Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A08
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: 119882356
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2655529 characters in sequence are not A, C, G, or T
File 166 of 362
Found at i:54649483 original size:27 final size:27
Alignment explanation
Indices: 54649453--54649517 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
54649443 GGGCATATTC
54649453 GTCATTTTACCATACAAGGG-TATTACG
1 GTCATTTTACCATACAAGGGCT-TTACG
* * * *
54649480 GTCACTTTACCCTATAGGGGCTTTACG
1 GTCATTTTACCATACAAGGGCTTTACG
*
54649507 GTCTTTTTACC
1 GTCATTTTACC
54649518 TATTAGGGGT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
27 30 0.97
28 1 0.03
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (27 bp):
GTCATTTTACCATACAAGGGCTTTACG
Found at i:54649519 original size:26 final size:28
Alignment explanation
Indices: 54649475--54649526 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
54649465 TACAAGGGTA
54649475 TTACGGTCACTTTACCCTA-TAGGGGCT
1 TTACGGTCACTTTACCCTATTAGGGGCT
**
54649502 TTACGGTCTTTTTA-CCTATTAGGGG
1 TTACGGTCACTTTACCCTATTAGGGG
54649527 TATTTTAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.38
Consensus pattern (28 bp):
TTACGGTCACTTTACCCTATTAGGGGCT
Found at i:54649684 original size:27 final size:26
Alignment explanation
Indices: 54649547--54649826 Score: 175
Period size: 27 Copynumber: 10.3 Consensus size: 26
54649537 ATTTCATCCT
* * * *
54649547 ACAAGGGTGTTTTGGTAAATCTATAA
1 ACAAGGGTATTTTGGTAATTTTACAA
** **
54649573 ACAAAGGGTATTTCAGTAATTTTGTAA
1 AC-AAGGGTATTTTGGTAATTTTACAA
* * *
54649600 ACCAATGGTATTTCT-ATAATTTTTAGAA
1 A-CAAGGGTATTT-TGGTAA-TTTTACAA
* **
54649628 AGTCAAGGGTATTTTTGTAATTTTGTAA
1 A--CAAGGGTATTTTGGTAATTTTACAA
*
54649656 ATCAAGGGTATTTTGGTAATTTAACAA
1 A-CAAGGGTATTTTGGTAATTTTACAA
** * *
54649683 ATTGAGGGTATTTCGGTAATTTCACAA
1 A-CAAGGGTATTTTGGTAATTTTACAA
*
54649710 ACTAGTGGTATTTTGGTAATTTTACAA
1 ACAAG-GGTATTTTGGTAATTTTACAA
*
54649737 ACTAGGGGTATTTTGGTAATTTTACAA
1 AC-AAGGGTATTTTGGTAATTTTACAA
* * **
54649764 ACTAGGGGTATTTTGGTAATTCTATCCT
1 AC-AAGGGTATTTTGGTAATTTTA-CAA
* * *
54649792 ACAGGGGTATTTTAGTAATTTCACAA
1 ACAAGGGTATTTTGGTAATTTTACAA
* *
54649818 TCGAGGGTA
1 ACAAGGGTA
54649827 AAATGGTAAT
Statistics
Matches: 204, Mismatches: 41, Indels: 18
0.78 0.16 0.07
Matches are distributed among these distances:
26 11 0.05
27 160 0.78
28 20 0.10
29 13 0.06
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.39
Consensus pattern (26 bp):
ACAAGGGTATTTTGGTAATTTTACAA
Found at i:54649751 original size:81 final size:81
Alignment explanation
Indices: 54649635--54649784 Score: 205
Period size: 81 Copynumber: 1.9 Consensus size: 81
54649625 GAAAGTCAAG
* ** *
54649635 GGTATTTTTGTAATTTTGTAAATCAAGGGTATTTTGGTAATTTAACAAA-TTGAGGGTATTTCGG
1 GGTATTTTGGTAATTTTACAAATCAAGGGTATTTTGGTAATTTAACAAACTAG-GGGTATTTCGG
54649699 TAATTTCACAAACTAGT
65 TAATTTCACAAACTAGT
* * *
54649716 GGTATTTTGGTAATTTTACAAA-CTAGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGG
1 GGTATTTTGGTAATTTTACAAATC-AAGGGTATTTTGGTAATTTAACAAACTAGGGGTATTTCGG
54649780 TAATT
65 TAATT
54649785 CTATCCTACA
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
80 1 0.02
81 57 0.95
82 2 0.03
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.43
Consensus pattern (81 bp):
GGTATTTTGGTAATTTTACAAATCAAGGGTATTTTGGTAATTTAACAAACTAGGGGTATTTCGGT
AATTTCACAAACTAGT
Found at i:54649801 original size:81 final size:81
Alignment explanation
Indices: 54649634--54649826 Score: 198
Period size: 81 Copynumber: 2.4 Consensus size: 81
54649624 AGAAAGTCAA
* ** *
54649634 GGGTATTTTTGTAATTTTGTAAATCAAGGGTATTTTGGTAATTTAACAAATTGAGGGTATTTCGG
1 GGGTATTTTAGTAATTTTACAAATCAAGGGTATTTTGGTAATTTAACAAATAGAGGGTATTTCGG
54649699 TAATTTCACAAACTAG
66 TAATTTCACAAACTAG
* * * * *
54649715 TGGTATTTTGGTAATTTTACAAA-CTAGGGGTATTTTGGTAATTTTACAAACTAG-GGGTATTTT
1 GGGTATTTTAGTAATTTTACAAATC-AAGGGTATTTTGGTAATTTAACAAA-TAGAGGGTATTTC
**
54649778 GGTAA-TTCTATCCTAC-AG
64 GGTAATTTC-A-CAAACTAG
* *
54649796 GGGTATTTTAGTAATTTCAC-AATCGAGGGTA
1 GGGTATTTTAGTAATTTTACAAATCAAGGGTA
54649827 AAATGGTAAT
Statistics
Matches: 92, Mismatches: 15, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
80 11 0.12
81 76 0.83
82 5 0.05
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.40
Consensus pattern (81 bp):
GGGTATTTTAGTAATTTTACAAATCAAGGGTATTTTGGTAATTTAACAAATAGAGGGTATTTCGG
TAATTTCACAAACTAG
Found at i:54649850 original size:27 final size:27
Alignment explanation
Indices: 54649816--54649907 Score: 123
Period size: 27 Copynumber: 3.4 Consensus size: 27
54649806 GTAATTTCAC
54649816 AATCGAGGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTTTGTA
*
54649843 TA-CTGAGGGTAAAATGGTAATTTTGTA
1 AATC-GAGGGTAAAATGGTAATTTTGTA
* * * *
54649870 AATCGAGGGTAAAACGATAATTCTATA
1 AATCGAGGGTAAAATGGTAATTTTGTA
54649897 AATCGAGGGTA
1 AATCGAGGGTA
54649908 CTTTGGTAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
26 1 0.02
27 55 0.96
28 1 0.02
ACGTcount: A:0.38, C:0.07, G:0.25, T:0.30
Consensus pattern (27 bp):
AATCGAGGGTAAAATGGTAATTTTGTA
Found at i:54649930 original size:54 final size:53
Alignment explanation
Indices: 54649796--54649932 Score: 125
Period size: 54 Copynumber: 2.5 Consensus size: 53
54649786 TATCCTACAG
* * * * * * * *
54649796 GGGTATTTTAGTAATTTCACAATCGAGGGTAAAATGGTAATTTTGTATACTGA
1 GGGTAATTTGGTAATTTTACAATCGAGGGTAAAACGATAATTCTATAAACTGA
**
54649849 GGGTAAAATGGTAATTTTGTA-AATCGAGGGTAAAACGATAATTCTATAAA-TCGA
1 GGGTAATTTGGTAA-TTT-TACAATCGAGGGTAAAACGATAATTCTATAAACT-GA
*
54649903 GGGTACTTTGGTAATTTTACAAGTCGAGGG
1 GGGTAATTTGGTAATTTTACAA-TCGAGGG
54649933 CATTTCAATA
Statistics
Matches: 66, Mismatches: 13, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
52 2 0.03
53 16 0.24
54 47 0.71
55 1 0.02
ACGTcount: A:0.34, C:0.08, G:0.25, T:0.34
Consensus pattern (53 bp):
GGGTAATTTGGTAATTTTACAATCGAGGGTAAAACGATAATTCTATAAACTGA
Found at i:54651512 original size:48 final size:47
Alignment explanation
Indices: 54651438--54651661 Score: 155
Period size: 48 Copynumber: 4.7 Consensus size: 47
54651428 AGGGTAAATT
* * * * * *
54651438 GCCGATGTCATGTCCTAGACACGGTCTTATAATGGCTCACATGTCGAG
1 GCCGATGCCATGTCC-AGACATGGTCTTACAATAGCTCACATCTCAAG
* * * *
54651486 GCCGATGCCATGTCTCAGACATGGTCTTACACTAGCTCTCGTCTCAAT
1 GCCGATGCCATGTC-CAGACATGGTCTTACAATAGCTCACATCTCAAG
* ** * **
54651534 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTTATAAT-GTG
1 GCCGATGCCATGT-CCAGACATGGTCTTACAATAGCTCACAT-CTCAAG
* * * * * * ** *
54651582 GCTGACGCTATGTCCTAGACATGGTCTTACACTAGCACACATATTGAT
1 GCCGATGCCATGTCC-AGACATGGTCTTACAATAGCTCACATCTCAAG
54651630 GCCGATGCCATGTCCCAGACATGGTCTT-CAAT
1 GCCGATGCCATGT-CCAGACATGGTCTTACAAT
54651662 GTCACAGACA
Statistics
Matches: 142, Mismatches: 28, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
47 7 0.05
48 130 0.92
49 5 0.04
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (47 bp):
GCCGATGCCATGTCCAGACATGGTCTTACAATAGCTCACATCTCAAG
Found at i:54651669 original size:21 final size:21
Alignment explanation
Indices: 54651639--54651678 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
54651629 TGCCGATGCC
*
54651639 ATGTCCCAGACATGGTCTTCA
1 ATGTCACAGACATGGTCTTCA
54651660 ATGTCACAGACATGGTCTT
1 ATGTCACAGACATGGTCTT
54651679 ACACTGGCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (21 bp):
ATGTCACAGACATGGTCTTCA
Found at i:54651776 original size:48 final size:47
Alignment explanation
Indices: 54651660--54651778 Score: 141
Period size: 47 Copynumber: 2.5 Consensus size: 47
54651650 ATGGTCTTCA
* * * **
54651660 ATGTCACAGACATGGTCTTACACTGGCTCTCATATATTTCCGATGCC
1 ATGTCCCAGACATGGTCTTACACTGGCTCTCATATATTGCAGACACC
* *
54651707 ATGTTCCAAACATGGTCTTACACTGGCTCTCATA-ATGTGGCAGACACC
1 ATGTCCCAGACATGGTCTTACACTGGCTCTCATATAT-T-GCAGACACC
*
54651755 ATGTCCCAGGCATGGTCTTACACT
1 ATGTCCCAGACATGGTCTTACACT
54651779 AGCACACATA
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
46 2 0.03
47 32 0.53
48 26 0.43
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.29
Consensus pattern (47 bp):
ATGTCCCAGACATGGTCTTACACTGGCTCTCATATATTGCAGACACC
Found at i:54654021 original size:49 final size:50
Alignment explanation
Indices: 54653892--54654027 Score: 177
Period size: 49 Copynumber: 2.8 Consensus size: 50
54653882 TGTAACACCA
* *
54653892 TTTGTGGACAAGCCACAAC-GACTTGTAGATAAACTACCACTAATAACAC
1 TTTGTGGACAAGCCACAACTGATTTGTAGATATACTACCACTAATAACAC
* * * * *
54653941 TTTGTGGACAAGCCACCACTGATATGCAGATATACTACCACTGATAA-AT
1 TTTGTGGACAAGCCACAACTGATTTGTAGATATACTACCACTAATAACAC
* *
54653990 TTTGTGGACAAGCCACTACTGGTTTGTAGATATACTAC
1 TTTGTGGACAAGCCACAACTGATTTGTAGATATACTAC
54654028 TGGAAACACA
Statistics
Matches: 75, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
49 53 0.71
50 22 0.29
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (50 bp):
TTTGTGGACAAGCCACAACTGATTTGTAGATATACTACCACTAATAACAC
Found at i:54654121 original size:18 final size:18
Alignment explanation
Indices: 54654094--54654134 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
54654084 GTTTCGGTAA
54654094 AATT-ATTATTGA-AAAAT
1 AATTAATTATT-ATAAAAT
*
54654111 ATTTAATTATTATAAAAT
1 AATTAATTATTATAAAAT
54654129 AATTAA
1 AATTAA
54654135 ATTGTACTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
AATTAATTATTATAAAAT
Found at i:54661321 original size:9 final size:9
Alignment explanation
Indices: 54661303--54661375 Score: 61
Period size: 9 Copynumber: 8.6 Consensus size: 9
54661293 TTTATTTAAG
54661303 TTAA-GTGT
1 TTAATGTGT
54661311 TTAATGTGT
1 TTAATGTGT
54661320 TT--TGTGT
1 TTAATGTGT
54661327 TTAATAAGTGT
1 TTAAT--GTGT
54661338 TTAAATGTGT
1 TT-AATGTGT
*
54661348 TTAATATG-
1 TTAATGTGT
54661356 TT--TGT-T
1 TTAATGTGT
54661362 TTAATGTGT
1 TTAATGTGT
54661371 TTAAT
1 TTAAT
54661376 TGCAAGTGTC
Statistics
Matches: 53, Mismatches: 2, Indels: 19
0.72 0.03 0.26
Matches are distributed among these distances:
6 4 0.08
7 7 0.13
8 9 0.17
9 18 0.34
10 6 0.11
11 6 0.11
12 3 0.06
ACGTcount: A:0.25, C:0.00, G:0.19, T:0.56
Consensus pattern (9 bp):
TTAATGTGT
Found at i:54661348 original size:21 final size:22
Alignment explanation
Indices: 54661322--54661375 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 22
54661312 TAATGTGTTT
54661322 TGTGTTTAATAAG-TGTTTAAA
1 TGTGTTTAATAAGTTGTTTAAA
* *
54661343 TGTGTTTAATATGTTTGTTTTAA
1 TGTGTTTAATAAG-TTGTTTAAA
54661366 TGTGTTTAAT
1 TGTGTTTAAT
54661376 TGCAAGTGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 12 0.41
23 17 0.59
ACGTcount: A:0.26, C:0.00, G:0.19, T:0.56
Consensus pattern (22 bp):
TGTGTTTAATAAGTTGTTTAAA
Found at i:54662844 original size:36 final size:36
Alignment explanation
Indices: 54662797--54662868 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
54662787 CTTATGATTG
54662797 TGGTTATGATATTTGTGTAGATCTCATGCTCATGAT
1 TGGTTATGATATTTGTGTAGATCTCATGCTCATGAT
54662833 TGGTTATGATATTTGTGTAGATCTCATGCTCATGAT
1 TGGTTATGATATTTGTGTAGATCTCATGCTCATGAT
54662869 ATGTGATGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.22, C:0.11, G:0.22, T:0.44
Consensus pattern (36 bp):
TGGTTATGATATTTGTGTAGATCTCATGCTCATGAT
Found at i:54664625 original size:27 final size:27
Alignment explanation
Indices: 54664595--54664884 Score: 314
Period size: 27 Copynumber: 10.7 Consensus size: 27
54664585 TTAGTTTACC
54664595 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* * *
54664622 AAATTACTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTA
* *
54664649 AAATCACAAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* * * ** *
54664676 TAATTACTAAAATACCCTTTATTTATA
1 AAATTACCAAAATACCCCTGGTTTGTA
*
54664703 AAATTACCAAAATACCCCTGGCTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
54664730 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* *
54664757 AAATTATCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
*
54664784 AAATTACCAAAATACCCCTGATTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
** ***
54664811 AAATTACTGAAATA-CCCTCGACCTGTA
1 AAATTACCAAAATACCCCT-GGTTTGTA
*** **
54664838 AAATTATTGAAATA-CCCTCGACTTGTA
1 AAATTACCAAAATACCCCT-GGTTTGTA
*
54664865 AAATTACCAAAGTACCCCTG
1 AAATTACCAAAATACCCCTG
54664885 ATTTACAGAA
Statistics
Matches: 224, Mismatches: 37, Indels: 4
0.85 0.14 0.02
Matches are distributed among these distances:
26 4 0.02
27 216 0.96
28 4 0.02
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGGTTTGTA
Found at i:54664934 original size:27 final size:27
Alignment explanation
Indices: 54664595--54664935 Score: 185
Period size: 27 Copynumber: 12.6 Consensus size: 27
54664585 TTAGTTTACC
* *
54664595 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACCGAAATACCCTC-GATTTGTA
** * * *
54664622 AAATTACTAAAATACCCTTGGTTTATA
1 AAATTACCGAAATACCCTCGATTTGTA
* ** *
54664649 AAATCACAAAAATACCC-CTGGTTTGTA
1 AAATTACCGAAATACCCTC-GATTTGTA
* ** ** *
54664676 TAATTACTAAAATACCCTTTATTTATA
1 AAATTACCGAAATACCCTCGATTTGTA
* **
54664703 AAATTACCAAAATACCC-CTGGCTTGTA
1 AAATTACCGAAATACCCTC-GATTTGTA
* *
54664730 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACCGAAATACCCTC-GATTTGTA
* * *
54664757 AAATTATCAAAATACCC-CTAGTTTGTA
1 AAATTACCGAAATACCCTCGA-TTTGTA
*
54664784 AAATTACCAAAATACCC-CTGATTTGTA
1 AAATTACCGAAATACCCTC-GATTTGTA
* **
54664811 AAATTACTGAAATACCCTCGACCTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
** *
54664838 AAATTATTGAAATACCCTCGACTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
**
54664865 AAATTACC-AAAGTACCC-CTGATTTACA
1 AAATTACCGAAA-TACCCTC-GATTTGTA
* * *** **
54664892 GAATTATCGTTTTACCCTCGATTTACA
1 AAATTACCGAAATACCCTCGATTTGTA
54664919 AAATTACCGAAATACCC
1 AAATTACCGAAATACCC
54664936 CTGTAGGGTA
Statistics
Matches: 255, Mismatches: 48, Indels: 22
0.78 0.15 0.07
Matches are distributed among these distances:
26 4 0.02
27 248 0.97
28 3 0.01
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (27 bp):
AAATTACCGAAATACCCTCGATTTGTA
Found at i:54664953 original size:27 final size:27
Alignment explanation
Indices: 54664920--54665176 Score: 352
Period size: 27 Copynumber: 9.5 Consensus size: 27
54664910 CGATTTACAA
54664920 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
54664947 AAATACCAAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
54664974 AATTACCGAAATAACCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
54665001 AATTATCGGAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
54665028 AATTACCGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
54665055 AATTACCGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
54665082 AATTATCGCAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
54665109 AATTACTGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** *
54665136 AATTACTAAAATACCCCTGTAGGGTGG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
54665163 AATTACCGAGATAC
1 AATTACCGAAATAC
54665177 TGTAACGCCC
Statistics
Matches: 202, Mismatches: 28, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 202 1.00
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:54665529 original size:26 final size:26
Alignment explanation
Indices: 54665500--54665607 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
54665490 TGGTACAAAT
54665500 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
54665526 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
54665552 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
54665578 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
54665604 TGAT
1 TGAT
54665608 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:54668708 original size:22 final size:22
Alignment explanation
Indices: 54668656--54668720 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
54668646 TTAAAGCCTT
* *
54668656 CTGATTATGGCTTTGTGTCAAC
1 CTGATTATGGCTCTGTGCCAAC
*
54668678 CT-ACATATGGCTCTGTGCCAAC
1 CTGA-TTATGGCTCTGTGCCAAC
*
54668700 CTGATTATGGCTGTGTGCCAA
1 CTGATTATGGCTCTGTGCCAA
54668721 ACGTATTTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 1 0.03
22 34 0.94
23 1 0.03
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (22 bp):
CTGATTATGGCTCTGTGCCAAC
Found at i:54668931 original size:27 final size:26
Alignment explanation
Indices: 54668901--54668980 Score: 97
Period size: 27 Copynumber: 3.0 Consensus size: 26
54668891 TATTACCTGT
*
54668901 TTCTGGTGGCTATGCCACAAATATCTG
1 TTCTGGTGGCTCTGCCAC-AATATCTG
* *
54668928 TTCTGGTGGTTCTGCCACAATATCAG
1 TTCTGGTGGCTCTGCCACAATATCTG
* *
54668954 TATCTGGTGACTCTGTCACAATATCTG
1 T-TCTGGTGGCTCTGCCACAATATCTG
54668981 ATAACTGAGC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
26 8 0.18
27 37 0.82
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (26 bp):
TTCTGGTGGCTCTGCCACAATATCTG
Found at i:54669162 original size:31 final size:31
Alignment explanation
Indices: 54669125--54669188 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
54669115 ACATTTTGAT
*
54669125 TTTTGATTC-AGTTACCTGATACTAATTCTGA
1 TTTTGATTCTA-TTACCTAATACTAATTCTGA
54669156 TTTTGATTCTATTACCTAATACTAATTCTGA
1 TTTTGATTCTATTACCTAATACTAATTCTGA
54669187 TT
1 TT
54669189 CTGTCACCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 30 0.97
32 1 0.03
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.48
Consensus pattern (31 bp):
TTTTGATTCTATTACCTAATACTAATTCTGA
Found at i:54669174 original size:25 final size:25
Alignment explanation
Indices: 54669146--54669216 Score: 97
Period size: 25 Copynumber: 2.8 Consensus size: 25
54669136 TTACCTGATA
* *
54669146 CTAATTCTGATTTTGATTCTATTAC
1 CTAATTCTGATTCTGATTCTATCAC
* * *
54669171 CTAATACTAATTCTGATTCTGTCAC
1 CTAATTCTGATTCTGATTCTATCAC
54669196 CTAATTCTGATTCTGATTCTA
1 CTAATTCTGATTCTGATTCTA
54669217 ATTCTAGTTC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.25, C:0.20, G:0.08, T:0.46
Consensus pattern (25 bp):
CTAATTCTGATTCTGATTCTATCAC
Found at i:54669274 original size:24 final size:24
Alignment explanation
Indices: 54669247--54669295 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
54669237 TCTTATTCTG
*
54669247 TAATGGGTTAAAGCCC-ATCTGGTA
1 TAATGGGCTAAAGCCCAAT-TGGTA
*
54669271 TAATGGGCTAAGGCCCAATTGGTA
1 TAATGGGCTAAAGCCCAATTGGTA
54669295 T
1 T
54669296 TGAAACTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 20 0.91
25 2 0.09
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.29
Consensus pattern (24 bp):
TAATGGGCTAAAGCCCAATTGGTA
Found at i:54681565 original size:49 final size:47
Alignment explanation
Indices: 54681508--54681777 Score: 209
Period size: 46 Copynumber: 5.7 Consensus size: 47
54681498 GGGTTAAGCT
* *
54681508 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTATCCTCATCGAG
1 GCCGATGCCATGTCCCAGACAT-GTCTTACACTAGCTATCGTC-TCAAG
* * * *
54681557 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTTGCGTATCCAT
1 GCCGATGCCATGTCCCAGACAT-GTCTTACACTAGCT-AT-CGTCTCAAG
* *
54681607 GTCGATGCCATGTCCCAGACACAT-TCTTACACT-GAC-AT-GTCTCGTA-
1 GCCGATGCCATGTCCCAG--ACATGTCTTACACTAG-CTATCGTCTC-AAG
* * *
54681653 GCTGATG-CATGTCCCAGACATGCCTTACACTAGCT-TACATCTCAAG
1 GCCGATGCCATGTCCCAGACATGTCTTACACTAGCTAT-CGTCTCAAG
* * *
54681699 GCCGATG-CATGT-CCTGAACATGTCTTACACTGGC-ATTCGTCTCAAT
1 GCCGATGCCATGTCCCAG-ACATGTCTTACACTAGCTA-TCGTCTCAAG
* *
54681745 GCCGATGCCATGTCCCATACATTATCTTACACT
1 GCCGATGCCATGTCCCAGACA-TGTCTTACACT
54681778 GGCACACAAA
Statistics
Matches: 180, Mismatches: 23, Indels: 37
0.75 0.10 0.15
Matches are distributed among these distances:
43 4 0.02
44 10 0.06
45 15 0.08
46 53 0.29
47 10 0.06
48 13 0.07
49 38 0.21
50 31 0.17
51 2 0.01
52 4 0.02
ACGTcount: A:0.23, C:0.31, G:0.18, T:0.28
Consensus pattern (47 bp):
GCCGATGCCATGTCCCAGACATGTCTTACACTAGCTATCGTCTCAAG
Found at i:54681773 original size:138 final size:145
Alignment explanation
Indices: 54681511--54681778 Score: 340
Period size: 138 Copynumber: 1.9 Consensus size: 145
54681501 TTAAGCTGCC
* * *
54681511 GATGCCATGTCCCAGACATGGTCTTACACTAGCTATCCTCATCGAGGCCGATGCCATGTCCCAGA
1 GATGCCATGTCCCAGACATGGCCTTACACTAGCTATCATCATCAAGGCCGATGCCATGTCCCAGA
* * *
54681576 CATGGTCTTACACTAGCTCTTGCGTATCCATGTCGATGCCATGTCCCAGACACATTCTTACACTG
66 CATGGTCTTACACTAGCTATTGCGTATCAATGCCGATGCCATGTCCCAGACACATTCTTACACTG
54681641 ACATGTCTCGTAGCT
131 ACATGTCTCGTAGCT
*
54681656 GATG-CATGTCCCAGACAT-GCCTTACACTAGCT-TACATC-TCAAGGCCGATG-CATGT-CCTG
1 GATGCCATGTCCCAGACATGGCCTTACACTAGCTAT-CATCATCAAGGCCGATGCCATGTCCCAG
* * * *
54681715 AACAT-GTCTTACACTGGC-ATT-CGTCTCAATGCCGATGCCATGTCCCATACA-TTATCTTACA
65 -ACATGGTCTTACACTAGCTATTGCGTATCAATGCCGATGCCATGTCCCAGACACAT-TCTTACA
54681776 CTG
128 CTG
54681779 GCACACAAAT
Statistics
Matches: 109, Mismatches: 11, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
137 1 0.01
138 36 0.33
139 2 0.02
140 15 0.14
141 9 0.08
142 12 0.11
143 16 0.15
144 14 0.13
145 4 0.04
ACGTcount: A:0.23, C:0.31, G:0.18, T:0.28
Consensus pattern (145 bp):
GATGCCATGTCCCAGACATGGCCTTACACTAGCTATCATCATCAAGGCCGATGCCATGTCCCAGA
CATGGTCTTACACTAGCTATTGCGTATCAATGCCGATGCCATGTCCCAGACACATTCTTACACTG
ACATGTCTCGTAGCT
Found at i:54690796 original size:101 final size:101
Alignment explanation
Indices: 54690680--54690952 Score: 370
Period size: 101 Copynumber: 2.7 Consensus size: 101
54690670 TAGTATCCTA
* * * * * *
54690680 CACTTAGTACTACACACGTGACTTATCCATCTGATACACGTAGTAGCCTGCACTTAGTACTACAC
1 CACTTAGTACTACACATGCGACCTAACAATCTGGTACACGTAGTAGCCTGCACTTAGTACTACAC
** *
54690745 ACGTGATCGAAGTTAAT-GGGTACGCATAGTA-GCTTG
66 ACGTGATCGAAACT-ATCGGGTACGCATAGCAGGC-TG
* * * *
54690781 TACTTAGTACTACACATGCGACCTAACAATCCGGTACACGTAATAGCTTGCACTTAGTACTACAC
1 CACTTAGTACTACACATGCGACCTAACAATCTGGTACACGTAGTAGCCTGCACTTAGTACTACAC
*
54690846 ACATGATCGAAACTATCGGGTACGCATAGCAGGCTG
66 ACGTGATCGAAACTATCGGGTACGCATAGCAGGCTG
*
54690882 CACTTAGTACTACACATGCGACCTAACAATCTGGTACACGTAGTAGGCTGCACTTAGTACTACAC
1 CACTTAGTACTACACATGCGACCTAACAATCTGGTACACGTAGTAGCCTGCACTTAGTACTACAC
*
54690947 ATGTGA
66 ACGTGA
54690953 CCTAAAACTG
Statistics
Matches: 149, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
100 2 0.01
101 145 0.97
102 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (101 bp):
CACTTAGTACTACACATGCGACCTAACAATCTGGTACACGTAGTAGCCTGCACTTAGTACTACAC
ACGTGATCGAAACTATCGGGTACGCATAGCAGGCTG
Found at i:54690918 original size:151 final size:150
Alignment explanation
Indices: 54690609--54690957 Score: 378
Period size: 151 Copynumber: 2.3 Consensus size: 150
54690599 ATCGAAGCTC
* * * * *
54690609 TCTGGTACGCATAGTAGCCTGCACTTAGTATTACACATGCGGCCTATCAATCTGGTACACGTAGT
1 TCTGGTACGCATAGTAG-CTGCACTTAGTACTACACATGCGACCTAACAATCCGGTACACGTAAT
* * ** * * * *
54690674 ATCCTACACTTAGTACTACACACGTGACTTATCCATCTGATACACGTAGTAGCCTGCACTTAGTA
65 AGCCTACACTTAGTACTACACACATGACGAAACCATCGGATACACATAGCAGCCTGCACTTAGTA
* * *
54690739 CTACACACGTGATCGAAGTTAA
130 CTACACACGCGACCGAAG-CAA
* *
54690761 T-GGGTACGCATAGTAGCTTGTACTTAGTACTACACATGCGACCTAACAATCCGGTACACGTAAT
1 TCTGGTACGCATAGTAGC-TGCACTTAGTACTACACATGCGACCTAACAATCCGGTACACGTAAT
* * * * * *
54690825 AGCTTGCACTTAGTACTACACACATGATCGAAACTATCGGGTACGCATAGCAGGCTGCACTTAGT
65 AGCCTACACTTAGTACTACACACATGA-CGAAACCATCGGATACACATAGCAGCCTGCACTTAGT
* *
54690890 ACTACACATGCGACCTAA-CAA
129 ACTACACACGCGACCGAAGCAA
* * *
54690911 TCTGGTACACGTAGTAGGCTGCACTTAGTACTACACATGTGACCTAA
1 TCTGGTACGCATAGTA-GCTGCACTTAGTACTACACATGCGACCTAA
54690958 AACTGTCTTA
Statistics
Matches: 162, Mismatches: 31, Indels: 9
0.80 0.15 0.04
Matches are distributed among these distances:
150 4 0.02
151 114 0.70
152 44 0.27
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (150 bp):
TCTGGTACGCATAGTAGCTGCACTTAGTACTACACATGCGACCTAACAATCCGGTACACGTAATA
GCCTACACTTAGTACTACACACATGACGAAACCATCGGATACACATAGCAGCCTGCACTTAGTAC
TACACACGCGACCGAAGCAA
Found at i:54691000 original size:52 final size:50
Alignment explanation
Indices: 54690609--54691003 Score: 305
Period size: 50 Copynumber: 7.8 Consensus size: 50
54690599 ATCGAAGCTC
* * * * * *
54690609 TCTGGTACGCATAGTAGCCTGCACTTAGTATTACACATGCGGCCTATCAA
1 TCTGGTACACATAGTAGGCTGCACTTAGTACTACACATGTGACCTAACAA
* ** * * * * *
54690659 TCTGGTACACGTAGTATCCTACACTTAGTACTACACACGTGACTTATCCA
1 TCTGGTACACATAGTAGGCTGCACTTAGTACTACACATGTGACCTAACAA
* * * * * * *
54690709 TCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTAA
1 TCTGGTACACATAGTAGGCTGCACTTAGTACTACACATGTGACCTAA--CAA
* * * *
54690761 T-GGGTACGCATAGTA-GCTTGTACTTAGTACTACACATGCGACCTAACAA
1 TCTGGTACACATAGTAGGC-TGCACTTAGTACTACACATGTGACCTAACAA
* * * ** ** *
54690810 TCCGGTACACGTAATA-GCTTGCACTTAGTACTACACACATGATCGAAACTA
1 TCTGGTACACATAGTAGGC-TGCACTTAGTACTACACATGTGA-CCTAACAA
* * * *
54690861 TCGGGTACGCATAGCAGGCTGCACTTAGTACTACACATGCGACCTAACAA
1 TCTGGTACACATAGTAGGCTGCACTTAGTACTACACATGTGACCTAACAA
*
54690911 TCTGGTACACGTAGTAGGCTGCACTTAGTACTACACATGTGACCTAA-AA
1 TCTGGTACACATAGTAGGCTGCACTTAGTACTACACATGTGACCTAACAA
* * *
54690960 -CTGTCTTAAACACATAGTAGCCTGCACATAGTACTACACATGTG
1 TCTG--GT--ACACATAGTAGGCTGCACTTAGTACTACACATGTG
54691004 TTCTCACAAC
Statistics
Matches: 274, Mismatches: 61, Indels: 18
0.78 0.17 0.05
Matches are distributed among these distances:
48 3 0.01
49 5 0.02
50 161 0.59
51 69 0.25
52 36 0.13
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.26
Consensus pattern (50 bp):
TCTGGTACACATAGTAGGCTGCACTTAGTACTACACATGTGACCTAACAA
Found at i:54691636 original size:30 final size:30
Alignment explanation
Indices: 54691592--54691650 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
54691582 CAAAAATCAT
* *
54691592 ACTTTTACAAATTTGCATTTTGACCCCTAA
1 ACTTTCACAAATTTGCACTTTGACCCCTAA
* * *
54691622 ACTTTCACATATTTGTACTTTGGCCCCTA
1 ACTTTCACAAATTTGCACTTTGACCCCTA
54691651 GGCTCGTAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.25, C:0.25, G:0.08, T:0.41
Consensus pattern (30 bp):
ACTTTCACAAATTTGCACTTTGACCCCTAA
Found at i:54693799 original size:13 final size:13
Alignment explanation
Indices: 54693781--54693805 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54693771 TAATTTATAT
54693781 GTGTGAAAATTTC
1 GTGTGAAAATTTC
54693794 GTGTGAAAATTT
1 GTGTGAAAATTT
54693806 TATCGTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:54699565 original size:49 final size:47
Alignment explanation
Indices: 54699379--54699883 Score: 826
Period size: 47 Copynumber: 10.7 Consensus size: 47
54699369 TTAGGATTCT
* *
54699379 ATGTGATGGATGTGAACA-TGCATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCG
54699426 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
54699473 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
54699520 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
54699569 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
* *
54699618 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCCAATGGTCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
*
54699665 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCCAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
54699714 ATGTGATGAATGTGAAAGTGTATATATGTGAT-A-----AATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
54699755 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
*
54699802 ATGTGATGAATGTGAAAGTGTATATATGTGATAATGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* *
54699849 ATGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
54699884 CCCCGAAGGG
Statistics
Matches: 438, Mismatches: 9, Indels: 22
0.93 0.02 0.05
Matches are distributed among these distances:
41 40 0.09
42 1 0.00
46 2 0.00
47 253 0.58
49 142 0.32
ACGTcount: A:0.32, C:0.08, G:0.29, T:0.30
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:54699642 original size:96 final size:96
Alignment explanation
Indices: 54699400--54699883 Score: 821
Period size: 96 Copynumber: 5.1 Consensus size: 96
54699390 GTGAACATGC
54699400 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
54699465 AATGGCCGATGTGATGAATGTGAAAGTG--T
66 AATGGCCGATGTGATGAATGTGAAAGTGTAT
54699494 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGC
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGC
54699559 CTAATGGCCGATGTGATGAATGTGAAAGTGTAT
64 CTAATGGCCGATGTGATGAATGTGAAAGTGTAT
*
54699592 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCC
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
*
54699657 AATGGTCGATGTGATGAATGTGAAAGTGTAT
66 AATGGCCGATGTGATGAATGTGAAAGTGTAT
*
54699688 ATATATGTGATAAGGCCCAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT-A-----
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
54699747 AATGGCCGATGTGATGAATGTGAAAGTG--T
66 AATGGCCGATGTGATGAATGTGAAAGTGTAT
*
54699776 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAATGCCT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
*
54699841 AATGGCCGATGTGATGGATGTGAAAGTGTAT
66 AATGGCCGATGTGATGAATGTGAAAGTGTAT
54699872 A-A-ATGTGATAAG
1 ATATATGTGATAAG
54699884 CCCCGAAGGG
Statistics
Matches: 372, Mismatches: 6, Indels: 24
0.93 0.01 0.06
Matches are distributed among these distances:
88 58 0.16
89 1 0.00
90 27 0.07
94 83 0.22
95 2 0.01
96 154 0.41
98 47 0.13
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (96 bp):
ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
AATGGCCGATGTGATGAATGTGAAAGTGTAT
Found at i:54700058 original size:37 final size:37
Alignment explanation
Indices: 54700002--54700080 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 37
54699992 CCGAGCTCTA
* * *
54700002 AAGACTCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
* *
54700039 AAGACCCGATAACTTCGTGTGGAGATTATGTTCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
54700076 AAGAC
1 AAGAC
54700081 TTTGCAATAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
37 35 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.28
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:54702019 original size:46 final size:43
Alignment explanation
Indices: 54701931--54702138 Score: 179
Period size: 46 Copynumber: 4.5 Consensus size: 43
54701921 GTATATCTGT
* * *
54701931 GCCGATGCCATGTCCCAGACATGGTCTTACACTGACACATCTCGTA
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCATCTC-AA
*
54701977 GTCGATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTCAA
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGC-T-CATCTCAA
* * * *
54702022 GGCTGATGCATGTCTCATACATGTCTTACACTAGCGCTCGTCTCAA
1 -GCCGATGCATGTCCCAGACATGTCTTACACT-G-GCTCATCTCAA
54702068 TGCCGATGCCATGT-CCAGACATGGTCTTACACTGGCTC-TCAT-AA
1 -GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCATC-TCAA
54702112 TGTGGCCGATGCATGTCCCAGACATGT
1 ----GCCGATGCATGTCCCAGACATGT
54702139 AAAGCGCACA
Statistics
Matches: 136, Mismatches: 14, Indels: 24
0.78 0.08 0.14
Matches are distributed among these distances:
44 16 0.12
45 20 0.15
46 66 0.49
47 32 0.24
48 2 0.01
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (43 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCATCTCAA
Found at i:54702123 original size:93 final size:91
Alignment explanation
Indices: 54701884--54702138 Score: 234
Period size: 93 Copynumber: 2.7 Consensus size: 91
54701874 GTTAGGTGCT
** *
54701884 GATGCCATGTCCAAGACATGGTCTTACACAAGCTCT-AGTATATCTGTGCCGATGCCATGTCCCA
1 GATGCCATGTCC-AGACATGGTCTTACACTGGCTCTCA-TA-ATATG-GCCGATG-CATGTCCCA
* *
54701948 GACATGGTCTTACACTGACACATCTCGTAGTC
61 GACAT-GTCTTACACTGACACATCTCATAGCC
* * * * *
54701980 GATG-CATGTCCCAGACAT-GTCTTACACTGGCT-TACAT-CTCAAGGCTGATGCATGTCTCATA
1 GATGCCATGT-CCAGACATGGTCTTACACTGGCTCT-CATAAT-ATGGCCGATGCATGTCCCAGA
* * *
54702041 CATGTCTTACACTAGCGCTCGTCTCA-ATGCC
63 CATGTCTTACACT-G-ACACATCTCATA-GCC
*
54702072 GATGCCATGTCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCATGTCCCAGACAT
1 GATGCCATGTCCAGACATGGTCTTACACTGGCTCTCATAATATGGCCGATGCATGTCCCAGACAT
54702137 GT
66 GT
54702139 AAAGCGCACA
Statistics
Matches: 129, Mismatches: 19, Indels: 25
0.75 0.11 0.14
Matches are distributed among these distances:
90 10 0.08
91 14 0.11
92 27 0.21
93 45 0.35
94 15 0.12
95 12 0.09
96 6 0.05
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (91 bp):
GATGCCATGTCCAGACATGGTCTTACACTGGCTCTCATAATATGGCCGATGCATGTCCCAGACAT
GTCTTACACTGACACATCTCATAGCC
Found at i:54712448 original size:48 final size:48
Alignment explanation
Indices: 54712389--54712729 Score: 574
Period size: 48 Copynumber: 7.1 Consensus size: 48
54712379 GCGGAAATTG
* * *
54712389 ATGTATAAGATATGTATATGTGGTAAAGCTGAATGGCTAATGTGAAAT
1 ATGTATGAGATAAGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
* * * *
54712437 ATGTATGAGATATGTATATGTGGAAAAGCCAAATGGCTAAAGTGAAAT
1 ATGTATGAGATAAGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
*
54712485 ATGTATGACATAAGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATAAGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
54712533 ATGTATGAGATAAGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATAAGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
*
54712581 ATGTATGAGATAAGTATATGTGGTAAAGCTGAATGGCTAATGTGAAAT
1 ATGTATGAGATAAGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
54712629 ATGTATGAGATAAGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATAAGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
* * *
54712677 ATGTATGAGATATGTATATGTGGTAAAGCCAAATGGCTAGTGTGAAAT
1 ATGTATGAGATAAGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
54712725 ATGTA
1 ATGTA
54712730 GGCGATGTGT
Statistics
Matches: 277, Mismatches: 16, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 277 1.00
ACGTcount: A:0.38, C:0.06, G:0.26, T:0.30
Consensus pattern (48 bp):
ATGTATGAGATAAGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
Found at i:54713014 original size:37 final size:37
Alignment explanation
Indices: 54712876--54713021 Score: 195
Period size: 37 Copynumber: 3.9 Consensus size: 37
54712866 GGAAATATAT
* * *
54712876 TCCGGGTAAGACCCGATGACTACTTGTGGAAATATAT-
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGAT-TTTG
** *
54712913 TCTAGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
54712950 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* **
54712987 TCCGGGTAAGACCCGATAACTTTGTGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
54713022 CATCTGAGCT
Statistics
Matches: 98, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
36 3 0.03
37 95 0.97
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:54714336 original size:40 final size:40
Alignment explanation
Indices: 54714279--54714676 Score: 546
Period size: 40 Copynumber: 10.0 Consensus size: 40
54714269 GAGAGTTATA
* *
54714279 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGT
* *
54714319 TCTATCCGGGCTAAGTCCCGAAGAGCATTTGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGT
* *
54714359 TATATCCGGGCTAAGTCCC-AAGAGCATTCGTGCTAGTGA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGT
* * *
54714398 TGTATCTGGGCTAAGTCCCGAAGAGCATTTGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGT
*
54714438 TATATCCGGGCTAAGTCCCGAAGAGCATTTGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGT
* *
54714478 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGT
* *
54714518 TGTATCCGGGCTAAGTCCCGAAGAGCATTTGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGT
* * * * *
54714558 TATATCCGGGCTAAGTCTCAAAGAGCATTTGTGCTAGAGT
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGT
* * *
54714598 TACATCAGGGTTAAGTCCCGAAGAGCATTCGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGT
* * * * *
54714638 TATAACTGGGCTAGGTCCCGAAGAGCAATCATGCTGGTG
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTG
54714677 ATGTGTATTC
Statistics
Matches: 315, Mismatches: 42, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
39 34 0.11
40 281 0.89
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (40 bp):
TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGT
Found at i:54714890 original size:25 final size:25
Alignment explanation
Indices: 54714840--54714890 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
54714830 TGTGTAACAA
* *
54714840 CAAATGAATAGGGGCACTATGTGTG
1 CAAATGAATAGAGGCACTATGAGTG
*
54714865 CAAATGAGTAGAGGCACTGA-GAGTG
1 CAAATGAATAGAGGCACT-ATGAGTG
54714890 C
1 C
54714891 GAGTTCTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 21 0.95
26 1 0.05
ACGTcount: A:0.33, C:0.14, G:0.33, T:0.20
Consensus pattern (25 bp):
CAAATGAATAGAGGCACTATGAGTG
Found at i:54714959 original size:29 final size:28
Alignment explanation
Indices: 54714887--54714977 Score: 94
Period size: 28 Copynumber: 3.2 Consensus size: 28
54714877 GGCACTGAGA
* *
54714887 GTGCGAGTTCTTCAACTGAGCACTATGT
1 GTGCGAGTTCTTTAATTGAGCACTATGT
**
54714915 GTGCGAGATT-GGTAATTGAGGCACTATGT
1 GTGCGAG-TTCTTTAATTGA-GCACTATGT
* * *
54714944 GTGCAAGTTCTTTAATCGAGCGCTATGT
1 GTGCGAGTTCTTTAATTGAGCACTATGT
54714972 GTGCGA
1 GTGCGA
54714978 AATCAGTCAG
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
28 27 0.54
29 23 0.46
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (28 bp):
GTGCGAGTTCTTTAATTGAGCACTATGT
Found at i:54718362 original size:48 final size:48
Alignment explanation
Indices: 54718296--54718684 Score: 661
Period size: 48 Copynumber: 8.1 Consensus size: 48
54718286 GCGGAAATTG
*
54718296 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATAAGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
** *
54718344 ATGTATGAGATTTGTATATGTGGTAAAGCCAAATGGCTAATGTGAAAT
1 ATGTATGAGATAAGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
* *
54718392 ACGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATAAGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
* *
54718440 ATGTATGACATAAGTATATGTGGTAAAGCCGAATGGTTAATGTGAAAT
1 ATGTATGAGATAAGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
*
54718488 ATGTATGAGATAAGTATATGTGGTTAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATAAGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
54718536 ATGTATGAGATAAGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATAAGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
*
54718584 ATGTATGAGATAAGTATATGTGGTAAAGCCGAATGACTAATGTGAAAT
1 ATGTATGAGATAAGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
* * *
54718632 ATGTATGAGATATGTATAAGTGGTAAAGCCGAATGGCTAGTGTGAAAT
1 ATGTATGAGATAAGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
54718680 ATGTA
1 ATGTA
54718685 GGCGATGTGT
Statistics
Matches: 323, Mismatches: 18, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 323 1.00
ACGTcount: A:0.37, C:0.06, G:0.26, T:0.31
Consensus pattern (48 bp):
ATGTATGAGATAAGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
Found at i:54718870 original size:37 final size:36
Alignment explanation
Indices: 54718820--54718958 Score: 199
Period size: 37 Copynumber: 3.8 Consensus size: 36
54718810 ACATGAAACT
54718820 TGGAAATATATTCCGGGTAAGACCCGATGACTACGTG
1 TGGAAAT-TATTCCGGGTAAGACCCGATGACTACGTG
*
54718857 TGGAAATATATTCCGGGTAAGACCCGATGACTACATG
1 TGGAAAT-TATTCCGGGTAAGACCCGATGACTACGTG
*
54718894 TGGAGATTATGTCCGGGTAAGACCCGATGACTACGTG
1 TGGAAATTAT-TCCGGGTAAGACCCGATGACTACGTG
*
54718931 TGGAGATT-TTGCCCGGGTAAGACCCGAT
1 TGGAAATTATT--CCGGGTAAGACCCGAT
54718959 AACTTTGTGT
Statistics
Matches: 96, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
35 1 0.01
36 4 0.04
37 91 0.95
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.24
Consensus pattern (36 bp):
TGGAAATTATTCCGGGTAAGACCCGATGACTACGTG
Found at i:54718969 original size:37 final size:36
Alignment explanation
Indices: 54718832--54718976 Score: 193
Period size: 37 Copynumber: 3.9 Consensus size: 36
54718822 GAAATATATT
*
54718832 CCGGGTAAGACCCGATGACTACGTGTGGAAATATATT-
1 CCGGGTAAGACCCGATGACTACGTGTGGAGAT-T-TTG
* *
54718869 CCGGGTAAGACCCGATGACTACATGTGGAGATTATG
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
54718905 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 -CCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* **
54718942 CCCGGGTAAGACCCGATAACTTTGTGTGGAGATTT
1 -CCGGGTAAGACCCGATGACTACGTGTGGAGATTT
54718977 CATCTGAGCT
Statistics
Matches: 97, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
35 1 0.01
36 1 0.01
37 95 0.98
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.26
Consensus pattern (36 bp):
CCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:54727745 original size:94 final size:91
Alignment explanation
Indices: 54727498--54727766 Score: 269
Period size: 94 Copynumber: 2.9 Consensus size: 91
54727488 ATAAGGTAAG
* * * * * *
54727498 GTGCTGATGCCATGTCTTAGACACGGTCTTACACTGG--CTCATATCTCAAGTCAATGCCATGTC
1 GTGCTGATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCATATGT--GGCCGATG-CATGTC
* *
54727561 CCAAACATGGTCTTACACTGACTATCCTCTC
63 CCAGACAT-GTCTTACACT-ACCATCCTCTC
* ** *
54727592 GTAGCCGATG-CATGTCCTAGACAT-ACCTTACACTGGCT-TACATCTTGTGGCCGATGCATGTC
1 GT-GCTGATGCCATGTCCTAGACATGGTCTTACACTGGCTCT-CAT-ATGTGGCCGATGCATGTC
* *
54727654 CCAGACATGTCTTACACTATCCCTCGTCTC
63 CCAGACATGTCTTACACTA-CCATCCTCTC
*
54727684 AGTGCTGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCATGTCC
1 -GTGCTGATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCAT-ATGTGGCCGATGCATGTCC
54727749 CAGACATGTCTTACACTA
64 CAGACATGTCTTACACTA
54727767 GCTCACATAA
Statistics
Matches: 145, Mismatches: 20, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
91 1 0.01
92 23 0.16
93 38 0.26
94 71 0.49
95 10 0.07
96 2 0.01
ACGTcount: A:0.22, C:0.30, G:0.19, T:0.29
Consensus pattern (91 bp):
GTGCTGATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCATATGTGGCCGATGCATGTCCCA
GACATGTCTTACACTACCATCCTCTC
Found at i:54727776 original size:46 final size:46
Alignment explanation
Indices: 54727595--54727776 Score: 181
Period size: 46 Copynumber: 3.9 Consensus size: 46
54727585 TCCTCTCGTA
* ** * * **
54727595 GCCGATGCATGTCCTAGACATACCTTACACTGGCTTACATCTTGTG
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCACATAATGTG
* * *
54727641 GCCGATGCATGTCCCAGACATGTCTTACACTATCCCTCGTC-TCA-GT-
1 GCCGATGCATGTCCCAGACATGTCTTACACTA--GCTC-ACATAATGTG
* * *
54727687 GCTGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCACATAATGTG
54727735 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCACATAA
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCACATAA
54727777 GTGACACAAA
Statistics
Matches: 113, Mismatches: 15, Indels: 16
0.78 0.10 0.11
Matches are distributed among these distances:
45 2 0.02
46 58 0.51
47 32 0.28
48 20 0.18
49 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (46 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCACATAATGTG
Found at i:54741327 original size:6 final size:6
Alignment explanation
Indices: 54741316--54741428 Score: 88
Period size: 6 Copynumber: 18.3 Consensus size: 6
54741306 TATCAAAACT
* *
54741316 AGAATC AGAATC AGAATC AGAATC AG-GTGAC AGAATC AGAATC AGTATC
1 AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC AGAATC
* * * *
54741365 AGGTAA-C AGAATC AAAATC AGAATC AGTATC AGGTAA-C AGAATC AAAATT
1 A-G-AATC AGAATC AGAATC AGAATC AGAATC A-G-AATC AGAATC AGAATC
*
54741415 AGAATC AGTATC AG
1 AGAATC AGAATC AG
54741429 GTAACAGAAT
Statistics
Matches: 85, Mismatches: 13, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
5 5 0.06
6 68 0.80
7 9 0.11
8 3 0.04
ACGTcount: A:0.47, C:0.15, G:0.19, T:0.19
Consensus pattern (6 bp):
AGAATC
Found at i:54741328 original size:18 final size:18
Alignment explanation
Indices: 54741316--54741396 Score: 58
Period size: 19 Copynumber: 4.4 Consensus size: 18
54741306 TATCAAAACT
*
54741316 AGAATCAGAATCAGAATC
1 AGAATCAAAATCAGAATC
**
54741334 AGAATC-AGGTGACAGAATC
1 AGAATCAAAAT--CAGAATC
**
54741353 AGAATCAGTATCAGGTAA-C
1 AGAATCAAAATCA-G-AATC
54741372 AGAATCAAAATCAGAATC
1 AGAATCAAAATCAGAATC
*
54741390 AGTATCA
1 AGAATCA
54741397 GGTAACAGAA
Statistics
Matches: 48, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
17 3 0.06
18 16 0.33
19 26 0.54
20 3 0.06
ACGTcount: A:0.47, C:0.16, G:0.19, T:0.19
Consensus pattern (18 bp):
AGAATCAAAATCAGAATC
Found at i:54741349 original size:25 final size:25
Alignment explanation
Indices: 54741321--54741391 Score: 115
Period size: 25 Copynumber: 2.8 Consensus size: 25
54741311 AAACTAGAAT
*
54741321 CAGAATCAGAATCAGAATCAGGTGA
1 CAGAATCAGAATCAGAATCAGGTAA
*
54741346 CAGAATCAGAATCAGTATCAGGTAA
1 CAGAATCAGAATCAGAATCAGGTAA
*
54741371 CAGAATCAAAATCAGAATCAG
1 CAGAATCAGAATCAGAATCAG
54741392 TATCAGGTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (25 bp):
CAGAATCAGAATCAGAATCAGGTAA
Found at i:54741352 original size:31 final size:31
Alignment explanation
Indices: 54741349--54741451 Score: 179
Period size: 31 Copynumber: 3.3 Consensus size: 31
54741339 CAGGTGACAG
54741349 AATCAGAATCAGTATCAGGTAACAGAATCAA
1 AATCAGAATCAGTATCAGGTAACAGAATCAA
54741380 AATCAGAATCAGTATCAGGTAACAGAATCAA
1 AATCAGAATCAGTATCAGGTAACAGAATCAA
* *
54741411 AATTAGAATCAGTATCAGGTAACAGAATAAAA
1 AATCAGAATCAGTATCAGGTAACAGAAT-CAA
54741443 AATCAGAAT
1 AATCAGAAT
54741452 GTGAATGCAA
Statistics
Matches: 68, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
31 58 0.85
32 10 0.15
ACGTcount: A:0.50, C:0.14, G:0.16, T:0.20
Consensus pattern (31 bp):
AATCAGAATCAGTATCAGGTAACAGAATCAA
Found at i:54741374 original size:19 final size:19
Alignment explanation
Indices: 54741352--54741409 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
54741342 GTGACAGAAT
54741352 CAGAATCAGTATCAGGTAA
1 CAGAATCAGTATCAGGTAA
*
54741371 CAGAATCA--A--A---AT
1 CAGAATCAGTATCAGGTAA
54741383 CAGAATCAGTATCAGGTAA
1 CAGAATCAGTATCAGGTAA
54741402 CAGAATCA
1 CAGAATCA
54741410 AAATTAGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
12 9 0.30
14 1 0.03
15 1 0.03
16 1 0.03
17 1 0.03
19 17 0.57
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.19
Consensus pattern (19 bp):
CAGAATCAGTATCAGGTAA
Found at i:54741408 original size:25 final size:25
Alignment explanation
Indices: 54741321--54741438 Score: 110
Period size: 31 Copynumber: 4.2 Consensus size: 25
54741311 AAACTAGAAT
* *
54741321 CAGAATCAGAATCAGAATCAGGTGA
1 CAGAATCAGAATCAGTATCAGGTAA
54741346 CAGAATCAGAATCAGTATCAGGTAA
1 CAGAATCAGAATCAGTATCAGGTAA
54741371 CAGAATCAAAATCAGAATCAGTATCAGGTAA
1 CAG------AATCAGAATCAGTATCAGGTAA
54741402 CAGAATCAAAATTAGAATCAGTATCAGGTAA
1 CAGAATC------AGAATCAGTATCAGGTAA
54741433 CAGAAT
1 CAGAAT
54741439 AAAAAATCAG
Statistics
Matches: 79, Mismatches: 2, Indels: 18
0.80 0.02 0.18
Matches are distributed among these distances:
25 30 0.38
31 49 0.62
ACGTcount: A:0.47, C:0.15, G:0.19, T:0.19
Consensus pattern (25 bp):
CAGAATCAGAATCAGTATCAGGTAA
Found at i:54741630 original size:27 final size:26
Alignment explanation
Indices: 54741588--54741661 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 26
54741578 GCTCAGTTAT
** *
54741588 CAGATATTGTAACAGAGTCACCAAATA
1 CAGATATTGTGGCAGAGCCACCAAA-A
* *
54741615 CAGATATTGTGGCAGAGCCACTAGAA
1 CAGATATTGTGGCAGAGCCACCAAAA
* *
54741641 CAGATAATGTGGCAAAGCCAC
1 CAGATATTGTGGCAGAGCCAC
54741662 TTAACAGAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
26 20 0.50
27 20 0.50
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.19
Consensus pattern (26 bp):
CAGATATTGTGGCAGAGCCACCAAAA
Found at i:54741677 original size:25 final size:26
Alignment explanation
Indices: 54741614--54741679 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 26
54741604 GTCACCAAAT
** *
54741614 ACAGATATTGTGGCAGAGCCACTAGA
1 ACAGATAACGTGGCAAAGCCACTAGA
* *
54741640 ACAGATAATGTGGCAAAGCCACT-TA
1 ACAGATAACGTGGCAAAGCCACTAGA
54741665 ACAGA-ATACGTGGCA
1 ACAGATA-ACGTGGCA
54741680 CAAAGCCATC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
24 1 0.03
25 13 0.37
26 21 0.60
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.18
Consensus pattern (26 bp):
ACAGATAACGTGGCAAAGCCACTAGA
Found at i:54741848 original size:22 final size:22
Alignment explanation
Indices: 54741820--54741884 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
54741810 GCAAATACGT
*
54741820 TTGGCACACAGCCATAATCAGG
1 TTGGCACAAAGCCATAATCAGG
* * *
54741842 TTGGCACAGAGCCAT-GTGTAGG
1 TTGGCACAAAGCCATAAT-CAGG
*
54741864 TTGACACAAAGCCATAATCAG
1 TTGGCACAAAGCCATAATCAG
54741885 AAGGCTTTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
21 1 0.03
22 32 0.94
23 1 0.03
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Found at i:54742367 original size:27 final size:27
Alignment explanation
Indices: 54742336--54742585 Score: 254
Period size: 27 Copynumber: 9.3 Consensus size: 27
54742326 AAGGTATCTC
* *
54742336 GGTAATTCCACCCTACAGGAGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTT
* * **
54742363 AGTAATTCTATCCTACAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTTT
*
54742390 GGTAATTCTACCCTACAGGGTTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTT
*
54742417 GGTAATTCTACCCTACAGGGGTATTTA
1 GGTAATTCTACCCTACAGGGGTATTTT
* *
54742444 GGTAATTCTACCTTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTT
*
54742471 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTT
* *** *
54742498 GGTAATTTTA-TAAACAAAGGGTATTTT
1 GGTAATTCTACCCTAC-AGGGGTATTTT
* * ** *
54742525 AGTAATTTTA-CAAACAATGGGTATTTT
1 GGTAATTCTACCCTAC-AGGGGTATTTT
*
54742552 GGTAATTCTATCCTACAGGGGTATTTCT
1 GGTAATTCTACCCTACAGGGGTATTT-T
54742580 -GTAATT
1 GGTAATT
54742586 TCACAATCGA
Statistics
Matches: 190, Mismatches: 30, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
26 2 0.01
27 184 0.97
28 4 0.02
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTT
Found at i:54742624 original size:27 final size:27
Alignment explanation
Indices: 54742590--54742787 Score: 218
Period size: 27 Copynumber: 7.3 Consensus size: 27
54742580 GTAATTTCAC
* *
54742590 AATCGAGGGTAAAACAGTAATTTTTTA
1 AATCGAGGGTAAAACAGTAATTCTGTA
** *
54742617 AA-CTGAGGGTAAAATGGTAATTTTGTA
1 AATC-GAGGGTAAAACAGTAATTCTGTA
* *
54742644 AATCAAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACAGTAATTCTGTA
* *
54742671 AATCGAGGGTAAAACGGTAATTCTATA
1 AATCGAGGGTAAAACAGTAATTCTGTA
* * *
54742698 TATCGAGGGTAAAATAGTAATTTTGTA
1 AATCGAGGGTAAAACAGTAATTCTGTA
* * *
54742725 TATCGAGGGTGAAACAGTAATTCTATA
1 AATCGAGGGTAAAACAGTAATTCTGTA
** *
54742752 AATCGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAACAGTAATTCTGTA
54742779 AATCGAGGG
1 AATCGAGGG
54742788 CATTTCAGTA
Statistics
Matches: 148, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
26 1 0.01
27 146 0.99
28 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.23, T:0.30
Consensus pattern (27 bp):
AATCGAGGGTAAAACAGTAATTCTGTA
Found at i:54742801 original size:81 final size:81
Alignment explanation
Indices: 54742590--54742787 Score: 281
Period size: 81 Copynumber: 2.4 Consensus size: 81
54742580 GTAATTTCAC
* * * *
54742590 AATCGAGGGTAAAACAGTAATTTTTTAAA-CTGAGGGTAAAATGGTAATTTTGTAAATCAAGGGT
1 AATCGAGGGTAAAACGGTAATTCTATAAATC-GAGGGTAAAATAGTAATTTTGTAAATCAAGGGT
* *
54742654 AAAACGGTAATTCTGTA
65 AAAACAGTAATTCTATA
* * * *
54742671 AATCGAGGGTAAAACGGTAATTCTATATATCGAGGGTAAAATAGTAATTTTGTATATCGAGGGTG
1 AATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAATAGTAATTTTGTAAATCAAGGGTA
54742736 AAACAGTAATTCTATA
66 AAACAGTAATTCTATA
*
54742752 AATCGAGGGTAAAATGGTAATTCTATAAATCGAGGG
1 AATCGAGGGTAAAACGGTAATTCTATAAATCGAGGG
54742788 CATTTCAGTA
Statistics
Matches: 104, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
81 103 0.99
82 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.23, T:0.30
Consensus pattern (81 bp):
AATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAATAGTAATTTTGTAAATCAAGGGTA
AAACAGTAATTCTATA
Found at i:54745721 original size:27 final size:27
Alignment explanation
Indices: 54745691--54745868 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 27
54745681 ATATTGAGTC
* *
54745691 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
54745718 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
54745745 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
54745773 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
54745800 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
** * *
54745827 CGCACACTTAGTGGAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
54745854 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54745869 GTACAATTTA
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 103 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:54745830 original size:82 final size:81
Alignment explanation
Indices: 54745712--54745867 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
54745702 TGCTATATAA
* *
54745712 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
54745777 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
54745794 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGGAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
54745858 CACTTAGTGC
65 CACTTAGTGC
54745868 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 16 0.24
82 50 0.76
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:54745851 original size:54 final size:54
Alignment explanation
Indices: 54745691--54745867 Score: 196
Period size: 54 Copynumber: 3.3 Consensus size: 54
54745681 ATATTGAGTC
* * * *
54745691 CGCACACTCAGTGCTAT-ATAATCAACTCGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGC-ATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
* ** * *
54745745 CGCACACTTAGTGC-TACATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCAT-CATAATC-AACTCGCACACTTAGTGCAACATAGTCAAAT
* ** *
54745800 CGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGGAACATAGTCAAAT
1 CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
54745854 CGCACACTTAGTGC
1 CGCACACTTAGTGC
54745868 TGTACAATTT
Statistics
Matches: 103, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
52 1 0.01
54 56 0.54
55 45 0.44
56 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:54753663 original size:27 final size:27
Alignment explanation
Indices: 54753633--54753728 Score: 129
Period size: 27 Copynumber: 3.5 Consensus size: 27
54753623 ATATTGAGTC
* *
54753633 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
54753660 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
54753687 CGTACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
54753715 CGCACACTTAGTGC
1 CGCACACTTAGTGC
54753729 CGCATGGTCC
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
27 43 0.73
28 16 0.27
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:54753779 original size:27 final size:27
Alignment explanation
Indices: 54753744--54753818 Score: 114
Period size: 27 Copynumber: 2.8 Consensus size: 27
54753734 GGTCCGCATG
*
54753744 GTCAATTCGCACACTTAGTGCATCATA
1 GTCAATTCGCACACTTAGTGCAACATA
* *
54753771 TTCATTTCGCACACTTAGTGCAACATA
1 GTCAATTCGCACACTTAGTGCAACATA
*
54753798 GTCAAATCGCACACTTAGTGC
1 GTCAATTCGCACACTTAGTGC
54753819 TGTACAATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (27 bp):
GTCAATTCGCACACTTAGTGCAACATA
Found at i:54755901 original size:6 final size:6
Alignment explanation
Indices: 54755883--54756010 Score: 93
Period size: 6 Copynumber: 20.8 Consensus size: 6
54755873 AAGAAACATT
* * *
54755883 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAGA ATCAG- GTGACAAA ATTAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA
* * *
54755932 ATCAGA ATCAGT ATCAGGTA A-CAGA ATCAAA ATCAGA ATCAGT ATCAGGTA
1 ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA ATCAGA ATCA-G-A
* *
54755983 A-CAGA ATCAAA ATCAGA ATCAGT ATCAG
1 ATCAGA ATCAGA ATCAGA ATCAGA ATCAG
54756011 GTAACAGAAT
Statistics
Matches: 96, Mismatches: 15, Indels: 22
0.72 0.11 0.17
Matches are distributed among these distances:
5 6 0.06
6 78 0.81
7 9 0.09
8 3 0.03
ACGTcount: A:0.48, C:0.16, G:0.17, T:0.20
Consensus pattern (6 bp):
ATCAGA
Found at i:54755904 original size:18 final size:18
Alignment explanation
Indices: 54755883--54756010 Score: 93
Period size: 19 Copynumber: 6.9 Consensus size: 18
54755873 AAGAAACATT
54755883 ATCAGAA-CTAGAATCAGA
1 ATCAGAATC-AGAATCAGA
54755901 ATCAGAATCAGAATCAG-
1 ATCAGAATCAGAATCAGA
* * *
54755918 GTGACAAAATTAGAATCAGA
1 AT--CAGAATCAGAATCAGA
*
54755938 ATCAGTATCAGGTAA-CAGA
1 ATCAGAATCA-G-AATCAGA
* *
54755957 ATCAAAATCAGAATCAGT
1 ATCAGAATCAGAATCAGA
*
54755975 ATCAGGTAA-CAGAATCAAA
1 ATCA-G-AATCAGAATCAGA
*
54755994 ATCAGAATCAGTATCAG
1 ATCAGAATCAGAATCAG
54756011 GTAACAGAAT
Statistics
Matches: 85, Mismatches: 15, Indels: 20
0.71 0.12 0.17
Matches are distributed among these distances:
17 5 0.06
18 36 0.42
19 39 0.46
20 5 0.06
ACGTcount: A:0.48, C:0.16, G:0.17, T:0.20
Consensus pattern (18 bp):
ATCAGAATCAGAATCAGA
Found at i:54755933 original size:31 final size:31
Alignment explanation
Indices: 54755892--54756033 Score: 212
Period size: 31 Copynumber: 4.5 Consensus size: 31
54755882 TATCAGAACT
* * *
54755892 AGAATCAGAATCAGAATCAGAATCAGGTGAC
1 AGAATCAAAATCAGAATCAGTATCAGGTAAC
* * *
54755923 AAAATTAGAATCAGAATCAGTATCAGGTAAC
1 AGAATCAAAATCAGAATCAGTATCAGGTAAC
54755954 AGAATCAAAATCAGAATCAGTATCAGGTAAC
1 AGAATCAAAATCAGAATCAGTATCAGGTAAC
54755985 AGAATCAAAATCAGAATCAGTATCAGGTAAC
1 AGAATCAAAATCAGAATCAGTATCAGGTAAC
*
54756016 AGAATAAAAAATCAGAAT
1 AGAAT-CAAAATCAGAAT
54756034 GTGAATGTAA
Statistics
Matches: 102, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
31 91 0.89
32 11 0.11
ACGTcount: A:0.50, C:0.14, G:0.17, T:0.19
Consensus pattern (31 bp):
AGAATCAAAATCAGAATCAGTATCAGGTAAC
Found at i:54756233 original size:26 final size:27
Alignment explanation
Indices: 54756170--54756243 Score: 105
Period size: 27 Copynumber: 2.8 Consensus size: 27
54756160 GCTCAGTTAT
* *
54756170 CAGATATTGTGACAGAGTCACCAGATA
1 CAGATATTGTGGCAGAGCCACCAGATA
54756197 CAGATATTGTGGCAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
* *
54756223 CAGATAATGTGGCAAAGCCAC
1 CAGATATTGTGGCAGAGCCAC
54756244 TTAACAGAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
26 20 0.47
27 23 0.53
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:54756428 original size:22 final size:23
Alignment explanation
Indices: 54756400--54756463 Score: 78
Period size: 22 Copynumber: 2.9 Consensus size: 23
54756390 AGGCAAATAC
*
54756400 GGTTGGCACACAGCCATAAT-CA
1 GGTTGGCACAAAGCCATAATGCA
* *
54756422 GGTTGGCACAGAGCCAT-ATGTA
1 GGTTGGCACAAAGCCATAATGCA
*
54756444 GGTTGACACAAAGCCATAAT
1 GGTTGGCACAAAGCCATAAT
54756464 TAGAAGGCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 2 0.06
22 32 0.89
23 2 0.06
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.20
Consensus pattern (23 bp):
GGTTGGCACAAAGCCATAATGCA
Found at i:54757084 original size:81 final size:80
Alignment explanation
Indices: 54756910--54757166 Score: 268
Period size: 81 Copynumber: 3.2 Consensus size: 80
54756900 TACCCCACAA
* * * * *
54756910 GGTATCTCGGTAATTCCACCATACAGGGGTATTTTAG-AATTCTACCCTACAAGGGTATTCCAGT
1 GGTATTTCAGTAATTCTACCATACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTCGA-T
54756974 AATTCTACCCTACAGG
65 AATTCTACCCTACAGG
** **
54756990 GGTATTTTGGTAATTCTACCATACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTACGAT
1 GGTATTTCAGTAATTCTACCATACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATT-CGAT
54757055 AATTCTACCCTACAGG
65 AATTCTACCCTACAGG
* * * * * ** *
54757071 GGTATTTCAGTAATTTTA-TAAACAAAGGGTATTTTAGTAATTTTA-CAAACAAGGGGTATTTTG
1 GGTATTTCAGTAATTCTACCATAC-AGGGGTATTTTAGTAATTCTACCCTAC-AGGGGTA-TTCG
* * *
54757134 GTAATTTTATCCTACAGG
63 ATAATTCTACCCTACAGG
54757152 GGTATTTCAGTAATT
1 GGTATTTCAGTAATT
54757167 TCACAATCGA
Statistics
Matches: 150, Mismatches: 22, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
80 38 0.25
81 108 0.72
82 4 0.03
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (80 bp):
GGTATTTCAGTAATTCTACCATACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTCGATA
ATTCTACCCTACAGG
Found at i:54757167 original size:27 final size:27
Alignment explanation
Indices: 54756893--54757166 Score: 234
Period size: 27 Copynumber: 10.2 Consensus size: 27
54756883 GGGCAAAATG
* * * * *
54756893 GTAATTTTACCCCACA-AGGTATCTCG
1 GTAATTCTACCCTACAGGGGTATTTCA
* * *
54756919 GTAATTCCACCATACAGGGGTATTTTA
1 GTAATTCTACCCTACAGGGGTATTTCA
* *
54756946 G-AATTCTACCCTACAAGGGTATTCCA
1 GTAATTCTACCCTACAGGGGTATTTCA
**
54756972 GTAATTCTACCCTACAGGGGTATTTTG
1 GTAATTCTACCCTACAGGGGTATTTCA
* *
54756999 GTAATTCTACCATACAGGGGTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTCA
*
54757026 GTAATTCTACCCTACAGGGGTATTAC-
1 GTAATTCTACCCTACAGGGGTATTTCA
54757052 GATAATTCTACCCTACAGGGGTATTTCA
1 G-TAATTCTACCCTACAGGGGTATTTCA
* *** * *
54757080 GTAATTTTA-TAAACAAAGGGTATTTTA
1 GTAATTCTACCCTAC-AGGGGTATTTCA
* ** **
54757107 GTAATTTTA-CAAACAAGGGGTATTTTG
1 GTAATTCTACCCTAC-AGGGGTATTTCA
* *
54757134 GTAATTTTATCCTACAGGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
54757161 GTAATT
1 GTAATT
54757167 TCACAATCGA
Statistics
Matches: 207, Mismatches: 35, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
26 36 0.17
27 167 0.81
28 4 0.02
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Consensus pattern (27 bp):
GTAATTCTACCCTACAGGGGTATTTCA
Found at i:54757205 original size:27 final size:27
Alignment explanation
Indices: 54757171--54757354 Score: 253
Period size: 27 Copynumber: 6.8 Consensus size: 27
54757161 GTAATTTCAC
54757171 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTTTGTA
** *
54757198 AA-CTGAGGGTAAAATAGTAATTTTTTA
1 AATC-GAGGGTAAAACGGTAATTTTGTA
54757225 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTTTGTA
* * *
54757252 AATCGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTTTGTA
*
54757279 AATCGAGGGTGAAACGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTTTGTA
* * *
54757306 AATCGAGGGTGAAACGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTTTGTA
*
54757333 AATCGAGGGTAAAATGGTAATT
1 AATCGAGGGTAAAACGGTAATT
54757355 CTACAAATCA
Statistics
Matches: 138, Mismatches: 17, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
26 1 0.01
27 136 0.99
28 1 0.01
ACGTcount: A:0.38, C:0.07, G:0.25, T:0.30
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTTTGTA
Found at i:54757363 original size:54 final size:54
Alignment explanation
Indices: 54757171--54757354 Score: 289
Period size: 54 Copynumber: 3.4 Consensus size: 54
54757161 GTAATTTCAC
* * *
54757171 AATCGAGGGTAAAACGGTAATTTTGTAAA-CTGAGGGTAAAATAGTAATTTTTTA
1 AATCGAGGGTAAAACGGTAATTTTGTAAATC-GAGGGTAAAATGGTAATTCTATA
54757225 AATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATA
* * *
54757279 AATCGAGGGTGAAACGGTAATTTTGTAAATCGAGGGTGAAACGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATA
*
54757333 AATCGAGGGTAAAATGGTAATT
1 AATCGAGGGTAAAACGGTAATT
54757355 CTACAAATCA
Statistics
Matches: 121, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
54 120 0.99
55 1 0.01
ACGTcount: A:0.38, C:0.07, G:0.25, T:0.30
Consensus pattern (54 bp):
AATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATA
Found at i:54763560 original size:49 final size:49
Alignment explanation
Indices: 54763488--54763588 Score: 184
Period size: 49 Copynumber: 2.1 Consensus size: 49
54763478 TCCTCAGGCG
*
54763488 TGCACGACAATTCATCAAACACTCTGATGGTGTTCTCTAAACAAAACTT
1 TGCACGACAATTCATCAAACACTCTGATGGTATTCTCTAAACAAAACTT
*
54763537 TGCACGACAATTCATTAAACACTCTGATGGTATTCTCTAAACAAAACTT
1 TGCACGACAATTCATCAAACACTCTGATGGTATTCTCTAAACAAAACTT
54763586 TGC
1 TGC
54763589 TTTCTCCGGG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.30
Consensus pattern (49 bp):
TGCACGACAATTCATCAAACACTCTGATGGTATTCTCTAAACAAAACTT
Found at i:54768829 original size:23 final size:23
Alignment explanation
Indices: 54768769--54768822 Score: 76
Period size: 21 Copynumber: 2.3 Consensus size: 23
54768759 ACGTATTATA
54768769 TATATTTTA-TA-ATTATTTACT
1 TATATTTTATTATATTATTTACT
54768790 TATATTTTATTATATTATATTACT
1 TATATTTTATTATATTAT-TTACT
54768814 TCATATTTT
1 T-ATATTTT
54768823 TCTATTATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 9 0.31
22 2 0.07
23 5 0.17
24 6 0.21
25 7 0.24
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (23 bp):
TATATTTTATTATATTATTTACT
Found at i:54768931 original size:18 final size:18
Alignment explanation
Indices: 54768900--54768937 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
54768890 TCACATAATA
*
54768900 TTTATATATTTTTATATT
1 TTTATATATTTTTACATT
54768918 TTTATAT-TATTTTACATT
1 TTTATATAT-TTTTACATT
54768936 TT
1 TT
54768938 AACAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTATATATTTTTACATT
Found at i:54769168 original size:21 final size:22
Alignment explanation
Indices: 54769134--54769177 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
54769124 TATTTCAAAA
*
54769134 TTCATTATTAATT-ACTATGTT
1 TTCATTATTAATTAAATATGTT
54769155 TTCATGTATT-ATTAAATATGTT
1 TTCAT-TATTAATTAAATATGTT
54769177 T
1 T
54769178 ATTATCTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (22 bp):
TTCATTATTAATTAAATATGTT
Found at i:54781785 original size:47 final size:47
Alignment explanation
Indices: 54781719--54782207 Score: 493
Period size: 47 Copynumber: 10.1 Consensus size: 47
54781709 GAAATGATAG
*
54781719 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
*
54781766 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
54781813 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
*
54781860 TAAGGCCAAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
* *
54781907 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
** *** * * * *
54781954 TAAGGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAA-TGTGA-AAGTGT-A
1 TAAGGCCTA-ATG-GCCGATG--TGAT-G--AATGTGA--AAGTGT-ATATGTGTGA
* * * *
54782008 TATATGTG-ATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTAA
1 TA-A-G-GCCTAATG-------GCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
*
54782064 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
*
54782111 TAAGGCCTAATGGCCGATGTG-TGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
* * * * * * * * **
54782157 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
54782204 TAAG
1 TAAG
54782208 TCCCGAAGGG
Statistics
Matches: 376, Mismatches: 42, Indels: 48
0.81 0.09 0.10
Matches are distributed among these distances:
46 40 0.11
47 267 0.71
48 2 0.01
49 3 0.01
51 3 0.01
52 1 0.00
53 1 0.00
54 17 0.05
55 18 0.05
56 16 0.04
57 1 0.00
58 1 0.00
59 3 0.01
61 3 0.01
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
Found at i:54781953 original size:16 final size:16
Alignment explanation
Indices: 54781932--54781974 Score: 70
Period size: 16 Copynumber: 2.7 Consensus size: 16
54781922 GATGTGATGA
54781932 ATGTGA-AAGTGTATAT
1 ATGTGATAAG-GTATAT
54781948 ATGTGATAAGGTATAT
1 ATGTGATAAGGTATAT
54781964 ATGTGATAAGG
1 ATGTGATAAGG
54781975 CCTAATAGCC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 23 0.88
17 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.28, T:0.35
Consensus pattern (16 bp):
ATGTGATAAGGTATAT
Found at i:54781962 original size:63 final size:63
Alignment explanation
Indices: 54781885--54782021 Score: 249
Period size: 63 Copynumber: 2.2 Consensus size: 63
54781875 GATGTGATGA
*
54781885 ATGTGA-AAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATAAG-GTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
54781948 ATGTGATAAGGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATAAGGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
54782011 ATGTGATAAGG
1 ATGTGATAAGG
54782022 CCTAATAGCC
Statistics
Matches: 72, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
63 69 0.96
64 3 0.04
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.31
Consensus pattern (63 bp):
ATGTGATAAGGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
Found at i:54781962 original size:110 final size:110
Alignment explanation
Indices: 54781838--54782068 Score: 401
Period size: 110 Copynumber: 2.1 Consensus size: 110
54781828 GATGTGATGA
* * *
54781838 ATGTGA-AAGTGTATATGTGTGATAAGGCCAAATGGCCGATGTGATGAATGTGAAAGTGTATATG
1 ATGTGATAAG-GTATATATGTGATAAGGCCAAATAGCCGATGTGATGAATGTGAAAGTGTATATA
54781902 TGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
65 TGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
*
54781948 ATGTGATAAGGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGATAAGGTATATATGTGATAAGGCCAAATAGCCGATGTGATGAATGTGAAAGTGTATATAT
54782013 GTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
66 GTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
*
54782058 ATGTAATAAGG
1 ATGTGATAAGG
54782069 CCTAATGGCC
Statistics
Matches: 115, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
110 112 0.97
111 3 0.03
ACGTcount: A:0.34, C:0.07, G:0.29, T:0.30
Consensus pattern (110 bp):
ATGTGATAAGGTATATATGTGATAAGGCCAAATAGCCGATGTGATGAATGTGAAAGTGTATATAT
GTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
Found at i:54781996 original size:157 final size:157
Alignment explanation
Indices: 54781791--54782115 Score: 562
Period size: 157 Copynumber: 2.1 Consensus size: 157
54781781 GATGTGATGA
* * *
54781791 ATGTGA-AAGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATG
1 ATGTGATAAG-GTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATA
* * *
54781855 TGTGATAAGGCCAAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAG
65 TGTGATAAGGCCAAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTAATAAGGCCTAATAG
54781920 CCGATGTGATGAATGTGAAAGTGTATAT
130 CCGATGTGATGAATGTGAAAGTGTATAT
54781948 ATGTGATAAGGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGATAAGGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATAT
* *
54782013 GTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTAATAAGGCCTAATGGC
66 GTGATAAGGCCAAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTAATAAGGCCTAATAGC
54782078 CGATGTGATGAATGTGAAAGTGTATAT
131 CGATGTGATGAATGTGAAAGTGTATAT
54782105 ATGTGATAAGG
1 ATGTGATAAGG
54782116 CCTAATGGCC
Statistics
Matches: 159, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
157 156 0.98
158 3 0.02
ACGTcount: A:0.33, C:0.07, G:0.29, T:0.30
Consensus pattern (157 bp):
ATGTGATAAGGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATAT
GTGATAAGGCCAAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTAATAAGGCCTAATAGC
CGATGTGATGAATGTGAAAGTGTATAT
Found at i:54782104 original size:204 final size:203
Alignment explanation
Indices: 54781744--54782156 Score: 738
Period size: 204 Copynumber: 2.0 Consensus size: 203
54781734 GATGTGATGA
*
54781744 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGT
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATAT
* * *
54781809 GTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCAAATGGC
66 GTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTAATAAGGCCAAATGGC
*
54781874 CGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
131 CGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTG-TGAATGTGAA
54781939 AGTGTATAT
195 AGTGTATAT
54781948 ATGTGATAAG-GTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATA
1 ATGTGA-AAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATA
*
54782012 TGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTAATAAGGCCTAATGG
65 TGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTAATAAGGCCAAATGG
*
54782077 CCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGTGAATGTGAA
130 CCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGTGAATGTGAA
54782142 AGTGTATAT
195 AGTGTATAT
54782151 ATGTGA
1 ATGTGA
54782157 CAGGGCCGAG
Statistics
Matches: 201, Mismatches: 7, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
203 25 0.12
204 173 0.86
205 3 0.01
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (203 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATAT
GTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTAATAAGGCCAAATGGC
CGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGTGAATGTGAAA
GTGTATAT
Found at i:54784355 original size:17 final size:16
Alignment explanation
Indices: 54784336--54784432 Score: 92
Period size: 17 Copynumber: 5.9 Consensus size: 16
54784326 TTCGAAAATC
54784336 AAAAAAAG-AAAAAAA
1 AAAAAAAGAAAAAAAA
* *
54784351 ACAAACAGAAAATAAAA
1 AAAAAAAGAAAA-AAAA
54784368 AAAAACAA-AAAACAAAA
1 AAAAA-AAGAAAA-AAAA
*
54784385 CAAAGAAAA-AAAACAAA
1 -AAA-AAAAGAAAAAAAA
54784402 AAAAAAAGAAAAAAAA
1 AAAAAAAGAAAAAAAA
54784418 AGAAAAAAGAAAAAA
1 A-AAAAAAGAAAAAA
54784433 GAGAGAAGAG
Statistics
Matches: 68, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
15 10 0.15
16 14 0.21
17 32 0.47
18 10 0.15
19 2 0.03
ACGTcount: A:0.87, C:0.06, G:0.06, T:0.01
Consensus pattern (16 bp):
AAAAAAAGAAAAAAAA
Found at i:54784362 original size:29 final size:28
Alignment explanation
Indices: 54784329--54784424 Score: 96
Period size: 25 Copynumber: 3.5 Consensus size: 28
54784319 TTGAGGTTTC
54784329 GAAAATCAAAAAAAGAA-AAAAAACAAACA
1 GAAAAT-AAAAAAA-AACAAAAAACAAACA
54784358 GAAAATAAAAAAAAACAAAAAACAAA-A
1 GAAAATAAAAAAAAACAAAAAACAAACA
* *
54784385 -CAAA-GAAAAAAAACAAAAAA-AAA-A
1 GAAAATAAAAAAAAACAAAAAACAAACA
*
54784409 GAAAAAAAAAGAAAAA
1 GAAAATAAAA-AAAAA
54784425 AGAAAAAAGA
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
24 4 0.07
25 18 0.31
26 6 0.10
27 8 0.14
28 17 0.29
29 6 0.10
ACGTcount: A:0.84, C:0.07, G:0.06, T:0.02
Consensus pattern (28 bp):
GAAAATAAAAAAAAACAAAAAACAAACA
Found at i:54784390 original size:46 final size:45
Alignment explanation
Indices: 54784330--54784432 Score: 143
Period size: 46 Copynumber: 2.3 Consensus size: 45
54784320 TGAGGTTTCG
* * * *
54784330 AAAATCAAAAAAAGAAAAAAAACAAACAGAAAATAAAAAAAAACA
1 AAAAACAAAAAAAGAAAAAAAACAAAAAAAAAAGAAAAAAAAACA
*
54784375 AAAAACAAAACAAAGAAAAAAAACAAAAAAAAAAGAAAAAAAAAGA
1 AAAAACAAAA-AAAGAAAAAAAACAAAAAAAAAAGAAAAAAAAACA
*
54784421 AAAAAGAAAAAA
1 AAAAACAAAAAA
54784433 GAGAGAAGAG
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
45 11 0.22
46 40 0.78
ACGTcount: A:0.85, C:0.07, G:0.06, T:0.02
Consensus pattern (45 bp):
AAAAACAAAAAAAGAAAAAAAACAAAAAAAAAAGAAAAAAAAACA
Found at i:54784425 original size:29 final size:28
Alignment explanation
Indices: 54784330--54784425 Score: 95
Period size: 31 Copynumber: 3.1 Consensus size: 28
54784320 TGAGGTTTCG
*
54784330 AAAATCAAAAAAAGAAAAAAAACAAACAGAA
1 AAAAACAAAAAAA-AAAAAAAA-AAA-AGAA
54784361 AATAAA-AAAAAACAAAAAACAAAACAAAGAAA
1 AA-AAACAAAAAA-AAAAAA-AAAA-AAAG-AA
54784393 AAAAACAAAAAAAAAAGAAAAAAAAAGAA
1 AAAAACAAAAAAAAAA-AAAAAAAAAGAA
54784422 AAAA
1 AAAA
54784426 GAAAAAAGAG
Statistics
Matches: 57, Mismatches: 1, Indels: 16
0.77 0.01 0.22
Matches are distributed among these distances:
29 6 0.11
30 4 0.07
31 27 0.47
32 20 0.35
ACGTcount: A:0.85, C:0.07, G:0.05, T:0.02
Consensus pattern (28 bp):
AAAAACAAAAAAAAAAAAAAAAAAAGAA
Found at i:54784430 original size:24 final size:23
Alignment explanation
Indices: 54784336--54784434 Score: 92
Period size: 26 Copynumber: 4.0 Consensus size: 23
54784326 TTCGAAAATC
54784336 AAAAAAAGAAAAAAAACAAACAGAA
1 AAAAAAAGAAAAAAAA-AAA-AGAA
*
54784361 AATAAAAA-AAAACAAAAAACAAAACA
1 AA-AAAAAGAAAA-AAAAAA-AAGA-A
*
54784387 AAGAAAAAAAACAAAAAAAAAAGAA
1 AA-AAAAAGAA-AAAAAAAAAAGAA
54784412 AAAAAAAGAAAAAAGAAAAAAGA
1 AAAAAAAGAAAAAA-AAAAAAGA
54784435 GAGAAGAGGA
Statistics
Matches: 63, Mismatches: 4, Indels: 15
0.77 0.05 0.18
Matches are distributed among these distances:
23 4 0.06
24 15 0.24
25 13 0.21
26 21 0.33
27 8 0.13
28 2 0.03
ACGTcount: A:0.86, C:0.06, G:0.07, T:0.01
Consensus pattern (23 bp):
AAAAAAAGAAAAAAAAAAAAGAA
Found at i:54784449 original size:1 final size:1
Alignment explanation
Indices: 54784336--54784432 Score: 77
Period size: 1 Copynumber: 97.0 Consensus size: 1
54784326 TTCGAAAATC
* * * * * * * * * *
54784336 AAAAAAAGAAAAAAAACAAACAGAAAATAAAAAAAAACAAAAAACAAAACAAAGAAAAAAAACAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
54784401 AAAAAAAAGAAAAAAAAAGAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
54784433 GAGAGAAGAG
Statistics
Matches: 70, Mismatches: 26, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 70 1.00
ACGTcount: A:0.87, C:0.06, G:0.06, T:0.01
Consensus pattern (1 bp):
A
Found at i:54785544 original size:413 final size:413
Alignment explanation
Indices: 54784472--54785708 Score: 2447
Period size: 414 Copynumber: 3.0 Consensus size: 413
54784462 GAGGCCAAGG
54784472 TGAAAACCCGCAAAGGGCGCCTTGTGACCAAAAGGGTTTTGAGTTGAAAACCTGAAAGGTGACTC
1 TGAAAACCCGCAAAGGGCGCCTTGTGACCAAAAGGGTTTTGAGTTGAAAACCTGAAAGGTGACTC
54784537 AAATTTTGAAGCATCTGATAATCTTTCTCAACAAAGAACGAAGAACGTTGCATACTGGGGCATCG
66 AAATTTTGAAGCATCTGATAATCTTTCTCAACAAAGAACGAAGAACGTTGCATACTGGGGCATCG
54784602 ACAGAGTACTTTGAATCTTCTAAACACATGCCTTCATGAAGTTGATGTATAAGCGCTCAAGCGGC
131 ACAGAGTACTTTGAATCTTCTAAACACATGCCTTCATGAAGTTGATGTATAAGCGCTCAAGCGGC
54784667 GATATCTAGGGCATCTAATTTTTGGCTTGTTTGCTATCTTTAGATTTTTTTTTCTTCTCAAAGAT
196 GATATCTAGGGCATCTAATTTTTGGCTTGTTTGCTATCTTTAGATTTTTTTTTCTTCTCAAAGAT
54784732 ACGCTTTCAGATTAATTTCCTTTGTATCTTTTTCGATAATTCATTCAAATCCAATTATTCTTAGA
261 ACGCTTTCAGATTAATTTCCTTTGTATCTTTTTCGATAATTCATTCAAATCCAATTATTCTTAGA
54784797 GATTTTTTTATCTTCCATTATTCTTTAAGTATGTTGCATTGAAATAATGATAGATGAACTAAATA
326 GATTTTTTTATCTTCCATTATTCTTTAAGTATGTTGCATTGAAATAATGATAGATGAACTAAATA
54784862 TGTTCACAAATGAAGTTTTGAGT
391 TGTTCACAAATGAAGTTTTGAGT
*
54784885 TGAAAACCCACAAAGGGCGCCTTGTGACCAAAAGGGTTTTGAGTTGAAAACCTGAAAGGTGACTC
1 TGAAAACCCGCAAAGGGCGCCTTGTGACCAAAAGGGTTTTGAGTTGAAAACCTGAAAGGTGACTC
54784950 AAATTTTGAAGCATCTGATAATCTTTCTCAACAAAGAACGAAGAACGTTGCATACTGGGGCATCG
66 AAATTTTGAAGCATCTGATAATCTTTCTCAACAAAGAACGAAGAACGTTGCATACTGGGGCATCG
54785015 ACAGAGTACTTTGAATCTTCTAAACACATGCCTTCATGAAGTTGATGTATAAGCGCTCAAGCGGC
131 ACAGAGTACTTTGAATCTTCTAAACACATGCCTTCATGAAGTTGATGTATAAGCGCTCAAGCGGC
54785080 GATATCTAGGGCATCTAATTTTTGGCTTGTTTGCTATCTTTAGATTTTTTTTTTCTTCTCAAAGA
196 GATATCTAGGGCATCTAATTTTTGGCTTGTTTGCTATCTTTAGA-TTTTTTTTTCTTCTCAAAGA
*
54785145 TAGGCTTTCAGATTAATTTCCTTTGTATCTTTTTCGATAATTCATTCAAATCCAATTATTCTTAG
260 TACGCTTTCAGATTAATTTCCTTTGTATCTTTTTCGATAATTCATTCAAATCCAATTATTCTTAG
54785210 AGATTTTTTTATCTTCCATTATTCTTTAAGTATGTTGCATTGAAATAATGATAGATGAACTAAAT
325 AGATTTTTTTATCTTCCATTATTCTTTAAGTATGTTGCATTGAAATAATGATAGATGAACTAAAT
54785275 ATGTTCACAAATGAAGTTTTGAGT
390 ATGTTCACAAATGAAGTTTTGAGT
54785299 TGAAAACCCGCAAAGGGCGCCTTGTGACCAAAAGGGTTTTGAGTTGAAAACCTGAAAGGTGACTC
1 TGAAAACCCGCAAAGGGCGCCTTGTGACCAAAAGGGTTTTGAGTTGAAAACCTGAAAGGTGACTC
54785364 AAATTTTGAAGCATCTGATAATCTTTCTCAACAAAGAACGAAGAACGTTGCATACTGGGGCATCG
66 AAATTTTGAAGCATCTGATAATCTTTCTCAACAAAGAACGAAGAACGTTGCATACTGGGGCATCG
54785429 ACAGAGTACTTTGAATCTTCTAAACACATGCCTTCATGAAGTTGATGTATAAGCGCTCAAGCGGC
131 ACAGAGTACTTTGAATCTTCTAAACACATGCCTTCATGAAGTTGATGTATAAGCGCTCAAGCGGC
54785494 GATATCTAGGGCATCTAATTTTTGGCTTGTTTGCTATCTTTAGATTTTTTTTTCTTCTCAAAGAT
196 GATATCTAGGGCATCTAATTTTTGGCTTGTTTGCTATCTTTAGATTTTTTTTTCTTCTCAAAGAT
54785559 ACGCTTTCAGATTAATTTCCTTTGTATCTTTTTCGATAATTCATTCAAATCCAATTATTCTTAGA
261 ACGCTTTCAGATTAATTTCCTTTGTATCTTTTTCGATAATTCATTCAAATCCAATTATTCTTAGA
54785624 GATTTTTTTATCTTCCATTATTCTTTAAGTATGTTGCATTGAAATAATGATAGATGAACTAAATA
326 GATTTTTTTATCTTCCATTATTCTTTAAGTATGTTGCATTGAAATAATGATAGATGAACTAAATA
54785689 TGTTCACAAATGAAGTTTTG
391 TGTTCACAAATGAAGTTTTG
54785709 CGCATTACTC
Statistics
Matches: 819, Mismatches: 4, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
413 408 0.50
414 411 0.50
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.36
Consensus pattern (413 bp):
TGAAAACCCGCAAAGGGCGCCTTGTGACCAAAAGGGTTTTGAGTTGAAAACCTGAAAGGTGACTC
AAATTTTGAAGCATCTGATAATCTTTCTCAACAAAGAACGAAGAACGTTGCATACTGGGGCATCG
ACAGAGTACTTTGAATCTTCTAAACACATGCCTTCATGAAGTTGATGTATAAGCGCTCAAGCGGC
GATATCTAGGGCATCTAATTTTTGGCTTGTTTGCTATCTTTAGATTTTTTTTTCTTCTCAAAGAT
ACGCTTTCAGATTAATTTCCTTTGTATCTTTTTCGATAATTCATTCAAATCCAATTATTCTTAGA
GATTTTTTTATCTTCCATTATTCTTTAAGTATGTTGCATTGAAATAATGATAGATGAACTAAATA
TGTTCACAAATGAAGTTTTGAGT
Found at i:54786514 original size:206 final size:205
Alignment explanation
Indices: 54786151--54786706 Score: 792
Period size: 206 Copynumber: 2.7 Consensus size: 205
54786141 GCAAATCGAG
* *
54786151 CTGAAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCAAAGACATAGCT
1 CTGAAGC-AGATCCAAGATGATTTGGCATCCTTATGCTTACAAGGAACAAATCGAA-ACATAGCT
* *
54786216 GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTATATTGTCAG
64 GATTTGGCTTTCACGTGCTTACGCTGAAACAAATCTAAGATGATTTGGCATCTCTATATTGTCAG
* * * **
54786281 AGAACAAATCAAAGTTTGGCGTCTCCATATTCGACAG-AGAGCAGATACATAGTAGATCTGGCCT
129 AGAACAAATCAAAGTTTGGCATCTCCATATTCGACAGAAG-GCAGACACATAGCAGATCTAACCT
* *
54786345 TCAGATGTTTATA
193 TCAGATGATTAAA
*
54786358 CTGAAGCAGATCCAAGATGATTTGGCATCCTTATGTTTACAAGGAACAAATCGAAATCATAGCTG
1 CTGAAGCAGATCCAAGATGATTTGGCATCCTTATGCTTACAAGGAACAAATCGAAA-CATAGCTG
* * *
54786423 ATTTAGCTTTCACGTGCTTATGCTGAAACAAGTCTAAGATGATTTGGCATCTCTATATTGTCAGA
65 ATTTGGCTTTCACGTGCTTACGCTGAAACAAATCTAAGATGATTTGGCATCTCTATATTGTCAGA
* * *
54786488 GAACAAGTCGAAGTTTGGCATCTCCATATTCGACGGAAGGCAGACACATAGCAGATCTAACCTTC
130 GAACAAATCAAAGTTTGGCATCTCCATATTCGACAGAAGGCAGACACATAGCAGATCTAACCTTC
54786553 AGATGATTAAA
195 AGATGATTAAA
* * * * *
54786564 CTGAAGCAGATCCAAGATGGTTTGGTATCATTTTGCTTACAAGGAGCAAATCGAAGACATAGCTG
1 CTGAAGCAGATCCAAGATGATTTGGCATCCTTATGCTTACAAGGAACAAATCGAA-ACATAGCTG
* * ** *
54786629 ATTTGGTTTTCGCGTGCTTACGCT-AAAGCAAATCTAAGATGATTTGGCATCTCCGTATTGTTAG
65 ATTTGGCTTTCACGTGCTTACGCTGAAA-CAAATCTAAGATGATTTGGCATCTCTATATTGTCAG
54786693 AGAACAAATCAAAG
129 AGAACAAATCAAAG
54786707 AAGCAGATTT
Statistics
Matches: 311, Mismatches: 34, Indels: 9
0.88 0.10 0.03
Matches are distributed among these distances:
205 4 0.01
206 297 0.95
207 10 0.03
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (205 bp):
CTGAAGCAGATCCAAGATGATTTGGCATCCTTATGCTTACAAGGAACAAATCGAAACATAGCTGA
TTTGGCTTTCACGTGCTTACGCTGAAACAAATCTAAGATGATTTGGCATCTCTATATTGTCAGAG
AACAAATCAAAGTTTGGCATCTCCATATTCGACAGAAGGCAGACACATAGCAGATCTAACCTTCA
GATGATTAAA
Found at i:54788526 original size:8 final size:8
Alignment explanation
Indices: 54788481--54788647 Score: 50
Period size: 8 Copynumber: 21.5 Consensus size: 8
54788471 TGAATATACG
54788481 TATTATAT
1 TATTATAT
*
54788489 ATATTTTAT
1 -TATTATAT
*
54788498 AATTAT-T
1 TATTATAT
54788505 TACTTATAT
1 TA-TTATAT
54788514 T-TTAT-T
1 TATTATAT
54788520 ATATTATAT
1 -TATTATAT
54788529 TACTTCATAT
1 TA-TT-ATAT
* *
54788539 TTTTCTAT
1 TATTATAT
*
54788547 TATCATAT
1 TATTATAT
*
54788555 TAATATA-
1 TATTATAT
* *
54788562 TATTTTAA
1 TATTATAT
* *
54788570 CA-CATAT
1 TATTATAT
* *
54788577 CATTA-CT
1 TATTATAT
54788584 TATTAT-T
1 TATTATAT
54788591 TATTATAT
1 TATTATAT
*
54788599 TATGT-TTT
1 TAT-TATAT
* *
54788607 TATCACA-
1 TATTATAT
*
54788614 TAATAT-T
1 TATTATAT
54788621 TA-TATAT
1 TATTATAT
*
54788628 TTTTATAT
1 TATTATAT
54788636 TATTATAT
1 TATTATAT
54788644 TATT
1 TATT
54788648 TTACATTTTA
Statistics
Matches: 113, Mismatches: 29, Indels: 33
0.65 0.17 0.19
Matches are distributed among these distances:
6 4 0.04
7 35 0.31
8 54 0.48
9 15 0.13
10 5 0.04
ACGTcount: A:0.34, C:0.07, G:0.01, T:0.59
Consensus pattern (8 bp):
TATTATAT
Found at i:54788548 original size:23 final size:23
Alignment explanation
Indices: 54788488--54788541 Score: 76
Period size: 21 Copynumber: 2.3 Consensus size: 23
54788478 ACGTATTATA
54788488 TATATTTTA-TA-ATTATTTACT
1 TATATTTTATTATATTATTTACT
54788509 TATATTTTATTATATTATATTACT
1 TATATTTTATTATATTAT-TTACT
54788533 TCATATTTT
1 T-ATATTTT
54788542 TCTATTATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 9 0.31
22 2 0.07
23 5 0.17
24 6 0.21
25 7 0.24
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (23 bp):
TATATTTTATTATATTATTTACT
Found at i:54788608 original size:40 final size:37
Alignment explanation
Indices: 54788564--54788638 Score: 89
Period size: 37 Copynumber: 1.9 Consensus size: 37
54788554 TTAATATATA
54788564 TTTTAACACATATCATTACTTAT-TATTTATTATATTATGT
1 TTTTAACACATA--A-TACTTATATATTT-TTATATTATGT
* *
54788604 TTTTATCACATAATATTTATATATTTTTATATTAT
1 TTTTAACACATAATACTTATATATTTTTATATTAT
54788639 TATATTATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
37 15 0.47
38 6 0.19
40 11 0.34
ACGTcount: A:0.33, C:0.08, G:0.01, T:0.57
Consensus pattern (37 bp):
TTTTAACACATAATACTTATATATTTTTATATTATGT
Found at i:54793792 original size:43 final size:43
Alignment explanation
Indices: 54793698--54793856 Score: 160
Period size: 43 Copynumber: 3.7 Consensus size: 43
54793688 TTACGCCATA
* * * * *
54793698 TCCCAGATATGGTCTTACTTGTTATCAC-ATATCGATGCCACTA
1 TCCCAGACATGGTCTTACATGTAATCACAATA-CGATGCCAATG
* * * * *
54793741 TCCTAGACAGGGTTTTACATGAAATC-GAATAACGATGCCAATG
1 TCCCAGACATGGTCTTACATGTAATCACAAT-ACGATGCCAATG
* * *
54793784 TCCCAGACATGGTCTTACACGTATTCACAATACAATGCCAATG
1 TCCCAGACATGGTCTTACATGTAATCACAATACGATGCCAATG
*
54793827 TCCCAGGCATGGTCTTACATGTAATCACAA
1 TCCCAGACATGGTCTTACATGTAATCACAA
54793857 CTCAGCAACC
Statistics
Matches: 92, Mismatches: 21, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
43 88 0.96
44 4 0.04
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (43 bp):
TCCCAGACATGGTCTTACATGTAATCACAATACGATGCCAATG
Found at i:54799232 original size:69 final size:70
Alignment explanation
Indices: 54799100--54799232 Score: 214
Period size: 69 Copynumber: 1.9 Consensus size: 70
54799090 TAGTTTATTA
* * * * *
54799100 CTAATTAATTTGCTGCTGTAATGCTGTAAATTATTGGCTGTCCAAATTAGGACAAATTTATGGTA
1 CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGTA
54799165 CTTAG
66 CTTAG
54799170 CTAATTAATATGCTGCTGTAATACT-TAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGT
1 CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGT
54799233 GTTATGTGCT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
69 35 0.60
70 23 0.40
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (70 bp):
CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGTA
CTTAG
Found at i:54800673 original size:47 final size:47
Alignment explanation
Indices: 54800619--54801309 Score: 1150
Period size: 47 Copynumber: 14.6 Consensus size: 47
54800609 TATTTGAATA
54800619 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
54800666 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
54800713 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
54800762 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
54800809 AATGTGAAAGTGTATATATGTGATAAGG-CTGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCT-AATGGCCGATGTGATG
54800856 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
54800905 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
54800952 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
54801001 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
54801048 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
54801095 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
54801142 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCTATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
54801189 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * *
54801236 AATGTGAAAGTGTATATATGTGATAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
54801283 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
54801310 TCCCGAAGGG
Statistics
Matches: 606, Mismatches: 30, Indels: 16
0.93 0.05 0.02
Matches are distributed among these distances:
46 2 0.00
47 471 0.78
49 131 0.22
50 2 0.00
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:54800781 original size:143 final size:143
Alignment explanation
Indices: 54800619--54801309 Score: 1169
Period size: 143 Copynumber: 4.9 Consensus size: 143
54800609 TATTTGAATA
54800619 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
54800684 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAAT
66 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAAT
*
54800749 AGCCGATGTGATG
131 GGCCGATGTGATG
54800762 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
*
54800827 TGTGATAAGGCTGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAAT
66 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAAT
54800892 GGCCGATGTGATG
131 GGCCGATGTGATG
* *
54800905 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATA
* * * *
54800970 TATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCGA
64 TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTA
*
54801033 ATGGCCAATGTGATG
129 ATGGCCGATGTGATG
54801048 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
* * *
54801113 TGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAAT
66 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAAT
*
54801176 GGCCTATGTGATG
131 GGCCGATGTGATG
54801189 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
* * * *
54801254 TGTGATAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATA-A-ATGTGATAAG
66 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAG
54801310 TCCCGAAGGG
Statistics
Matches: 523, Mismatches: 21, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
141 189 0.36
142 1 0.00
143 290 0.55
145 43 0.08
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (143 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAAT
GGCCGATGTGATG
Found at i:54807764 original size:61 final size:61
Alignment explanation
Indices: 54807669--54807783 Score: 221
Period size: 61 Copynumber: 1.9 Consensus size: 61
54807659 TATTTGAGTA
54807669 ATTTTATGGGATATTAATGTAATAAAAGAAAATGAAAGAAAGAAAAAGCATTACCATTGTC
1 ATTTTATGGGATATTAATGTAATAAAAGAAAATGAAAGAAAGAAAAAGCATTACCATTGTC
*
54807730 ATTTTATGGGATATTAATGTAATAAAAGAAAATGAAAGAAAGAAAAAGTATTAC
1 ATTTTATGGGATATTAATGTAATAAAAGAAAATGAAAGAAAGAAAAAGCATTAC
54807784 TTTTGAGAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 53 1.00
ACGTcount: A:0.51, C:0.04, G:0.17, T:0.28
Consensus pattern (61 bp):
ATTTTATGGGATATTAATGTAATAAAAGAAAATGAAAGAAAGAAAAAGCATTACCATTGTC
Found at i:54810931 original size:40 final size:40
Alignment explanation
Indices: 54810759--54810924 Score: 262
Period size: 40 Copynumber: 4.2 Consensus size: 40
54810749 AACCCAAGTA
* * * *
54810759 CCTTCAGGATTTAG-CCGGATATAGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
*
54810798 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
*
54810838 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAGATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
*
54810878 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
54810918 CCTTCGG
1 CCTTCGG
54810925 ATCTTAGTCC
Statistics
Matches: 119, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
39 12 0.10
40 107 0.90
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
Found at i:54812318 original size:13 final size:13
Alignment explanation
Indices: 54812300--54812325 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
54812290 TTTTTATTTT
54812300 TTAACATAAAATA
1 TTAACATAAAATA
54812313 TTAACATAAAATA
1 TTAACATAAAATA
54812326 ATTATAATAT
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:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (13 bp):
TTAACATAAAATA
Found at i:54812730 original size:27 final size:27
Alignment explanation
Indices: 54812688--54812863 Score: 172
Period size: 27 Copynumber: 6.5 Consensus size: 27
54812678 CATGACAACT
* * *
54812688 AAGAATAGCCTCTATGGCAAACTCTTA
1 AAGAATAGCCTTTATGGCGAACTCTGA
* * * *
54812715 ATGAATAGTCTTTATGGCGTACTCTAA
1 AAGAATAGCCTTTATGGCGAACTCTGA
* ** *
54812742 AAGAATAGACTTTATGATGAACTTTGA
1 AAGAATAGCCTTTATGGCGAACTCTGA
**
54812769 AAGAATAGCCTTTATGATGAACTCTGA
1 AAGAATAGCCTTTATGGCGAACTCTGA
* *
54812796 AAGAATAGACCTTTTTGGCAAACTCTGA
1 AAGAATAG-CCTTTATGGCGAACTCTGA
* * *
54812824 AAGAATAGACTTTATGGCGACCTTTGA
1 AAGAATAGCCTTTATGGCGAACTCTGA
*
54812851 AAGAATAACCTTT
1 AAGAATAGCCTTT
54812864 GTTGCAAACT
Statistics
Matches: 122, Mismatches: 26, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
27 99 0.81
28 23 0.19
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (27 bp):
AAGAATAGCCTTTATGGCGAACTCTGA
Found at i:54812875 original size:27 final size:26
Alignment explanation
Indices: 54812761--54812905 Score: 98
Period size: 27 Copynumber: 5.3 Consensus size: 26
54812751 CTTTATGATG
* *
54812761 AACTTTGAAAGAATAGCCTTTATG-A
1 AACTTTGAAAGAATAACCTTTTTGCA
*
54812786 TGAACTCTGAAAGAATAGACCTTTTTGGCA
1 --AACTTTGAAAGAATA-ACCTTTTT-GCA
* * *
54812816 AACTCTGAAAGAATAGA-CTTTATGGCG
1 AACTTTGAAAGAATA-ACCTTT-TTGCA
*
54812843 ACCTTTGAAAGAATAACCTTTGTTGCA
1 AACTTTGAAAGAATAACCTTT-TTGCA
* * *
54812870 AACTTTAAAAAGAAT-GCCTTTGTGACA
1 AACTTT-GAAAGAATAACCTTTTTG-CA
54812897 AACTTTGAA
1 AACTTTGAA
54812906 TGGATCGCTT
Statistics
Matches: 96, Mismatches: 15, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
26 5 0.05
27 58 0.60
28 31 0.32
29 1 0.01
30 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.30
Consensus pattern (26 bp):
AACTTTGAAAGAATAACCTTTTTGCA
Found at i:54812882 original size:55 final size:55
Alignment explanation
Indices: 54812688--54812884 Score: 159
Period size: 54 Copynumber: 3.6 Consensus size: 55
54812678 CATGACAACT
* * * * * * * *
54812688 AAGAATAG-CCTCTATGGCAAACTCTTAATGAATAGTCTTTATGGCGTACTCTAA
1 AAGAATAGACCTTTTTGGCAAACTCTAAAAGAATAGACTTTATGACGAACTCTGA
* *** * * * *
54812742 AAGAATAGA-CTTTATGATGAACTTTGAAAGAATAGCCTTTATGATGAACTCTGA
1 AAGAATAGACCTTTTTGGCAAACTCTAAAAGAATAGACTTTATGACGAACTCTGA
* * * *
54812796 AAGAATAGACCTTTTTGGCAAACTCTGAAAGAATAGACTTTATGGCGACCTTTGA
1 AAGAATAGACCTTTTTGGCAAACTCTAAAAGAATAGACTTTATGACGAACTCTGA
*
54812851 AAGAATA-ACCTTTGTT-GCAAACTTTAAAAAGAAT
1 AAGAATAGACCTTT-TTGGCAAACTCT-AAAAGAAT
54812885 GCCTTTGTGA
Statistics
Matches: 115, Mismatches: 24, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
54 64 0.56
55 51 0.44
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (55 bp):
AAGAATAGACCTTTTTGGCAAACTCTAAAAGAATAGACTTTATGACGAACTCTGA
Found at i:54814827 original size:23 final size:23
Alignment explanation
Indices: 54814801--54814845 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
54814791 TGTTGGATAC
54814801 TTAGTTTATTCTACTTGTCCATT
1 TTAGTTTATTCTACTTGTCCATT
54814824 TTAGTTTATTCTACTTGTCCAT
1 TTAGTTTATTCTACTTGTCCAT
54814846 ACATTATCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.18, C:0.18, G:0.09, T:0.56
Consensus pattern (23 bp):
TTAGTTTATTCTACTTGTCCATT
Found at i:54815170 original size:29 final size:29
Alignment explanation
Indices: 54815135--54815194 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
54815125 TCCTAAAGAC
54815135 TTTCCTTTCAGAGATTTGCCACAAAGGCG
1 TTTCCTTTCAGAGATTTGCCACAAAGGCG
* *
54815164 TTTCCTTTCATAGATTTTCCACAAAGGCG
1 TTTCCTTTCAGAGATTTGCCACAAAGGCG
54815193 TT
1 TT
54815195 CTTAAATAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (29 bp):
TTTCCTTTCAGAGATTTGCCACAAAGGCG
Found at i:54815555 original size:53 final size:53
Alignment explanation
Indices: 54815463--54815569 Score: 135
Period size: 53 Copynumber: 2.0 Consensus size: 53
54815453 TTAAATTTCT
* *
54815463 CCATATGATGCCATAACCCACCAATTATGATCTTGCATGATATGATCTTCTTC
1 CCATATGATGCCATAACCCACCAATTAAGATCTTACATGATATGATCTTCTTC
* * * * *
54815516 CCATATGATGCCATAATCCACTAGTTACAG-TCTTACATGATATGGTTTTCTTC
1 CCATATGATGCCATAACCCACCAATTA-AGATCTTACATGATATGATCTTCTTC
54815569 C
1 C
54815570 TATCATAACC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
53 45 0.98
54 1 0.02
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.36
Consensus pattern (53 bp):
CCATATGATGCCATAACCCACCAATTAAGATCTTACATGATATGATCTTCTTC
Found at i:54824194 original size:16 final size:16
Alignment explanation
Indices: 54824173--54824205 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
54824163 TGAGGTACCA
*
54824173 CAGATACTATTGTATT
1 CAGATACTAATGTATT
54824189 CAGATACTAATGTATT
1 CAGATACTAATGTATT
54824205 C
1 C
54824206 CACCATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.39
Consensus pattern (16 bp):
CAGATACTAATGTATT
Found at i:54833132 original size:21 final size:20
Alignment explanation
Indices: 54833093--54833132 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
54833083 TATGAATGAG
54833093 TTTTGATGATTGATGATAGA
1 TTTTGATGATTGATGATAGA
* *
54833113 TTTTGAATGGTTGTTGATAG
1 TTTTG-ATGATTGATGATAG
54833133 TGAAACAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (20 bp):
TTTTGATGATTGATGATAGA
Found at i:54840432 original size:17 final size:18
Alignment explanation
Indices: 54840406--54840450 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
54840396 CGAAGCAACG
*
54840406 ATCA-CAAAAACGTA-AA
1 ATCATCAAAAACCTAGAA
54840422 ATCATCAAAAACCTAGAA
1 ATCATCAAAAACCTAGAA
54840440 ATCATCAAAAA
1 ATCATCAAAAA
54840451 TCGAGTCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 4 0.15
17 9 0.35
18 13 0.50
ACGTcount: A:0.60, C:0.20, G:0.04, T:0.16
Consensus pattern (18 bp):
ATCATCAAAAACCTAGAA
Found at i:54845379 original size:46 final size:46
Alignment explanation
Indices: 54845325--54845494 Score: 152
Period size: 46 Copynumber: 3.6 Consensus size: 46
54845315 GACAAGGGCT
54845325 AGTGTAAGACATGTCCGGGACATGCATCGGCCT-CGAGACCT-A-AGCC
1 AGTGTAAGACATGTCCGGGACATGCATCGG-CTACGAGA--TGATAGCC
* *
54845371 AGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATGATAGTC
1 AGTGTAAGACATGTCCGGGACATGCATCGGCTACGAGATGATAGCC
* ** * *
54845417 AGTGTAAGACCATGTCGGGGACATGGCATCAACT-TGAAAT-ATGAGCC
1 AGTGTAAGA-CATGTCCGGGACAT-GCATCGGCTACGAGATGAT-AGCC
**
54845464 AGTGTAAGACCATGTCTAGGACATGGCATCG
1 AGTGTAAGA-CATGTCCGGGACAT-GCATCG
54845495 ACACCTTACC
Statistics
Matches: 107, Mismatches: 11, Indels: 11
0.83 0.09 0.09
Matches are distributed among these distances:
44 1 0.01
45 3 0.03
46 48 0.45
47 48 0.45
48 7 0.07
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (46 bp):
AGTGTAAGACATGTCCGGGACATGCATCGGCTACGAGATGATAGCC
Found at i:54845467 original size:47 final size:48
Alignment explanation
Indices: 54845367--54845493 Score: 154
Period size: 47 Copynumber: 2.7 Consensus size: 48
54845357 TCGAGACCTA
** *
54845367 AGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTACGAGATGAT
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCAACTACGAAATGAT
* * *
54845413 AGTCAGTGTAAGACCATGTCGGGGACATGGCATCAACT-TGAAAT-AT
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCAACTACGAAATGAT
*
54845459 GAGCCAGTGTAAGACCATGTCTAGGACATGGCATC
1 -AGCCAGTGTAAGACCATGTCTGGGACATGGCATC
54845494 GACACCTTAC
Statistics
Matches: 69, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
46 14 0.20
47 48 0.70
48 7 0.10
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (48 bp):
AGCCAGTGTAAGACCATGTCTGGGACATGGCATCAACTACGAAATGAT
Found at i:54845478 original size:140 final size:141
Alignment explanation
Indices: 54845225--54845494 Score: 330
Period size: 140 Copynumber: 1.9 Consensus size: 141
54845215 GTCCCTTGTT
* * * *
54845225 TAAGCTAGTATAAGACATGTTTGGGACATGCATCGGCCACATTATGAGAACCAGTGTAGGACCAT
1 TAAGCCAGTATAAGACATGTCTGGGACATGCATCGGCCACATGATGAGAACCAGTGTAAGACCAT
* * * * * * *
54845290 GTCTGGGACATGGCATTAGCATTGAGACAAGGGCTAGTGTAAGACATGTCCGGGACAT-GCATCG
66 GTCGGGGACATGGCATCAACATTGAAACAAGAGCCAGTGTAAGACATGTCCAGGACATGGCATCG
54845354 GCCTCGAGACC
131 GCCTCGAGACC
* * * **
54845365 TAAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCTACGA-GATGATAGTCAGTGTAAGACCA
1 TAAGCCAGTATAAGACATGTCTGGGACATGCATCGGCCAC-ATGATGAGAACCAGTGTAAGACCA
* * *
54845429 TGTCGGGGACATGGCATCAAC-TTGAAATATGAGCCAGTGTAAGACCATGTCTAGGACATGGCAT
65 TGTCGGGGACATGGCATCAACATTGAAACAAGAGCCAGTGTAAGA-CATGTCCAGGACATGGCAT
54845493 CG
129 CG
54845495 ACACCTTACC
Statistics
Matches: 108, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
139 18 0.17
140 83 0.77
141 7 0.06
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (141 bp):
TAAGCCAGTATAAGACATGTCTGGGACATGCATCGGCCACATGATGAGAACCAGTGTAAGACCAT
GTCGGGGACATGGCATCAACATTGAAACAAGAGCCAGTGTAAGACATGTCCAGGACATGGCATCG
GCCTCGAGACC
Found at i:54848316 original size:64 final size:64
Alignment explanation
Indices: 54848236--54848419 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
54848226 AGACATTATG
* * * *
54848236 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGGCAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * *
54848300 ATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
54848365 AA
63 AA
* * *
54848367 AT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCACCATGT-GTACAAGAGAGC
1 ATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTAG-ACAAGAGAGC
54848420 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 25 0.26
66 21 0.21
67 32 0.33
ACGTcount: A:0.28, C:0.17, G:0.32, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:54867630 original size:13 final size:13
Alignment explanation
Indices: 54867612--54867643 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
54867602 CTCGTGTGAG
54867612 CAGGCCCATGTCA
1 CAGGCCCATGTCA
54867625 CAGGCCCATGTCA
1 CAGGCCCATGTCA
54867638 CAGGCC
1 CAGGCC
54867644 ATTCGACAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.22, C:0.41, G:0.25, T:0.12
Consensus pattern (13 bp):
CAGGCCCATGTCA
Found at i:54869480 original size:18 final size:18
Alignment explanation
Indices: 54869453--54869500 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
54869443 CGAAGCAACG
*
54869453 ATCA-CAAAAACGTAGAA
1 ATCATCAAAAACCTAGAA
*
54869470 ATCTTCAAAAACCTAGAA
1 ATCATCAAAAACCTAGAA
54869488 ATCATCAAAAACC
1 ATCATCAAAAACC
54869501 GAGTCAAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 3 0.11
18 24 0.89
ACGTcount: A:0.54, C:0.23, G:0.06, T:0.17
Consensus pattern (18 bp):
ATCATCAAAAACCTAGAA
Found at i:54876878 original size:20 final size:20
Alignment explanation
Indices: 54876853--54876898 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
54876843 TAGGGACTAA
* *
54876853 AATGAAAAGTTGTAAAATTT
1 AATGAAAAATTCTAAAATTT
54876873 AATGAAAAATTCTAAAATTT
1 AATGAAAAATTCTAAAATTT
*
54876893 TATGAA
1 AATGAA
54876899 TACATGTGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.52, C:0.02, G:0.11, T:0.35
Consensus pattern (20 bp):
AATGAAAAATTCTAAAATTT
Found at i:54881156 original size:47 final size:47
Alignment explanation
Indices: 54881097--54881661 Score: 986
Period size: 47 Copynumber: 11.9 Consensus size: 47
54881087 TAGTATGGCG
54881097 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
54881144 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
54881191 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
54881238 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCC
*
54881287 TAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
54881334 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
* *
54881381 TAATAGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCC
54881430 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
54881477 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
*
54881524 TAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
* *
54881571 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
* * * * * *
54881618 GAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
54881662 TCCCAAGGGC
Statistics
Matches: 496, Mismatches: 18, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
47 405 0.82
49 91 0.18
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
Found at i:54881353 original size:143 final size:141
Alignment explanation
Indices: 54881097--54881661 Score: 986
Period size: 143 Copynumber: 4.0 Consensus size: 141
54881087 TAGTATGGCG
*
54881097 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 TAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
54881162 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
66 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
54881227 GTGATAAGGCC
131 GTGATAAGGCC
* *
54881238 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATAGCCGATGTGAT
1 TAATAGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGAT
54881303 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
64 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
54881368 ATGTGATAAGGCC
129 ATGTGATAAGGCC
*
54881381 TAATAGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCGATGTGAT
1 TAATAGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGAT
54881446 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
64 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
54881511 ATGTGATAAGGCC
129 ATGTGATAAGGCC
54881524 TAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 TAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * * * *
54881589 ATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAAT
66 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
54881654 GTGATAAG
131 GTGATAAG
54881662 TCCCAAGGGC
Statistics
Matches: 409, Mismatches: 13, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
141 129 0.32
143 280 0.68
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.29
Consensus pattern (141 bp):
TAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
GTGATAAGGCC
Found at i:54881835 original size:37 final size:37
Alignment explanation
Indices: 54881779--54881857 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
54881769 CCGAGCTCTA
* *
54881779 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
54881816 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
54881853 AAGAC
1 AAGAC
54881858 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:54883783 original size:43 final size:43
Alignment explanation
Indices: 54883722--54883824 Score: 188
Period size: 43 Copynumber: 2.4 Consensus size: 43
54883712 TTGGTTTTCA
*
54883722 GCACTAAGTGTGCAGGCAATAAGTGTTCACGATTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGATTGTGAGATTG
*
54883765 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGATTGTGAGATTG
54883808 GCACTAAGTGTGCGGGC
1 GCACTAAGTGTGCGGGC
54883825 TTGAAATGCA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 58 1.00
ACGTcount: A:0.24, C:0.16, G:0.34, T:0.26
Consensus pattern (43 bp):
GCACTAAGTGTGCGGGCAATAAGTGTTCACGATTGTGAGATTG
Done.