Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D07
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: 56457815
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1765025 characters in sequence are not A, C, G, or T
File 2 of 189
Found at i:410897 original size:48 final size:45
Alignment explanation
Indices: 410845--410943 Score: 117
Period size: 48 Copynumber: 2.1 Consensus size: 45
410835 GCGGGGGCGA
* *
410845 TGGTGGAGGCGGAGGAGGAGAGTACACAGGTGGCGGCGGAGGTGGAGG
1 TGGTGAAGGCGGAGGAGGAGAGTACAC---TGGCGGCGGAGGCGGAGG
* * * *
410893 TGGTGAAGGGGGAGGGGGAGAGTATACTGGCGGCGGCGGCGGAGG
1 TGGTGAAGGCGGAGGAGGAGAGTACACTGGCGGCGGAGGCGGAGG
410938 TGGTGA
1 TGGTGA
410944 TTGTGGAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
45 22 0.49
48 23 0.51
ACGTcount: A:0.19, C:0.10, G:0.59, T:0.12
Consensus pattern (45 bp):
TGGTGAAGGCGGAGGAGGAGAGTACACTGGCGGCGGAGGCGGAGG
Found at i:422136 original size:19 final size:19
Alignment explanation
Indices: 422112--422182 Score: 51
Period size: 19 Copynumber: 3.8 Consensus size: 19
422102 TTAAATAATT
422112 TTTTAAACATTTTAAAATA
1 TTTTAAACATTTTAAAATA
*** *
422131 TTTTAATTTTTTTATAAT-
1 TTTTAAACATTTTAAAATA
*
422149 TTTT--ACATTTTAAAACAA
1 TTTTAAACATTTTAAAA-TA
422167 TTTTAATA-ATTTTAAA
1 TTTTAA-ACATTTTAAA
422183 TACTTTTTAT
Statistics
Matches: 38, Mismatches: 9, Indels: 9
0.68 0.16 0.16
Matches are distributed among these distances:
16 7 0.18
18 8 0.21
19 14 0.37
20 8 0.21
21 1 0.03
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTTAAACATTTTAAAATA
Found at i:425750 original size:27 final size:27
Alignment explanation
Indices: 425709--425811 Score: 156
Period size: 27 Copynumber: 3.8 Consensus size: 27
425699 TAGTATTGGC
425709 GCCTATCT-GGAAGGCGCCAATGGTGGT
1 GCCTATCTAGG-AGGCGCCAATGGTGGT
* *
425736 GCCTATTTGGGAGGCGCCAATGGTGGT
1 GCCTATCTAGGAGGCGCCAATGGTGGT
425763 GCCTATCTAGGAGGCGCCAATGGTGGT
1 GCCTATCTAGGAGGCGCCAATGGTGGT
425790 GCCATAT-TAGGAGGCGCCAATG
1 GCC-TATCTAGGAGGCGCCAATG
425812 CTGTGATTTT
Statistics
Matches: 71, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
27 66 0.93
28 5 0.07
ACGTcount: A:0.19, C:0.21, G:0.37, T:0.22
Consensus pattern (27 bp):
GCCTATCTAGGAGGCGCCAATGGTGGT
Found at i:429402 original size:16 final size:15
Alignment explanation
Indices: 429371--429412 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
429361 ACAAAATCAA
*
429371 ATAAAATTTAATTAT
1 ATAAAAGTTAATTAT
429386 ATAAAAGTTACATTAT
1 ATAAAAGTTA-ATTAT
*
429402 ATAAAAATTAA
1 ATAAAAGTTAA
429413 ATAAGTTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (15 bp):
ATAAAAGTTAATTAT
Found at i:429578 original size:38 final size:38
Alignment explanation
Indices: 429524--429597 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
429514 TAAAAAACCC
429524 AAACTTTTAATAAAATGATTTTTAATTTTTTTATAATT
1 AAACTTTTAATAAAATGATTTTTAATTTTTTTATAATT
*
429562 AAACTTTTAATGAAATGATTTTTAATTTTTTTATAA
1 AAACTTTTAATAAAATGATTTTTAATTTTTTTATAA
429598 ACTTTATATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (38 bp):
AAACTTTTAATAAAATGATTTTTAATTTTTTTATAATT
Found at i:429836 original size:19 final size:19
Alignment explanation
Indices: 429814--430153 Score: 117
Period size: 19 Copynumber: 17.5 Consensus size: 19
429804 CATACAAAAT
*
429814 TACAATATTACAATATTCA
1 TACAAAATTACAATATTCA
*
429833 TACAAAAAAATTGCAATATTCA
1 TAC---AAAATTACAATATTCA
*
429855 TACAAAATTATAATA-T--
1 TACAAAATTACAATATTCA
*
429871 TACAACATT-C-ATA-T-A
1 TACAAAATTACAATATTCA
* *
429886 -A-AAAAATATAATATTCA
1 TACAAAATTACAATATTCA
*
429903 TACAAAATTACAA-AAT--
1 TACAAAATTACAATATTCA
*
429919 TACAATATT-C-ATA--CA
1 TACAAAATTACAATATTCA
* *
429934 -AAAAAATTGCAATATTCA
1 TACAAAATTACAATATTCA
429952 TACAAAACTATAATATTACAATATTCA
1 TAC---A--A-AAT-T-ACAATATTCA
*
429979 TACAAAAAATTTATAATATTCA
1 TAC--AAAA-TTACAATATTCA
430001 TACAAAATTACAATATTCA
1 TACAAAATTACAATATTCA
* *
430020 TACAAAAAATTACTA-ATCCAA
1 TAC--AAAATTACAATATTC-A
*
430041 AACTATAAA-TACAAATTTAATT-A
1 TAC-A-AAATTAC-AA--T-ATTCA
*
430064 TAAAATAATTACAATATTCA
1 TACAA-AATTACAATATTCA
*
430084 TACAACATTACAATATTCA
1 TACAAAATTACAATATTCA
* *
430103 TAAAAAAATTATAATATTCA
1 T-ACAAAATTACAATATTCA
*
430123 TACAAAAAATTTAAAATATTCA
1 TAC--AAAA-TTACAATATTCA
430145 TACAAAATT
1 TACAAAATT
430154 CTAATCTAAA
Statistics
Matches: 244, Mismatches: 34, Indels: 86
0.67 0.09 0.24
Matches are distributed among these distances:
13 4 0.02
14 12 0.05
15 6 0.02
16 20 0.08
17 1 0.00
18 6 0.02
19 56 0.23
20 37 0.15
21 21 0.09
22 49 0.20
23 8 0.03
24 3 0.01
25 5 0.02
26 4 0.02
27 12 0.05
ACGTcount: A:0.55, C:0.13, G:0.01, T:0.32
Consensus pattern (19 bp):
TACAAAATTACAATATTCA
Found at i:429850 original size:30 final size:27
Alignment explanation
Indices: 429793--430017 Score: 213
Period size: 27 Copynumber: 9.1 Consensus size: 27
429783 ATATCCTCAC
*
429793 ATTACAATGTTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAATTACAAT
429820 ATTACAATATTCATAC-AAA--A-AA-
1 ATTACAATATTCATACAAAATTACAAT
* *
429842 ATTGCAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAATTACAAT
* *
429869 ATTACAACATTCATATAAAA--A-AAT
1 ATTACAATATTCATACAAAATTACAAT
*
429893 A-T--AATATTCATACAAAATTACAAA
1 ATTACAATATTCATACAAAATTACAAT
429917 ATTACAATATTCATAC-AAA--A-AA-
1 ATTACAATATTCATACAAAATTACAAT
* * *
429939 ATTGCAATATTCATACAAAACTATAAT
1 ATTACAATATTCATACAAAATTACAAT
429966 ATTACAATATTCATAC-AAA--A-AAT
1 ATTACAATATTCATACAAAATTACAAT
*
429989 -TTATAATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAATTACAAT
430015 ATT
1 ATT
430018 CATACAAAAA
Statistics
Matches: 166, Mismatches: 11, Indels: 42
0.76 0.05 0.19
Matches are distributed among these distances:
21 13 0.08
22 44 0.27
23 18 0.11
24 10 0.06
25 5 0.03
26 16 0.10
27 60 0.36
ACGTcount: A:0.53, C:0.13, G:0.01, T:0.32
Consensus pattern (27 bp):
ATTACAATATTCATACAAAATTACAAT
Found at i:429872 original size:49 final size:49
Alignment explanation
Indices: 429750--430017 Score: 334
Period size: 49 Copynumber: 5.5 Consensus size: 49
429740 AAAATAATCA
* * *
429750 CAATATTCATACAAAAAATTACAATATTACAATATATCCT-C----ACATTA
1 CAATATTCATAC--AAAATTACAATATTACAATAT-TCATACAAAAAAATTG
*
429797 CAATGTTCATACAAAATTACAATATTACAATATTCATACAAAAAAATTG
1 CAATATTCATACAAAATTACAATATTACAATATTCATACAAAAAAATTG
* * *
429846 CAATATTCATACAAAATTATAATATTACAACATTCATATAAAAAAATAT-
1 CAATATTCATACAAAATTACAATATTACAATATTCATACAAAAAAAT-TG
*
429895 -AATATTCATACAAAATTACAAAATTACAATATTCATACAAAAAAATTG
1 CAATATTCATACAAAATTACAATATTACAATATTCATACAAAAAAATTG
* * * *
429943 CAATATTCATACAAAACTATAATATTACAATATTCATACAAAAAATTTA
1 CAATATTCATACAAAATTACAATATTACAATATTCATACAAAAAAATTG
*
429992 TAATATTCATACAAAATTACAATATT
1 CAATATTCATACAAAATTACAATATT
430018 CATACAAAAA
Statistics
Matches: 193, Mismatches: 20, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
44 3 0.02
45 22 0.11
47 12 0.06
48 42 0.22
49 113 0.59
50 1 0.01
ACGTcount: A:0.53, C:0.14, G:0.01, T:0.32
Consensus pattern (49 bp):
CAATATTCATACAAAATTACAATATTACAATATTCATACAAAAAAATTG
Found at i:429915 original size:97 final size:98
Alignment explanation
Indices: 429802--430017 Score: 380
Period size: 97 Copynumber: 2.2 Consensus size: 98
429792 CATTACAATG
*
429802 TTCATACAAAATTACAATATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAATTATA
1 TTCATACAAAATTACAATATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAACTATA
*
429867 ATATTACAACATTCATATAAAAAA-ATATAATA
66 ATATTACAACATTCATACAAAAAATATATAATA
*
429899 TTCATACAAAATTACAAAATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAACTATA
1 TTCATACAAAATTACAATATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAACTATA
* *
429964 ATATTACAATATTCATACAAAAAATTTATAATA
66 ATATTACAACATTCATACAAAAAATATATAATA
429997 TTCATACAAAATTACAATATT
1 TTCATACAAAATTACAATATT
430018 CATACAAAAA
Statistics
Matches: 112, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
97 85 0.76
98 27 0.24
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.32
Consensus pattern (98 bp):
TTCATACAAAATTACAATATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAACTATA
ATATTACAACATTCATACAAAAAATATATAATA
Found at i:429946 original size:22 final size:22
Alignment explanation
Indices: 429869--430151 Score: 191
Period size: 22 Copynumber: 12.9 Consensus size: 22
429859 AAATTATAAT
* *
429869 ATTACAACATTCATATAAAAAA
1 ATTACAATATTCATACAAAAAA
*
429891 A-TATAATATTCATACAAAATTACAAA
1 ATTACAATATTCATAC--AA--A-AAA
429917 ATTACAATATTCATACAAAAAA
1 ATTACAATATTCATACAAAAAA
*
429939 ATTGCAATATTCATACAAAACTATAA
1 ATTACAATATTCATAC-AAA--A-AA
429965 TATTACAATATTCATACAAAAAA
1 -ATTACAATATTCATACAAAAAA
* *
429988 TTTATAATATTCATAC---AAA
1 ATTACAATATTCATACAAAAAA
430007 ATTACAATATTCATAC-AAAAA
1 ATTACAATATTCATACAAAAAA
* * *
430028 ATTACTA-ATCCA-A-AACTATAA
1 ATTACAATATTCATACAA--AAAA
* * *
430049 A-TACAA-ATTTAATTATAAAATA
1 ATTACAATA-TTCA-TACAAAAAA
*
430071 ATTACAATATTCATAC---AAC
1 ATTACAATATTCATACAAAAAA
430090 ATTACAATATTCAT--AAAAAA
1 ATTACAATATTCATACAAAAAA
*
430110 ATTATAATATTCATACAAAAAA
1 ATTACAATATTCATACAAAAAA
* *
430132 TTTAAAATATTCATACAAAA
1 ATTACAATATTCATACAAAA
430152 TTCTAATCTA
Statistics
Matches: 208, Mismatches: 26, Indels: 54
0.72 0.09 0.19
Matches are distributed among these distances:
19 34 0.16
20 24 0.12
21 26 0.12
22 62 0.30
23 17 0.08
24 4 0.02
25 4 0.02
26 9 0.04
27 28 0.13
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.31
Consensus pattern (22 bp):
ATTACAATATTCATACAAAAAA
Found at i:437509 original size:33 final size:33
Alignment explanation
Indices: 437469--437537 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
437459 AATTGTTGCT
437469 TTAGTCCTTCAAAA-TTTAAAAAACATGAAGTTA
1 TTAGTCCTTCAAAATTTTAAAAAAC-TGAAGTTA
*
437502 TTAGTCCTTCAAAATTTTAAAAATCTGAAGTTA
1 TTAGTCCTTCAAAATTTTAAAAAACTGAAGTTA
437535 TTA
1 TTA
437538 TGTGGTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 25 0.74
34 9 0.26
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.38
Consensus pattern (33 bp):
TTAGTCCTTCAAAATTTTAAAAAACTGAAGTTA
Found at i:439986 original size:132 final size:131
Alignment explanation
Indices: 439749--440144 Score: 472
Period size: 132 Copynumber: 3.0 Consensus size: 131
439739 TCTTACCCAA
* * ** *** *
439749 TAAATTTGTCACTTCTTCAGGCAATCTCATGTACTCATACTTTCGACTAAGTTGGGAGATAAAAC
1 TAAATCTGTCACTTCTTCAGGTAGCCTCATGTACTCGGGCTCTCGACTAAGTTGGGAGATAAAAC
** * *
439814 CTCGGCCCAATCGGGGATAATGCTGAACATGTTGAGGGGCTTGTCGACTTTGGGTAGATGACACT
66 CTCGGCCTGATCGGGGATAATACTGGACATGTTGAGGGGCTTGTCG-CTTTGGGTAGATGACACT
439879 TC
130 TC
** * *
439881 TAAATCTGTCACTTCTTC-GCGTAGCCTTGTGTACTCTGGCTCTCGACTAAGTCGGGAGATAAAA
1 TAAATCTGTCACTTCTTCAG-GTAGCCTCATGTACTCGGGCTCTCGACTAAGTTGGGAGATAAAA
* * * * * *
439945 CCTCGGCCTGATCGAGGACAATACTGGACATGTTGAGGGGCTCGTTGGTTCTGGGTAGATAACAC
65 CCTCGGCCTGATCGGGGATAATACTGGACATGTTGAGGGGCTTGTCGCTT-TGGGTAGATGACAC
440010 TTC
129 TTC
* *
440013 TAAATTTGTCACTTCTTCAGGTAGCCTCATGTACTCGGGCTCTCGATTAAGTTGGGAGATAAAAC
1 TAAATCTGTCACTTCTTCAGGTAGCCTCATGTACTCGGGCTCTCGACTAAGTTGGGAGATAAAAC
* * * * *
440078 CTCGGCTTGATTGGGGATAATATTGGACATGTTGAGGGGTTTGTCGGCTTTGGGCA-ATTGACAC
66 CTCGGCCTGATCGGGGATAATACTGGACATGTTGAGGGGCTTGTC-GCTTTGGGTAGA-TGACAC
440142 TTC
129 TTC
440145 AAAAACTTTT
Statistics
Matches: 221, Mismatches: 38, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
131 4 0.02
132 213 0.96
133 4 0.02
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (131 bp):
TAAATCTGTCACTTCTTCAGGTAGCCTCATGTACTCGGGCTCTCGACTAAGTTGGGAGATAAAAC
CTCGGCCTGATCGGGGATAATACTGGACATGTTGAGGGGCTTGTCGCTTTGGGTAGATGACACTT
C
Found at i:444447 original size:13 final size:14
Alignment explanation
Indices: 444423--444488 Score: 50
Period size: 13 Copynumber: 4.6 Consensus size: 14
444413 AAAAACAATT
444423 ATTTTTTCTATTTC
1 ATTTTTTCTATTTC
444437 ATTTTTT-TATTTC
1 ATTTTTTCTATTTC
*
444450 -TTTATTTACCTTTTTC
1 ATTT-TTT--CTATTTC
444466 --TTTTTCTATTTGC
1 ATTTTTTCTATTT-C
444479 ATTTCTTTCT
1 ATTT-TTTCT
444489 TCTTTTGCCA
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
12 8 0.19
13 10 0.24
14 10 0.24
15 4 0.10
16 10 0.24
ACGTcount: A:0.12, C:0.15, G:0.02, T:0.71
Consensus pattern (14 bp):
ATTTTTTCTATTTC
Found at i:444485 original size:18 final size:18
Alignment explanation
Indices: 444462--444496 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
444452 TATTTACCTT
444462 TTTCTTT-TTCTATTTGCA
1 TTTCTTTCTTCT-TTTGCA
444480 TTTCTTTCTTCTTTTGC
1 TTTCTTTCTTCTTTTGC
444497 CATAAACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.06, C:0.20, G:0.06, T:0.69
Consensus pattern (18 bp):
TTTCTTTCTTCTTTTGCA
Found at i:444713 original size:16 final size:16
Alignment explanation
Indices: 444685--444740 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
444675 GAGATAAGAG
444685 GAAAGAAAG-GAGAATA
1 GAAA-AAAGAGAGAATA
*
444701 GAAAAAAGAGAGAAGA
1 GAAAAAAGAGAGAATA
*
444717 GAGAAGAA-AGAGAATAA
1 GA-AAAAAGAGAGAAT-A
444734 GAAAAAA
1 GAAAAAA
444741 AAAGAAAGGC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 4 0.12
16 22 0.67
17 7 0.21
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.04
Consensus pattern (16 bp):
GAAAAAAGAGAGAATA
Found at i:444726 original size:18 final size:17
Alignment explanation
Indices: 444675--444729 Score: 60
Period size: 16 Copynumber: 3.2 Consensus size: 17
444665 GGTTGTTTAT
*
444675 GAGATAAGAGGAAAGAAA
1 GAGAGAAGA-GAAAGAAA
*
444693 G-GAGAATAGAAA-AAA
1 GAGAGAAGAGAAAGAAA
444708 GAGAGAAGAGAGAAGAAA
1 GAGAGAAGAGA-AAGAAA
444726 GAGA
1 GAGA
444730 ATAAGAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 4 0.13
16 12 0.39
17 7 0.23
18 8 0.26
ACGTcount: A:0.62, C:0.00, G:0.35, T:0.04
Consensus pattern (17 bp):
GAGAGAAGAGAAAGAAA
Found at i:450446 original size:146 final size:148
Alignment explanation
Indices: 450175--450482 Score: 421
Period size: 146 Copynumber: 2.1 Consensus size: 148
450165 AATTATGATC
*
450175 TTTTTAAAGAAAAGAGAATTTAGATTTTTAAAAATAAAAATATGTTTTTTAGTCATTTTAAAGGA
1 TTTTTAAAGAAAAGAGAATTTAGATTTTT-AAAATAAAAATATGCTTTTTAGTCATTTTAAAGGA
* *
450240 AAAGATTAAAATTTTAAAACAAAGTTTTAATCTTTTTCAACTATTTCGAAATAAAGCTTTGATTT
65 AAAGATTAAAATTTTAAAACAAAATTTTAATCTTTTTCAACTATTTCGAAATAAAACTTTGATTT
* *
450305 TAAAGAAAAATAGTGATTT
130 TAAAGAAAAATAGTAATTG
*
450324 TCTTTTAAA-AAAAGAGAAAGTTTAGATTTTT-AAA-AACAA-AT-CTTTTTAGTCATTTTAAAG
1 T-TTTTAAAGAAAAGAG-AA-TTTAGATTTTTAAAATAAAAATATGCTTTTTAGTCATTTTAAAG
* * * *
450384 GAAAA-ATTTAAATTTTTAAAATAAAATTTTGATCTTTTTCAACTATTTTGAAATAAAACTTTGA
63 GAAAAGA-TTAAAATTTTAAAACAAAATTTTAATCTTTTTCAACTATTTCGAAATAAAACTTTGA
* *
450448 TTTTTAAGAAAAGTAGTAATTG
127 TTTTAAAGAAAAATAGTAATTG
450470 TTTTTAAAGAAAA
1 TTTTTAAAGAAAA
450483 CTTTAATTTT
Statistics
Matches: 142, Mismatches: 12, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
145 8 0.06
146 97 0.68
147 2 0.01
148 4 0.03
149 11 0.08
150 9 0.06
151 11 0.08
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (148 bp):
TTTTTAAAGAAAAGAGAATTTAGATTTTTAAAATAAAAATATGCTTTTTAGTCATTTTAAAGGAA
AAGATTAAAATTTTAAAACAAAATTTTAATCTTTTTCAACTATTTCGAAATAAAACTTTGATTTT
AAAGAAAAATAGTAATTG
Found at i:453518 original size:17 final size:17
Alignment explanation
Indices: 453496--453529 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
453486 ATCCACTAAT
*
453496 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
453513 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
453530 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:458146 original size:17 final size:17
Alignment explanation
Indices: 458124--458157 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
458114 ATCCACTAAT
*
458124 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
458141 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
458158 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:475998 original size:18 final size:19
Alignment explanation
Indices: 475967--476006 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
475957 AAAATTTATT
* *
475967 AAAATAATACAAAATTACA
1 AAAAAAATACAAAATCACA
475986 AAAAAAATA-AAAATCACA
1 AAAAAAATACAAAATCACA
476004 AAA
1 AAA
476007 GCATAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.75, C:0.10, G:0.00, T:0.15
Consensus pattern (19 bp):
AAAAAAATACAAAATCACA
Found at i:476377 original size:15 final size:14
Alignment explanation
Indices: 476348--476374 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
476338 CAATTTTATA
476348 ATTTTTTAAAATTC
1 ATTTTTTAAAATTC
476362 ATTTTTTAAAATT
1 ATTTTTTAAAATT
476375 TCAAAAATCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTTTTTAAAATTC
Found at i:476409 original size:27 final size:27
Alignment explanation
Indices: 476379--476463 Score: 73
Period size: 29 Copynumber: 3.0 Consensus size: 27
476369 AAAATTTCAA
*
476379 AAATCTATATTTTTTATTTTCAATTTT
1 AAATTTATATTTTTTATTTTCAATTTT
* * *
476406 AAATATTTTAATTTTT-TTTACAATTTTT
1 AAAT-TTATATTTTTTATTTTCAA-TTTT
* *
476434 ATAATTTTATATTTTTGAATTTCAATTTT
1 A-AA-TTTATATTTTTTATTTTCAATTTT
476463 A
1 A
476464 TAAAAATTTC
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
27 10 0.23
28 13 0.30
29 15 0.34
30 6 0.14
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.62
Consensus pattern (27 bp):
AAATTTATATTTTTTATTTTCAATTTT
Found at i:476513 original size:97 final size:97
Alignment explanation
Indices: 476333--476510 Score: 211
Period size: 97 Copynumber: 1.8 Consensus size: 97
476323 TTTGAAAATC
* * * *
476333 TTTTACAATTTTATAATTTTTTAAAATTCATTTTTTAAAATTTCAAAAATCTATATTTTTTATTT
1 TTTTACAATTTTATAATTTTTTAAAATTCATTTTTAAAAATTTCAAAAATCTAAATTTATTATTA
*
476398 TCAATTTTAAATATTTTAATTTTTTTTACAAT
66 TCAATTTCAAATATTTTAATTTTTTTTACAAT
* * * * *
476430 TTTTATAATTTTAT-A-TTTTTGAATTTCAATTTTATAAAAATTTCCAAAATTTAAATTTATT-T
1 TTTTACAATTTTATAATTTTTTAAAATTC-ATTTT-TAAAAATTTCAAAAATCTAAATTTATTAT
476492 TAT-AATTTCAAATGATTTT
64 TATCAATTTCAAAT-ATTTT
476511 TAAAACAATT
Statistics
Matches: 68, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
95 19 0.28
96 14 0.21
97 35 0.51
ACGTcount: A:0.36, C:0.06, G:0.01, T:0.57
Consensus pattern (97 bp):
TTTTACAATTTTATAATTTTTTAAAATTCATTTTTAAAAATTTCAAAAATCTAAATTTATTATTA
TCAATTTCAAATATTTTAATTTTTTTTACAAT
Found at i:478660 original size:63 final size:61
Alignment explanation
Indices: 478546--478670 Score: 171
Period size: 63 Copynumber: 2.0 Consensus size: 61
478536 GGTTCAATAC
* * *
478546 CATTGTAAGGTGATTGTAGTAACCTTTTTCTATAATTGTAGTTTAAAGCTTTTATCCAAAT
1 CATTGTAAGGTCATTGTAGTAACCTTTTTCTATAATTGCAATTTAAAGCTTTTATCCAAAT
* *
478607 CATTGTGAGGTCATTGTAGTAACCCCATTTTT-TATAATTGCAATTTAAGGCTTTTATCCAAAT
1 CATTGTAAGGTCATTGTAGTAA--CC-TTTTTCTATAATTGCAATTTAAAGCTTTTATCCAAAT
478670 C
1 C
478671 TTATCAATTT
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
61 20 0.36
63 31 0.55
64 5 0.09
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.42
Consensus pattern (61 bp):
CATTGTAAGGTCATTGTAGTAACCTTTTTCTATAATTGCAATTTAAAGCTTTTATCCAAAT
Found at i:484523 original size:17 final size:18
Alignment explanation
Indices: 484493--484538 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
484483 ATTTAAATTG
484493 CGGTCGCGGTCGCGTTTT
1 CGGTCGCGGTCGCGTTTT
484511 CGGTCGC-GTCGCG-TTT
1 CGGTCGCGGTCGCGTTTT
484527 --GTCGCGGTCGCG
1 CGGTCGCGGTCGCG
484539 GACATAACGG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.19
15 6 0.22
16 3 0.11
17 6 0.22
18 7 0.26
ACGTcount: A:0.00, C:0.30, G:0.41, T:0.28
Consensus pattern (18 bp):
CGGTCGCGGTCGCGTTTT
Found at i:486351 original size:14 final size:14
Alignment explanation
Indices: 486313--486355 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
486303 TAAAATGTAC
486313 AATATAATTAAA-T
1 AATATAATTAAATT
486326 AATATAAATTAAATT
1 AATAT-AATTAAATT
*
486341 AA-ATAATTTAATT
1 AATATAATTAAATT
486354 AA
1 AA
486356 CTGTTTACCC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 15 0.56
14 9 0.33
15 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATAATTAAATT
Found at i:488842 original size:3 final size:3
Alignment explanation
Indices: 488836--488932 Score: 77
Period size: 3 Copynumber: 32.0 Consensus size: 3
488826 TAAAAAAATT
**
488836 TAA TAA TAA TAA TAA TAA TGG TAA TAAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
* * * * * * ** * *
488882 TCA TGA TGA TGA TGA TGA TGG TAT TAA TAA TAA TAA TAA TAA CAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
488930 TAA
1 TAA
488933 AAATCTTAAA
Statistics
Matches: 81, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
3 78 0.96
4 3 0.04
ACGTcount: A:0.56, C:0.02, G:0.09, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:502699 original size:49 final size:50
Alignment explanation
Indices: 502551--502797 Score: 284
Period size: 49 Copynumber: 4.8 Consensus size: 50
502541 GATAATAACA
* ** *
502551 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGT-CTCGG
* * * *
502602 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
*
502652 TGCCAACGCCATGTCCCAGACAT-GTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
* * *
502701 TGCCCATGCCATGTCCCA-ACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC--G-TC-T-CGG
*
502755 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
502798 TTACCCAAAT
Statistics
Matches: 167, Mismatches: 20, Indels: 13
0.83 0.10 0.06
Matches are distributed among these distances:
48 4 0.02
49 58 0.35
50 28 0.17
51 34 0.20
52 2 0.01
53 1 0.01
54 2 0.01
55 17 0.10
56 21 0.13
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
Found at i:502910 original size:13 final size:13
Alignment explanation
Indices: 502889--502920 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
502879 GCTTGGATCA
*
502889 TCATCAAATAAAT
1 TCATAAAATAAAT
502902 TCATAAAATAAAT
1 TCATAAAATAAAT
502915 TCATAA
1 TCATAA
502921 TTGCTGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:503166 original size:30 final size:30
Alignment explanation
Indices: 503131--503188 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
503121 CCTCGACTCT
*
503131 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
503161 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
503189 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:511167 original size:3 final size:3
Alignment explanation
Indices: 511154--511183 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
511144 AAGACACAGC
511154 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AA
511184 AGCATTTAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:511413 original size:19 final size:19
Alignment explanation
Indices: 511391--511441 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
511381 ATATAAATTC
511391 TAAAAGTAATTAATTTAAA
1 TAAAAGTAATTAATTTAAA
**
511410 TAAAAGTAATTTTTTTAAA
1 TAAAAGTAATTAATTTAAA
511429 -AAAA-TAA-TAATTT
1 TAAAAGTAATTAATTT
511442 CAAGTGATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
16 4 0.14
17 3 0.11
18 4 0.14
19 17 0.61
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (19 bp):
TAAAAGTAATTAATTTAAA
Found at i:520743 original size:17 final size:16
Alignment explanation
Indices: 520705--520744 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
520695 AACTCCAGAT
520705 TTTTTTATTTTTAATA
1 TTTTTTATTTTTAATA
* *
520721 TATTTTATTTTTTATAA
1 TTTTTTATTTTTAAT-A
520738 TTTTTTA
1 TTTTTTA
520745 ATAATTTACT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTTATTTTTAATA
Found at i:522744 original size:26 final size:27
Alignment explanation
Indices: 522694--522744 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
522684 GCAGATAATA
*
522694 AAAATTTTTGAATTTTAAAGTAAATCT
1 AAAATTTTTGAATTTTAAAGAAAATCT
* *
522721 AAAA-TTTTGATTTTTATAGAAAAT
1 AAAATTTTTGAATTTTAAAGAAAAT
522745 TCAAATATCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 17 0.81
27 4 0.19
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (27 bp):
AAAATTTTTGAATTTTAAAGAAAATCT
Found at i:525288 original size:149 final size:149
Alignment explanation
Indices: 525016--525612 Score: 932
Period size: 149 Copynumber: 4.0 Consensus size: 149
525006 GATCAGCACT
* * *
525016 TTTTCCATCGTTTGATTTATTATCATCGCCATTGACATGGAAAGACCCGTATTTTTTAGGTCGGT
1 TTTTCCATCATTTGATTTATTATCATCACCATTGACATGGAAAGACCCGTATTTTTTAAGTCGGT
* * **
525081 CCTAGAGAACACTTACAGAGATTAGAAGAGTTCCAGTGTGAAGAGATAATC-AGACAAGTAAAG-
66 CCTAGAGAACAATTACAGAGATCAGAAGAGTTCCAGTGTGAAGAGGCAATCAAG-CAAGTAAAGA
525144 TGCAAACACGAGGGATACCTG
130 T-CAAACACGAGGGATACCTG
525165 TTTTCCATCATTTGATTTATTATCATCACCATTGACATGGAAAGACCCGTATTTTTTAAGTCGGT
1 TTTTCCATCATTTGATTTATTATCATCACCATTGACATGGAAAGACCCGTATTTTTTAAGTCGGT
* *
525230 CCTAGAGAACAATTACAGAGATCAGAAGAGTTTCAGTATGAAGAGGCAATCAAGCAAGTAAAGAT
66 CCTAGAGAACAATTACAGAGATCAGAAGAGTTCCAGTGTGAAGAGGCAATCAAGCAAGTAAAGAT
*
525295 CAAACACGAGTGATACCTG
131 CAAACACGAGGGATACCTG
525314 TTTTCCATCATTTGATTTATTATCATCACCATTGACATGGAAAGACCCGTATTTTTTAAGTCGGT
1 TTTTCCATCATTTGATTTATTATCATCACCATTGACATGGAAAGACCCGTATTTTTTAAGTCGGT
* * * *
525379 CCTAGAGAACAATTACAGAGATCAGAAGAGTTTCAGTGTGAAGATGCGATCAGGCAAGTAAAGAT
66 CCTAGAGAACAATTACAGAGATCAGAAGAGTTCCAGTGTGAAGAGGCAATCAAGCAAGTAAAGAT
525444 CAAACACGAGGGATACCTG
131 CAAACACGAGGGATACCTG
* *
525463 TTTTCCATAATTTGATTTATTATCTTCACCATTGACATGGAAAGACCCGTATTTTTT-AGTTCGG
1 TTTTCCATCATTTGATTTATTATCATCACCATTGACATGGAAAGACCCGTATTTTTTAAG-TCGG
* * * * *
525527 TCCTGGAGAA-AAGTTACAGAGATCAGAAGAGTTCCAATGCGAAGAGGCAATTAGGCAAGTAAAG
65 TCCTAGAGAACAA-TTACAGAGATCAGAAGAGTTCCAGTGTGAAGAGGCAATCAAGCAAGTAAAG
*
525591 ATCAAACACAAGGGATACCTG
129 ATCAAACACGAGGGATACCTG
525612 T
1 T
525613 GGCTGTGGGA
Statistics
Matches: 419, Mismatches: 25, Indels: 8
0.93 0.06 0.02
Matches are distributed among these distances:
148 4 0.01
149 412 0.98
150 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (149 bp):
TTTTCCATCATTTGATTTATTATCATCACCATTGACATGGAAAGACCCGTATTTTTTAAGTCGGT
CCTAGAGAACAATTACAGAGATCAGAAGAGTTCCAGTGTGAAGAGGCAATCAAGCAAGTAAAGAT
CAAACACGAGGGATACCTG
Found at i:531284 original size:18 final size:18
Alignment explanation
Indices: 531239--531295 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
531229 AATATTTTTC
531239 TAAATTTTATATGAAAAGA
1 TAAA-TTTATATGAAAAGA
* *
531258 TAAAATTATCTGAAAA-A
1 TAAATTTATATGAAAAGA
531275 TAATATTTAT-T-AAAAG-
1 TAA-ATTTATATGAAAAGA
531291 TAAAT
1 TAAAT
531296 GACTTTTTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
15 2 0.06
16 7 0.21
17 5 0.15
18 15 0.45
19 4 0.12
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (18 bp):
TAAATTTATATGAAAAGA
Found at i:533737 original size:18 final size:17
Alignment explanation
Indices: 533711--533744 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
533701 ATATAAAGTT
533711 TTGGTAATTTCATTTTG
1 TTGGTAATTTCATTTTG
*
533728 TTGGTGAATTTTATTTT
1 TTGGT-AATTTCATTTT
533745 ATTTTTTGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.18, C:0.03, G:0.18, T:0.62
Consensus pattern (17 bp):
TTGGTAATTTCATTTTG
Found at i:533760 original size:22 final size:23
Alignment explanation
Indices: 533717--533763 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
533707 AGTTTTGGTA
533717 ATTTCATTTTGTTGGTGAATTTT
1 ATTTCATTTTGTTGGTGAATTTT
*
533740 ATTTTATTTT-TTGGT-ATATTTT
1 ATTTCATTTTGTTGGTGA-ATTTT
533762 AT
1 AT
533764 ACCCGTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 1 0.05
22 12 0.55
23 9 0.41
ACGTcount: A:0.19, C:0.02, G:0.13, T:0.66
Consensus pattern (23 bp):
ATTTCATTTTGTTGGTGAATTTT
Found at i:537434 original size:14 final size:14
Alignment explanation
Indices: 537415--537448 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
537405 GTGAATTTTT
537415 TAATTTG-TGAAATA
1 TAATTTGAT-AAATA
537429 TAATTTGATAAATA
1 TAATTTGATAAATA
537443 TAATTT
1 TAATTT
537449 AATTCAGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 18 0.95
15 1 0.05
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (14 bp):
TAATTTGATAAATA
Found at i:542482 original size:3 final size:3
Alignment explanation
Indices: 542476--542500 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
542466 CAACAATTGT
542476 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
542501 GTGCTGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:554928 original size:44 final size:44
Alignment explanation
Indices: 554832--555121 Score: 132
Period size: 43 Copynumber: 6.7 Consensus size: 44
554822 TTTTAACCCA
* * ** * *
554832 CTCCACTGTAACTTCAGGGAGATAGGAT-AGTGTCTTCGATCTG
1 CTCCACTGTAACTTCAGGGGGATAAGATCTCTGGCTTCAATCTG
*
554875 CTCCGCTGTAA-TCTC-GGGGAGATAAGATCTCTGGCTTCAATCTG
1 CTCCACTGTAACT-TCAGGGG-GATAAGATCTCTGGCTTCAATCTG
* ** *
554919 CTCCACTGTAACTTCAGGGGGATAAGATCTGCAAT-TCTTCGGTCTA
1 CTCCACTGTAACTTCAGGGGGATAAGATCT-C--TGGCTTCAATCTG
* * * * * * *
554965 CTCCACTGTAACCTCAGAGAGATAAGA-C-CT-GATGCGATCTA
1 CTCCACTGTAACTTCAGGGGGATAAGATCTCTGGCTTCAATCTG
* * * *** * *
555006 CTCTACTGTAAC-TCAGAGAGATAAGATC-CTTTATTTTAATCCG
1 CTCCACTGTAACTTCAGGGGGATAAGATCTC-TGGCTTCAATCTG
* * * ** *
555049 CTCCACTGTAACTTCAGGGAGATAGGAT-TATATCTTCGATCTG
1 CTCCACTGTAACTTCAGGGGGATAAGATCTCTGGCTTCAATCTG
* * * *
555092 CTCCGCTGTAACCTCAGGGAGACAAGATCT
1 CTCCACTGTAACTTCAGGGGGATAAGATCT
555122 GCATTTCTTC
Statistics
Matches: 192, Mismatches: 41, Indels: 27
0.74 0.16 0.10
Matches are distributed among these distances:
40 14 0.07
41 21 0.11
42 5 0.03
43 66 0.34
44 47 0.24
45 7 0.04
46 31 0.16
47 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (44 bp):
CTCCACTGTAACTTCAGGGGGATAAGATCTCTGGCTTCAATCTG
Found at i:554972 original size:46 final size:44
Alignment explanation
Indices: 554832--555207 Score: 262
Period size: 46 Copynumber: 8.7 Consensus size: 44
554822 TTTTAACCCA
* *
554832 CTCCACTGTAACTTCAGGGAGATAGGAT-AG-TGTCTTCGATCTG
1 CTCCACTGTAACTTCAGGGAGATAAGATCTGAT-TCTTCGATCTG
* * * * *
554875 CTCCGCTGTAA-TCTCGGGGAGATAAGATCT-CTGGCTTCAATCTG
1 CTCCACTGTAACT-TCAGGGAGATAAGATCTGAT-TCTTCGATCTG
* * *
554919 CTCCACTGTAACTTCAGGGGGATAAGATCTGCAATTCTTCGGTCTA
1 CTCCACTGTAACTTCAGGGAGATAAGATCTG--ATTCTTCGATCTG
* * * * *
554965 CTCCACTGTAACCTCAGAGAGATAAGACCTGA---TGCGATCTA
1 CTCCACTGTAACTTCAGGGAGATAAGATCTGATTCTTCGATCTG
* * * * *
555006 CTCTACTGTAAC-TCAGAGAGATAAGATCCTTTATT-TT-AATCCG
1 CTCCACTGTAACTTCAGGGAGATAAGAT-C-TGATTCTTCGATCTG
*
555049 CTCCACTGTAACTTCAGGGAGATAGGAT-T-ATATCTTCGATCTG
1 CTCCACTGTAACTTCAGGGAGATAAGATCTGAT-TCTTCGATCTG
* * * *
555092 CTCCGCTGTAACCTCAGGGAGACAAGATCTGCATTTCTTCGGTCTG
1 CTCCACTGTAACTTCAGGGAGATAAGATCTG-A-TTCTTCGATCTG
* * * *
555138 TTCCACTGTAA-TCTCAGGGAGATAAGACCTGA-T-GT-GATCTT
1 CTCCACTGTAACT-TCAGGGAGATAAGATCTGATTCTTCGATCTG
* *
555179 CTCTACTGTAACTTCAGAGAGATAAGATC
1 CTCCACTGTAACTTCAGGGAGATAAGATC
555208 CTTTAATCCG
Statistics
Matches: 263, Mismatches: 49, Indels: 44
0.74 0.14 0.12
Matches are distributed among these distances:
40 16 0.06
41 48 0.18
42 7 0.03
43 66 0.25
44 52 0.20
45 2 0.01
46 70 0.27
47 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (44 bp):
CTCCACTGTAACTTCAGGGAGATAAGATCTGATTCTTCGATCTG
Found at i:555121 original size:173 final size:169
Alignment explanation
Indices: 554874--555291 Score: 504
Period size: 173 Copynumber: 2.4 Consensus size: 169
554864 TCTTCGATCT
* ** * ** * *
554874 GCTCCGCTGTAATCTCGGGGAGATAAGATCT-CTGGCTTCAATCTGCTCCACTGTAACTTCAGGG
1 GCTCCACTGTAATCTCAAGGAGATAGGAT-TACTATCTTCGATCTGCTCCGCTGTAAC-TCAGGG
* *
554938 GGATAAGATCTGCAATTCTTCGGTCTACTCCACTGTAACCTCAGAGAGATAAGACCTGATGCGAT
64 AGACAAGATCTGCAATTCTTCGGTCTACTCCACTGTAACCTCAGAGAGATAAGACCTGATGCGAT
555003 CTACTCTACTGTAAC-TCAGAGAGATAAGATCCTTTATTTTAATCC
129 CTACTCTACTGTAACTTCAGAGAGATAAGATCC-----TTTAATCC
*
555048 GCTCCACTGTAA-CTTCAGGGAGATAGGATTA-TATCTTCGATCTGCTCCGCTGTAACCTCAGGG
1 GCTCCACTGTAATC-TCAAGGAGATAGGATTACTATCTTCGATCTGCTCCGCTGTAA-CTCAGGG
* ** * * *
555111 AGACAAGATCTGCATTTCTTCGGTCTGTTCCACTGTAATCTCAGGGAGATAAGACCTGATGTGAT
64 AGACAAGATCTGCAATTCTTCGGTCTACTCCACTGTAACCTCAGAGAGATAAGACCTGATGCGAT
*
555176 CTTCTCTACTGTAACTTCAGAGAGATAAGATCCTTTAATCC
129 CTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTAATCC
* * *
555217 GCTCCATTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTGCTTCGCTGTTAA-TCAGGGA
1 GCTCCACTGTAATCTCAAGGAGATAGGATTACTATCTTCGATCTGCTCCGCTG-TAACTCAGGG-
*
555281 AGGCAAGATCT
64 AGACAAGATCT
555292 CTTCTTCAAC
Statistics
Matches: 215, Mismatches: 21, Indels: 20
0.84 0.08 0.08
Matches are distributed among these distances:
169 41 0.19
170 30 0.14
171 3 0.01
173 99 0.46
174 42 0.20
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (169 bp):
GCTCCACTGTAATCTCAAGGAGATAGGATTACTATCTTCGATCTGCTCCGCTGTAACTCAGGGAG
ACAAGATCTGCAATTCTTCGGTCTACTCCACTGTAACCTCAGAGAGATAAGACCTGATGCGATCT
ACTCTACTGTAACTTCAGAGAGATAAGATCCTTTAATCC
Found at i:556624 original size:1 final size:1
Alignment explanation
Indices: 556618--556644 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
556608 CTCTCCAAAG
556618 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
556645 AGGAAGCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:568150 original size:34 final size:34
Alignment explanation
Indices: 568085--568150 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
568075 TTTAATAATA
* ** *
568085 TTAATAATAATGCTAAATAATAATTATAATAGTT
1 TTAATAATAATGATAAATAATAAAAAAAATAGTT
568119 TTAATAATAAT-ATATAATAATAAAAAAAATAG
1 TTAATAATAATGATA-AATAATAAAAAAAATAG
568151 CACATATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 2 0.07
34 25 0.93
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.36
Consensus pattern (34 bp):
TTAATAATAATGATAAATAATAAAAAAAATAGTT
Found at i:570562 original size:18 final size:18
Alignment explanation
Indices: 570516--570551 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
570506 TATCATGTAT
570516 TATATTAG-ATTTTATAAA
1 TATATTAGTA-TTTATAAA
570534 TATATTAGTATTTATAAA
1 TATATTAGTATTTATAAA
570552 ATTTTATGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 16 0.94
19 1 0.06
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (18 bp):
TATATTAGTATTTATAAA
Found at i:573558 original size:243 final size:234
Alignment explanation
Indices: 573107--574209 Score: 1182
Period size: 243 Copynumber: 4.8 Consensus size: 234
573097 CAAAATAAAT
*
573107 AATCATGAAAAATCACGGAAA-AATAG-AATCCAATTCAGTATGACTAACAATTCGATTATATAA
1 AATCAT-AAAAATCAC-GAAACAATAGCAATCCAATTCAGTATGACTAACGATTCGATTATATAA
* * *
573170 ACAC--AAGCTATATGTATAAAATCAAA-CGATGAATCGTATTTCGTTCCTATTAGACTAACCCT
64 ACACAAAAGCTATATGTATACATTCAAACCGATGAATCGTATTTCGTTCCTATTAGACTATCCCT
* * * * *
573232 ATCAAATAAGGTTTCATATAAGTAACTATTTGCATTTCAATTTCTGTTCCTCGTACCA-AACCAA
129 ATCGAATAAGGTTTCATATAAGTAACCATTTGCATTTCAATTTCCGTTCCTCATA-CAGAACCGA
573296 TCCAATGACAACCCTCCATTCAAAATACATAATCATGAAAATTA
193 TCCAATGACAACCCTCCATTCAAAATACATAATCATGAAAA--A
*
573340 CTTGTAATCTCATAAAAATCACGAAACAATAGCAATCCAATTCAGTATGACTAATGATTCGATTA
1 -----AA--TCATAAAAATCACGAAACAATAGCAATCCAATTCAGTATGACTAACGATTCGATTA
* * * *
573405 TATAAACACAAAAGCTATATGTATAGATTCAAACCAATGAATCATATTTCGTTCCTATAAGACTA
59 TATAAACACAAAAGCTATATGTATACATTCAAACCGATGAATCGTATTTCGTTCCTATTAGACTA
* * * *
573470 TCCCTATCGAATAAGGTGTCGTATAAGTAACCATTTGCATTTCAATTTCCATTCCTCGTACAGAA
124 TCCCTATCGAATAAGGTTTCATATAAGTAACCATTTGCATTTCAATTTCCGTTCCTCATACAGAA
*
573535 CCGATCCAATGACAACCCTCCATTCAAAATACATGAAAATCACTTG--TAA
189 CCGATCCAATGACAACCCTCCATTCAAAATACAT---AATCA--TGAAAAA
** * * * * *
573584 TCTCATAAACATCACGGAACAACAGCAATCCAATTCAGTATGACTAATGATTCGATTATACAAAC
1 AATCATAAAAATCACGAAACAATAGCAATCCAATTCAGTATGACTAACGATTCGATTATATAAAC
* * * * *
573649 ACAAAAGCTATATGTAGACATTCGAACCGATGATTTGTA-TTCATTCCTATTAGACTATCCCTAT
66 ACAAAAGCTATATGTATACATTCAAACCGATGAATCGTATTTCGTTCCTATTAGACTATCCCTAT
* * * * * *
573713 CGAATAAGGTTTCCTATAAGTAACCATTTGCGTTTAAATTTCCATTCCTCATACTGAACTGATCC
131 CGAATAAGGTTTCATATAAGTAACCATTTGCATTTCAATTTCCGTTCCTCATACAGAACCGATCC
*
573778 AATGACAACCCTCCATTCAAAGTACATAATCATG---AA
196 AATGACAACCCTCCATTCAAAATACATAATCATGAAAAA
* *
573814 AATC------AT---GGAACAATAGCAATCCAATTCAGTATGATTAACGATTCGATTATATAAAC
1 AATCATAAAAATCACGAAACAATAGCAATCCAATTCAGTATGACTAACGATTCGATTATATAAAC
* *
573870 ACAAAAGCTATATGTATACATTCAAACCGATGAGTCGTATTTCATTCCTATTAGACTATCCCTAT
66 ACAAAAGCTATATGTATACATTCAAACCGATGAATCGTATTTCGTTCCTATTAGACTATCCCTAT
* *
573935 CGAATAAGGATTCATATAAGTAACCATTTG------------CGTTCCTCATACCGAACCGATCC
131 CGAATAAGGTTTCATATAAGTAACCATTTGCATTTCAATTTCCGTTCCTCATACAGAACCGATCC
*
573988 AATGACAACCCTCCATTCAAAATACATAATC---AAGAA
196 AATGACAACCCTCCATTCAAAATACATAATCATGAAAAA
*
574024 AATC-----AAT---G-AACAAAAGCAATCCAATTCAGTATGACTAACGATTCGATTATATAAAC
1 AATCATAAAAATCACGAAACAATAGCAATCCAATTCAGTATGACTAACGATTCGATTATATAAAC
* * * *
574080 AC-AAAGCTATATATATATAGATTCAAACCGACGAATCGTATTTTGTTCCTATTAGACTATCCCC
66 ACAAAAGC--TATATGTATACATTCAAACCGATGAATCGTATTTCGTTCCTATTAGACTAT-CCC
* * ** * * * *
574144 TACCGAATAAGGTTTCCTATAAACAACCACTCGCATTCCAATTTCCGTTCCTCATACCGAACCGA
128 TATCGAATAAGGTTTCATATAAGTAACCATTTGCATTTCAATTTCCGTTCCTCATACAGAACCGA
574209 T
193 T
574210 AAACATATTT
Statistics
Matches: 762, Mismatches: 70, Indels: 80
0.84 0.08 0.09
Matches are distributed among these distances:
209 5 0.01
210 104 0.14
211 48 0.06
212 29 0.04
221 81 0.11
222 53 0.07
224 23 0.03
230 4 0.01
231 2 0.00
233 5 0.01
236 107 0.14
237 91 0.12
238 6 0.01
239 14 0.02
240 43 0.06
242 22 0.03
243 116 0.15
244 1 0.00
246 6 0.01
248 2 0.00
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.29
Consensus pattern (234 bp):
AATCATAAAAATCACGAAACAATAGCAATCCAATTCAGTATGACTAACGATTCGATTATATAAAC
ACAAAAGCTATATGTATACATTCAAACCGATGAATCGTATTTCGTTCCTATTAGACTATCCCTAT
CGAATAAGGTTTCATATAAGTAACCATTTGCATTTCAATTTCCGTTCCTCATACAGAACCGATCC
AATGACAACCCTCCATTCAAAATACATAATCATGAAAAA
Found at i:574574 original size:185 final size:191
Alignment explanation
Indices: 574250--574662 Score: 631
Period size: 185 Copynumber: 2.2 Consensus size: 191
574240 AATTGTTGAA
* *
574250 AGTAACATTGAAATAAACTAAAACCAGATAACCGAGGACTCCGATTATATAAACTCAAAAGCTAT
1 AGTAACATTGAAATAAACTAAAACCAGATAACCAAGGACTCCGATTATATAAACACAAAAGCTAT
* *
574315 ATGTATAAATTCAAACGGATGAATCGTATTACGTTCCTAGTAGACTATCCCCTGTCGAATAAGGT
66 ATGTATAAATTCAAACGGATGAATCGCATTACATTCCTAGTAGACTATCCCCTGTCGAATAAGGT
* **
574380 GT-TAT-A-TAA-G-TTGTGTTCCGATTTTTGCTCCTCGTACCGAACCGATCAGCATTCCT
131 GTCAATAAGTAACGATTGTGTTCCGATTTCCGCTCCTCGTACCGAACCGATCAGCATTCCT
*
574436 AGTAACATTGAAATAAACTAAAACCAAATAACCAAGGACT-CGATTATATAAACACAAAAGCTAT
1 AGTAACATTGAAATAAACTAAAACCAGATAACCAAGGACTCCGATTATATAAACACAAAAGCTAT
* * * *
574500 ATGTATAAATTCAAACTGATGAATCGCATTTCATTCCTATTAGACTATCCCCTGTCGAATAATGT
66 ATGTATAAATTCAAACGGATGAATCGCATTACATTCCTAGTAGACTATCCCCTGTCGAATAAGGT
* *
574565 GTCATATAAGTAACGATTTGTGTTCCGATTTCCGTTCCTCGTACCGAACCGATCCGCATTCCT
131 GTCA-ATAAGTAACGA-TTGTGTTCCGATTTCCGCTCCTCGTACCGAACCGATCAGCATTCCT
*
574628 AGTAAAATTGAAATAAACTAAAACCAGATAACCAA
1 AGTAACATTGAAATAAACTAAAACCAGATAACCAA
574663 ATGACAACCC
Statistics
Matches: 204, Mismatches: 16, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
185 84 0.41
186 38 0.19
187 2 0.01
188 1 0.00
189 3 0.01
190 1 0.00
192 75 0.37
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.29
Consensus pattern (191 bp):
AGTAACATTGAAATAAACTAAAACCAGATAACCAAGGACTCCGATTATATAAACACAAAAGCTAT
ATGTATAAATTCAAACGGATGAATCGCATTACATTCCTAGTAGACTATCCCCTGTCGAATAAGGT
GTCAATAAGTAACGATTGTGTTCCGATTTCCGCTCCTCGTACCGAACCGATCAGCATTCCT
Found at i:576416 original size:10 final size:10
Alignment explanation
Indices: 576401--576425 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
576391 TTTATAACTC
576401 AATTATGAAA
1 AATTATGAAA
576411 AATTATGAAA
1 AATTATGAAA
576421 AATTA
1 AATTA
576426 CAAACGATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (10 bp):
AATTATGAAA
Found at i:579003 original size:5 final size:5
Alignment explanation
Indices: 578997--579040 Score: 70
Period size: 5 Copynumber: 8.8 Consensus size: 5
578987 ATATATATAT
* *
578997 CATAT CATAC CATAC CATAC CATAC CATAC CATAC CATAT CATA
1 CATAC CATAC CATAC CATAC CATAC CATAC CATAC CATAC CATA
579041 ATCATTGTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.41, C:0.34, G:0.00, T:0.25
Consensus pattern (5 bp):
CATAC
Found at i:582950 original size:14 final size:14
Alignment explanation
Indices: 582931--582957 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
582921 CTAAGTAGCG
582931 TTGTTATTTTATTA
1 TTGTTATTTTATTA
582945 TTGTTATTTTATT
1 TTGTTATTTTATT
582958 GAGCTCGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.00, G:0.07, T:0.74
Consensus pattern (14 bp):
TTGTTATTTTATTA
Found at i:590680 original size:51 final size:48
Alignment explanation
Indices: 590580--590694 Score: 194
Period size: 48 Copynumber: 2.4 Consensus size: 48
590570 GCCATCCACC
*
590580 GCAACTCCGCCGCCAACTACCACTCCTGCCACACCACCACCAACCGCA
1 GCAACTCCGCCGCCAACTAACACTCCTGCCACACCACCACCAACCGCA
* *
590628 GCAACTCCGCCGCCAACTAACACTCCTTCTACACCACCACCAACCGCA
1 GCAACTCCGCCGCCAACTAACACTCCTGCCACACCACCACCAACCGCA
*
590676 GCAGCTCCGCCGCCAACTA
1 GCAACTCCGCCGCCAACTA
590695 GTCCTCCCTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 63 1.00
ACGTcount: A:0.27, C:0.51, G:0.11, T:0.10
Consensus pattern (48 bp):
GCAACTCCGCCGCCAACTAACACTCCTGCCACACCACCACCAACCGCA
Found at i:596982 original size:14 final size:14
Alignment explanation
Indices: 596963--596989 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
596953 ATTTATCCCT
596963 AAAATTTATGTATC
1 AAAATTTATGTATC
596977 AAAATTTATGTAT
1 AAAATTTATGTAT
596990 AATTTTAAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (14 bp):
AAAATTTATGTATC
Found at i:603369 original size:17 final size:19
Alignment explanation
Indices: 603343--603380 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
603333 ATTATTTTTT
603343 TTAAAGATTAA-AA-TAAA
1 TTAAAGATTAAGAATTAAA
*
603360 TTAAATATTAAGAATTAAA
1 TTAAAGATTAAGAATTAAA
603379 TT
1 TT
603381 TATCATTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 10 0.56
18 2 0.11
19 6 0.33
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (19 bp):
TTAAAGATTAAGAATTAAA
Found at i:605231 original size:16 final size:16
Alignment explanation
Indices: 605210--605241 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
605200 TCAAAAAAGA
*
605210 AAAATCTGAATAGTTG
1 AAAATCCGAATAGTTG
605226 AAAATCCGAATAGTTG
1 AAAATCCGAATAGTTG
605242 GGTGACCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.09, G:0.19, T:0.28
Consensus pattern (16 bp):
AAAATCCGAATAGTTG
Found at i:608736 original size:41 final size:41
Alignment explanation
Indices: 608679--608761 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
608669 AAAAAAAAGT
608679 ATTTTCAGTACTTAATTGAACAAGAACCAATAATGGCCACA
1 ATTTTCAGTACTTAATTGAACAAGAACCAATAATGGCCACA
608720 ATTTTCAGTACTTAATTGAACAAGAACCAATAATGGCCACA
1 ATTTTCAGTACTTAATTGAACAAGAACCAATAATGGCCACA
608761 A
1 A
608762 AATTACCCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (41 bp):
ATTTTCAGTACTTAATTGAACAAGAACCAATAATGGCCACA
Found at i:613239 original size:30 final size:31
Alignment explanation
Indices: 613205--613264 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
613195 AAACCTTTTA
*
613205 TTTTCTCCC-AAAAGTTTTACTCCC-TCCCAC
1 TTTTC-CCCTAAAAATTTTACTCCCTTCCCAC
*
613235 TTTTCCCCTAAAAATTTTATTCCCTTCCCA
1 TTTTCCCCTAAAAATTTTACTCCCTTCCCA
613265 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 3 0.12
30 18 0.69
31 5 0.19
ACGTcount: A:0.22, C:0.37, G:0.02, T:0.40
Consensus pattern (31 bp):
TTTTCCCCTAAAAATTTTACTCCCTTCCCAC
Found at i:614140 original size:6 final size:6
Alignment explanation
Indices: 614129--614155 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
614119 AAGAATGATT
614129 ATTCAA ATTCAA ATTCAA ATTCAA ATT
1 ATTCAA ATTCAA ATTCAA ATTCAA ATT
614156 AATTAAAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (6 bp):
ATTCAA
Found at i:616090 original size:21 final size:21
Alignment explanation
Indices: 616066--616106 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
616056 CCGAATTCAA
616066 TTTAAACAAAAAAATATATAT
1 TTTAAACAAAAAAATATATAT
** *
616087 TTTAATTATAAAAATATATA
1 TTTAAACAAAAAAATATATA
616107 AATCATTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
TTTAAACAAAAAAATATATAT
Found at i:616573 original size:12 final size:12
Alignment explanation
Indices: 616556--616580 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
616546 AAAAACAGAC
616556 TGTTTTGTTTTT
1 TGTTTTGTTTTT
616568 TGTTTTGTTTTT
1 TGTTTTGTTTTT
616580 T
1 T
616581 ATAATTGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (12 bp):
TGTTTTGTTTTT
Found at i:617281 original size:199 final size:198
Alignment explanation
Indices: 616900--617456 Score: 681
Period size: 199 Copynumber: 2.8 Consensus size: 198
616890 AACAGGTGCG
* * *
616900 AGAATTTTCTTTCCTACCAAACACGCTCAAACATCCATATTCTTTTTCAGTTTTTCACCACCCCT
1 AGAATTTTCTTTCCTACCAAACACGCTCAAACATTCATATTCTTTTTCAGTTTTTCACCATCCTT
* * ** * * *
616965 AATTCCATTTCTTCCAGATTTTTCACTCTGCTAAGCAAACCACTAATCTTGTTTCCGTATTTTTG
66 TATT-CATTTCTTTCACTTTTTTCACTCTGCCAAGCAAACCACTAATCTCGTTTTCGTATTTTTG
* ** *
617030 CTTTACAATCTATGAACAAGAAAGCTAACGAAGATGATGCTAATCTTTTGTAATGCAGCTAAGTG
130 CTTTACAATCTATGAACAAGAAAGCTAATGAAGACAAAGCTAATCTTTTGTAATGCAGCTAAGTG
617095 AACA
195 AACA
* *
617099 AGAATTCTT-TTTCCTACCAAACACGCTCAAACATTCATATTCTTTTTCAGTTTTTCACCTTCTT
1 AGAATT-TTCTTTCCTACCAAACACGCTCAAACATTCATATTCTTTTTCAGTTTTTCACCATCCT
***
617163 TTATTCATTCTTCTGTTTTTTTTTTTCACTCTGCCAAGCAAACCACTAA-CTCGTTTTCGTATTT
65 TTATTCA-T-TTCT-TTCACTTTTTTCACTCTGCCAAGCAAACCACTAATCTCGTTTTCGTATTT
* *
617227 TTGCTTTACTATCTATGAACAAGAAAGCTAATGAAGACAAAGCTAATC-TTTGTAATGCAGTTAA
127 TTGCTTTACAATCTATGAACAAGAAAGCTAATGAAGACAAAGCTAATCTTTTGTAATGCAGCTAA
* *
617291 GTGAGCC
192 GTGAACA
* * * * * * * ** *
617298 GGAATTTTCTTCCCTACCTAAGACACTCAAACATTAATGTTCTTTTTTGGTTTTTCACCATCCTA
1 AGAATTTTCTTTCCTACCAAACACGCTCAAACATTCATATTCTTTTTCAGTTTTTCACCATCCTT
* * * * *
617363 TATCCATTTC-TTCCCTTTTTTCTACTCTGCCAAGCTAACCACTAATCTCATTTTCCTAATTTTT
66 TATTCATTTCTTTCACTTTTTTC-ACTCTGCCAAGCAAACCACTAATCTCGTTTTCGT-ATTTTT
617427 GCTTTACAATCTATGAACAAGAAAGCTAAT
129 GCTTTACAATCTATGAACAAGAAAGCTAAT
617457 TATTTCCTTC
Statistics
Matches: 308, Mismatches: 42, Indels: 17
0.84 0.11 0.05
Matches are distributed among these distances:
195 9 0.03
196 21 0.07
197 12 0.04
198 40 0.13
199 136 0.44
200 62 0.20
201 28 0.09
ACGTcount: A:0.28, C:0.24, G:0.10, T:0.39
Consensus pattern (198 bp):
AGAATTTTCTTTCCTACCAAACACGCTCAAACATTCATATTCTTTTTCAGTTTTTCACCATCCTT
TATTCATTTCTTTCACTTTTTTCACTCTGCCAAGCAAACCACTAATCTCGTTTTCGTATTTTTGC
TTTACAATCTATGAACAAGAAAGCTAATGAAGACAAAGCTAATCTTTTGTAATGCAGCTAAGTGA
ACA
Found at i:626950 original size:22 final size:23
Alignment explanation
Indices: 626924--626972 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
626914 TACAAGCACT
*
626924 TATA-TGATAATA-ATAAGATATA
1 TATATTGAAAATACATAAG-TATA
626946 TATATTTGAAAATACATAAGTATA
1 TATA-TTGAAAATACATAAGTATA
626970 TAT
1 TAT
626973 GAATAGAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 4 0.17
24 14 0.61
25 5 0.22
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.39
Consensus pattern (23 bp):
TATATTGAAAATACATAAGTATA
Found at i:627017 original size:3 final size:3
Alignment explanation
Indices: 627006--627061 Score: 69
Period size: 3 Copynumber: 18.7 Consensus size: 3
626996 CAATAATACC
* * *
627006 AAT ACT AAT AAT AGT AA- AGAT GAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
627051 AAT AAT AAT AA
1 AAT AAT AAT AA
627062 AGTTAACAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
2 1 0.02
3 44 0.98
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:628568 original size:46 final size:44
Alignment explanation
Indices: 628510--628871 Score: 191
Period size: 41 Copynumber: 8.4 Consensus size: 44
628500 CACTGCATCT
* * *
628510 TCAGGGGGATAAGATCTGCAATTCTTCGGTCTACTCCACTGTAACC
1 TCAGGGAGATAAGATCTG--ATTCTTCGATCTGCTCCACTGTAACC
* * * * * *
628556 TCAGAGAGATAAGACCTGA---TGCGATCTACTCTACTGTAACT
1 TCAGGGAGATAAGATCTGATTCTTCGATCTGCTCCACTGTAACC
* * * * * *
628597 TCAGAGAAATAAGATCCTTTATT-TT-AATCCGCTCCACTGTAACT
1 TCAGGGAGATAAGAT-C-TGATTCTTCGATCTGCTCCACTGTAACC
* *
628641 TCAGGGAGATAGGAT-T-ATATCTTCGATCTGCTCCGCTGTAACC
1 TCAGGGAGATAAGATCTGAT-TCTTCGATCTGCTCCACTGTAACC
* * * *
628684 TCAGGGAGACAAGATCTGCAATTCTTCGGTCTGTTCCACTGTAATC
1 TCAGGGAGATAAGATCTG--ATTCTTCGATCTGCTCCACTGTAACC
* * * * *
628730 TCAGGGAGATAAGACCTGA-T-GT-GATCTTCTCTACTGTAACT
1 TCAGGGAGATAAGATCTGATTCTTCGATCTGCTCCACTGTAACC
* * * * *
628771 TCAGAGAGATAAGATCCT--TT-AT--ATCCGCTCCATTGTAATC
1 TCAGGGAGATAAGAT-CTGATTCTTCGATCTGCTCCACTGTAACC
* * * * *
628811 TCAAGGAGATAGGAT-T-ACTATCTTTGATCTGCTCCGCTGTAATC
1 TCAGGGAGATAAGATCTGA-T-TCTTCGATCTGCTCCACTGTAACC
628855 TCAGGGAGATAAGATCT
1 TCAGGGAGATAAGATCT
628872 CTGGCTTCAA
Statistics
Matches: 241, Mismatches: 55, Indels: 41
0.72 0.16 0.12
Matches are distributed among these distances:
38 1 0.00
40 27 0.11
41 62 0.26
42 7 0.03
43 31 0.13
44 58 0.24
45 2 0.01
46 51 0.21
47 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (44 bp):
TCAGGGAGATAAGATCTGATTCTTCGATCTGCTCCACTGTAACC
Found at i:628609 original size:87 final size:87
Alignment explanation
Indices: 628508--628786 Score: 269
Period size: 87 Copynumber: 3.2 Consensus size: 87
628498 TCCACTGCAT
* * * *
628508 CTTCAGGGGGATAAGATCTGCAATTCTTCGGTCTACTCCACTGTAACCTCAGAGAGATAAGACCT
1 CTTCAGAGAGATAAGATCTGCAATTCTTCGGTCTGCTCCACTGTAACCTCAGGGAGATAAGACCT
628573 GATGCGATCTACTCTACTGTAA
66 GATGCGATCTACTCTACTGTAA
* ** ** * * * *
628595 CTTCAGAGAAATAAGATCCT-TTATT-TT-AATCCGCTCCACTGTAACTTCAGGGAGATAGGA-T
1 CTTCAGAGAGATAAGAT-CTGCAATTCTTCGGTCTGCTCCACTGTAACCTCAGGGAGATAAGACC
* * * **
628656 TATATCTTCGATCTGCTCCGCTGTAA
65 T-GA--TGCGATCTACTCTACTGTAA
* * * * *
628682 CCTCAGGGAGACAAGATCTGCAATTCTTCGGTCTGTTCCACTGTAATCTCAGGGAGATAAGACCT
1 CTTCAGAGAGATAAGATCTGCAATTCTTCGGTCTGCTCCACTGTAACCTCAGGGAGATAAGACCT
* *
628747 GATGTGATCTTCTCTACTGTAA
66 GATGCGATCTACTCTACTGTAA
628769 CTTCAGAGAGATAAGATC
1 CTTCAGAGAGATAAGATC
628787 CTTTATATCC
Statistics
Matches: 143, Mismatches: 41, Indels: 16
0.71 0.20 0.08
Matches are distributed among these distances:
84 1 0.01
85 27 0.19
86 4 0.03
87 79 0.55
88 4 0.03
89 27 0.19
90 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (87 bp):
CTTCAGAGAGATAAGATCTGCAATTCTTCGGTCTGCTCCACTGTAACCTCAGGGAGATAAGACCT
GATGCGATCTACTCTACTGTAA
Found at i:628935 original size:86 final size:85
Alignment explanation
Indices: 628831--629042 Score: 241
Period size: 86 Copynumber: 2.5 Consensus size: 85
628821 AGGATTACTA
* * * *
628831 TCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT-CTGGCTTCAATCT-GCTCCAATG
1 TCTTTGATCTGCTTCGCTGTAAT-GCAGGAAGACAAGATCTACT-GCTTCAA-CTAGCTCCAATG
628894 CAACCGATGGAGGCAAGGCTTTG
63 CAACCGATGGAGGCAAGGCTTTG
* * * *
628917 TCTTTGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTACTTCTTTAACTAGCTCCACTGCA
1 TCTTTGATCTGCTTCGCTG-TAATGCAGGAAGACAAGATCTACTGCTTCAACTAGCTCCAATGCA
* *
628982 ATCGATGGATGCAAGGCTTTG
65 ACCGATGGAGGCAAGGCTTTG
* *
629003 T-TTTCGATCTGCTTCGCTGTCAATGCAGAAAGGCAAGATC
1 TCTTT-GATCTGCTTCGCTGT-AATGCAGGAAGACAAGATC
629043 CTTTGTCTTC
Statistics
Matches: 110, Mismatches: 11, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
85 6 0.05
86 98 0.89
87 6 0.05
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (85 bp):
TCTTTGATCTGCTTCGCTGTAATGCAGGAAGACAAGATCTACTGCTTCAACTAGCTCCAATGCAA
CCGATGGAGGCAAGGCTTTG
Found at i:630301 original size:1 final size:1
Alignment explanation
Indices: 630295--630323 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
630285 CTCTCCAAAG
630295 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
630324 AGGAAGCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:641791 original size:22 final size:23
Alignment explanation
Indices: 641765--641813 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
641755 TACAAGCACT
*
641765 TATA-TGATAATA-ATAAGATATA
1 TATATTGAAAATACATAAG-TATA
641787 TATATTTGAAAATACATAAGTATA
1 TATA-TTGAAAATACATAAGTATA
641811 TAT
1 TAT
641814 GAATAGAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 4 0.17
24 14 0.61
25 5 0.22
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.39
Consensus pattern (23 bp):
TATATTGAAAATACATAAGTATA
Found at i:641858 original size:3 final size:3
Alignment explanation
Indices: 641847--641902 Score: 69
Period size: 3 Copynumber: 18.7 Consensus size: 3
641837 CAATAATACC
* * *
641847 AAT ACT AAT AAT AGT AA- AGAT GAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
641892 AAT AAT AAT AA
1 AAT AAT AAT AA
641903 AGTTAACAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
2 1 0.02
3 44 0.98
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:643573 original size:3 final size:3
Alignment explanation
Indices: 643567--643607 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
643557 AGCATTTTGG
643567 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
643608 AACTTAGCCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:651887 original size:3 final size:3
Alignment explanation
Indices: 651879--651904 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
651869 GGGAAAGCAA
651879 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
651905 AGGCAACATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:653553 original size:19 final size:20
Alignment explanation
Indices: 653509--653563 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
653499 ATCAATAAAT
653509 ATTTAAATTATATTTTTATA
1 ATTTAAATTATATTTTTATA
* * *
653529 ATTTAATTTATTTTTTTATT
1 ATTTAAATTATATTTTTATA
* *
653549 ATTAAAATTAAATTT
1 ATTTAAATTATATTT
653564 AAGTTAGGCC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTAAATTATATTTTTATA
Found at i:660843 original size:128 final size:128
Alignment explanation
Indices: 660691--661061 Score: 460
Period size: 130 Copynumber: 2.9 Consensus size: 128
660681 AACGAAATCG
* * **
660691 CTTTGCTTTTTTAAAAATTAGAATATTGTATTCGTAAATTTATTCAAAATCGATCTAAACTAAAA
1 CTTTGCTTTTTTAAAAACTAGAATATTGTATTCGTAAATTTATTCAAAATCGATCCAAACCGAAA
*
660756 TGTTATCCGCCTAACTTATTGATGTTTGTTTTCACTGTTGTTTATGGTTCAT-TTGATGTGGCT
66 TGTTATCCGCCTAACTTATTGATGTTTGTTTTTACTGTTGTTTATGGTTCATCTT-ATGTGGCT
* ** * *
660819 CTTTGCTTTTTTAAAAACTAGAATACTGTAACCGTAAATTTGTTCAAAATCGATCCAAGCCGAAA
1 CTTTGCTTTTTTAAAAACTAGAATATTGTATTCGTAAATTTATTCAAAATCGATCCAAACCGAAA
* *
660884 TGTTATTCGCCTAACTTATTGATGTGTT-TACTTTTACTGTTGTTTATGGTTCATCTTATGTGGT
66 TGTTATCCGCCTAACTTATTGATGT-TTGT--TTTTACTGTTGTTTATGGTTCATCTTATGTGGC
660948 T
128 T
* * * * *
660949 CATTGCTTTTTTAAAAGCTAAAACATTGTAATT-GTAAATTTATTCAAAACCGATCCAAACCGAA
1 CTTTGCTTTTTTAAAAACTAGAATATTGT-ATTCGTAAATTTATTCAAAATCGATCCAAACCGAA
** * * *
661013 ATGTTATCTACCTAACTTATTGGTGTGTTTGTTTTTACTATTATTTATG
65 ATGTTATCCGCCTAACTTATT-G-ATGTTTGTTTTTACTGTTGTTTATG
661062 CGGTTCTTTG
Statistics
Matches: 207, Mismatches: 28, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
128 81 0.39
129 2 0.01
130 114 0.55
131 6 0.03
132 4 0.02
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (128 bp):
CTTTGCTTTTTTAAAAACTAGAATATTGTATTCGTAAATTTATTCAAAATCGATCCAAACCGAAA
TGTTATCCGCCTAACTTATTGATGTTTGTTTTTACTGTTGTTTATGGTTCATCTTATGTGGCT
Found at i:663891 original size:14 final size:13
Alignment explanation
Indices: 663865--663898 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
663855 TATAAAATTT
663865 TAATAAATAAAAA
1 TAATAAATAAAAA
*
663878 TATTAAATTAAAAA
1 TAATAAA-TAAAAA
663892 TAATAAA
1 TAATAAA
663899 AATATATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
TAATAAATAAAAA
Found at i:670928 original size:25 final size:26
Alignment explanation
Indices: 670870--670928 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 26
670860 CTCTCAATGT
*
670870 TTATATTTTTTTTGTCAATTTAATCC
1 TTATATTTTTTTTGTCAATTGAATCC
*
670896 TTAT-TTTTTTTTGTC-A-TGAATTGC
1 TTATATTTTTTTTGTCAATTGAA-TCC
670920 TTATATTTT
1 TTATATTTT
670929 AAGATATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
23 3 0.10
24 7 0.24
25 15 0.52
26 4 0.14
ACGTcount: A:0.20, C:0.08, G:0.07, T:0.64
Consensus pattern (26 bp):
TTATATTTTTTTTGTCAATTGAATCC
Found at i:679642 original size:24 final size:24
Alignment explanation
Indices: 679615--679666 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
679605 TTCGTAGGTC
* *
679615 AAATAAATTATACTAATAAATGTT
1 AAATAAATCATACTAATAAATATT
*
679639 AAATATATCATACTAATAAATATT
1 AAATAAATCATACTAATAAATATT
679663 AAAT
1 AAAT
679667 CATCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.37
Consensus pattern (24 bp):
AAATAAATCATACTAATAAATATT
Found at i:694844 original size:21 final size:20
Alignment explanation
Indices: 694816--694854 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
694806 TTTGGGATTA
*
694816 AAATATGACAATGATAATCC
1 AAATATGAAAATGATAATCC
694836 AAATGATGAAAATGATAAT
1 AAAT-ATGAAAATGATAAT
694855 TATTTTTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.54, C:0.08, G:0.13, T:0.26
Consensus pattern (20 bp):
AAATATGAAAATGATAATCC
Found at i:700258 original size:63 final size:64
Alignment explanation
Indices: 700191--700315 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 64
700181 CTCTTTTAAA
* * *
700191 TTTTTTTC-AAAAATCTCATTAATCTCACAAAATTTTTAAAAATTTTAATTAGATCC-CCAAATT
1 TTTTTTTCAAAAAAT-TCATCAAACTCACAAAATTTTTAAAAATTTTAATTAGACCCTCCAAATT
** * * *
700254 TTTTTTTCAAAAAATTCATCAAACTCGTAAAATTTTTGAAATTTTTATTTAGACCCTCCAAA
1 TTTTTTTCAAAAAATTCATCAAACTCACAAAATTTTTAAAAATTTTAATTAGACCCTCCAAA
700316 ACTTAGTCTC
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
63 41 0.79
64 11 0.21
ACGTcount: A:0.38, C:0.16, G:0.03, T:0.42
Consensus pattern (64 bp):
TTTTTTTCAAAAAATTCATCAAACTCACAAAATTTTTAAAAATTTTAATTAGACCCTCCAAATT
Found at i:704536 original size:3 final size:3
Alignment explanation
Indices: 704528--704557 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
704518 TTCATGGCCT
704528 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
704558 TTAGTAACTA
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:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:704797 original size:12 final size:12
Alignment explanation
Indices: 704782--704806 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
704772 TTTCTTTGCC
704782 TTTTTCTTTCTT
1 TTTTTCTTTCTT
704794 TTTTTCTTTCTT
1 TTTTTCTTTCTT
704806 T
1 T
704807 CTTTATTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTCTTTCTT
Found at i:705099 original size:16 final size:16
Alignment explanation
Indices: 705078--705108 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
705068 CTATACATAT
705078 TATAATTACAAAATTA
1 TATAATTACAAAATTA
*
705094 TATAATTAGAAAATT
1 TATAATTACAAAATT
705109 TTGGGAGTCG
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:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (16 bp):
TATAATTACAAAATTA
Found at i:708782 original size:29 final size:29
Alignment explanation
Indices: 708737--708792 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
708727 ATATTTTAAG
* *
708737 TTATTTTCACTATTAAAATA-TAAAATAT
1 TTATTTTCACTAGTAAAAAATTAAAATAT
*
708765 TTATTTTTACATAGTAAAAAATTAAAAT
1 TTATTTTCAC-TAGTAAAAAATTAAAAT
708793 TAATTATGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 9 0.39
29 8 0.35
30 6 0.26
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (29 bp):
TTATTTTCACTAGTAAAAAATTAAAATAT
Found at i:709232 original size:25 final size:26
Alignment explanation
Indices: 709194--709266 Score: 76
Period size: 25 Copynumber: 2.7 Consensus size: 26
709184 TATCAAATTT
*
709194 AAAATTAATAAATTATGTTTATTAA-
1 AAAATTATTAAATTATGTTTATTAAG
* * *
709219 AAAGTTATTAAATTGTGTTTTTTAAGG
1 AAAATTATTAAATTATGTTTATTAA-G
709246 AAAATTTTATTAAATTATGTT
1 AAAA--TTATTAAATTATGTT
709267 GAATACTTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
25 21 0.55
27 3 0.08
29 14 0.37
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (26 bp):
AAAATTATTAAATTATGTTTATTAAG
Found at i:711738 original size:31 final size:28
Alignment explanation
Indices: 711699--711765 Score: 73
Period size: 31 Copynumber: 2.3 Consensus size: 28
711689 TAGATATTAT
* *
711699 ATTTATACATGAGCTTTGGTTTAATGTGCA
1 ATTTATACATAAACTTT-GTTTAA-GTGCA
*
711729 ATTTAATACATAAACTTTGTTTTAGTGCA
1 ATTT-ATACATAAACTTTGTTTAAGTGCA
711758 A-TTATACA
1 ATTTATACA
711766 CGTGAAACTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
27 5 0.15
28 2 0.06
29 6 0.18
30 9 0.27
31 11 0.33
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.43
Consensus pattern (28 bp):
ATTTATACATAAACTTTGTTTAAGTGCA
Found at i:712658 original size:15 final size:16
Alignment explanation
Indices: 712638--712668 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
712628 AAGTTCCTAA
712638 CTATATATGT-CTTAT
1 CTATATATGTACTTAT
712653 CTATATATGTACTTAT
1 CTATATATGTACTTAT
712669 AAGACAAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.29, C:0.13, G:0.06, T:0.52
Consensus pattern (16 bp):
CTATATATGTACTTAT
Found at i:713942 original size:17 final size:19
Alignment explanation
Indices: 713916--713961 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
713906 TATTTATTAT
713916 ATATTATAAAT-A-TAAAA
1 ATATTATAAATAATTAAAA
*
713933 ATATTTTAAATAATTAAAA
1 ATATTATAAATAATTAAAA
*
713952 ATAATATAAA
1 ATATTATAAA
713962 AATGTCAGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 10 0.42
18 1 0.04
19 13 0.54
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
ATATTATAAATAATTAAAA
Found at i:716296 original size:19 final size:19
Alignment explanation
Indices: 716252--716289 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
716242 TTTGGGTTGG
716252 AAAATTA-A-ATAAATTTT
1 AAAATTATACATAAATTTT
716269 AAAATTATACATAAATTTT
1 AAAATTATACATAAATTTT
716288 AA
1 AA
716290 TTTTATATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.37
18 1 0.05
19 11 0.58
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAATTATACATAAATTTT
Found at i:716432 original size:29 final size:31
Alignment explanation
Indices: 716274--716434 Score: 95
Period size: 31 Copynumber: 5.2 Consensus size: 31
716264 ATTTTAAAAT
* * *
716274 TATACATAAATTTTAATTTTATATGTAATT-
1 TATATATAAATTTTAATTTAATGTGTAATTA
*
716304 TGATATATAAATTTTAATTT--GGTGTAATTA
1 T-ATATATAAATTTTAATTTAATGTGTAATTA
** *
716334 TATATACATGTACAACTTTT-ATTGT--TGACTAAATA
1 TATAT--A--TA-AA-TTTTAATT-TAATGTGTAATTA
* *
716369 TATACATAAATTTTAATTTAATGTGTAATTT
1 TATATATAAATTTTAATTTAATGTGTAATTA
* *
716400 TATATATGAATTTTGATTT-A-GTGTAATTA
1 TATATATAAATTTTAATTTAATGTGTAATTA
716429 TATATA
1 TATATA
716435 CACGTCAAAT
Statistics
Matches: 103, Mismatches: 16, Indels: 25
0.72 0.11 0.17
Matches are distributed among these distances:
29 30 0.29
30 8 0.08
31 42 0.41
33 3 0.03
34 5 0.05
35 15 0.15
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.50
Consensus pattern (31 bp):
TATATATAAATTTTAATTTAATGTGTAATTA
Found at i:716450 original size:95 final size:94
Alignment explanation
Indices: 716270--716447 Score: 268
Period size: 95 Copynumber: 1.9 Consensus size: 94
716260 ATAAATTTTA
* *
716270 AAATTATACATAAATTTTAATTTTATATGTAATTTGATATATAAATTTTAATTTGGTGTAATTAT
1 AAATTATACATAAATTTTAATTTAATATGTAATTTGATATATAAATTTTAATTTAGTGTAATTAT
*
716335 ATATACATGTACAACTTTTATTGTTGACT
66 ATATACACGTACAACTTTTATTGTTGACT
* * * *
716364 AAATATATACATAAATTTTAATTTAATGTGTAATTTTATATATGAATTTTGATTTAGTGTAATTA
1 AAAT-TATACATAAATTTTAATTTAATATGTAATTTGATATATAAATTTTAATTTAGTGTAATTA
*
716429 TATATACACGT-CAAATTTT
65 TATATACACGTACAACTTTT
716448 TATCGTGGAC
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
94 11 0.15
95 64 0.85
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.48
Consensus pattern (94 bp):
AAATTATACATAAATTTTAATTTAATATGTAATTTGATATATAAATTTTAATTTAGTGTAATTAT
ATATACACGTACAACTTTTATTGTTGACT
Found at i:717577 original size:15 final size:16
Alignment explanation
Indices: 717550--717590 Score: 68
Period size: 15 Copynumber: 2.7 Consensus size: 16
717540 TTGATTCTGA
717550 TTATAATTA-TTTTAT
1 TTATAATTATTTTTAT
717565 TTAT-ATTATTTTTAT
1 TTATAATTATTTTTAT
717580 TTATAATTATT
1 TTATAATTATT
717591 CAAATAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.17
15 14 0.58
16 6 0.25
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATAATTATTTTTAT
Found at i:724370 original size:22 final size:22
Alignment explanation
Indices: 724343--724386 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
724333 ATTGTGATAA
724343 AAGGATTTGACCAGAGTCTGAT
1 AAGGATTTGACCAGAGTCTGAT
724365 AAGGATTTGACCAGAGTCTGAT
1 AAGGATTTGACCAGAGTCTGAT
724387 TGGTTCCAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.27
Consensus pattern (22 bp):
AAGGATTTGACCAGAGTCTGAT
Found at i:731519 original size:133 final size:125
Alignment explanation
Indices: 731240--731535 Score: 385
Period size: 126 Copynumber: 2.3 Consensus size: 125
731230 AACAATGACA
* * * * * * *
731240 ACAATCACAATCATAATAAAGCTAAACATTAACCAATGATTTTAATAATAGTTAAACTGGGAATT
1 ACAATCATAATCATAATATAGTTAAAAATTAACCAATGAATTGAATAATAGTTAAACTGAGAATT
731305 AAACCCTAAACCCTAAAACTAATTAGTAGGCATCAAACAAGAGTAAAATAACGCAATAAC
66 AAACCCTAAACCCTAAAACTAATTAGTAGGCATCAAACAAGAGTAAAATAACGCAATAAC
* * * * *
731365 AGCAATCATAATAATATTATAGTTAAAAATTAACCAGTGAATTGGATAATAGTTAAGCTGAGAAT
1 A-CAATCATAATCATAATATAGTTAAAAATTAACCAATGAATTGAATAATAGTTAAACTGAGAAT
* *
731430 TAAACCCTAAACCCTAATACTTAAATTAAGTAGTAGGCGTCAAACAAGAGTAAAAATAACGCAAT
65 TAAACCCTAAACCCTAAAAC-T-AA-T---TAGTAGGCATCAAACAAGAGT-AAAATAACGCAAT
731495 AAC
123 AAC
731498 GACAATCATAATCATAATATAGTTAAAAATTAACCAAT
1 -ACAATCATAATCATAATATAGTTAAAAATTAACCAAT
731536 TAGTTCAATC
Statistics
Matches: 145, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
125 1 0.01
126 70 0.48
127 1 0.01
128 2 0.01
129 1 0.01
132 20 0.14
133 49 0.34
134 1 0.01
ACGTcount: A:0.49, C:0.15, G:0.11, T:0.25
Consensus pattern (125 bp):
ACAATCATAATCATAATATAGTTAAAAATTAACCAATGAATTGAATAATAGTTAAACTGAGAATT
AAACCCTAAACCCTAAAACTAATTAGTAGGCATCAAACAAGAGTAAAATAACGCAATAAC
Found at i:733428 original size:24 final size:23
Alignment explanation
Indices: 733392--733438 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
733382 ATTAGAAATA
*
733392 ATAAAAATTAAAATTAAAATTAG
1 ATAAAAATAAAAATTAAAATTAG
*
733415 ATAAAAATAAAAAATTAAAGTTAG
1 ATAAAAAT-AAAAATTAAAATTAG
733439 TAATGATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (23 bp):
ATAAAAATAAAAATTAAAATTAG
Found at i:735223 original size:2 final size:2
Alignment explanation
Indices: 735218--735245 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
735208 TTATTACGTG
735218 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
735246 GTTAAAAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:736294 original size:3 final size:3
Alignment explanation
Indices: 736286--736341 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
736276 TGTAGATAGA
*
736286 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAG
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
736334 AAT AAT AA
1 AAT AAT AA
736342 ATTTTGTTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:738193 original size:92 final size:92
Alignment explanation
Indices: 738036--738214 Score: 304
Period size: 92 Copynumber: 1.9 Consensus size: 92
738026 CTTTACCCTG
* * *
738036 AATATAACTAGCTTGAAGTTTTAGAATTCACACAAAATGGGAGGTGAAGGGAGGCTTCCTTTTGG
1 AATATAACTAGCTCGAAGTTTTAGAATTCACACAAAATGAGAGGTGAAGGGAAGCTTCCTTTTGG
738101 CTTGATCTTAATGACAAAACTTTGCCC
66 CTTGATCTTAATGACAAAACTTTGCCC
*
738128 AATATGACTAGCTCGAAGTTTTAGAATTCACACAAAATGAGAGGTGAAGGGAAGCTTCCTTTTGG
1 AATATAACTAGCTCGAAGTTTTAGAATTCACACAAAATGAGAGGTGAAGGGAAGCTTCCTTTTGG
* *
738193 CTTGGTCTTAATGGCAAAACTT
66 CTTGATCTTAATGACAAAACTT
738215 AAGAGAGACG
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
92 81 1.00
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (92 bp):
AATATAACTAGCTCGAAGTTTTAGAATTCACACAAAATGAGAGGTGAAGGGAAGCTTCCTTTTGG
CTTGATCTTAATGACAAAACTTTGCCC
Found at i:749190 original size:2 final size:2
Alignment explanation
Indices: 749183--749224 Score: 66
Period size: 2 Copynumber: 20.5 Consensus size: 2
749173 GGTTGAACAA
*
749183 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT ACT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A
749225 AGCTTGTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:753810 original size:26 final size:26
Alignment explanation
Indices: 753775--753945 Score: 76
Period size: 26 Copynumber: 6.8 Consensus size: 26
753765 GTAGCTCTTA
*
753775 TGAGCGTCCCGTTATATGGCTCTTCT
1 TGAGCTTCCCGTTATATGGCTCTTCT
*
753801 TGAGCTTCCCGATTA-AAGGCTCTT-T
1 TGAGCTTCCCG-TTATATGGCTCTTCT
* *
753826 GTTAGCTTCCCGTTAGTA---CTC-GCT
1 -TGAGCTTCCCGTTA-TATGGCTCTTCT
* * * *
753850 TGAACTTCCTGTTATATGGCT-ATCC
1 TGAGCTTCCCGTTATATGGCTCTTCT
* * ** *
753875 GGTGCTTTTCGTTA-ATTGCTCTTC-
1 TGAGCTTCCCGTTATATGGCTCTTCT
* * *
753899 GGAGCTACTCGTTATA-GGCTCTT-T
1 TGAGCTTCCCGTTATATGGCTCTTCT
*
753923 GTGAGCTTCCCGTTATATTGCTC
1 -TGAGCTTCCCGTTATATGGCTC
753946 GAATAAGCTT
Statistics
Matches: 106, Mismatches: 25, Indels: 28
0.67 0.16 0.18
Matches are distributed among these distances:
22 2 0.02
23 11 0.10
24 26 0.25
25 31 0.29
26 32 0.30
27 4 0.04
ACGTcount: A:0.15, C:0.25, G:0.21, T:0.40
Consensus pattern (26 bp):
TGAGCTTCCCGTTATATGGCTCTTCT
Found at i:753919 original size:24 final size:25
Alignment explanation
Indices: 753892--753939 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
753882 TTCGTTAATT
*
753892 GCTCTTCG-GAGCTACTCGTTATAG
1 GCTCTTCGTGAGCTACCCGTTATAG
* *
753916 GCTCTTTGTGAGCTTCCCGTTATA
1 GCTCTTCGTGAGCTACCCGTTATA
753940 TTGCTCGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.15, C:0.25, G:0.23, T:0.38
Consensus pattern (25 bp):
GCTCTTCGTGAGCTACCCGTTATAG
Found at i:759230 original size:142 final size:143
Alignment explanation
Indices: 759010--759299 Score: 530
Period size: 142 Copynumber: 2.0 Consensus size: 143
759000 AAATTTAGAT
759010 ATTAAATTAAGAAAAAAATTATAAAAATCAAATTGAGAGAATGTGCGGGTAAAAATGTATTTAAA
1 ATTAAATTAAGAAAAAAATTATAAAAATCAAATTGAGAGAATGTGCGGGTAAAAATGTATTTAAA
759075 CTTTTTTATTAATTATTTTATTACCATAATAATATTTGATGTTAAAGGGAACGTTATTAATTAGA
66 CTTTTTTATTAATTATTTTATTACCATAATAATATTTGATGTTAAA-GGAACGTTATTAATTAGA
*
759140 GAAAATCCATATTC
130 GAAAATCCACATTC
759154 -TTAAATTAAG-AAAAAATTATAAAAATCAAATTGAGAGAATGTGCGGGTAAAAATGTATTTAAA
1 ATTAAATTAAGAAAAAAATTATAAAAATCAAATTGAGAGAATGTGCGGGTAAAAATGTATTTAAA
* *
759217 CTTTTTTATTAATTATTTTATTGCCATAATAATATTTGATGTTAAAGGAACGTTATTAATTTGAG
66 CTTTTTTATTAATTATTTTATTACCATAATAATATTTGATGTTAAAGGAACGTTATTAATTAGAG
759282 AAAATCCACATTC
131 AAAATCCACATTC
759295 ATTAA
1 ATTAA
759300 TGAATTATGA
Statistics
Matches: 142, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
141 30 0.21
142 102 0.72
143 10 0.07
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (143 bp):
ATTAAATTAAGAAAAAAATTATAAAAATCAAATTGAGAGAATGTGCGGGTAAAAATGTATTTAAA
CTTTTTTATTAATTATTTTATTACCATAATAATATTTGATGTTAAAGGAACGTTATTAATTAGAG
AAAATCCACATTC
Found at i:759502 original size:3 final size:3
Alignment explanation
Indices: 759494--759528 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
759484 AGGTGTTTCT
759494 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
759529 CATCAATTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:759595 original size:21 final size:22
Alignment explanation
Indices: 759552--759596 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
759542 AAAATAAGAT
759552 AATACAAAGATTAATACTTACA
1 AATACAAAGATTAATACTTACA
759574 AATACAAA-ATCTAATA-TTACA
1 AATACAAAGAT-TAATACTTACA
759595 AA
1 AA
759597 CAGGGAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.58, C:0.13, G:0.02, T:0.27
Consensus pattern (22 bp):
AATACAAAGATTAATACTTACA
Found at i:768414 original size:85 final size:84
Alignment explanation
Indices: 768221--768564 Score: 385
Period size: 85 Copynumber: 4.1 Consensus size: 84
768211 ACAAAAACGA
** *
768221 TATATATACAATTTCCAAAAGAACATTTTAGGTTTCAATAAATCATA---T-TCCACTCCTATAC
1 TATATATATGATTTCCAAAAGAACATTTTAGGTTTCAATAAATCATATTTTGTTC-CTCCTATAC
768282 AAACCGGAGTAGACTATCCCC
65 AAACCGGAGTAGACTAT-CCC
* * *
768303 TATATATA-GAATTTCCAAAAGAACATTTTATGTTTCCATAGATCATATTTTGTTCCTCCTATAC
1 TATATATATG-ATTTCCAAAAGAACATTTTAGGTTTCAATAAATCATATTTTGTTCCTCCTATAC
* *
768367 AAACCAGAGAAGACTATCCC
65 AAACCGGAGTAGACTATCCC
* *
768387 TATATATATGATTTCCAAAAAGAACATTTTAGGTTTCAATAAATCATATTTCGTTCCTACTATAC
1 TATATATATGATTTCC-AAAAGAACATTTTAGGTTTCAATAAATCATATTTTGTTCCTCCTATAC
768452 AAACCGGAGTAGACTATCCC
65 AAACCGGAGTAGACTATCCC
* * * * * * * ** *
768472 TATATATGTAATTCCCAAAAGAACAGTTTGGGTTCCAATAAATCGTACTCCT-TTCCTCCTATAT
1 TATATATATGATTTCCAAAAGAACATTTTAGGTTTCAATAAATCATA-TTTTGTTCCTCCTATAC
* * *
768536 GAACCGGAGAAGACCATCCC
65 AAACCGGAGTAGACTATCCC
*
768556 TATACATAT
1 TATATATAT
768565 AGGTATATAA
Statistics
Matches: 223, Mismatches: 31, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
82 42 0.19
84 78 0.35
85 101 0.45
86 2 0.01
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.32
Consensus pattern (84 bp):
TATATATATGATTTCCAAAAGAACATTTTAGGTTTCAATAAATCATATTTTGTTCCTCCTATACA
AACCGGAGTAGACTATCCC
Found at i:768548 original size:169 final size:166
Alignment explanation
Indices: 768221--768565 Score: 439
Period size: 169 Copynumber: 2.1 Consensus size: 166
768211 ACAAAAACGA
* *
768221 TATATATACAATTTCCAAAAGAACATTTTAGGTTTCAATAAATCATATTCCACTCCTATACAAAC
1 TATATATATAATTTCCAAAAGAACATTTTAGGTTTCAATAAATCATATTCCACTACTATACAAAC
* * * * *
768286 CGGAGTAGACTATCCCCTATATATAGAATTTCCAAAAGAACATTTTATGTTTCCATAGATCATAT
66 CGGAGTAGACTATCCCCTATATATAGAATTCCCAAAAGAACAGTTTAGGGTTCCATAAATCATAT
** *
768351 TTTGTTCCTCCTATACAAACCAGAGAAGACTATCCC
131 CCTGTTCCTCCTATACAAACCAGAGAAGACCATCCC
*
768387 TATATATATGATTTCCAAAAAGAACATTTTAGGTTTCAATAAATCATATTTCGTTC-CTACTATA
1 TATATATATAATTTCC-AAAAGAACATTTTAGGTTTCAATAAATCATA-TTC---CACTACTATA
768451 CAAACCGGAGTAGACTAT-CCCTATATAT-GTAATTCCCAAAAGAACAGTTT-GGGTTCCAATAA
61 CAAACCGGAGTAGACTATCCCCTATATATAG-AATTCCCAAAAGAACAGTTTAGGGTTCC-ATAA
* ** *
768513 ATCGTACTCCT-TTCCTCCTATATGAACCGGAGAAGACCATCCC
124 ATCATA-TCCTGTTCCTCCTATACAAACCAGAGAAGACCATCCC
*
768556 TATACATATA
1 TATATATATA
768566 GGTATATAAT
Statistics
Matches: 154, Mismatches: 17, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
166 14 0.09
167 31 0.20
168 9 0.06
169 72 0.47
170 27 0.18
171 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.32
Consensus pattern (166 bp):
TATATATATAATTTCCAAAAGAACATTTTAGGTTTCAATAAATCATATTCCACTACTATACAAAC
CGGAGTAGACTATCCCCTATATATAGAATTCCCAAAAGAACAGTTTAGGGTTCCATAAATCATAT
CCTGTTCCTCCTATACAAACCAGAGAAGACCATCCC
Found at i:769711 original size:15 final size:17
Alignment explanation
Indices: 769691--769723 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
769681 TGGTATTATA
769691 ATAATTT-T-TTATTTG
1 ATAATTTATGTTATTTG
769706 ATAATTTATGTTATTTG
1 ATAATTTATGTTATTTG
769723 A
1 A
769724 ACGAATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 1 0.06
17 8 0.50
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (17 bp):
ATAATTTATGTTATTTG
Found at i:770978 original size:45 final size:45
Alignment explanation
Indices: 770884--770988 Score: 111
Period size: 45 Copynumber: 2.3 Consensus size: 45
770874 ATTGATTAAC
* * * * ** *
770884 ACCATAGTTGAAACACACTATGGCATTATACCGGAATTAAATAAT
1 ACCATAGTTGAAAGAAACTATGGCATCATACCGAAAACAAATAAG
* *
770929 ACCATAGTTGAAAGAAACTATGGCATCATACCGAAAACGAGTAAG
1 ACCATAGTTGAAAGAAACTATGGCATCATACCGAAAACAAATAAG
* *
770974 ACCATGGCTGAAAGA
1 ACCATAGTTGAAAGA
770989 TGTTATGGCA
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.21
Consensus pattern (45 bp):
ACCATAGTTGAAAGAAACTATGGCATCATACCGAAAACAAATAAG
Found at i:771013 original size:45 final size:45
Alignment explanation
Indices: 770964--771079 Score: 151
Period size: 45 Copynumber: 2.6 Consensus size: 45
770954 TCATACCGAA
* * * * *
770964 AACGAGTAAGACCATGGCTGAAAGATGTTATGGCATCCCGATTTT
1 AACGAGTAAGACCATAGCTGAAAGACGTTATGGCATCACAATTCT
* *
771009 AACGAGTAAAACCATAGTTGAAAGACGTTATGGCATCACAATTCT
1 AACGAGTAAGACCATAGCTGAAAGACGTTATGGCATCACAATTCT
* *
771054 AACAAGTAAGACCATAGCTAAAAGAC
1 AACGAGTAAGACCATAGCTGAAAGAC
771080 ACAATGGCAT
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 60 1.00
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.22
Consensus pattern (45 bp):
AACGAGTAAGACCATAGCTGAAAGACGTTATGGCATCACAATTCT
Found at i:771087 original size:45 final size:45
Alignment explanation
Indices: 770993--771091 Score: 108
Period size: 45 Copynumber: 2.2 Consensus size: 45
770983 GAAAGATGTT
* * * * * * ***
770993 ATGGCATCCCGATTTTAACGAGTAAAACCATAGTTGAAAGACGTT
1 ATGGCATCACAATTCTAACAAGTAAAACCATAGCTAAAAGACACA
*
771038 ATGGCATCACAATTCTAACAAGTAAGACCATAGCTAAAAGACACA
1 ATGGCATCACAATTCTAACAAGTAAAACCATAGCTAAAAGACACA
771083 ATGGCATCA
1 ATGGCATCA
771092 TGAACCAGAC
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.22
Consensus pattern (45 bp):
ATGGCATCACAATTCTAACAAGTAAAACCATAGCTAAAAGACACA
Found at i:788815 original size:27 final size:27
Alignment explanation
Indices: 788774--788876 Score: 127
Period size: 27 Copynumber: 3.8 Consensus size: 27
788764 TAGTATTGGC
*
788774 GCCTATTTGGAAGGCTCCAATGGTGGT
1 GCCTATTTGGAAGGCGCCAATGGTGGT
*
788801 GCCTATTTGGGAGGCGCCAATGGTGGT
1 GCCTATTTGGAAGGCGCCAATGGTGGT
* * *
788828 GCCTATGTAGCAGGCGCCAATGGTGGT
1 GCCTATTTGGAAGGCGCCAATGGTGGT
* *
788855 GCC-ATATTAGAAGGCGCTAATG
1 GCCTAT-TTGGAAGGCGCCAATG
788877 CTGTGATTTT
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
26 2 0.03
27 65 0.97
ACGTcount: A:0.20, C:0.19, G:0.35, T:0.25
Consensus pattern (27 bp):
GCCTATTTGGAAGGCGCCAATGGTGGT
Found at i:788980 original size:18 final size:20
Alignment explanation
Indices: 788938--788984 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 20
788928 AAAACGGAAG
788938 AAAGAAGAAGGAAGGAAGCA
1 AAAGAAGAAGGAAGGAAGCA
* *
788958 GAAGAA-AA-GAAGGAAGGA
1 AAAGAAGAAGGAAGGAAGCA
788976 AAAGAAGAA
1 AAAGAAGAA
788985 AAAAGTAGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 14 0.61
19 4 0.17
20 5 0.22
ACGTcount: A:0.64, C:0.02, G:0.34, T:0.00
Consensus pattern (20 bp):
AAAGAAGAAGGAAGGAAGCA
Found at i:788987 original size:22 final size:23
Alignment explanation
Indices: 788934--788987 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
788924 TACAAAAACG
*
788934 GAAGAAAGAAGAAGGAAGGAAGCA
1 GAAGAAA-AAGAAGGAAGGAAGAA
788958 GAAG-AAAAGAAGGAAGGAA-AA
1 GAAGAAAAAGAAGGAAGGAAGAA
788979 GAAGAAAAA
1 GAAGAAAAA
788988 AGTAGGTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 5 0.18
22 17 0.61
23 2 0.07
24 4 0.14
ACGTcount: A:0.65, C:0.02, G:0.33, T:0.00
Consensus pattern (23 bp):
GAAGAAAAAGAAGGAAGGAAGAA
Found at i:792867 original size:38 final size:38
Alignment explanation
Indices: 792824--792905 Score: 146
Period size: 38 Copynumber: 2.2 Consensus size: 38
792814 AAAAAGTCAG
792824 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTAT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTAT
* *
792862 TTATAATTAAACTTTTAATGAAATGATTTTTAATTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTAT
792900 TTATAA
1 TTATAA
792906 ACTTTATATG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (38 bp):
TTATAATTAAACTTTTAATAAAATGATTTTTAATTTAT
Found at i:793136 original size:27 final size:26
Alignment explanation
Indices: 793100--793438 Score: 264
Period size: 27 Copynumber: 14.1 Consensus size: 26
793090 ATATCCCCAC
793100 ATTACAATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAATTA-AAT
793127 ATTACAATATTCATAC-AAA--AAA-
1 ATTACAATATTCATACAAAATTAAAT
*
793149 ATTGCAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAATTA-AAT
*
793176 ATTACAATATTCATACAACATTACAAT
1 ATTACAATATTCATACAAAATTA-AAT
*
793203 ATT-C-ATA---A-A-AAAATT-AT-
1 ATTACAATATTCATACAAAATTAAAT
*
793220 -----AATATTCATACAAAATTACAAA
1 ATTACAATATTCATACAAAATTA-AAT
*
793242 ACTACAATATTCATAC-AAA--AAA-
1 ATTACAATATTCATACAAAATTAAAT
*
793264 ATTGCAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAATTA-AAT
793291 ATTACAATATTCATACAAAA--AAAT
1 ATTACAATATTCATACAAAATTAAAT
*
793315 A-T--AATATTCATACAAAATTACAAA
1 ATTACAATATTCATACAAAATTA-AAT
793339 ATTACAATATTCATAC--AA--AAA-
1 ATTACAATATTCATACAAAATTAAAT
* *
793360 ATTGCAATATTCATACAAAACTATAAT
1 ATTACAATATTCATACAAAATTA-AAT
793387 ATTACAATATTCATAC-AAA--AAAT
1 ATTACAATATTCATACAAAATTAAAT
*
793410 -TTATAATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAATTA-AAT
793436 ATT
1 ATT
793439 CATACAAAAA
Statistics
Matches: 257, Mismatches: 14, Indels: 82
0.73 0.04 0.23
Matches are distributed among these distances:
14 3 0.01
17 1 0.00
18 2 0.01
19 6 0.02
20 5 0.02
21 32 0.12
22 46 0.18
23 21 0.08
24 10 0.04
25 11 0.04
26 19 0.07
27 101 0.39
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.32
Consensus pattern (26 bp):
ATTACAATATTCATACAAAATTAAAT
Found at i:793164 original size:96 final size:92
Alignment explanation
Indices: 793047--793550 Score: 364
Period size: 96 Copynumber: 5.5 Consensus size: 92
793037 AATTAATTAT
* * *
793047 AAAATAATTACAATATTCATACAAAAAATTACAATA-T-TACAATA-TATCCCCACATTACAATA
1 AAAAAAATTACAATATTCATACAAAAAATTACAATATTATACAAAACTAT---AACATTACAATA
793109 TTCATACAAAATTACAATATTACAATATTCATAC
63 TTCATACAAAA--A-AATATT-CAATATTCATAC
* * * *
793143 AAAAAAATTGCAATATTCATAC--AAAATTATAATA-T-TACAATATTCATACAACATTACAATA
1 AAAAAAATTACAATATTCATACAAAAAATTACAATATTATACAA-A-AC-TATAACATTACAATA
*
793204 TTCATA-AAAAAATTA-T-AATATTCATAC
63 TTCATACAAAAAAATATTCAATATTCATAC
* * * *
793231 AAAATTACAAAACTACAATATTCATACAAAAAAATTGCAATATTCATACAAAATTATAATATTAC
1 --AA--A-AAAATTACAATATTCATAC-AAAAAATTACAATATT-ATACAAAACTATAACATTAC
793296 AATATTCATACAAAAAAATA-T-AATATTCATAC
59 AATATTCATACAAAAAAATATTCAATATTCATAC
* *
793328 AAAATTACAAAATTACAATATTCATACAAAAAATTGCAATATTCATACAAAACTATAATATTACA
1 --AA--A-AAAATTACAATATTCATACAAAAAATTACAATATT-ATACAAAACTATAACATTACA
*
793393 ATATTCATAC-AAAAAAT-TTATAATATTCATAC
60 ATATTCATACAAAAAAATATT-CAATATTCATAC
*
793425 ---AAAATTACAATATTCATACAAAAAATTAC--TA--ATCCAAAACTATAA-A-TACAA-ATTT
1 AAAAAAATTACAATATTCATACAAAAAATTACAATATTATACAAAACTATAACATTACAATA-TT
* * * *
793480 AATTATAAAATAAT-TACAATATTCATAC
65 CA-TACAAAAAAATATTCAATATTCATAC
* *
793508 ---AACATTACAATATTCATA-AAAAAATTATAATATTCATACAAAA
1 AAAAAAATTACAATATTCATACAAAAAATTACAATATT-ATACAAAA
793551 AATTTAAAAT
Statistics
Matches: 352, Mismatches: 29, Indels: 63
0.79 0.07 0.14
Matches are distributed among these distances:
81 1 0.00
82 17 0.05
83 31 0.09
84 22 0.06
87 9 0.03
88 11 0.03
89 28 0.08
90 3 0.01
91 3 0.01
92 2 0.01
93 17 0.05
94 21 0.06
95 25 0.07
96 96 0.27
97 58 0.16
98 3 0.01
99 5 0.01
ACGTcount: A:0.54, C:0.14, G:0.01, T:0.31
Consensus pattern (92 bp):
AAAAAAATTACAATATTCATACAAAAAATTACAATATTATACAAAACTATAACATTACAATATTC
ATACAAAAAAATATTCAATATTCATAC
Found at i:793177 original size:49 final size:46
Alignment explanation
Indices: 793052--793447 Score: 229
Period size: 49 Copynumber: 8.5 Consensus size: 46
793042 ATTATAAAAT
* * *
793052 AATTACAATATTCATACAAAAAATTACAATATTACAATA-T-ATCCCCA
1 AATTACAATATTCATAC--AAAATTATAATATTACAATATTCAT-ACAA
* *
793099 CATTACAATATTCATACAAAATTACAATATTACAATATTCATACAAAAA
1 AATTACAATATTCATACAAAATTATAATATTACAATATTCATAC---AA
*
793148 AATTGCAATATTCATACAAAATTATAATATTACAATATTCATACAA
1 AATTACAATATTCATACAAAATTATAATATTACAATATTCATACAA
* * *
793194 CATTACAATATTCATAAAAAAATTATAATATTCATACAA-AAT--TACAA
1 AATTACAATATTCAT-ACAAAATTATAATA-T--TACAATATTCATACAA
* ** *
793241 AACTACAATATTCATACAAAAAAATTGCAATATTCATACAAAATT-AT--AA
1 AATTACAATATTCATAC---AAAATTATAATA-T--TACAATATTCATACAA
* * *
793290 TATTACAATATTCATACAAAAAAATATAATATTCATACAA-AAT--TACAA
1 AATTACAATATTCATAC--AAAATTATAATA-T--TACAATATTCATACAA
** *
793338 AATTACAATATTCATACAAAAAATTGCAATATT-C-ATA--CAAAACTATA
1 AATTACAATATTCATAC--AAAATTATAATATTACAATATTC-ATAC-A-A
*
793385 ATATTACAATATTCATAC-AAA--A-AAT-TTATAATATTCATACAA
1 A-ATTACAATATTCATACAAAATTATAATATTACAATATTCATACAA
793427 AATTACAATATTCATACAAAA
1 AATTACAATATTCATACAAAA
793448 AATTACTAAT
Statistics
Matches: 291, Mismatches: 30, Indels: 61
0.76 0.08 0.16
Matches are distributed among these distances:
41 18 0.06
42 8 0.03
43 5 0.02
44 5 0.02
45 27 0.09
46 20 0.07
47 54 0.19
48 66 0.23
49 80 0.27
50 7 0.02
51 1 0.00
ACGTcount: A:0.54, C:0.14, G:0.01, T:0.31
Consensus pattern (46 bp):
AATTACAATATTCATACAAAATTATAATATTACAATATTCATACAA
Found at i:793225 original size:115 final size:114
Alignment explanation
Indices: 793100--793574 Score: 422
Period size: 115 Copynumber: 4.2 Consensus size: 114
793090 ATATCCCCAC
793100 ATTACAATATTCATACAAAATTACAATATTACAATATTCATACAAAAAAATTGCAATATTCATAC
1 ATTACAATATTCATACAAAATTACAA-ATTACAATATTCATACAAAAAAATTGCAATATTCATAC
*
793165 AAAATTATAATATTACAATATTCATACAACATTACAATATTCATAAAAAA
65 AAAATTATAATATTACAATATTCATACAAAATTACAATATTCATAAAAAA
* *
793215 ATTATAATATTCATACAAAATTACAAAACTACAATATTCATACAAAAAAATTGCAATATTCATAC
1 ATTACAATATTCATACAAAATTAC-AAATTACAATATTCATACAAAAAAATTGCAATATTCATAC
* *
793280 AAAATTATAATATTACAATATTCATACAAAAAAATATAATATTCATACAAAATTACAAA
65 AAAATTATAATATTACAATATTCATAC--AAAATTACAATATTCAT----AA--A-AAA
* *
793339 ATTACAATATTCATAC--AA--A-AAATTGCAATATTCATACAAAACTATAATATTACAATATTC
1 ATTACAATATTCATACAAAATTACAAATTACAATATTCATAC-AAA--A-AA-ATTGCAATATTC
*
793399 ATAC-AAA--A-AAT-TTATAATATTCATACAAAATTACAATATTCATACAAAAA
61 ATACAAAATTATAATATTACAATATTCATACAAAATTACAATATTCATA-AAAAA
* * * * * * *
793449 ATTAC--TA---ATCCAAAACTATAAA-TACAA-ATTTAATTATAAAATAATTACAATATTCATA
1 ATTACAATATTCATACAAAATTACAAATTACAATA-TTCA-TACAAAAAAATTGCAATATTCATA
* * *
793507 CAACATTACAATATT-C-ATA---A-A-AAAATTATAATATTCATACAAAAA
64 CAAAATTATAATATTACAATATTCATACAAAATTACAATATTCATA-AAAAA
*
793552 ATTTAAAATATTCATACAAAATT
1 A-TTACAATATTCATACAAAATT
793575 CTAATCTAAA
Statistics
Matches: 303, Mismatches: 23, Indels: 74
0.76 0.06 0.19
Matches are distributed among these distances:
103 24 0.08
104 4 0.01
105 20 0.07
106 5 0.02
107 3 0.01
108 7 0.02
109 22 0.07
110 15 0.05
111 1 0.00
112 1 0.00
113 1 0.00
115 87 0.29
116 17 0.06
117 14 0.05
118 30 0.10
119 6 0.02
120 2 0.01
121 3 0.01
122 7 0.02
123 16 0.05
124 18 0.06
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.32
Consensus pattern (114 bp):
ATTACAATATTCATACAAAATTACAAATTACAATATTCATACAAAAAAATTGCAATATTCATACA
AAATTATAATATTACAATATTCATACAAAATTACAATATTCATAAAAAA
Found at i:793339 original size:97 final size:96
Alignment explanation
Indices: 793195--793434 Score: 428
Period size: 97 Copynumber: 2.5 Consensus size: 96
793185 TTCATACAAC
793195 ATTACAATATTCATA-AAAAAATTATAATATTCATACAAAATTACAAAACTACAATATTCATACA
1 ATTACAATATTCATACAAAAAATTATAATATTCATACAAAATTACAAAACTACAATATTCATAC-
*
793259 AAAAAATTGCAATATTCATACAAAATTATAAT
65 AAAAAATTGCAATATTCATACAAAACTATAAT
* *
793291 ATTACAATATTCATACAAAAAAATATAATATTCATACAAAATTACAAAATTACAATATTCATACA
1 ATTACAATATTCATACAAAAAATTATAATATTCATACAAAATTACAAAACTACAATATTCATACA
793356 AAAAATTGCAATATTCATACAAAACTATAAT
66 AAAAATTGCAATATTCATACAAAACTATAAT
793387 ATTACAATATTCATACAAAAAATTTATAATATTCATACAAAATTACAA
1 ATTACAATATTCATACAAAAAA-TTATAATATTCATACAAAATTACAA
793435 TATTCATACA
Statistics
Matches: 138, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
96 68 0.49
97 70 0.51
ACGTcount: A:0.55, C:0.13, G:0.01, T:0.31
Consensus pattern (96 bp):
ATTACAATATTCATACAAAAAATTATAATATTCATACAAAATTACAAAACTACAATATTCATACA
AAAAATTGCAATATTCATACAAAACTATAAT
Found at i:793561 original size:22 final size:21
Alignment explanation
Indices: 793127--793572 Score: 112
Period size: 19 Copynumber: 20.0 Consensus size: 21
793117 AAATTACAAT
*
793127 ATTACAATATTCATACAAAAAA
1 ATTAAAATATTCATAC-AAAAA
**
793149 ATTGCAATATTCATAC--AAA
1 ATTAAAATATTCATACAAAAA
* *
793168 ATTATAATATTACAATATTCATACAAC
1 ATTAAAATATT-C-ATA--CA-A-AAA
*
793195 ATTACAATATTCATA-AAAAA
1 ATTAAAATATTCATACAAAAA
*
793215 ATTATAATATTCATACAAAATTACAAA
1 ATTAAAATATTCATAC---A--A-AAA
* *
793242 ACTACAATATTCATACAAAAAA
1 ATTAAAATATTCATAC-AAAAA
**
793264 ATTGCAATATTCATAC--AAA
1 ATTAAAATATTCATACAAAAA
*
793283 ATTATAATATTACAATATTCATACAAAA
1 ATTAAAATATT-C-ATA--C--A-AAAA
* *
793311 AAATATAATATTCATACAAAATTACAAA
1 -ATTAAAATATTCATAC---A--A-AAA
*
793339 ATTACAATATTCATACAAAAA
1 ATTAAAATATTCATACAAAAA
**
793360 ATTGCAATATTCATAC--AAA
1 ATTAAAATATTCATACAAAAA
* *
793379 ACTATAATATTACAATATTCATACAAAA
1 ATTAAAATATT-C-ATA--C--A-AAAA
*
793407 AATTTATAATATTCATAC--AAA
1 -A-TTAAAATATTCATACAAAAA
*
793428 ATTACAATATTCATACAAAAA
1 ATTAAAATATTCATACAAAAA
** * * * *
793449 ATTACTA-ATCCAAAACTATAA
1 ATTAAAATATTC-ATACAAAAA
* *
793470 A-TACAAAT-TTAATTATAAAATA
1 ATTA-AAATATTCA-TACAAAA-A
* *
793492 ATTACAATATTCATAC--AAC
1 ATTAAAATATTCATACAAAAA
*
793511 ATTACAATATTCATA-AAAAA
1 ATTAAAATATTCATACAAAAA
*
793531 ATTATAATATTCATACAAAAA
1 ATTAAAATATTCATACAAAAA
793552 ATTTAAAATATTCATACAAAA
1 A-TTAAAATATTCATACAAAA
793573 TTCTAATCTA
Statistics
Matches: 328, Mismatches: 44, Indels: 104
0.69 0.09 0.22
Matches are distributed among these distances:
19 64 0.20
20 44 0.13
21 58 0.18
22 59 0.18
23 9 0.03
24 2 0.01
25 6 0.02
26 5 0.02
27 47 0.14
28 13 0.04
29 12 0.04
30 9 0.03
ACGTcount: A:0.55, C:0.13, G:0.01, T:0.32
Consensus pattern (21 bp):
ATTAAAATATTCATACAAAAA
Found at i:793573 original size:83 final size:85
Alignment explanation
Indices: 793333--793573 Score: 246
Period size: 83 Copynumber: 2.8 Consensus size: 85
793323 CATACAAAAT
** *
793333 TACAAAATTACAATATTCATACAAAAAATTGCAATATTCATACAAAACTATAATATTACAATATT
1 TACAAAATTACAATATTCATACAAAAAATTATAATATTCATAC-AAA--A-AAT-TTAAAATATT
*
793398 CATACAAAA-AATTTATAATATTCA
61 CATACAAAATAATTTACAATATTCA
* * * * *
793422 TACAAAATTACAATATTCATACAAAAAATTACT-A-ATCCAAAACTATAAA--TACAAAT-TTAA
1 TACAAAATTACAATATTCATACAAAAAATTA-TAATATTC-ATACAAAAAATTTA-AAATATTCA
*
793482 TTATAAAATAA-TTACAATATTCA
63 -TACAAAATAATTTACAATATTCA
*
793505 TACAACATTACAATATTCATA-AAAAAATTATAATATTCATACAAAAAATTTAAAATATTCATAC
1 TACAAAATTACAATATTCATACAAAAAATTATAATATTCATACAAAAAATTTAAAATATTCATAC
793569 AAAAT
66 AAAAT
793574 TCTAATCTAA
Statistics
Matches: 125, Mismatches: 17, Indels: 26
0.74 0.10 0.15
Matches are distributed among these distances:
81 1 0.01
82 22 0.18
83 54 0.43
84 7 0.06
85 2 0.02
86 1 0.01
88 4 0.03
89 34 0.27
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (85 bp):
TACAAAATTACAATATTCATACAAAAAATTATAATATTCATACAAAAAATTTAAAATATTCATAC
AAAATAATTTACAATATTCA
Found at i:793574 original size:20 final size:20
Alignment explanation
Indices: 793497--793574 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 20
793487 AAATAATTAC
* *
793497 AATATTCATACAACA-TTAC
1 AATATTCATACAAAATTTAA
* * *
793516 AATATTCATAAAAAAATTAT
1 AATATTCATACAAAATTTAA
793536 AATATTCATACAAAAAATTTAA
1 AATATTCATAC--AAAATTTAA
793558 AATATTCATACAAAATT
1 AATATTCATACAAAATT
793575 CTAATCTAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
19 13 0.26
20 19 0.38
22 18 0.36
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (20 bp):
AATATTCATACAAAATTTAA
Done.