Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 166 of 310
Found at i:54421157 original size:41 final size:39
Alignment explanation
Indices: 54421112--54421277 Score: 113
Period size: 42 Copynumber: 4.0 Consensus size: 39
54421102 AAATGCCACA
*
54421112 ATTGCTTTAGCTTTAGCGGCGTTTATGAAAAAAA-CACTGCT
1 ATTGCTTTA-CTTTTGCGGCGTTTATGAAAAAAAGC-C-GCT
* *
54421153 ATTGCTTTACTGTTTGTGGCATTTATGAGAAAAAAGCCGCT
1 ATTGCTTTACT-TTTGCGGCGTTTATGA-AAAAAAGCCGCT
* * *
54421194 ATAGTTTTAACCTTTTGCGGCGTTTATGAGAAAAATA-CCACT
1 ATTGCTTT-A-CTTTTGCGGCGTTTATGA-AAAAA-AGCCGCT
* * * *
54421236 ATAG-TTATAACCTTTTGCGGCGTTTATGCATAAACGCCGCT
1 ATTGCTT-T-A-CTTTTGCGGCGTTTATGAAAAAAAGCCGCT
54421277 A
1 A
54421278 CTATTTTACA
Statistics
Matches: 105, Mismatches: 12, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
40 2 0.02
41 42 0.40
42 57 0.54
43 4 0.04
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.35
Consensus pattern (39 bp):
ATTGCTTTACTTTTGCGGCGTTTATGAAAAAAAGCCGCT
Found at i:54421220 original size:42 final size:41
Alignment explanation
Indices: 54421122--54421263 Score: 155
Period size: 42 Copynumber: 3.4 Consensus size: 41
54421112 ATTGCTTTAG
* * *
54421122 CTTTAGCGGCGTTTATGA-AAAAAACACTGCTATTGCTTT-A-
1 CTTTTGCGGCGTTTATGAGAAAAAAC-C-GCTATAGTTTTAAC
* *
54421162 CTGTTTGTGGCATTTATGAGAAAAAAGCCGCTATAGTTTTAAC
1 CT-TTTGCGGCGTTTATGAGAAAAAA-CCGCTATAGTTTTAAC
* *
54421205 CTTTTGCGGCGTTTATGAGAAAAATACCACTATAGTTATAAC
1 CTTTTGCGGCGTTTATGAGAAAAA-ACCGCTATAGTTTTAAC
54421247 CTTTTGCGGCGTTTATG
1 CTTTTGCGGCGTTTATG
54421264 CATAAACGCC
Statistics
Matches: 87, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
40 2 0.02
41 22 0.25
42 59 0.68
43 4 0.05
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (41 bp):
CTTTTGCGGCGTTTATGAGAAAAAACCGCTATAGTTTTAAC
Found at i:54430197 original size:40 final size:34
Alignment explanation
Indices: 54430152--54430236 Score: 100
Period size: 34 Copynumber: 2.4 Consensus size: 34
54430142 CCAAAATTAT
54430152 TATTTTAGAAAATTTTTAAAATATTAACTTTATATATATA
1 TATTTTAG-AAATTTTTAAAAT-TT-A---TATATATATA
*
54430192 TATTTTAGAATTTTTTAAAATTTATATATATATA
1 TATTTTAGAAATTTTTAAAATTTATATATATATA
54430226 TATTTTA-AAAT
1 TATTTTAGAAAT
54430237 ATAAATTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
33 3 0.07
34 17 0.40
37 1 0.02
38 2 0.05
39 12 0.28
40 8 0.19
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (34 bp):
TATTTTAGAAATTTTTAAAATTTATATATATATA
Found at i:54430224 original size:38 final size:40
Alignment explanation
Indices: 54430152--54430228 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 40
54430142 CCAAAATTAT
*
54430152 TATTTTAGAAAATTTTTAAAATATTAACTTTATATATATA
1 TATTTTAGAAAATTTTTAAAATATTAACTATATATATATA
*
54430192 TATTTTAG-AATTTTTTAAAAT-TT-A-TATATATATATA
1 TATTTTAGAAAATTTTTAAAATATTAACTATATATATATA
54430228 T
1 T
54430229 TTTAAAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 12 0.34
37 1 0.03
38 2 0.06
39 12 0.34
40 8 0.23
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (40 bp):
TATTTTAGAAAATTTTTAAAATATTAACTATATATATATA
Found at i:54442512 original size:46 final size:45
Alignment explanation
Indices: 54442444--54442796 Score: 192
Period size: 46 Copynumber: 7.6 Consensus size: 45
54442434 TTATTTGTGT
*
54442444 GCTAGTGTAAGACATGTCTGGGACATGCGTCGGCCACCTTATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCA-CTTATGAGA
54442490 GCTAGTGTAAGACCATGT-TGGGACATGGCATCGG-CA-TTGA-GACAAGA
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCACTT-ATG---AGA
* * * ** *
54442537 GCTAGTGTAAGACATGTTTGGGACATGCATTGGCCTCGAGATTA-A
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-TTATGAGA
*
54442582 GCTAGTGTAAGATCATGTCTGGGACATGGCATCGG-CA-TTGAGACGAGA
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCACTT---ATGAGA
* * * **
54442630 GCTAGTGTAAGACATGTCTGAGACATGTATCGGCCTCAAGATGTA-A
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-TTATG-AGA
* * * * * *
54442676 ACCAATGTAAGACATGTCTGGGACAT-CATCGGCTAC-GA-GATGT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACTTATGA-GA
* *
54442719 G-TCAGTGTAAGACTATGTCTGGGACATGGCATCAG-CACGGATATGTGAGA
1 GCT-AGTGTAAGAC-ATGTCTGGGACAT-GCATCGGCCAC---T-TATGAGA
* *
54442769 GCTAATGTAAAACCATGTCTGGGACATG
1 GCTAGTGTAAGA-CATGTCTGGGACATG
54442797 GTATTGGCCT
Statistics
Matches: 235, Mismatches: 37, Indels: 67
0.69 0.11 0.20
Matches are distributed among these distances:
41 1 0.00
42 1 0.00
43 11 0.05
44 16 0.07
45 23 0.10
46 84 0.36
47 58 0.25
48 14 0.06
49 1 0.00
50 22 0.09
51 4 0.02
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.24
Consensus pattern (45 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACTTATGAGA
Found at i:54442538 original size:47 final size:47
Alignment explanation
Indices: 54442444--54442903 Score: 240
Period size: 47 Copynumber: 9.8 Consensus size: 47
54442434 TTATTTGTGT
*
54442444 GCTAGTGTAAGACATGTCTGGGACAT-GCGTCGGCCACCTT-ATG---AGA
1 GCTAGTGTAAGACATGTCTGGGACATGGCATCGG-CA--TTGA-GACAAGA
54442490 GCTAGTGTAAGACCATGT-TGGGACATGGCATCGGCATTGAGACAAGA
1 GCTAGTGTAAGA-CATGTCTGGGACATGGCATCGGCATTGAGACAAGA
* * * * **
54442537 GCTAGTGTAAGACATGTTTGGGACAT-GCATTGGCCTCGAGATTA-A
1 GCTAGTGTAAGACATGTCTGGGACATGGCATCGGCATTGAGACAAGA
*
54442582 GCTAGTGTAAGATCATGTCTGGGACATGGCATCGGCATTGAGACGAGA
1 GCTAGTGTAAGA-CATGTCTGGGACATGGCATCGGCATTGAGACAAGA
* * * ** *
54442630 GCTAGTGTAAGACATGTCTGAGACAT-GTATCGGCCTCAAGATGTAA-A
1 GCTAGTGTAAGACATGTCTGGGACATGGCATCGGCATTGAGA--CAAGA
* * * * *
54442677 -CCAATGTAAGACATGTCTGGGACAT--CATCGGC--T-ACGAGATGT
1 GCTAGTGTAAGACATGTCTGGGACATGGCATCGGCATTGA-GACAAGA
* ** * **
54442719 G-TCAGTGTAAGACTATGTCTGGGACATGGCATCAGCACGGATATGTGAGA
1 GCT-AGTGTAAGAC-ATGTCTGGGACATGGCATCGGCATTGAGA--CAAGA
* * * * * ** *
54442769 GCTAATGTAAAACCATGTCTGGGACATGGTATTGGCCTTGATTTCAATA
1 GCTAGTGTAAGA-CATGTCTGGGACATGGCATCGGCATTGA-GACAAGA
* ** * *
54442818 G-TCAGTGTAAGACCATATCTGGGACATGGCATCAAC-TTGATG-GATGA
1 GCT-AGTGTAAGA-CATGTCTGGGACATGGCATCGGCATTGA-GACAAGA
* * *
54442865 GCCAGTGTAAGACCATATCTGGGACATGGCATCAGCATT
1 GCTAGTGTAAGA-CATGTCTGGGACATGGCATCGGCATT
54442904 ATACCTTATG
Statistics
Matches: 323, Mismatches: 61, Indels: 58
0.73 0.14 0.13
Matches are distributed among these distances:
41 1 0.00
42 1 0.00
43 11 0.03
44 16 0.05
45 20 0.06
46 92 0.28
47 96 0.30
48 23 0.07
49 30 0.09
50 30 0.09
51 3 0.01
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.25
Consensus pattern (47 bp):
GCTAGTGTAAGACATGTCTGGGACATGGCATCGGCATTGAGACAAGA
Found at i:54442605 original size:93 final size:92
Alignment explanation
Indices: 54442444--54442708 Score: 338
Period size: 93 Copynumber: 2.9 Consensus size: 92
54442434 TTATTTGTGT
* * *** *
54442444 GCTAGTGTAAGACATGTCTGGGACATGCGTCGGCCACCTTATGAGAGCTAGTGTAAGACCATGT-
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCAAGATTA-AGCTAGTGTAAGA-CATGTC
54442508 TGGGACATGGCATCGGCATTGAGACAAGA
64 TGGGACATGGCATCGGCATTGAGACAAGA
* * *
54442537 GCTAGTGTAAGACATGTTTGGGACATGCATTGGCCTCGAGATTAAGCTAGTGTAAGATCATGTCT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCAAGATTAAGCTAGTGTAAGA-CATGTCT
*
54442602 GGGACATGGCATCGGCATTGAGACGAGA
65 GGGACATGGCATCGGCATTGAGACAAGA
* * * * *
54442630 GCTAGTGTAAGACATGTCTGAGACATGTATCGGCCTCAAGATGTAAACCAATGTAAGACATGTCT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCAAGAT-TAAGCTAGTGTAAGACATGTCT
54442695 GGGACAT--CATCGGC
65 GGGACATGGCATCGGC
54442709 TACGAGATGT
Statistics
Matches: 152, Mismatches: 18, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
91 7 0.05
92 18 0.12
93 115 0.76
94 12 0.08
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.24
Consensus pattern (92 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCAAGATTAAGCTAGTGTAAGACATGTCTG
GGACATGGCATCGGCATTGAGACAAGA
Found at i:54450667 original size:46 final size:46
Alignment explanation
Indices: 54450608--54450820 Score: 195
Period size: 46 Copynumber: 4.6 Consensus size: 46
54450598 ATTGATACGA
* * * * *
54450608 AAGCTAGTG-AAGACATGTCTAGGACATACACCAGCCTGGAGATGT
1 AAGCCAGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGATGT
* * *
54450653 AAGCCAGTGTAAGACTATGTCTAGGACATGGCATCGGCATTGAGACG-
1 AAGCCAGTGTAAGAC-ATGTCTAGGACAT-GCATCGGCCTCGAGATGT
* * * *
54450700 AGAGCTAGTGTAAGACATGTCTAGGACATGCATTGGCCTCAAGATTT
1 A-AGCCAGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGATGT
*
54450747 AAGCCAGTGTAAGACATGTC-AGGGACATGCATCGG-CTATGAGATGT
1 AAGCCAGTGTAAGACATGTCTA-GGACATGCATCGGCCT-CGAGATGT
* *
54450793 --GTCAGTGTAAGACCATGTCTAGAACATG
1 AAGCCAGTGTAAGA-CATGTCTAGGACATG
54450821 ACATTGGAAT
Statistics
Matches: 138, Mismatches: 21, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
44 11 0.08
45 23 0.17
46 52 0.38
47 28 0.20
48 24 0.17
ACGTcount: A:0.31, C:0.18, G:0.28, T:0.23
Consensus pattern (46 bp):
AAGCCAGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGATGT
Found at i:54450758 original size:94 final size:93
Alignment explanation
Indices: 54450585--54450827 Score: 273
Period size: 94 Copynumber: 2.6 Consensus size: 93
54450575 CATGTATGAA
* * * * *** **
54450585 ACATGGCATCGACATTGATACGAAAGCTAGTG-AAGACATGTCTAGGACATACACCAGCCTGGAG
1 ACATGGCATCGGCATTGAGACGAGAGCTAGTGTAAGACATGTCTAGGACATGCATTGGCCTCAAG
54450649 ATGTAAGCCAGTGTAAGACTATGTCTA-GG
66 ATGTAAGCCAGTGTAAGAC-ATGTC-AGGG
54450678 ACATGGCATCGGCATTGAGACGAGAGCTAGTGTAAGACATGTCTAGGACATGCATTGGCCTCAAG
1 ACATGGCATCGGCATTGAGACGAGAGCTAGTGTAAGACATGTCTAGGACATGCATTGGCCTCAAG
*
54450743 ATTTAAGCCAGTGTAAGACATGTCAGGG
66 ATGTAAGCCAGTGTAAGACATGTCAGGG
* * * *
54450771 ACAT-GCATCGGC-TATGAGATGTG-TC-AGTGTAAGACCATGTCTAGAACATGACATTGG
1 ACATGGCATCGGCAT-TGAGACGAGAGCTAGTGTAAGA-CATGTCTAGGACATG-CATTGG
54450828 AATGTATATA
Statistics
Matches: 131, Mismatches: 14, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
90 9 0.07
91 16 0.12
92 22 0.17
93 40 0.31
94 44 0.34
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (93 bp):
ACATGGCATCGGCATTGAGACGAGAGCTAGTGTAAGACATGTCTAGGACATGCATTGGCCTCAAG
ATGTAAGCCAGTGTAAGACATGTCAGGG
Found at i:54451021 original size:47 final size:47
Alignment explanation
Indices: 54450843--54451021 Score: 177
Period size: 47 Copynumber: 3.7 Consensus size: 47
54450833 ATATAGGTGT
* *
54450843 TAGTGTAAGACCATGTCTAGGACATGGCATCAGCACGAAT-ATGTGA-GAGC
1 TAGTGTAAGACCATGTCTGGGACATGGCATC-G-AC--TTGATG-GATGAGC
* * ** * *
54450893 TAGTGTAAGACCATGTATGGGACATTGCGCCGACCTCGATTTCGAT-AG-
1 TAGTGTAAGACCATGTCTGGGACATGGCATCGA-CTTGA--TGGATGAGC
54450941 TCAGTGTAAGACCATGTCTGGGACATGGCATCGACTTGATGGATGAGC
1 T-AGTGTAAGACCATGTCTGGGACATGGCATCGACTTGATGGATGAGC
54450989 TAGTGTAAGACCATGTCTGGGACATGGCATCGA
1 TAGTGTAAGACCATGTCTGGGACATGGCATCGA
54451022 TATTATACAT
Statistics
Matches: 107, Mismatches: 14, Indels: 19
0.76 0.10 0.14
Matches are distributed among these distances:
46 4 0.04
47 34 0.32
48 8 0.07
49 34 0.32
50 27 0.25
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (47 bp):
TAGTGTAAGACCATGTCTGGGACATGGCATCGACTTGATGGATGAGC
Found at i:54453529 original size:51 final size:50
Alignment explanation
Indices: 54453355--54453633 Score: 317
Period size: 50 Copynumber: 5.5 Consensus size: 50
54453345 TGAGAACACA
* * * ** * *
54453355 TGTGTAGTACTATGTGCAGGCTACTATGTGTTTAAGACGGTTTTAGGTCAGG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCCGATGG--TTAGGTCACG
*
54453407 TGTTTAGTACTAAGTGCAGGCTACTACGTGTATCCGATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCCGATGGTTAGGTCACG
* * * * * * *
54453457 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCAATAGCTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCCGAT-GGTTAGGTCACG
*
54453508 TGTGTAGTACTAAGTGTAGGCTACTACGTGTATCCGATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCCGATGGTTAGGTCACG
* * * * *
54453558 TGTGTAGTACTAAGTGCAGGCTACTACGTATA-CTAGATTGTTAGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATC-CGATGGTTAGGTCACG
*
54453608 TGTTTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
54453634 TGCATACTAG
Statistics
Matches: 194, Mismatches: 31, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
49 1 0.01
50 118 0.61
51 42 0.22
52 33 0.17
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (50 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCCGATGGTTAGGTCACG
Found at i:54453631 original size:151 final size:152
Alignment explanation
Indices: 54453355--54453636 Score: 397
Period size: 151 Copynumber: 1.9 Consensus size: 152
54453345 TGAGAACACA
* * * * *
54453355 TGTGTAGTACTATGTGCAGGCTACTATGTGTTTAAGACGGTTTTAGGTCAGGTGTTTAGTACTAA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATAAGACGG-TTTAGGTCACGTGTGTAGTACTAA
* * *
54453420 GTGCAGGCTACTACGTGTATCCGATGGTTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATG
65 GTGCAGGCTACTACGTATATCAGATGGTTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTATG
54453485 CGTACCCAATAGCTTCGATCACG
130 CGTACCCAATAGCTTCGATCACG
* ** *
54453508 TGTGTAGTACTAAGTGTAGGCTACTACGTGTATCCGATGG-TTAGGTCACGTGTGTAGTACTAAG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATAAGACGGTTTAGGTCACGTGTGTAGTACTAAG
* * *
54453572 TGCAGGCTACTACGTATA-CTAGATTGTTAGGTCGCATGTTTAGTACTAAGTGCAGGCTACTATG
66 TGCAGGCTACTACGTATATC-AGATGGTTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTATG
54453636 C
130 C
54453637 ATACTAGAGA
Statistics
Matches: 113, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
150 1 0.01
151 79 0.70
153 33 0.29
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.32
Consensus pattern (152 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTATAAGACGGTTTAGGTCACGTGTGTAGTACTAAG
TGCAGGCTACTACGTATATCAGATGGTTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGC
GTACCCAATAGCTTCGATCACG
Found at i:54459339 original size:27 final size:27
Alignment explanation
Indices: 54459309--54459486 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
54459299 ATATTGAGTC
* * * *
54459309 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
54459336 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54459363 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
54459391 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
54459418 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
54459445 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54459472 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54459487 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:54459448 original size:82 final size:81
Alignment explanation
Indices: 54459330--54459485 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
54459320 TGCTATATAA
* *
54459330 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
54459395 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
54459412 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
54459476 CACTTAGTGC
65 CACTTAGTGC
54459486 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:54467402 original size:27 final size:27
Alignment explanation
Indices: 54467372--54467549 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
54467362 ATATTGAGTC
* * * *
54467372 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
54467399 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54467426 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
54467454 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
54467481 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
54467508 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54467535 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54467550 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:54467511 original size:82 final size:81
Alignment explanation
Indices: 54467393--54467548 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
54467383 TGCTATATAA
* *
54467393 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
54467458 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
54467475 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
54467539 CACTTAGTGC
65 CACTTAGTGC
54467549 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:54471793 original size:50 final size:49
Alignment explanation
Indices: 54471719--54471865 Score: 183
Period size: 50 Copynumber: 3.0 Consensus size: 49
54471709 TGTTTTAGAC
*
54471719 GATT-TTAGGTCAAGTGTGTAGTACTAAGTGAAGGCTACTACGTGTATCC-
1 GATTGTTAGGTCAA-TGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CCA
*
54471768 G-TTGGTTAGGTCACATGTGTAGTACTAAGTGCAGGCTACAACGTGTACCA
1 GATT-GTTAGGTCA-ATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCA
* * *
54471818 GATTGTTAGGCCATATGTGTAGTATTAAGTGCAGGCTACTATGTGTAC
1 GATTGTTAGGTCA-ATGTGTAGTACTAAGTGCAGGCTACTACGTGTAC
54471866 TAGAGAGCTT
Statistics
Matches: 86, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
48 2 0.02
49 3 0.03
50 78 0.91
51 3 0.03
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.32
Consensus pattern (49 bp):
GATTGTTAGGTCAATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCA
Found at i:54474834 original size:34 final size:34
Alignment explanation
Indices: 54474791--54474859 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
54474781 AACGCCGATG
54474791 GTTAGAACTGCTAAAAGACTATAAGCTTGTGATT
1 GTTAGAACTGCTAAAAGACTATAAGCTTGTGATT
*
54474825 GTTAGAACTGCTAAAAGACTATGAGCTTGTGATT
1 GTTAGAACTGCTAAAAGACTATAAGCTTGTGATT
54474859 G
1 G
54474860 ACTATCACCC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.32
Consensus pattern (34 bp):
GTTAGAACTGCTAAAAGACTATAAGCTTGTGATT
Found at i:54477251 original size:125 final size:125
Alignment explanation
Indices: 54477100--54477349 Score: 446
Period size: 125 Copynumber: 2.0 Consensus size: 125
54477090 TGATGATGAA
*
54477100 AAATGAAAGATATGTTTTAGCTTAACATATTTTGTATTGGAATTTTTGATAATTTTGAGTAATAA
1 AAATGAAAGATATGTTTTAGCTTAACATATTTTGTATTGGAATTTTTAATAATTTTGAGTAATAA
* *
54477165 GGACTTAATTGCAAAAATAATAATTTAAGGGTCTAAAATTTGAAATTAATGAAATATATG
66 GGACTTAATTGCAAAAATAATAATTTAAGGGACTAAAATGTGAAATTAATGAAATATATG
*
54477225 AAATGAAAGATATGTTTTAGCTTAACATATTTTGTATTGGAATTTTTAATAATTTTGAGTAATTA
1 AAATGAAAGATATGTTTTAGCTTAACATATTTTGTATTGGAATTTTTAATAATTTTGAGTAATAA
* *
54477290 GGACTTAATTGCAAAAATAATAATTTGAGGGACTGAAATGTGAAATTAATGAAATATATG
66 GGACTTAATTGCAAAAATAATAATTTAAGGGACTAAAATGTGAAATTAATGAAATATATG
54477350 GACTCGTATG
Statistics
Matches: 119, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
125 119 1.00
ACGTcount: A:0.41, C:0.04, G:0.16, T:0.39
Consensus pattern (125 bp):
AAATGAAAGATATGTTTTAGCTTAACATATTTTGTATTGGAATTTTTAATAATTTTGAGTAATAA
GGACTTAATTGCAAAAATAATAATTTAAGGGACTAAAATGTGAAATTAATGAAATATATG
Found at i:54478123 original size:39 final size:39
Alignment explanation
Indices: 54478080--54478158 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
54478070 GTAAGAATTT
54478080 ATTTGATATTTACATGAGATAAGGTAAGTAAATATTAAG
1 ATTTGATATTTACATGAGATAAGGTAAGTAAATATTAAG
54478119 ATTTGATATTTACATGAGATAAGGTAAGTAAATATTAAG
1 ATTTGATATTTACATGAGATAAGGTAAGTAAATATTAAG
54478158 A
1 A
54478159 ATATTTGTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.44, C:0.03, G:0.18, T:0.35
Consensus pattern (39 bp):
ATTTGATATTTACATGAGATAAGGTAAGTAAATATTAAG
Found at i:54484217 original size:45 final size:44
Alignment explanation
Indices: 54484132--54484217 Score: 127
Period size: 45 Copynumber: 1.9 Consensus size: 44
54484122 TATGTAATTT
* *
54484132 GAACTCATTGAGTTGTGTTTGAGTTTATGATATATGTGACATCC
1 GAACTCATTGAGTTGTGTCTGAGTTTATGATATATATGACATCC
* *
54484176 GAACTCATTGAGTTGTGGTCTGAGTTTGTGATATGTATGACA
1 GAACTCATTGAGTTGT-GTCTGAGTTTATGATATATATGACA
54484218 CATGTTTTGG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 16 0.43
45 21 0.57
ACGTcount: A:0.24, C:0.10, G:0.26, T:0.40
Consensus pattern (44 bp):
GAACTCATTGAGTTGTGTCTGAGTTTATGATATATATGACATCC
Found at i:54486045 original size:13 final size:13
Alignment explanation
Indices: 54486029--54486061 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
54486019 TTTAATTAAA
*
54486029 TTAGTTAATTAGT
1 TTAGATAATTAGT
54486042 TTAGATAATTAGT
1 TTAGATAATTAGT
54486055 TTA-ATAA
1 TTAGATAA
54486062 ACAAACCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:54491410 original size:7 final size:6
Alignment explanation
Indices: 54491354--54491437 Score: 59
Period size: 6 Copynumber: 14.7 Consensus size: 6
54491344 TCCTCCTATT
* * * * *
54491354 TTTTTA TTCTTA TTCTTA TTCTTA -TTTTA -TTTTA TTTTTC TTTTTC
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
* * * *
54491400 TTTTGA TTTTTA TTTTCA -TTTCA ATTTTA -TTTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
54491438 GAAAATATAT
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
5 19 0.28
6 48 0.72
ACGTcount: A:0.15, C:0.08, G:0.01, T:0.75
Consensus pattern (6 bp):
TTTTTA
Found at i:54501355 original size:15 final size:15
Alignment explanation
Indices: 54501335--54501368 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
54501325 AGGTATTTTT
54501335 GAAAGTGTCACCATG
1 GAAAGTGTCACCATG
54501350 GAAAGTGTCACCATG
1 GAAAGTGTCACCATG
54501365 GAAA
1 GAAA
54501369 AAGGTTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.18
Consensus pattern (15 bp):
GAAAGTGTCACCATG
Found at i:54520681 original size:3 final size:3
Alignment explanation
Indices: 54520666--54520719 Score: 83
Period size: 3 Copynumber: 18.3 Consensus size: 3
54520656 TTATTTTCTT
* *
54520666 TAA TAA CAA TAA TAA TGA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
54520713 TAA TAA T
1 TAA TAA T
54520720 GGGAAAAAAG
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:54521076 original size:23 final size:23
Alignment explanation
Indices: 54521050--54521093 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
54521040 AACATAAACA
*
54521050 AACATGTTCGTGAACGCTAAATG
1 AACATGTTCGCGAACGCTAAATG
*
54521073 AACATGTTCGCGAATGCTAAA
1 AACATGTTCGCGAACGCTAAA
54521094 CGAATCGAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.25
Consensus pattern (23 bp):
AACATGTTCGCGAACGCTAAATG
Found at i:54525991 original size:17 final size:18
Alignment explanation
Indices: 54525956--54525991 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
54525946 CAAGTAAGCA
*
54525956 CACGGGCGTGTGCCCAGG
1 CACGGGCATGTGCCCAGG
54525974 CACGGGCATGTG-CCAGG
1 CACGGGCATGTGCCCAGG
54525991 C
1 C
54525992 CATATGATCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.14, C:0.33, G:0.42, T:0.11
Consensus pattern (18 bp):
CACGGGCATGTGCCCAGG
Found at i:54528850 original size:42 final size:41
Alignment explanation
Indices: 54528738--54528856 Score: 125
Period size: 43 Copynumber: 2.8 Consensus size: 41
54528728 ACTAAGATGT
* *
54528738 GATTACATGTAAGACCATGTCTGGGACATTGGCATCGTTAATC
1 GATT-CATGTAAGACCATGTCTGGGATA-TGGCATCGATAATC
*
54528781 GATTTCATGTAAGA-CACTGTCTGGGATAGTGGCATCGAT-GTGC
1 GA-TTCATGTAAGACCA-TGTCTGGGATA-TGGCATCGATAAT-C
* *
54528824 GATTCATGTAAGACCATATCTAGGATATGGCAT
1 GATTCATGTAAGACCATGTCTGGGATATGGCAT
54528857 TGTACGAGCT
Statistics
Matches: 66, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
41 6 0.09
42 23 0.35
43 35 0.53
44 2 0.03
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (41 bp):
GATTCATGTAAGACCATGTCTGGGATATGGCATCGATAATC
Found at i:54540564 original size:280 final size:280
Alignment explanation
Indices: 54540063--54540623 Score: 1095
Period size: 280 Copynumber: 2.0 Consensus size: 280
54540053 GGAAATCCTG
54540063 TTTGAACCTTAGGAATATTTTAGGATACGAATGACTTGTCACTAAGAACTATGTGATCTGAACTC
1 TTTGAACCTTAGGAATATTTTAGGATACGAATGACTTGTCACTAAGAACTATGTGATCTGAACTC
*
54540128 ATTGAGTTGTGGTCTGAGTTCATGATGTATGTGACACATGTTTTGGCGTCTGGGTATTGGTCCCA
66 ATTGAGTTGTGGTCTGAGTTCATAATGTATGTGACACATGTTTTGGCGTCTGGGTATTGGTCCCA
54540193 CATATTCTACCTGTGGCTGGGTAGTCCGGCATGTGTTGCAGAAACCTGACAACCTATGTGAGCAG
131 CATATTCTACCTGTGGCTGGGTAGTCCGGCATGTGTTGCAGAAACCTGACAACCTATGTGAGCAG
*
54540258 ACCTGTGAGTAGCTTGAAAGCAAGCAACACGTGATATGTGATATGAGGTAGTGTTGGCTACATAT
196 ACCTGTCAGTAGCTTGAAAGCAAGCAACACGTGATATGTGATATGAGGTAGTGTTGGCTACATAT
54540323 GAGACACTTAGGTGCAAGAT
261 GAGACACTTAGGTGCAAGAT
54540343 TTTGAACCTTAGGAATATTTTAGGATACGAATGACTTGTCACTAAGAACTATGTGATCTGAACTC
1 TTTGAACCTTAGGAATATTTTAGGATACGAATGACTTGTCACTAAGAACTATGTGATCTGAACTC
54540408 ATTGAGTTGTGGTCTGAGTTCATAATGTATGTGACACATGTTTTGGCGTCTGGGTATTGGTCCCA
66 ATTGAGTTGTGGTCTGAGTTCATAATGTATGTGACACATGTTTTGGCGTCTGGGTATTGGTCCCA
54540473 CATATTCTACCTGTGGCTGGGTAGTCCGGCATGTGTTGCAGAAACCTGACAACCTATGTGAGCAG
131 CATATTCTACCTGTGGCTGGGTAGTCCGGCATGTGTTGCAGAAACCTGACAACCTATGTGAGCAG
*
54540538 ACTTGTCAGTAGCTTGAAAGCAAGCAACACGTGATATGTGATATGAGGTAGTGTTGGCTACATAT
196 ACCTGTCAGTAGCTTGAAAGCAAGCAACACGTGATATGTGATATGAGGTAGTGTTGGCTACATAT
54540603 GAGACACTTAGGTGCAAGAT
261 GAGACACTTAGGTGCAAGAT
54540623 T
1 T
54540624 CTGATGTATC
Statistics
Matches: 278, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
280 278 1.00
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (280 bp):
TTTGAACCTTAGGAATATTTTAGGATACGAATGACTTGTCACTAAGAACTATGTGATCTGAACTC
ATTGAGTTGTGGTCTGAGTTCATAATGTATGTGACACATGTTTTGGCGTCTGGGTATTGGTCCCA
CATATTCTACCTGTGGCTGGGTAGTCCGGCATGTGTTGCAGAAACCTGACAACCTATGTGAGCAG
ACCTGTCAGTAGCTTGAAAGCAAGCAACACGTGATATGTGATATGAGGTAGTGTTGGCTACATAT
GAGACACTTAGGTGCAAGAT
Found at i:54546808 original size:18 final size:19
Alignment explanation
Indices: 54546787--54546826 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
54546777 TTTTTTTTTG
54546787 AAAACA-CGAAAATTTTCA
1 AAAACACCGAAAATTTTCA
* *
54546805 AAAACACCGAAATTTTTTA
1 AAAACACCGAAAATTTTCA
54546824 AAA
1 AAA
54546827 CAAGAGGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.55, C:0.15, G:0.05, T:0.25
Consensus pattern (19 bp):
AAAACACCGAAAATTTTCA
Found at i:54546919 original size:17 final size:17
Alignment explanation
Indices: 54546781--54546918 Score: 127
Period size: 17 Copynumber: 8.0 Consensus size: 17
54546771 GAGATTTTTT
54546781 TTTTTGAAAACACGAAAA
1 TTTTTG-AAACACGAAAA
** *
54546799 TTTTCAAAAACACCGAAAT
1 TTTT-TGAAACA-CGAAAA
* * **
54546818 TTTTTAAAACAAGAGGA
1 TTTTTGAAACACGAAAA
* *
54546835 TTTTTGAAATATGAAAA
1 TTTTTGAAACACGAAAA
*
54546852 ATTTTGAAAACACGAAAA
1 TTTTTG-AAACACGAAAA
*
54546870 TTTTTGAAACACGGAAA
1 TTTTTGAAACACGAAAA
54546887 TTTTTGAAA-ACGAAAA
1 TTTTTGAAACACGAAAA
54546903 TTTTTGAAACAC-AAAA
1 TTTTTGAAACACGAAAA
54546919 AGACCAAGAG
Statistics
Matches: 97, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
16 19 0.20
17 40 0.41
18 29 0.30
19 9 0.09
ACGTcount: A:0.49, C:0.10, G:0.12, T:0.30
Consensus pattern (17 bp):
TTTTTGAAACACGAAAA
Found at i:54547251 original size:20 final size:18
Alignment explanation
Indices: 54547235--54547286 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 18
54547225 TTATTTTGTG
54547235 CTTTTTTTTTTCTTTTTT
1 CTTTTTTTTTTCTTTTTT
* *
54547253 CCTTTTTTCTTCTTTTTCTT
1 CTTTTTTTTTTC-TTTT-TT
54547273 CCTTTTTTTTTTCT
1 -CTTTTTTTTTTCT
54547287 ACTGGGCTGC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
18 10 0.37
19 4 0.15
20 3 0.11
21 10 0.37
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (18 bp):
CTTTTTTTTTTCTTTTTT
Found at i:54547796 original size:29 final size:29
Alignment explanation
Indices: 54547763--54547879 Score: 94
Period size: 30 Copynumber: 3.9 Consensus size: 29
54547753 TGTAATTTTT
*
54547763 AGAAAATTTAGGATTAAAATGAAATTTAA
1 AGAAAATTTAGGGTTAAAATGAAATTTAA
* * *
54547792 TGAAAGTTTAGGGGTCT-AAGTGAAATTTAA
1 AGAAAATTTA-GGGT-TAAAATGAAATTTAA
* *
54547822 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAATTT-AGGGTTAAAATGAAATTTAA
* * *
54547851 GGAAAAGTTTAGGGGTCAAAATGCAATTT
1 AGAAAA-TTTA-GGGTTAAAATGAAATTT
54547880 TTATTTTTTT
Statistics
Matches: 72, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
29 14 0.19
30 56 0.78
31 2 0.03
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.30
Consensus pattern (29 bp):
AGAAAATTTAGGGTTAAAATGAAATTTAA
Found at i:54547818 original size:30 final size:30
Alignment explanation
Indices: 54547778--54547879 Score: 134
Period size: 30 Copynumber: 3.4 Consensus size: 30
54547768 ATTTAGGATT
*
54547778 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* * *
54547808 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
*
54547838 AAAATGAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAGGGGTC
*
54547868 AAAATGCAATTT
1 AAAATGAAATTT
54547880 TTATTTTTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 2 0.03
30 60 0.97
ACGTcount: A:0.44, C:0.04, G:0.23, T:0.29
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Found at i:54548344 original size:54 final size:55
Alignment explanation
Indices: 54548156--54548373 Score: 299
Period size: 54 Copynumber: 4.1 Consensus size: 55
54548146 CACGTGAGCC
* *
54548156 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTG-AAAACAGAATTTGCAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTG-AA
*
54548211 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATAGAAAATT---
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAG-AAATTGAA
* *
54548265 ---GCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATT-AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
*
54548316 AAGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
54548371 AAG
1 AAG
54548374 TAGAAATTGA
Statistics
Matches: 147, Mismatches: 7, Indels: 18
0.85 0.04 0.10
Matches are distributed among these distances:
49 5 0.03
50 14 0.10
51 29 0.20
54 46 0.31
55 37 0.25
56 6 0.04
57 6 0.04
58 4 0.03
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (55 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
Found at i:54548352 original size:105 final size:104
Alignment explanation
Indices: 54548159--54548365 Score: 326
Period size: 105 Copynumber: 2.0 Consensus size: 104
54548149 GTGAGCCAAG
* *
54548159 GCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAACAGAATTTGCAAAAGGCTCAACTCA
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATT-CAAAAGGCTCAACTCA
*
54548224 CCTCTCGCAATATGAGTTGATTTTTTGAAAAATAGAAAATT
65 CCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAAATT
* *
54548265 GCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATT-AAAAGGCTCAACTCA
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAACAGAAATTCAAAAGGCTCAACTCA
*
54548329 CCTTTCGCAATATGAGTTGATTTTTGAAAAACAGAAA
65 CCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA
54548366 TTGAAAAGTA
Statistics
Matches: 94, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
104 16 0.17
105 34 0.36
106 34 0.36
107 10 0.11
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (104 bp):
GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTCAAAAGGCTCAACTCAC
CTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAAATT
Found at i:54548371 original size:14 final size:14
Alignment explanation
Indices: 54548352--54548386 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
54548342 GAGTTGATTT
54548352 TTGAAAAACAGAAA
1 TTGAAAAACAGAAA
**
54548366 TTGAAAAGTAGAAA
1 TTGAAAAACAGAAA
54548380 TTGAAAA
1 TTGAAAA
54548387 TACCTCAGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.60, C:0.03, G:0.17, T:0.20
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:54548480 original size:13 final size:14
Alignment explanation
Indices: 54548452--54548484 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
54548442 TTTTTGAAAC
54548452 ACAGAAATTAAAAA
1 ACAGAAATTAAAAA
54548466 ACAGAAATT-AAAA
1 ACAGAAATTAAAAA
54548479 ACAGAA
1 ACAGAA
54548485 TTTGAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.70, C:0.09, G:0.09, T:0.12
Consensus pattern (14 bp):
ACAGAAATTAAAAA
Found at i:54548492 original size:14 final size:14
Alignment explanation
Indices: 54548445--54548492 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
54548435 ATTTTTTTTT
*
54548445 TTGAAACACAGAAA
1 TTGAAAAACAGAAA
*
54548459 TTAAAAAACAGAAA
1 TTGAAAAACAGAAA
*
54548473 TT-AAAAACAGAAT
1 TTGAAAAACAGAAA
54548486 TTGAAAA
1 TTGAAAA
54548493 GACCTCAGCG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
13 12 0.40
14 18 0.60
ACGTcount: A:0.62, C:0.08, G:0.10, T:0.19
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:54562626 original size:17 final size:17
Alignment explanation
Indices: 54562417--54562863 Score: 181
Period size: 17 Copynumber: 25.1 Consensus size: 17
54562407 CGGAAATTTT
* *
54562417 TTTTTAAAATACGAGAA
1 TTTTTAAAACACGAAAA
*
54562434 TTTTTGAAAACACGAGAA
1 TTTTT-AAAACACGAAAA
* *
54562452 TTTGT-AAACACGAATA
1 TTTTTAAAACACGAAAA
54562468 -TTTTAGAAACACGAAAA
1 TTTTTA-AAACACGAAAA
* *
54562485 TTTTTGGAAAAAAACGAAAT
1 TTTTT---AAAACACGAAAA
**
54562505 TTTCTTAAAACACGACATTTT
1 TTT-TTAAAACACGA-A--AA
* **
54562526 TTTTTGAAACACGGGAA
1 TTTTTAAAACACGAAAA
* **
54562543 TTTTTAAAACAAGACATT
1 TTTTTAAAACACGA-AAA
* *
54562561 TTTTTGAAACA--AAATTT
1 TTTTTAAAACACGAAA--A
54562578 TTTTTAAAA-A--AAAA
1 TTTTTAAAACACGAAAA
* * *
54562592 ATTTT-AAATACGAGAA
1 TTTTTAAAACACGAAAA
54562608 TTTTTAAAACACGAAAA
1 TTTTTAAAACACGAAAA
54562625 TTTTTAAAACACGGAAAA
1 TTTTTAAAACAC-GAAAA
*
54562643 TTTTTTTTTTAAAACACGAAATTTT
1 -----TTTTTAAAACACGAAA---A
*
54562668 TTTTTGAAAACAAGAAAA
1 TTTTT-AAAACACGAAAA
* * *
54562686 TTTTTGAAACACTAGAA
1 TTTTTAAAACACGAAAA
* *
54562703 TTTTGAAAACACGAAGA
1 TTTTTAAAACACGAAAA
* * *
54562720 TTTTTGAAACATGAGAA
1 TTTTTAAAACACGAAAA
**
54562737 TTTTTAAAAGCACGAGGA
1 TTTTTAAAA-CACGAAAA
* * *
54562755 TTATTGAAAGCACGAAGA
1 TT-TTTAAAACACGAAAA
* * *
54562773 TTTATAAAAAACGACAA
1 TTTTTAAAACACGAAAA
* *
54562790 TTTTTGAAATACGAGAAA
1 TTTTTAAAACACGA-AAA
* *
54562808 TTTTTTAAACGCGAAAA
1 TTTTTAAAACACGAAAA
*
54562825 TTTTTTTCAAACACGAAAA
1 --TTTTTAAAACACGAAAA
* *
54562844 CTTTTGAAAACGCGAAAA
1 -TTTTTAAAACACGAAAA
54562862 TT
1 TT
54562864 CGAAAATTTC
Statistics
Matches: 325, Mismatches: 72, Indels: 66
0.70 0.16 0.14
Matches are distributed among these distances:
13 3 0.01
14 5 0.02
15 4 0.01
16 21 0.06
17 121 0.37
18 91 0.28
19 21 0.06
20 26 0.08
21 17 0.05
22 4 0.01
23 12 0.04
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (17 bp):
TTTTTAAAACACGAAAA
Found at i:54562664 original size:21 final size:21
Alignment explanation
Indices: 54562625--54562690 Score: 87
Period size: 21 Copynumber: 3.0 Consensus size: 21
54562615 AACACGAAAA
54562625 TTTTTAAAACACGGAAAATTTTT
1 TTTTTAAAACAC-G-AAATTTTT
54562648 TTTTTAAAACACGAAATTTTT
1 TTTTTAAAACACGAAATTTTT
* * *
54562669 TTTTGAAAACAAGAAAATTTT
1 TTTTTAAAACACGAAATTTTT
54562690 T
1 T
54562691 GAAACACTAG
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
21 27 0.68
22 1 0.03
23 12 0.30
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.44
Consensus pattern (21 bp):
TTTTTAAAACACGAAATTTTT
Found at i:54562830 original size:19 final size:19
Alignment explanation
Indices: 54562808--54562863 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 19
54562798 ATACGAGAAA
54562808 TTTTTT-AAACGCGAAAAT
1 TTTTTTAAAACGCGAAAAT
* *
54562826 TTTTTTCAAACACGAAAA-
1 TTTTTTAAAACGCGAAAAT
* *
54562844 CTTTTGAAAACGCGAAAAT
1 TTTTTTAAAACGCGAAAAT
54562863 T
1 T
54562864 CGAAAATTTC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 20 0.67
19 10 0.33
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (19 bp):
TTTTTTAAAACGCGAAAAT
Found at i:54562907 original size:18 final size:17
Alignment explanation
Indices: 54562858--54562908 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
54562848 TGAAAACGCG
54562858 AAAATTCGAAAATTTCT
1 AAAATTCGAAAATTTCT
* * *
54562875 AAAATACGAGTAATTTTT
1 AAAATTCGA-AAATTTCT
54562893 AAAGATTCGAAAATTT
1 AAA-ATTCGAAAATTT
54562909 GAAACAAGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
17 8 0.30
18 14 0.52
19 5 0.19
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.35
Consensus pattern (17 bp):
AAAATTCGAAAATTTCT
Found at i:54563431 original size:15 final size:15
Alignment explanation
Indices: 54563413--54563482 Score: 88
Period size: 15 Copynumber: 4.7 Consensus size: 15
54563403 CTTTTTCTTC
*
54563413 CTTTTTTTTTTTTTT
1 CTTTTTTTCTTTTTT
*
54563428 CTTTTTTCCTTTTTT
1 CTTTTTTTCTTTTTT
54563443 CTTTTTTTCTTTTTT
1 CTTTTTTTCTTTTTT
**
54563458 CTTCTTTTTCTTCCTT
1 CTT-TTTTTCTTTTTT
54563474 -TTTTTTTCT
1 CTTTTTTTCT
54563483 GCTGGGCTGC
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
14 7 0.14
15 32 0.65
16 10 0.20
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
CTTTTTTTCTTTTTT
Found at i:54563438 original size:23 final size:23
Alignment explanation
Indices: 54563405--54563466 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
54563395 TGAACCCCCT
54563405 TTTTCTTCCTTTTTTTTTTTTTTC
1 TTTT-TTCCTTTTTTTTTTTTTTC
*
54563429 TTTTTTCCTTTTTTCTTTTTTTC
1 TTTTTTCCTTTTTTTTTTTTTTC
*
54563452 TTTTTT-CTTCTTTTT
1 TTTTTTCCTTTTTTTT
54563467 CTTCCTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 7 0.20
23 24 0.69
24 4 0.11
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (23 bp):
TTTTTTCCTTTTTTTTTTTTTTC
Found at i:54563467 original size:16 final size:16
Alignment explanation
Indices: 54563404--54563469 Score: 82
Period size: 16 Copynumber: 4.1 Consensus size: 16
54563394 TTGAACCCCC
54563404 TTTTTCTTCCTTTTT-T
1 TTTTTCTT-CTTTTTCT
*
54563420 TTTTTTTTCTTTTTTCCT
1 TTTTTCTTC-TTTTT-CT
54563438 TTTTTCTT-TTTTTCT
1 TTTTTCTTCTTTTTCT
54563453 TTTTTCTTCTTTTTCT
1 TTTTTCTTCTTTTTCT
54563469 T
1 T
54563470 CCTTTTTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
15 11 0.25
16 25 0.57
18 8 0.18
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTCTTCTTTTTCT
Found at i:54563478 original size:23 final size:23
Alignment explanation
Indices: 54563425--54563482 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
54563415 TTTTTTTTTT
* **
54563425 TTTCTTTTTTCCTTTTTTCTTTT
1 TTTCTTTTTTCTTTTTTTCTTCC
54563448 TTTCTTTTTTCTTCTTTTTCTTCC
1 TTTCTTTTTTCTT-TTTTTCTTCC
54563472 TTT-TTTTTTCT
1 TTTCTTTTTTCT
54563483 GCTGGGCTGC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 20 0.65
24 11 0.35
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (23 bp):
TTTCTTTTTTCTTTTTTTCTTCC
Found at i:54563767 original size:3 final size:3
Alignment explanation
Indices: 54563761--54563819 Score: 73
Period size: 3 Copynumber: 18.0 Consensus size: 3
54563751 TTTTTTTTTT
54563761 TTC TTC TTTC TTC TTC TCTC TTTC TTTC TTC TTC TTC TTC TTCC TTC
1 TTC TTC -TTC TTC TTC T-TC -TTC -TTC TTC TTC TTC TTC TT-C TTC
54563808 TTC TTC TTC TTC
1 TTC TTC TTC TTC
54563820 AAAACCGAGC
Statistics
Matches: 52, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
3 37 0.71
4 14 0.27
5 1 0.02
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:54563774 original size:10 final size:10
Alignment explanation
Indices: 54563761--54563819 Score: 72
Period size: 10 Copynumber: 6.3 Consensus size: 10
54563751 TTTTTTTTTT
54563761 TTCTTCTTTC
1 TTCTTCTTTC
*
54563771 TTCTTCTCTC
1 TTCTTCTTTC
54563781 -T-TTCTTTC
1 TTCTTCTTTC
54563789 TTCTTC-TTC
1 TTCTTCTTTC
*
54563798 TTCTTCCTTC
1 TTCTTCTTTC
54563808 TTCTTC-TTC
1 TTCTTCTTTC
54563817 TTC
1 TTC
54563820 AAAACCGAGC
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
8 6 0.14
9 17 0.39
10 21 0.48
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (10 bp):
TTCTTCTTTC
Found at i:54564207 original size:29 final size:29
Alignment explanation
Indices: 54564174--54564290 Score: 94
Period size: 30 Copynumber: 3.9 Consensus size: 29
54564164 TATAATTTTT
*
54564174 AGAAAATTTAGGATTAAAATGAAATTTAA
1 AGAAAATTTAGGGTTAAAATGAAATTTAA
* * *
54564203 TGAAAGTTTAGGGGTCT-AAGTGAAATTTAA
1 AGAAAATTTA-GGGT-TAAAATGAAATTTAA
* *
54564233 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAATTT-AGGGTTAAAATGAAATTTAA
* * *
54564262 GGAAAAGTTTAGGGGTCAAAATGCAATTT
1 AGAAAA-TTTA-GGGTTAAAATGAAATTT
54564291 TTATTTTTTA
Statistics
Matches: 72, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
29 14 0.19
30 56 0.78
31 2 0.03
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.30
Consensus pattern (29 bp):
AGAAAATTTAGGGTTAAAATGAAATTTAA
Found at i:54564229 original size:30 final size:30
Alignment explanation
Indices: 54564189--54564290 Score: 134
Period size: 30 Copynumber: 3.4 Consensus size: 30
54564179 ATTTAGGATT
*
54564189 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* * *
54564219 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
*
54564249 AAAATGAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAGGGGTC
*
54564279 AAAATGCAATTT
1 AAAATGAAATTT
54564291 TTATTTTTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 2 0.03
30 60 0.97
ACGTcount: A:0.44, C:0.04, G:0.23, T:0.29
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Found at i:54569058 original size:6 final size:6
Alignment explanation
Indices: 54569047--54569074 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
54569037 GCGTATAATA
54569047 GCAGAT GCAGAT GCAGAT GCAGAT GCAG
1 GCAGAT GCAGAT GCAGAT GCAGAT GCAG
54569075 TGTAGTGGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.18, G:0.36, T:0.14
Consensus pattern (6 bp):
GCAGAT
Found at i:54579506 original size:30 final size:30
Alignment explanation
Indices: 54579470--54579560 Score: 164
Period size: 30 Copynumber: 3.0 Consensus size: 30
54579460 TAAGGAGGTA
54579470 TGATACATTTGGGACAATTCAACTAGAGAC
1 TGATACATTTGGGACAATTCAACTAGAGAC
*
54579500 TGATACATTTGGAACAATTCAACTAGAGAC
1 TGATACATTTGGGACAATTCAACTAGAGAC
*
54579530 TGATACATTTGAGACAATTCAACTAGAGAC
1 TGATACATTTGGGACAATTCAACTAGAGAC
54579560 T
1 T
54579561 TGTTACAAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 58 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.27
Consensus pattern (30 bp):
TGATACATTTGGGACAATTCAACTAGAGAC
Found at i:54584708 original size:47 final size:48
Alignment explanation
Indices: 54584655--54584745 Score: 130
Period size: 47 Copynumber: 1.9 Consensus size: 48
54584645 ACATAGGGCA
**
54584655 TAATGTCGATACTATGTCTTAGACAT-GTCTTACACTAGCTCTCGTCT
1 TAATGTCGATACTATGTCCCAGACATGGTCTTACACTAGCTCTCGTCT
* * *
54584702 TAATGTCGATGCTATGTCCCAGACATGGTCTTTCACTGGCTCTC
1 TAATGTCGATACTATGTCCCAGACATGGTCTTACACTAGCTCTC
54584746 ATAATGTGGC
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
47 23 0.61
48 15 0.39
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (48 bp):
TAATGTCGATACTATGTCCCAGACATGGTCTTACACTAGCTCTCGTCT
Found at i:54590590 original size:18 final size:19
Alignment explanation
Indices: 54590546--54590590 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
54590536 ATTTAAAATT
54590546 TTAT-AAATTTTTAAAACA
1 TTATCAAATTTTTAAAACA
*
54590564 TTATTAAATTTTATAAAA-A
1 TTATCAAATTTT-TAAAACA
54590583 -TATCAAAT
1 TTATCAAAT
54590591 AAATTTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 11 0.46
19 8 0.33
20 5 0.21
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (19 bp):
TTATCAAATTTTTAAAACA
Found at i:54590621 original size:20 final size:20
Alignment explanation
Indices: 54590578--54590624 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
54590568 TAAATTTTAT
* * **
54590578 AAAAATATCAAATAAATTTC
1 AAAAATTTCAAAAAAATTAA
54590598 AAAAATTTCAAAAAAATTAA
1 AAAAATTTCAAAAAAATTAA
54590618 AAAAATT
1 AAAAATT
54590625 AATTTAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAAATTTCAAAAAAATTAA
Found at i:54596873 original size:46 final size:45
Alignment explanation
Indices: 54596767--54596925 Score: 203
Period size: 46 Copynumber: 3.7 Consensus size: 45
54596757 CATATGACCT
*
54596767 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
54596810 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
*
54596856 CTTATCACTTTATCACTTGATCAGATAA--GT-G-T-AG---CCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
54596893 CTTATCACTTTGTCTCTTGATCAGATAAGTGTA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTA
54596926 ACCACTTATC
Statistics
Matches: 104, Mismatches: 6, Indels: 15
0.83 0.05 0.12
Matches are distributed among these distances:
37 29 0.28
39 2 0.02
40 2 0.02
42 1 0.01
43 9 0.09
44 6 0.06
45 21 0.20
46 34 0.33
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (45 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
Found at i:54596894 original size:37 final size:37
Alignment explanation
Indices: 54596852--54596954 Score: 170
Period size: 37 Copynumber: 2.8 Consensus size: 37
54596842 AGCTGAAGCT
* *
54596852 ACCACTTATCACTTTATCACTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
*
54596889 GCCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
*
54596926 ACCACTTATCACTTTGTTTCTTGATCAGA
1 ACCACTTATCACTTTGTCTCTTGATCAGA
54596955 AGTACTCAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (37 bp):
ACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
Found at i:54600151 original size:114 final size:114
Alignment explanation
Indices: 54599951--54600182 Score: 367
Period size: 114 Copynumber: 2.0 Consensus size: 114
54599941 AAATTAGAAT
* * * *
54599951 TGTAGACGACATAATAATCCTTCTCAGTATTTAAATCAAATGCTCACTTTGATTTTTTTGCGGGA
1 TGTAGACGACATAATAATCCTTCTCAATATTTAAATCAAATGCTCAATTTGATTCTTTTGCGAGA
* *
54600016 CTATAGACTTATTTAGATTATCTTCTA-AAGTATGTTGTCTTTATTGCAA
66 CTACAGACTTATTTAGATTATCTTC-AGAAGTATGTTGTCTTTATCGCAA
*
54600065 TGTAGACGACATAATAATCCTTCTCAATATTTGAATCAAATGCTCAATTTGATTCTTTTGCGAGA
1 TGTAGACGACATAATAATCCTTCTCAATATTTAAATCAAATGCTCAATTTGATTCTTTTGCGAGA
* *
54600130 GTACGGACTTATTTAGATTATCTTCAGAAGTATGTTGTCTTTATCGCAA
66 CTACAGACTTATTTAGATTATCTTCAGAAGTATGTTGTCTTTATCGCAA
54600179 TGTA
1 TGTA
54600183 AACGTTCCTA
Statistics
Matches: 108, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
113 1 0.01
114 107 0.99
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (114 bp):
TGTAGACGACATAATAATCCTTCTCAATATTTAAATCAAATGCTCAATTTGATTCTTTTGCGAGA
CTACAGACTTATTTAGATTATCTTCAGAAGTATGTTGTCTTTATCGCAA
Found at i:54606950 original size:21 final size:21
Alignment explanation
Indices: 54606924--54606993 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
54606914 CTATCATTGA
*
54606924 TTAATAAGTAAATCTAAAACC
1 TTAATAAGTAAATCTAGAACC
*
54606945 TTAATAA-AACAATGCT-GAA-C
1 TTAATAAGTA-AAT-CTAGAACC
**
54606965 AAAATAAGTAAATCTAGAACC
1 TTAATAAGTAAATCTAGAACC
54606986 TTAATAAG
1 TTAATAAG
54606994 ACAATGCTAA
Statistics
Matches: 37, Mismatches: 7, Indels: 10
0.69 0.13 0.19
Matches are distributed among these distances:
19 2 0.05
20 13 0.35
21 20 0.54
22 2 0.05
ACGTcount: A:0.53, C:0.13, G:0.09, T:0.26
Consensus pattern (21 bp):
TTAATAAGTAAATCTAGAACC
Found at i:54610293 original size:24 final size:26
Alignment explanation
Indices: 54610266--54610315 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
54610256 AAATGTATGT
54610266 ACATAACAT-ATATG-AAAAATATAA
1 ACATAACATAATATGTAAAAATATAA
* *
54610290 ACATGATATAATATGTAAAAATATAA
1 ACATAACATAATATGTAAAAATATAA
54610316 TATAGTATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
25 5 0.23
26 10 0.45
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.28
Consensus pattern (26 bp):
ACATAACATAATATGTAAAAATATAA
Found at i:54610510 original size:3 final size:3
Alignment explanation
Indices: 54610502--54610802 Score: 77
Period size: 3 Copynumber: 100.7 Consensus size: 3
54610492 AAATAACGAC
* *
54610502 TAA TAA TAA TAA TAA TAT TAGA -AA TAA TAA TGA -AA TATA TAA -AA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TA-A TAA TAA
* * * *
54610546 -AA GAA -AA T-A TAA T-A TAA TAG TAA TAT TAA -AA TAA -AG TAA TTAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
* *
54610589 -AA TAG TAC T-A TATA TAA -ATA TATA TACA TACA TATA TAA T-A TACA
1 TAA TAA TAA TAA TA-A TAA TA-A TA-A TA-A TA-A TA-A TAA TAA TA-A
* *
54610634 TACA CTAA TAT TAA TAA TAA TAA TAA -AA CTAGA -AA TAA TAA TAA TTAG
1 TA-A -TAA TAA TAA TAA TAA TAA TAA TAA -TA-A TAA TAA TAA TAA -TAA
* * * ** *
54610682 TAA TAA TAA TACG TTA GAA -AA TAA TTAA T-A TGT TAA TAA AAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA
* * * *
54610727 TAG TAA TGAA -AA TAA TAC TAA CAG TAA TAA TAA -AGA TAA TAA TAGA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TA-A
* *
54610773 -AA TAA -AA TAA TAG TAA TAA TAT TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
54610803 TGTAAAAAAA
Statistics
Matches: 222, Mismatches: 41, Indels: 70
0.67 0.12 0.21
Matches are distributed among these distances:
2 34 0.15
3 144 0.65
4 41 0.18
5 3 0.01
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:54610632 original size:17 final size:16
Alignment explanation
Indices: 54610606--54610637 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
54610596 CTATATATAA
54610606 ATATATATACATACAT
1 ATATATATACATACAT
54610622 ATATAATATACATACA
1 ATAT-ATATACATACA
54610638 CTAATATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (16 bp):
ATATATATACATACAT
Found at i:54616052 original size:19 final size:20
Alignment explanation
Indices: 54616024--54616062 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
54616014 TCCCATTATT
54616024 TATTTATTTTT-TGTTTTAA
1 TATTTATTTTTATGTTTTAA
*
54616043 TATTTGTTTTTATGTTTTAA
1 TATTTATTTTTATGTTTTAA
54616063 ATGTATTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.72
Consensus pattern (20 bp):
TATTTATTTTTATGTTTTAA
Found at i:54616080 original size:25 final size:23
Alignment explanation
Indices: 54616043--54616088 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
54616033 TTTGTTTTAA
*
54616043 TATTTGTTTTTATGTTTTAAATG
1 TATTTGTTTTTATATTTTAAATG
54616066 TATTTGATTTATTATATTTTAAA
1 TATTTG-TTT-TTATATTTTAAA
54616089 GTTTTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 3 0.15
25 11 0.55
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (23 bp):
TATTTGTTTTTATATTTTAAATG
Found at i:54622458 original size:21 final size:21
Alignment explanation
Indices: 54622434--54622473 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
54622424 TGCAGATGTA
54622434 ATATATA-ATTAAAATTATATT
1 ATATATATATT-AAATTATATT
*
54622455 ATATTTATATTAAATTATA
1 ATATATATATTAAATTATA
54622474 AAAAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATATATATATTAAATTATATT
Found at i:54627414 original size:49 final size:49
Alignment explanation
Indices: 54627353--54627458 Score: 126
Period size: 49 Copynumber: 2.2 Consensus size: 49
54627343 CCATACAACG
* * * * *
54627353 GGAAGCTTATCCGGGCTGTATAATGGGAAGCTTAT-AAGAGCCA-TATTCA
1 GGAAGCTCATCCGAGCT-AATAACGGGAAGCTT-TGAAGAGCCATTAATCA
*
54627402 GGAAGCTCATCCGAGCTAATAACGGGTAGCTTTGAAGAGCCATTAATCA
1 GGAAGCTCATCCGAGCTAATAACGGGAAGCTTTGAAGAGCCATTAATCA
54627451 GGAAGCTC
1 GGAAGCTC
54627459 CATCTAGCCA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
47 1 0.02
48 20 0.41
49 28 0.57
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (49 bp):
GGAAGCTCATCCGAGCTAATAACGGGAAGCTTTGAAGAGCCATTAATCA
Found at i:54632201 original size:30 final size:30
Alignment explanation
Indices: 54632167--54632232 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 30
54632157 TACTCATACA
**
54632167 AGTCCACAG-ATTTCATTTATTTCACATTTT
1 AGTCCACAGAATTT-ATAAATTTCACATTTT
*
54632197 AGTCC-CTGAATTTATAAATTTCACATTTT
1 AGTCCACAGAATTTATAAATTTCACATTTT
*
54632226 AGCCCAC
1 AGTCCAC
54632233 TTTACTCAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
29 20 0.67
30 10 0.33
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.41
Consensus pattern (30 bp):
AGTCCACAGAATTTATAAATTTCACATTTT
Found at i:54635278 original size:12 final size:10
Alignment explanation
Indices: 54635249--54635277 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
54635239 CCATATAGAT
54635249 AATCATATAG
1 AATCATATAG
54635259 AATCATATAG
1 AATCATATAG
54635269 AATCATATA
1 AATCATATA
54635278 TATATACTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.52, C:0.10, G:0.07, T:0.31
Consensus pattern (10 bp):
AATCATATAG
Found at i:54637843 original size:378 final size:377
Alignment explanation
Indices: 54637149--54637907 Score: 1322
Period size: 378 Copynumber: 2.0 Consensus size: 377
54637139 AGAGAAAAAG
54637149 TACCAATAATAACACCAGGTGCAGTAGCATCCTCACATGCACGAATAGCATATGTTCTGACTGGT
1 TACCAATAATAACACCAGGTGCAGTAGCATCCTCACATGCACGAATAGCATATGTTCTGACTGGT
*
54637214 GCCCGTGCTTCAGATCTAATAGTTGAATCTGTTGTCGTACCCCAGCTACCATCACATTTCCGGGA
66 GCCCGTGCTTCAGATCTAATAGTTGAATCTGTTGTCATACCCCAGCTACCATCACATTTCCGGGA
*
54637279 TTACGAGGTGGTCTACCTTTCGTGGTAGGATTGCTTGGCCTTGAAGTTTGAACAGTTTCTTTCTC
131 TTACGAGGTGGTCTACCTTTCATGGTAGGATTGCTTGGCCTTGAAGTTTGAACAGTTTCTTTCTC
*
54637344 AAGCTTTTCTGGGCAATCTCTCAAATAGTGGTCAAAGGAACCACATCTAAAGCAAGCTCTACTTT
196 AAGCTTTTCTGGGCAATATCTCAAATAGTGGTCAAAGGAACCACATCTAAAGCAAGCTCTACTTT
54637409 TCATGCCACACTCTCCAAAATGAAGTTTATTACAGTGCTTGCATATGGGTTTGGTATTTCTAACA
261 TCATGCCACACTCTCCAAAATGAAGTTTATTACAGTGCTTGCATATGGGTTTGGTATTTCTAACA
*
54637474 CTGTTCGCACTTACTACAGATGTAGCCTGAGATCTTAAACTGGAACGTTGAA
326 CTGTCCGCACTTACTACAGATGTAGCCTGAGATCTTAAACTGGAACGTTGAA
* * *
54637526 TACCAATAATAACACCAGGTGCAGTAGCATTCTCACGTGCATGAATAGCATATGTTCT-AGCTGG
1 TACCAATAATAACACCAGGTGCAGTAGCATCCTCACATGCACGAATAGCATATGTTCTGA-CTGG
* * * * *
54637590 TGCTCGTGCTTTAGATCTAATAGTTGAATCTTTTGTCATACCCCGGCTACCACTCACATTTTCGG
65 TGCCCGTGCTTCAGATCTAATAGTTGAATCTGTTGTCATACCCCAGCTACCA-TCACATTTCCGG
* *
54637655 GATTACGAGGTGGTCTACCTTTCATGGTGGGATTGCTTGGCCTTGAAGTTTGAACAGTTTTTTTC
129 GATTACGAGGTGGTCTACCTTTCATGGTAGGATTGCTTGGCCTTGAAGTTTGAACAGTTTCTTTC
*
54637720 TCAAGCTTTTCTGGGCAATATCTCAAATAGTGGTCAAAGGAACCACATCTAAAGCAAGCTCTTCT
194 TCAAGCTTTTCTGGGCAATATCTCAAATAGTGGTCAAAGGAACCACATCTAAAGCAAGCTCTACT
**
54637785 TTTCATGCGGCACTCTCCAAAATGAAGTTTATTACAGTGCTTGCATATGGGTTTGGTATTTCTAA
259 TTTCATGCCACACTCTCCAAAATGAAGTTTATTACAGTGCTTGCATATGGGTTTGGTATTTCTAA
* *
54637850 CACTGTCCGCACTTACTACAGATGTAGCCTGAGATCTTGAACTGGAATGTTGAA
324 CACTGTCCGCACTTACTACAGATGTAGCCTGAGATCTTAAACTGGAACGTTGAA
54637904 TACC
1 TACC
54637908 TCTAAGTCTC
Statistics
Matches: 361, Mismatches: 19, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
376 1 0.00
377 106 0.29
378 254 0.70
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (377 bp):
TACCAATAATAACACCAGGTGCAGTAGCATCCTCACATGCACGAATAGCATATGTTCTGACTGGT
GCCCGTGCTTCAGATCTAATAGTTGAATCTGTTGTCATACCCCAGCTACCATCACATTTCCGGGA
TTACGAGGTGGTCTACCTTTCATGGTAGGATTGCTTGGCCTTGAAGTTTGAACAGTTTCTTTCTC
AAGCTTTTCTGGGCAATATCTCAAATAGTGGTCAAAGGAACCACATCTAAAGCAAGCTCTACTTT
TCATGCCACACTCTCCAAAATGAAGTTTATTACAGTGCTTGCATATGGGTTTGGTATTTCTAACA
CTGTCCGCACTTACTACAGATGTAGCCTGAGATCTTAAACTGGAACGTTGAA
Found at i:54638682 original size:27 final size:28
Alignment explanation
Indices: 54638652--54638708 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
54638642 ATTTTTGATG
54638652 AAATGAGCTATTTG-GG-CTAATTTGTGA
1 AAATGAGCT-TTTGAGGACTAATTTGTGA
*
54638679 AAATGAGGTTTTGAAGGACTAATTTGTGA
1 AAATGAGCTTTTG-AGGACTAATTTGTGA
54638708 A
1 A
54638709 TTTAACATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 4 0.15
27 8 0.31
28 2 0.08
29 12 0.46
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.35
Consensus pattern (28 bp):
AAATGAGCTTTTGAGGACTAATTTGTGA
Found at i:54639813 original size:12 final size:13
Alignment explanation
Indices: 54639796--54639827 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
54639786 GCAAATGTTG
54639796 AGTTTTG-TGCAT
1 AGTTTTGATGCAT
54639808 AGTTTTGATGCAT
1 AGTTTTGATGCAT
54639821 -GTTTTGA
1 AGTTTTGA
54639828 AATGTGCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.19, C:0.06, G:0.25, T:0.50
Consensus pattern (13 bp):
AGTTTTGATGCAT
Found at i:54642689 original size:29 final size:29
Alignment explanation
Indices: 54642626--54642693 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
54642616 TAATCAACCG
54642626 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
54642655 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
54642684 CGCACACTTA
1 CGCACACTTA
54642694 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:54642805 original size:174 final size:174
Alignment explanation
Indices: 54642515--54642842 Score: 629
Period size: 174 Copynumber: 1.9 Consensus size: 174
54642505 AACTCAAGGT
*
54642515 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
54642580 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
54642645 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
54642689 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
54642754 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
*
54642819 ACTTTAAACTCGCACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
54642843 TGTACAATTT
Statistics
Matches: 151, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
174 151 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:54642834 original size:29 final size:30
Alignment explanation
Indices: 54642795--54642873 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
54642785 CTTAATAATC
54642795 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
54642825 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
54642854 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
54642874 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:54649248 original size:93 final size:93
Alignment explanation
Indices: 54649141--54649311 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
54649131 GCCCCTAAGT
* *
54649141 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
54649206 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
54649234 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
54649299 CGAGTTCGGATGC
66 CGAGTTCGGATGC
54649312 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:54649308 original size:46 final size:46
Alignment explanation
Indices: 54649136--54649308 Score: 219
Period size: 46 Copynumber: 3.7 Consensus size: 46
54649126 AACCCGCCCC
* * *
54649136 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
*
54649182 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
54649230 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
54649275 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
54649309 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 61 0.56
47 29 0.27
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:54649765 original size:30 final size:30
Alignment explanation
Indices: 54649731--54649790 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
54649721 ATTTAATACG
54649731 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
54649761 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
54649791 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:54651488 original size:22 final size:20
Alignment explanation
Indices: 54651453--54651496 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
54651443 CAATTTTTGT
54651453 AAATAACAATTAC-ACAATTC
1 AAATAACAATTACAAC-ATTC
54651473 AAATATACAACTTACAACATTC
1 AAATA-ACAA-TTACAACATTC
54651495 AA
1 AA
54651497 TTCAAACATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 5 0.24
21 4 0.19
22 10 0.48
23 2 0.10
ACGTcount: A:0.55, C:0.20, G:0.00, T:0.25
Consensus pattern (20 bp):
AAATAACAATTACAACATTC
Found at i:54655734 original size:41 final size:41
Alignment explanation
Indices: 54655677--54655861 Score: 271
Period size: 41 Copynumber: 4.5 Consensus size: 41
54655667 GGCTTTACCG
**
54655677 GCGTTTTTATAAAAGCGCCGCTAATGCTCTGGTCTTTAGCA
1 GCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGTCTTTAGCA
* *
54655718 GCGTTTTTGGAGAAGCGCCGCTAATGCTCTGGTCTTTAGCG
1 GCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGTCTTTAGCA
* * * * *
54655759 GCATTTCTGGAAAAGTGCCGCTAAAGCTCAGGTCTTTAGCA
1 GCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGTCTTTAGCA
*
54655800 GCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGTCTTTAGCG
1 GCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGTCTTTAGCA
*
54655841 GCGTTTTTTGAAAAGCGCCGC
1 GCGTTTTTGGAAAAGCGCCGC
54655862 AAAAACATTT
Statistics
Matches: 126, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 126 1.00
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (41 bp):
GCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGTCTTTAGCA
Found at i:54656254 original size:22 final size:22
Alignment explanation
Indices: 54656204--54656282 Score: 65
Period size: 22 Copynumber: 3.6 Consensus size: 22
54656194 ATATGATTTA
54656204 GAGTTTAAGGTTTA-GGAGTTACT
1 GAGTTTAAGGTTTATGGA-TTA-T
*
54656227 -ATTTTAAGGTTTATGGATTAT
1 GAGTTTAAGGTTTATGGATTAT
* * *
54656248 GAGTTTAGGGGTTATGGTTTA-
1 GAGTTTAAGGTTTATGGATTAT
* *
54656269 CAGTTTATGGTTTA
1 GAGTTTAAGGTTTA
54656283 AGATTTAGGG
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
21 12 0.26
22 31 0.67
23 3 0.07
ACGTcount: A:0.24, C:0.03, G:0.28, T:0.46
Consensus pattern (22 bp):
GAGTTTAAGGTTTATGGATTAT
Found at i:54656281 original size:7 final size:7
Alignment explanation
Indices: 54656229--54656322 Score: 53
Period size: 7 Copynumber: 13.3 Consensus size: 7
54656219 GAGTTACTAT
*
54656229 TTTAAGG
1 TTTATGG
54656236 TTTATGG
1 TTTATGG
*
54656243 ATTATGAG
1 TTTATG-G
*
54656251 TTTAGGG
1 TTTATGG
*
54656258 GTTATGG
1 TTTATGG
**
54656265 TTTACAG
1 TTTATGG
54656272 TTTATGG
1 TTTATGG
* *
54656279 TTTAAGA
1 TTTATGG
*
54656286 TTTAGGG
1 TTTATGG
*
54656293 TTTAAGG
1 TTTATGG
* **
54656300 GTTGCGG
1 TTTATGG
54656307 TTTATGG
1 TTTATGG
*
54656314 TTTAAGG
1 TTTATGG
54656321 TT
1 TT
54656323 ATAGATTAAG
Statistics
Matches: 63, Mismatches: 23, Indels: 2
0.72 0.26 0.02
Matches are distributed among these distances:
7 58 0.92
8 5 0.08
ACGTcount: A:0.21, C:0.02, G:0.31, T:0.46
Consensus pattern (7 bp):
TTTATGG
Found at i:54656522 original size:16 final size:17
Alignment explanation
Indices: 54656503--54656544 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
54656493 AAATTCTTTA
54656503 TAAATAATTT-ATATAT
1 TAAATAATTTAATATAT
54656519 TAAATAATTTAATATAT
1 TAAATAATTTAATATAT
54656536 TAAAATAAT
1 T-AAATAAT
54656545 GATTATAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 10 0.42
17 7 0.29
18 7 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAATAATTTAATATAT
Found at i:54656755 original size:21 final size:22
Alignment explanation
Indices: 54656737--54656777 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
54656727 ATGGTTTATT
54656737 GTTTAAGGGTT-GGGATTTAAA
1 GTTTAAGGGTTAGGGATTTAAA
*
54656758 GTTTAGGGGTTAGGGATTTA
1 GTTTAAGGGTTAGGGATTTA
54656778 GGGTTTTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.24, C:0.00, G:0.37, T:0.39
Consensus pattern (22 bp):
GTTTAAGGGTTAGGGATTTAAA
Found at i:54657032 original size:23 final size:23
Alignment explanation
Indices: 54657004--54657050 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
54656994 AACTAATAAT
54657004 TTTTAACAAATAAAATAAA-AAAA
1 TTTTAACAAAT-AAATAAATAAAA
54657027 TTTTAACAAATAAATAAATAAAA
1 TTTTAACAAATAAATAAATAAAA
54657050 T
1 T
54657051 CACTAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (23 bp):
TTTTAACAAATAAATAAATAAAA
Found at i:54657136 original size:38 final size:39
Alignment explanation
Indices: 54657053--54657137 Score: 109
Period size: 39 Copynumber: 2.2 Consensus size: 39
54657043 AATAAAATCA
*
54657053 CTAAAAATAAGCATTAGCGGCGCTTTTCGGAAAACGCCG
1 CTAAAAATAAGCATTAGCGGCGCTTTTCAGAAAACGCCG
* * *
54657092 CTAAAAATGAGCATTAGTGGCG-TTTTTAGAAAAGCGCCG
1 CTAAAAATAAGCATTAGCGGCGCTTTTCAGAAAA-CGCCG
*
54657131 CAAAAAA
1 CTAAAAA
54657138 ACTAGGCCCA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
38 9 0.22
39 31 0.77
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.21
Consensus pattern (39 bp):
CTAAAAATAAGCATTAGCGGCGCTTTTCAGAAAACGCCG
Found at i:54658006 original size:38 final size:38
Alignment explanation
Indices: 54657926--54658007 Score: 112
Period size: 38 Copynumber: 2.2 Consensus size: 38
54657916 GGTTACAAAC
* * * *
54657926 TTTATCTGTTTTTTATATGTTTATCTCACAAATTTTCT
1 TTTATCTGCTTTTTACATGTTTATCTCACAAATGTTCG
54657964 TTTATCTGCTTTTTACATGTTTATCTCACAAA-GTTCGG
1 TTTATCTGCTTTTTACATGTTTATCTCACAAATGTTC-G
54658002 TTTATC
1 TTTATC
54658008 AATTGTTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
37 3 0.08
38 36 0.92
ACGTcount: A:0.21, C:0.16, G:0.09, T:0.55
Consensus pattern (38 bp):
TTTATCTGCTTTTTACATGTTTATCTCACAAATGTTCG
Found at i:54662213 original size:43 final size:43
Alignment explanation
Indices: 54662166--54662350 Score: 232
Period size: 43 Copynumber: 4.3 Consensus size: 43
54662156 TTTATTTTTT
* *
54662166 AAGCGTCGCTAAAGGTTGTGGTCTTTAGCGGCGTTTTTGGGAA
1 AAGCGTCGCTAAAGGTTATGGTCTTTAGCGGCGTTTGTGGGAA
* *
54662209 AAGCGTCGCTAAAGGTCA-GAGTCTTTAGCGGCGTTTGTCGGAA
1 AAGCGTCGCTAAAGGTTATG-GTCTTTAGCGGCGTTTGTGGGAA
*
54662252 AAGCGTCGCTAAA-GTTCATCGTCTTTAGCGGCGTTTGTGGGAA
1 AAGCGTCGCTAAAGGTT-ATGGTCTTTAGCGGCGTTTGTGGGAA
* * ** *
54662295 AAGCGCCGCTAAAGGTCATGACCTTTAGCGGCGCTTGTGGG-A
1 AAGCGTCGCTAAAGGTTATGGTCTTTAGCGGCGTTTGTGGGAA
*
54662337 AAGCGCCGCTAAAG
1 AAGCGTCGCTAAAG
54662351 TTAGAGACGC
Statistics
Matches: 125, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
42 18 0.14
43 105 0.84
44 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.26
Consensus pattern (43 bp):
AAGCGTCGCTAAAGGTTATGGTCTTTAGCGGCGTTTGTGGGAA
Found at i:54662258 original size:86 final size:86
Alignment explanation
Indices: 54662166--54662350 Score: 259
Period size: 86 Copynumber: 2.2 Consensus size: 86
54662156 TTTATTTTTT
* * * *
54662166 AAGCGTCGCTAAAGGTT-GTGGTCTTTAGCGGCGTTTTTGGGAAAAGCGTCGCTAAAGGTCA-GA
1 AAGCGTCGCTAAAGGTTCATCGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGA
* *
54662229 GTCTTTAGCGGCGTTTGTCGGAA
66 -CCTTTAGCGGCGCTTGT-GGAA
54662252 AAGCGTCGCTAAA-GTTCATCGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGA
1 AAGCGTCGCTAAAGGTTCATCGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGA
*
54662316 CCTTTAGCGGCGCTTGTGGGA
66 CCTTTAGCGGCGCTTGTGGAA
*
54662337 AAGCGCCGCTAAAG
1 AAGCGTCGCTAAAG
54662351 TTAGAGACGC
Statistics
Matches: 88, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
85 18 0.20
86 68 0.77
87 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.26
Consensus pattern (86 bp):
AAGCGTCGCTAAAGGTTCATCGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGA
CCTTTAGCGGCGCTTGTGGAA
Found at i:54663983 original size:5 final size:5
Alignment explanation
Indices: 54663973--54664065 Score: 75
Period size: 5 Copynumber: 17.6 Consensus size: 5
54663963 ATTGATATCC
*
54663973 AAATA AAATA AAATA AAATAA TAAATA ATAA-A TAATA AAATA AAATA
1 AAATA AAATA AAATA AAAT-A -AAATA A-AATA AAATA AAATA AAATA
*
54664020 AAATA ATAA-A TAATGA ATAATA AAATAA AAATA AAGA-A AAATA AAA
1 AAATA A-AATA AAAT-A A-AATA AAAT-A AAATA AA-ATA AAATA AAA
54664066 ATTGGGTTGC
Statistics
Matches: 73, Mismatches: 4, Indels: 22
0.74 0.04 0.22
Matches are distributed among these distances:
4 5 0.07
5 46 0.63
6 15 0.21
7 7 0.10
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (5 bp):
AAATA
Found at i:54664000 original size:7 final size:7
Alignment explanation
Indices: 54663988--54664053 Score: 71
Period size: 7 Copynumber: 8.9 Consensus size: 7
54663978 AAATAAAATA
54663988 AAATAAT
1 AAATAAT
54663995 AAATAAT
1 AAATAAT
54664002 AAATAAT
1 AAATAAT
54664009 AAAATAAAAT
1 -AAAT--AAT
54664019 AAAATAAT
1 -AAATAAT
54664027 AAATAAT
1 AAATAAT
*
54664034 GAATAAT
1 AAATAAT
54664041 AAAATAA-
1 -AAATAAT
54664048 AAATAA
1 AAATAA
54664054 AGAAAAATAA
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
6 6 0.11
7 27 0.51
8 12 0.23
10 8 0.15
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (7 bp):
AAATAAT
Found at i:54664011 original size:32 final size:32
Alignment explanation
Indices: 54663974--54664054 Score: 144
Period size: 32 Copynumber: 2.5 Consensus size: 32
54663964 TTGATATCCA
54663974 AATAAAATAAAATAAAATAATAAATAATAAAT
1 AATAAAATAAAATAAAATAATAAATAATAAAT
*
54664006 AATAAAATAAAATAAAATAATAAATAATGAAT
1 AATAAAATAAAATAAAATAATAAATAATAAAT
54664038 AATAAAATAAAAATAAA
1 AATAAAAT-AAAATAAA
54664055 GAAAAATAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 39 0.83
33 8 0.17
ACGTcount: A:0.75, C:0.00, G:0.01, T:0.23
Consensus pattern (32 bp):
AATAAAATAAAATAAAATAATAAATAATAAAT
Found at i:54664067 original size:22 final size:20
Alignment explanation
Indices: 54663973--54664065 Score: 82
Period size: 22 Copynumber: 4.4 Consensus size: 20
54663963 ATTGATATCC
54663973 AAATAAAAT-AAAATAAAATA
1 AAATAAAATAAAAATAAAA-A
*
54663993 ATAA-ATAATAAATAATAAAATA
1 A-AATAAAATAAA-AATAAAA-A
*
54664015 AAATAAAATAATAAATAATGAA
1 AAATAAAATAA-AAATAA-AAA
*
54664037 TAATAAAATAAAAATAAAGAA
1 AAATAAAATAAAAATAAA-AA
54664058 AAATAAAA
1 AAATAAAA
54664066 ATTGGGTTGC
Statistics
Matches: 60, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
20 5 0.08
21 21 0.35
22 32 0.53
23 2 0.03
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (20 bp):
AAATAAAATAAAAATAAAAA
Found at i:54667685 original size:10 final size:10
Alignment explanation
Indices: 54667658--54667706 Score: 64
Period size: 10 Copynumber: 4.9 Consensus size: 10
54667648 TTAAATTCTA
54667658 AAAGATAAAT
1 AAAGATAAAT
54667668 ATAA-ATAAAT
1 A-AAGATAAAT
*
54667678 AAAGATAATT
1 AAAGATAAAT
54667688 AAAGATAAAT
1 AAAGATAAAT
*
54667698 GAAGATAAA
1 AAAGATAAA
54667707 AGCTAAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
9 2 0.06
10 30 0.88
11 2 0.06
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:54687319 original size:21 final size:22
Alignment explanation
Indices: 54687288--54687329 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
54687278 TTCAATAACA
54687288 CTTAACATGGTC-TAATTATACT
1 CTTAACATGGTCTTAA-TATACT
54687310 CTTAA-ATGGTCTTAATATAC
1 CTTAACATGGTCTTAATATAC
54687330 CTCATTGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (22 bp):
CTTAACATGGTCTTAATATACT
Found at i:54692001 original size:39 final size:39
Alignment explanation
Indices: 54691945--54692107 Score: 195
Period size: 39 Copynumber: 4.2 Consensus size: 39
54691935 GTATGAGATT
* * *
54691945 GAAAATATATCCAGACATGAGGTCTGCAGGCTATATGCTG
1 GAAAA-ATATCCGGACATGAGGTCCGCAGGCTATATGCTA
54691985 GAAAAATATCCGGACATGA--TCCGCAGGCTATATGCTA
1 GAAAAATATCCGGACATGAGGTCCGCAGGCTATATGCTA
* * *
54692022 GAAATATATCTGGACATGAGATCCGCAGGCTATATGCTA
1 GAAAAATATCCGGACATGAGGTCCGCAGGCTATATGCTA
* * * ** *
54692061 GAAATATATCCGGACTTGAGGTTCGCAGGCTACGTGCTG
1 GAAAAATATCCGGACATGAGGTCCGCAGGCTATATGCTA
54692100 GAAAAATA
1 GAAAAATA
54692108 CTTGGGTTAA
Statistics
Matches: 108, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
37 33 0.31
39 70 0.65
40 5 0.05
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (39 bp):
GAAAAATATCCGGACATGAGGTCCGCAGGCTATATGCTA
Found at i:54692330 original size:2 final size:2
Alignment explanation
Indices: 54692325--54692382 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
54692315 ACGATATATA
*
54692325 TG TG TG TG TG TG TG TG TG TG TG TA TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
54692367 TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG
54692383 AATGAATTCG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.02, C:0.00, G:0.48, T:0.50
Consensus pattern (2 bp):
TG
Found at i:54695472 original size:28 final size:26
Alignment explanation
Indices: 54695432--54695490 Score: 75
Period size: 28 Copynumber: 2.2 Consensus size: 26
54695422 GTAAGCATTT
*
54695432 AATTTATAGATTTTATACTTTTTAAATA
1 AATTTATAGATTTT-TAATTTTTAAA-A
54695460 AATTTA-ATGATTTTTAATTTTTAAAA
1 AATTTATA-GATTTTTAATTTTTAAAA
54695486 AATTT
1 AATTT
54695491 TATATATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 6 0.21
27 11 0.38
28 12 0.41
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (26 bp):
AATTTATAGATTTTTAATTTTTAAAA
Found at i:54695501 original size:29 final size:28
Alignment explanation
Indices: 54695436--54695515 Score: 83
Period size: 27 Copynumber: 2.8 Consensus size: 28
54695426 GCATTTAATT
*
54695436 TATAGATTTTATACTTTTTAAATAAATTTA
1 TATAGATTTT-TAATTTTTAAA-AAATTTA
54695466 -AT-GATTTTTAATTTTTAAAAAATTTTA
1 TATAGATTTTTAATTTTTAAAAAA-TTTA
* *
54695493 TATATATTTTTAAAATTTTAAAA
1 TATAGATTTTT-AATTTTTAAAA
54695516 TTTTAAAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
26 3 0.07
27 14 0.33
28 8 0.19
29 8 0.19
30 10 0.23
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (28 bp):
TATAGATTTTTAATTTTTAAAAAATTTA
Found at i:54695513 original size:8 final size:8
Alignment explanation
Indices: 54695500--54695529 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
54695490 TTATATATAT
54695500 TTTTAAAA
1 TTTTAAAA
54695508 TTTTAAAA
1 TTTTAAAA
54695516 TTTTAAAA
1 TTTTAAAA
54695524 TTTTAA
1 TTTTAA
54695530 TTAAATATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
TTTTAAAA
Found at i:54697286 original size:15 final size:14
Alignment explanation
Indices: 54697266--54697308 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
54697256 GAAAATTACG
*
54697266 TATTTAATATATATA
1 TATTTAATAAATA-A
54697281 TATTTAA-AAATAA
1 TATTTAATAAATAA
54697294 TATTTAATAAATAA
1 TATTTAATAAATAA
54697308 T
1 T
54697309 GAAACATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 8 0.31
14 11 0.42
15 7 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TATTTAATAAATAA
Found at i:54698151 original size:31 final size:29
Alignment explanation
Indices: 54698116--54698184 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
54698106 CATAGTGAGT
* * *
54698116 AAAATATTACAAATTAATAATGTTAGTGACC
1 AAAATATAACAAATTAA-AAT-TGAATGACC
*
54698147 AAAATATAATAAATTAAAATTGAATGACC
1 AAAATATAACAAATTAAAATTGAATGACC
*
54698176 AAAACATAA
1 AAAATATAA
54698185 TTTAAACCAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 15 0.45
30 3 0.09
31 15 0.45
ACGTcount: A:0.57, C:0.09, G:0.07, T:0.28
Consensus pattern (29 bp):
AAAATATAACAAATTAAAATTGAATGACC
Found at i:54703169 original size:82 final size:82
Alignment explanation
Indices: 54703032--54703189 Score: 298
Period size: 82 Copynumber: 1.9 Consensus size: 82
54703022 CTATCTCTGA
*
54703032 GAATCTCCATACCAAGTATCTTCTTTGCTGGTCCTAAATCTTTCATCTCAAATTCTTCACTTAGT
1 GAATCTCCATACCAAGTATATTCTTTGCTGGTCCTAAATCTTTCATCTCAAATTCTTCACTTAGT
54703097 TGGGCTTTGACCTTTGG
66 TGGGCTTTGACCTTTGG
*
54703114 GAATCTCCATACCAAGTATATTCTTTGTTGGTCCTAAATCTTTCATCTCAAATTCTTCACTTAGT
1 GAATCTCCATACCAAGTATATTCTTTGCTGGTCCTAAATCTTTCATCTCAAATTCTTCACTTAGT
54703179 TGGGCTTTGAC
66 TGGGCTTTGAC
54703190 ATTTCTTATC
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 74 1.00
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.41
Consensus pattern (82 bp):
GAATCTCCATACCAAGTATATTCTTTGCTGGTCCTAAATCTTTCATCTCAAATTCTTCACTTAGT
TGGGCTTTGACCTTTGG
Found at i:54715324 original size:13 final size:13
Alignment explanation
Indices: 54715306--54715331 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
54715296 AATTGTTGCG
54715306 TGCAAATATGCAA
1 TGCAAATATGCAA
54715319 TGCAAATATGCAA
1 TGCAAATATGCAA
54715332 GTGTACACGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (13 bp):
TGCAAATATGCAA
Found at i:54726987 original size:30 final size:30
Alignment explanation
Indices: 54726932--54726993 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
54726922 CACTAAGCAA
54726932 GTTTCATATACATGTATCATCCATTT-CAT
1 GTTTCATATACATGTATCATCCATTTCCAT
54726961 GTTTCAATATATCATGTAAT-AT-CATTTCCAT
1 GTTTC-ATATA-CATGT-ATCATCCATTTCCAT
54726992 GT
1 GT
54726994 ATTTCCATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
29 5 0.17
30 10 0.34
31 12 0.41
32 2 0.07
ACGTcount: A:0.29, C:0.18, G:0.08, T:0.45
Consensus pattern (30 bp):
GTTTCATATACATGTATCATCCATTTCCAT
Found at i:54727013 original size:9 final size:10
Alignment explanation
Indices: 54726984--54727016 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
54726974 ATGTAATATC
54726984 ATTTCCATGT
1 ATTTCCATGT
54726994 ATTTCCATGT
1 ATTTCCATGT
54727004 ATTT-CATGT
1 ATTTCCATGT
54727013 ATTT
1 ATTT
54727017 ACCTGTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 9 0.39
10 14 0.61
ACGTcount: A:0.21, C:0.15, G:0.09, T:0.55
Consensus pattern (10 bp):
ATTTCCATGT
Found at i:54727241 original size:24 final size:26
Alignment explanation
Indices: 54727205--54727269 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 26
54727195 GAATTGGTAA
* *
54727205 AAGCTCATTCGAGCTGA-GAATC-GT
1 AAGCTCATACGAGCTGACAAATCTGT
54727229 AAGCTC-TCACGAGCT-ACAAATCTGT
1 AAGCTCAT-ACGAGCTGACAAATCTGT
54727254 AAGCTCATACGAGCTG
1 AAGCTCATACGAGCTG
54727270 TGGTGTGTCC
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
23 2 0.06
24 16 0.47
25 15 0.44
26 1 0.03
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.23
Consensus pattern (26 bp):
AAGCTCATACGAGCTGACAAATCTGT
Found at i:54731195 original size:4 final size:4
Alignment explanation
Indices: 54731186--54731297 Score: 50
Period size: 4 Copynumber: 28.2 Consensus size: 4
54731176 TTGATTCTGA
* * * **
54731186 TATT TATT TATT CATT TACT TGTT TATT TA-T TCCT TATT CTATT TACTT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT -TATT TA-TT
* * * * * * * * * *
54731235 TATT CATT TATC TGTT CATT TACT CA-T TATT TCTA T-TT TAGT CATT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
54731281 TATT TATT TATT TATT T
1 TATT TATT TATT TATT T
54731298 TTGTTTCAAT
Statistics
Matches: 76, Mismatches: 27, Indels: 10
0.67 0.24 0.09
Matches are distributed among these distances:
3 6 0.08
4 62 0.82
5 8 0.11
ACGTcount: A:0.21, C:0.12, G:0.03, T:0.64
Consensus pattern (4 bp):
TATT
Found at i:54731239 original size:41 final size:41
Alignment explanation
Indices: 54731186--54731272 Score: 115
Period size: 41 Copynumber: 2.1 Consensus size: 41
54731176 TTGATTCTGA
* * *
54731186 TATTTATTTATTCATTTA-CTTGTTTATTTATTCCTTA-TTC
1 TATTTATTTATTCATTTATC-TGTTCATTTACTCATTATTTC
54731226 TATTTACTTTATTCATTTATCTGTTCATTTACTCATTATTTC
1 TATTTA-TTTATTCATTTATCTGTTCATTTACTCATTATTTC
54731268 TATTT
1 TATTT
54731273 TAGTCATTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
40 6 0.15
41 26 0.63
42 9 0.22
ACGTcount: A:0.21, C:0.14, G:0.02, T:0.63
Consensus pattern (41 bp):
TATTTATTTATTCATTTATCTGTTCATTTACTCATTATTTC
Found at i:54731620 original size:6 final size:6
Alignment explanation
Indices: 54731609--54731642 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
54731599 GGCATCTAGC
54731609 ATTTTT ATTTTT ACTTTTT ATTTTTT ATTTTT AT
1 ATTTTT ATTTTT A-TTTTT A-TTTTT ATTTTT AT
54731643 CACTTTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 14 0.54
7 12 0.46
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (6 bp):
ATTTTT
Found at i:54731628 original size:13 final size:12
Alignment explanation
Indices: 54731609--54731642 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
54731599 GGCATCTAGC
54731609 ATTTTTATTTTT
1 ATTTTTATTTTT
54731621 ACTTTTTATTTTTT
1 A-TTTTTA-TTTTT
54731635 ATTTTTAT
1 ATTTTTAT
54731643 CACTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 2 0.10
13 12 0.60
14 6 0.30
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (12 bp):
ATTTTTATTTTT
Found at i:54732986 original size:7 final size:7
Alignment explanation
Indices: 54732974--54733013 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
54732964 ATATGTGCTC
54732974 TATTTAT
1 TATTTAT
54732981 TATTTAT
1 TATTTAT
54732988 TATTTAT
1 TATTTAT
54732995 TATTTAT
1 TATTTAT
54733002 TATTTAT
1 TATTTAT
54733009 TATTT
1 TATTT
54733014 GCTTCAAGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TATTTAT
Found at i:54739597 original size:19 final size:19
Alignment explanation
Indices: 54739573--54739609 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
54739563 AAATCAATTG
*
54739573 GGAATATAAATTTGTCAAA
1 GGAATATAAATTTATCAAA
54739592 GGAATATAAATTTATCAA
1 GGAATATAAATTTATCAA
54739610 TTTTGACAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.05, G:0.14, T:0.32
Consensus pattern (19 bp):
GGAATATAAATTTATCAAA
Found at i:54746821 original size:43 final size:42
Alignment explanation
Indices: 54746744--54746862 Score: 141
Period size: 43 Copynumber: 2.8 Consensus size: 42
54746734 CACATAGTAC
* * * *
54746744 CATACCAATGCCATATCCTAGATATGGTCGTACAT-AGGATCT
1 CATATCAATGCCATATCCCAGATATGGTCTTACATGA-AATCT
* *
54746786 CATATCAATGCCAATAGCCCAGCTATGGTCTTACATGAAATCT
1 CATATCAATGCC-ATATCCCAGATATGGTCTTACATGAAATCT
* *
54746829 CATATCGATGCCATATCTCAGATATGGTCTTACA
1 CATATCAATGCCATATCCCAGATATGGTCTTACA
54746863 CAAAAATAGG
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
42 30 0.46
43 34 0.52
44 1 0.02
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.29
Consensus pattern (42 bp):
CATATCAATGCCATATCCCAGATATGGTCTTACATGAAATCT
Found at i:54762257 original size:78 final size:78
Alignment explanation
Indices: 54762125--54762279 Score: 256
Period size: 78 Copynumber: 2.0 Consensus size: 78
54762115 GAATGAACAA
* *
54762125 GGAGGAGAGATGTTAAGTGTTGCGGCATCAACAAAGTATTTTGGATCTCCGAAACACATATCAAG
1 GGAGGAGAGATGCTAAGTCTTGCGGCATCAACAAAGTATTTTGGATCTCCGAAACACATATCAAG
54762190 TTCAAAAGGGTCC
66 TTCAAAAGGGTCC
* * * *
54762203 GGAGGAGAGATGCTACGTCTTGGGGTATCAACAAAGTATTTTGGATCTCTGAAACACATATCAAG
1 GGAGGAGAGATGCTAAGTCTTGCGGCATCAACAAAGTATTTTGGATCTCCGAAACACATATCAAG
54762268 TTCAAAAGGGTC
66 TTCAAAAGGGTC
54762280 TTCGAGAAGT
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
78 71 1.00
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25
Consensus pattern (78 bp):
GGAGGAGAGATGCTAAGTCTTGCGGCATCAACAAAGTATTTTGGATCTCCGAAACACATATCAAG
TTCAAAAGGGTCC
Found at i:54763016 original size:44 final size:44
Alignment explanation
Indices: 54762953--54763715 Score: 439
Period size: 44 Copynumber: 16.9 Consensus size: 44
54762943 TATAATAGTG
* *
54762953 AATCTTATCTCCCTAAAGTTGCAGTGGAACAGATTGAAGCCACT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACT
* * * ** * * * *** *
54762997 AATCTCATATCTCTGAAGTTTTAGTAGAGTAGATTTAATATAACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA-GCCACT
* * *
54763042 AATCTTAT-TCCCCTAAAGTTGCAGTGG-GACAGGTTGAAGCTATCAT
1 AATCTTATCT-CCCTGAAGTTGCAGTGGAG-CAGATTGAAGCCA-C-T
* *
54763088 GGCAGATCTTATCTCCCTGAAGTTGCAGTAGAGTAGATTGAAGCCACT
1 ---A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACT
* * * *
54763136 AATCTCATTTCCCTGAAGTTGCAGT-GAGACAGGTTGAAGCTATCATGGCG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAG-CAGATTGAAGC---CA---CT
* * *
54763186 GATCTTATCTCCCTGAAGTTGTAGTGGAGTAGATTGAAGCCACT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACT
* *
54763230 AA-CATTATCTCCCTGAAGTTGCAGTAGAGTAGATTGAAGCCACT
1 AATC-TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACT
* * * * * * **
54763274 AATCTTATCTCCCTAAAGTTGTAATGGAACAGGTTAAAGTTAC-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACT
* **
54763317 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAGCCAAA
1 AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACT
* * * ** *
54763362 AATCTTATCTCCCTAAAGTTGCAGTGGAGTAGATTAAAGATAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCA-CT
* *
54763407 AATCTTAT-TCTCCTGAAGTTGCAATGG-GACA-AGTTGAAGCTATCAT
1 AATCTTATCTC-CCTGAAGTTGCAGTGGAG-CAGA-TTGAAGCCA-C-T
*
54763453 GGCAGATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCCACT
1 ---A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACT
* * * * * ** *
54763501 AACCTCATCTCCTTAAAGTTGTAGTGGAGCA-AGTTGAAGTTA-A
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTGAAGCCACT
* ** *
54763544 AAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGATAGT
1 AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACT
* * ** * * ** *
54763589 GAATATTATCTCCCCGAAGTTATAGTGGAGTAGATTAAAGTAACA
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACT
* * * ** * *** *
54763634 AATCTTATTTCTCTGAAGTTACAGTGGAATATATTGAAATTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACT
* * *
54763678 AATCTTATCTCCCTGAAGTTGTAGTGGGGTAGATTGAA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA
54763716 ACAACAAATT
Statistics
Matches: 554, Mismatches: 125, Indels: 80
0.73 0.16 0.11
Matches are distributed among these distances:
43 9 0.02
44 331 0.60
45 99 0.18
46 2 0.00
47 4 0.01
48 2 0.00
49 4 0.01
50 94 0.17
51 9 0.02
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.30
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACT
Found at i:54763520 original size:227 final size:227
Alignment explanation
Indices: 54763234--54763653 Score: 619
Period size: 227 Copynumber: 1.9 Consensus size: 227
54763224 GCCACTAACA
* *
54763234 TTATCTCCCTGAAGTTGCAGTAGAGTAGATTGAAGCCACTAATCTTATCTCCCTAAAGTTGTAAT
1 TTATCTCCCTGAAGTTGCAGTAGAGTAGATTGAAGCCACTAACCTCATCTCCCTAAAGTTGTAAT
* * *
54763299 GGAACAGGTTAAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAGCCA-AAA
66 GGAACAAGTTAAAGTTAAAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAGACAGAAA
* * * *
54763363 ATCTTATCTCCCTAAAGTTGCAGTGGAGTAGATTAAAGATAGCAAATCTTA-TTCTCCTGAAGTT
131 ATATTATCTCCCCAAAGTTACAGTGGAGTAGATTAAAG-TAACAAATCTTATTTCT-CTGAAGTT
54763427 GCAATGGGACAAGTTGAAGCTATCATGGCAGATC
194 GCAATGGGACAAGTTGAAGCTATCATGGCAGATC
* * *
54763461 TTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCCACTAACCTCATCTCCTTAAAGTTGTAGT
1 TTATCTCCCTGAAGTTGCAGTAGAGTAGATTGAAGCCACTAACCTCATCTCCCTAAAGTTGTAAT
* * * * * **
54763526 GGAGCAAGTTGAAGTTAAAAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGATAGTGA
66 GGAACAAGTTAAAGTTAAAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAGACAGAAA
* *
54763591 ATATTATCTCCCCGAAGTTATAGTGGAGTAGATTAAAGTAACAAATCTTATTTCTCTGAAGTT
131 ATATTATCTCCCCAAAGTTACAGTGGAGTAGATTAAAGTAACAAATCTTATTTCTCTGAAGTT
54763654 ACAGTGGAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
227 132 0.78
228 38 0.22
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.30
Consensus pattern (227 bp):
TTATCTCCCTGAAGTTGCAGTAGAGTAGATTGAAGCCACTAACCTCATCTCCCTAAAGTTGTAAT
GGAACAAGTTAAAGTTAAAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAGACAGAAA
ATATTATCTCCCCAAAGTTACAGTGGAGTAGATTAAAGTAACAAATCTTATTTCTCTGAAGTTGC
AATGGGACAAGTTGAAGCTATCATGGCAGATC
Found at i:54763682 original size:271 final size:271
Alignment explanation
Indices: 54763093--54763698 Score: 670
Period size: 271 Copynumber: 2.2 Consensus size: 271
54763083 ATCATGGCAG
* * * * * ** * * *
54763093 ATCTTATCTCCCTGAAGTTGCAGTAGAGTAGATTGAAGCCA-CTAATCTCATTTCCCTGAAGTTG
1 ATCTTATCTCCCTAAAGTTACAGTGGAATAGATTAAAGATAGCAAATCTTATCTCCCTGAAGTTG
* * * *
54763157 CAGTGAGACAGGTTGAAGCTATCATGGCGGATCTTATCTCCCTGAAGTTGTAGTGGAGTAGATTG
66 CAATGAGACAAGTTGAAGCTATCATGGCAGATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTG
* * * *
54763222 AAGCCACTAACATTATCTCCCTGAAGTTGCAGTAGAGTAGATTGAAGCCACTAATCTTATCTCCC
131 AAGCCACTAACATCATCTCCCTAAAGTTGCAGTAGAGAAGATTGAAGCCACAAATCTTATCTCCC
* * * * *
54763287 TAAAGTTGTAATGGAACAGGTTAAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAAT
196 TAAAGTTGTAATGGAACAGATTAAAGATACAAGTATTATCTCCCCGAAGTTACAGTGGAGCAAAT
*
54763352 TGAAGCCAAAA
261 TAAAGCCAAAA
* *
54763363 ATCTTATCTCCCTAAAGTTGCAGTGGAGTAGATTAAAGATAGCAAATCTTAT-TCTCCTGAAGTT
1 ATCTTATCTCCCTAAAGTTACAGTGGAATAGATTAAAGATAGCAAATCTTATCTC-CCTGAAGTT
*
54763427 GCAATGGGACAAGTTGAAGCTATCATGGCAGATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATT
65 GCAATGAGACAAGTTGAAGCTATCATGGCAGATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATT
* * * * **
54763492 GAAGCCACTAACCTCATCTCCTTAAAGTTGTAGTGGAGCAAG-TTGAAGTTA-AAAGTCTTATCT
130 GAAGCCACTAACATCATCTCCCTAAAGTTGCAGTAGAG-AAGATTGAAGCCACAAA-TCTTATCT
* * * * * *
54763555 CCCTGAAGTTGTAGTGGAGCAGATTGAAGATAGTGAA-TATTATCTCCCCGAAGTTATAGTGGAG
193 CCCTAAAGTTGTAATGGAACAGATTAAAGATA--CAAGTATTATCTCCCCGAAGTTACAGTGGAG
* * *
54763619 TAGATTAAAG-TAACAA
256 CAAATTAAAGCCAA-AA
* * * * *
54763635 ATCTTATTTCTCTGAAGTTACAGTGGAATATATTGAAA-TTA-CAAATCTTATCTCCCTGAAGTT
1 ATCTTATCTCCCTAAAGTTACAGTGGAATAGATT-AAAGATAGCAAATCTTATCTCCCTGAAGTT
54763698 G
65 G
54763699 TAGTGGGGTA
Statistics
Matches: 283, Mismatches: 44, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
270 40 0.14
271 172 0.61
272 66 0.23
273 5 0.02
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.30
Consensus pattern (271 bp):
ATCTTATCTCCCTAAAGTTACAGTGGAATAGATTAAAGATAGCAAATCTTATCTCCCTGAAGTTG
CAATGAGACAAGTTGAAGCTATCATGGCAGATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTG
AAGCCACTAACATCATCTCCCTAAAGTTGCAGTAGAGAAGATTGAAGCCACAAATCTTATCTCCC
TAAAGTTGTAATGGAACAGATTAAAGATACAAGTATTATCTCCCCGAAGTTACAGTGGAGCAAAT
TAAAGCCAAAA
Found at i:54766372 original size:23 final size:23
Alignment explanation
Indices: 54766342--54766430 Score: 103
Period size: 23 Copynumber: 3.9 Consensus size: 23
54766332 AGCTTACTAT
*
54766342 TTTTAGCTC-ATTGGAGCTTACCG
1 TTTTAGCTCGA-TAGAGCTTACCG
*
54766365 TTTTAGCTCGATAGAGCTTACTG
1 TTTTAGCTCGATAGAGCTTACCG
*
54766388 -TTTAGCTCGATAGAGCTTACCA
1 TTTTAGCTCGATAGAGCTTACCG
*
54766410 TTTCAGCTC-ATTAGAGCTTAC
1 TTTTAGCTCGA-TAGAGCTTAC
54766431 TGTTCATCAG
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
22 21 0.36
23 36 0.62
24 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.37
Consensus pattern (23 bp):
TTTTAGCTCGATAGAGCTTACCG
Found at i:54766394 original size:22 final size:22
Alignment explanation
Indices: 54766355--54766430 Score: 100
Period size: 22 Copynumber: 3.4 Consensus size: 22
54766345 TAGCTCATTG
54766355 GAGCTTACCGTTTTAGCTCGATA
1 GAGCTTACCG-TTTAGCTCGATA
*
54766378 GAGCTTACTGTTTAGCTCGATA
1 GAGCTTACCGTTTAGCTCGATA
*
54766400 GAGCTTACCATTTCAGCTC-ATTA
1 GAGCTTACCGTTT-AGCTCGA-TA
54766423 GAGCTTAC
1 GAGCTTAC
54766431 TGTTCATCAG
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
22 24 0.50
23 24 0.50
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (22 bp):
GAGCTTACCGTTTAGCTCGATA
Done.