--187101 Score: 299
Period size: 101 Copynumber: 1.8 Consensus size: 103
186904 CTTTTTGTTT
* * * *
186914 CGTATAGGAATTCATATACTCACGATGACACTGAATCATCGGACCTTTAATTCGTCATGGATTCA
1 CGTAAAGGAATTCATATACTCACGATGACACTGAATCATCGGACCTTTAATCCGTAAGGGATTCA
*
186979 TTTACTCACGATGACACTTAGTCATCAGACCTTTAATC
66 ATTACTCACGATGACACTTAGTCATCAGACCTTTAATC
* *
187017 CGTAAAGG-ATTCAT-TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAGGGATTCA
1 CGTAAAGGAATTCATATACTCACGATGACACTGAATCATCGGACCTTTAATCCGTAAGGGATTCA
187080 ATTACTCACGATGACACTTAGT
66 ATTACTCACGATGACACTTAGT
187102 TATCGGACTC
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 65 0.83
102 6 0.08
103 7 0.09
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (103 bp):
CGTAAAGGAATTCATATACTCACGATGACACTGAATCATCGGACCTTTAATCCGTAAGGGATTCA
ATTACTCACGATGACACTTAGTCATCAGACCTTTAATC
Found at i:188019 original size:17 final size:17
Alignment explanation
Indices: 187997--188030 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
187987 CACAAAACAT
187997 GCAAAATAACCATTCTC
1 GCAAAATAACCATTCTC
188014 GCAAAATAACCATTCTC
1 GCAAAATAACCATTCTC
188031 ACACACAACT
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:0.41, C:0.29, G:0.06, T:0.24
Consensus pattern (17 bp):
GCAAAATAACCATTCTC
Found at i:189001 original size:40 final size:40
Alignment explanation
Indices: 188946--189027 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
188936 AATTTAAGCA
188946 TGCACATTTCATAAAATAAACACTTCAACTTATTTTATAT
1 TGCACATTTCATAAAATAAACACTTCAACTTATTTTATAT
188986 TGCACATTTCATAAAATAAACACTTCAACTTATTTTATAT
1 TGCACATTTCATAAAATAAACACTTCAACTTATTTTATAT
189026 TG
1 TG
189028 GATAAATTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.39, C:0.17, G:0.04, T:0.40
Consensus pattern (40 bp):
TGCACATTTCATAAAATAAACACTTCAACTTATTTTATAT
Found at i:189154 original size:29 final size:30
Alignment explanation
Indices: 189113--189171 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
189103 GAATTGGATC
189113 AAATCAAAATTTCATGTATAAAATTGCACA
1 AAATCAAAATTTCATGTATAAAATTGCACA
**
189143 AAATC-AAATTTCATGTATACGATTGCACA
1 AAATCAAAATTTCATGTATAAAATTGCACA
189172 TTAAACCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (30 bp):
AAATCAAAATTTCATGTATAAAATTGCACA
Found at i:192028 original size:5 final size:5
Alignment explanation
Indices: 191985--192027 Score: 68
Period size: 5 Copynumber: 8.6 Consensus size: 5
191975 TTTGGTTATT
* *
191985 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTTA TTTTA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTT
192028 TGTTAGTAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (5 bp):
TTTAA
Found at i:198912 original size:21 final size:21
Alignment explanation
Indices: 198888--198927 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
198878 TACTTATTAG
198888 TACTAACAAAATAAAATTACT
1 TACTAACAAAATAAAATTACT
*
198909 TACTAACAAAATTAAATTA
1 TACTAACAAAATAAAATTA
198928 AATTAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.30
Consensus pattern (21 bp):
TACTAACAAAATAAAATTACT
Found at i:199301 original size:14 final size:13
Alignment explanation
Indices: 199276--199319 Score: 61
Period size: 13 Copynumber: 3.2 Consensus size: 13
199266 CTCTCCTTAT
199276 TTTTTTTCTCTTTC
1 TTTTTTT-TCTTTC
199290 TTCTTTTTTCTTTC
1 TT-TTTTTTCTTTC
*
199304 TTTTTTTCCTTTC
1 TTTTTTTTCTTTC
199317 TTT
1 TTT
199320 CTTCTTGGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 13 0.46
14 10 0.36
15 5 0.18
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTTTTCTTTC
Found at i:199730 original size:24 final size:24
Alignment explanation
Indices: 199698--199745 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
199688 ATGCTATTTG
199698 GGTAATTAATTATATGGGGGTGTT
1 GGTAATTAATTATATGGGGGTGTT
199722 GGTAATTAATTATATGGGGGTGTT
1 GGTAATTAATTATATGGGGGTGTT
199746 ATTTTGGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.33, T:0.42
Consensus pattern (24 bp):
GGTAATTAATTATATGGGGGTGTT
Found at i:209283 original size:27 final size:27
Alignment explanation
Indices: 209253--209307 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
209243 TGCCGCTTTC
*
209253 CAGATGGGTACCATAGGTGCTACCTAT
1 CAGATGGGCACCATAGGTGCTACCTAT
* * *
209280 CAGATGGGCACCATTGGTGTTCCCTAT
1 CAGATGGGCACCATAGGTGCTACCTAT
209307 C
1 C
209308 TGACAGGCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.27
Consensus pattern (27 bp):
CAGATGGGCACCATAGGTGCTACCTAT
Found at i:211627 original size:17 final size:17
Alignment explanation
Indices: 211586--211633 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 17
211576 AGAAAACATG
*
211586 ATAAAAAGAAAAATGAA
1 ATAAAAAAAAAAATGAA
*
211603 ATAGAAAAAAAAAATTAA
1 ATA-AAAAAAAAAATGAA
*
211621 TTAAAAAAAAAAA
1 ATAAAAAAAAAAA
211634 AAGCCCACTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (17 bp):
ATAAAAAAAAAAATGAA
Found at i:212342 original size:34 final size:33
Alignment explanation
Indices: 212288--212351 Score: 110
Period size: 34 Copynumber: 1.9 Consensus size: 33
212278 AAAAATTATA
212288 TTTAATACAATAAATATTTATTATATTTATTTT
1 TTTAATACAATAAATATTTATTATATTTATTTT
*
212321 TTTAATATAATAAAATATTTATTATATTTAT
1 TTTAATACAAT-AAATATTTATTATATTTAT
212352 GGTTATCTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 10 0.34
34 19 0.66
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (33 bp):
TTTAATACAATAAATATTTATTATATTTATTTT
Found at i:212459 original size:16 final size:16
Alignment explanation
Indices: 212438--212471 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
212428 TAGCGTATTA
212438 TATTTTAAAAAAAAAT
1 TATTTTAAAAAAAAAT
*
212454 TATTTTAAATAAAAAT
1 TATTTTAAAAAAAAAT
212470 TA
1 TA
212472 ATATACAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TATTTTAAAAAAAAAT
Found at i:215786 original size:100 final size:99
Alignment explanation
Indices: 215605--215797 Score: 266
Period size: 100 Copynumber: 1.9 Consensus size: 99
215595 AATGCACCTG
* * * * *
215605 CATATTTCGTGTAAAAATTTGCGATTCCAGAAAGAGAAAAAAGATACATTTTTATCCAAAAGAAT
1 CATATTTCGTGTAAAAATTTGCAATTCCAAAAAGACAAAAAAGACACATTTTTACCCAAAAGAAT
**
215670 AGGTTAGAGAAAGCAGTGTCAAATATATATAGGT
66 ACATTAGAGAAAGCAGTGTCAAATATATATAGGT
215704 CATATTTTC-TGTAAAAATTT-CAATTCCAAAAAGACCCAAAAAA-ACACATTTTTGACCCAAAA
1 CATA-TTTCGTGTAAAAATTTGCAATTCCAAAAAGA--CAAAAAAGACACATTTTT-ACCCAAAA
215766 GAATACATTAGAGAAAGCAGTGTCAAATATAT
62 GAATACATTAGAGAAAGCAGTGTCAAATATAT
215798 TAGAGGGATA
Statistics
Matches: 83, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
98 12 0.14
99 24 0.29
100 47 0.57
ACGTcount: A:0.45, C:0.13, G:0.14, T:0.27
Consensus pattern (99 bp):
CATATTTCGTGTAAAAATTTGCAATTCCAAAAAGACAAAAAAGACACATTTTTACCCAAAAGAAT
ACATTAGAGAAAGCAGTGTCAAATATATATAGGT
Found at i:218530 original size:6 final size:6
Alignment explanation
Indices: 218519--218553 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
218509 CTTTTCTTGG
* *
218519 TCCCTA TCCCTA TCCTTA TCTCTA TCCCTA TCCCT
1 TCCCTA TCCCTA TCCCTA TCCCTA TCCCTA TCCCT
218554 GTGGTGATCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.14, C:0.46, G:0.00, T:0.40
Consensus pattern (6 bp):
TCCCTA
Found at i:220942 original size:22 final size:22
Alignment explanation
Indices: 220916--220957 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
220906 TTTAGTAAAA
*
220916 AAGGAAAAATTTAGGTTTTCTC
1 AAGGAAAAACTTAGGTTTTCTC
*
220938 AAGGAAAAACTTGGGTTTTC
1 AAGGAAAAACTTAGGTTTTC
220958 ACGAAGAACT
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:0.36, C:0.10, G:0.21, T:0.33
Consensus pattern (22 bp):
AAGGAAAAACTTAGGTTTTCTC
Found at i:221514 original size:3 final size:3
Alignment explanation
Indices: 221506--221530 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
221496 TACGAATGTG
221506 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
221531 CATAATAAAT
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:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:222518 original size:29 final size:30
Alignment explanation
Indices: 222473--222546 Score: 123
Period size: 30 Copynumber: 2.5 Consensus size: 30
222463 ATATTAAGTC
* *
222473 TACTATAAAATAACTTTTCAC-CAAAAAAA
1 TACTATAAAATACCTTTTCACAAAAAAAAA
222502 TACTATAAAATACCTTTTCACAAAAAAAAA
1 TACTATAAAATACCTTTTCACAAAAAAAAA
222532 TACTATAAAATACCT
1 TACTATAAAATACCT
222547 AACTATATCT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
29 20 0.48
30 22 0.52
ACGTcount: A:0.54, C:0.18, G:0.00, T:0.28
Consensus pattern (30 bp):
TACTATAAAATACCTTTTCACAAAAAAAAA
Found at i:222886 original size:18 final size:18
Alignment explanation
Indices: 222813--222888 Score: 62
Period size: 18 Copynumber: 4.1 Consensus size: 18
222803 TCCCTCAACA
* **
222813 AAAAATTAAAAAATTTCC
1 AAAAATTCAAAAATTTAT
*
222831 AAAATATTCAAACTAATTTTT
1 AAAA-ATTCAAA--AATTTAT
* **
222852 AAAAATCCAAATGTTTAT
1 AAAAATTCAAAAATTTAT
222870 AAAAATTCAAAAATTTAT
1 AAAAATTCAAAAATTTAT
222888 A
1 A
222889 TTTTTAAAAA
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
18 24 0.53
19 6 0.13
20 6 0.13
21 9 0.20
ACGTcount: A:0.55, C:0.09, G:0.01, T:0.34
Consensus pattern (18 bp):
AAAAATTCAAAAATTTAT
Done.