Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 36 of 150
Found at i:9697947 original size:13 final size:14
Alignment explanation
Indices: 9697915--9697951 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
9697905 GCCATACAAT
9697915 TTATGATATATGTA
1 TTATGATATATGTA
9697929 TGTATGATATATG-A
1 T-TATGATATATGTA
9697943 TTATGATAT
1 TTATGATAT
9697952 GCTTGTGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 8 0.36
14 3 0.14
15 11 0.50
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
TTATGATATATGTA
Found at i:9698219 original size:25 final size:25
Alignment explanation
Indices: 9698177--9698224 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
9698167 GGTAGGACAT
* *
9698177 GATATGACATGTTTTGTTATGATTC
1 GATATGACATGATATGTTATGATTC
*
9698202 GATATGATATGATATGTTATGAT
1 GATATGACATGATATGTTATGAT
9698225 ACATTATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.29, C:0.04, G:0.21, T:0.46
Consensus pattern (25 bp):
GATATGACATGATATGTTATGATTC
Found at i:9698225 original size:20 final size:20
Alignment explanation
Indices: 9698202--9698249 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
9698192 GTTATGATTC
* *
9698202 GATATGATATGATATGTTAT
1 GATATGATATAATATGTTAA
*
9698222 GATA-CATTATAATATGTTAA
1 GATATGA-TATAATATGTTAA
9698242 GATATGAT
1 GATATGAT
9698250 CTATATGGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
19 1 0.05
20 20 0.91
21 1 0.05
ACGTcount: A:0.40, C:0.02, G:0.17, T:0.42
Consensus pattern (20 bp):
GATATGATATAATATGTTAA
Found at i:9699911 original size:18 final size:18
Alignment explanation
Indices: 9699890--9699924 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9699880 TGCATTTGTA
* *
9699890 TCTGAATTTGATTATGCG
1 TCTGAATCTGAATATGCG
9699908 TCTGAATCTGAATATGC
1 TCTGAATCTGAATATGC
9699925 ATATGTATCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.40
Consensus pattern (18 bp):
TCTGAATCTGAATATGCG
Found at i:9703872 original size:18 final size:17
Alignment explanation
Indices: 9703849--9703904 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 17
9703839 CGTTTGCATT
9703849 TGTATCTGACTCTGATTA
1 TGTATCTGA-TCTGATTA
* *
9703867 TGTATCTGAATCTAAATA
1 TGTATCTG-ATCTGATTA
*
9703885 TGCATCTGTATCTGATTA
1 TGTATCTG-ATCTGATTA
9703903 TG
1 TG
9703905 AAATACATCT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
18 30 0.97
19 1 0.03
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (17 bp):
TGTATCTGATCTGATTA
Found at i:9707196 original size:41 final size:41
Alignment explanation
Indices: 9707139--9707331 Score: 151
Period size: 41 Copynumber: 4.7 Consensus size: 41
9707129 AATATAACTT
* *
9707139 ACCTGATACAATACATCGACACAAAGACTGCTAGGCTCAAG
1 ACCTGATACAATACATCGACACAAAGCCTGCTAGGCTCAAA
* * * *
9707180 ACCTGATACAACACATCGGCACGAAA-CCTGCTAGACACAAA
1 ACCTGATACAATACATCGACAC-AAAGCCTGCTAGGCTCAAA
* * *
9707221 ACCTGATATAATACA-CCAGCACGAAGCCTGCTAGGCTCAAA
1 ACCTGATACAATACATCGA-CACAAAGCCTGCTAGGCTCAAA
* ** * * * *
9707262 GCCT-ATTACGGTACACCGGCACGAAGCCTGCTAGGCACAAA
1 ACCTGA-TACAATACATCGACACAAAGCCTGCTAGGCTCAAA
* * *
9707303 GCCAGATATAATACA-CTGACACAAAGCCT
1 ACCTGATACAATACATC-GACACAAAGCCT
9707332 ACTAAGCAAA
Statistics
Matches: 119, Mismatches: 26, Indels: 14
0.75 0.16 0.09
Matches are distributed among these distances:
40 5 0.04
41 109 0.92
42 5 0.04
ACGTcount: A:0.37, C:0.30, G:0.18, T:0.16
Consensus pattern (41 bp):
ACCTGATACAATACATCGACACAAAGCCTGCTAGGCTCAAA
Found at i:9707330 original size:82 final size:82
Alignment explanation
Indices: 9707143--9707331 Score: 206
Period size: 82 Copynumber: 2.3 Consensus size: 82
9707133 TAACTTACCT
* * *
9707143 GATACAATACA-TCGACACAAAGACTGCTAGGCTCAAGACCTGATACAACACATCGGCACGAAAC
1 GATATAATACACT-GACACAAAGCCTGCTAGGCTCAAGACCTGATACAACACACCGGCACGAAAC
*
9707207 CTGCTAGACACAAAACCT
65 CTGCTAGACACAAAACCA
* * ***
9707225 GATATAATACAC-CAGCACGAAGCCTGCTAGGCTCAA-AGCCT-ATTACGGTACACCGGCACGAA
1 GATATAATACACTGA-CACAAAGCCTGCTAGGCTCAAGA-CCTGA-TACAACACACCGGCACGAA
* * *
9707287 GCCTGCTAGGCACAAAGCCA
63 ACCTGCTAGACACAAAACCA
9707307 GATATAATACACTGACACAAAGCCT
1 GATATAATACACTGACACAAAGCCT
9707332 ACTAAGCAAA
Statistics
Matches: 88, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
81 3 0.03
82 84 0.95
83 1 0.01
ACGTcount: A:0.38, C:0.29, G:0.18, T:0.15
Consensus pattern (82 bp):
GATATAATACACTGACACAAAGCCTGCTAGGCTCAAGACCTGATACAACACACCGGCACGAAACC
TGCTAGACACAAAACCA
Found at i:9707345 original size:82 final size:81
Alignment explanation
Indices: 9707196--9707374 Score: 198
Period size: 82 Copynumber: 2.2 Consensus size: 81
9707186 TACAACACAT
* * * * * **
9707196 CGGCACGAAACCTGCTAGACACAAAACCTGATATAATACACCAGCACGAAGCCTGCTAGGCTCAA
1 CGGCACGAAGCCTGCTAGACACAAAACCAGATATAATACACCAGCACAAAGCCTACTAAGCAAAA
* * *
9707261 AGCCTATTACGGTACA
66 AGCCTAATAAGATACA
* * *
9707277 CCGGCACGAAGCCTGCTAGGCACAAAGCCAGATATAATACA-CTGACACAAAGCCTACTAAGCAA
1 -CGGCACGAAGCCTGCTAGACACAAAACCAGATATAATACACCAG-CACAAAGCCTACTAAGCAA
*
9707341 AAAGCCTAATAATATACA
64 AAAGCCTAATAAGATACA
*
9707359 CTGCACGAAGCCTGCT
1 CGGCACGAAGCCTGCT
9707375 GGATTCAAGG
Statistics
Matches: 81, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 17 0.21
82 64 0.79
ACGTcount: A:0.37, C:0.29, G:0.18, T:0.16
Consensus pattern (81 bp):
CGGCACGAAGCCTGCTAGACACAAAACCAGATATAATACACCAGCACAAAGCCTACTAAGCAAAA
AGCCTAATAAGATACA
Found at i:9713305 original size:2 final size:2
Alignment explanation
Indices: 9713298--9713330 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
9713288 AGTAAAAGAA
*
9713298 AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9713331 CATGTATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9713928 original size:7 final size:7
Alignment explanation
Indices: 9713913--9713945 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
9713903 ACTTATATTC
9713913 AAAAA-A
1 AAAAAGA
9713919 AAAAAGA
1 AAAAAGA
9713926 AAAAAGA
1 AAAAAGA
9713933 AAAAACGA
1 AAAAA-GA
9713941 AAAAA
1 AAAAA
9713946 AGATGGGACT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 5 0.20
7 13 0.52
8 7 0.28
ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:9723736 original size:22 final size:23
Alignment explanation
Indices: 9723710--9723754 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
9723700 CATGATAGTG
*
9723710 GTATCATGACACCC-TTACAATA
1 GTATCATGACACCCATGACAATA
* *
9723732 GTATCGTGAGACCCATGACAATA
1 GTATCATGACACCCATGACAATA
9723755 TGGAATTAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (23 bp):
GTATCATGACACCCATGACAATA
Found at i:9734273 original size:3 final size:3
Alignment explanation
Indices: 9734265--9734289 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
9734255 GCTACTCAAC
9734265 CTA CTA CTA CTA CTA CTA CTA CTA C
1 CTA CTA CTA CTA CTA CTA CTA CTA C
9734290 AGTGGAGTGC
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:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CTA
Found at i:9764997 original size:20 final size:21
Alignment explanation
Indices: 9764974--9765012 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
9764964 TTATGATGTT
9764974 ATAAAATGTTTA-ATGTGATA
1 ATAAAATGTTTATATGTGATA
**
9764994 ATAATGTGTTTATATGTGA
1 ATAAAATGTTTATATGTGA
9765013 GCAAACTACT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (21 bp):
ATAAAATGTTTATATGTGATA
Found at i:9776290 original size:19 final size:20
Alignment explanation
Indices: 9776258--9776295 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
9776248 AATGATAATA
*
9776258 AAAGAATAAG-AAAATAAAG
1 AAAGAAGAAGAAAAATAAAG
*
9776277 AAAGAAGAATAAAAATAAA
1 AAAGAAGAAGAAAAATAAA
9776296 CAAGAAATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.11
Consensus pattern (20 bp):
AAAGAAGAAGAAAAATAAAG
Found at i:9779841 original size:41 final size:41
Alignment explanation
Indices: 9779633--9779841 Score: 310
Period size: 41 Copynumber: 5.1 Consensus size: 41
9779623 AAGTGTAACC
*
9779633 GGGGCACGTAAGTGCAATTCAGGGGTACCGAAGTACAAATA
1 GGGGCACGTAAGTGCAATTCAGGGGTACCAAAGTACAAATA
* * * ** *
9779674 AGGGCATGTAAGTGCAATTTAGCAGTACCAAAGTACAAACA
1 GGGGCACGTAAGTGCAATTCAGGGGTACCAAAGTACAAATA
*
9779715 GGGACACGTAAGTGCAATTCAGGGGTACCAAAGTACAAATA
1 GGGGCACGTAAGTGCAATTCAGGGGTACCAAAGTACAAATA
* *
9779756 GGGGCACATAAATGCAATTCAGGGGTACCAAAGTACAAATA
1 GGGGCACGTAAGTGCAATTCAGGGGTACCAAAGTACAAATA
* *
9779797 GGGGCACGTAAGTGCAATTCAGGGGTACCGAAGTACAAACA
1 GGGGCACGTAAGTGCAATTCAGGGGTACCAAAGTACAAATA
9779838 GGGG
1 GGGG
9779842 ATAATTAACA
Statistics
Matches: 147, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 147 1.00
ACGTcount: A:0.37, C:0.17, G:0.29, T:0.17
Consensus pattern (41 bp):
GGGGCACGTAAGTGCAATTCAGGGGTACCAAAGTACAAATA
Found at i:9793923 original size:32 final size:32
Alignment explanation
Indices: 9793878--9793946 Score: 113
Period size: 32 Copynumber: 2.2 Consensus size: 32
9793868 TGTCCCTGCT
*
9793878 TTGT-AAGGATGTTGAGTATTGGGGTTCATAC
1 TTGTCAAGGATGTTGAGAATTGGGGTTCATAC
*
9793909 TTGTCAAGGATGTTGAGAATTGGGGTTCATAT
1 TTGTCAAGGATGTTGAGAATTGGGGTTCATAC
9793941 TTGTCA
1 TTGTCA
9793947 CTCATTATGT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
31 4 0.11
32 31 0.89
ACGTcount: A:0.23, C:0.07, G:0.30, T:0.39
Consensus pattern (32 bp):
TTGTCAAGGATGTTGAGAATTGGGGTTCATAC
Found at i:9797932 original size:22 final size:22
Alignment explanation
Indices: 9797907--9797952 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
9797897 TCTGCTATTG
9797907 TTTGTTGTTGTTTTGCTGCCAT
1 TTTGTTGTTGTTTTGCTGCCAT
*
9797929 TTTGTTGTTGTTTTGCTGTCAT
1 TTTGTTGTTGTTTTGCTGCCAT
9797951 TT
1 TT
9797953 CACTATTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.04, C:0.11, G:0.22, T:0.63
Consensus pattern (22 bp):
TTTGTTGTTGTTTTGCTGCCAT
Found at i:9799379 original size:19 final size:19
Alignment explanation
Indices: 9799352--9799390 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
9799342 TATTATATGT
*
9799352 TATTTTAAAAATGTACTTG
1 TATTCTAAAAATGTACTTG
* *
9799371 TATTCTAAATATGTAGTTG
1 TATTCTAAAAATGTACTTG
9799390 T
1 T
9799391 CATTGATAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.33, C:0.05, G:0.13, T:0.49
Consensus pattern (19 bp):
TATTCTAAAAATGTACTTG
Found at i:9799533 original size:6 final size:7
Alignment explanation
Indices: 9799518--9799542 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
9799508 ATTTCTTTTA
9799518 TTTTCTT
1 TTTTCTT
9799525 TTTTCTT
1 TTTTCTT
9799532 TTTTCTT
1 TTTTCTT
9799539 TTTT
1 TTTT
9799543 ATCATTTTAA
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):
TTTTCTT
Found at i:9803325 original size:138 final size:138
Alignment explanation
Indices: 9803050--9803603 Score: 871
Period size: 138 Copynumber: 4.0 Consensus size: 138
9803040 ACATAGATAA
9803050 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATA
* * * *
9803115 -AAA-AATTATATTAATTAATTTTGGTCAAAATATAAAAGACAT-AGAAACTAATATTATTTCGG
66 TAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGA-AAATTAATATTCTTTTGG
*
9803177 AATGAATAT
130 AAAGAATAT
* *
9803186 AATTAATATATGAATTTGATTCATACAAAATATTAGTTGTATATATTTTACCAAATTTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATA
* *
9803251 TAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTTGA
66 TAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGA
9803316 AAGAATAT
131 AAGAATAT
* *
9803324 AATTAATATATGAATTTGATTCATACAAAATATCAATTGTATATATTTTACCGAATTTGTTAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATA
* * * *
9803389 TAAATAGTTATATAAAATAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGA
66 TAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGA
9803454 AAGAATAT
131 AAGAATAT
* *
9803462 AATTAATATATGAATTTGGTCCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATA
* * * * * *
9803527 TAAACAGTTATATTAATAAATTTCGATCAAAATAAAAAAGATATGAAAATTAATATTCTTTTAGA
66 TAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGA
9803592 AAGAATAT
131 AAGAATAT
9803600 AATT
1 AATT
9803604 CATTTTTCTA
Statistics
Matches: 384, Mismatches: 31, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
136 63 0.16
137 3 0.01
138 318 0.83
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.39
Consensus pattern (138 bp):
AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATA
TAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGA
AAGAATAT
Found at i:9803706 original size:75 final size:75
Alignment explanation
Indices: 9803579--9803725 Score: 235
Period size: 75 Copynumber: 2.0 Consensus size: 75
9803569 ATGAAAATTA
*
9803579 ATATTCTTTTAGAAAGAATATAATTCATTTTTCTAACTTTCCTTTTGTCTTCTCTATTAAT-AAG
1 ATATTCTTTTAGAAAGAATATAATTCATTTTTCTAACTTTCCTTTTGCCTTCTCTATTAATAAAG
9803643 GAAATAATGCT
66 G-AATAATGCT
* *
9803654 ATATTCTTTTGGAAAGAATATAATTCCTTTTTCTAACTTTCCATTTT-CCTTCTCTATTAATAAA
1 ATATTCTTTTAGAAAGAATATAATTCATTTTTCTAACTTTCC-TTTTGCCTTCTCTATTAATAAA
9803718 GGAATAAT
65 GGAATAAT
9803726 CCTGGTTTTC
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
75 59 0.88
76 8 0.12
ACGTcount: A:0.32, C:0.14, G:0.07, T:0.46
Consensus pattern (75 bp):
ATATTCTTTTAGAAAGAATATAATTCATTTTTCTAACTTTCCTTTTGCCTTCTCTATTAATAAAG
GAATAATGCT
Found at i:9804298 original size:17 final size:17
Alignment explanation
Indices: 9804276--9804308 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
9804266 ATGAATGAAA
9804276 AAATGTTAG-GGCAATTG
1 AAATGTT-GTGGCAATTG
9804293 AAATGTTGTGGCAATT
1 AAATGTTGTGGCAATT
9804309 CTCAAAGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.07
17 14 0.93
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.33
Consensus pattern (17 bp):
AAATGTTGTGGCAATTG
Found at i:9807315 original size:30 final size:30
Alignment explanation
Indices: 9807281--9807379 Score: 85
Period size: 30 Copynumber: 3.3 Consensus size: 30
9807271 TCGATCTATC
*
9807281 AAAAGGGATAGCT-TCGACTATCAAATTATG
1 AAAAGGGAT-GCTAACGACTATCAAATTATG
* * * * *
9807311 AAAAGAGATGGTGACGAC-ACTCGAATAATG
1 AAAAGGGATGCTAACGACTA-TCAAATTATG
* * *
9807341 TAAAGGGATGGTAACGACCATCAAATTATG
1 AAAAGGGATGCTAACGACTATCAAATTATG
9807371 AAAAGGGAT
1 AAAAGGGAT
9807380 AACTTTGGTT
Statistics
Matches: 55, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
29 3 0.05
30 51 0.93
31 1 0.02
ACGTcount: A:0.42, C:0.12, G:0.24, T:0.21
Consensus pattern (30 bp):
AAAAGGGATGCTAACGACTATCAAATTATG
Found at i:9818803 original size:27 final size:25
Alignment explanation
Indices: 9818773--9818840 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 25
9818763 GTTCCAACCT
* *
9818773 ACAGCTTGTGTGAGCAGGCCCATTTTC
1 ACAGCTCGTGTGAGCAGACCCA--TTC
* * *
9818800 ACAGCTCATGTGAGCATACCGATTC
1 ACAGCTCGTGTGAGCAGACCCATTC
9818825 ACAGCTCGTGTGAGCA
1 ACAGCTCGTGTGAGCA
9818841 TACATGTACA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 18 0.51
27 17 0.49
ACGTcount: A:0.24, C:0.26, G:0.25, T:0.25
Consensus pattern (25 bp):
ACAGCTCGTGTGAGCAGACCCATTC
Found at i:9832322 original size:24 final size:22
Alignment explanation
Indices: 9832270--9832322 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 22
9832260 AACTTTACAT
9832270 CTCAAAAAATTATAAAAAAAAA
1 CTCAAAAAATTATAAAAAAAAA
* * *
9832292 CTTAAAAATATATATAAAAGAATA
1 CTCAAAAA-AT-TATAAAAAAAAA
9832316 CTCAAAA
1 CTCAAAA
9832323 CCCTACACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 7 0.28
23 2 0.08
24 16 0.64
ACGTcount: A:0.66, C:0.09, G:0.02, T:0.23
Consensus pattern (22 bp):
CTCAAAAAATTATAAAAAAAAA
Found at i:9837168 original size:40 final size:41
Alignment explanation
Indices: 9837092--9837169 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 41
9837082 TTTTCTAAAA
*
9837092 ATATTTAAATATTAATATAAAATATTATAATGTTAACATTC
1 ATATTTAAATATTAATATAAAATAATATAATGTTAACATTC
* ** * *
9837133 ATATTT-AATATTTATATTTAATAATCTAATTTTAACA
1 ATATTTAAATATTAATATAAAATAATATAATGTTAACA
9837170 ATAAATGTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
40 25 0.81
41 6 0.19
ACGTcount: A:0.46, C:0.05, G:0.01, T:0.47
Consensus pattern (41 bp):
ATATTTAAATATTAATATAAAATAATATAATGTTAACATTC
Found at i:9837317 original size:25 final size:25
Alignment explanation
Indices: 9837289--9837346 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
9837279 TAATATATAG
* ** *
9837289 TTAAAAATATATTTATATTAATATT
1 TTAAAAATAAATACATATTAAAATT
9837314 TTAAAAATAAATACATATTAAAATT
1 TTAAAAATAAATACATATTAAAATT
9837339 TTAAAAAT
1 TTAAAAAT
9837347 TTTAATAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (25 bp):
TTAAAAATAAATACATATTAAAATT
Found at i:9837569 original size:18 final size:17
Alignment explanation
Indices: 9837529--9837576 Score: 71
Period size: 18 Copynumber: 2.8 Consensus size: 17
9837519 TATTATTAAG
*
9837529 TTTA-TATAAGATATTA
1 TTTATTATAAAATATTA
9837545 TTTATTATAAAATATTA
1 TTTATTATAAAATATTA
9837562 TCTTATTATAAAATA
1 T-TTATTATAAAATA
9837577 AATTTTGATT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 4 0.14
17 12 0.41
18 13 0.45
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (17 bp):
TTTATTATAAAATATTA
Found at i:9842850 original size:3 final size:3
Alignment explanation
Indices: 9842842--9842871 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
9842832 TTTGCTTTTA
9842842 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
9842872 TTTCCTTGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:9849127 original size:19 final size:18
Alignment explanation
Indices: 9849105--9849146 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
9849095 AAATAAAGTT
9849105 TGATTAATAATTTATTAAA
1 TGATTAATAATTTA-TAAA
* *
9849124 TGATTACTTATTTATAAA
1 TGATTAATAATTTATAAA
9849142 T-ATTA
1 TGATTA
9849147 TATATTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 4 0.19
18 5 0.24
19 12 0.57
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (18 bp):
TGATTAATAATTTATAAA
Found at i:9852602 original size:29 final size:30
Alignment explanation
Indices: 9852568--9852630 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
9852558 TTTAATGTGC
*
9852568 AATTTTAT-TCATG-AATTTTGATTTTATAT
1 AATTTTATAT-ATGAAATTTTGATTTGATAT
*
9852597 AATTTTATATATGAAATTTTGATTTGATTT
1 AATTTTATATATGAAATTTTGATTTGATAT
9852627 AATT
1 AATT
9852631 CTCACAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 11 0.37
30 19 0.63
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.57
Consensus pattern (30 bp):
AATTTTATATATGAAATTTTGATTTGATAT
Found at i:9855169 original size:21 final size:22
Alignment explanation
Indices: 9855145--9855201 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
9855135 ACATAGGTTG
9855145 CAAGTCTCGAGACTTAGG-C-AA
1 CAAGTCTCGAGACTT-GGCCTAA
* *
9855166 CAAGTATCAAGACTTGGCCTAA
1 CAAGTCTCGAGACTTGGCCTAA
9855188 -AAGTCTCGAGACTT
1 CAAGTCTCGAGACTT
9855202 CGACTATAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 2 0.07
21 26 0.87
22 2 0.07
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (22 bp):
CAAGTCTCGAGACTTGGCCTAA
Found at i:9855212 original size:21 final size:21
Alignment explanation
Indices: 9855146--9855214 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
9855136 CATAGGTTGC
*
9855146 AAGTCTCGAGACTTAGGC-AA
1 AAGTCTCGAGACTTAGACTAA
* * * *
9855166 CAAGTATCAAGACTTGGCCTAA
1 -AAGTCTCGAGACTTAGACTAA
* *
9855188 AAGTCTCGAGACTTCGACTAT
1 AAGTCTCGAGACTTAGACTAA
9855209 AAGTCT
1 AAGTCT
9855215 TTATACTTAG
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
21 36 0.95
22 2 0.05
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (21 bp):
AAGTCTCGAGACTTAGACTAA
Found at i:9857741 original size:20 final size:21
Alignment explanation
Indices: 9857718--9857773 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 21
9857708 TTAAAATTAA
*
9857718 TAAAACTTGATTAA-TTAAAT
1 TAAAACTTAATTAACTTAAAT
*
9857738 TAAACCTTAATTAACTT-AAT
1 TAAAACTTAATTAACTTAAAT
9857758 GCT-AAACTTAATTAAC
1 --TAAAACTTAATTAAC
9857774 CAAATGTTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 15 0.50
21 14 0.47
22 1 0.03
ACGTcount: A:0.46, C:0.12, G:0.04, T:0.38
Consensus pattern (21 bp):
TAAAACTTAATTAACTTAAAT
Found at i:9857779 original size:21 final size:22
Alignment explanation
Indices: 9857738--9857779 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
9857728 TTAATTAAAT
**
9857738 TAAACCTTAATTAACTTAATGC
1 TAAACCTTAATTAACCAAATGC
9857760 TAAA-CTTAATTAACCAAATG
1 TAAACCTTAATTAACCAAATG
9857780 TTAGTGGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (22 bp):
TAAACCTTAATTAACCAAATGC
Found at i:9864174 original size:15 final size:16
Alignment explanation
Indices: 9864154--9864186 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
9864144 GCAATAAAAA
9864154 TTCAGTACTT-AATTT
1 TTCAGTACTTAAATTT
9864169 TTCAGTACTTAAATTT
1 TTCAGTACTTAAATTT
9864185 TT
1 TT
9864187 AGTTTATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.27, C:0.12, G:0.06, T:0.55
Consensus pattern (16 bp):
TTCAGTACTTAAATTT
Found at i:9875093 original size:22 final size:21
Alignment explanation
Indices: 9875065--9875106 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
9875055 TGAATGGGGA
*
9875065 AGTGGAAGGATGGAAAGAGTAG
1 AGTGGAAAGATGGAAA-AGTAG
9875087 AGTGGAAAGATGGAAAAGTA
1 AGTGGAAAGATGGAAAAGTA
9875107 ATAAATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.45, C:0.00, G:0.40, T:0.14
Consensus pattern (21 bp):
AGTGGAAAGATGGAAAAGTAG
Found at i:9890837 original size:21 final size:21
Alignment explanation
Indices: 9890799--9890838 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
9890789 GCCAAGCCGT
**
9890799 TTTAGGATTTTAGTTTAGTAG
1 TTTAGGATTTTAAATTAGTAG
9890820 TTTAGGATTTTAAATTAGT
1 TTTAGGATTTTAAATTAGT
9890839 TATATTTTAT
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:0.28, C:0.00, G:0.20, T:0.53
Consensus pattern (21 bp):
TTTAGGATTTTAAATTAGTAG
Found at i:9895170 original size:14 final size:15
Alignment explanation
Indices: 9895151--9895185 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
9895141 ATTTGGTCCC
9895151 TTTTTATTCTTTT-T
1 TTTTTATTCTTTTAT
*
9895165 TTTTTATTTTTTTAT
1 TTTTTATTCTTTTAT
9895180 TTTTTA
1 TTTTTA
9895186 ATTAAATGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.11, C:0.03, G:0.00, T:0.86
Consensus pattern (15 bp):
TTTTTATTCTTTTAT
Found at i:9895382 original size:2 final size:2
Alignment explanation
Indices: 9895375--9895399 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9895365 TGTGCACATG
9895375 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
9895400 TTTAAATGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9899844 original size:6 final size:6
Alignment explanation
Indices: 9899833--9899872 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
9899823 TGAAAGTGAT
*
9899833 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG -GAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
9899873 TGGTTAGGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 4 0.13
6 27 0.87
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:9901288 original size:88 final size:88
Alignment explanation
Indices: 9901137--9901714 Score: 852
Period size: 88 Copynumber: 6.6 Consensus size: 88
9901127 GTGAAGATAA
* * ** * *
9901137 CAGATCTTGCCTTCCTGTACTGGTAGCGAAGCAGATCAAAGACACCAGCCTTGCCTCCTTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
9901202 GCAGCGGAGCAGGCTAAAAATAG
66 GCAGCGGAGCAGGCTAAAAATAG
*
9901225 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCTTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
9901290 GTAGCGGAGCAGGCTAAAAATAG
66 GCAGCGGAGCAGGCTAAAAATAG
* * * *
9901313 CAGATCTTACCTTCCTGCACCTACAACGAAGCAGATCGAA-ATCGCCAGCCTTGCCTCCCTGGGT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGA-CACCAGCCTTGCCTCCCTGGGT
*
9901377 TGCAACGGAGCAGGCTAAAAATAG
65 TGCAGCGGAGCAGGCTAAAAATAG
* * *
9901401 CAGATCTTGCCTTCCTACACCGACAGCGAAGCAGATCGAAGACACCAGCATTGCCTCCCTAGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
9901466 GCAGCGGAGCAGGCTAAAAATAG
66 GCAGCGGAGCAGGCTAAAAATAG
* * * *
9901489 CAGATCTTACCTACCTGCACCGACAGCGAAGCAGATCAAATACACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
9901554 GCAGTGGAGCAGGCTAAAAATAG
66 GCAGCGGAGCAGGCTAAAAATAG
* * *
9901577 CAGATCTTGCCTTCCTGCATCAACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCACTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* * *
9901642 GCAGCGGAGCGGGTTAAAAGTAG
66 GCAGCGGAGCAGGCTAAAAATAG
* * * * *
9901665 CAGATCTTGCATTCCTACACCGACAGCGAAGCAGATTGATGACCCCAGCC
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCC
9901715 CTATCTCCCT
Statistics
Matches: 439, Mismatches: 49, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
87 1 0.00
88 437 1.00
89 1 0.00
ACGTcount: A:0.28, C:0.29, G:0.24, T:0.19
Consensus pattern (88 bp):
CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
GCAGCGGAGCAGGCTAAAAATAG
Found at i:9901777 original size:44 final size:44
Alignment explanation
Indices: 9901714--9902172 Score: 498
Period size: 44 Copynumber: 10.7 Consensus size: 44
9901704 TGACCCCAGC
*
9901714 CCTATCTCCCTAGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
* * *
9901758 CCTATCTCCCTGGACAGCAGTGGAATAGGTTGAAGATTGAGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
* * *
9901802 TCTATCTCCCTGGGCAGCAGTGGAATAGATTAAAGA----G--T
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
*
9901840 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAATATTGTGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
*
9901884 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGAGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
* * ** * *
9901928 TCTATTTCCCTGGGAAGTAGTGGAATAGATT-AA-A----GAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
** *
9901966 CCTATCTCTTTGGACAGCAGTGGAATAGGTTAAAGATTGTGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
* *
9902010 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
* * * ** * * *
9902054 TCTATCTCCCTGGGCAGCAGTGGATTAAATTGAAGATCGT-AGGT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGA-AT
* * *
9902098 CCTATTTCCCTGGTCAGCAGTGGAATAGGTTGAAA-ATCGTGAAC
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTT-AAAGATTGTGAAT
*
9902142 CCTATCTCCCTGAG-CAGCAGTGGAGTAGGTT
1 CCTATCTCCCTG-GTCAGCAGTGGAATAGGTT
9902173 GAAAATAGCA
Statistics
Matches: 347, Mismatches: 52, Indels: 32
0.81 0.12 0.07
Matches are distributed among these distances:
38 60 0.17
39 2 0.01
40 2 0.01
42 2 0.01
43 3 0.01
44 274 0.79
45 4 0.01
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (44 bp):
CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
Found at i:9901939 original size:126 final size:126
Alignment explanation
Indices: 9901714--9902175 Score: 685
Period size: 126 Copynumber: 3.6 Consensus size: 126
9901704 TGACCCCAGC
* *
9901714 CCTATCTCCCTAGTCAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGACAGCAGT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAGCAGT
9901779 GGAATAGGTTGAAGATTGAGAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTAAAGAGT
66 GGAATAGGTTGAAGATTGAGAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTAAAGAGT
*
9901840 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAATATTGTGAATCCTATCTCCCTGGTCAGCAGT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAGCAGT
* * * * *
9901905 GGAATAGGTTAAAGATTGAGAATTCTATTTCCCTGGGAAGTAGTGGAATAGATTAAAGAAT
66 GGAATAGGTTGAAGATTGAGAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTAAAGAGT
** *
9901966 CCTATCTCTTTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAGCAGT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAGCAGT
* *
9902031 GGAATAGGTTGAAGATTGAGAATTCTATCTCCCTGGGCAGCAGTGGATTAAATTGAAGATCGTAG
66 GGAATAGGTTGAAGATTGAGAATTCTATCTCCCTGGGCAGCAGTGGAATAGATT-AA-A--G-A-
9902096 GT
125 GT
* * *
9902098 CCTATTTCCCTGGTCAGCAGTGGAATAGGTTGAAA-ATCGTGAACCCTATCTCCCTGAG-CAGCA
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTT-AAAGATTGTGAATCCTATCTCCCTG-GTCAGCA
*
9902161 GTGGAGTAGGTTGAA
64 GTGGAATAGGTTGAA
9902176 AATAGCAGGT
Statistics
Matches: 302, Mismatches: 26, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
126 227 0.75
127 2 0.01
128 1 0.00
130 1 0.00
131 1 0.00
132 66 0.22
133 4 0.01
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (126 bp):
CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAGCAGT
GGAATAGGTTGAAGATTGAGAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTAAAGAGT
Found at i:9904062 original size:12 final size:11
Alignment explanation
Indices: 9904045--9904080 Score: 54
Period size: 12 Copynumber: 3.1 Consensus size: 11
9904035 ATTTGGTCCC
9904045 TTTTTATTTCTT
1 TTTTTATTT-TT
9904057 TTTTTATTTTT
1 TTTTTATTTTT
9904068 TTATTTATTTTT
1 TT-TTTATTTTT
9904080 T
1 T
9904081 AATTAAATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 4 0.17
12 19 0.83
ACGTcount: A:0.11, C:0.03, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTATTTTT
Found at i:9904284 original size:2 final size:2
Alignment explanation
Indices: 9904277--9904315 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
9904267 TGTGCACATG
9904277 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9904316 TNNNNNNNNN
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9923709 original size:17 final size:17
Alignment explanation
Indices: 9923660--9923697 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
9923650 CATGGGATGG
*
9923660 CACATGGGCGTGTGGCT
1 CACATAGGCGTGTGGCT
9923677 CACATAGGCGTGTGGCT
1 CACATAGGCGTGTGGCT
9923694 CACA
1 CACA
9923698 CGGACGTGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (17 bp):
CACATAGGCGTGTGGCT
Found at i:9925225 original size:44 final size:43
Alignment explanation
Indices: 9925175--9925289 Score: 103
Period size: 44 Copynumber: 2.7 Consensus size: 43
9925165 TGTGTTATCT
*
9925175 TGTAAGACCACGTATGGGACATTGGCATCGACT-TGCGACTTACG
1 TGTAAGACCACGTATGGGACATTGGCATCGA-TATGCGA-TTACA
* * *
9925219 TGTAAGACTCTATC-TA--GGACAGTGCCATCGATATGTGATTACA
1 TGTAAGAC-C-A-CGTATGGGACATTGGCATCGATATGCGATTACA
* *
9925262 TGTAAGACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCACGTATGGGACATTGGCAT
9925290 TGTACGAGAT
Statistics
Matches: 56, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
40 1 0.02
41 2 0.04
42 1 0.02
43 22 0.39
44 25 0.45
45 1 0.02
46 3 0.05
47 1 0.02
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (43 bp):
TGTAAGACCACGTATGGGACATTGGCATCGATATGCGATTACA
Found at i:9927294 original size:18 final size:19
Alignment explanation
Indices: 9927259--9927296 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
9927249 TGAAAATGAA
*
9927259 TCATTTCTCATTTTCATTT
1 TCATTTCTCATTTCCATTT
9927278 TCATTTC-CATTTCCATTT
1 TCATTTCTCATTTCCATTT
9927296 T
1 T
9927297 GAGAAAACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.61
Consensus pattern (19 bp):
TCATTTCTCATTTCCATTT
Found at i:9927414 original size:19 final size:19
Alignment explanation
Indices: 9927379--9927417 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
9927369 CAACGTCTAG
*
9927379 AGTGTGAATACCGCAACTA
1 AGTGTGAATACCACAACTA
*
9927398 AGTGTGAATACTACAACTA
1 AGTGTGAATACCACAACTA
9927417 A
1 A
9927418 ATATATGAAT
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:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (19 bp):
AGTGTGAATACCACAACTA
Found at i:9929363 original size:43 final size:43
Alignment explanation
Indices: 9929316--9929399 Score: 114
Period size: 43 Copynumber: 2.0 Consensus size: 43
9929306 TATGTGATTG
*
9929316 ATATTGAAATGGAAAAGATAAAAAATGAATACGAGATGAGAAA
1 ATATTGAAATAGAAAAGATAAAAAATGAATACGAGATGAGAAA
* * * * *
9929359 ATATTGAAATAGAAAATATGATAAATGATTATGAGATGAGA
1 ATATTGAAATAGAAAAGATAAAAAATGAATACGAGATGAGA
9929400 TATGAAATGA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.55, C:0.01, G:0.20, T:0.24
Consensus pattern (43 bp):
ATATTGAAATAGAAAAGATAAAAAATGAATACGAGATGAGAAA
Found at i:9930757 original size:49 final size:49
Alignment explanation
Indices: 9930703--9930803 Score: 157
Period size: 49 Copynumber: 2.1 Consensus size: 49
9930693 TCTAGAGAGG
** * *
9930703 ATAAATAATGATAAGATTGTAGACAGTGGAAGACTAAGTTTAGCAATGT
1 ATAAATAATGATAAGAGAGTAGACAGTGGAAGACCAAGTTTAGAAATGT
*
9930752 ATAAATAGTGATAAGAGAGTAGACAGTGGAAGACCAAGTTTAGAAATGT
1 ATAAATAATGATAAGAGAGTAGACAGTGGAAGACCAAGTTTAGAAATGT
9930801 ATA
1 ATA
9930804 GCATAATTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.45, C:0.06, G:0.24, T:0.26
Consensus pattern (49 bp):
ATAAATAATGATAAGAGAGTAGACAGTGGAAGACCAAGTTTAGAAATGT
Found at i:9942236 original size:2 final size:2
Alignment explanation
Indices: 9942190--9942222 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
9942180 ACAATTAATG
9942190 AT AT GAT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9942223 ATAGTTAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 26 0.90
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9942387 original size:11 final size:12
Alignment explanation
Indices: 9942365--9942393 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
9942355 TGCAAAAGAA
9942365 AGAAAGAAAAAG
1 AGAAAGAAAAAG
9942377 AGAAA-AAAAAG
1 AGAAAGAAAAAG
9942388 AGAAAG
1 AGAAAG
9942394 TCACGCACCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AGAAAGAAAAAG
Found at i:9944323 original size:30 final size:29
Alignment explanation
Indices: 9944300--9944418 Score: 172
Period size: 30 Copynumber: 4.1 Consensus size: 29
9944290 GTATATGTTT
*
9944300 TATATATTGCCGAATTGA-TTGTATATGGG
1 TATACATTGCCGAATTGATTTGTATAT-GG
9944329 TATACATTGCCGAATTGATTTGTATATGG
1 TATACATTGCCGAATTGATTTGTATATGG
*
9944358 ATATACATTGCCGAATTGATTTTTATATGG
1 -TATACATTGCCGAATTGATTTGTATATGG
*
9944388 -ATATATTGCCGAATTGATTTGTATAT-G
1 TATACATTGCCGAATTGATTTGTATATGG
9944415 TATA
1 TATA
9944419 TGTATACATA
Statistics
Matches: 83, Mismatches: 4, Indels: 7
0.88 0.04 0.07
Matches are distributed among these distances:
27 1 0.01
28 27 0.33
29 19 0.23
30 36 0.43
ACGTcount: A:0.29, C:0.08, G:0.19, T:0.43
Consensus pattern (29 bp):
TATACATTGCCGAATTGATTTGTATATGG
Found at i:9944406 original size:58 final size:59
Alignment explanation
Indices: 9944300--9944419 Score: 181
Period size: 58 Copynumber: 2.1 Consensus size: 59
9944290 GTATATGTTT
*
9944300 TATATATTGCCGAATTGATTGTATATGGGTATACATTGCCGAATTGATTTGTATATGGA
1 TATACATTGCCGAATTGATTGTATATGGGTATACATTGCCGAATTGATTTGTATATGGA
* * *
9944359 TATACATTGCCGAATTGATTTTTATAT-GG-ATATATTGCCGAATTGATTTGTATATGTA
1 TATACATTGCCGAATTGA-TTGTATATGGGTATACATTGCCGAATTGATTTGTATATGGA
9944417 TAT
1 TAT
9944420 GTATACATAT
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
58 30 0.54
59 19 0.34
60 7 0.12
ACGTcount: A:0.29, C:0.08, G:0.19, T:0.43
Consensus pattern (59 bp):
TATACATTGCCGAATTGATTGTATATGGGTATACATTGCCGAATTGATTTGTATATGGA
Found at i:9944614 original size:41 final size:42
Alignment explanation
Indices: 9944569--9944647 Score: 124
Period size: 41 Copynumber: 1.9 Consensus size: 42
9944559 GAGGTGTGAT
* *
9944569 TTCGTGTAAGACCATGTCTGGGACATTGGCATC-ATATATGA
1 TTCGTATAAGACCATGTCTGGGACAGTGGCATCGATATATGA
*
9944610 TTCGTATAAGACCCTGTCTGGGACAGTGGCATCGATAT
1 TTCGTATAAGACCATGTCTGGGACAGTGGCATCGATAT
9944648 GCGTTAACAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
41 30 0.88
42 4 0.12
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30
Consensus pattern (42 bp):
TTCGTATAAGACCATGTCTGGGACAGTGGCATCGATATATGA
Found at i:9958138 original size:30 final size:30
Alignment explanation
Indices: 9958102--9958182 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 30
9958092 AATTAATATG
**
9958102 GCACACAACCATGTGAGTAGGCCATGTGTA
1 GCACACAACTGTGTGAGTAGGCCATGTGTA
* * * * *
9958132 GCACACAACTGTTTAAGTAGACCGTGTGTT
1 GCACACAACTGTGTGAGTAGGCCATGTGTA
9958162 GCACACAACTGTGTGAGTAGG
1 GCACACAACTGTGTGAGTAGG
9958183 TTGTGTATTA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.23
Consensus pattern (30 bp):
GCACACAACTGTGTGAGTAGGCCATGTGTA
Found at i:9961910 original size:19 final size:17
Alignment explanation
Indices: 9961872--9961921 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
9961862 TAATTTAAAA
*
9961872 TATATTAAAAATAAATT
1 TATATTAAATATAAATT
9961889 TATATTAAATATATAATAT
1 TATATTAAATATA-AAT-T
* *
9961908 TATTTTTAATATAA
1 TATATTAAATATAA
9961922 TATAAAGATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 12 0.43
18 4 0.14
19 12 0.43
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATTAAATATAAATT
Found at i:9963619 original size:21 final size:19
Alignment explanation
Indices: 9963575--9963628 Score: 51
Period size: 21 Copynumber: 2.8 Consensus size: 19
9963565 TTTTTGGATT
*
9963575 TAAA-TTGTT-TTCTTATA
1 TAAATTTGTTATTTTTATA
9963592 TAAATTT-TATATTTTTATAA
1 TAAATTTGT-TATTTTTAT-A
9963612 TAATATTTGTTATTTTT
1 TAA-ATTTGTTATTTTT
9963629 TTAAATATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
17 5 0.17
18 3 0.10
19 6 0.20
20 4 0.13
21 11 0.37
22 1 0.03
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (19 bp):
TAAATTTGTTATTTTTATA
Found at i:9964051 original size:5 final size:5
Alignment explanation
Indices: 9964041--9964065 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
9964031 CAATTTAAGG
9964041 TTAAA TTAAA TTAAA TTAAA TTAAA
1 TTAAA TTAAA TTAAA TTAAA TTAAA
9964066 GGGTCTGCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TTAAA
Found at i:9967525 original size:11 final size:11
Alignment explanation
Indices: 9967509--9967534 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
9967499 CTAGCATGTC
9967509 AATTTTATTAA
1 AATTTTATTAA
9967520 AATTTTATTAA
1 AATTTTATTAA
9967531 AATT
1 AATT
9967535 ATTTCAGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
AATTTTATTAA
Found at i:9969988 original size:20 final size:21
Alignment explanation
Indices: 9969960--9969998 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
9969950 TACTTTGTCC
*
9969960 AAACTTTTTCTAAG-TGTTCA
1 AAACATTTTCTAAGATGTTCA
9969980 AAACATTTTCTAAGATGTT
1 AAACATTTTCTAAGATGTT
9969999 TGGAAGTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (21 bp):
AAACATTTTCTAAGATGTTCA
Found at i:9996350 original size:21 final size:20
Alignment explanation
Indices: 9996321--9996387 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 20
9996311 CTAATGTATG
9996321 ATAACTTTAAATAATATAATTA
1 ATAA-TTTAAATAATATAA-TA
* *
9996343 ATAATTTAAATCATAAAACT-
1 ATAATTTAAATAATATAA-TA
* *
9996363 ATATTTTAAATTATACTAATA
1 ATAATTTAAATAATA-TAATA
9996384 ATAA
1 ATAA
9996388 GCTTAAAAAC
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
20 14 0.39
21 18 0.50
22 4 0.11
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (20 bp):
ATAATTTAAATAATATAATA
Found at i:9999840 original size:13 final size:13
Alignment explanation
Indices: 9999822--9999846 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9999812 TAAAAGAGTT
9999822 ATTAATTAAAAAG
1 ATTAATTAAAAAG
9999835 ATTAATTAAAAA
1 ATTAATTAAAAA
9999847 AATAAAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (13 bp):
ATTAATTAAAAAG
Found at i:10003196 original size:35 final size:35
Alignment explanation
Indices: 10003156--10003223 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
10003146 CATCTTCGGA
* *
10003156 GCTTGGTAAATATGGAAAGTGATCTTTAAAGATGT
1 GCTTGGCAAATATGGAAAGTGATCTTCAAAGATGT
*
10003191 GCTTGGCAAATATGGAATGTGATCTTCAAAGAT
1 GCTTGGCAAATATGGAAAGTGATCTTCAAAGAT
10003224 ATGTGATCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.34, C:0.09, G:0.25, T:0.32
Consensus pattern (35 bp):
GCTTGGCAAATATGGAAAGTGATCTTCAAAGATGT
Found at i:10004227 original size:18 final size:18
Alignment explanation
Indices: 10004206--10004244 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
10004196 TGGTATAAGC
10004206 TTTATTTTTCTTATT-ATT
1 TTTATTTTTCTT-TTGATT
10004224 TTTATTTTTCTTTTGATT
1 TTTATTTTTCTTTTGATT
10004242 TTT
1 TTT
10004245 CTTCCTTTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.13, C:0.05, G:0.03, T:0.79
Consensus pattern (18 bp):
TTTATTTTTCTTTTGATT
Found at i:10004882 original size:3 final size:3
Alignment explanation
Indices: 10004874--10004951 Score: 129
Period size: 3 Copynumber: 25.3 Consensus size: 3
10004864 CCTTTTTAGC
10004874 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
10004922 ATT ATT ATTT CTT CATT ATT ATT ATT ATT A
1 ATT ATT A-TT ATT -ATT ATT ATT ATT ATT A
10004952 CTATACTAGT
Statistics
Matches: 71, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
3 67 0.94
4 4 0.06
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:10005334 original size:22 final size:20
Alignment explanation
Indices: 10005297--10005338 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
10005287 TTTATATTTT
10005297 TATATCTTATAATTTATGTA
1 TATATCTTATAATTTATGTA
*
10005317 TATATTTTAATAATTTTATGTA
1 TATATCTT-ATAA-TTTATGTA
10005339 CATACATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 4 0.21
22 8 0.42
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (20 bp):
TATATCTTATAATTTATGTA
Found at i:10009677 original size:7 final size:7
Alignment explanation
Indices: 10009665--10009728 Score: 51
Period size: 7 Copynumber: 8.9 Consensus size: 7
10009655 TCAGACTCAA
10009665 AAAAAAC
1 AAAAAAC
10009672 AAAAAAAC
1 -AAAAAAC
10009680 AAAAATA-
1 AAAAA-AC
10009687 AAAACAA-
1 AAAA-AAC
10009694 AAAAAATC
1 AAAAAA-C
*
10009702 AAAAATC
1 AAAAAAC
*
10009709 AAAAATC
1 AAAAAAC
*
10009716 AAAAAAT
1 AAAAAAC
10009723 AAAAAA
1 AAAAAA
10009729 ATCAAAGTCA
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
6 2 0.04
7 33 0.67
8 14 0.29
ACGTcount: A:0.83, C:0.09, G:0.00, T:0.08
Consensus pattern (7 bp):
AAAAAAC
Found at i:10009689 original size:14 final size:14
Alignment explanation
Indices: 10009666--10009727 Score: 61
Period size: 14 Copynumber: 4.4 Consensus size: 14
10009656 CAGACTCAAA
*
10009666 AAAAACAAAAAAAC
1 AAAAATAAAAAAAC
*
10009680 AAAAATAAAAACAAA
1 AAAAATAAAAA-AAC
* *
10009695 AAAAATCAAAAATC
1 AAAAATAAAAAAAC
* *
10009709 AAAAATCAAAAAAT
1 AAAAATAAAAAAAC
10009723 AAAAA
1 AAAAA
10009728 AATCAAAGTC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
14 28 0.70
15 12 0.30
ACGTcount: A:0.82, C:0.10, G:0.00, T:0.08
Consensus pattern (14 bp):
AAAAATAAAAAAAC
Found at i:10009699 original size:30 final size:31
Alignment explanation
Indices: 10009663--10009734 Score: 96
Period size: 30 Copynumber: 2.4 Consensus size: 31
10009653 GTTCAGACTC
*
10009663 AAAAAAAACAAAAAAACAAAAAT-AAAAACA-
1 AAAAAAATCAAAAAAACAAAAATCAAAAA-AT
*
10009693 AAAAAAATC-AAAAATCAAAAATCAAAAAAT
1 AAAAAAATCAAAAAAACAAAAATCAAAAAAT
10009723 AAAAAAATCAAA
1 AAAAAAATCAAA
10009735 GTCAAAAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
29 13 0.35
30 22 0.59
31 2 0.05
ACGTcount: A:0.82, C:0.10, G:0.00, T:0.08
Consensus pattern (31 bp):
AAAAAAATCAAAAAAACAAAAATCAAAAAAT
Found at i:10009713 original size:8 final size:8
Alignment explanation
Indices: 10009664--10009734 Score: 62
Period size: 8 Copynumber: 9.4 Consensus size: 8
10009654 TTCAGACTCA
*
10009664 AAAAAAAC
1 AAAAAATC
*
10009672 AAAAAAAC
1 AAAAAATC
10009680 -AAAAAT-
1 AAAAAATC
*
10009686 AAAAACA-A
1 AAAAA-ATC
10009694 AAAAAATC
1 AAAAAATC
10009702 -AAAAATC
1 AAAAAATC
10009709 -AAAAATC
1 AAAAAATC
*
10009716 AAAAAATA
1 AAAAAATC
10009724 AAAAAATC
1 AAAAAATC
10009732 AAA
1 AAA
10009735 GTCAAAAATA
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
7 24 0.44
8 30 0.56
ACGTcount: A:0.82, C:0.10, G:0.00, T:0.08
Consensus pattern (8 bp):
AAAAAATC
Found at i:10009739 original size:22 final size:22
Alignment explanation
Indices: 10009665--10009742 Score: 65
Period size: 22 Copynumber: 3.5 Consensus size: 22
10009655 TCAGACTCAA
*
10009665 AAAAAACAAAAAA-ACAAAAAT-
1 AAAAATCAAAAAATA-AAAAATC
*
10009686 AAAAA-CAAAAAAAATCAAAAATC
1 AAAAATC-AA-AAAATAAAAAATC
10009709 AAAAATCAAAAAATAAAAAAATC
1 AAAAATCAAAAAATAAAA-AATC
*
10009732 -AAAGTCAAAAA
1 AAAAATCAAAAA
10009743 TAGGAGAAAG
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
20 1 0.02
21 7 0.15
22 28 0.58
23 11 0.23
24 1 0.02
ACGTcount: A:0.79, C:0.10, G:0.01, T:0.09
Consensus pattern (22 bp):
AAAAATCAAAAAATAAAAAATC
Found at i:10009743 original size:29 final size:29
Alignment explanation
Indices: 10009662--10009744 Score: 100
Period size: 29 Copynumber: 2.9 Consensus size: 29
10009652 AGTTCAGACT
*
10009662 CAAAAAAAA-CAAAAAAACAAAAATAAAAA
1 CAAAAAAAATC-AAAAATCAAAAATAAAAA
10009691 CAAAAAAAATCAAAAATCAAAAATCAAAAA
1 CAAAAAAAATCAAAAATCAAAAAT-AAAAA
*
10009721 -ATAAAAAAATC-AAAGTCAAAAATA
1 CA-AAAAAAATCAAAAATCAAAAATA
10009745 GGAGAAAGAG
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
28 1 0.02
29 33 0.67
30 15 0.31
ACGTcount: A:0.78, C:0.11, G:0.01, T:0.10
Consensus pattern (29 bp):
CAAAAAAAATCAAAAATCAAAAATAAAAA
Found at i:10009778 original size:5 final size:6
Alignment explanation
Indices: 10009747--10009786 Score: 53
Period size: 6 Copynumber: 6.3 Consensus size: 6
10009737 CAAAAATAGG
*
10009747 AGAAAG AGAAATA AGAAAAA AGAAAA AGAAAA AGAAAA AG
1 AGAAAA AGAAA-A AG-AAAA AGAAAA AGAAAA AGAAAA AG
10009787 GAGAGGTCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
6 23 0.74
7 5 0.16
8 3 0.10
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.03
Consensus pattern (6 bp):
AGAAAA
Found at i:10012005 original size:88 final size:88
Alignment explanation
Indices: 10011857--10012789 Score: 1351
Period size: 88 Copynumber: 10.6 Consensus size: 88
10011847 ATGAAGTTGC
* * *
10011857 AGATCCTGCCTTCCTGCATTGACAGCGAAGCAGGTCAAAGATACAAACCTTGCCTCTCTCGGTTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
* * *
10011922 T-AGCGGAGCTGGTTGAAAACAAC
66 TGA-TGGAGCTGGTTGAAGACAAA
* *
10011945 AGATCTTGCCTTCCTGTC-TTTACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGCT
1 AGATCTTGCCTTCCTG-CATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTT
* *
10012009 GTGATGGAGCTAGTTGAAGAGAAA
65 GTGATGGAGCTGGTTGAAGACAAA
*
10012033 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGTTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
10012098 TGATGGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
* *
10012121 CGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGATACAAACCTTGCCTCTCTCGGTTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
*
10012186 TAATGGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
* *
10012209 AGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGCTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
*
10012274 TGATGGAGCTGGTTGAAAACAAA
66 TGATGGAGCTGGTTGAAGACAAA
* * * * *
10012297 AGATCCTGCCTTCCTGTATTGACAGCGAACCAGGTCGAAGACACAAACCTTGCCTCTTTCGCTTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
*
10012362 TGATGGGGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
* * *
10012385 AGATCTTGCCTTCCTACATTGACAGCGAAGCAGGTCGAAGATACAAACCTTTCCTCTCTCGGTTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
10012450 TGATGGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
** *
10012473 AGATCTTGCCTTCCTATATTGATAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
10012538 TGATGGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
* * *
10012561 AGATCTTGCTTTCCTGTATTGACAGCAAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
10012626 TGATGGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
* * * *
10012649 AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAA-A-ACAAAGCCTTACCT-TCATTGGT
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAA-CCTTGCCTCTC-TCGGT
* * * **
10012711 TG-CAGTGGAACTGGTTAAAGA-AGC
64 TGTGA-TGGAGCTGGTTGAAGACAAA
* * * *
10012735 AGATCTTGCCTTCCTGCATTAACAGTGAAGCAGATCGAAAACA-AAAGCCTTGCCT
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAA-CCTTGCCT
10012790 TCATTGGTTG
Statistics
Matches: 774, Mismatches: 63, Indels: 17
0.91 0.07 0.02
Matches are distributed among these distances:
86 47 0.06
87 41 0.05
88 684 0.88
89 2 0.00
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.25
Consensus pattern (88 bp):
AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
TGATGGAGCTGGTTGAAGACAAA
Found at i:10012856 original size:55 final size:56
Alignment explanation
Indices: 10012761--10012880 Score: 215
Period size: 55 Copynumber: 2.2 Consensus size: 56
10012751 CATTAACAGT
10012761 GAAGCAGATCGAAAACAAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAA
1 GAAGCAGATCGAAAACAAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAA
* *
10012817 GAAGTAGATCGAAAACAAAA-CCTTTCCTTCATTGGTTGCAGTGGAGCTGGTTAAA
1 GAAGCAGATCGAAAACAAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAA
10012872 GAAGCAGAT
1 GAAGCAGAT
10012881 TTTGCCTTCC
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
55 42 0.69
56 19 0.31
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (56 bp):
GAAGCAGATCGAAAACAAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAA
Found at i:10013656 original size:50 final size:50
Alignment explanation
Indices: 10013014--10013658 Score: 698
Period size: 50 Copynumber: 12.9 Consensus size: 50
10013004 AAACCATAGT
* *
10013014 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTAACA
* ** * *
10013064 TTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTAACA
* *
10013114 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTAACA
* ** * *
10013164 TTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTAACA
* * *
10013214 TTGCAATTAAAAAGATTGAAGCTACAACAGTGGATCTTACTTTCCTAGCA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTAACA
* ** * *
10013264 TTGCAGTGGAATAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTAACA
* * * *
10013314 TTGCAATTAAAAAGATTGAAGCTACAATAGCGGATCTTACTTTCCTAGCG
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTAACA
* ** * * *
10013364 TTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCACTGACA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTAACA
* * *
10013414 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCG
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTAACA
* ** *** *
10013464 TTGCAGTGGAGCGGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTAACA
* * * * *
10013514 TTGTAATTAAAAAGATTAAAGCTACAACAGTGGATCTTATTTCCC-AGGCA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTA-ACA
* **** * * ** * *
10013564 ATGCAGCGGAACAGATTGAAGCCACAATGGCGAATCTTACTTCCCCAACA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTAACA
* * * ** *
10013614 TTGCAACTCAAAAGATTGAAGCCACAATGGCGAATCTTACTTCCC
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCC
10013659 AGGCAGTATA
Statistics
Matches: 486, Mismatches: 107, Indels: 4
0.81 0.18 0.01
Matches are distributed among these distances:
50 485 1.00
51 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (50 bp):
TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTAACA
Found at i:10013663 original size:100 final size:100
Alignment explanation
Indices: 10013014--10013655 Score: 1034
Period size: 100 Copynumber: 6.4 Consensus size: 100
10013004 AAACCATAGT
10013014 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTGGAACAGA
10013079 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
66 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
10013114 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTGGAACAGA
10013179 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
66 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* *
10013214 TTGCAATTAAAAAGATTGAAGCTACAACAGTGGATCTTACTTTCCTAGCATTGCAGTGGAATAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTGGAACAGA
10013279 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
66 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* *
10013314 TTGCAATTAAAAAGATTGAAGCTACAATAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTGGAACAGA
*
10013379 TTGAAGCTACAACAGCGGATCTTACTTCACTGACA
66 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* * *
10013414 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAGCGGA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTGGAACAGA
10013479 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
66 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* * * * * *
10013514 TTGTAATTAAAAAGATTAAAGCTACAACAGTGGATCTTA-TTTCCCAGGCAATGCAGCGGAACAG
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTA-GCATTGCAGTGGAACAG
* ** * **
10013578 ATTGAAGCCACAATGGCGAATCTTACTTCCCCAACA
65 ATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* * * ** *
10013614 TTGCAACTCAAAAGATTGAAGCCACAATGGCGAATCTTACTT
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTT
10013656 CCCAGGCAGT
Statistics
Matches: 505, Mismatches: 35, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
99 6 0.01
100 497 0.98
101 2 0.00
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.26
Consensus pattern (100 bp):
TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTGGAACAGA
TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
Found at i:10013680 original size:50 final size:49
Alignment explanation
Indices: 10013547--10013701 Score: 127
Period size: 50 Copynumber: 3.1 Consensus size: 49
10013537 ACAACAGTGG
* * * * *
10013547 ATCTTATTTCCCAGGCAATGCAGCGGAACAGATTGAAGCCACAATGGCGA
1 ATCTTACTTCCCAGGCAGT-AAGTGGAAAAGATTGAAGCCACAATGGCGA
* * * *
10013597 ATCTTACTTCCCCA-ACATTGCAACT-CAAAAGATTGAAGCCACAATGGCGA
1 ATCTTACTT-CCCAGGCA--GTAAGTGGAAAAGATTGAAGCCACAATGGCGA
* * *
10013647 ATCTTACTTCCCAGGCAGTATAGTGGAATAGATTAAAGCCA-AATTGGTGA
1 ATCTTACTTCCCAGGCAGTA-AGTGGAAAAGATTGAAGCCACAA-TGGCGA
10013697 ATCTT
1 ATCTT
10013702 GTTTCTCCAA
Statistics
Matches: 82, Mismatches: 16, Indels: 14
0.73 0.14 0.12
Matches are distributed among these distances:
48 2 0.02
49 8 0.10
50 67 0.82
51 5 0.06
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.25
Consensus pattern (49 bp):
ATCTTACTTCCCAGGCAGTAAGTGGAAAAGATTGAAGCCACAATGGCGA
Found at i:10013699 original size:100 final size:100
Alignment explanation
Indices: 10013014--10013739 Score: 465
Period size: 100 Copynumber: 7.3 Consensus size: 100
10013004 AAACCATAGT
* * * * * * *
10013014 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTA-GCATTGCAGTGGAACAG
1 TTGCAATTAAAAAGATTAAAGCCACAACAGCGAATCTTAC-TTCCCAGGCAATACAGCGGAACAG
* * ** * **
10013078 ATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
65 ATTAAAGCCACAATGGCGAATCTTACTTCCCCAACA
* * * * * * *
10013114 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTA-GCATTGCAGTGGAACAG
1 TTGCAATTAAAAAGATTAAAGCCACAACAGCGAATCTTAC-TTCCCAGGCAATACAGCGGAACAG
* * ** * **
10013178 ATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
65 ATTAAAGCCACAATGGCGAATCTTACTTCCCCAACA
* * * * * * * * *
10013214 TTGCAATTAAAAAGATTGAAGCTACAACAGTGGATCTTACTTTCCTA-GCATTGCAGTGGAATAG
1 TTGCAATTAAAAAGATTAAAGCCACAACAGCGAATCTTAC-TTCCCAGGCAATACAGCGGAACAG
* * ** * **
10013278 ATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
65 ATTAAAGCCACAATGGCGAATCTTACTTCCCCAACA
* * * * * ** * *
10013314 TTGCAATTAAAAAGATTGAAGCTACAATAGCGGATCTTACTTTCCTA-GCGTTGCAGTGGAACAG
1 TTGCAATTAAAAAGATTAAAGCCACAACAGCGAATCTTAC-TTCCCAGGCAATACAGCGGAACAG
* * ** * * **
10013378 ATTGAAGCTACAACAGCGGATCTTACTTCACTGACA
65 ATTAAAGCCACAATGGCGAATCTTACTTCCCCAACA
* * * * ** * * * *
10013414 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTA-GCGTTGCAGTGGAGCGG
1 TTGCAATTAAAAAGATTAAAGCCACAACAGCGAATCTTAC-TTCCCAGGCAATACAGCGGAACAG
* * ** * **
10013478 ATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
65 ATTAAAGCCACAATGGCGAATCTTACTTCCCCAACA
* * * * * *
10013514 TTGTAATTAAAAAGATTAAAGCTACAACAGTGGATCTTATTTCCCAGGCAATGCAGCGGAACAGA
1 TTGCAATTAAAAAGATTAAAGCCACAACAGCGAATCTTACTTCCCAGGCAATACAGCGGAACAGA
*
10013579 TTGAAGCCACAATGGCGAATCTTACTTCCCCAACA
66 TTAAAGCCACAATGGCGAATCTTACTTCCCCAACA
* * * ** * * * *
10013614 TTGCAACTCAAAAGATTGAAGCCACAATGGCGAATCTTACTTCCCAGGCAGTATAGTGGAATAGA
1 TTGCAATTAAAAAGATTAAAGCCACAACAGCGAATCTTACTTCCCAGGCAATACAGCGGAACAGA
* ** *
10013679 TTAAAGCCA-AATTGGTGAATCTTGTTTCTCCAACA
66 TTAAAGCCACAA-TGGCGAATCTTACTTCCCCAACA
*
10013714 TTGCAGTTAAAAAGATTAAAGCCACA
1 TTGCAATTAAAAAGATTAAAGCCACA
10013740 TCGGTGAATC
Statistics
Matches: 573, Mismatches: 51, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
99 7 0.01
100 566 0.99
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (100 bp):
TTGCAATTAAAAAGATTAAAGCCACAACAGCGAATCTTACTTCCCAGGCAATACAGCGGAACAGA
TTAAAGCCACAATGGCGAATCTTACTTCCCCAACA
Found at i:10013773 original size:25 final size:25
Alignment explanation
Indices: 10013727--10013776 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
10013717 CAGTTAAAAA
* * *
10013727 GATTAAAGCCACATCGGTGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
*
10013752 GATTAAAGCTACAACAGCGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
10013777 ACGCCCCAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (25 bp):
GATTAAAGCCACAACAGCGAATCTT
Found at i:10014023 original size:25 final size:25
Alignment explanation
Indices: 10013977--10014026 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
10013967 CAGTTAAAAA
* * *
10013977 GATTAAAGCCACATCGGTGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
*
10014002 GATTAAAGCTACAACAGCGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
10014027 ACGCCCCAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (25 bp):
GATTAAAGCCACAACAGCGAATCTT
Found at i:10014251 original size:125 final size:125
Alignment explanation
Indices: 10013668--10014239 Score: 1090
Period size: 125 Copynumber: 4.6 Consensus size: 125
10013658 CAGGCAGTAT
*
10013668 AGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCAACATTGCAGTTAAAAAGATTAA
1 AGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAAGATTAA
10013733 AGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATGC
66 AGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATGC
*
10013793 AGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCTGACATTGCAGTTAAAAAGATTAA
1 AGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAAGATTAA
*
10013858 AGCCACATCGGTGAATCTTAATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATGC
66 AGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATGC
*
10013918 AGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCAACATTGCAGTTAAAAAGATTAA
1 AGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAAGATTAA
10013983 AGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATGC
66 AGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATGC
10014043 AGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAAGATTAA
1 AGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAAGATTAA
* *
10014108 AGCCACATCGGTGAATCTTGATTAAAACTACAACAGCGAATCTTACGCCCCAAGTGATGC
66 AGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATGC
10014168 AGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAAGATTAA
1 AGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAAGATTAA
10014233 AGCCACA
66 AGCCACA
10014240 ATGGCGAATC
Statistics
Matches: 438, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
125 438 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (125 bp):
AGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAAGATTAA
AGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATGC
Found at i:10014417 original size:44 final size:43
Alignment explanation
Indices: 10014323--10014518 Score: 153
Period size: 44 Copynumber: 4.5 Consensus size: 43
10014313 AGAACCAAAG
* * * * * *
10014323 TCTTATCCCCCTGAAGATGCAGTGGGGCAAATTGAAGGTACAA-A
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAA-G-CCAAGA
* *
10014367 TATTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCCA-AGA
** * * **
10014411 TCTTATCTCCCTG-AGATTACAACGGAGCAGATCGAAGACACTA
1 TCTTATCTCCCTGAAG-TTACAGTGGAGCAGATTGAAGCCAAGA
* * * * *
10014454 TCCTATATCCCTGAAGTTACAGTGGAGCGGATTAAAACCACAGA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCCA-AGA
*
10014498 TCTTATCTCTCTGAAGTTACA
1 TCTTATCTCCCTGAAGTTACA
10014519 ACAGAGTAGA
Statistics
Matches: 117, Mismatches: 30, Indels: 10
0.75 0.19 0.06
Matches are distributed among these distances:
42 2 0.02
43 32 0.27
44 83 0.71
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (43 bp):
TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCCAAGA
Found at i:10015562 original size:18 final size:18
Alignment explanation
Indices: 10015541--10015579 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
10015531 TGGTATAAGC
10015541 TTTATTTTTCTTCTT-ATT
1 TTTATTTTTCTT-TTGATT
10015559 TTTATTTTTCTTTTGATT
1 TTTATTTTTCTTTTGATT
10015577 TTT
1 TTT
10015580 CTTCCTTTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.10, C:0.08, G:0.03, T:0.79
Consensus pattern (18 bp):
TTTATTTTTCTTTTGATT
Found at i:10016215 original size:3 final size:3
Alignment explanation
Indices: 10016207--10016231 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
10016197 CCTTTTTAGC
10016207 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
10016232 NNNNNNNNNN
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:10018826 original size:18 final size:19
Alignment explanation
Indices: 10018799--10018837 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
10018789 TGGTGGTCTA
*
10018799 TTATTGGGTAGAAT-TTTT
1 TTATTAGGTAGAATATTTT
*
10018817 TTATTAGGTATAATATTTT
1 TTATTAGGTAGAATATTTT
10018836 TT
1 TT
10018838 GTGAAAAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.59
Consensus pattern (19 bp):
TTATTAGGTAGAATATTTT
Found at i:10019250 original size:22 final size:22
Alignment explanation
Indices: 10019209--10019265 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 22
10019199 TTTTAATTAT
10019209 ATTTATTA-TTAACAAAATTTA
1 ATTTATTATTTAACAAAATTTA
*
10019230 GTTTATTATTTAA-AAATATTTA
1 ATTTATTATTTAACAAA-ATTTA
10019252 ATTTAAATTATTTA
1 ATTT--ATTATTTA
10019266 TTTTTAAGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 10 0.33
22 12 0.40
24 8 0.27
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
ATTTATTATTTAACAAAATTTA
Found at i:10021084 original size:12 final size:12
Alignment explanation
Indices: 10021067--10021097 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
10021057 GAAGCAGGGG
10021067 AGAAAAAGCGAA
1 AGAAAAAGCGAA
*
10021079 AGAAAAAGGGAA
1 AGAAAAAGCGAA
10021091 AGAAAAA
1 AGAAAAA
10021098 TAAAAGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.71, C:0.03, G:0.26, T:0.00
Consensus pattern (12 bp):
AGAAAAAGCGAA
Found at i:10022286 original size:37 final size:38
Alignment explanation
Indices: 10022186--10022295 Score: 87
Period size: 37 Copynumber: 2.8 Consensus size: 38
10022176 GACCTCGAGT
* *
10022186 CGATGAGACACTGGGTGTCACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA--A-CTTTCTTCGGATAGATC
** ** * **
10022227 CGATGAGGTACTGGGTACCAACTTTCTTCGGCTTTA-C
1 CGATGAGACACTGGGTGTCAACTTTCTTCGGATAGATC
10022264 CGATGAGACACTGGGTGTCAACTGTTGCTTCG
1 CGATGAGACACTGGGTGTCAACT-TT-CTTCG
10022296 AACTATCAAA
Statistics
Matches: 54, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
37 19 0.35
38 13 0.24
39 6 0.11
41 16 0.30
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (38 bp):
CGATGAGACACTGGGTGTCAACTTTCTTCGGATAGATC
Found at i:10031312 original size:3 final size:3
Alignment explanation
Indices: 10031304--10031343 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
10031294 GTTGTGGCGT
*
10031304 TTG TTG TTG CTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
10031344 AAATTAGGGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.03, G:0.33, T:0.65
Consensus pattern (3 bp):
TTG
Found at i:10031374 original size:6 final size:6
Alignment explanation
Indices: 10031363--10031387 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
10031353 GAGGAATTAA
10031363 GGTTAG GGTTAG GGTTAG GGTTAG G
1 GGTTAG GGTTAG GGTTAG GGTTAG G
10031388 AATGGGGGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.52, T:0.32
Consensus pattern (6 bp):
GGTTAG
Found at i:10031568 original size:3 final size:3
Alignment explanation
Indices: 10031562--10031604 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
10031552 GGAGAAGAAA
* * *
10031562 TTG TTG TTG TTG TTG CTG TTG TTG TTG TTG TTG CTG TTT TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
10031605 AAGAGAAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.05, G:0.30, T:0.65
Consensus pattern (3 bp):
TTG
Found at i:10034775 original size:50 final size:50
Alignment explanation
Indices: 10034660--10034904 Score: 213
Period size: 50 Copynumber: 4.8 Consensus size: 50
10034650 TAATAACATA
* ** * ** * **
10034660 CCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTTTTGT-ATTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTG
* * * * **
10034709 CCAATGCCATATCCCAGATATGATCTTACATTGGAGTTCTCATATCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTG
* ** *
10034759 CCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTG
* *
10034809 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAACCTCAATGATG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GGTG
* * *
10034865 CCAATGCCATGTCCCAAACATGGCCTTACATGGGATCTCT
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
10034905 TTACCCAAAT
Statistics
Matches: 156, Mismatches: 33, Indels: 7
0.80 0.17 0.04
Matches are distributed among these distances:
49 34 0.22
50 81 0.52
53 2 0.01
56 39 0.25
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (50 bp):
CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTG
Found at i:10039156 original size:26 final size:26
Alignment explanation
Indices: 10039122--10039171 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
10039112 TCCTATAACC
*
10039122 CTCTTAGAGTTTGTTAAAAAAAAACT
1 CTCTTAGAGTTTGTAAAAAAAAAACT
10039148 CTCTTAGAGTTTGTAAAAAAAAAA
1 CTCTTAGAGTTTGTAAAAAAAAAA
10039172 AAAACACTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (26 bp):
CTCTTAGAGTTTGTAAAAAAAAAACT
Found at i:10044407 original size:16 final size:16
Alignment explanation
Indices: 10044386--10044419 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
10044376 TTCACAAAAA
10044386 TTACCAATGAGGTAAT
1 TTACCAATGAGGTAAT
* *
10044402 TTACCAGTGGGGTAAT
1 TTACCAATGAGGTAAT
10044418 TT
1 TT
10044420 TATAATTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (16 bp):
TTACCAATGAGGTAAT
Found at i:10044493 original size:25 final size:26
Alignment explanation
Indices: 10044455--10044506 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
10044445 AAGTTGTAAG
10044455 TAAAAAAATATCTTTAGA-AATTTTC
1 TAAAAAAATATCTTTAGAGAATTTTC
* *
10044480 TAAAATAATCTCTTTAGAGAATTTTC
1 TAAAAAAATATCTTTAGAGAATTTTC
10044506 T
1 T
10044507 TTCTACAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (26 bp):
TAAAAAAATATCTTTAGAGAATTTTC
Found at i:10044646 original size:16 final size:16
Alignment explanation
Indices: 10044627--10044664 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
10044617 AAATTAATAT
10044627 AATATTTATCAAGATA
1 AATATTTATCAAGATA
10044643 AATATTTATCAAGATA
1 AATATTTATCAAGATA
10044659 AATATT
1 AATATT
10044665 AGATTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.39
Consensus pattern (16 bp):
AATATTTATCAAGATA
Found at i:10054277 original size:75 final size:75
Alignment explanation
Indices: 10054133--10054278 Score: 213
Period size: 75 Copynumber: 1.9 Consensus size: 75
10054123 GACAGCATTG
* *
10054133 AATGTGAGCCCAGCTTTAGTTGGATAAACCAACAATGTTTGCGCCCAACGCTAGTTGGATATATC
1 AATGTGAGCCCAGCTTTAGTTGGATAAACCAACAATGTTTGCGCCCAACGCTAGTCGGATAAATC
10054198 GATGATAATA
66 GATGATAATA
* * * * *
10054208 AATGTGAGCCCAGCTTTAGTTGGATGAACCAACAGTGTTTGTGCTCAGCGCTAGTCGGATAAA-C
1 AATGTGAGCCCAGCTTTAGTTGGATAAACCAACAATGTTTGCGCCCAACGCTAGTCGGATAAATC
10054272 TGATGAT
66 -GATGAT
10054279 TGTGTGCCCA
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
74 1 0.02
75 62 0.98
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.28
Consensus pattern (75 bp):
AATGTGAGCCCAGCTTTAGTTGGATAAACCAACAATGTTTGCGCCCAACGCTAGTCGGATAAATC
GATGATAATA
Found at i:10057233 original size:31 final size:31
Alignment explanation
Indices: 10057154--10057222 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
10057144 GTTACAAGAT
**
10057154 AGTCATTAAACTATTTAAAAGTTTTCATTTA
1 AGTCATTAAACTATTCGAAAGTTTTCATTTA
*
10057185 AGTCATTAAACTATTCGAAAGTTTTTATTTA
1 AGTCATTAAACTATTCGAAAGTTTTCATTTA
10057216 AGTCATT
1 AGTCATT
10057223 GTATTATTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.36, C:0.10, G:0.09, T:0.45
Consensus pattern (31 bp):
AGTCATTAAACTATTCGAAAGTTTTCATTTA
Found at i:10057787 original size:43 final size:43
Alignment explanation
Indices: 10057446--10057791 Score: 369
Period size: 43 Copynumber: 8.1 Consensus size: 43
10057436 TTTCTCACGT
* ** * * * *
10057446 AAACGCCGTTAAAGAACATGATCTTTAGCGGCACTTTTACCA-C
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTA-TAGA
* ** * *
10057489 AAACGCCGCTAAAGATCATGACCTTTAGCGGCG-TTTAAATA-T
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTT-TATAGA
**
10057531 AAGTGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTATA-A
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTATAGA
* *
10057573 GAAACACCGCTAAAGGTCATGTTCTTTAGCGACGCTTTTATAAGA
1 -AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTAT-AGA
* * * * *
10057618 AAA-GCCGTTAAATGTCAAGTTCTTTAGCAGCGCTTTTATAGC
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTATAGA
* * * * *
10057660 AAACGCCGCTAAAGGTCATGTTCTTTAACGACACTTTTCTAGC
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTATAGA
*
10057703 AAACGCCGCTAAAGGTCATCTTCTTTAGCGGCGCTTTTATAGA
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTATAGA
*
10057746 AAACGCCACTAAAGGTCATGTTCTTTAGCGGCGCTTTTATAGA
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTATAGA
10057789 AAA
1 AAA
10057792 GACCACTAAC
Statistics
Matches: 256, Mismatches: 41, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
42 40 0.16
43 211 0.82
44 4 0.02
45 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (43 bp):
AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTATAGA
Found at i:10058097 original size:21 final size:19
Alignment explanation
Indices: 10058065--10058104 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 19
10058055 TCGTACTTTC
10058065 TACTCTGCTCTGCTTCCCT
1 TACTCTGCTCTGCTTCCCT
10058084 TACTACTGCCTCTGCTTCCCT
1 TACT-CTG-CTCTGCTTCCCT
10058105 CGCTGCTACC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.21
20 3 0.16
21 12 0.63
ACGTcount: A:0.07, C:0.42, G:0.10, T:0.40
Consensus pattern (19 bp):
TACTCTGCTCTGCTTCCCT
Found at i:10063181 original size:9 final size:9
Alignment explanation
Indices: 10063163--10063467 Score: 224
Period size: 9 Copynumber: 32.6 Consensus size: 9
10063153 TATTTATGTA
*
10063163 TTATGCAAG
1 TTATGTAAG
10063172 TTATGTAAG
1 TTATGTAAG
*
10063181 TTATGTGAG
1 TTATGTAAG
10063190 TTATGTAAG
1 TTATGTAAG
*
10063199 TTATGATATG
1 TTATG-TAAG
*
10063209 ATATATATAAG
1 -T-TATGTAAG
10063220 TTAT-TAAG
1 TTATGTAAG
10063228 TTATGTAAG
1 TTATGTAAG
*
10063237 TTATGTGAG
1 TTATGTAAG
*
10063246 TTATGTAAA
1 TTATGTAAG
*
10063255 TTATGGTATG
1 TTAT-GTAAG
*
10063265 ATATATATAAG
1 -T-TATGTAAG
10063276 TTAT-TAAG
1 TTATGTAAG
10063284 TTATGTAAG
1 TTATGTAAG
*
10063293 TTATGTGAG
1 TTATGTAAG
10063302 TTATGTAAG
1 TTATGTAAG
*
10063311 TTATGGTATGATA
1 TTAT-GTA--A-G
*
10063324 TATATATAAG
1 T-TATGTAAG
10063334 TTAT-TAAG
1 TTATGTAAG
*
10063342 TTATGCAAG
1 TTATGTAAG
*
10063351 TTATGTGAG
1 TTATGTAAG
*
10063360 TTATGTAAA
1 TTATGTAAG
*
10063369 TTATGATATG
1 TTATG-TAAG
*
10063379 ATATATATAAG
1 -T-TATGTAAG
10063390 TTAT-TAAG
1 TTATGTAAG
*
10063398 TTAAGTAAG
1 TTATGTAAG
*
10063407 TTATGTGAG
1 TTATGTAAG
*
10063416 TTATTTAAG
1 TTATGTAAG
*
10063425 TTATGGTATG
1 TTAT-GTAAG
*
10063435 ATATATATAAG
1 -T-TATGTAAG
10063446 TTAT-TAAG
1 TTATGTAAG
*
10063454 TTAAGTAAG
1 TTATGTAAG
10063463 TTATG
1 TTATG
10063468 GTATGACTGA
Statistics
Matches: 236, Mismatches: 38, Indels: 44
0.74 0.12 0.14
Matches are distributed among these distances:
8 38 0.16
9 143 0.61
10 19 0.08
11 17 0.07
12 13 0.06
13 3 0.01
14 3 0.01
ACGTcount: A:0.36, C:0.01, G:0.20, T:0.44
Consensus pattern (9 bp):
TTATGTAAG
Found at i:10063233 original size:56 final size:56
Alignment explanation
Indices: 10063127--10063467 Score: 502
Period size: 56 Copynumber: 6.0 Consensus size: 56
10063117 AGTATAATTA
* * * *
10063127 AGTTATATAACTTATGATATGATATATATTTATGTATTATGCAAGTTATGTAAGTTATGTG
1 AGTTATGTAAGTTATGATATGATATATA--TAAG--TTAT-TAAGTTATGTAAGTTATGTG
10063188 AGTTATGTAAGTTATGATATGATATATATAAGTTATTAAGTTATGTAAGTTATGTG
1 AGTTATGTAAGTTATGATATGATATATATAAGTTATTAAGTTATGTAAGTTATGTG
* *
10063244 AGTTATGTAAATTATGGTATGATATATATAAGTTATTAAGTTATGTAAGTTATGTG
1 AGTTATGTAAGTTATGATATGATATATATAAGTTATTAAGTTATGTAAGTTATGTG
* *
10063300 AGTTATGTAAGTTATGGTATGATATATATATAAGTTATTAAGTTATGCAAGTTATGTG
1 AGTTATGTAAGTTATGATATG--ATATATATAAGTTATTAAGTTATGTAAGTTATGTG
* *
10063358 AGTTATGTAAATTATGATATGATATATATAAGTTATTAAGTTAAGTAAGTTATGTG
1 AGTTATGTAAGTTATGATATGATATATATAAGTTATTAAGTTATGTAAGTTATGTG
* * *
10063414 AGTTATTTAAGTTATGGTATGATATATATAAGTTATTAAGTTAAGTAAGTTATG
1 AGTTATGTAAGTTATGATATGATATATATAAGTTATTAAGTTATGTAAGTTATG
10063468 GTATGACTGA
Statistics
Matches: 263, Mismatches: 15, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
56 177 0.67
57 4 0.02
58 53 0.20
59 3 0.01
61 26 0.10
ACGTcount: A:0.36, C:0.01, G:0.19, T:0.44
Consensus pattern (56 bp):
AGTTATGTAAGTTATGATATGATATATATAAGTTATTAAGTTATGTAAGTTATGTG
Found at i:10063371 original size:114 final size:112
Alignment explanation
Indices: 10063127--10063467 Score: 529
Period size: 114 Copynumber: 3.0 Consensus size: 112
10063117 AGTATAATTA
* * * *
10063127 AGTTATATAACTTATGATATGATATATATTTATGTATTATGCAAGTTATGTAAGTTATGTGAGTT
1 AGTTATGTAAATTATGATATGATATATA--TAAG--TTAT-TAAGTTATGTAAGTTATGTGAGTT
*
10063192 ATGTAAGTTATGATATGATATATATAAGTTATTAAGTTATGTAAGTTATGTG
61 ATGTAAGTTATGGTATGATATATATAAGTTATTAAGTTATGTAAGTTATGTG
*
10063244 AGTTATGTAAATTATGGTATGATATATATAAGTTATTAAGTTATGTAAGTTATGTGAGTTATGTA
1 AGTTATGTAAATTATGATATGATATATATAAGTTATTAAGTTATGTAAGTTATGTGAGTTATGTA
*
10063309 AGTTATGGTATGATATATATATAAGTTATTAAGTTATGCAAGTTATGTG
66 AGTTATGGTATG--ATATATATAAGTTATTAAGTTATGTAAGTTATGTG
* *
10063358 AGTTATGTAAATTATGATATGATATATATAAGTTATTAAGTTAAGTAAGTTATGTGAGTTATTTA
1 AGTTATGTAAATTATGATATGATATATATAAGTTATTAAGTTATGTAAGTTATGTGAGTTATGTA
*
10063423 AGTTATGGTATGATATATATAAGTTATTAAGTTAAGTAAGTTATG
66 AGTTATGGTATGATATATATAAGTTATTAAGTTATGTAAGTTATG
10063468 GTATGACTGA
Statistics
Matches: 210, Mismatches: 12, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
112 70 0.33
113 4 0.02
114 108 0.51
115 3 0.01
117 25 0.12
ACGTcount: A:0.36, C:0.01, G:0.19, T:0.44
Consensus pattern (112 bp):
AGTTATGTAAATTATGATATGATATATATAAGTTATTAAGTTATGTAAGTTATGTGAGTTATGTA
AGTTATGGTATGATATATATAAGTTATTAAGTTATGTAAGTTATGTG
Found at i:10063376 original size:170 final size:172
Alignment explanation
Indices: 10063127--10063467 Score: 551
Period size: 170 Copynumber: 2.0 Consensus size: 172
10063117 AGTATAATTA
* * *
10063127 AGTTATATAACTTATGATATGATATATATTTATGTATTATGCAAGTTATGTAAGTTATGTGAGTT
1 AGTTATATAACTTATGATATGATATATATATAAG-ATTATGCAAGTTATGCAAGTTATGTGAGTT
* *
10063192 ATGTAAGTTATGATATGATATATATAAGTTATTAAGTTATGTAAGTTATGTGAGTTATGTAAATT
65 ATGTAAATTATGATATGATATATATAAGTTATTAAGTTAAGTAAGTTATGTGAGTTATGTAAATT
*
10063257 ATGGTATGATATATATAAGTTATTAAGTTATGTAAGTTATGTG
130 ATGGTATGATATATATAAGTTATTAAGTTAAGTAAGTTATGTG
* * * *
10063300 AGTTATGTAAGTTATGGTATGATATATATATAAG-TTAT-TAAGTTATGCAAGTTATGTGAGTTA
1 AGTTATATAACTTATGATATGATATATATATAAGATTATGCAAGTTATGCAAGTTATGTGAGTTA
* *
10063363 TGTAAATTATGATATGATATATATAAGTTATTAAGTTAAGTAAGTTATGTGAGTTATTTAAGTTA
66 TGTAAATTATGATATGATATATATAAGTTATTAAGTTAAGTAAGTTATGTGAGTTATGTAAATTA
10063428 TGGTATGATATATATAAGTTATTAAGTTAAGTAAGTTATG
131 TGGTATGATATATATAAGTTATTAAGTTAAGTAAGTTATG
10063468 GTATGACTGA
Statistics
Matches: 156, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
170 123 0.79
171 4 0.03
173 29 0.19
ACGTcount: A:0.36, C:0.01, G:0.19, T:0.44
Consensus pattern (172 bp):
AGTTATATAACTTATGATATGATATATATATAAGATTATGCAAGTTATGCAAGTTATGTGAGTTA
TGTAAATTATGATATGATATATATAAGTTATTAAGTTAAGTAAGTTATGTGAGTTATGTAAATTA
TGGTATGATATATATAAGTTATTAAGTTAAGTAAGTTATGTG
Found at i:10069147 original size:41 final size:41
Alignment explanation
Indices: 10069115--10069235 Score: 197
Period size: 41 Copynumber: 3.0 Consensus size: 41
10069105 CCCACTAGAC
* *
10069115 TTATAGCCTGATTCAGATCACCGGTACGTAGCCTGCTAGGT
1 TTATAACCTGATTCAGATCACCGGCACGTAGCCTGCTAGGT
*
10069156 TTATAACCTGATTCAGATCACCGGCACGTATCCTGCTAGGT
1 TTATAACCTGATTCAGATCACCGGCACGTAGCCTGCTAGGT
**
10069197 TTATAACCTGATTCAGATCACCGGCAATTAGCCTGCTAG
1 TTATAACCTGATTCAGATCACCGGCACGTAGCCTGCTAG
10069236 ACTTAAAGTC
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 74 1.00
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.29
Consensus pattern (41 bp):
TTATAACCTGATTCAGATCACCGGCACGTAGCCTGCTAGGT
Found at i:10070015 original size:2 final size:2
Alignment explanation
Indices: 10070008--10070062 Score: 51
Period size: 2 Copynumber: 28.0 Consensus size: 2
10069998 CAATAACTTT
* * *
10070008 TA TA TA TA TA TA TG TA TA TA TA T- TC TA GCA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
*
10070049 CA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
10070063 CATGCTTATT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
1 2 0.05
2 40 0.93
3 1 0.02
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:10075304 original size:28 final size:28
Alignment explanation
Indices: 10075264--10075319 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
10075254 CTAATGAATG
10075264 TGGTAAATTACTCATTCGAGAACAACTA
1 TGGTAAATTACTCATTCGAGAACAACTA
10075292 TGGTAAATTACTCATTCGAGAACAACTA
1 TGGTAAATTACTCATTCGAGAACAACTA
10075320 ACCCGTGACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (28 bp):
TGGTAAATTACTCATTCGAGAACAACTA
Found at i:10080607 original size:16 final size:15
Alignment explanation
Indices: 10080566--10080607 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
10080556 CACTTTTTGG
10080566 GTTTTATTTT-AATA
1 GTTTTATTTTAAATA
*
10080580 GTTTAGATTTTAAATTA
1 GTTT-TATTTTAAA-TA
10080597 GTTTTATTTTA
1 GTTTTATTTTA
10080608 TTTACAAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 4 0.17
15 5 0.22
16 8 0.35
17 6 0.26
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.62
Consensus pattern (15 bp):
GTTTTATTTTAAATA
Found at i:10083710 original size:25 final size:25
Alignment explanation
Indices: 10083681--10083754 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
10083671 TAGAGATTGA
10083681 CTTTTTCAACTATTATGATTTAGTC
1 CTTTTTCAACTATTATGATTTAGTC
* * *
10083706 CTTTTT--GC--TTA--ATTAACT-
1 CTTTTTCAACTATTATGATTTAGTC
*
10083724 ATTTTTCAACTATTATGATTTAGTC
1 CTTTTTCAACTATTATGATTTAGTC
10083749 CTTTTT
1 CTTTTT
10083755 GCTTAATTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 14
0.61 0.14 0.25
Matches are distributed among these distances:
18 5 0.15
19 5 0.15
20 1 0.03
21 3 0.09
22 3 0.09
23 1 0.03
24 5 0.15
25 11 0.32
ACGTcount: A:0.23, C:0.15, G:0.07, T:0.55
Consensus pattern (25 bp):
CTTTTTCAACTATTATGATTTAGTC
Found at i:10083743 original size:43 final size:43
Alignment explanation
Indices: 10083682--10083768 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
10083672 AGAGATTGAC
10083682 TTTTTCAACTATTATGATTTAGTCCTTTTTGCTTAATTAACTA
1 TTTTTCAACTATTATGATTTAGTCCTTTTTGCTTAATTAACTA
10083725 TTTTTCAACTATTATGATTTAGTCCTTTTTGCTTAATTAACTA
1 TTTTTCAACTATTATGATTTAGTCCTTTTTGCTTAATTAACTA
10083768 T
1 T
10083769 CTAAACATTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.25, C:0.14, G:0.07, T:0.54
Consensus pattern (43 bp):
TTTTTCAACTATTATGATTTAGTCCTTTTTGCTTAATTAACTA
Found at i:10085624 original size:16 final size:16
Alignment explanation
Indices: 10085603--10085646 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
10085593 AAAGGCTTTT
10085603 TTTTAATTTGTTTTAA
1 TTTTAATTTGTTTTAA
*
10085619 TTTTAATTT-TCTTTAT
1 TTTTAATTTGT-TTTAA
*
10085635 TTTTCATTTGTT
1 TTTTAATTTGTT
10085647 CATTTTCTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 1 0.04
16 22 0.92
17 1 0.04
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.73
Consensus pattern (16 bp):
TTTTAATTTGTTTTAA
Found at i:10087263 original size:30 final size:30
Alignment explanation
Indices: 10087227--10087288 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
10087217 TCCTTAAAAG
10087227 TATGGGAACACTCAGTGATTGGGTGAGCTC
1 TATGGGAACACTCAGTGATTGGGTGAGCTC
10087257 TATGGGAACACTCAGTGATTGGGTGAGCTC
1 TATGGGAACACTCAGTGATTGGGTGAGCTC
10087287 TA
1 TA
10087289 AACTTAATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.24, C:0.16, G:0.32, T:0.27
Consensus pattern (30 bp):
TATGGGAACACTCAGTGATTGGGTGAGCTC
Found at i:10088908 original size:29 final size:29
Alignment explanation
Indices: 10088696--10088897 Score: 228
Period size: 29 Copynumber: 7.0 Consensus size: 29
10088686 ATTTGTGACA
* *
10088696 ATCTCTGTTATAAAGAAGCCTTTGTGGCG
1 ATCTCTGTTATAAGGAAGCCTTTGTGGTG
10088725 ATCTCTGTTATAAGGAAGCCTTTGTGGTG
1 ATCTCTGTTATAAGGAAGCCTTTGTGGTG
* *
10088754 ATCTCTGTTATAAGAAAGCCTTTGTAGTG
1 ATCTCTGTTATAAGGAAGCCTTTGTGGTG
*
10088783 AT-TATTGTTATAAAGG-AGCCTTTGTGGTG
1 ATCT-CTGTTAT-AAGGAAGCCTTTGTGGTG
* * * ***
10088812 ATCTCTATCATAAGGAAGCCTTTCTAACG
1 ATCTCTGTTATAAGGAAGCCTTTGTGGTG
* * * **
10088841 ATCTCTATTGTAAGGAAGCCTTTATGGCA
1 ATCTCTGTTATAAGGAAGCCTTTGTGGTG
10088870 ATCTCTGTTATAAGGAAGCCTTTGTGGT
1 ATCTCTGTTATAAGGAAGCCTTTGTGGT
10088898 TGTTTTTGTT
Statistics
Matches: 145, Mismatches: 24, Indels: 8
0.82 0.14 0.05
Matches are distributed among these distances:
28 5 0.03
29 136 0.94
30 4 0.03
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (29 bp):
ATCTCTGTTATAAGGAAGCCTTTGTGGTG
Found at i:10095517 original size:36 final size:36
Alignment explanation
Indices: 10095460--10095533 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 36
10095450 GGAGGAGCAC
*
10095460 ATCAGTCAGAATAGATTCGAAAGCCTACTGAACTGA
1 ATCAGTCAAAATAGATTCGAAAGCCTACTGAACTGA
* * *
10095496 ATCAGTCAAAATA-TTTCCGAAAGGCTGCTGAACTGA
1 ATCAGTCAAAATAGATT-CGAAAGCCTACTGAACTGA
10095532 AT
1 AT
10095534 AGAGTTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 2 0.06
36 31 0.94
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (36 bp):
ATCAGTCAAAATAGATTCGAAAGCCTACTGAACTGA
Found at i:10095545 original size:16 final size:16
Alignment explanation
Indices: 10095524--10095556 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
10095514 GAAAGGCTGC
10095524 TGAACTGAATAGAGTT
1 TGAACTGAATAGAGTT
10095540 TGAACTGAATAGAGTT
1 TGAACTGAATAGAGTT
10095556 T
1 T
10095557 ACTCTTTCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.33
Consensus pattern (16 bp):
TGAACTGAATAGAGTT
Found at i:10102066 original size:18 final size:18
Alignment explanation
Indices: 10102043--10102078 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
10102033 TGAGTCATCG
10102043 AACGAATCCAAAATGGAA
1 AACGAATCCAAAATGGAA
10102061 AACGAATCCAAAATGGAA
1 AACGAATCCAAAATGGAA
10102079 GCTAACTCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.17, G:0.17, T:0.11
Consensus pattern (18 bp):
AACGAATCCAAAATGGAA
Done.