Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold78
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: 2238306
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 23262 characters in sequence are not A, C, G, or T
File 6 of 15
Found at i:843674 original size:18 final size:17
Alignment explanation
Indices: 843632--843675 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
843622 TAAGTAATAA
843632 TAATTTAAAAAATAATT
1 TAATTTAAAAAATAATT
843649 TAATTTTAAAAAATTACA-T
1 TAA-TTTAAAAAA-TA-ATT
843668 TAATTTAA
1 TAATTTAA
843676 TTAATAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 3 0.12
18 14 0.58
19 6 0.25
20 1 0.04
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
TAATTTAAAAAATAATT
Found at i:847551 original size:13 final size:13
Alignment explanation
Indices: 847533--847560 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
847523 TTTTAACCTT
847533 TAAACTCTAAGTA
1 TAAACTCTAAGTA
847546 TAAACTCTAAGTA
1 TAAACTCTAAGTA
847559 TA
1 TA
847561 TAGATAACAT
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:0.46, C:0.14, G:0.07, T:0.32
Consensus pattern (13 bp):
TAAACTCTAAGTA
Found at i:847794 original size:16 final size:16
Alignment explanation
Indices: 847773--847810 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
847763 AACTATATTT
*
847773 AATTATTGTTAAATTA
1 AATTATTATTAAATTA
847789 AATTATTATTAAATTA
1 AATTATTATTAAATTA
*
847805 TATTAT
1 AATTAT
847811 AATTCAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
AATTATTATTAAATTA
Found at i:848100 original size:25 final size:27
Alignment explanation
Indices: 848057--848111 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
848047 TATTTTTAAA
** *
848057 ATTTTTAAAATAATGATAAT-TAATTT
1 ATTTTTAAAATAAAAATAATATAATAT
848083 ATTTTT-AAATAAAAATAATATAATAT
1 ATTTTTAAAATAAAAATAATATAATAT
848109 ATT
1 ATT
848112 AATATCAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 11 0.44
26 14 0.56
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (27 bp):
ATTTTTAAAATAAAAATAATATAATAT
Found at i:850237 original size:26 final size:23
Alignment explanation
Indices: 850180--850244 Score: 76
Period size: 26 Copynumber: 2.7 Consensus size: 23
850170 ACGATCCTTT
*
850180 TAATTTTAATTATATTTTATATA
1 TAATTTAAATTATATTTTATATA
*
850203 TAATATAAATATATATGTTTATATAA
1 TAATTTAAAT-TATAT-TTTATAT-A
850229 TAATTTAAAATTATAT
1 TAATTT-AAATTATAT
850245 AATATACAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
23 8 0.23
24 5 0.14
25 7 0.20
26 11 0.31
27 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TAATTTAAATTATATTTTATATA
Found at i:850760 original size:2 final size:2
Alignment explanation
Indices: 850753--850790 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
850743 TGATGTATAT
*
850753 TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
850791 ACGCACACAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:851239 original size:2 final size:2
Alignment explanation
Indices: 851227--851258 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
851217 ATCCATGGAG
*
851227 TA TA TA CA 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 TA TA TA
851259 ATGGTTTGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:852170 original size:16 final size:17
Alignment explanation
Indices: 852144--852177 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
852134 CGAATTCGAA
852144 TATTTTCAAATTTAAAT
1 TATTTTCAAATTTAAAT
852161 TATTTT-AAATTTAAAT
1 TATTTTCAAATTTAAAT
852177 T
1 T
852178 TGATTTTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTTTCAAATTTAAAT
Found at i:853026 original size:27 final size:28
Alignment explanation
Indices: 852961--853026 Score: 66
Period size: 27 Copynumber: 2.4 Consensus size: 28
852951 CATTTTTATG
* *
852961 CCCTTCTCCTATCTGACTAAACCGATAGC
1 CCCTTCT-CTTTCTCACTAAACCGATAGC
*
852990 CTCTTC-CTTTCTCACTAAACC-AGTA-C
1 CCCTTCTCTTTCTCACTAAACCGA-TAGC
853016 CCCTTCTCTTT
1 CCCTTCTCTTT
853027 TCAGATTGCC
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
26 7 0.23
27 19 0.61
29 5 0.16
ACGTcount: A:0.20, C:0.39, G:0.06, T:0.35
Consensus pattern (28 bp):
CCCTTCTCTTTCTCACTAAACCGATAGC
Found at i:854444 original size:16 final size:16
Alignment explanation
Indices: 854420--854450 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
854410 TAAATATTTT
854420 TATTAATTATTTATTA
1 TATTAATTATTTATTA
*
854436 TATTTATTATTTATT
1 TATTAATTATTTATT
854451 TAACATTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATTAATTATTTATTA
Found at i:855012 original size:15 final size:15
Alignment explanation
Indices: 854988--855019 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
854978 GAATGTGTTA
854988 AATATAAATATATTT
1 AATATAAATATATTT
*
855003 AATATGAATATATTT
1 AATATAAATATATTT
855018 AA
1 AA
855020 ATTTTTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (15 bp):
AATATAAATATATTT
Found at i:855389 original size:13 final size:13
Alignment explanation
Indices: 855341--855389 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
855331 AATATAAATG
855341 TAATAAATATTATCA
1 TAATAAATATTA--A
855356 TAATTAAATATTAA
1 TAA-TAAATATTAA
**
855370 TTTTAAATATTAA
1 TAATAAATATTAA
855383 TAATAAA
1 TAATAAA
855390 AAATTAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 15 0.52
14 2 0.07
15 3 0.10
16 9 0.31
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (13 bp):
TAATAAATATTAA
Found at i:856245 original size:14 final size:15
Alignment explanation
Indices: 856217--856248 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
856207 CGAGTTTAAA
856217 TTATTTTATATTTTT
1 TTATTTTATATTTTT
856232 TTATTTTA-ATTTTT
1 TTATTTTATATTTTT
856246 TTA
1 TTA
856249 AAATATCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (15 bp):
TTATTTTATATTTTT
Found at i:857935 original size:9 final size:9
Alignment explanation
Indices: 857921--857956 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
857911 AAGATTTTTT
857921 AAAATATTA
1 AAAATATTA
857930 AAAATATTA
1 AAAATATTA
857939 AAAAT-TTA
1 AAAATATTA
857947 AAAA-ATTA
1 AAAATATTA
857955 AA
1 AA
857957 TAAATTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 12 0.46
9 14 0.54
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
AAAATATTA
Found at i:857954 original size:16 final size:18
Alignment explanation
Indices: 857921--857956 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
857911 AAGATTTTTT
857921 AAAATATTAAAAATATTA
1 AAAATATTAAAAATATTA
857939 AAAAT-TTAAAAA-ATTA
1 AAAATATTAAAAATATTA
857955 AA
1 AA
857957 TAAATTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 7 0.39
18 5 0.28
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAATATTAAAAATATTA
Found at i:857961 original size:9 final size:8
Alignment explanation
Indices: 857919--857964 Score: 56
Period size: 8 Copynumber: 5.5 Consensus size: 8
857909 TAAAGATTTT
*
857919 TTAAAATA
1 TTAAAAAA
857927 TTAAAAATA
1 TTAAAAA-A
*
857936 TTAAAAAT
1 TTAAAAAA
857944 TTAAAAAA
1 TTAAAAAA
857952 TTAAATAAA
1 TTAAA-AAA
857961 TTAA
1 TTAA
857965 TATTAAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
8 18 0.55
9 15 0.45
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
TTAAAAAA
Found at i:859284 original size:23 final size:23
Alignment explanation
Indices: 859253--859299 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
859243 GCTCAAATAC
859253 ACCTATCATTTATAGATATTATA
1 ACCTATCATTTATAGATATTATA
*
859276 ACCTGTCATTTATAGATATTATA
1 ACCTATCATTTATAGATATTATA
859299 A
1 A
859300 AATGAACCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.43
Consensus pattern (23 bp):
ACCTATCATTTATAGATATTATA
Found at i:864452 original size:85 final size:86
Alignment explanation
Indices: 864285--864443 Score: 191
Period size: 86 Copynumber: 1.9 Consensus size: 86
864275 GGTTAAATCG
* * * ***
864285 ACAAGTCAACAAAGGATGAAAAGAATTTACTTGGGACTAAGTCAACAGGTAGCTGTTGAATAAAA
1 ACAAGTCAACAAAGGATGAAAAGAATTTACTTGGGACTAAGCCAACAAGTAACTAAAGAATAAAA
*
864350 AAGTTGACCGGGCATGAACCA
66 AAGTTAACCGGGCATGAACCA
* *
864371 ACAAGTCAACAAAGGATGAAAAG-ATTTA-TTCGGGACTAAGCCGACAAGTAAAC-AAAGGAT-A
1 ACAAGTCAACAAAGGATGAAAAGAATTTACTT-GGGACTAAGCCAACAAGT-AACTAAAGAATAA
864432 AAAAGTTAACCG
64 AAAAGTTAACCG
864444 AGAGATGAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
84 14 0.23
85 23 0.37
86 25 0.40
ACGTcount: A:0.45, C:0.15, G:0.22, T:0.18
Consensus pattern (86 bp):
ACAAGTCAACAAAGGATGAAAAGAATTTACTTGGGACTAAGCCAACAAGTAACTAAAGAATAAAA
AAGTTAACCGGGCATGAACCA
Found at i:864777 original size:84 final size:83
Alignment explanation
Indices: 864586--864943 Score: 321
Period size: 85 Copynumber: 4.2 Consensus size: 83
864576 AAATTTACTT
* * * *
864586 GGGACTAAGTCGACAGGTAAACAATGGGATGAA-GGTTGACCGAAGACTGAGTTGACAAGTCA-C
1 GGGACTAAGCCGA-AGGTAAACAAT-GGATGAAGGGTTGACCGGAGACTGAGCTGACAGGTCACC
* * * *
864649 CATCGGGGTAATAGATTTACCG
64 CA-AGGGATAA-GGGTTTACCG
* * * * * * * *
864671 AGGACTAAGCCGACGGGCAAACAATGGATGAAGGGTTGACCGGGGACTAAACCGACAAGTCACCC
1 GGGACTAAGCCGA-AGGTAAACAATGGATGAAGGGTTGACCGGAGACTGAGCTGACAGGTCACCC
*
864736 AAGGGATAAGGGTTTACCA
65 AAGGGATAAGGGTTTACCG
* * *
864755 GGGACTGAGCCGATAGGTAAACAAAGGATGAA-GGTTGACCGGAGACTGAGCTGACAGGTCA-AC
1 GGGACTAAGCCGA-AGGTAAACAATGGATGAAGGGTTGACCGGAGACTGAGCTGACAGGTCACCC
** ** *
864818 AAAAGATGGGAGGTTTAACG
65 AAGGGATAAG-GGTTTACCG
* *
864838 GGGACTAAGCCGAAGGGTAAACCATGGATGAAGGGTTGACCGGAGATTGAGCTGACAGGTCACCA
1 GGGACTAAGCCGAA-GGTAAACAATGGATGAAGGGTTGACCGGAGACTGAGCTGACAGGTCACC-
* *
864903 TAAGGG-TAATGGGTTTACTG
64 CAAGGGATAA-GGGTTTACCG
864923 GGGACTAAGCCGACAGGTAAA
1 GGGACTAAGCCGA-AGGTAAA
864944 TAATAAGATG
Statistics
Matches: 219, Mismatches: 45, Indels: 18
0.78 0.16 0.06
Matches are distributed among these distances:
82 8 0.04
83 58 0.26
84 68 0.31
85 77 0.35
86 8 0.04
ACGTcount: A:0.33, C:0.17, G:0.33, T:0.17
Consensus pattern (83 bp):
GGGACTAAGCCGAAGGTAAACAATGGATGAAGGGTTGACCGGAGACTGAGCTGACAGGTCACCCA
AGGGATAAGGGTTTACCG
Found at i:864849 original size:83 final size:84
Alignment explanation
Indices: 864672--864899 Score: 246
Period size: 83 Copynumber: 2.7 Consensus size: 84
864662 GATTTACCGA
* * * * * * * * *
864672 GGACTAAGCCGACGGGCAAACAATGGATGAAGGGTTGACCGGGGACTAAACCGACAAGTCACCCA
1 GGACTAAGCCGAAGGGTAAACAAAGGATGAAGGGTTGACCGGAGACTGAGCTGACAGGTCA-ACA
** ** *
864737 AGGGATAAG-GGTTTACCAG
65 AAAGATGGGAGGTTTAACAG
*
864756 GGACTGAGCCGATA-GGTAAACAAAGGATGAA-GGTTGACCGGAGACTGAGCTGACAGGTCAACA
1 GGACTAAGCCGA-AGGGTAAACAAAGGATGAAGGGTTGACCGGAGACTGAGCTGACAGGTCAACA
*
864819 AAAGATGGGAGGTTTAACGG
65 AAAGATGGGAGGTTTAACAG
* * *
864839 GGACTAAGCCGAAGGGTAAACCATGGATGAAGGGTTGACCGGAGATTGAGCTGACAGGTCA
1 GGACTAAGCCGAAGGGTAAACAAAGGATGAAGGGTTGACCGGAGACTGAGCTGACAGGTCA
864900 CCATAAGGGT
Statistics
Matches: 120, Mismatches: 20, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
82 8 0.07
83 58 0.48
84 54 0.45
ACGTcount: A:0.33, C:0.18, G:0.34, T:0.15
Consensus pattern (84 bp):
GGACTAAGCCGAAGGGTAAACAAAGGATGAAGGGTTGACCGGAGACTGAGCTGACAGGTCAACAA
AAGATGGGAGGTTTAACAG
Found at i:865086 original size:42 final size:42
Alignment explanation
Indices: 864971--865476 Score: 185
Period size: 42 Copynumber: 11.9 Consensus size: 42
864961 TTTCTTGGGA
* * * *
864971 CTGAGTCGACAGGCAAATAAAGAGATGAAGAAGTCTCCTGGGT
1 CTGAGCCGACAGGCAGACAAAGA-ATGAAGAAGTCTCCTGGAT
* * ** * *
865014 CTGAGCCGACGGGCAGACGATTAATAAAGAAGTCTCTTGGAT
1 CTGAGCCGACAGGCAGACAAAGAATGAAGAAGTCTCCTGGAT
* * * *
865056 CTGAGCCTATAGGTAGACAAAGAATGAAGAAGTCTCC-CGAGT
1 CTGAGCCGACAGGCAGACAAAGAATGAAGAAGTCTCCTGGA-T
* * * * *
865098 CTAAGCCGA-TGAGCAAACAAA-AGATGAAAAAGTCT-CTCGGGT
1 CTGAGCCGACAG-GCAGACAAAGA-ATGAAGAAGTCTCCT-GGAT
* * * * *
865140 CTAAGCTGACGGGCAGACGAAAG-ATAAATAAGTCTCCTAGG-T
1 CTGAGCCGACAGGCAGAC-AAAGAATGAAGAAGTCTCCT-GGAT
* * * * * * *
865182 CTAAGCTGACAGGCAAATAAAGAAAGGATAAAGAAGGTCTCCCGGGT
1 CTGAGCCGACAGGCAGACAAAG--A--ATGAAGAA-GTCTCCTGGAT
* * * * * *
865229 CTAAGTCAACGGGCAGA-AAAGAGATGAAGAAGTCT-TTCGAGT
1 CTGAGCCGACAGGCAGACAAAGA-ATGAAGAAGTCTCCTGGA-T
* * * * *
865271 CTGAGCTGACGGGCA-AAAAAGAGATGAAGAAGTCTCCCGGGT
1 CTGAGCCGACAGGCAGACAAAGA-ATGAAGAAGTCTCCTGGAT
* * * *
865313 CTAAGCCGACGGGTAGA-AAAGAGATGAAGAAATCTTCC--GAGT
1 CTGAGCCGACAGGCAGACAAAGA-ATGAAGAAGTC-TCCTGGA-T
** *
865355 CTGAGCCGATGGGCAGA-AAAGAGATGAAGAAGTCTCCCAGG-T
1 CTGAGCCGACAGGCAGACAAAGA-ATGAAGAAGTCT-CCTGGAT
* * * * * *
865397 CTAAGCCGATAGGCAAACAAAGAGATGACGAAGTCTCCCGGGT
1 CTGAGCCGACAGGCAGACAAAGA-ATGAAGAAGTCTCCTGGAT
* * * *
865440 CTAAGCCGACGGGCAGACAAAGGATAAAGAAGGTCTC
1 CTGAGCCGACAGGCAGACAAAGAATGAAGAA-GTCTC
865477 TAGTGGTTGG
Statistics
Matches: 358, Mismatches: 77, Indels: 56
0.73 0.16 0.11
Matches are distributed among these distances:
41 13 0.04
42 231 0.65
43 80 0.22
44 2 0.01
46 13 0.04
47 19 0.05
ACGTcount: A:0.36, C:0.19, G:0.29, T:0.17
Consensus pattern (42 bp):
CTGAGCCGACAGGCAGACAAAGAATGAAGAAGTCTCCTGGAT
Found at i:865173 original size:84 final size:83
Alignment explanation
Indices: 865074--865448 Score: 319
Period size: 84 Copynumber: 4.4 Consensus size: 83
865064 ATAGGTAGAC
*
865074 AAAGA-ATGAAGAAGTCTCCCGAGTCTAAGCCGATGAGCAAACAAAAGATGAAAAAGTCTCTCGG
1 AAAGAGATGAAGAAGTCTCCCGAGTCTAAGCCGATGAGCAAA-AAAAGATGAAAAAGTCTCCCGG
*
865138 GTCTAAGCTGACGGGCAGA
65 GTCTAAGCCGACGGGCAGA
* * * * * *
865157 CGAA-AGATAAATAAGTCT-CCTAGGTCTAAGCTGA-CAGGCAAATAAAGAAAGGAT-AAAGAAG
1 -AAAGAGATGAAGAAGTCTCCCGA-GTCTAAGCCGATGA-GC--A-AAA-AAA-GATGAAA-AA-
* *
865218 GTCTCCCGGGTCTAAGTCAACGGGCAGA
56 GTCTCCCGGGTCTAAGCCGACGGGCAGA
** * * * * *
865246 AAAGAGATGAAGAAGTCTTTCGAGTCTGAGCTGACGGGCAAAAAAGAGATGAAGAAGTCTCCCGG
1 AAAGAGATGAAGAAGTCTCCCGAGTCTAAGCCGATGAGCAAAAAA-AGATGAAAAAGTCTCCCGG
*
865311 GTCTAAGCCGACGGGTAGA
65 GTCTAAGCCGACGGGCAGA
* * * * * * *
865330 AAAGAGATGAAGAAATCTTCCGAGTCTGAGCCGATGGGCAGAAAAGAGATGAAGAAGTCTCCCAG
1 AAAGAGATGAAGAAGTCTCCCGAGTCTAAGCCGATGAGCA-AAAAAAGATGAAAAAGTCTCCCGG
** *
865395 GTCTAAGCCGATAGGCAAA
65 GTCTAAGCCGACGGGCAGA
* *
865414 CAAAGAGATGACGAAGTCTCCCGGGTCTAAGCCGA
1 -AAAGAGATGAAGAAGTCTCCCGAGTCTAAGCCGA
865449 CGGGCAGACA
Statistics
Matches: 237, Mismatches: 37, Indels: 33
0.77 0.12 0.11
Matches are distributed among these distances:
83 5 0.02
84 118 0.50
85 40 0.17
86 8 0.03
87 9 0.04
88 7 0.03
89 48 0.20
90 2 0.01
ACGTcount: A:0.37, C:0.19, G:0.28, T:0.16
Consensus pattern (83 bp):
AAAGAGATGAAGAAGTCTCCCGAGTCTAAGCCGATGAGCAAAAAAAGATGAAAAAGTCTCCCGGG
TCTAAGCCGACGGGCAGA
Found at i:865399 original size:215 final size:210
Alignment explanation
Indices: 864977--865471 Score: 509
Period size: 215 Copynumber: 2.3 Consensus size: 210
864967 GGGACTGAGT
* * * * * * ***
864977 CGACAGGCAAATAAAGAGATGAAGAAGTCTCCTGGGTCTGAGCCGACGGGCAGACGATTAATAAA
1 CGACAGGCAAACAAAGAGATAAAGAAGTCTCCCGGGTCTAAGCCAACGGGCAGACAAAGGATAAA
* ** * *
865042 GAAGTCTCTTGGA-TCTGAGCCT-ATAGGTAGACAAAGAATGAAGAAGTCTCCCGAGTCTAAGCC
66 GAAGTCT-TTCGAGTCTGAG-CTGACGGGCA-AAAAAGAATGAAGAAGTCTCCCGAGTCTAAGCC
* * * * *
865105 GATGAGCAAACAAAAGATGAAAAAGTCTCTCGGGTCTAAGCTGACGGGCAGACGAAAGATAAATA
128 GACGAGCAAACAAAAGATGAAAAAGTCTCTCGAGTCTAAGCCGACGGGCAGACAAAAGATAAAGA
*
865170 AGTCTCCTAGGTCTAAGC
193 AGTCTCCCAGGTCTAAGC
* * *
865188 TGACAGGCAAATAAAGAAAGGATAAAGAAGGTCTCCCGGGTCTAAGTCAACGGGCAGA-AAAGAG
1 CGACAGGCAAACAAAG--A-GATAAAGAA-GTCTCCCGGGTCTAAGCCAACGGGCAGACAAAG-G
* *
865252 ATGAAGAAGTCTTTCGAGTCTGAGCTGACGGGCAAAAAAGAGATGAAGAAGTCTCCCGGGTCTAA
61 ATAAAGAAGTCTTTCGAGTCTGAGCTGACGGGCAAAAAAGA-ATGAAGAAGTCTCCCGAGTCTAA
* * * * *
865317 GCCGACGGGTAGAA-AAGAGATGAAGAAA-TCT-TCCGAGTCTGAGCCGATGGGCAGA-AAAGAG
125 GCCGACGAGCA-AACAAAAGATGAA-AAAGTCTCT-CGAGTCTAAGCCGACGGGCAGACAAA-AG
*
865378 ATGAAGAAGTCTCCCAGGTCTAAGC
186 ATAAAGAAGTCTCCCAGGTCTAAGC
* * * *
865403 CGATAGGCAAACAAAGAGATGACGAAGTCTCCCGGGTCTAAGCCGACGGGCAGACAAAGGATAAA
1 CGACAGGCAAACAAAGAGATAAAGAAGTCTCCCGGGTCTAAGCCAACGGGCAGACAAAGGATAAA
865468 GAAG
66 GAAG
865472 GTCTCTAGTG
Statistics
Matches: 234, Mismatches: 37, Indels: 26
0.79 0.12 0.09
Matches are distributed among these distances:
211 50 0.21
212 11 0.05
213 2 0.01
214 24 0.10
215 142 0.61
216 5 0.02
ACGTcount: A:0.37, C:0.18, G:0.29, T:0.16
Consensus pattern (210 bp):
CGACAGGCAAACAAAGAGATAAAGAAGTCTCCCGGGTCTAAGCCAACGGGCAGACAAAGGATAAA
GAAGTCTTTCGAGTCTGAGCTGACGGGCAAAAAAGAATGAAGAAGTCTCCCGAGTCTAAGCCGAC
GAGCAAACAAAAGATGAAAAAGTCTCTCGAGTCTAAGCCGACGGGCAGACAAAAGATAAAGAAGT
CTCCCAGGTCTAAGC
Found at i:865441 original size:127 final size:126
Alignment explanation
Indices: 865070--865470 Score: 342
Period size: 131 Copynumber: 3.1 Consensus size: 126
865060 GCCTATAGGT
* * * * * * * *
865070 AGACAAAGAATGAAGAAGTCTCCCGAGTCTAAGCCGATGAGCA-AACAAAAGATGAAAAAGTCTC
1 AGACAAAGGATAAAGAAATCTTCCGAGTCTGAGCCGATGGGCAGAA-AAGAGATGAAGAAGTCTC
* * * * ** * * ** * *
865134 TCGGGTCTAAGCTGACGGGCAGACGAA-AGATAAATAAGTCTCCTAGGTCTAAGCTGACAGGC
65 CCGAGTCTAAGCCGACAGGCA-AAAAAGAGATGAAGAAGTCTCCCGGGTCTAAGCCGACGGGC
* * * * * * * * *
865196 AAATAAAGAAAGGATAAAGAAGGTCTCCCGGGTCTAAGTCAACGGGCAGAAAAGAGATGAAGAAG
1 ----AGACAAAGGATAAAGAA-ATCTTCCGAGTCTGAGCCGATGGGCAGAAAAGAGATGAAGAAG
** * * *
865261 TCTTTCGAGTCTGAGCTGACGGGCAAAAAAGAGATGAAGAAGTCTCCCGGGTCTAAGCCGACGGG
61 TCTCCCGAGTCTAAGCCGACAGGCAAAAAAGAGATGAAGAAGTCTCCCGGGTCTAAGCCGACGGG
*
865326 T
126 C
*
865327 AGA-AAAGAGATGAAGAAATCTTCCGAGTCTGAGCCGATGGGCAGAAAAGAGATGAAGAAGTCTC
1 AGACAAAG-GATAAAGAAATCTTCCGAGTCTGAGCCGATGGGCAGAAAAGAGATGAAGAAGTCTC
* *
865391 CC-AGGTCTAAGCCGATAGGCAAACAAAGAGATGACGAAGTCTCCCGGGTCTAAGCCGACGGGC
65 CCGA-GTCTAAGCCGACAGGCAAA-AAAGAGATGAAGAAGTCTCCCGGGTCTAAGCCGACGGGC
865454 AGACAAAGGATAAAGAA
1 AGACAAAGGATAAAGAA
865471 GGTCTCTAGT
Statistics
Matches: 223, Mismatches: 41, Indels: 17
0.79 0.15 0.06
Matches are distributed among these distances:
125 1 0.00
126 59 0.26
127 58 0.26
128 4 0.02
130 16 0.07
131 83 0.37
132 2 0.01
ACGTcount: A:0.38, C:0.18, G:0.28, T:0.15
Consensus pattern (126 bp):
AGACAAAGGATAAAGAAATCTTCCGAGTCTGAGCCGATGGGCAGAAAAGAGATGAAGAAGTCTCC
CGAGTCTAAGCCGACAGGCAAAAAAGAGATGAAGAAGTCTCCCGGGTCTAAGCCGACGGGC
Found at i:866181 original size:73 final size:73
Alignment explanation
Indices: 866041--866181 Score: 203
Period size: 73 Copynumber: 1.9 Consensus size: 73
866031 TAAATACTAT
* * * *
866041 TGTTATCTAAAATGCAGATGCAGGTGAAACGATGCAAATGCAAACATCAATAAAAGGGCAAATGC
1 TGTTATCTAAAATGCAGATGCAAGTGAAACAATGCAAATGCAAACATCAATAAAAGGACAAAAGC
866106 ATATGGAA
66 ATATGGAA
* * *
866114 TGTTATCTAAAATGTAGATGCAAGTGAAACAATGCAAATGCAAGCATCAATAGGAA-GACAAAAG
1 TGTTATCTAAAATGCAGATGCAAGTGAAACAATGCAAATGCAAACATCAATA-AAAGGACAAAAG
866178 CATA
65 CATA
866182 CAAAAGATGC
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
73 58 0.97
74 2 0.03
ACGTcount: A:0.45, C:0.13, G:0.21, T:0.21
Consensus pattern (73 bp):
TGTTATCTAAAATGCAGATGCAAGTGAAACAATGCAAATGCAAACATCAATAAAAGGACAAAAGC
ATATGGAA
Found at i:872549 original size:11 final size:11
Alignment explanation
Indices: 872533--872571 Score: 53
Period size: 10 Copynumber: 3.5 Consensus size: 11
872523 CGTTTTTCTA
872533 TTTTTTCCTTT
1 TTTTTTCCTTT
872544 TTTTTT-CTTT
1 TTTTTTCCTTT
872554 TTTTTCTCTCTTT
1 TTTTT-TC-CTTT
872567 TTTTT
1 TTTTT
872572 GCCCGAGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 9 0.36
11 7 0.28
13 9 0.36
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTCCTTT
Found at i:872550 original size:20 final size:22
Alignment explanation
Indices: 872525--872571 Score: 71
Period size: 20 Copynumber: 2.2 Consensus size: 22
872515 AATCCCATCG
872525 TTTTTCTATTTTTTC-CT-TTT
1 TTTTTCTATTTTTTCTCTCTTT
*
872545 TTTTTCTTTTTTTTCTCTCTTT
1 TTTTTCTATTTTTTCTCTCTTT
872567 TTTTT
1 TTTTT
872572 GCCCGAGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 14 0.58
21 2 0.08
22 8 0.33
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (22 bp):
TTTTTCTATTTTTTCTCTCTTT
Found at i:873444 original size:167 final size:165
Alignment explanation
Indices: 873106--873470 Score: 422
Period size: 167 Copynumber: 2.2 Consensus size: 165
873096 ATATTAGATG
* * * * *
873106 AATTTTAAAT-CAAGAAAAATCCCCCCGAAAATATTTACGGAGTAGAAAACTCGATTTTTTAAAA
1 AATTTTAAATCCATGAAAAATCCCCCCGAAAAAAATTACGAAGTAGAAAACTCGATTTTCTAAAA
*
873170 ACAGAATAATTTCAAAGAAAAATTCAAAACTCATGAAAATAAATTAATTTGTCAAAACAGATTTA
66 ACAGAATAATTTCAAAGAAAAATTAAAAACTCATGAAAATAAATTAATTTGTCAAAACAGATTTA
* * *
873235 GTATGAATTAAATAATGATATTTGATGAATTTTAAA
131 G-ATGAATCAAATAATAATATTTGATAAATTTTAAA
* *
873271 AATTTTAAATCCATGAAAAATTCCCCCGAAAAAAATTATGAAGTAGAAAA-TAACG-TATTTCTA
1 AATTTTAAATCCATGAAAAATCCCCCCGAAAAAAATTACGAAGTAGAAAACT--CGAT-TTTCTA
* * * * *
873334 AAAA-AGAGA-AATTTCAAGGAAAAATTTAAAAACTTATGAAAATTAATTAATTTTTGAAAACTA
63 AAAACAGA-ATAATTTCAAAGAAAAA-TTAAAAACTCATGAAAATAAATTAATTTGTCAAAAC-A
*
873397 -ATTTA-ATGAGGATCAAATGATAATATTTGATAAATTTTAAA
125 GATTTAGATGA--ATCAAATAATAATATTTGATAAATTTTAAA
* *
873438 AATTTTAAATCCATG-AAAATCCTCTCGAAAAAA
1 AATTTTAAATCCATGAAAAATCCCCCCGAAAAAA
873471 TTTTCAGAAA
Statistics
Matches: 171, Mismatches: 20, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
165 15 0.09
166 66 0.39
167 89 0.52
168 1 0.01
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.31
Consensus pattern (165 bp):
AATTTTAAATCCATGAAAAATCCCCCCGAAAAAAATTACGAAGTAGAAAACTCGATTTTCTAAAA
ACAGAATAATTTCAAAGAAAAATTAAAAACTCATGAAAATAAATTAATTTGTCAAAACAGATTTA
GATGAATCAAATAATAATATTTGATAAATTTTAAA
Found at i:874409 original size:18 final size:18
Alignment explanation
Indices: 874372--874428 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
874362 TATATTATAA
*
874372 TTATATTTA-A-AATATT
1 TTATATTTATATAATTTT
874388 TTATATTTATATAATTTT
1 TTATATTTATATAATTTT
*
874406 TTATATTT-TAATAATTAT
1 TTATATTTAT-ATAATTTT
874424 TTATA
1 TTATA
874429 CGTTAATACT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
16 9 0.25
17 2 0.06
18 25 0.69
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTATATTTATATAATTTT
Found at i:874434 original size:18 final size:18
Alignment explanation
Indices: 874398--874436 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
874388 TTATATTTAT
* **
874398 ATAATTTTTTATATTTTA
1 ATAATTATTTATACGTTA
874416 ATAATTATTTATACGTTA
1 ATAATTATTTATACGTTA
874434 ATA
1 ATA
874437 CTTTAACAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (18 bp):
ATAATTATTTATACGTTA
Found at i:874660 original size:27 final size:28
Alignment explanation
Indices: 874604--874676 Score: 78
Period size: 27 Copynumber: 2.6 Consensus size: 28
874594 TCTTGTATTC
*
874604 AAATATTTTATTATATTATAATTATATTTA
1 AAATATTTTA-TAT-TTATAATAATATTTA
*
874634 AAATATTTTATATTTAT-ATAATTTTTA
1 AAATATTTTATATTTATAATAATATTTA
*
874661 ATAT-TTTTATACTTTA
1 AAATATTTTATA-TTTA
874677 ACAATAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
26 7 0.18
27 15 0.38
28 4 0.10
29 3 0.08
30 10 0.26
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (28 bp):
AAATATTTTATATTTATAATAATATTTA
Found at i:874666 original size:18 final size:18
Alignment explanation
Indices: 874625--874671 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
874615 TATATTATAA
874625 TTATATTTA-A-AATATT
1 TTATATTTATATAATATT
874641 TTATATTTATATAAT-TT
1 TTATATTTATATAATATT
*
874658 TTAATATTTTTATA
1 TT-ATATTTATATA
874672 CTTTAACAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 9 0.33
17 5 0.19
18 13 0.48
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATATTTATATAATATT
Found at i:874915 original size:16 final size:16
Alignment explanation
Indices: 874865--874985 Score: 81
Period size: 16 Copynumber: 7.8 Consensus size: 16
874855 TATTTAAATA
*
874865 TTTTATTATATAATAAT
1 TTTTATTATAT-ATATT
* *
874882 TTATATT-TAAAATATT
1 TTTTATTAT-ATATATT
874898 TTTTATT-TATATATT
1 TTTTATTATATATATT
*
874913 TTTTATTATATATATA
1 TTTTATTATATATATT
** * *
874929 TTAAAATATTTATATT
1 TTTTATTATATATATT
* *
874945 ATTT-TTA-AAATATT
1 TTTTATTATATATATT
* *
874959 TTATA-TGTATATATT
1 TTTTATTATATATATT
874974 TTTTATTATATA
1 TTTTATTATATA
874986 AATATTAAAA
Statistics
Matches: 76, Mismatches: 23, Indels: 11
0.69 0.21 0.10
Matches are distributed among these distances:
14 8 0.11
15 25 0.33
16 36 0.47
17 7 0.09
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (16 bp):
TTTTATTATATATATT
Found at i:874921 original size:14 final size:14
Alignment explanation
Indices: 874893--874985 Score: 64
Period size: 15 Copynumber: 6.2 Consensus size: 14
874883 TATATTTAAA
874893 ATATTTTTTATTTAT
1 ATATTTTTTA-TTAT
874908 ATATTTTTTATTAT
1 ATATTTTTTATTAT
*
874922 ATATATATTAAAATATT-T
1 ATAT-T-TT---TTATTAT
* *
874940 ATATTATTTT-TAAA
1 ATATT-TTTTATTAT
*
874954 ATATTTTATATGTAT
1 ATATTTTTTAT-TAT
874969 ATATTTTTTATTAT
1 ATATTTTTTATTAT
874983 ATA
1 ATA
874986 AATATTAAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 17
0.71 0.09 0.20
Matches are distributed among these distances:
13 4 0.06
14 21 0.34
15 22 0.35
16 2 0.03
17 4 0.06
18 5 0.08
19 4 0.06
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (14 bp):
ATATTTTTTATTAT
Found at i:874921 original size:18 final size:17
Alignment explanation
Indices: 874896--874930 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
874886 ATTTAAAATA
*
874896 TTTTTTATTTATATATT
1 TTTTTTATATATATATT
874913 TTTTATTATATATATATT
1 TTTT-TTATATATATATT
874931 AAAATATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTTATATATATATT
Found at i:874941 original size:20 final size:20
Alignment explanation
Indices: 874918--874970 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 20
874908 ATATTTTTTA
874918 TTATATATATATTAAAATA-T
1 TTATAT-TATATTAAAATATT
*
874938 TTATATTATTTTTAAAATATT
1 TTATATTA-TATTAAAATATT
874959 TTATATGTATAT
1 TTATAT-TATAT
874971 ATTTTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 2 0.07
20 15 0.54
21 9 0.32
22 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
TTATATTATATTAAAATATT
Found at i:874960 original size:61 final size:61
Alignment explanation
Indices: 874882--874998 Score: 198
Period size: 61 Copynumber: 1.9 Consensus size: 61
874872 ATATAATAAT
* * *
874882 TTATATTTAAAATATTTTTTATTTATATATTTTTTATTATATATATATTAAAATATTTATA
1 TTATATTTAAAATATTTTATATGTATATATTTTTTATTATATAAATATTAAAATATTTATA
*
874943 TTATTTTTAAAATATTTTATATGTATATATTTTTTATTATATAAATATTAAAATAT
1 TTATATTTAAAATATTTTATATGTATATATTTTTTATTATATAAATATTAAAATAT
874999 AAAAAATTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 52 1.00
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (61 bp):
TTATATTTAAAATATTTTATATGTATATATTTTTTATTATATAAATATTAAAATATTTATA
Found at i:875022 original size:61 final size:59
Alignment explanation
Indices: 874897--875030 Score: 171
Period size: 61 Copynumber: 2.2 Consensus size: 59
874887 TTTAAAATAT
* ** * *
874897 TTTTTAT-TTATATATTTTTTATTATATATATATTAAAATATTTATATTATTTTTAAAA
1 TTTTTATATTATATATTTTTTATTATATAAATATTAAAATATAAAAATTATTTTCAAAA
* *
874955 TATTTTATATGTATATATTTTTTATTATATAAATATTAAAATATAAAAAATTATTTTCATAC
1 T-TTTTATAT-TATATATTTTTTATTATATAAATATTAAAATAT-AAAAATTATTTTCAAAA
875017 TTTTTATATTATAT
1 TTTTTATATTATAT
875031 TATATTATAT
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
58 1 0.02
59 6 0.09
60 6 0.09
61 40 0.62
62 12 0.18
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (59 bp):
TTTTTATATTATATATTTTTTATTATATAAATATTAAAATATAAAAATTATTTTCAAAA
Found at i:875050 original size:12 final size:12
Alignment explanation
Indices: 875018--875070 Score: 60
Period size: 12 Copynumber: 4.7 Consensus size: 12
875008 TTTTCATACT
875018 TTTTATATTATA
1 TTTTATATTATA
875030 --TTATATTATA
1 TTTTATATTATA
*
875040 TTTTATTTTATA
1 TTTTATATTATA
875052 TTTTA-ATTAT-
1 TTTTATATTATA
875062 TATTTATAT
1 T-TTTATAT
875071 GTTTAATATT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
10 11 0.31
11 8 0.23
12 16 0.46
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTATATTATA
Found at i:875364 original size:15 final size:15
Alignment explanation
Indices: 875338--875376 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
875328 TTATTAATAT
*
875338 TTTTTTATATAATTAA
1 TTTTTAATA-AATTAA
875354 TATTTTAATAAATTAA
1 T-TTTTAATAAATTAA
875370 TTTTTAA
1 TTTTTAA
875377 ATTTAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 6 0.29
16 8 0.38
17 7 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTTTAATAAATTAA
Found at i:875364 original size:43 final size:42
Alignment explanation
Indices: 875291--875399 Score: 107
Period size: 43 Copynumber: 2.6 Consensus size: 42
875281 ATACTACGTG
* * * *
875291 ATATATTTTTA-ATAATGTAAAATTAAAATAAATTTATTTATTA
1 ATATTTTTTTATATAAT-TAATATTTAAATAAATTAATTT-TTA
*
875334 ATATTTTTTTATATAATTAATATTTTAATAAATTAATTTTTA
1 ATATTTTTTTATATAATTAATATTTAAATAAATTAATTTTTA
** *
875376 A-ATTTAATAATATAATT-ATATTTA
1 ATATTTTTTTATATAATTAATATTTA
875400 TTATGCGCAT
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
40 6 0.11
41 13 0.23
42 4 0.07
43 28 0.50
44 5 0.09
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (42 bp):
ATATTTTTTTATATAATTAATATTTAAATAAATTAATTTTTA
Found at i:877680 original size:20 final size:20
Alignment explanation
Indices: 877651--877697 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
877641 GATTAATGAA
877651 ATTG-AAAGCTCAATATTTT
1 ATTGAAAAGCTCAATATTTT
877670 ATTGAAAAGCTCAATATTTT
1 ATTGAAAAGCTCAATATTTT
877690 ATTGAAAA
1 ATTGAAAA
877698 CTATACATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 4 0.15
20 23 0.85
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.38
Consensus pattern (20 bp):
ATTGAAAAGCTCAATATTTT
Found at i:878367 original size:27 final size:27
Alignment explanation
Indices: 878303--878373 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
878293 AAACAAGCCT
* * *
878303 CCATATTTGACAAATACAAAGGAAATCA
1 CCATTTTTGACAAACACAAA-GAAACCA
878331 CCATTTTTGACAAACACAAA-ATAACCA
1 CCATTTTTGACAAACACAAAGA-AACCA
878358 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
878374 AATGGGTGGC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.51
28 18 0.46
ACGTcount: A:0.46, C:0.23, G:0.07, T:0.24
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAGAAACCA
Found at i:880149 original size:21 final size:22
Alignment explanation
Indices: 880123--880168 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
880113 ATCTGTTGAA
* *
880123 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGTGGAGTACT
880144 ACTCCACCTGCTGTGGAGTACT
1 ACTCCACCTGCTGTGGAGTACT
880166 ACT
1 ACT
880169 TGTCTGAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.33
Consensus pattern (22 bp):
ACTCCACCTGCTGTGGAGTACT
Found at i:882817 original size:24 final size:27
Alignment explanation
Indices: 882744--882814 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
882734 AAACAAGCCT
* *
882744 CCATATTTGACAAATACAAAGGA-AACCA
1 CCATTTTTGACAAACACAAA--ATAACCA
882772 CCATTTTTGACAAACACAAAATAACCA
1 CCATTTTTGACAAACACAAAATAACCA
882799 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
882815 AATGGGTGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.23
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAATAACCA
Found at i:883064 original size:22 final size:22
Alignment explanation
Indices: 883020--883065 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
883010 AAAATATTGA
*
883020 TATATTATTTTATATTGATATT
1 TATATTATTTTATATTGAAATT
*
883042 TATATTTTTTTATAATT-AAATT
1 TATATTATTTTAT-ATTGAAATT
883064 TA
1 TA
883066 AGTAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (22 bp):
TATATTATTTTATATTGAAATT
Found at i:883259 original size:23 final size:24
Alignment explanation
Indices: 883233--883279 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
883223 TAATTTTTCG
883233 TTAATAATATAATT-ATATTATTT
1 TTAATAATATAATTCATATTATTT
** *
883256 TTAATGTTATAATTCATGTTATTT
1 TTAATAATATAATTCATATTATTT
883280 GCTATCATCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.57
Consensus pattern (24 bp):
TTAATAATATAATTCATATTATTT
Found at i:883578 original size:18 final size:19
Alignment explanation
Indices: 883555--883600 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
883545 TGCTTTTTTA
883555 ATATATTTTT-ATTTATTT
1 ATATATTTTTAATTTATTT
*
883573 ATATATTTTTTAATTTTTTT
1 ATATA-TTTTTAATTTATTT
883593 A-ATATTTT
1 ATATATTTT
883601 AATAATCGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 9 0.36
19 8 0.32
20 8 0.32
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
ATATATTTTTAATTTATTT
Found at i:883606 original size:20 final size:18
Alignment explanation
Indices: 883548--883600 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 18
883538 ATTAGATTGC
*
883548 TTTTTTAATATATTTTTAT
1 TTTTTTAATAT-TTTTAAT
*
883567 TTATTTATATATTTTTTAAT
1 TTTTTTA-ATA-TTTTTAAT
883587 TTTTTTAATATTTT
1 TTTTTTAATATTTT
883601 AATAATCGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 4 0.14
19 9 0.31
20 15 0.52
21 1 0.03
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTTAATATTTTTAAT
Found at i:885420 original size:2 final size:2
Alignment explanation
Indices: 885413--885446 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
885403 TCATTATTTA
885413 AT AT AT 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 AT AT AT
885447 GTGTGTGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:885548 original size:27 final size:28
Alignment explanation
Indices: 885527--885585 Score: 75
Period size: 30 Copynumber: 2.1 Consensus size: 28
885517 TATTTCGTTT
*
885527 ATGAT-TTTTAAAAATTTAATTTTATCC
1 ATGATCTTTTAAAAATTTAATTTCATCC
*
885554 ATGATCTTTTAAAAATTTTCAAATTCATCC
1 ATGATCTTTTAAAAA-TTT-AATTTCATCC
885584 AT
1 AT
885586 TTCATCACTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 5 0.19
28 9 0.33
29 3 0.11
30 10 0.37
ACGTcount: A:0.37, C:0.12, G:0.03, T:0.47
Consensus pattern (28 bp):
ATGATCTTTTAAAAATTTAATTTCATCC
Found at i:886796 original size:13 final size:13
Alignment explanation
Indices: 886778--886804 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
886768 TCTAAAATTA
886778 TTTTTTTACTTTT
1 TTTTTTTACTTTT
886791 TTTTTTTACTTTT
1 TTTTTTTACTTTT
886804 T
1 T
886805 AACAATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTTTACTTTT
Found at i:887599 original size:23 final size:22
Alignment explanation
Indices: 887521--887616 Score: 76
Period size: 20 Copynumber: 4.4 Consensus size: 22
887511 TAATTTTTTT
* *
887521 TTAAATTTTTTATATTAATTTAA
1 TTAAA-TTTATATATTATTTTAA
* *
887544 -T-ATTTTATTTATTATTTTAA
1 TTAAATTTATATATTATTTTAA
*
887564 -AAAATATTAATATATTATTTTATA
1 TTAAAT-TT-ATATATTATTTTA-A
887588 TTAAATTTATATA-T-TTTTAA
1 TTAAATTTATATATTATTTTAA
887608 TTAAATTTA
1 TTAAATTTA
887617 AATAAAATAT
Statistics
Matches: 60, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
20 24 0.40
21 8 0.13
22 4 0.07
23 17 0.28
24 3 0.05
25 4 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TTAAATTTATATATTATTTTAA
Found at i:887641 original size:21 final size:21
Alignment explanation
Indices: 887606--887669 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
887596 ATATATTTTT
*
887606 AATTAAATTTAAATAAAATATTT
1 AATTAAA-TTAAATAAAAT-TTA
*
887629 TATTAAA-TAAATAATAATTTA
1 AATTAAATTAAATAA-AATTTA
887650 AATTAAATTAAAT-AAATTTA
1 AATTAAATTAAATAAAATTTA
887670 TAAAATAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
20 6 0.17
21 16 0.44
22 8 0.22
23 6 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AATTAAATTAAATAAAATTTA
Found at i:887670 original size:39 final size:40
Alignment explanation
Indices: 887608--887687 Score: 101
Period size: 39 Copynumber: 2.0 Consensus size: 40
887598 ATATTTTTAA
* * *
887608 TTAAATTTAAATAAAATATTTTATTAAAT-AAATAATAAT
1 TTAAATTTAAATAAAATAATTTATAAAATAAAAAAATAAT
*
887647 TTAAA-TTAAATTAAATAAATTTATAAAATAAAAAAATAAT
1 TTAAATTTAAATAAAAT-AATTTATAAAATAAAAAAATAAT
887687 T
1 T
887688 ATTTTTTAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
38 10 0.29
39 15 0.43
40 10 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (40 bp):
TTAAATTTAAATAAAATAATTTATAAAATAAAAAAATAAT
Found at i:887673 original size:22 final size:21
Alignment explanation
Indices: 887630--887691 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
887620 AAAATATTTT
887630 ATTAAATAAATAATAATTTAA
1 ATTAAATAAATAATAATTTAA
*
887651 ATTAAATTAAATAA-ATTTATAA
1 ATTAAA-TAAATAATAATT-TAA
* * *
887673 AATAAAAAAATAATTATTT
1 ATTAAATAAATAATAATTT
887692 TTTAACAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
21 16 0.48
22 17 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
ATTAAATAAATAATAATTTAA
Found at i:887919 original size:17 final size:18
Alignment explanation
Indices: 887889--887963 Score: 57
Period size: 17 Copynumber: 4.2 Consensus size: 18
887879 AATTAAACAG
* *
887889 TAAAAAAATTATAAAA-A
1 TAAAATAATAATAAAATA
887906 TAAAATAATAATAAAATA
1 TAAAATAATAATAAAATA
* *
887924 TAATATAA-AATATAATA
1 TAAAATAATAATAAAATA
* *
887941 CGAATATAAT-ATAAATATA
1 -TAAAATAATAATAAA-ATA
887960 TAAA
1 TAAA
887964 TTTATTAAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
17 22 0.48
18 21 0.46
19 3 0.07
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (18 bp):
TAAAATAATAATAAAATA
Found at i:887933 original size:23 final size:23
Alignment explanation
Indices: 887905--887962 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 23
887895 AATTATAAAA
887905 ATAAAATAATAATA-AAATATAAT
1 ATAAAAT-ATAATACAAATATAAT
*
887928 ATAAAATATAATACGAATATAAT
1 ATAAAATATAATACAAATATAAT
887951 ATAAATATATAA
1 ATAAA-ATATAA
887963 ATTTATTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
22 6 0.19
23 20 0.62
24 6 0.19
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (23 bp):
ATAAAATATAATACAAATATAAT
Found at i:887957 original size:11 final size:10
Alignment explanation
Indices: 887904--887963 Score: 59
Period size: 11 Copynumber: 5.6 Consensus size: 10
887894 AAATTATAAA
887904 AATAAAATAAT
1 AATAAAAT-AT
887915 AATAAAATAT
1 AATAAAATAT
887925 AATATAAAATAT
1 -A-ATAAAATAT
*
887937 AATACGAATAT
1 AATA-AAATAT
887948 AATATAAATAT
1 AATA-AAATAT
887959 -ATAAA
1 AATAAA
887964 TTTATTAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
9 2 0.05
10 8 0.19
11 24 0.56
12 9 0.21
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (10 bp):
AATAAAATAT
Found at i:887962 original size:13 final size:12
Alignment explanation
Indices: 887910--887962 Score: 63
Period size: 12 Copynumber: 4.3 Consensus size: 12
887900 TAAAAATAAA
887910 ATAATAATAAAAT
1 ATAAT-ATAAAAT
887923 ATAATATAAAAT
1 ATAATATAAAAT
**
887935 ATAATA-CGAAT
1 ATAATATAAAAT
887946 ATAATATAAATAT
1 ATAATATAAA-AT
887959 ATAA
1 ATAA
887963 ATTTATTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
11 9 0.26
12 14 0.41
13 11 0.32
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (12 bp):
ATAATATAAAAT
Found at i:888047 original size:44 final size:46
Alignment explanation
Indices: 887975--888062 Score: 135
Period size: 44 Copynumber: 2.0 Consensus size: 46
887965 TTATTAAAAT
* *
887975 TTTTATAATATAAATTATAATCTTTAAAAAATATAAAAATATAATA
1 TTTTATAATATAAATTATAATATATAAAAAATATAAAAATATAATA
*
888021 TTTTA-AATAT-AATTATAATATATAAAAAATATATAAATATAA
1 TTTTATAATATAAATTATAATATATAAAAAATATAAAAATATAA
888063 CATCAATATA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
44 29 0.74
45 5 0.13
46 5 0.13
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (46 bp):
TTTTATAATATAAATTATAATATATAAAAAATATAAAAATATAATA
Found at i:888061 original size:24 final size:23
Alignment explanation
Indices: 887982--888062 Score: 69
Period size: 24 Copynumber: 3.5 Consensus size: 23
887972 AATTTTTATA
*
887982 ATATAAATTATAATCTTTAAAAAAT
1 ATATAAA-TATAAT-ATTAAAAAAT
* **
888007 ATAAAAATATAATATT--TTAA-
1 ATATAAATATAATATTAAAAAAT
*
888027 ATATAATTATAATATATAAAAAAT
1 ATATAAATATAATAT-TAAAAAAT
888051 ATATAAATATAA
1 ATATAAATATAA
888063 CATCAATATA
Statistics
Matches: 43, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
20 13 0.30
21 3 0.07
23 4 0.09
24 17 0.40
25 6 0.14
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (23 bp):
ATATAAATATAATATTAAAAAAT
Found at i:889320 original size:10 final size:10
Alignment explanation
Indices: 889307--889341 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
889297 TTTATTTGAT
889307 TTAATTTAAA
1 TTAATTTAAA
*
889317 TTAATTTAAT
1 TTAATTTAAA
*
889327 TTGATTTAAA
1 TTAATTTAAA
889337 TTAAT
1 TTAAT
889342 ATTTAATAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (10 bp):
TTAATTTAAA
Found at i:889328 original size:20 final size:20
Alignment explanation
Indices: 889300--889341 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
889290 GAAATTATTT
*
889300 ATTTGATTTAATTTAAATTA
1 ATTTAATTTAATTTAAATTA
*
889320 ATTTAATTTGATTTAAATTA
1 ATTTAATTTAATTTAAATTA
889340 AT
1 AT
889342 ATTTAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (20 bp):
ATTTAATTTAATTTAAATTA
Found at i:890493 original size:17 final size:16
Alignment explanation
Indices: 890470--890509 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
890460 ACAAGGGAAT
890470 TAATAAAATAAATAAA
1 TAATAAAATAAATAAA
* *
890486 TAAATAAATTAGATAAA
1 T-AATAAAATAAATAAA
890503 TAATAAA
1 TAATAAA
890510 TTTTTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (16 bp):
TAATAAAATAAATAAA
Found at i:891156 original size:22 final size:22
Alignment explanation
Indices: 891112--891157 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
891102 AAAATATTGA
*
891112 TATATTATTTTATATTGATATT
1 TATATTATTTTATATTGAAATT
*
891134 TATATTTTTTTATAATT-AAATT
1 TATATTATTTTAT-ATTGAAATT
891156 TA
1 TA
891158 AATAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (22 bp):
TATATTATTTTATATTGAAATT
Found at i:894640 original size:9 final size:9
Alignment explanation
Indices: 894627--894657 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
894617 TACTAATGGT
*
894627 ATATAAATT
1 ATATAAATC
894636 ATATAAATC
1 ATATAAATC
894645 ATATAAATC
1 ATATAAATC
894654 ATAT
1 ATAT
894658 TCTTAATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (9 bp):
ATATAAATC
Found at i:895709 original size:30 final size:30
Alignment explanation
Indices: 895675--895755 Score: 76
Period size: 30 Copynumber: 2.6 Consensus size: 30
895665 ACTTAAGTTC
*
895675 ATTTTATTATTTAAAAATAT-TAAAAATATT
1 ATTTTATTAATTAAAAATATAT-AAAATATT
**
895705 ATTTT-TATAATTAAATTTATATAAAATATT
1 ATTTTAT-TAATTAAAAATATATAAAATATT
*
895735 ATTTTTATTAAATAAATAATA
1 A-TTTTATTAATTAAA-AATA
895756 ATTTAAATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
29 1 0.03
30 24 0.60
31 12 0.30
32 3 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (30 bp):
ATTTTATTAATTAAAAATATATAAAATATT
Found at i:896233 original size:18 final size:17
Alignment explanation
Indices: 896210--896243 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
896200 TGAAATATTT
896210 TTTTATTAATAAAATATA
1 TTTTATT-ATAAAATATA
*
896228 TTTTATTTTAAAATAT
1 TTTTATTATAAAATAT
896244 TTTAAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTATTATAAAATATA
Found at i:896246 original size:10 final size:10
Alignment explanation
Indices: 896231--896273 Score: 54
Period size: 10 Copynumber: 4.3 Consensus size: 10
896221 AAATATATTT
896231 TATTTTAAAA
1 TATTTTAAAA
896241 TATTTTAAAA
1 TATTTTAAAA
896251 TA--TTAAAA
1 TATTTTAAAA
896259 TATTATATAAAA
1 TATT-T-TAAAA
896271 TAT
1 TAT
896274 GATTTAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
8 8 0.28
10 12 0.41
11 1 0.03
12 8 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
TATTTTAAAA
Found at i:896258 original size:18 final size:20
Alignment explanation
Indices: 896235--896273 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
896225 ATATTTTATT
896235 TTAAAATATT-T-TAAAATA
1 TTAAAATATTATATAAAATA
896253 TTAAAATATTATATAAAATA
1 TTAAAATATTATATAAAATA
896273 T
1 T
896274 GATTTAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.53
19 1 0.05
20 8 0.42
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAAAATATTATATAAAATA
Found at i:896619 original size:22 final size:23
Alignment explanation
Indices: 896578--896625 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
896568 CTTAATAAAA
896578 AAATATTTTAATAATATAAT-AT
1 AAATATTTTAATAATATAATAAT
* * *
896600 AAATGTTTTAATATTTTAATAAT
1 AAATATTTTAATAATATAATAAT
896623 AAA
1 AAA
896626 AAAATAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
AAATATTTTAATAATATAATAAT
Found at i:896639 original size:30 final size:30
Alignment explanation
Indices: 896579--896644 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
896569 TTAATAAAAA
* * *
896579 AATATTTTAATAATATAATATAAATGTTTT
1 AATATTTTAATAATAAAAAATAAATATTTT
896609 AATATTTTAATAATAAAAAA-ATAATATTTT
1 AATATTTTAATAATAAAAAATA-AATATTTT
896639 -ATATTT
1 AATATTT
896645 CATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 7 0.22
30 25 0.78
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (30 bp):
AATATTTTAATAATAAAAAATAAATATTTT
Found at i:896816 original size:16 final size:15
Alignment explanation
Indices: 896789--896845 Score: 71
Period size: 16 Copynumber: 3.7 Consensus size: 15
896779 TGATGATAAA
896789 ATATTATTAAAATATT
1 ATATT-TTAAAATATT
896805 ACTATTTTAAAATATT
1 A-TATTTTAAAATATT
*
896821 A-ATATTAAAATATT
1 ATATTTTAAAATATT
896835 ATAATTTTAAA
1 AT-ATTTTAAA
896846 TGTTTTAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
14 13 0.36
16 19 0.53
17 4 0.11
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATTTTAAAATATT
Found at i:896828 original size:14 final size:15
Alignment explanation
Indices: 896793--896835 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
896783 GATAAAATAT
896793 TATTAAAATATTACTA
1 TATTAAAATATTAC-A
*
896809 TTTTAAAATATTA-A
1 TATTAAAATATTACA
896823 TATTAAAATATTA
1 TATTAAAATATTA
896836 TAATTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 13 0.52
16 12 0.48
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
TATTAAAATATTACA
Found at i:896862 original size:30 final size:30
Alignment explanation
Indices: 896785--896864 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 30
896775 TATTTGATGA
896785 TAAAATATT-AT--TAAAATATTACTATTT
1 TAAAATATTAATAATAAAATATTACTATTT
*
896812 TAAAATATTAATATTAAAATATTA-TAATTT
1 TAAAATATTAATAATAAAATATTACT-ATTT
* *
896842 TAAATGTTTTAATAAT-AAATATT
1 TAAA-ATATTAATAATAAAATATT
896865 TTAAGAATTA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
27 9 0.20
28 2 0.04
29 1 0.02
30 25 0.56
31 8 0.18
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (30 bp):
TAAAATATTAATAATAAAATATTACTATTT
Found at i:898913 original size:2 final size:2
Alignment explanation
Indices: 898906--898962 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
898896 CCATGGAGCC
898906 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
*
898948 TA TA TA TT TA TA TA T
1 TA TA TA TA TA TA TA T
898963 GGTTTTTGGC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:899316 original size:2 final size:2
Alignment explanation
Indices: 899309--899349 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
899299 CATATTGTTA
899309 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
899350 CAATAAATGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:899641 original size:25 final size:25
Alignment explanation
Indices: 899598--899672 Score: 93
Period size: 25 Copynumber: 3.1 Consensus size: 25
899588 TGAAAGCTTG
*
899598 TATTATTGTTTATAATAATATTTAAA
1 TATTATT-TTTATATTAATATTTAAA
*
899624 TATTATTTTTATATTAATATTTATA
1 TATTATTTTTATATTAATATTTAAA
*
899649 TA-TATTTTTA-ATCAA-ATTTAAA
1 TATTATTTTTATATTAATATTTAAA
899671 TA
1 TA
899673 AAAATATTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
22 8 0.18
23 4 0.09
24 8 0.18
25 18 0.40
26 7 0.16
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (25 bp):
TATTATTTTTATATTAATATTTAAA
Found at i:909813 original size:2 final size:2
Alignment explanation
Indices: 909801--909837 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
909791 TATAGTCTTT
*
909801 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
909838 GGGGTTAGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:914926 original size:2 final size:2
Alignment explanation
Indices: 914919--914949 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
914909 AATCTATTTA
*
914919 AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
914950 CACACGCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:920684 original size:24 final size:24
Alignment explanation
Indices: 920656--920701 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
920646 AATAAAAATT
920656 AGCCACCAATTTTGACAAACAACA
1 AGCCACCAATTTTGACAAACAACA
* *
920680 AGCCACCATTTTTTACAAACAA
1 AGCCACCAATTTTGACAAACAA
920702 AAATAACCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.28, G:0.07, T:0.22
Consensus pattern (24 bp):
AGCCACCAATTTTGACAAACAACA
Found at i:920729 original size:28 final size:27
Alignment explanation
Indices: 920682--920758 Score: 79
Period size: 28 Copynumber: 2.9 Consensus size: 27
920672 AAACAACAAG
* *
920682 CCACCATTTTTTAC-AA-ACAAAAATAA
1 CCACCATATTTGACAAATACAAAAA-AA
*
920708 CCACCATATTTGACAAATACAAAGGAAA
1 CCACCATATTTGACAAATACAAA-AAAA
*
920736 CCACCATATTTGATAAATA-AAAA
1 CCACCATATTTGACAAATACAAAA
920759 GAGTAGCATT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
26 12 0.28
27 5 0.12
28 25 0.58
29 1 0.02
ACGTcount: A:0.51, C:0.21, G:0.05, T:0.23
Consensus pattern (27 bp):
CCACCATATTTGACAAATACAAAAAAA
Found at i:920759 original size:28 final size:28
Alignment explanation
Indices: 920706--920759 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
920696 AAACAAAAAT
*
920706 AACCACCATATTTGACAAATACAAAGGA
1 AACCACCATATTTGACAAATAAAAAGGA
*
920734 AACCACCATATTTGATAAATAAAAAG
1 AACCACCATATTTGACAAATAAAAAG
920760 AGTAGCATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.52, C:0.19, G:0.09, T:0.20
Consensus pattern (28 bp):
AACCACCATATTTGACAAATAAAAAGGA
Found at i:922060 original size:2 final size:2
Alignment explanation
Indices: 922053--922083 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
922043 ATCGGAATAT
922053 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
922084 TTTTTTTCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:926313 original size:28 final size:28
Alignment explanation
Indices: 926259--926314 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
926249 TATTCATGTC
* *
926259 ATATTTTTATTATTTTTTATGTAATTTT
1 ATATTTTTATCATATTTTATGTAATTTT
*
926287 ATATTTTGTATCATATTTTA-GTTATTTT
1 ATATTTT-TATCATATTTTATGTAATTTT
926315 TTCATATCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 14 0.58
29 10 0.42
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (28 bp):
ATATTTTTATCATATTTTATGTAATTTT
Found at i:927362 original size:20 final size:20
Alignment explanation
Indices: 927337--927376 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
927327 GTCCCCTCAG
927337 AATTTGTAAGCTCATTTTTT
1 AATTTGTAAGCTCATTTTTT
927357 AATTTGTAAGCTCATTTTTT
1 AATTTGTAAGCTCATTTTTT
927377 CTCTTCTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.55
Consensus pattern (20 bp):
AATTTGTAAGCTCATTTTTT
Found at i:928086 original size:27 final size:27
Alignment explanation
Indices: 928052--928143 Score: 91
Period size: 28 Copynumber: 3.4 Consensus size: 27
928042 GCCACCCATT
928052 TATTTGTCAAAAATGGTGGTTAT-TTTG
1 TATTTGTCAAAAATGGTGGTT-TCTTTG
* *
928079 TGTTTGTCAAAAATAGTGGTTTCCTTTG
1 TATTTGTCAAAAATGGTGGTTT-CTTTG
* * * *
928107 TATTTGTCAAATATGGAGGCTT-GTT-
1 TATTTGTCAAAAATGGTGGTTTCTTTG
928132 TATTTGTCAAAA
1 TATTTGTCAAAA
928144 TTTGTGGCTA
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
25 11 0.20
26 3 0.06
27 19 0.35
28 21 0.39
ACGTcount: A:0.26, C:0.08, G:0.21, T:0.46
Consensus pattern (27 bp):
TATTTGTCAAAAATGGTGGTTTCTTTG
Found at i:928107 original size:28 final size:27
Alignment explanation
Indices: 928052--928117 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 27
928042 GCCACCCATT
*
928052 TATTTGTCAAAAATGGTGGTTATTTTG
1 TATTTGTCAAAAATAGTGGTTATTTTG
*
928079 TGTTTGTCAAAAATAGTGGTT-TCCTTTG
1 TATTTGTCAAAAATAGTGGTTAT--TTTG
928107 TATTTGTCAAA
1 TATTTGTCAAA
928118 TATGGAGGCT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 1 0.03
27 19 0.56
28 14 0.41
ACGTcount: A:0.26, C:0.08, G:0.20, T:0.47
Consensus pattern (27 bp):
TATTTGTCAAAAATAGTGGTTATTTTG
Found at i:932659 original size:27 final size:27
Alignment explanation
Indices: 932625--932695 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
932615 GCCACCCATT
932625 TGTTTGTCAAAAATGGTGGTTAT-TTTG
1 TGTTTGTCAAAAATGGTGGTT-TCTTTG
*
932652 TGTTTGTCAAAAATAGTGGTTTCCTTTG
1 TGTTTGTCAAAAATGGTGGTTT-CTTTG
* *
932680 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
932696 AGGCTTGTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.53
28 17 0.45
ACGTcount: A:0.24, C:0.07, G:0.23, T:0.46
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTTCTTTG
Found at i:935285 original size:2 final size:2
Alignment explanation
Indices: 935278--935316 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
935268 AATCTCTAGC
935278 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
935317 GAATTATGAA
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:936136 original size:50 final size:50
Alignment explanation
Indices: 936077--936175 Score: 189
Period size: 50 Copynumber: 2.0 Consensus size: 50
936067 GATATCACAT
*
936077 AATATTTGTTTAGATGATAATATTTTACGACAAAAGTTTTAAGATTTTCA
1 AATATTTGTTTAGATGATAATATTTTACGAAAAAAGTTTTAAGATTTTCA
936127 AATATTTGTTTAGATGATAATATTTTACGAAAAAAGTTTTAAGATTTTC
1 AATATTTGTTTAGATGATAATATTTTACGAAAAAAGTTTTAAGATTTTC
936176 GAAAAATTGT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.44
Consensus pattern (50 bp):
AATATTTGTTTAGATGATAATATTTTACGAAAAAAGTTTTAAGATTTTCA
Found at i:936179 original size:21 final size:23
Alignment explanation
Indices: 936148--936191 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
936138 AGATGATAAT
936148 ATTTTACGAAAAA-AGTTTTAAG
1 ATTTTACGAAAAATAGTTTTAAG
*
936170 ATTTT-CGAAAAATTGTTTTAAG
1 ATTTTACGAAAAATAGTTTTAAG
936192 TGGATGGCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.41
Consensus pattern (23 bp):
ATTTTACGAAAAATAGTTTTAAG
Found at i:936186 original size:50 final size:50
Alignment explanation
Indices: 936077--936187 Score: 179
Period size: 50 Copynumber: 2.2 Consensus size: 50
936067 GATATCACAT
* *
936077 AATATTTGTTTAGATGATAATATTTTACGACAAAAGTTTTAAGATTTTCA
1 AATAATTGTTTAGATGATAATATTTTACGAAAAAAGTTTTAAGATTTTCA
*
936127 AATATTTGTTTAGATGATAATATTTTACGAAAAAAGTTTTAAGATTTTCGA
1 AATAATTGTTTAGATGATAATATTTTACGAAAAAAGTTTTAAGATTTTC-A
936178 AA-AATTGTTT
1 AATAATTGTTT
936188 TAAGTGGATG
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
50 55 0.95
51 3 0.05
ACGTcount: A:0.39, C:0.05, G:0.13, T:0.44
Consensus pattern (50 bp):
AATAATTGTTTAGATGATAATATTTTACGAAAAAAGTTTTAAGATTTTCA
Found at i:938680 original size:2 final size:2
Alignment explanation
Indices: 938673--938701 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
938663 AATCTCTAGC
938673 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 T
938702 GAATTATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:942160 original size:25 final size:24
Alignment explanation
Indices: 942127--942179 Score: 97
Period size: 25 Copynumber: 2.2 Consensus size: 24
942117 GGTGTTATTA
942127 CATATATAATTCATATTAATTTAG
1 CATATATAATTCATATTAATTTAG
942151 CATACTATAATTCATATTAATTTAG
1 CATA-TATAATTCATATTAATTTAG
942176 CATA
1 CATA
942180 AATTAATTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 4 0.14
25 24 0.86
ACGTcount: A:0.42, C:0.11, G:0.04, T:0.43
Consensus pattern (24 bp):
CATATATAATTCATATTAATTTAG
Found at i:943729 original size:38 final size:38
Alignment explanation
Indices: 943646--943776 Score: 129
Period size: 38 Copynumber: 3.4 Consensus size: 38
943636 TCAAAGAGAG
* * * * *
943646 TTCAATTTGGAATTCTCTAGCCACCAGCCACCGGCC-AA
1 TTCAAATT-GAATTCTCTAGCCATCAGTCGCCAGCCAAA
* * * * **
943684 TTCCAAATTGAATTCTCTAGTCGTCAGTCGCCGGTCATT
1 TT-CAAATTGAATTCTCTAGCCATCAGTCGCCAGCCAAA
943723 TTCAAATTGAATTCTCTAGCCATCAGTCGCCAGCCAAA
1 TTCAAATTGAATTCTCTAGCCATCAGTCGCCAGCCAAA
*
943761 TTAAAATTGAATTCTC
1 TTCAAATTGAATTCTC
943777 CAACCGTCAA
Statistics
Matches: 75, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
38 68 0.91
39 7 0.09
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (38 bp):
TTCAAATTGAATTCTCTAGCCATCAGTCGCCAGCCAAA
Found at i:948396 original size:38 final size:38
Alignment explanation
Indices: 948354--948454 Score: 139
Period size: 38 Copynumber: 2.7 Consensus size: 38
948344 AGCCACCGAC
* ** *
948354 CAATTCCAAATTGAATTCTCTAGTCGTCAGCCGTCGGT
1 CAATTTCAAATTGAATTCTCTAACCGTCAGCCGTCAGT
* * *
948392 CAATTTTAAATTGAATTCTTTAACCGTCAGTCGTCAGT
1 CAATTTCAAATTGAATTCTCTAACCGTCAGCCGTCAGT
948430 CAATTTCAAATTGAATTCTCTAACC
1 CAATTTCAAATTGAATTCTCTAACC
948455 ATCAACTAAT
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 54 1.00
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.36
Consensus pattern (38 bp):
CAATTTCAAATTGAATTCTCTAACCGTCAGCCGTCAGT
Found at i:950258 original size:42 final size:42
Alignment explanation
Indices: 950211--950302 Score: 105
Period size: 43 Copynumber: 2.2 Consensus size: 42
950201 GCATTTGTCT
* * *
950211 TTCAAC-TTTTTCTTTGAGGGTACTGGTGGGTAACTGGGCAGG
1 TTCAACGTTTTACTTT-AGGATACTGGTGGGTAAATGGGCAGG
* *
950253 TTCAACGGTTTTAGTTTTGGATACTGGTGGGTAAATGGGCAGG
1 TTCAAC-GTTTTACTTTAGGATACTGGTGGGTAAATGGGCAGG
*
950296 TTGAACG
1 TTCAACG
950303 GTTTGGTTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
42 7 0.17
43 28 0.67
44 7 0.17
ACGTcount: A:0.20, C:0.12, G:0.34, T:0.35
Consensus pattern (42 bp):
TTCAACGTTTTACTTTAGGATACTGGTGGGTAAATGGGCAGG
Found at i:950326 original size:42 final size:43
Alignment explanation
Indices: 950236--950331 Score: 115
Period size: 43 Copynumber: 2.3 Consensus size: 43
950226 GAGGGTACTG
* * **
950236 GTGGGTAACTGGGCAGGTTCAACGGTTTTAGTTTTGGATACTG
1 GTGGGTAAATGGGCAGGTTCAACGGTTTTAGTTTTGGACACCA
* *
950279 GTGGGTAAATGGGCAGGTTGAACGG-TTTGGTTTTTGG-CACCA
1 GTGGGTAAATGGGCAGGTTCAACGGTTTTAG-TTTTGGACACCA
950321 GTGGGTAAATG
1 GTGGGTAAATG
950332 AGCATTTCAA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
42 17 0.37
43 29 0.63
ACGTcount: A:0.20, C:0.10, G:0.38, T:0.32
Consensus pattern (43 bp):
GTGGGTAAATGGGCAGGTTCAACGGTTTTAGTTTTGGACACCA
Found at i:954169 original size:20 final size:20
Alignment explanation
Indices: 954144--954181 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
954134 AGAGAGAATG
*
954144 CTTGAGAGGGATGAGGGATA
1 CTTGAGAGGGAGGAGGGATA
954164 CTTGAGAGGGAGGAGGGA
1 CTTGAGAGGGAGGAGGGA
954182 GCTTCCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.05, G:0.50, T:0.16
Consensus pattern (20 bp):
CTTGAGAGGGAGGAGGGATA
Found at i:954255 original size:24 final size:24
Alignment explanation
Indices: 954228--954297 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 24
954218 AATAAAAATT
*
954228 AGCCACCAATTTTGACAAACAACA
1 AGCCACCAATTTTGACAAACAAAA
*
954252 AGCCA-TAATTTTTGACAAACAAAA
1 AGCCACCAA-TTTTGACAAACAAAA
*
954276 AGGAACCACCATTTTTGACAAA
1 A-G--CCACCAATTTTGACAAA
954298 TACAAAGTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
23 2 0.05
24 20 0.54
25 1 0.03
27 13 0.35
28 1 0.03
ACGTcount: A:0.46, C:0.23, G:0.10, T:0.21
Consensus pattern (24 bp):
AGCCACCAATTTTGACAAACAAAA
Found at i:954297 original size:27 final size:27
Alignment explanation
Indices: 954230--954326 Score: 101
Period size: 27 Copynumber: 3.7 Consensus size: 27
954220 TAAAAATTAG
* *
954230 CCACCAATTTTGACAAACAACAA-G--
1 CCACCATTTTTGACAAACAAAAAGGAA
**
954254 CCATAATTTTTGACAAACAAAAAGGAA
1 CCACCATTTTTGACAAACAAAAAGGAA
* * *
954281 CCACCATTTTTGACAAATACAAAGTAA
1 CCACCATTTTTGACAAACAAAAAGGAA
*
954308 CCACCATTGTTGACAAACA
1 CCACCATTTTTGACAAACA
954327 CATGGTGGCT
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
24 19 0.32
25 1 0.02
27 39 0.66
ACGTcount: A:0.45, C:0.24, G:0.09, T:0.22
Consensus pattern (27 bp):
CCACCATTTTTGACAAACAAAAAGGAA
Found at i:954345 original size:24 final size:25
Alignment explanation
Indices: 954314--954371 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 25
954304 GTAACCACCA
*
954314 TTGTTGACAAACAC-ATGGTGGCTT
1 TTGTTGACAAACACAAGGGTGGCTT
*
954338 TTGTTGACAAACACAAAGGGTGGTTT
1 TTGTTGACAAACAC-AAGGGTGGCTT
954364 TTGTTGAC
1 TTGTTGAC
954372 TAGCCACCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 14 0.47
26 16 0.53
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (25 bp):
TTGTTGACAAACACAAGGGTGGCTT
Found at i:956261 original size:21 final size:22
Alignment explanation
Indices: 956235--956280 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
956225 ATCTGTTGAA
* *
956235 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGTGGAGTACT
956256 ACTCCACCTGCTGTGGAGTACT
1 ACTCCACCTGCTGTGGAGTACT
956278 ACT
1 ACT
956281 TGTCTGAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.33
Consensus pattern (22 bp):
ACTCCACCTGCTGTGGAGTACT
Found at i:958778 original size:20 final size:20
Alignment explanation
Indices: 958753--958790 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
958743 AGAGAGAATG
*
958753 CTTGAGAGGGATGAGGGATA
1 CTTGAGAGGGAGGAGGGATA
958773 CTTGAGAGGGAGGAGGGA
1 CTTGAGAGGGAGGAGGGA
958791 GCTTCCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.05, G:0.50, T:0.16
Consensus pattern (20 bp):
CTTGAGAGGGAGGAGGGATA
Found at i:958864 original size:24 final size:24
Alignment explanation
Indices: 958837--958906 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 24
958827 AATAAAAATT
*
958837 AGCCACCAATTTTGACAAACAACA
1 AGCCACCAATTTTGACAAACAAAA
*
958861 AGCCA-TAATTTTTGACAAACAAAA
1 AGCCACCAA-TTTTGACAAACAAAA
*
958885 AGGAACCACCATTTTTGACAAA
1 A-G--CCACCAATTTTGACAAA
958907 TACAAAGTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
23 2 0.05
24 20 0.54
25 1 0.03
27 13 0.35
28 1 0.03
ACGTcount: A:0.46, C:0.23, G:0.10, T:0.21
Consensus pattern (24 bp):
AGCCACCAATTTTGACAAACAAAA
Found at i:958906 original size:27 final size:27
Alignment explanation
Indices: 958839--958935 Score: 101
Period size: 27 Copynumber: 3.7 Consensus size: 27
958829 TAAAAATTAG
* *
958839 CCACCAATTTTGACAAACAACAA-G--
1 CCACCATTTTTGACAAACAAAAAGGAA
**
958863 CCATAATTTTTGACAAACAAAAAGGAA
1 CCACCATTTTTGACAAACAAAAAGGAA
* * *
958890 CCACCATTTTTGACAAATACAAAGTAA
1 CCACCATTTTTGACAAACAAAAAGGAA
*
958917 CCACCATTGTTGACAAACA
1 CCACCATTTTTGACAAACA
958936 CATGGTGCTT
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
24 19 0.32
25 1 0.02
27 39 0.66
ACGTcount: A:0.45, C:0.24, G:0.09, T:0.22
Consensus pattern (27 bp):
CCACCATTTTTGACAAACAAAAAGGAA
Found at i:960222 original size:26 final size:28
Alignment explanation
Indices: 960177--960250 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 28
960167 ATAAGTCACA
960177 ATTTTTTACAAACAAAAAAG-AACCACC
1 ATTTTTTACAAACAAAAAAGTAACCACC
* * *
960204 ATTTTTTACAAA-TATAAAGTAACCACT
1 ATTTTTTACAAACAAAAAAGTAACCACC
*
960231 ATTTTTGACAAACACAAAAA
1 ATTTTTTACAAACA-AAAAA
960251 ACGGCTTGTA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
26 5 0.13
27 29 0.76
29 4 0.11
ACGTcount: A:0.50, C:0.18, G:0.04, T:0.28
Consensus pattern (28 bp):
ATTTTTTACAAACAAAAAAGTAACCACC
Found at i:961969 original size:27 final size:27
Alignment explanation
Indices: 961938--962010 Score: 92
Period size: 27 Copynumber: 2.7 Consensus size: 27
961928 AAAAACCACT
* *
961938 CTTTGTGTTTGTCAAAAATGGTGGTTA
1 CTTTGTGTTTGTCAAAAATAGTGATTA
* *
961965 CTTTGTATTTGTCAAAAATAGTGATTC
1 CTTTGTGTTTGTCAAAAATAGTGATTA
* *
961992 CTTTTTGTTTGTTAAAAAT
1 CTTTGTGTTTGTCAAAAAT
962011 TGTAGCTTGT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.26, C:0.08, G:0.18, T:0.48
Consensus pattern (27 bp):
CTTTGTGTTTGTCAAAAATAGTGATTA
Found at i:963330 original size:15 final size:15
Alignment explanation
Indices: 963306--963340 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
963296 TTTAAATATA
963306 TTTT-TAATTTAATC
1 TTTTATAATTTAATC
*
963320 TTTTATAATTTAATT
1 TTTTATAATTTAATC
963335 TTTTAT
1 TTTTAT
963341 TAACTTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTATAATTTAATC
Found at i:967375 original size:50 final size:50
Alignment explanation
Indices: 967316--967426 Score: 195
Period size: 50 Copynumber: 2.2 Consensus size: 50
967306 GATATCACAT
*
967316 AATATTTGTTTAGATGATAATATTTTACGACAAAAGTTTTAAGATTTTCG
1 AATATTTGTTTAGATGATAATATTTTACGAAAAAAGTTTTAAGATTTTCG
967366 AATATTTGTTTAGATGATAATATTTTACGAAAAAAGTTTTAAGATTTTCG
1 AATATTTGTTTAGATGATAATATTTTACGAAAAAAGTTTTAAGATTTTCG
* *
967416 AAAAATTGTTT
1 AATATTTGTTT
967427 TAAGTGGATG
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 58 1.00
ACGTcount: A:0.38, C:0.05, G:0.14, T:0.44
Consensus pattern (50 bp):
AATATTTGTTTAGATGATAATATTTTACGAAAAAAGTTTTAAGATTTTCG
Found at i:967418 original size:21 final size:23
Alignment explanation
Indices: 967387--967430 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
967377 AGATGATAAT
967387 ATTTTACGAAAAA-AGTTTTAAG
1 ATTTTACGAAAAATAGTTTTAAG
*
967409 ATTTT-CGAAAAATTGTTTTAAG
1 ATTTTACGAAAAATAGTTTTAAG
967431 TGGATGACAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.41
Consensus pattern (23 bp):
ATTTTACGAAAAATAGTTTTAAG
Found at i:971155 original size:11 final size:12
Alignment explanation
Indices: 971127--971159 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
971117 GGTCAAGGTT
971127 AAAGTCAAATATC
1 AAAGTC-AATATC
971140 AAAGTCAATA-C
1 AAAGTCAATATC
971151 AAAGTCAAT
1 AAAGTCAAT
971160 CGAGATCCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.50
12 4 0.20
13 6 0.30
ACGTcount: A:0.55, C:0.15, G:0.09, T:0.21
Consensus pattern (12 bp):
AAAGTCAATATC
Found at i:975423 original size:17 final size:18
Alignment explanation
Indices: 975373--975423 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 18
975363 AATAAATTAG
*
975373 TAGACAAGT-TAAAGAA-
1 TAGACAAATATAAAGAAT
*
975389 TAGACAAATATATA-AAT
1 TAGACAAATATAAAGAAT
975406 TAGACAAA-ATAAAGAAT
1 TAGACAAATATAAAGAAT
975423 T
1 T
975424 CTTTTAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 14 0.48
17 15 0.52
ACGTcount: A:0.59, C:0.06, G:0.12, T:0.24
Consensus pattern (18 bp):
TAGACAAATATAAAGAAT
Found at i:975490 original size:28 final size:28
Alignment explanation
Indices: 975429--975490 Score: 65
Period size: 28 Copynumber: 2.2 Consensus size: 28
975419 GAATTCTTTT
* *
975429 AAAAAATAAATAAAGTCAATTAAATTAA
1 AAAAAATAAATAAAGTCAATAAAAATAA
975457 AGAAAAAT-AATAAAG-CAAATAAAAAATAA
1 A-AAAAATAAATAAAGTC-AAT-AAAAATAA
975486 AAAAA
1 AAAAA
975491 GGGCATAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
27 1 0.03
28 15 0.52
29 13 0.45
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (28 bp):
AAAAAATAAATAAAGTCAATAAAAATAA
Found at i:980362 original size:2 final size:2
Alignment explanation
Indices: 980355--980383 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
980345 GTATTTAAAT
980355 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 T
980384 GGTTTTTAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:982883 original size:22 final size:21
Alignment explanation
Indices: 982842--982883 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
982832 ATATTTTATT
*
982842 TAAATTTAATTATAAGATATA
1 TAAATTTAATTATAAAATATA
982863 TAAATATTAA-TATAAAA-ATA
1 TAAAT-TTAATTATAAAATATA
982883 T
1 T
982884 TTTTTTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 11 0.58
22 4 0.21
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATA
Found at i:984035 original size:16 final size:16
Alignment explanation
Indices: 984014--984044 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
984004 TGTATATTTT
*
984014 TATTAATTATTTATTA
1 TATTAATAATTTATTA
984030 TATTAATAATTTATT
1 TATTAATAATTTATT
984045 TAGTATTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTAATAATTTATTA
Found at i:990706 original size:2 final size:2
Alignment explanation
Indices: 990701--990726 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
990691 ACACACACAC
990701 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
990727 GCATTTAGCT
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):
AT
Done.