Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 164 of 322
Found at i:53794929 original size:12 final size:12
Alignment explanation
Indices: 53794906--53794943 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
53794896 ATATACAGAC
53794906 ATATATAAAAAAA
1 ATATA-AAAAAAA
53794919 ATA-AAAGAAAAA
1 ATATAAA-AAAAA
53794931 ATATAAAAAAAA
1 ATATAAAAAAAA
53794943 A
1 A
53794944 CCTTTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
11 2 0.09
12 15 0.65
13 6 0.26
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.16
Consensus pattern (12 bp):
ATATAAAAAAAA
Found at i:53795258 original size:3 final size:3
Alignment explanation
Indices: 53795250--53795286 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
53795240 TATCATTTAC
53795250 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
53795287 ACTTGTACTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:53795420 original size:12 final size:12
Alignment explanation
Indices: 53795405--53795433 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
53795395 ATATTGTTTA
53795405 TATTATTACTAT
1 TATTATTACTAT
53795417 TATTATTACTAT
1 TATTATTACTAT
53795429 TATTA
1 TATTA
53795434 CTATTTCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (12 bp):
TATTATTACTAT
Found at i:53795489 original size:3 final size:3
Alignment explanation
Indices: 53795483--53795805 Score: 98
Period size: 3 Copynumber: 107.0 Consensus size: 3
53795473 ATCTCGTTTC
* * * * * * *
53795483 ATT ATT ATC ATT CTT ATT AAT A-C ATT ATT ACT ATT ATT TTT ATT TTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * * * *
53795530 ATT TTT ATT ACT ATT ACT -TT ATT ATT ATT ACT ACT ACT GTT ATT TTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
** *
53795577 ATT AAC A-T ATT ATT -TT -TT ATC A-T ATT ATT ATT -TCCT ATT -TT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT--T ATT ATT
* *
53795618 -TT ATAT ATT ATT ATT ATT ATT AATGT ACT ATT ATT TTCT ATTT ATT
1 ATT AT-T ATT ATT ATT ATT ATT -AT-T ATT ATT ATT AT-T A-TT ATT
* * * * * * *
53795664 ACT ATT ATT AAT ATT TTT TTT CTTT AGT ATT ATC ATT ATT ATT A-T
1 ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT
* * *
53795709 ATT ATT -TGT CTT ATT AATGT ATT GTT ATT ATT -TCCT ACTT AGCT ATT
1 ATT ATT AT-T ATT ATT -AT-T ATT ATT ATT ATT AT--T A-TT A-TT ATT
* * * *
53795756 ATT ACT ATT ATT ATT TTT ACT ATT ATA ATT ATT ATT AATT -TT -TT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT
53795800 ATT ATT
1 ATT ATT
53795806 CTCTTACATT
Statistics
Matches: 236, Mismatches: 58, Indels: 52
0.68 0.17 0.15
Matches are distributed among these distances:
2 21 0.09
3 184 0.78
4 26 0.11
5 4 0.02
6 1 0.00
ACGTcount: A:0.28, C:0.08, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:53795552 original size:20 final size:20
Alignment explanation
Indices: 53795527--53795580 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
53795517 TATTTTTATT
*
53795527 TTTATTTTTATTACTATTAC
1 TTTATTTTTATTACTACTAC
*
53795547 TTTATTATTATTACTACTAC
1 TTTATTTTTATTACTACTAC
53795567 TGTTATTTTTATTA
1 T-TTATTTTTATTA
53795581 ACATATTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.26, C:0.09, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTATTTTTATTACTACTAC
Found at i:53795663 original size:34 final size:34
Alignment explanation
Indices: 53795611--53795675 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
53795601 TTATTATTTC
*
53795611 CTATTTTTTATATATTATTATTATTATTAATGTA
1 CTATTTTTTATATATTATTACTATTATTAATGTA
*
53795645 CTATTATTTTCTAT-TTATTACTATTATTAAT
1 CTATT-TTTTATATATTATTACTATTATTAAT
53795676 ATTTTTTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 21 0.75
35 7 0.25
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.62
Consensus pattern (34 bp):
CTATTTTTTATATATTATTACTATTATTAATGTA
Found at i:53798782 original size:48 final size:48
Alignment explanation
Indices: 53798711--53798802 Score: 166
Period size: 48 Copynumber: 1.9 Consensus size: 48
53798701 TTTAAGAAAA
*
53798711 TATGGCAATTAAAGGAAATTCAAGAATTTATAGTGGTTCAACTTCAGT
1 TATGGCAATTAAAGGAAATTCAAGAATCTATAGTGGTTCAACTTCAGT
*
53798759 TATGGTAATTAAAGGAAATTCAAGAATCTATAGTGGTTCAACTT
1 TATGGCAATTAAAGGAAATTCAAGAATCTATAGTGGTTCAACTT
53798803 AAATTACTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (48 bp):
TATGGCAATTAAAGGAAATTCAAGAATCTATAGTGGTTCAACTTCAGT
Found at i:53800873 original size:91 final size:91
Alignment explanation
Indices: 53800692--53800887 Score: 297
Period size: 91 Copynumber: 2.2 Consensus size: 91
53800682 ACTCTTTGTA
* *
53800692 TAAAGGTTGGTATATGCATGCCTAAAGCAACGCTTAAATAAGAGTTGGCTTTGTCTAGTCCTAAG
1 TAAAGGTTGGGATATGCATGCCTAAAGCAACGCTTAAATAAGAGTTGGCTTTATCTAGTCCTAAG
53800757 ACGACACTTTTGGGGCAACACTTTCC
66 ACGACACTTTTGGGGCAACACTTTCC
* * **
53800783 TAAAGGTTGGGATATGTATGCCTAAAGCAACGCTTGAATAAGAGTTAGTTTTTATCTAGTCCTAA
1 TAAAGGTTGGGATATGCATGCCTAAAGCAACGCTTAAATAAGAGTT-GGCTTTATCTAGTCCTAA
*
53800848 GACGACACTTTTGTGGCAACA-TTTCC
65 GACGACACTTTTGGGGCAACACTTTCC
53800874 T-AAGTGTTGGGATA
1 TAAAG-GTTGGGATA
53800888 GACTATGCTT
Statistics
Matches: 96, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
90 3 0.03
91 58 0.60
92 35 0.36
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (91 bp):
TAAAGGTTGGGATATGCATGCCTAAAGCAACGCTTAAATAAGAGTTGGCTTTATCTAGTCCTAAG
ACGACACTTTTGGGGCAACACTTTCC
Found at i:53801071 original size:132 final size:132
Alignment explanation
Indices: 53800787--53801387 Score: 830
Period size: 132 Copynumber: 4.5 Consensus size: 132
53800777 CTTTCCTAAA
* * * *
53800787 GGTTGGGATATGTATGCCTAAAGCAACGCTTGAATAAGAGTTAGTTTTTATCTAGTCCTAAGACG
1 GGTTGGGATATGTATGCCTAAGGCAACGCTTGAATAAGAGTTGGCTTTTGTCTAGTCCTAAGACG
*
53800852 ACACTTTTGTGGCAACA-TTTCCTAAGTGTTGGGATAGACTATGCTTTGGCCAACTCTTTGTATA
66 ACACTTTTGTGGCGACACTTTCCTAAGTGTTGGGATAGACTATGCTTTGGCCAACTCTTTGTATA
53800916 AG
131 AG
* * *
53800918 GGTTGGTATATGTATGCCTAAGGCAACGCTTGAATAAAAGTTGGCTTTTGTATAGTCCTAAGACG
1 GGTTGGGATATGTATGCCTAAGGCAACGCTTGAATAAGAGTTGGCTTTTGTCTAGTCCTAAGACG
* *
53800983 ACACTTTTGTGGCGACATTTTACTAAGTGTTGGGATAGACTATGCTTTGGCCAACTCTTTGTATA
66 ACACTTTTGTGGCGACACTTTCCTAAGTGTTGGGATAGACTATGCTTTGGCCAACTCTTTGTATA
53801048 AG
131 AG
* * * *
53801050 GGTAGGGATATGTATGTCTAAGGCAACGCTTGAATAAAAGTTGGCTTTTGTATAGTCCTAAGACG
1 GGTTGGGATATGTATGCCTAAGGCAACGCTTGAATAAGAGTTGGCTTTTGTCTAGTCCTAAGACG
* * *
53801115 ACACTTTTTTGGTGACACTTTCCTAAGTGTTGGGATAGACTATGCTTTGGTCAACTCTTTGTATA
66 ACACTTTTGTGGCGACACTTTCCTAAGTGTTGGGATAGACTATGCTTTGGCCAACTCTTTGTATA
53801180 AG
131 AG
* * *
53801182 GGTTGGGATATGTATGCCTAAGGCAACGCTTGAATAAGAGTTGGCTTTGGTCTCGTTCTAAGACG
1 GGTTGGGATATGTATGCCTAAGGCAACGCTTGAATAAGAGTTGGCTTTTGTCTAGTCCTAAGACG
* * * *
53801247 ATAATTTT-TGTGCGACACTTTCCGAAGTGTTGGGATAGACCGGCCTACATATGCTTTAGCCAAC
66 ACACTTTTGTG-GCGACACTTTCCTAAGTGTTGGGAT--A---G---AC-TATGCTTTGGCCAAC
53801311 TCTTTGTATAAG
121 TCTTTGTATAAG
* * * * *
53801323 GGTTGGGATATGCATGCCAAAGGCAACGCATAAATAAGAGTTGGC-TTTGTCCAGTCCTAAGACG
1 GGTTGGGATATGTATGCCTAAGGCAACGCTTGAATAAGAGTTGGCTTTTGTCTAGTCCTAAGACG
53801387 A
66 A
53801388 TATATATTTT
Statistics
Matches: 421, Mismatches: 38, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
131 76 0.18
132 259 0.62
134 1 0.00
137 1 0.00
140 18 0.04
141 66 0.16
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (132 bp):
GGTTGGGATATGTATGCCTAAGGCAACGCTTGAATAAGAGTTGGCTTTTGTCTAGTCCTAAGACG
ACACTTTTGTGGCGACACTTTCCTAAGTGTTGGGATAGACTATGCTTTGGCCAACTCTTTGTATA
AG
Found at i:53801500 original size:130 final size:130
Alignment explanation
Indices: 53801265--53801505 Score: 322
Period size: 130 Copynumber: 1.9 Consensus size: 130
53801255 TGTGCGACAC
* * *
53801265 TTTCCGAAGTGTTGGGATAGACCGGCCTACATATGCTTTAGCCAACTCTTTGTATAAGGGTTGGG
1 TTTCCGAAGTGTTGGGATAGACCGGCCGACATACGCTTTAGCCAACTCTTTATATAAGGGTTGGG
**
53801330 ATATGCATGCCAAAGGCAACGCATAAATAAGAGTTGGCTTTGTCCAGTCCTAAGACGATATATAT
66 ATATGCATGCCAAAGGCAACGCATAAATAAGAGTCAGCTTTGTCCAGTCCTAAGACGATATATAT
* ** ** * *
53801395 TTTCCTAAGTGTTGGGATAGACTTGCCGACATACGC-TTAGGTTAACTTTTTATATAAGGGTTGT
1 TTTCCGAAGTGTTGGGATAGACCGGCCGACATACGCTTTA-GCCAACTCTTTATATAAGGGTTGG
** * *
53801459 GATATGCATGCTTAATGCAACGCTTAAATAAGAGTCAGCTTTGTCCA
65 GATATGCATGCCAAAGGCAACGCATAAATAAGAGTCAGCTTTGTCCA
53801506 ACACTATGCC
Statistics
Matches: 94, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
129 3 0.03
130 91 0.97
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (130 bp):
TTTCCGAAGTGTTGGGATAGACCGGCCGACATACGCTTTAGCCAACTCTTTATATAAGGGTTGGG
ATATGCATGCCAAAGGCAACGCATAAATAAGAGTCAGCTTTGTCCAGTCCTAAGACGATATATAT
Found at i:53801636 original size:7 final size:7
Alignment explanation
Indices: 53801615--53801686 Score: 81
Period size: 7 Copynumber: 10.0 Consensus size: 7
53801605 CATGCCTAAT
53801615 GGGTTTA
1 GGGTTTA
53801622 GGGTGTTTA
1 -GG-GTTTA
53801631 GGGTTTA
1 GGGTTTA
*
53801638 GGGCTTA
1 GGGTTTA
*
53801645 GGATTTA
1 GGGTTTA
53801652 GGGTTTA
1 GGGTTTA
* *
53801659 TGGCTTA
1 GGGTTTA
53801666 GGGTTTA
1 GGGTTTA
53801673 GGGTTTA
1 GGGTTTA
*
53801680 GGATTTA
1 GGGTTTA
53801687 AGAGTTGGCC
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
7 45 0.83
8 4 0.07
9 5 0.09
ACGTcount: A:0.17, C:0.03, G:0.39, T:0.42
Consensus pattern (7 bp):
GGGTTTA
Found at i:53801652 original size:21 final size:21
Alignment explanation
Indices: 53801627--53801681 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
53801617 GTTTAGGGTG
53801627 TTTAGGGTTTAGGGCTTAGGA
1 TTTAGGGTTTAGGGCTTAGGA
* *
53801648 TTTAGGGTTTATGGCTTAGGG
1 TTTAGGGTTTAGGGCTTAGGA
53801669 TTTAGGGTTTAGG
1 TTTAGGGTTTAGG
53801682 ATTTAAGAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.16, C:0.04, G:0.38, T:0.42
Consensus pattern (21 bp):
TTTAGGGTTTAGGGCTTAGGA
Found at i:53801858 original size:7 final size:7
Alignment explanation
Indices: 53801839--53801964 Score: 76
Period size: 7 Copynumber: 17.4 Consensus size: 7
53801829 AGCTTATATA
53801839 TTTA-GG
1 TTTAGGG
53801845 TTGTAGGG
1 TT-TAGGG
53801853 TTTAGGG
1 TTTAGGG
* *
53801860 TTTTGGA
1 TTTAGGG
53801867 TTTAGGG
1 TTTAGGG
*
53801874 TTTATGAG
1 TTTA-GGG
53801882 TTTAGGG
1 TTTAGGG
53801889 TTTAGGG
1 TTTAGGG
* *
53801896 TGTATGGT
1 TTTA-GGG
*
53801904 TTTAAGG
1 TTTAGGG
*
53801911 TTTAGGAT
1 TTTAGG-G
*
53801919 TTTATGG
1 TTTAGGG
*
53801926 TTTTGAGG
1 TTTAG-GG
*
53801934 TTTAAGG
1 TTTAGGG
53801941 TTT-GTGG
1 TTTAG-GG
*
53801948 TTTAAGG
1 TTTAGGG
*
53801955 CTTAGGG
1 TTTAGGG
53801962 TTT
1 TTT
53801965 TGATAAAAAT
Statistics
Matches: 88, Mismatches: 24, Indels: 15
0.69 0.19 0.12
Matches are distributed among these distances:
6 2 0.02
7 61 0.69
8 25 0.28
ACGTcount: A:0.17, C:0.01, G:0.35, T:0.48
Consensus pattern (7 bp):
TTTAGGG
Found at i:53801887 original size:15 final size:14
Alignment explanation
Indices: 53801851--53801964 Score: 79
Period size: 15 Copynumber: 7.9 Consensus size: 14
53801841 TAGGTTGTAG
53801851 GGTTTAGGGTTT-T
1 GGTTTAGGGTTTAT
53801864 GGATTTAGGGTTTAT
1 GG-TTTAGGGTTTAT
*
53801879 GAGTTTAGGGTTTAG
1 G-GTTTAGGGTTTAT
* * *
53801894 GGTGTATGGTTTTAA
1 GGTTTA-GGGTTTAT
*
53801909 GGTTTAGGATTTTAT
1 GGTTTAGG-GTTTAT
* *
53801924 GGTTTTGAGGTTTAA
1 GGTTTAG-GGTTTAT
*
53801939 GGTTT-GTGGTTTAA
1 GGTTTAG-GGTTTAT
*
53801953 GGCTTAGGGTTT
1 GGTTTAGGGTTT
53801965 TGATAAAAAT
Statistics
Matches: 83, Mismatches: 11, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
13 2 0.02
14 33 0.40
15 46 0.55
16 2 0.02
ACGTcount: A:0.17, C:0.01, G:0.35, T:0.47
Consensus pattern (14 bp):
GGTTTAGGGTTTAT
Found at i:53806220 original size:76 final size:75
Alignment explanation
Indices: 53806094--53806430 Score: 434
Period size: 76 Copynumber: 4.5 Consensus size: 75
53806084 GCGCGTCCTA
* *
53806094 AGGCTCAATTCACCTCTCGCAATATGAGTTGATTTTTGAAACATACAAAAAATTGACAATACCTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAACATAC-AAAAATTGAAAATACCTC
*
53806159 ATCATGTCTTG
65 AGCATGTCTTG
*
53806170 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAACATACAAAAAATTGACAATACCTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAACATAC-AAAAATTGAAAATACCTC
53806235 AGCATGTCTTG
65 AGCATGTCTTG
* * *** *
53806246 AGGCTCAACTCGCCTCTCGCAATACGAGTTGATTTTTTTGACA-ACACAAATT-AAAATTACCTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAACATACAAAAATTGAAAA-TACCTC
*
53806309 AGCATGTGAAC-CG
65 AGCATGT---CTTG
*
53806322 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA-AT--AGAAATTGAAAATACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAACATACAAAAATTGAAAATACCTCA
* *
53806384 ACGTGTCTTG
66 GCATGTCTTG
**
53806394 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
53806431 TTNNNNNNNN
Statistics
Matches: 233, Mismatches: 21, Indels: 18
0.86 0.08 0.07
Matches are distributed among these distances:
71 1 0.00
72 36 0.15
73 3 0.01
74 36 0.15
75 7 0.03
76 149 0.64
77 1 0.00
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (75 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAACATACAAAAATTGAAAATACCTCA
GCATGTCTTG
Found at i:53806599 original size:74 final size:74
Alignment explanation
Indices: 53806478--53806630 Score: 261
Period size: 74 Copynumber: 2.1 Consensus size: 74
53806468 NNNNNNNNNN
*
53806478 TTTTTTTGAAAATAGAAATTAAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAAT
1 TTTTTTTGAAAATAGAAATTAAAATTACCTCAGCGTGTCCCGAGGCTCAACCCACCTCTCGCAAT
*
53806543 ATGAGTTGA
66 ATAAGTTGA
**
53806552 TTTTTTTGAAAATAGAAATTAAAATTACCTCAGCGTGTCCCGAGGCTCAACCCATTTCTCGCAAT
1 TTTTTTTGAAAATAGAAATTAAAATTACCTCAGCGTGTCCCGAGGCTCAACCCACCTCTCGCAAT
53806617 ATAAGTTGA
66 ATAAGTTGA
*
53806626 ATTTT
1 TTTTT
53806631 GAAAACGGAA
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.33
Consensus pattern (74 bp):
TTTTTTTGAAAATAGAAATTAAAATTACCTCAGCGTGTCCCGAGGCTCAACCCACCTCTCGCAAT
ATAAGTTGA
Found at i:53814716 original size:16 final size:16
Alignment explanation
Indices: 53814691--53814726 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
53814681 ACATAAACTC
*
53814691 AATAAAATATTTAATA
1 AATAAAATATATAATA
*
53814707 AATAATATATATAATA
1 AATAAAATATATAATA
53814723 AATA
1 AATA
53814727 GCAACCATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AATAAAATATATAATA
Found at i:53817602 original size:41 final size:41
Alignment explanation
Indices: 53817545--53817638 Score: 127
Period size: 41 Copynumber: 2.3 Consensus size: 41
53817535 CAATCCCGTG
* ** * *
53817545 AATATATTACCTATGCACATGGAGTTGTCCGATGAAATAAT
1 AATATGTTACCTATGCACATAAAGTGGTCCCATGAAATAAT
*
53817586 AATATGTTACCTATGCACATAAAGTGGTCCCATGGAATAAT
1 AATATGTTACCTATGCACATAAAGTGGTCCCATGAAATAAT
53817627 AATATGTT-CCTA
1 AATATGTTACCTA
53817639 ATAAAGTCAT
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 4 0.09
41 43 0.91
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (41 bp):
AATATGTTACCTATGCACATAAAGTGGTCCCATGAAATAAT
Found at i:53827084 original size:19 final size:19
Alignment explanation
Indices: 53827062--53827113 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
53827052 ATAATTAATT
*
53827062 AAATTTTTAAATTTTAAAA
1 AAATTTTTAAATTTCAAAA
*** *
53827081 AAATTCAAAAAATTCAAAA
1 AAATTTTTAAATTTCAAAA
53827100 AATATTTTTAAATT
1 AA-ATTTTTAAATT
53827114 AAAAATAATT
Statistics
Matches: 23, Mismatches: 9, Indels: 1
0.70 0.27 0.03
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (19 bp):
AAATTTTTAAATTTCAAAA
Found at i:53827092 original size:9 final size:9
Alignment explanation
Indices: 53827078--53827102 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
53827068 TTAAATTTTA
53827078 AAAAAATTC
1 AAAAAATTC
53827087 AAAAAATTC
1 AAAAAATTC
53827096 AAAAAAT
1 AAAAAAT
53827103 ATTTTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAAAATTC
Found at i:53833352 original size:25 final size:25
Alignment explanation
Indices: 53833324--53833445 Score: 74
Period size: 25 Copynumber: 4.9 Consensus size: 25
53833314 CANCTCTTCC
53833324 GAGCCATA-TAACAGGAAGCTCATGT
1 GAGCCA-AGTAACAGGAAGCTCATGT
* * **
53833349 GAGCTAAGTAACGGGAAGCTCATAC
1 GAGCCAAGTAACAGGAAGCTCATGT
* *
53833374 GAG-C-TGTATATCGGGAAGCTCATG-
1 GAGCCAAGTA-A-CAGGAAGCTCATGT
* * *
53833398 GAAGCAAAGTATC-GAGAAGCTCATGA
1 G-AGCCAAGTAACAG-GAAGCTCATGT
*
53833424 GAGCCAAGTATCAGGAAGCTCA
1 GAGCCAAGTAACAGGAAGCTCA
53833446 AGAGAGCTGT
Statistics
Matches: 77, Mismatches: 11, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
23 3 0.04
24 4 0.05
25 65 0.84
26 2 0.03
27 3 0.04
ACGTcount: A:0.35, C:0.19, G:0.28, T:0.18
Consensus pattern (25 bp):
GAGCCAAGTAACAGGAAGCTCATGT
Found at i:53833441 original size:50 final size:50
Alignment explanation
Indices: 53833335--53833445 Score: 120
Period size: 50 Copynumber: 2.2 Consensus size: 50
53833325 AGCCATATAA
* * **
53833335 CAGGAAGCTCATGTGAGCTAAGTAACGGGAAGCTCATACGAGCTGTATAT
1 CAGGAAGCTCATGTGAGCAAAGTAACGAGAAGCTCATACGAGCTCAATAT
* *
53833385 CGGGAAGCTCATG-GAAGCAAAGTATCGAGAAGCTCATGA-GAGC-CAAGTAT
1 CAGGAAGCTCATGTG-AGCAAAGTAACGAGAAGCTCAT-ACGAGCTCAA-TAT
53833435 CAGGAAGCTCA
1 CAGGAAGCTCA
53833446 AGAGAGCTGT
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
49 2 0.04
50 48 0.94
51 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.29, T:0.18
Consensus pattern (50 bp):
CAGGAAGCTCATGTGAGCAAAGTAACGAGAAGCTCATACGAGCTCAATAT
Found at i:53833450 original size:25 final size:24
Alignment explanation
Indices: 53833337--53833452 Score: 85
Period size: 25 Copynumber: 4.7 Consensus size: 24
53833327 CCATATAACA
* * *
53833337 GGAAGCTCATGTGAGCTAAGTAAC
1 GGAAGCTCATGAGAGCAAAGTATC
**
53833361 GGGAAGCTCAT-ACGAGCTGTA-TATC
1 -GGAAGCTCATGA-GAGC-AAAGTATC
53833386 GGGAAGCTCATG-GAAGCAAAGTATC
1 -GGAAGCTCATGAG-AGCAAAGTATC
*
53833411 GAGAAGCTCATGAGAGCCAAGTATC
1 G-GAAGCTCATGAGAGCAAAGTATC
*
53833436 AGGAAGCTCAAGAGAGC
1 -GGAAGCTCATGAGAGC
53833453 TGTTGTGTGT
Statistics
Matches: 75, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
24 3 0.04
25 69 0.92
26 3 0.04
ACGTcount: A:0.34, C:0.18, G:0.30, T:0.17
Consensus pattern (24 bp):
GGAAGCTCATGAGAGCAAAGTATC
Found at i:53834392 original size:15 final size:16
Alignment explanation
Indices: 53834374--53834408 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
53834364 TGATGTGAAT
53834374 AATAT-AAAATATTAG
1 AATATCAAAATATTAG
53834389 AATATCAAAATATTAG
1 AATATCAAAATATTAG
53834405 AATA
1 AATA
53834409 ATAATAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.60, C:0.03, G:0.06, T:0.31
Consensus pattern (16 bp):
AATATCAAAATATTAG
Found at i:53834580 original size:20 final size:20
Alignment explanation
Indices: 53834523--53834582 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 20
53834513 AATACTACAT
53834523 AAATATGTACAT-ATATAAA
1 AAATATGTACATAATATAAA
** *
53834542 AAATAAATACGTGATAATATTAA
1 AAATATGTAC---ATAATATAAA
53834565 AAATATGTACATAATATA
1 AAATATGTACATAATATA
53834583 GTGTAAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
19 8 0.26
20 7 0.23
22 2 0.06
23 14 0.45
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.32
Consensus pattern (20 bp):
AAATATGTACATAATATAAA
Found at i:53834621 original size:22 final size:23
Alignment explanation
Indices: 53834560--53834630 Score: 81
Period size: 25 Copynumber: 3.0 Consensus size: 23
53834550 ACGTGATAAT
*
53834560 ATTAAAAATATGTACATAATATA
1 ATTAAAAATATATACATAATATA
* *
53834583 GTGTAAAAAATACATACATAATATA
1 AT-T-AAAAATATATACATAATATA
*
53834608 ATT-AAAATATATACATAAGATA
1 ATTAAAAATATATACATAATATA
53834630 A
1 A
53834631 CATGTAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
22 18 0.45
23 1 0.03
24 2 0.05
25 19 0.47
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (23 bp):
ATTAAAAATATATACATAATATA
Found at i:53834682 original size:25 final size:25
Alignment explanation
Indices: 53834646--53834777 Score: 91
Period size: 25 Copynumber: 5.6 Consensus size: 25
53834636 AAAAAAAAAT
*
53834646 ATATATAAATAATATAGTATTAAAG
1 ATATATACATAATATAGTATTAAAG
* *
53834671 ATATATACATAAAATAGTA-TAATAT
1 ATATATACATAATATAGTATTAA-AG
* * *
53834696 ATATATACGTAATATAGAATT-TAG
1 ATATATACATAATATAGTATTAAAG
* *
53834720 A-ATATACCTAATATA-T-TAAAAG
1 ATATATACATAATATAGTATTAAAG
* * *
53834742 A-ATATATATAAAATAATATT-AAG
1 ATATATACATAATATAGTATTAAAG
*
53834765 AAATATA-ATAATA
1 ATATATACATAATA
53834778 ACAAAAAAAG
Statistics
Matches: 84, Mismatches: 17, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
21 1 0.01
22 14 0.17
23 23 0.27
24 11 0.13
25 34 0.40
26 1 0.01
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.35
Consensus pattern (25 bp):
ATATATACATAATATAGTATTAAAG
Found at i:53834759 original size:50 final size:50
Alignment explanation
Indices: 53834639--53834760 Score: 131
Period size: 50 Copynumber: 2.4 Consensus size: 50
53834629 AACATGTAAA
*
53834639 AAAAAATATATATAAATAATATAGTATTAAAGATATATACATAAAATAGT
1 AAAAAATATATATAAATAATATAGAATTAAAGATATATACATAAAATAGT
* * ** * * * *
53834689 ATAATATATATATACGTAATATAGAATT-TAGA-ATATACCTAATATATT
1 AAAAAATATATATAAATAATATAGAATTAAAGATATATACATAAAATAGT
53834737 AAAAGAATATATATAAAATAATAT
1 AAAA-AATATATAT-AAATAATAT
53834761 TAAGAAATAT
Statistics
Matches: 57, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
48 16 0.28
49 11 0.19
50 30 0.53
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.34
Consensus pattern (50 bp):
AAAAAATATATATAAATAATATAGAATTAAAGATATATACATAAAATAGT
Found at i:53835299 original size:30 final size:30
Alignment explanation
Indices: 53835265--53835380 Score: 214
Period size: 30 Copynumber: 3.9 Consensus size: 30
53835255 GGGGTGGTAG
* *
53835265 AGTGTGGCTAGTGGAGTAGGTAGTGGAGCA
1 AGTGTGGCTAGTGGAGTTGGTGGTGGAGCA
53835295 AGTGTGGCTAGTGGAGTTGGTGGTGGAGCA
1 AGTGTGGCTAGTGGAGTTGGTGGTGGAGCA
53835325 AGTGTGGCTAGTGGAGTTGGTGGTGGAGCA
1 AGTGTGGCTAGTGGAGTTGGTGGTGGAGCA
53835355 AGTGTGGCTAGTGGAGTTGGTGGTGG
1 AGTGTGGCTAGTGGAGTTGGTGGTGG
53835381 CAAAAGCTAG
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 84 1.00
ACGTcount: A:0.17, C:0.06, G:0.50, T:0.27
Consensus pattern (30 bp):
AGTGTGGCTAGTGGAGTTGGTGGTGGAGCA
Found at i:53836305 original size:88 final size:88
Alignment explanation
Indices: 53836020--53836314 Score: 309
Period size: 88 Copynumber: 3.4 Consensus size: 88
53836010 GTGATCCTGA
* * **
53836020 GCTCAACTCATTTCTCGCAATATGAATTGACTCTTTAAAAC-TAGACATT--AAAAACAGAAATT
1 GCTCAACTCATTTCTCGCAATATGAGTTGATTCTTTAAAACATA-A-ATTGAAAAAACATTAATT
* * *
53836082 GAAAATAGCTCAGCACGTGAGCCAAG
64 GAAAATACCTCAG-ACGTGACCCGAG
* * * * *
53836108 GCTCAACTCACTTCTCGCAATATAAGTTGATT-TTTAAAACCA-AATTTGTAAAACAGATT--TT
1 GCTCAACTCATTTCTCGCAATATGAGTTGATTCTTTAAAA-CATAAATTG-AAAAAACATTAATT
* *
53836169 GAAAATACCTCGGTATGTGACCCGAG
64 GAAAATACCTCAG-ACGTGACCCGAG
* *
53836195 GCTCAACTCATTTCTCGTAATATGAGTTGATTCTTGAAAAGCATAAATTGAAAAAACATTAATTG
1 GCTCAACTCATTTCTCGCAATATGAGTTGATTCTTTAAAA-CATAAATTGAAAAAACATTAATTG
*
53836260 AAAATACCTCAG-CGTGCCCCGAG
65 AAAATACCTCAGACGTGACCCGAG
*
53836283 GCTCAACTCATTTCTCACAATATGAGTTGATT
1 GCTCAACTCATTTCTCGCAATATGAGTTGATT
53836315 TTTTGATGAA
Statistics
Matches: 170, Mismatches: 28, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
86 2 0.01
87 59 0.35
88 85 0.50
89 10 0.06
90 14 0.08
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (88 bp):
GCTCAACTCATTTCTCGCAATATGAGTTGATTCTTTAAAACATAAATTGAAAAAACATTAATTGA
AAATACCTCAGACGTGACCCGAG
Found at i:53836313 original size:175 final size:174
Alignment explanation
Indices: 53836002--53836317 Score: 415
Period size: 175 Copynumber: 1.8 Consensus size: 174
53835992 TTATTCTTTA
* *
53836002 CTCGGCATGTGATCCTGAGCTCAACTCATTTCTCGCAATATGAATTGACTCTTTAAAACTAGACA
1 CTCGGCATGTGATCCCGAGCTCAACTCATTTCTCGCAATATGAATTGACTCTTGAAAACTAGACA
* * *
53836067 TTAAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACTTCTCGCAATATA
66 TTAAAAACAGAAATTGAAAATACCTCAG-ACGTGACCCAAGGCTCAACTCACTTCTCACAATATA
53836132 AGTTGATTTTTAAAACCAAATTTGTAAAACAGATTTTGAAAATAC
130 AGTTGATTTTTAAAACCAAATTTGTAAAACAGATTTTGAAAATAC
* * * *
53836177 CTCGGTATGTGA-CCCGAGGCTCAACTCATTTCTCGTAATATGAGTTGATTCTTGAAAAGCATA-
1 CTCGGCATGTGATCCCGA-GCTCAACTCATTTCTCGCAATATGAATTGACTCTTGAAAA-C-TAG
** * * *
53836240 A-ATTGAAAAAACATTAATTGAAAATACCTCAG-CGTGCCCCGAGGCTCAACTCATTTCTCACAA
63 ACATT--AAAAACAGAAATTGAAAATACCTCAGACGTGACCCAAGGCTCAACTCACTTCTCACAA
*
53836303 TATGAGTTGATTTTT
126 TATAAGTTGATTTTT
53836318 TGATGAACAA
Statistics
Matches: 121, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
174 4 0.03
175 90 0.74
176 2 0.02
177 25 0.21
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (174 bp):
CTCGGCATGTGATCCCGAGCTCAACTCATTTCTCGCAATATGAATTGACTCTTGAAAACTAGACA
TTAAAAACAGAAATTGAAAATACCTCAGACGTGACCCAAGGCTCAACTCACTTCTCACAATATAA
GTTGATTTTTAAAACCAAATTTGTAAAACAGATTTTGAAAATAC
Found at i:53836446 original size:64 final size:65
Alignment explanation
Indices: 53836365--53836490 Score: 200
Period size: 64 Copynumber: 2.0 Consensus size: 65
53836355 AGGCTCAACT
* *
53836365 CACCTCTCGCAACATGAGTTGATTTTTTTGAAAAACAGAAGTT-AAAAACACCTCAGCGTGTGAC
1 CACCTCTCACAACATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAACACCTCAGCGTGTGAC
* * *
53836429 CACCTCTCACAATATGAGTTGATTTTTTTGACAAACAGAAATTGAAAAATACCTCAGCGTGT
1 CACCTCTCACAACATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAACACCTCAGCGTGT
53836491 AAGCCAAGGC
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
64 39 0.70
65 17 0.30
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.29
Consensus pattern (65 bp):
CACCTCTCACAACATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAACACCTCAGCGTGTGAC
Found at i:53836524 original size:142 final size:137
Alignment explanation
Indices: 53836295--53836568 Score: 388
Period size: 141 Copynumber: 2.0 Consensus size: 137
53836285 TCAACTCATT
** * * *
53836295 TCTCACAATATGAGTTGATTTTTTGATGAACAAAAATTAAAACTACCTTAACGTGTCCTGAGGCT
1 TCTCACAATATGAGTTGATTTTTTGACAAACAAAAATTAAAAATACCTCAACGTGTCCTAAGGCT
* *
53836360 CAACTCACCTCTCGCAACATGAGTTGATTTTTTTGAAAAACAGAAGTTAAAAACACCTCAGCGTG
66 CAACTCACCTCTCGCAACATGAGTTGA-TTTTTTGAAAAACAGAAATTAAAAACACCTCAGCATG
53836425 TGACCACC
130 TGACCACC
* *
53836433 TCTCACAATATGAGTTGATTTTTTTGACAAACAGAAATTGAAAAATACCTCAGCGTGTAAGCC-A
1 TCTCACAATATGAGTTGA-TTTTTTGACAAACAAAAATT-AAAAATACCTCAACGTGT---CCTA
* *
53836497 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAAACACCTCAG
61 AGGCTCAACTCACCTCTCGCAACATGAGTTGATTTTTTGAAAAACAGAAATTAAAAACACCTCAG
53836562 CATGTGA
126 CATGTGA
53836569 GGCTCAACTC
Statistics
Matches: 120, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
138 18 0.15
139 17 0.14
140 15 0.12
141 37 0.31
142 31 0.26
143 2 0.02
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.28
Consensus pattern (137 bp):
TCTCACAATATGAGTTGATTTTTTGACAAACAAAAATTAAAAATACCTCAACGTGTCCTAAGGCT
CAACTCACCTCTCGCAACATGAGTTGATTTTTTGAAAAACAGAAATTAAAAACACCTCAGCATGT
GACCACC
Found at i:53836591 original size:71 final size:72
Alignment explanation
Indices: 53836429--53836784 Score: 303
Period size: 71 Copynumber: 4.7 Consensus size: 72
53836419 AGCGTGTGAC
* * *
53836429 CACCTCTCACAATATGAGTTGATTTTTTTGACAAACAGAAATTGAAAAATACCTCAGC-GTGTAA
1 CACCTCTCGCAATATGAGTTGA-TTTTTTGAAAAACAGAAATTG-AAAATACCTCAGCACTGT--
53836493 GCCAAGGCTCAACT
62 G---AGGCTCAACT
*
53836507 CACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAAACACCTCAGCA-TGTGAGG
1 CACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAAATACCTCAGCACTGTGAGG
53836571 CTCAACT
66 CTCAACT
* *
53836578 CACCTCTCGCAATATGAGTTGATTTTTTAAAAACATAGATTGAGCAGAAATTGAAAATACCTCAA
1 CACCTCTCGCAATATGAGTTGATTTTTT---GA-A-A-A---A-CAGAAATTGAAAATACCTCAG
*
53836643 CGAGTCT-TGAGGTTCAACT
56 C-A--CTGTGAGGCTCAACT
* ** * *
53836662 CACCTCTCGCAATATGAGTTGATCTTTTG---ATGATAAATTGAAAATACCTCAATGTGACT-TG
1 CACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAAATACCTC-A-G-CACTGTG
*
53836723 AGGTTCAACT
63 AGGCTCAACT
*
53836733 CATCTCTCGCAATATGAGTTGATTTTTTGAATTAAAACAGAAATTGAAAATA
1 CACCTCTCGCAATATGAGTTGATTTTTTG-A--AAAACAGAAATTGAAAATA
53836785 GAAATGGAAA
Statistics
Matches: 235, Mismatches: 19, Indels: 49
0.78 0.06 0.16
Matches are distributed among these distances:
71 96 0.41
72 1 0.00
73 1 0.00
74 2 0.01
75 2 0.01
76 16 0.07
77 35 0.15
78 21 0.09
80 1 0.00
81 20 0.09
82 1 0.00
84 38 0.16
85 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (72 bp):
CACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAAATACCTCAGCACTGTGAGG
CTCAACT
Found at i:53836675 original size:155 final size:151
Alignment explanation
Indices: 53836328--53836870 Score: 453
Period size: 155 Copynumber: 3.6 Consensus size: 151
53836318 TGATGAACAA
* * *
53836328 AAATT-AAAACTACCTTAACGTGTCCTGAGGCTCAACTCACCTCTCGCAACATGAGTTGATTTTT
1 AAATTGAAAA-TACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTT
* * * *
53836392 TTGAAAAACAGAAGTTAAAAACACCTCAGC--GT---GT-GAC-CACCTCTCACAATATGAGTTG
64 TTGAAAAACAGAAATTGAAAACACCTCAGCATGTGAGGTCAACTCACCTCTCGCAATATGAGTTG
**
53836450 ATTTTTT--TGAC-AA---ACAG
129 ATTTTTTAAAAACAAATTGACAG
* **
53836467 AAATTGAAAAATACCTCAGCGTGTAAGC-CAAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
1 AAATTG-AAAATACCTCAACGTGT---CTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
53836531 TTTTGAAAAACAGAAATTGAAAACACCTCAGCATGTGAGGCTCAACTCACCTCTCGCAATATGAG
62 TTTTGAAAAACAGAAATTGAAAACACCTCAGCATGTGAGG-TCAACTCACCTCTCGCAATATGAG
53836596 TTGATTTTTTAAAAACATAGATTGAGCAG
126 TTGATTTTTTAAAAACA-A-ATTGA-CAG
* * *
53836625 AAATTGAAAATACCTCAACGAGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGTTGATCTTTT
1 AAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
** * * * *
53836690 G---ATGATAAATTGAAAATACCTCAATGTGACT-TGAGGTTCAACTCATCTCTCGCAATATGAG
66 GAAAAACAGAAATTGAAAACACCTC-A-G-CA-TGTGAGG-TCAACTCACCTCTCGCAATATGAG
*
53836751 TTGATTTTTTGAATTAAAACAGAAATTGAAAATAG
126 TTGATTTTTT--A--AAAAC--AAATTG---ACAG
* * * * *
53836786 AAATGGAAAACACCTC-A-GCGTATTGAGGTTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
1 AAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
53836849 GAATTAAAACAGAAATTGAAAA
66 G-A--AAAACAGAAATTGAAAA
53836871 TAGAAATGGA
Statistics
Matches: 329, Mismatches: 33, Indels: 58
0.78 0.08 0.14
Matches are distributed among these distances:
139 5 0.02
140 11 0.03
141 36 0.11
142 31 0.09
143 3 0.01
146 1 0.00
147 1 0.00
148 2 0.01
149 27 0.08
151 2 0.01
152 17 0.05
153 2 0.01
154 3 0.01
155 76 0.23
156 1 0.00
157 17 0.05
158 9 0.03
159 53 0.16
160 2 0.01
161 17 0.05
162 1 0.00
165 12 0.04
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (151 bp):
AAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
GAAAAACAGAAATTGAAAACACCTCAGCATGTGAGGTCAACTCACCTCTCGCAATATGAGTTGAT
TTTTTAAAAACAAATTGACAG
Found at i:53836852 original size:88 final size:88
Alignment explanation
Indices: 53836720--53836936 Score: 407
Period size: 88 Copynumber: 2.5 Consensus size: 88
53836710 TCAATGTGAC
*
53836720 TTGAGGTTCAACTCATCTCTCGCAATATGAGTTGATTTTTTGAATTAAAACAGAAATTGAAAATA
1 TTGAGGTTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAATTAAAACAGAAATTGAAAATA
53836785 GAAATGGAAAACACCTCAGCGTA
66 GAAATGGAAAACACCTCAGCGTA
53836808 TTGAGGTTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAATTAAAACAGAAATTGAAAATA
1 TTGAGGTTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAATTAAAACAGAAATTGAAAATA
53836873 GAAATGGAAAACACCTCAGCGTA
66 GAAATGGAAAACACCTCAGCGTA
* *
53836896 TTGAGGTTCAACTCACTTCTCGCAATATGAGCTGATTTTTT
1 TTGAGGTTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
53836937 TGAAACACAT
Statistics
Matches: 126, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 126 1.00
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.31
Consensus pattern (88 bp):
TTGAGGTTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAATTAAAACAGAAATTGAAAATA
GAAATGGAAAACACCTCAGCGTA
Found at i:53837104 original size:77 final size:77
Alignment explanation
Indices: 53836968--53837427 Score: 408
Period size: 77 Copynumber: 5.9 Consensus size: 77
53836958 AAAAACAAAT
** ** * *
53836968 TAAAAATAGAATTTGAAAGGACCTC-GACGTGTGGCCCGAGACTCAACTCACCTATCGCAATATG
1 TAAAAATAGAATTTGAAAAAACCTCAGA-GTGT--CTTGAGGCTCAACTCACCTCTCGCAATATG
53837032 AGTTGATTTTTTTGA
63 AGTTGATTTTTTTGA
*
53837047 TAAAAATAGAATTTGAAAAAATCTCAGAGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGT
1 TAAAAATAGAATTTGAAAAAACCTCAGAGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGT
53837112 TGATTTTTTTGA
66 TGATTTTTTTGA
* *
53837124 TAAAAATAGAATTTGAAAAAATCTCAGAGTGTCTTGAGGCTCAACTCACCTCTCGCAATTTGAGT
1 TAAAAATAGAATTTGAAAAAACCTCAGAGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGT
53837189 TGA--TTTTTGA
66 TGATTTTTTTGA
* * ** * *
53837199 CAAACA-A-AATTTGAAATTACCTC--AGCGTCTTGAGGCTCAACTCACTTCTCGCAATATGAGT
1 TAAAAATAGAATTTGAAAAAACCTCAGAGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGT
53837260 TGATTTTTTTTGAAACATAA
66 TGA-TTTTTTTG-------A
* * * * *
53837280 GTTAAAAAAACGAAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATAT
1 --TAAAAATA-G-AATTTGAAAAAACCTCAGAGTGTCTTGAGGCTCAACTCACCTCTCGCAATAT
**
53837345 GAGTTGA--AATTT-A
62 GAGTTGATTTTTTTGA
* * * ** *
53837358 -AACACAA-A-AA-TTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTTGCAATATGA
1 TAA-A-AATAGAATTTGAAAAAACCTCAGAGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
*
53837419 GCTGATTTT
64 GTTGATTTT
53837428 GAAAAAGTAG
Statistics
Matches: 326, Mismatches: 32, Indels: 51
0.80 0.08 0.12
Matches are distributed among these distances:
71 38 0.12
72 52 0.16
73 15 0.05
74 7 0.02
75 13 0.04
76 2 0.01
77 110 0.34
78 1 0.00
79 26 0.08
80 2 0.01
81 1 0.00
83 4 0.01
84 1 0.00
86 3 0.01
87 14 0.04
89 37 0.11
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.30
Consensus pattern (77 bp):
TAAAAATAGAATTTGAAAAAACCTCAGAGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGT
TGATTTTTTTGA
Found at i:53837330 original size:160 final size:160
Alignment explanation
Indices: 53837136--53837427 Score: 417
Period size: 160 Copynumber: 1.8 Consensus size: 160
53837126 AAAATAGAAT
* * * **
53837136 TTGAAAAAATCTCAGAGTGTCTTGAGGCTCAACTCACCTCTCGCAATTTGAGTTGATTTTTGACA
1 TTGAAAAAACCTCAGAGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTT-A-A
* * ** * *
53837201 A-ACAAAATTTGAAATTACCTCAGCGT-CTTGAGGCTCAACTCACTTCTCGCAATATGAGTTGAT
64 ACACAAAAATTGAAAATACCTCAGCGTCCCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGAT
53837264 TTTTTTTGAAACATAAGTTAAAAAAACGAAAA
129 TTTTTTTGAAACATAAGTTAAAAAAACGAAAA
* *
53837296 TTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTTAAAC
1 TTGAAAAAACCTCAGAGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTTAAAC
*
53837361 ACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTTGCAATATGAGCTGATT
66 ACAAAAATTGAAAATACCTCAGCGT-CCCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGATT
53837426 TT
130 TT
53837428 GAAAAAGTAG
Statistics
Matches: 115, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
158 2 0.02
159 24 0.21
160 54 0.47
161 35 0.30
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (160 bp):
TTGAAAAAACCTCAGAGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTTAAAC
ACAAAAATTGAAAATACCTCAGCGTCCCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTT
TTTTTGAAACATAAGTTAAAAAAACGAAAA
Found at i:53838282 original size:43 final size:44
Alignment explanation
Indices: 53838234--53838344 Score: 163
Period size: 44 Copynumber: 2.5 Consensus size: 44
53838224 CTTCAGTAGA
* *
53838234 ACGCCC-TTTCAGGTTTTTATCC-TAATCTTTTATGTTAATCAAG
1 ACGCCCTTTTCGGGTTTTCA-CCTTAATCTTTTATGTTAATCAAG
* *
53838277 ACGCCCTTTTCGGGTTTTCACCTTGATCTTTTTTGTTAATCAAG
1 ACGCCCTTTTCGGGTTTTCACCTTAATCTTTTATGTTAATCAAG
53838321 ACGCCCTTTTCGGGTTTTCACCTT
1 ACGCCCTTTTCGGGTTTTCACCTT
53838345 GATCACCCTT
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
43 8 0.13
44 54 0.87
ACGTcount: A:0.17, C:0.24, G:0.14, T:0.44
Consensus pattern (44 bp):
ACGCCCTTTTCGGGTTTTCACCTTAATCTTTTATGTTAATCAAG
Found at i:53838306 original size:44 final size:44
Alignment explanation
Indices: 53838258--53838348 Score: 173
Period size: 44 Copynumber: 2.1 Consensus size: 44
53838248 TTTTATCCTA
53838258 ATCTTTTATGTTAATCAAGACGCCCTTTTCGGGTTTTCACCTTG
1 ATCTTTTATGTTAATCAAGACGCCCTTTTCGGGTTTTCACCTTG
*
53838302 ATCTTTTTTGTTAATCAAGACGCCCTTTTCGGGTTTTCACCTTG
1 ATCTTTTATGTTAATCAAGACGCCCTTTTCGGGTTTTCACCTTG
53838346 ATC
1 ATC
53838349 ACCCTTTTTT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.18, C:0.23, G:0.15, T:0.44
Consensus pattern (44 bp):
ATCTTTTATGTTAATCAAGACGCCCTTTTCGGGTTTTCACCTTG
Found at i:53845853 original size:16 final size:15
Alignment explanation
Indices: 53845827--53845861 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
53845817 TGATGTGAAT
53845827 AATATAAAATATTAA
1 AATATAAAATATTAA
*
53845842 AATATCAAAATATTAG
1 AATAT-AAAATATTAA
53845858 AATA
1 AATA
53845862 ATAATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (15 bp):
AATATAAAATATTAA
Found at i:53846033 original size:20 final size:20
Alignment explanation
Indices: 53845976--53846035 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 20
53845966 AATACTACAT
53845976 AAATATGTACAT-ATATAAA
1 AAATATGTACATAATATAAA
** *
53845995 AAATAAATACGTGATAATATTAA
1 AAATATGTAC---ATAATATAAA
53846018 AAATATGTACATAATATA
1 AAATATGTACATAATATA
53846036 GTGTAAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
19 8 0.26
20 7 0.23
22 2 0.06
23 14 0.45
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.32
Consensus pattern (20 bp):
AAATATGTACATAATATAAA
Found at i:53846074 original size:22 final size:23
Alignment explanation
Indices: 53846013--53846083 Score: 81
Period size: 25 Copynumber: 3.0 Consensus size: 23
53846003 ACGTGATAAT
*
53846013 ATTAAAAATATGTACATAATATA
1 ATTAAAAATATATACATAATATA
* *
53846036 GTGTAAAAAATACATACATAATATA
1 AT-T-AAAAATATATACATAATATA
*
53846061 ATT-AAAATATATACATAAGATA
1 ATTAAAAATATATACATAATATA
53846083 A
1 A
53846084 CATGTAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
22 18 0.45
23 1 0.03
24 2 0.05
25 19 0.47
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (23 bp):
ATTAAAAATATATACATAATATA
Found at i:53846130 original size:25 final size:24
Alignment explanation
Indices: 53846102--53846233 Score: 110
Period size: 23 Copynumber: 5.6 Consensus size: 24
53846092 AAAAAAATAT
*
53846102 ATATATAAATAATATAGTATTAAAG
1 ATATATACATAATATAGTATT-AAG
* *
53846127 ATATATACATAAAATAGTA-TAAT
1 ATATATACATAATATAGTATTAAG
* * *
53846150 ATATATACGTAATATAGAATTTAG
1 ATATATACATAATATAGTATTAAG
* * *
53846174 A-ATATACCTAATATATTA-AAAG
1 ATATATACATAATATAGTATTAAG
* *
53846196 AATATATATATAATATAATATTAAG
1 -ATATATACATAATATAGTATTAAG
*
53846221 AAATATA-ATAATA
1 ATATATACATAATA
53846234 ACAAAAAAAA
Statistics
Matches: 85, Mismatches: 18, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
22 2 0.02
23 39 0.46
24 24 0.28
25 20 0.24
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.36
Consensus pattern (24 bp):
ATATATACATAATATAGTATTAAG
Found at i:53846209 original size:24 final size:23
Alignment explanation
Indices: 53846182--53846233 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
53846172 AGAATATACC
*
53846182 TAATATATTA-AAAGAATATATATA
1 TAATATAATATAAAGAA-ATATA-A
*
53846206 TAATATAATATTAAGAAATATAA
1 TAATATAATATAAAGAAATATAA
53846229 TAATA
1 TAATA
53846234 ACAAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.24
24 14 0.56
25 5 0.20
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (23 bp):
TAATATAATATAAAGAAATATAA
Found at i:53851730 original size:8 final size:7
Alignment explanation
Indices: 53851697--53851731 Score: 61
Period size: 7 Copynumber: 4.9 Consensus size: 7
53851687 TTACACATAA
53851697 CCAAAAT
1 CCAAAAT
53851704 CCAAAAT
1 CCAAAAT
53851711 CCAAAAT
1 CCAAAAT
53851718 CCAAAATT
1 CCAAAA-T
53851726 CCAAAA
1 CCAAAA
53851732 GTATGTTCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 20 0.74
8 7 0.26
ACGTcount: A:0.57, C:0.29, G:0.00, T:0.14
Consensus pattern (7 bp):
CCAAAAT
Found at i:53856849 original size:23 final size:23
Alignment explanation
Indices: 53856822--53856936 Score: 117
Period size: 23 Copynumber: 4.9 Consensus size: 23
53856812 ATAGCTCGTA
*
53856822 AGAGCTTACTGTTTCAGCTCATT
1 AGAGCTTACTGTTTCAGCTCAAT
* * *
53856845 GGAGCTTACCGATTCAGCTCGAA-
1 AGAGCTTACTGTTTCAGCTC-AAT
*
53856868 AGAGCTTATTG-TTCAGCTCAAT
1 AGAGCTTACTGTTTCAGCTCAAT
*
53856890 AGAGCTTACCGTTTTCAGCTCAAT
1 AGAGCTTACTG-TTTCAGCTCAAT
*
53856914 AGAGCTTATTGTTTATCAGCTCA
1 AGAGCTTACTG-TT-TCAGCTCA
53856937 GGAGGAGCTT
Statistics
Matches: 76, Mismatches: 11, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
21 2 0.03
22 17 0.22
23 25 0.33
24 24 0.32
25 8 0.11
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (23 bp):
AGAGCTTACTGTTTCAGCTCAAT
Found at i:53856907 original size:46 final size:45
Alignment explanation
Indices: 53856814--53856926 Score: 147
Period size: 46 Copynumber: 2.5 Consensus size: 45
53856804 GACTCACCAT
* * * *
53856814 AGCTCGTAAGAGCTTACTGTTTCAGCTCATTGGAGCTTACCGATTC
1 AGCTCGAAAGAGCTTATTG-TTCAGCTCAATAGAGCTTACCGATTC
*
53856860 AGCTCGAAAGAGCTTATTGTTCAGCTCAATAGAGCTTACCGTTTTC
1 AGCTCGAAAGAGCTTATTGTTCAGCTCAATAGAGCTTACCG-ATTC
53856906 AGCTC-AATAGAGCTTATTGTT
1 AGCTCGAA-AGAGCTTATTGTT
53856927 TATCAGCTCA
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
45 22 0.37
46 38 0.63
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (45 bp):
AGCTCGAAAGAGCTTATTGTTCAGCTCAATAGAGCTTACCGATTC
Found at i:53857842 original size:40 final size:40
Alignment explanation
Indices: 53857797--53857874 Score: 156
Period size: 40 Copynumber: 1.9 Consensus size: 40
53857787 TCGGGCTGAG
53857797 AAAGCATAGCCTTCGGGCGTTTTAAGTGGGGGATAAAAAC
1 AAAGCATAGCCTTCGGGCGTTTTAAGTGGGGGATAAAAAC
53857837 AAAGCATAGCCTTCGGGCGTTTTAAGTGGGGGATAAAA
1 AAAGCATAGCCTTCGGGCGTTTTAAGTGGGGGATAAAA
53857875 CCCCCCATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.32, C:0.14, G:0.31, T:0.23
Consensus pattern (40 bp):
AAAGCATAGCCTTCGGGCGTTTTAAGTGGGGGATAAAAAC
Found at i:53858607 original size:11 final size:11
Alignment explanation
Indices: 53858581--53858626 Score: 56
Period size: 11 Copynumber: 3.8 Consensus size: 11
53858571 TACTACTGTT
53858581 TTATTATTCATCA
1 TTATTATT--TCA
53858594 TTATTATTTCA
1 TTATTATTTCA
53858605 TTATTATTTCA
1 TTATTATTTCA
53858616 CTTAGTTATTT
1 -TTA-TTATTT
53858627 GTTACCTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 14 0.45
12 3 0.10
13 14 0.45
ACGTcount: A:0.26, C:0.11, G:0.02, T:0.61
Consensus pattern (11 bp):
TTATTATTTCA
Found at i:53858700 original size:15 final size:15
Alignment explanation
Indices: 53858680--53858723 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
53858670 CTACTACATA
*
53858680 TATTATTCTCATTAT
1 TATTATTATCATTAT
53858695 TATTATTATCATTAT
1 TATTATTATCATTAT
*
53858710 TA-TACTATCATTAT
1 TATTATTATCATTAT
53858724 AATTTAATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.57
Consensus pattern (15 bp):
TATTATTATCATTAT
Found at i:53860475 original size:21 final size:21
Alignment explanation
Indices: 53860451--53860490 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
53860441 AAGATATACT
*
53860451 TATATAAATATATATTAAAGA
1 TATATAAATATATAATAAAGA
*
53860472 TATATACATATATAATAAA
1 TATATAAATATATAATAAA
53860491 ATACATGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (21 bp):
TATATAAATATATAATAAAGA
Found at i:53863191 original size:25 final size:23
Alignment explanation
Indices: 53863149--53863194 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
53863139 TCTTATTTTT
*
53863149 TATTTGTTTTTATGTTTTAAATG
1 TATTTGTTTTTATATTTTAAATG
53863172 TATTTGATTTATTATATTTTAAA
1 TATTTG-TTT-TTATATTTTAAA
53863195 GTTTTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 3 0.15
25 11 0.55
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (23 bp):
TATTTGTTTTTATATTTTAAATG
Found at i:53866984 original size:23 final size:23
Alignment explanation
Indices: 53866951--53866997 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
53866941 TTTTTGGATG
*
53866951 TATTTCTAGAAGAATTACCAGGT
1 TATTTCCAGAAGAATTACCAGGT
*
53866974 TATTTCCAGAAGAATTTCCAGGT
1 TATTTCCAGAAGAATTACCAGGT
53866997 T
1 T
53866998 TACCGCTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (23 bp):
TATTTCCAGAAGAATTACCAGGT
Found at i:53871069 original size:23 final size:22
Alignment explanation
Indices: 53871039--53871162 Score: 101
Period size: 23 Copynumber: 5.3 Consensus size: 22
53871029 GGACTCACCA
53871039 CAGCTCATAAGAGCTTACTGTTT
1 CAGCTCA-AAGAGCTTACTGTTT
** *
53871062 CAGCTCATTGGAGCTTACCGATTT
1 CAGCTCA-AAGAGCTTACTG-TTT
*
53871086 -AGCTCGAAAGAGCTTAGTGTTT
1 CAGCTC-AAAGAGCTTACTGTTT
53871108 -AGCTCAATAGAGCTTACCAT-TTT
1 CAGCTCAA-AGAGCTTA-C-TGTTT
53871131 CAGCTCAATAGAGCTTACTGTTTAT
1 CAGCTCAA-AGAGCTTACTG-TT-T
53871156 CAGCTCA
1 CAGCTCA
53871163 GGAGGAGCTT
Statistics
Matches: 84, Mismatches: 8, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
21 2 0.02
22 17 0.20
23 34 0.40
24 23 0.27
25 8 0.10
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.33
Consensus pattern (22 bp):
CAGCTCAAAGAGCTTACTGTTT
Found at i:53871107 original size:46 final size:46
Alignment explanation
Indices: 53871039--53871162 Score: 146
Period size: 46 Copynumber: 2.6 Consensus size: 46
53871029 GGACTCACCA
* *
53871039 CAGCTCATAAGAGCTTACTGTTTCAGCTCATTGGAGCTTACCGA-TTT
1 CAGCTCA-AAGAGCTTACTGTTTCAGCTCAATAGAGCTTACC-ATTTT
*
53871086 -AGCTCGAAAGAGCTTAGTGTTT-AGCTCAATAGAGCTTACCATTTT
1 CAGCTC-AAAGAGCTTACTGTTTCAGCTCAATAGAGCTTACCATTTT
53871131 CAGCTCAATAGAGCTTACTGTTTATCAGCTCA
1 CAGCTCAA-AGAGCTTACTG-TT-TCAGCTCA
53871163 GGAGGAGCTT
Statistics
Matches: 66, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
44 1 0.02
45 21 0.32
46 34 0.52
47 3 0.05
48 1 0.02
49 6 0.09
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.33
Consensus pattern (46 bp):
CAGCTCAAAGAGCTTACTGTTTCAGCTCAATAGAGCTTACCATTTT
Found at i:53889047 original size:14 final size:14
Alignment explanation
Indices: 53889028--53889055 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
53889018 TGACACAATC
53889028 AGAACAAATTTCCA
1 AGAACAAATTTCCA
53889042 AGAACAAATTTCCA
1 AGAACAAATTTCCA
53889056 TAAATAATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.21, G:0.07, T:0.21
Consensus pattern (14 bp):
AGAACAAATTTCCA
Found at i:53892425 original size:17 final size:17
Alignment explanation
Indices: 53892403--53892436 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
53892393 CTGAGGCTTG
*
53892403 TAAAGAAGCTATTTGGT
1 TAAAGAAACTATTTGGT
*
53892420 TAAAGAAACTCTTTGGT
1 TAAAGAAACTATTTGGT
53892437 GAACTCAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (17 bp):
TAAAGAAACTATTTGGT
Found at i:53898620 original size:23 final size:22
Alignment explanation
Indices: 53898589--53898631 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
53898579 GAGGTCAAAA
* *
53898589 TATATTTTTATCATTTATTAATT
1 TATAATTTTAACATTT-TTAATT
53898612 TATAATTTTAACATTTTTAA
1 TATAATTTTAACATTTTTAA
53898632 AAGGCTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (22 bp):
TATAATTTTAACATTTTTAATT
Found at i:53904361 original size:26 final size:25
Alignment explanation
Indices: 53904320--53904370 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
53904310 TGTACAATTG
*
53904320 AAATATAAACACTTAT-TAATATTT
1 AAATATAAACAATTATATAATATTT
*
53904344 AAATATTACAACAATTATATCATATTT
1 AAATA-TA-AACAATTATATAATATTT
53904371 CACTTGTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 5 0.23
25 2 0.09
26 8 0.36
27 7 0.32
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (25 bp):
AAATATAAACAATTATATAATATTT
Found at i:53905794 original size:38 final size:37
Alignment explanation
Indices: 53905714--53905794 Score: 96
Period size: 36 Copynumber: 2.2 Consensus size: 37
53905704 TTCTTTCCTT
*
53905714 TTTTATTATATTATAATATATATACTTAAACATTAATA
1 TTTT-TTATATTATAATATATATACTTAAACATTAACA
53905752 -TTTTTATATTATAATATATATA-TAATAAAC-TTACACA
1 TTTTTTATATTATAATATATATACT--TAAACATTA-ACA
53905789 TTTTTT
1 TTTTTT
53905795 TAATCTTATA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
35 1 0.03
36 22 0.58
37 10 0.26
38 5 0.13
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (37 bp):
TTTTTTATATTATAATATATATACTTAAACATTAACA
Found at i:53910252 original size:5 final size:5
Alignment explanation
Indices: 53910242--53910282 Score: 82
Period size: 5 Copynumber: 8.2 Consensus size: 5
53910232 GAACAAATAT
53910242 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG A
53910283 ATTCCATCTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.39
Consensus pattern (5 bp):
ATTCG
Found at i:53910397 original size:15 final size:16
Alignment explanation
Indices: 53910372--53910404 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
53910362 CTCAAAAATT
*
53910372 TTTTCATTCGATTTGA
1 TTTTCATTCGATTCGA
53910388 TTTT-ATTCGATTCGA
1 TTTTCATTCGATTCGA
53910403 TT
1 TT
53910405 GAACGCTCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.18, C:0.12, G:0.12, T:0.58
Consensus pattern (16 bp):
TTTTCATTCGATTCGA
Found at i:53913249 original size:44 final size:44
Alignment explanation
Indices: 53913194--53913289 Score: 140
Period size: 44 Copynumber: 2.2 Consensus size: 44
53913184 AGTTAAATTA
* *
53913194 TAATTTTAATTTCCCACTTAAACT-TCGATTAGTGTAAGTTATTT
1 TAATATTAATTTCCCACTTAAACTCT-GACTAGTGTAAGTTATTT
* *
53913238 TAATATTAATTTCTCACTTAAACTCTGACTAGTGTAGGTTATTT
1 TAATATTAATTTCCCACTTAAACTCTGACTAGTGTAAGTTATTT
53913282 TAATATTA
1 TAATATTA
53913290 TTTGACCTAC
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
44 46 0.98
45 1 0.02
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.47
Consensus pattern (44 bp):
TAATATTAATTTCCCACTTAAACTCTGACTAGTGTAAGTTATTT
Found at i:53915613 original size:8 final size:8
Alignment explanation
Indices: 53915600--53915628 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
53915590 TTATGTTTAG
53915600 TATATTAT
1 TATATTAT
53915608 TATATTAT
1 TATATTAT
53915616 TATATTAT
1 TATATTAT
53915624 TATAT
1 TATAT
53915629 AATAAAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATATTAT
Found at i:53915661 original size:5 final size:5
Alignment explanation
Indices: 53915651--53915686 Score: 65
Period size: 5 Copynumber: 7.4 Consensus size: 5
53915641 TTATGTTTTA
53915651 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT A-TAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
53915687 AAACTAAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.13
5 26 0.87
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
ATTAT
Found at i:53917027 original size:18 final size:19
Alignment explanation
Indices: 53917004--53917042 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
53916994 ATATATAGAT
53917004 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
53917022 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
53917041 AT
1 AT
53917043 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:53917392 original size:39 final size:39
Alignment explanation
Indices: 53917282--53917416 Score: 112
Period size: 39 Copynumber: 3.4 Consensus size: 39
53917272 GACCTCGAGT
* * * *
53917282 CGATGAGACACTGGGTGTCACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA-AATATTACTTCGGCTAG-TC
** ** * *
53917323 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
* *
53917361 CGATGAGACACTGGGTGTCAAATATTGCTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAAATATTACTTCG-GCTAGTC
*
53917400 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
53917417 CCATATTGGT
Statistics
Matches: 73, Mismatches: 19, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
Found at i:53918252 original size:22 final size:22
Alignment explanation
Indices: 53918227--53918270 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
53918217 GCACCTCCAT
53918227 ATGC-CAACGCACAGCCCCGTAC
1 ATGCACAACGCACA-CCCCGTAC
*
53918249 ATGCACCACGCACACCCCGTAC
1 ATGCACAACGCACACCCCGTAC
53918271 CTTCAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.27, C:0.48, G:0.16, T:0.09
Consensus pattern (22 bp):
ATGCACAACGCACACCCCGTAC
Found at i:53920147 original size:25 final size:25
Alignment explanation
Indices: 53920112--53920161 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
53920102 GGACACACCA
*
53920112 CAGCTCTTATGAGCTTCCCGATACT
1 CAGCTCGTATGAGCTTCCCGATACT
53920137 CAGCTCGTATGAGCTTCCCGATACT
1 CAGCTCGTATGAGCTTCCCGATACT
53920162 TAGTTTGCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.20, C:0.32, G:0.18, T:0.30
Consensus pattern (25 bp):
CAGCTCGTATGAGCTTCCCGATACT
Found at i:53920173 original size:25 final size:25
Alignment explanation
Indices: 53920120--53920176 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
53920110 CACAGCTCTT
*
53920120 ATGAGCTTCCCGATACTCAGCTCGT
1 ATGAGCTTCCCGATACTCAGCTCGC
* * *
53920145 ATGAGCTTCCCGATACTTAGTTTGC
1 ATGAGCTTCCCGATACTCAGCTCGC
53920170 ATGAGCT
1 ATGAGCT
53920177 CCCTGTTATG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (25 bp):
ATGAGCTTCCCGATACTCAGCTCGC
Found at i:53925372 original size:230 final size:230
Alignment explanation
Indices: 53924969--53925428 Score: 920
Period size: 230 Copynumber: 2.0 Consensus size: 230
53924959 AATAGGATTA
53924969 CCCGTCTGGGCTAAATCCTCAATGCACATATATTCTTCGGGAGGCTCGATCATTCGAGAAACACC
1 CCCGTCTGGGCTAAATCCTCAATGCACATATATTCTTCGGGAGGCTCGATCATTCGAGAAACACC
53925034 CGTCCGGGCTAGATCTTTTCCATACTCGAGATCACGGATTACCCGTCAGGCTAAATCCTTATTGC
66 CGTCCGGGCTAGATCTTTTCCATACTCGAGATCACGGATTACCCGTCAGGCTAAATCCTTATTGC
53925099 AACATATGCAGGATCTCTTTACACATATCAATGAGGGTTTATCCATCGAATTCCCTTTGTCAATC
131 AACATATGCAGGATCTCTTTACACATATCAATGAGGGTTTATCCATCGAATTCCCTTTGTCAATC
53925164 TTATCCGAGACATTTTTCACATGTTACCGTCAAAC
196 TTATCCGAGACATTTTTCACATGTTACCGTCAAAC
53925199 CCCGTCTGGGCTAAATCCTCAATGCACATATATTCTTCGGGAGGCTCGATCATTCGAGAAACACC
1 CCCGTCTGGGCTAAATCCTCAATGCACATATATTCTTCGGGAGGCTCGATCATTCGAGAAACACC
53925264 CGTCCGGGCTAGATCTTTTCCATACTCGAGATCACGGATTACCCGTCAGGCTAAATCCTTATTGC
66 CGTCCGGGCTAGATCTTTTCCATACTCGAGATCACGGATTACCCGTCAGGCTAAATCCTTATTGC
53925329 AACATATGCAGGATCTCTTTACACATATCAATGAGGGTTTATCCATCGAATTCCCTTTGTCAATC
131 AACATATGCAGGATCTCTTTACACATATCAATGAGGGTTTATCCATCGAATTCCCTTTGTCAATC
53925394 TTATCCGAGACATTTTTCACATGTTACCGTCAAAC
196 TTATCCGAGACATTTTTCACATGTTACCGTCAAAC
53925429 ATACATTTCT
Statistics
Matches: 230, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
230 230 1.00
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.30
Consensus pattern (230 bp):
CCCGTCTGGGCTAAATCCTCAATGCACATATATTCTTCGGGAGGCTCGATCATTCGAGAAACACC
CGTCCGGGCTAGATCTTTTCCATACTCGAGATCACGGATTACCCGTCAGGCTAAATCCTTATTGC
AACATATGCAGGATCTCTTTACACATATCAATGAGGGTTTATCCATCGAATTCCCTTTGTCAATC
TTATCCGAGACATTTTTCACATGTTACCGTCAAAC
Found at i:53931749 original size:15 final size:16
Alignment explanation
Indices: 53931729--53931763 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
53931719 TGTTTCAGGT
53931729 AAAAAA-AATTTATAA
1 AAAAAAGAATTTATAA
*
53931744 AAAAAAGAATTTCTAA
1 AAAAAAGAATTTATAA
53931760 AAAA
1 AAAA
53931764 TATATTGACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.23
Consensus pattern (16 bp):
AAAAAAGAATTTATAA
Found at i:53934382 original size:15 final size:15
Alignment explanation
Indices: 53934364--53934410 Score: 59
Period size: 11 Copynumber: 3.5 Consensus size: 15
53934354 ATTAGTATAA
53934364 AATATTTTGAAAATT
1 AATATTTTGAAAATT
53934379 AATA-TTT---AATT
1 AATATTTTGAAAATT
53934390 AA-ATTTTGAAAATT
1 AATATTTTGAAAATT
53934404 AATATTT
1 AATATTT
53934411 AATTAAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
10 1 0.04
11 9 0.33
14 9 0.33
15 8 0.30
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (15 bp):
AATATTTTGAAAATT
Found at i:53934398 original size:25 final size:25
Alignment explanation
Indices: 53934367--53934418 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
53934357 AGTATAAAAT
53934367 ATTTTGAAAATTAATATTTAATTAA
1 ATTTTGAAAATTAATATTTAATTAA
53934392 ATTTTGAAAATTAATATTTAATTAA
1 ATTTTGAAAATTAATATTTAATTAA
53934417 AT
1 AT
53934419 AAACAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (25 bp):
ATTTTGAAAATTAATATTTAATTAA
Found at i:53934426 original size:25 final size:25
Alignment explanation
Indices: 53934373--53934429 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
53934363 AAATATTTTG
****
53934373 AAAATTAATATTTAATTAAATTTTG
1 AAAATTAATATTTAATTAAATAAAC
53934398 AAAATTAATATTTAATTAAATAAAC
1 AAAATTAATATTTAATTAAATAAAC
53934423 AAAATTA
1 AAAATTA
53934430 TCTTCTAGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (25 bp):
AAAATTAATATTTAATTAAATAAAC
Found at i:53934626 original size:21 final size:21
Alignment explanation
Indices: 53934575--53934614 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
53934565 AATTTTATCG
53934575 AGAGGAAAAAGTTAAAAATAA
1 AGAGGAAAAAGTTAAAAATAA
53934596 AGAGGAAAAAGTTAAAAAT
1 AGAGGAAAAAGTTAAAAAT
53934615 CAGAAGTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.20, T:0.15
Consensus pattern (21 bp):
AGAGGAAAAAGTTAAAAATAA
Found at i:53941564 original size:26 final size:25
Alignment explanation
Indices: 53941535--53941634 Score: 130
Period size: 26 Copynumber: 3.9 Consensus size: 25
53941525 TCTCGTCCCT
53941535 ATTTTATCCCTAGTAAAATTTTGACG
1 ATTTTA-CCCTAGTAAAATTTTGACG
* *
53941561 ATTTTACCCTGGT-AAATTTTAACG
1 ATTTTACCCTAGTAAAATTTTGACG
*
53941585 ATTTTACCCTCGATAAAATTTTGACG
1 ATTTTACCCTAG-TAAAATTTTGACG
*
53941611 ATTTTACCCTTAATAAAATTTTGA
1 ATTTTACCC-TAGTAAAATTTTGA
53941635 GAAAATATGT
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
24 21 0.32
25 7 0.11
26 36 0.55
27 1 0.02
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (25 bp):
ATTTTACCCTAGTAAAATTTTGACG
Found at i:53944196 original size:20 final size:19
Alignment explanation
Indices: 53944144--53944198 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
53944134 TCAAAATGAA
* *
53944144 TAAAATATAAAAAAACTATT
1 TAAAA-ATAAATAAACAATT
*
53944164 TAAAAAGATAATAAACAATTT
1 TAAAAATA-AATAAACAA-TT
53944185 TAAAAATAAATAAA
1 TAAAAATAAATAAA
53944199 GTAAAAAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 2 0.07
20 18 0.62
21 9 0.31
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (19 bp):
TAAAAATAAATAAACAATT
Found at i:53946478 original size:44 final size:44
Alignment explanation
Indices: 53946406--53946742 Score: 211
Period size: 44 Copynumber: 7.5 Consensus size: 44
53946396 AATCCACTCT
* *
53946406 ACTGCAACTTCAGGGAGATAAGGCTTGTAATTTTAACCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGGCTTGTAATTTCAACCAGCTCC
* * *
53946450 ACTGCAACTTC-GGGAAGATGAGGTTTGTAATTTCGACCAGCTCC
1 ACTGCAACTTCAGGG-AGATAAGGCTTGTAATTTCAACCAGCTCC
* * * * * * * *
53946494 ACTGCAACTTTAGAGAGATAAGATCTGTGATTCATAGCTTCAATCTGTTCT
1 ACTGCAACTTCAGGGAGATAAG-GCT-TG--T-A-A-TTTCAACCAGCTCC
* * ** * *
53946545 ACTGCAACTTCAGGAAAATAAGATTTGCT-ATCTTCAGCCCGCTCC
1 ACTGCAACTTCAGGGAGATAAGGCTTG-TAAT-TTCAACCAGCTCC
* * * *
53946590 ACTGCAACTTCAGGGAGATAAGGCTTGT--TTT-GACCTGTTCT
1 ACTGCAACTTCAGGGAGATAAGGCTTGTAATTTCAACCAGCTCC
* * * ** * *
53946631 ACTGCAACTTCAGAGAGA-CAGGATCTGTAATTTTCAGTCTGCTCT
1 ACTGCAACTTCAGGGAGATAAGGCT-TGTAA-TTTCAACCAGCTCC
* *
53946676 ACTGCAACTTCAGGGAGATAAGGCTTGTAACTTCAACCTA-TTCC
1 ACTGCAACTTCAGGGAGATAAGGCTTGTAATTTCAACC-AGCTCC
*
53946720 ACTACAACTTCAGGGAGATAAGG
1 ACTGCAACTTCAGGGAGATAAGG
53946743 TTAGTGGTTG
Statistics
Matches: 221, Mismatches: 55, Indels: 34
0.71 0.18 0.11
Matches are distributed among these distances:
40 4 0.02
41 25 0.11
42 2 0.01
43 4 0.02
44 84 0.38
45 63 0.29
46 6 0.03
48 2 0.01
49 3 0.01
50 2 0.01
51 26 0.12
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.29
Consensus pattern (44 bp):
ACTGCAACTTCAGGGAGATAAGGCTTGTAATTTCAACCAGCTCC
Found at i:53957733 original size:12 final size:12
Alignment explanation
Indices: 53957711--53957749 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
53957701 TTTTAGCTAA
*
53957711 CTGTTCTTGCA-
1 CTGTGCTTGCAT
53957722 CTTGTGCTTGCAT
1 C-TGTGCTTGCAT
53957735 CTGTGCTTGCAT
1 CTGTGCTTGCAT
53957747 CTG
1 CTG
53957750 CTCCTGTATC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 1 0.04
12 23 0.92
13 1 0.04
ACGTcount: A:0.08, C:0.26, G:0.23, T:0.44
Consensus pattern (12 bp):
CTGTGCTTGCAT
Found at i:53957960 original size:18 final size:18
Alignment explanation
Indices: 53957934--53957968 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
53957924 ATGTAATGCA
53957934 AATGCATGAATACAAAAG
1 AATGCATGAATACAAAAG
* *
53957952 AATGGATGAATGCAAAA
1 AATGCATGAATACAAAA
53957969 AGAGGCGTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.09, G:0.20, T:0.17
Consensus pattern (18 bp):
AATGCATGAATACAAAAG
Found at i:53961837 original size:33 final size:33
Alignment explanation
Indices: 53961787--53961854 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
53961777 AATGTAAAAC
* *
53961787 AATTTAAGAAAAGATAATATATATATATATATA
1 AATTTAAGAAAAGATAATATACATATATACATA
* *
53961820 AATTTTAGAACAA-ATAATATACATATGTACATA
1 AATTTAAGAA-AAGATAATATACATATATACATA
53961853 AA
1 AA
53961855 AGTAAAACAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 28 0.93
34 2 0.07
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (33 bp):
AATTTAAGAAAAGATAATATACATATATACATA
Found at i:53965465 original size:44 final size:46
Alignment explanation
Indices: 53965415--53965502 Score: 153
Period size: 47 Copynumber: 1.9 Consensus size: 46
53965405 ACGACCTTAA
53965415 TATAATTATGTAAACATT-AA-AATAATAAAATAATAATTTACAAG
1 TATAATTATGTAAACATTAAATAATAATAAAATAATAATTTACAAG
53965459 TATAATTATGTAAACATTAAAATAATAATAAAATAATAATTTAC
1 TATAATTATGTAAACATT-AAATAATAATAAAATAATAATTTAC
53965503 TCGTCAGAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
44 18 0.44
46 2 0.05
47 21 0.51
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (46 bp):
TATAATTATGTAAACATTAAATAATAATAAAATAATAATTTACAAG
Found at i:53966033 original size:13 final size:13
Alignment explanation
Indices: 53966017--53966046 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
53966007 ATATATTAAT
53966017 TTATATTATTATA
1 TTATATTATTATA
53966030 TTATATTATTATA
1 TTATATTATTATA
53966043 TTAT
1 TTAT
53966047 TATATATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTATATTATTATA
Found at i:53970657 original size:14 final size:14
Alignment explanation
Indices: 53970638--53970664 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
53970628 GAGGCAAGTC
53970638 GAGAGTGTGTTTGG
1 GAGAGTGTGTTTGG
53970652 GAGAGTGTGTTTG
1 GAGAGTGTGTTTG
53970665 ACTAAGGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.48, T:0.37
Consensus pattern (14 bp):
GAGAGTGTGTTTGG
Found at i:53971597 original size:41 final size:41
Alignment explanation
Indices: 53971551--53971636 Score: 154
Period size: 41 Copynumber: 2.1 Consensus size: 41
53971541 CAAATCAGGT
53971551 ATGATTTTTGTCTTCGAATTTAGTAAAAAAAGAACCTTATA
1 ATGATTTTTGTCTTCGAATTTAGTAAAAAAAGAACCTTATA
* *
53971592 ATGATTTTTGTCTTTGAATTTAGTAAAAAAATAACCTTATA
1 ATGATTTTTGTCTTCGAATTTAGTAAAAAAAGAACCTTATA
53971633 ATGA
1 ATGA
53971637 CAATTAAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.41
Consensus pattern (41 bp):
ATGATTTTTGTCTTCGAATTTAGTAAAAAAAGAACCTTATA
Found at i:53972015 original size:15 final size:15
Alignment explanation
Indices: 53971983--53972119 Score: 91
Period size: 15 Copynumber: 8.8 Consensus size: 15
53971973 CACAATAGCG
53971983 GAAAAACC-CAATAGAA
1 GAAAAACCACAAT--AA
*
53971999 GAAAAACCAGAATAA
1 GAAAAACCACAATAA
*
53972014 GAAAAACCACAAAAA
1 GAAAAACCACAATAA
* *
53972029 CTATAAA-CACAATAGCA
1 -GAAAAACCACAATA--A
*
53972046 GAAAAACCAGAATAA
1 GAAAAACCACAATAA
* *
53972061 GAAAAAACACAAAAA
1 GAAAAACCACAATAA
* *
53972076 CTATAAA-CACAATAGCA
1 -GAAAAACCACAATA--A
*
53972093 GAAAAACCAGAATAA
1 GAAAAACCACAATAA
53972108 GAAAAACCACAA
1 GAAAAACCACAA
53972120 AACCTATAAA
Statistics
Matches: 93, Mismatches: 19, Indels: 19
0.71 0.15 0.15
Matches are distributed among these distances:
15 52 0.56
16 24 0.26
17 17 0.18
ACGTcount: A:0.65, C:0.18, G:0.09, T:0.07
Consensus pattern (15 bp):
GAAAAACCACAATAA
Found at i:53972049 original size:47 final size:47
Alignment explanation
Indices: 53971986--53972157 Score: 281
Period size: 47 Copynumber: 3.7 Consensus size: 47
53971976 AATAGCGGAA
* *
53971986 AAACCCAATAGAAGAAAAACCAGAATAAGAAAAACCACAAAAACTAT
1 AAACACAATAGCAGAAAAACCAGAATAAGAAAAACCACAAAAACTAT
*
53972033 AAACACAATAGCAGAAAAACCAGAATAAGAAAAAACACAAAAACTAT
1 AAACACAATAGCAGAAAAACCAGAATAAGAAAAACCACAAAAACTAT
*
53972080 AAACACAATAGCAGAAAAACCAGAATAAGAAAAACCACAAAACCTAT
1 AAACACAATAGCAGAAAAACCAGAATAAGAAAAACCACAAAAACTAT
* * *
53972127 AAACAAAATAGCAGAAAAACCAAAATCAGAA
1 AAACACAATAGCAGAAAAACCAGAATAAGAA
53972158 TAAGGTAAAA
Statistics
Matches: 117, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 117 1.00
ACGTcount: A:0.65, C:0.19, G:0.09, T:0.08
Consensus pattern (47 bp):
AAACACAATAGCAGAAAAACCAGAATAAGAAAAACCACAAAAACTAT
Found at i:53972068 original size:63 final size:63
Alignment explanation
Indices: 53971928--53972053 Score: 209
Period size: 63 Copynumber: 2.0 Consensus size: 63
53971918 CTAGAGACAG
* * *
53971928 CAATAGCAGAAAAACCAGAATAAGAAGACCTACAAAAACTATAAACACAATAGCGGAAAAACC
1 CAATAGAAGAAAAACCAGAATAAGAAAACCTACAAAAACTATAAACACAATAGCAGAAAAACC
53971991 CAATAGAAGAAAAACCAGAATAAGAAAAACC-ACAAAAACTATAAACACAATAGCAGAAAAACC
1 CAATAGAAGAAAAACCAGAATAAG-AAAACCTACAAAAACTATAAACACAATAGCAGAAAAACC
53972054 AGAATAAGAA
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
63 54 0.92
64 5 0.08
ACGTcount: A:0.60, C:0.20, G:0.11, T:0.09
Consensus pattern (63 bp):
CAATAGAAGAAAAACCAGAATAAGAAAACCTACAAAAACTATAAACACAATAGCAGAAAAACC
Found at i:53972069 original size:32 final size:31
Alignment explanation
Indices: 53971970--53972072 Score: 84
Period size: 32 Copynumber: 3.3 Consensus size: 31
53971960 CAAAAACTAT
* *
53971970 AAACACAATAGCGGAAAAACCCAATAGAAGAAA
1 AAACACAATAGCAGAAAAA-CCAA-AAAAGAAA
* * ** *
53972003 AACCAGAATA--AGAAAAACCACAAAAACTAT
1 AAACACAATAGCAGAAAAACCA-AAAAAGAAA
*
53972033 AAACACAATAGCAGAAAAACCAGAATAAGAAA
1 AAACACAATAGCAGAAAAACCA-AAAAAGAAA
53972065 AAACACAA
1 AAACACAA
53972073 AAACTATAAA
Statistics
Matches: 53, Mismatches: 14, Indels: 7
0.72 0.19 0.09
Matches are distributed among these distances:
30 15 0.28
31 7 0.13
32 23 0.43
33 8 0.15
ACGTcount: A:0.64, C:0.18, G:0.11, T:0.07
Consensus pattern (31 bp):
AAACACAATAGCAGAAAAACCAAAAAAGAAA
Found at i:53973159 original size:17 final size:17
Alignment explanation
Indices: 53973137--53973189 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
53973127 TGAATTCTAG
53973137 TAGCTAGAAGGATCAAA
1 TAGCTAGAAGGATCAAA
* *
53973154 TAGCT--ATGGAT--AG
1 TAGCTAGAAGGATCAAA
53973167 TAGCTAGAAGGATCAAA
1 TAGCTAGAAGGATCAAA
53973184 TAGCTA
1 TAGCTA
53973190 TGGAATTCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
13 6 0.21
15 10 0.36
17 12 0.43
ACGTcount: A:0.42, C:0.11, G:0.25, T:0.23
Consensus pattern (17 bp):
TAGCTAGAAGGATCAAA
Found at i:53973170 original size:30 final size:30
Alignment explanation
Indices: 53973134--53973193 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
53973124 AGTTGAATTC
53973134 TAGTAGCTAGAAGGATCAAATAGCTATGGA
1 TAGTAGCTAGAAGGATCAAATAGCTATGGA
53973164 TAGTAGCTAGAAGGATCAAATAGCTATGGA
1 TAGTAGCTAGAAGGATCAAATAGCTATGGA
53973194 ATTCAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.40, C:0.10, G:0.27, T:0.23
Consensus pattern (30 bp):
TAGTAGCTAGAAGGATCAAATAGCTATGGA
Found at i:53973519 original size:35 final size:35
Alignment explanation
Indices: 53973480--53973549 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
53973470 CTAATCAATC
53973480 TATTTTGGGGATTAATTTGAAAAGTTATCATAGTA
1 TATTTTGGGGATTAATTTGAAAAGTTATCATAGTA
53973515 TATTTTGGGGATTAATTTGAAAAGTTATCATAGTA
1 TATTTTGGGGATTAATTTGAAAAGTTATCATAGTA
53973550 AAAAAGTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.34, C:0.03, G:0.20, T:0.43
Consensus pattern (35 bp):
TATTTTGGGGATTAATTTGAAAAGTTATCATAGTA
Found at i:53975319 original size:3 final size:3
Alignment explanation
Indices: 53975313--53975358 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
53975303 TTAAAAAAAG
53975313 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
53975359 GTGCCGATCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:53986631 original size:12 final size:12
Alignment explanation
Indices: 53986616--53986649 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
53986606 AATAAATAAA
53986616 TAAATTAAAATC
1 TAAATTAAAATC
53986628 TAAATCT-AAATC
1 TAAAT-TAAAATC
53986640 TAAATTAAAA
1 TAAATTAAAA
53986650 AAATTAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 1 0.05
12 18 0.90
13 1 0.05
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.32
Consensus pattern (12 bp):
TAAATTAAAATC
Found at i:53990385 original size:35 final size:35
Alignment explanation
Indices: 53990262--53990386 Score: 144
Period size: 35 Copynumber: 3.6 Consensus size: 35
53990252 TCCTCATTGA
* * * * *
53990262 AATACCACACCTACATTTTACAACTCGGTATGGGA-
1 AATACCATACCTACGTTTCAAAACTCAGTAT-GGAT
* **
53990297 AATGCCATACCTACGTTTCTTAACTCAGTATGGAT
1 AATACCATACCTACGTTTCAAAACTCAGTATGGAT
53990332 AATACCATACCTACGTTTCAAAACTCAGTATGGAT
1 AATACCATACCTACGTTTCAAAACTCAGTATGGAT
* *
53990367 GATACCATACCTGCGTTTCA
1 AATACCATACCTACGTTTCA
53990387 CAAATTTGCC
Statistics
Matches: 77, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
34 3 0.04
35 74 0.96
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.30
Consensus pattern (35 bp):
AATACCATACCTACGTTTCAAAACTCAGTATGGAT
Found at i:53998220 original size:15 final size:15
Alignment explanation
Indices: 53998188--53998229 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
53998178 AACATTTTAA
*
53998188 AATAAAATAATACAT
1 AATAAATTAATACAT
53998203 AATAAATTAATA-ATT
1 AATAAATTAATACA-T
*
53998218 AATAATTTAATA
1 AATAAATTAATA
53998230 TGTGTATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 1 0.04
15 23 0.96
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (15 bp):
AATAAATTAATACAT
Found at i:53998325 original size:19 final size:19
Alignment explanation
Indices: 53998285--53998329 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
53998275 AAATTTTAAG
*
53998285 TAATATAATGAATAGTAAA
1 TAATATAATGAATAATAAA
*
53998304 TAATATAAT-AGATAATATA
1 TAATATAATGA-ATAATAAA
53998323 TAATATA
1 TAATATA
53998330 CATAACTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 1 0.04
19 22 0.96
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.36
Consensus pattern (19 bp):
TAATATAATGAATAATAAA
Found at i:54000940 original size:210 final size:210
Alignment explanation
Indices: 54000382--54001169 Score: 1315
Period size: 210 Copynumber: 3.7 Consensus size: 210
54000372 CCCATTGAAT
* * *
54000382 GTGGAGATGCTAGACTTCGATTTGTTCTCTGACAATACAGAGATGACAAATCATCTTAGATTTGC
1 GTGGAAATGCCAGACTTCGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGC
* *
54000447 TTCATCGTAAACATGTGAAAGCCAAATCAGCTATATCTTCGATCTGCTCCCCGCTGAATACAGAG
66 TTCATCGTAAACATGTGAAAGCCAAATCAACTATATCTTCGATCTGCTCCCCGCCGAATACAGAG
* * * *
54000512 AGATAAGACCTGTCATCTTGGATCTGCTTCAGTGTAAACATCTGAAGGTAAGATCTGCTATGTGT
131 AGATAAGATCTGTCATCTTGGATCTGCTTCAGTGTAAACATCAGAAGGTGAGATTTGCTATGTGT
*
54000577 TTGCCTTCCATCAAA
196 CTGCCTTCCATCAAA
*
54000592 GTGGAAATGCCAGACTTCGATTTATTCTCTGACAGATACAGAGACGACAAATCATCTTAGATTTG
1 GTGGAAATGCCAGACTTCGATTTGTTCTCTGACA-ATACAGAGACGACAAATCATCTTAGATTTG
* * *
54000657 CTTTATTGTAAACATGTGAAAGCCAAATCAACTATATCTTCGATCTGCTCCCCGCCGAATATAGA
65 CTTCATCGTAAACATGTGAAAGCCAAATCAACTATATCTTCGATCTGCTCCCCGCCGAATACAGA
54000722 GAGATAAGATCTGTCATCTTGGATCTGCTTCAGTGTAAACATCAGAAGGTGAGATTTGCTATGTG
130 GAGATAAGATCTGTCATCTTGGATCTGCTTCAGTGTAAACATCAGAAGGTGAGATTTGCTATGTG
54000787 TCTGCCTTCCATCAAA
195 TCTGCCTTCCATCAAA
* *
54000803 GTGGAAATGCCAGACTTCGATTTGTTTTCTGACAATATAGAGACGACAAATCATCTTAGATTTGC
1 GTGGAAATGCCAGACTTCGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGC
* *
54000868 TTTATTGTAAACATGTGAAAGCCAAATCAACTATATCTTCGATCTGCTCCCCGCCGAATACAGAG
66 TTCATCGTAAACATGTGAAAGCCAAATCAACTATATCTTCGATCTGCTCCCCGCCGAATACAGAG
54000933 AGATAAGATCTGTCATCTTGGATCTGCTTCAGTGTAAACATCAGAAGGTGAGATTTGCTATGTGT
131 AGATAAGATCTGTCATCTTGGATCTGCTTCAGTGTAAACATCAGAAGGTGAGATTTGCTATGTGT
54000998 CTGCCTTCCATCAAA
196 CTGCCTTCCATCAAA
* * * *
54001013 GTGGAAATGCCAGACTTCGATTTGTTTTCTGACAATATAGAGACGACAAATCATCTTGGATTTGA
1 GTGGAAATGCCAGACTTCGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGC
* * ** *
54001078 TTCATCATAAACACGTGAAAGCCAAATCAGTTATGTCTTCGATCTGCTCCCCGCCGAATACAGAG
66 TTCATCGTAAACATGTGAAAGCCAAATCAACTATATCTTCGATCTGCTCCCCGCCGAATACAGAG
*
54001143 AGATAAGATCTGTCATATTGGATCTGC
131 AGATAAGATCTGTCATCTTGGATCTGC
54001170 CCTGAGAATG
Statistics
Matches: 549, Mismatches: 28, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
210 352 0.64
211 197 0.36
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.30
Consensus pattern (210 bp):
GTGGAAATGCCAGACTTCGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGC
TTCATCGTAAACATGTGAAAGCCAAATCAACTATATCTTCGATCTGCTCCCCGCCGAATACAGAG
AGATAAGATCTGTCATCTTGGATCTGCTTCAGTGTAAACATCAGAAGGTGAGATTTGCTATGTGT
CTGCCTTCCATCAAA
Found at i:54009228 original size:15 final size:14
Alignment explanation
Indices: 54009186--54009235 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
54009176 ATAACTTTGA
*
54009186 ATGCAAATGATGTG
1 ATGCAAATGATGAG
54009200 ATG-AAATGTTATGAG
1 ATGCAAATG--ATGAG
54009215 ATGCAAATGCATGA-
1 ATGCAAATG-ATGAG
54009229 ATGCAAA
1 ATGCAAA
54009236 AAGAATATCG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 5 0.16
14 10 0.32
15 11 0.35
16 5 0.16
ACGTcount: A:0.42, C:0.08, G:0.24, T:0.26
Consensus pattern (14 bp):
ATGCAAATGATGAG
Found at i:54013667 original size:422 final size:422
Alignment explanation
Indices: 54012822--54013668 Score: 1608
Period size: 422 Copynumber: 2.0 Consensus size: 422
54012812 AAATAACATG
54012822 AACATACGTTTAATGAAAAAAATCATACTAGGGTAAATATAAGATAATAAACAAATAAAAACATG
1 AACATACGTTTAATGAAAAAAATCATACTAGGGTAAATATAAGATAATAAACAAATAAAAACATG
54012887 AGTAAACTAAAAGAAAAACATAATACATGCAAAAATTATACAACAATATATATCATAAAATAGCA
66 AGTAAACTAAAAGAAAAACATAATACATGCAAAAATTATACAACAATATATATCATAAAATAGCA
*
54012952 CATAAAAGAAATAATTAAACATAGCATATAAAAAAATGAAACTATGCACAAATAAGATAAATGAC
131 CATAAAAGAAATAATTAAACATAGCAAATAAAAAAATGAAACTATGCACAAATAAGATAAATGAC
54013017 ATACACTAAAAAAATGAATAAATAGAACATTTACAAATTATAAAAATATAATGCAATAGTTCAAA
196 ATACACTAAAAAAATGAATAAATAGAACATTTACAAATTATAAAAATATAATGCAATAGTTCAAA
54013082 ATACATGAAATGATAATATAATATATATATGCATAGAAAATATATATTTGAAAATAAACTATATA
261 ATACATGAAATGATAATATAATATATATATGCATAGAAAATATATATTTGAAAATAAACTATATA
* *
54013147 AAGAGTTAAATATTATAATATATAAAATACATAATCCAATGTATAAAAGATAGGAATAAATATAC
326 AAAAGTTAAATATTATAATATATAAAATACATAATCAAATGTATAAAAGATAGGAATAAATATAC
54013212 ATATTTGAAAAATGATGAAATTAAAATAAAAAA
391 ATATTTGAAAAATGATGAAATT-AAATAAAAAA
54013245 AACATACGTTTAAT-AAAAAAATCATACTAGGGTAAATATAAGATAATAAACAAATAAAAACATG
1 AACATACGTTTAATGAAAAAAATCATACTAGGGTAAATATAAGATAATAAACAAATAAAAACATG
*
54013309 AGTAAACTAAAAGAAAAACATAATACATGCAAAAATTATATAACAATATATATCATAAAATAGCA
66 AGTAAACTAAAAGAAAAACATAATACATGCAAAAATTATACAACAATATATATCATAAAATAGCA
54013374 CATAAAAGAAATAATTAAACATAGCAAATAAAAAAATGAAACTATGCACAAATAAGATAAATGAC
131 CATAAAAGAAATAATTAAACATAGCAAATAAAAAAATGAAACTATGCACAAATAAGATAAATGAC
54013439 ATACACTAAAAAAATGAATAAATAGAACATTTACAAATTATAAAAATATAATGCAATAGTTCAAA
196 ATACACTAAAAAAATGAATAAATAGAACATTTACAAATTATAAAAATATAATGCAATAGTTCAAA
54013504 ATACATGAAATGATAATATAATATATATACATGCATAGAAAATATATATTTGAAAATAAACTATA
261 ATACATGAAATGATAATATAATATATAT--ATGCATAGAAAATATATATTTGAAAATAAACTATA
54013569 TAAAAAGGTTAAATATTATAATATATAAAATACATAATCAAATGTATAAAAGATAGGAATAAATA
324 TAAAAA-GTTAAATATTATAATATATAAAATACATAATCAAATGTATAAAAGATAGGAATAAATA
54013634 TACATATTTGAAAAATGATGAAATTAAA-AAAAAA
388 TACATATTTGAAAAATGATGAAATTAAATAAAAAA
54013668 A
1 A
54013669 GGTTGAAAAA
Statistics
Matches: 417, Mismatches: 4, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
422 271 0.65
423 21 0.05
424 43 0.10
425 82 0.20
ACGTcount: A:0.58, C:0.08, G:0.08, T:0.26
Consensus pattern (422 bp):
AACATACGTTTAATGAAAAAAATCATACTAGGGTAAATATAAGATAATAAACAAATAAAAACATG
AGTAAACTAAAAGAAAAACATAATACATGCAAAAATTATACAACAATATATATCATAAAATAGCA
CATAAAAGAAATAATTAAACATAGCAAATAAAAAAATGAAACTATGCACAAATAAGATAAATGAC
ATACACTAAAAAAATGAATAAATAGAACATTTACAAATTATAAAAATATAATGCAATAGTTCAAA
ATACATGAAATGATAATATAATATATATATGCATAGAAAATATATATTTGAAAATAAACTATATA
AAAAGTTAAATATTATAATATATAAAATACATAATCAAATGTATAAAAGATAGGAATAAATATAC
ATATTTGAAAAATGATGAAATTAAATAAAAAA
Found at i:54013788 original size:26 final size:26
Alignment explanation
Indices: 54013749--54013800 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
54013739 AGAAATTTGA
*
54013749 GTGAACGCTTTCAAGAATTCTTATTT
1 GTGAACGCTCTCAAGAATTCTTATTT
*
54013775 GTGAATGCTCTCAAGAATTCTTATTT
1 GTGAACGCTCTCAAGAATTCTTATTT
54013801 CTTCCCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (26 bp):
GTGAACGCTCTCAAGAATTCTTATTT
Found at i:54013955 original size:22 final size:21
Alignment explanation
Indices: 54013925--54013990 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 21
54013915 TACAAATTAA
54013925 ATCTCCAAGATTACAAGATCAT
1 ATCTCCAAGATTAC-AGATCAT
* * *
54013947 ATCTTCAAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
* *
54013968 ATCT--AAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
54013987 ATCT
1 ATCT
54013991 AAGATTGTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
19 19 0.46
21 10 0.24
22 12 0.29
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (21 bp):
ATCTCCAAGATTACAGATCAT
Found at i:54013977 original size:19 final size:19
Alignment explanation
Indices: 54013942--54014039 Score: 146
Period size: 19 Copynumber: 5.2 Consensus size: 19
54013932 AGATTACAAG
54013942 ATCATATCTTCAAGATTGCAT
1 ATCATATC-T-AAGATTGCAT
54013963 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
54013982 ATCATATCTAAGATTG--T
1 ATCATATCTAAGATTGCAT
* *
54013999 ATCATATCTGATATTGCAT
1 ATCATATCTAAGATTGCAT
54014018 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
54014037 ATC
1 ATC
54014040 CCTAAAGATT
Statistics
Matches: 71, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
17 15 0.21
19 47 0.66
20 1 0.01
21 8 0.11
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (19 bp):
ATCATATCTAAGATTGCAT
Found at i:54014006 original size:36 final size:37
Alignment explanation
Indices: 54013942--54014039 Score: 135
Period size: 36 Copynumber: 2.6 Consensus size: 37
54013932 AGATTACAAG
54013942 ATCATATCTTCAAGATTGCATATCATATCTAAGATTGCAT
1 ATCATATC-T-AAGATTG-ATATCATATCTAAGATTGCAT
* *
54013982 ATCATATCTAAGATTG-TATCATATCTGATATTGCAT
1 ATCATATCTAAGATTGATATCATATCTAAGATTGCAT
54014018 ATCATATCTAAGATTGCATATC
1 ATCATATCTAAGATTG-ATATC
54014040 CCTAAAGATT
Statistics
Matches: 54, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
36 34 0.63
38 11 0.20
39 1 0.02
40 8 0.15
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (37 bp):
ATCATATCTAAGATTGATATCATATCTAAGATTGCAT
Found at i:54015262 original size:70 final size:70
Alignment explanation
Indices: 54015180--54015450 Score: 258
Period size: 70 Copynumber: 3.9 Consensus size: 70
54015170 AATCTTATTG
* * * * *
54015180 ATTATTTGACTAGTGTTAGGCACAATTATCGTTGGTTTATCCAACTAGCGTTGGGCGCAAAACAC
1 ATTATTCGACTAGTGCTAGGCACAATTATCGTTGGCTTATCCAACTAGCGCTGGGCGCAAAACAT
*
54015245 CGTCA
66 CATCA
* * * * * * *
54015250 ATTATTCAACTAGTGCTAGCCACACTTATTGTTGGCTTATCCAACTAGCACTGGGCGTAAAAAAT
1 ATTATTCGACTAGTGCTAGGCACAATTATCGTTGGCTTATCCAACTAGCGCTGGGCGCAAAACAT
* *
54015315 CTTCG
66 CATCA
* ** * * * *
54015320 ATTGTTCGACTAGTATTGGGCACACTTATCGTTGGCTTATCCAACTATCGCTGGGCGTAAAACAT
1 ATTATTCGACTAGTGCTAGGCACAATTATCGTTGGCTTATCCAACTAGCGCTGGGCGCAAAACAT
*
54015385 TATCA
66 CATCA
* * * * *
54015390 ATTATTTGACTAGTGCTGGGTA-AACTTATTGTTGG-TATATCCAACTAGTGCTGGGCGCAAA
1 ATTATTCGACTAGTGCTAGGCACAA-TTATCGTTGGCT-TATCCAACTAGCGCTGGGCGCAAA
54015451 GAGATTATTG
Statistics
Matches: 162, Mismatches: 37, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
69 2 0.01
70 160 0.99
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (70 bp):
ATTATTCGACTAGTGCTAGGCACAATTATCGTTGGCTTATCCAACTAGCGCTGGGCGCAAAACAT
CATCA
Found at i:54015444 original size:140 final size:140
Alignment explanation
Indices: 54015187--54015446 Score: 342
Period size: 140 Copynumber: 1.9 Consensus size: 140
54015177 TTGATTATTT
* * * *
54015187 GACTAGTGTTAGGCACAATTATCGTTGGTTTATCCAACTAGCGTTGGGCGCAAAACACCGTCAAT
1 GACTAGTATTAGGCACAATTATCGTTGGCTTATCCAACTAGCGCTGGGCGCAAAACACCATCAAT
*
54015252 TATTCAACTAGTGCTAGCCACACTTATTGTTGGCTTATCCAACTAGCACTGGGCGTAAAAAATCT
66 TATTCAACTAGTGCTAGCCAAACTTATTGTTGGCTTATCCAACTAGCACTGGGCGTAAAAAATCT
54015317 TCGATTGTTC
131 TCGATTGTTC
* * * * **
54015327 GACTAGTATTGGGCACACTTATCGTTGGCTTATCCAACTATCGCTGGGCGTAAAACATTATCAAT
1 GACTAGTATTAGGCACAATTATCGTTGGCTTATCCAACTAGCGCTGGGCGCAAAACACCATCAAT
** * ** **
54015392 TATTTGACTAGTGCTGGGTAAACTTATTGTTGG-TATATCCAACTAGTGCTGGGCG
66 TATTCAACTAGTGCTAGCCAAACTTATTGTTGGCT-TATCCAACTAGCACTGGGCG
54015447 CAAAGAGATT
Statistics
Matches: 101, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
139 1 0.01
140 100 0.99
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (140 bp):
GACTAGTATTAGGCACAATTATCGTTGGCTTATCCAACTAGCGCTGGGCGCAAAACACCATCAAT
TATTCAACTAGTGCTAGCCAAACTTATTGTTGGCTTATCCAACTAGCACTGGGCGTAAAAAATCT
TCGATTGTTC
Found at i:54026527 original size:40 final size:38
Alignment explanation
Indices: 54026471--54026625 Score: 150
Period size: 40 Copynumber: 3.9 Consensus size: 38
54026461 TGATACACCA
*
54026471 GCACAAAGCCTGCTAGGCATCAAGCCCGATAACTACAAT
1 GCACAAAGCCTGCTAGGCA-CAAGCCCGATAAATACAAT
54026510 GACACAAAGCCTGCTAGGCACTAAGCCCGATAAATACACCA-
1 G-CACAAAGCCTGCTAGGCAC-AAGCCCGATAAATACA--AT
* * * * *
54026551 GCACAAAGCCTGCTAGGCATAAATCCCTATAATTACACT
1 GCACAAAGCCTGCTAGGCA-CAAGCCCGATAAATACAAT
** * *
54026590 GGTGCAAAGCTTGCTAGGCACTAGCCCGATAAATAC
1 -GCACAAAGCCTGCTAGGCACAAGCCCGATAAATAC
54026626 TCAATACAAG
Statistics
Matches: 95, Mismatches: 14, Indels: 14
0.77 0.11 0.11
Matches are distributed among these distances:
39 13 0.14
40 80 0.84
41 1 0.01
42 1 0.01
ACGTcount: A:0.35, C:0.29, G:0.18, T:0.17
Consensus pattern (38 bp):
GCACAAAGCCTGCTAGGCACAAGCCCGATAAATACAAT
Found at i:54026598 original size:80 final size:79
Alignment explanation
Indices: 54026463--54026625 Score: 236
Period size: 80 Copynumber: 2.1 Consensus size: 79
54026453 AGACAATTTG
*
54026463 ATACACCAGCACAAAGCCTGCTAGGCATCAAGCCCGATAACTACAATGACACAAAGCCTGCTAGG
1 ATACACCAGCACAAAGCCTGCTAGGCATAAAGCCCGATAACTACAATGACACAAAGCCTGCTAGG
54026528 CACTAAGCCCGATAA
66 CACT-AGCCCGATAA
* * * * *** *
54026543 ATACACCAGCACAAAGCCTGCTAGGCATAAATCCCTATAATTACACTGGTGCAAAGCTTGCTAGG
1 ATACACCAGCACAAAGCCTGCTAGGCATAAAGCCCGATAACTACAATGACACAAAGCCTGCTAGG
54026608 CACTAGCCCGATAA
66 CACTAGCCCGATAA
54026622 ATAC
1 ATAC
54026626 TCAATACAAG
Statistics
Matches: 74, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
79 14 0.19
80 60 0.81
ACGTcount: A:0.36, C:0.29, G:0.17, T:0.17
Consensus pattern (79 bp):
ATACACCAGCACAAAGCCTGCTAGGCATAAAGCCCGATAACTACAATGACACAAAGCCTGCTAGG
CACTAGCCCGATAA
Found at i:54030055 original size:40 final size:40
Alignment explanation
Indices: 54030011--54030101 Score: 173
Period size: 40 Copynumber: 2.3 Consensus size: 40
54030001 CTTTTGCAGC
54030011 TTTTACAATTTATTCCCTTTCTTCTAATTAACTAACTAAA
1 TTTTACAATTTATTCCCTTTCTTCTAATTAACTAACTAAA
54030051 TTTTACAATTTATTCCCTTTCTTCTAATTAACTAACTAAA
1 TTTTACAATTTATTCCCTTTCTTCTAATTAACTAACTAAA
*
54030091 TTTTATAATTT
1 TTTTACAATTT
54030102 CTTAACCAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.51
Consensus pattern (40 bp):
TTTTACAATTTATTCCCTTTCTTCTAATTAACTAACTAAA
Found at i:54034204 original size:151 final size:151
Alignment explanation
Indices: 54033930--54034232 Score: 554
Period size: 151 Copynumber: 2.0 Consensus size: 151
54033920 CATCTTGACC
54033930 GTCAGCTTGTGTGAGCAGACCCGTTGATAGCTCGAGAGTGAGCATTATATGAGATATGAGATTGA
1 GTCAGCTTGTGTGAGCAGACCCGTTGATAGCTCGAGAGTGAGCATTATATGAGATATGAGATTGA
* * * *
54033995 GATAACTTTGGCTATGTATTGGCACTTGGGGTGTGAGATTCCTGAGTATCTGATATTAATTCAAA
66 GATAACTTTGGCTATGTATTGGCACTTAGGGTGTGAAATCCCCGAGTATCTGATATTAATTCAAA
54034060 TAGTTCAACAGGTATATCGAT
131 TAGTTCAACAGGTATATCGAT
54034081 GTCAGCTTGTGTGAGCAGACCCGTTGATAGCTCGAGAGTGAGCATTATATGAGATATGAGATTGA
1 GTCAGCTTGTGTGAGCAGACCCGTTGATAGCTCGAGAGTGAGCATTATATGAGATATGAGATTGA
54034146 GATAACTTTGGCTATGTATTGGCACTTAGGGTGT-ACAATCCCCGAGTATCTGATATTAATTCAA
66 GATAACTTTGGCTATGTATTGGCACTTAGGGTGTGA-AATCCCCGAGTATCTGATATTAATTCAA
54034210 ATAGTTCAACAGGTATATCGAT
130 ATAGTTCAACAGGTATATCGAT
54034232 G
1 G
54034233 AACTGAAAGA
Statistics
Matches: 147, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
150 1 0.01
151 146 0.99
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (151 bp):
GTCAGCTTGTGTGAGCAGACCCGTTGATAGCTCGAGAGTGAGCATTATATGAGATATGAGATTGA
GATAACTTTGGCTATGTATTGGCACTTAGGGTGTGAAATCCCCGAGTATCTGATATTAATTCAAA
TAGTTCAACAGGTATATCGAT
Found at i:54041018 original size:21 final size:21
Alignment explanation
Indices: 54040992--54041031 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
54040982 GGCCATATGG
*
54040992 CTACTTCACACGTCCGTGTGA
1 CTACTTCACACGCCCGTGTGA
54041013 CTACTTCACACGCCCGTGT
1 CTACTTCACACGCCCGTGT
54041032 ACGCTAATAG
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:0.17, C:0.38, G:0.17, T:0.28
Consensus pattern (21 bp):
CTACTTCACACGCCCGTGTGA
Found at i:54041490 original size:19 final size:19
Alignment explanation
Indices: 54041450--54041492 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
54041440 AGCTAGATCA
*
54041450 CATATACAATAAATATTGC
1 CATATACAATAAATACTGC
*
54041469 CATATACACATCAATACT-C
1 CATATACA-ATAAATACTGC
54041488 CATAT
1 CATAT
54041493 TTCCATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.44, C:0.23, G:0.02, T:0.30
Consensus pattern (19 bp):
CATATACAATAAATACTGC
Found at i:54041968 original size:40 final size:40
Alignment explanation
Indices: 54041870--54042050 Score: 159
Period size: 40 Copynumber: 4.5 Consensus size: 40
54041860 TGATACACTA
** * * *
54041870 GCACAAAGCCTGCTAGGCAC-ATAGCCCGATAAAATACACTG
1 GCACAAAGGTTGCTAGGCACTA-AGCCTGAT-AAACACACCG
* ** *
54041911 GCACGAAGCCTGCTAGGCACTAAGCTTGATAAACACACCG
1 GCACAAAGGTTGCTAGGCACTAAGCCTGATAAACACACCG
* * * *
54041951 GCACAAAGGTTGTTAGGCACTAAGCCCGATAAATACACTG
1 GCACAAAGGTTGCTAGGCACTAAGCCTGATAAACACACCG
* ** *
54041991 GCACAAAGGCTGCTAGGCAGAAAGCCTGAT-AACTACATCG
1 GCACAAAGGTTGCTAGGCACTAAGCCTGATAAAC-ACACCG
*
54042031 GCACAAAGCTTGCTAGGCAC
1 GCACAAAGGTTGCTAGGCAC
54042051 AGAACCCAAT
Statistics
Matches: 114, Mismatches: 24, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
39 2 0.02
40 86 0.75
41 25 0.22
42 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.23, T:0.16
Consensus pattern (40 bp):
GCACAAAGGTTGCTAGGCACTAAGCCTGATAAACACACCG
Found at i:54042021 original size:80 final size:81
Alignment explanation
Indices: 54041870--54042051 Score: 244
Period size: 80 Copynumber: 2.3 Consensus size: 81
54041860 TGATACACTA
* * *
54041870 GCACAAAGCCTGCTAGGCACATAGCCCGATAAAATACACTGGCACGAAGCCTGCTAGGCACTAAG
1 GCACAAAGCTTGCTAGGCACATAGCCCGATAAAATACACTGGCACAAAGCCTGCTAGGCACAAAG
*
54041935 CTTGATAAAC-ACACCG
66 CCTGAT-AACTACACCG
* * * *
54041951 GCACAAAGGTTGTTAGGCAC-TAAGCCCGAT-AAATACACTGGCACAAAGGCTGCTAGGCAGAAA
1 GCACAAAGCTTGCTAGGCACAT-AGCCCGATAAAATACACTGGCACAAAGCCTGCTAGGCACAAA
*
54042014 GCCTGATAACTACATCG
65 GCCTGATAACTACACCG
54042031 GCACAAAGCTTGCTAGGCACA
1 GCACAAAGCTTGCTAGGCACA
54042052 GAACCCAATA
Statistics
Matches: 87, Mismatches: 11, Indels: 6
0.84 0.11 0.06
Matches are distributed among these distances:
79 3 0.03
80 59 0.68
81 25 0.29
ACGTcount: A:0.35, C:0.27, G:0.23, T:0.16
Consensus pattern (81 bp):
GCACAAAGCTTGCTAGGCACATAGCCCGATAAAATACACTGGCACAAAGCCTGCTAGGCACAAAG
CCTGATAACTACACCG
Found at i:54044333 original size:23 final size:24
Alignment explanation
Indices: 54044307--54044357 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
54044297 CAAAAAAAAT
* * *
54044307 AAAATATATTCTAAAAA-AAGAGG
1 AAAACATAATCTAAAAATAAGAAG
*
54044330 AAAACCTAATCTAAAAATAAGAAG
1 AAAACATAATCTAAAAATAAGAAG
54044354 AAAA
1 AAAA
54044358 AAAAGAAAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.65, C:0.08, G:0.10, T:0.18
Consensus pattern (24 bp):
AAAACATAATCTAAAAATAAGAAG
Found at i:54044358 original size:13 final size:13
Alignment explanation
Indices: 54044342--54044375 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
54044332 AACCTAATCT
*
54044342 AAAAATAAG-AAG
1 AAAAAAAAGAAAG
54044354 AAAAAAAAGAAAG
1 AAAAAAAAGAAAG
54044367 AAAAAAAAG
1 AAAAAAAAG
54044376 CTAATCTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (13 bp):
AAAAAAAAGAAAG
Found at i:54045392 original size:35 final size:35
Alignment explanation
Indices: 54045343--54045493 Score: 169
Period size: 35 Copynumber: 4.3 Consensus size: 35
54045333 AATTTTGTAC
*
54045343 AATACTTATAGCTCGTTTATTGTTACAACTCACAT
1 AATACTTATAGCTCGTGTATTGTTACAACTCACAT
* * * *
54045378 AATACTTATGGCTCGTGTATCGTTACAACTCATAC
1 AATACTTATAGCTCGTGTATTGTTACAACTCACAT
*
54045413 AATACTTATAGCTCGTGTATTGTTACATCTCACAT
1 AATACTTATAGCTCGTGTATTGTTACAACTCACAT
* ** *** *
54045448 AATAGTTAT-GACTCACGTATCACTACAACTTACAT
1 AATACTTATAG-CTCGTGTATTGTTACAACTCACAT
54045483 AATACTTATAG
1 AATACTTATAG
54045494 TTTGCATGTT
Statistics
Matches: 95, Mismatches: 19, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
34 1 0.01
35 93 0.98
36 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (35 bp):
AATACTTATAGCTCGTGTATTGTTACAACTCACAT
Found at i:54045415 original size:70 final size:70
Alignment explanation
Indices: 54045340--54045493 Score: 209
Period size: 70 Copynumber: 2.2 Consensus size: 70
54045330 TACAATTTTG
* * ** **
54045340 TACAATACTTATAGCTCGTTTATTGTTACAACTCACATAATACTTATGGCTCGTGTATCGTTACA
1 TACAATACTTATAGCTCGTGTATTGTTACAACTCACATAATACTTATGACTCACGTATCACTACA
54045405 ACTCA
66 ACTCA
* *
54045410 TACAATACTTATAGCTCGTGTATTGTTACATCTCACATAATAGTTATGACTCACGTATCACTACA
1 TACAATACTTATAGCTCGTGTATTGTTACAACTCACATAATACTTATGACTCACGTATCACTACA
*
54045475 ACTTA
66 ACTCA
* *
54045480 CATAATACTTATAG
1 TACAATACTTATAG
54045494 TTTGCATGTT
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
70 73 1.00
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.36
Consensus pattern (70 bp):
TACAATACTTATAGCTCGTGTATTGTTACAACTCACATAATACTTATGACTCACGTATCACTACA
ACTCA
Done.