Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A03
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: 108673976
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 5040000 characters in sequence are not A, C, G, or T
File 267 of 333
Found at i:88261841 original size:38 final size:40
Alignment explanation
Indices: 88261798--88261906 Score: 159
Period size: 40 Copynumber: 2.7 Consensus size: 40
88261788 CTTGATATAT
*
88261798 TATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAA
1 TATATATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGTAA
88261838 TATATATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGT-A
1 TATATATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGTAA
* *
88261877 -CTATATCCGGGCTTAAAGTTCCGCAGGCTT
1 TATATATCCGGG-TTAAA-TCCCGCAGGCTT
88261907 TGAGCTAGTG
Statistics
Matches: 64, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
38 10 0.16
39 6 0.09
40 48 0.75
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.30
Consensus pattern (40 bp):
TATATATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGTAA
Found at i:88267622 original size:28 final size:27
Alignment explanation
Indices: 88267585--88267683 Score: 67
Period size: 28 Copynumber: 3.4 Consensus size: 27
88267575 AAGTTAACTA
88267585 GGCCTTAGCCCATATCAATATTAATCTG
1 GGCC-TAGCCCATATCAATATTAATCTG
*
88267613 GGCCATAGCCCCT-TACAATATCAGAGTATAT-TG
1 GGCC-TAGCCCATAT-CAATAT-----TA-ATCTG
* *
88267646 GGCCTAGCCCATATCAGTATCAATCTG
1 GGCCTAGCCCATATCAATATTAATCTG
88267673 GGCCGTAGCCC
1 GGCC-TAGCCC
88267684 TATTACAAGT
Statistics
Matches: 56, Mismatches: 5, Indels: 20
0.69 0.06 0.25
Matches are distributed among these distances:
26 2 0.04
27 8 0.14
28 23 0.41
32 12 0.21
33 9 0.16
34 2 0.04
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.26
Consensus pattern (27 bp):
GGCCTAGCCCATATCAATATTAATCTG
Found at i:88267658 original size:60 final size:60
Alignment explanation
Indices: 88267585--88267719 Score: 175
Period size: 60 Copynumber: 2.2 Consensus size: 60
88267575 AAGTTAACTA
* *
88267585 GGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCC-CTTACAATATC-AGAGTATATTG
1 GGCC-TAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAA-ATCAAGA-TATATTG
* * *
88267646 GGCCTAGCCCATATCAGTATCAATCTGGGCCGTAGCCCTATTACAAGTCAAGATATATTG
1 GGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAAATCAAGATATATTG
*
88267706 GGCCTTGCCCATAT
1 GGCCTAGCCCATAT
88267720 TGACACAGTT
Statistics
Matches: 66, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
60 53 0.80
61 13 0.20
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (60 bp):
GGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAAATCAAGATATATTG
Found at i:88267737 original size:20 final size:19
Alignment explanation
Indices: 88267712--88267767 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
88267702 ATTGGGCCTT
*
88267712 GCCCATATTGACACAGTTGG
1 GCCCATATTAACACAGTT-G
* *
88267732 GCCCATTTTAATACAGTTG
1 GCCCATATTAACACAGTTG
* *
88267751 GCCCATAATAAAACAGT
1 GCCCATATTAACACAGT
88267768 CTCATATATT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (19 bp):
GCCCATATTAACACAGTTG
Found at i:88268086 original size:26 final size:26
Alignment explanation
Indices: 88268057--88268119 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
88268047 AAAATTAACC
* *
88268057 CTAGGGGTATAATGGTCATTTTGCAT-
1 CTAGGGGTATAATGATAATTTT-CATA
*
88268083 CTAGGGGTAAAATGATAATTTTCATA
1 CTAGGGGTATAATGATAATTTTCATA
88268109 CTTAGGGGTAT
1 C-TAGGGGTAT
88268120 TTCAGTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
25 3 0.10
26 20 0.65
27 8 0.26
ACGTcount: A:0.29, C:0.10, G:0.25, T:0.37
Consensus pattern (26 bp):
CTAGGGGTATAATGATAATTTTCATA
Found at i:88269076 original size:19 final size:19
Alignment explanation
Indices: 88269054--88269093 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
88269044 AGATTCGGCT
88269054 AGTTGGAAAAGAAAATCAA
1 AGTTGGAAAAGAAAATCAA
88269073 AGTTGGAAAAGAAAATCAA
1 AGTTGGAAAAGAAAATCAA
88269092 AG
1 AG
88269094 GAATAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.57, C:0.05, G:0.23, T:0.15
Consensus pattern (19 bp):
AGTTGGAAAAGAAAATCAA
Found at i:88269952 original size:3 final size:3
Alignment explanation
Indices: 88269944--88269973 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
88269934 AACACCACAT
88269944 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
88269974 CCATAGCAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:88278107 original size:23 final size:23
Alignment explanation
Indices: 88278081--88278146 Score: 91
Period size: 23 Copynumber: 2.9 Consensus size: 23
88278071 AATCTGTCAG
*
88278081 AATAAAA-AAAATTAAAATGTAAA
1 AATAAAATAAAA-TAAAATGAAAA
88278104 AATAAAATAAAATAAAAT-AAAA
1 AATAAAATAAAATAAAATGAAAA
88278126 AATAAAATAAAAATAAAATGA
1 AATAAAAT-AAAATAAAATGA
88278147 CTAAATTAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
22 11 0.28
23 23 0.59
24 5 0.13
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (23 bp):
AATAAAATAAAATAAAATGAAAA
Found at i:88278112 original size:5 final size:5
Alignment explanation
Indices: 88278102--88278144 Score: 59
Period size: 5 Copynumber: 8.0 Consensus size: 5
88278092 TTAAAATGTA
88278102 AAAAT AAAAT AAAAT AAAAT AAAAAAT AAAAT AAAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT --AAAAT AAAAT -AAAAT AAAAT
88278145 GACTAAATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 25 0.71
6 5 0.14
7 5 0.14
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:88278129 original size:17 final size:18
Alignment explanation
Indices: 88278086--88278143 Score: 68
Period size: 18 Copynumber: 3.2 Consensus size: 18
88278076 GTCAGAATAA
88278086 AAAAAATTAAAATGTAAAAAT
1 AAAAAA-TAAAA--TAAAAAT
88278107 --AAAATAAAAT-AAAAT
1 AAAAAATAAAATAAAAAT
88278122 AAAAAATAAAATAAAAAT
1 AAAAAATAAAATAAAAAT
88278140 AAAA
1 AAAA
88278144 TGACTAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
15 5 0.15
16 1 0.03
17 10 0.29
18 14 0.41
19 4 0.12
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (18 bp):
AAAAAATAAAATAAAAAT
Found at i:88278157 original size:28 final size:25
Alignment explanation
Indices: 88278081--88278165 Score: 90
Period size: 23 Copynumber: 3.4 Consensus size: 25
88278071 AATCTGTCAG
*
88278081 AATAAAA-AAAATTAAAATG-TAAA
1 AATAAAATAAAAATAAAATGATAAA
88278104 AATAAAAT-AAAATAAAAT-A-AAA
1 AATAAAATAAAAATAAAATGATAAA
88278126 AATAAAATAAAAATAAAATGACTAAA
1 AATAAAATAAAAATAAAATGA-TAAA
88278152 TTAATACAAATAAA
1 --AATA-AAATAAA
88278166 TTTTTCTTAA
Statistics
Matches: 52, Mismatches: 1, Indels: 12
0.80 0.02 0.18
Matches are distributed among these distances:
22 11 0.21
23 26 0.50
24 1 0.02
26 3 0.06
28 4 0.08
29 7 0.13
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (25 bp):
AATAAAATAAAAATAAAATGATAAA
Found at i:88279259 original size:26 final size:26
Alignment explanation
Indices: 88279229--88279279 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
88279219 CCACATGGCC
*
88279229 GTGTGTAAGCCCTTGTGGCTCACACA
1 GTGTGTAAGCCCGTGTGGCTCACACA
*
88279255 GTGTGTAAGCTCGTGTGGCTCACAC
1 GTGTGTAAGCCCGTGTGGCTCACAC
88279280 GGCCATGTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.18, C:0.25, G:0.29, T:0.27
Consensus pattern (26 bp):
GTGTGTAAGCCCGTGTGGCTCACACA
Found at i:88281662 original size:24 final size:24
Alignment explanation
Indices: 88281635--88281688 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
88281625 ATTTAGTATT
*
88281635 TATTAGTATAAAATATCTAACATC
1 TATTAGCATAAAATATCTAACATC
* * * *
88281659 TATTAGCATAATATATTTGACATT
1 TATTAGCATAAAATATCTAACATC
88281683 TATTAG
1 TATTAG
88281689 AAATAAGGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (24 bp):
TATTAGCATAAAATATCTAACATC
Found at i:88291214 original size:50 final size:50
Alignment explanation
Indices: 88291150--88291381 Score: 193
Period size: 50 Copynumber: 4.6 Consensus size: 50
88291140 GTTATGTGTA
*
88291150 TAGTACTAAATGCAGGCTACTACGTGTACCAGGTAGTTAGGTCACATGTG
1 TAGTACTAAGTGCAGGCTACTACGTGTACCAGGTAGTTAGGTCACATGTG
* * * * ** * * *
88291200 TAGTACTAAGTGCAGGATACTATGCGTACCCGACAACTTCA-ATCACGTGTG
1 TAGTACTAAGTGCAGGCTACTACGTGTACCAG-GTAGTT-AGGTCACATGTG
** * ** * * *
88291251 TAGTACTAAGCACAGGCTACTACATGTATAAGATGGTTAGGTCACGTGTG
1 TAGTACTAAGTGCAGGCTACTACGTGTACCAGGTAGTTAGGTCACATGTG
* * *
88291301 TAGTACTAAGTGCAGGCTATTACATGTACC-GG-A-TTATTGGTCGCATGTG
1 TAGTACTAAGTGCAGGCTACTACGTGTACCAGGTAGTTA--GGTCACATGTG
* *
88291350 TAGTACTAAGTGCAGGCTACTATGCGTACCAG
1 TAGTACTAAGTGCAGGCTACTACGTGTACCAG
88291382 ATAGCTTCGG
Statistics
Matches: 139, Mismatches: 37, Indels: 12
0.74 0.20 0.06
Matches are distributed among these distances:
47 3 0.02
49 37 0.27
50 64 0.46
51 34 0.24
52 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (50 bp):
TAGTACTAAGTGCAGGCTACTACGTGTACCAGGTAGTTAGGTCACATGTG
Found at i:88291417 original size:150 final size:152
Alignment explanation
Indices: 88291098--88291382 Score: 344
Period size: 150 Copynumber: 1.9 Consensus size: 152
88291088 AACACATCTA
* ** * * *
88291098 TAGTACTATGTGCAGGCTACCATGTGTTTAAGATGGTTTTAGGTTATGTGTATAGTACTAAATGC
1 TAGTAATATGTGCAGGCTACCACATGTATAAGATGG-TTTAGGTCACGTGTATAGTACTAAATGC
*
88291163 AGGCTACTACGTGTACCAGGTAGTTAGGTCACATGTGTAGTACTAAGTGCAGGATACTATGCGTA
65 AGGCTACTACATGTACCAGGTAGTTAGGTCACATGTGTAGTACTAAGTGCAGGATACTATGCGTA
* *
88291228 CCCGACAACTTCAATCACGTGTG
130 CCAGACAACTTCAATCAAGTGTG
* * ** * * *
88291251 TAGTACTAAGCACAGGCTACTACATGTATAAGATGG-TTAGGTCACGTGTGTAGTACTAAGTGCA
1 TAGTAATATGTGCAGGCTACCACATGTATAAGATGGTTTAGGTCACGTGTATAGTACTAAATGCA
* * *
88291315 GGCTATTACATGTACC-GG-A-TTATTGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGT
66 GGCTACTACATGTACCAGGTAGTTA--GGTCACATGTGTAGTACTAAGTGCAGGATACTATGCGT
88291377 ACCAGA
129 ACCAGA
88291383 TAGCTTCGGT
Statistics
Matches: 114, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
148 3 0.03
149 1 0.01
150 43 0.38
151 38 0.33
153 29 0.25
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (152 bp):
TAGTAATATGTGCAGGCTACCACATGTATAAGATGGTTTAGGTCACGTGTATAGTACTAAATGCA
GGCTACTACATGTACCAGGTAGTTAGGTCACATGTGTAGTACTAAGTGCAGGATACTATGCGTAC
CAGACAACTTCAATCAAGTGTG
Found at i:88297840 original size:26 final size:26
Alignment explanation
Indices: 88297811--88297918 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
88297801 TGGTACAAAT
88297811 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
88297837 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
88297863 TCATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
88297889 TGATAATGGTTTAGGCAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
88297915 TGAT
1 TGAT
88297919 GGGCATTTCA
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 74 1.00
ACGTcount: A:0.32, C:0.09, G:0.23, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:88299622 original size:27 final size:27
Alignment explanation
Indices: 88299539--88299643 Score: 115
Period size: 27 Copynumber: 3.9 Consensus size: 27
88299529 AGGAAGCGTC
* *
88299539 CTGGTGGCTATGCCACAATTATTTG-AT
1 CTGGTGGCTCTGCCACAA-TATCTGTAT
* *
88299566 CTCGTGGCTCTGCCATATATATCTGT-T
1 CTGGTGGCTCTGCCACA-ATATCTGTAT
88299593 CTGGTGGCTCTGCCACAATATCTGTAT
1 CTGGTGGCTCTGCCACAATATCTGTAT
* * *
88299620 CTGGTGACTTTGTCACAATATCTG
1 CTGGTGGCTCTGCCACAATATCTG
88299644 GCAGTCTCGC
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
26 8 0.12
27 57 0.86
28 1 0.02
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATATCTGTAT
Found at i:88304905 original size:26 final size:26
Alignment explanation
Indices: 88304876--88304983 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
88304866 TGGTACAAAT
*
88304876 TGATAATGGGTTAGGTAAATGTCCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
88304902 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
88304928 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
88304954 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
88304980 TGAT
1 TGAT
88304984 GGGCATTTCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:88306694 original size:27 final size:27
Alignment explanation
Indices: 88306597--88306701 Score: 135
Period size: 27 Copynumber: 3.9 Consensus size: 27
88306587 AGGAAGCGTC
*
88306597 CTGGTGGCTATGCCACAATTATCTG-AT
1 CTGGTGGCTCTGCCACAA-TATCTGTAT
88306624 CTGGTGGCTCTGCCACATATATCTGT-T
1 CTGGTGGCTCTGCCACA-ATATCTGTAT
88306651 CTGGTGGCTCTGCCACAATATCTGTAT
1 CTGGTGGCTCTGCCACAATATCTGTAT
* *
88306678 CTGGTGACT-TCGTCACAATATCTG
1 CTGGTGGCTCT-GCCACAATATCTG
88306702 GCAGCCTCGC
Statistics
Matches: 71, Mismatches: 3, Indels: 8
0.87 0.04 0.10
Matches are distributed among these distances:
26 9 0.13
27 61 0.86
28 1 0.01
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATATCTGTAT
Found at i:88308196 original size:50 final size:50
Alignment explanation
Indices: 88308142--88308391 Score: 225
Period size: 50 Copynumber: 5.0 Consensus size: 50
88308132 TAAGATGGTT
** * *
88308142 TTAGGTCATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
1 TTAGGTCACATGTGTAGTACTAAGTGTAGGCTACTACGCGTACCAGATAG
* * * * * *
88308192 TTAGGTCGCATGTGTAGTACTAAGTGTAGGTTACTATGCGTACCCGACAAC
1 TTAGGTCACATGTGTAGTACTAAGTGTAGGCTACTACGCGTACCAGA-TAG
* * * * *
88308243 TTCA-ATCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGG
1 TT-AGGTCACATGTGTAGTACTAAGTGTAGGCTACTACGCGTACCAGATAG
* * * ** ** *
88308293 TTAGTTCACGTATGTAGTACTAAGTGTAGGCTACTACAAGTACTGGATTG
1 TTAGGTCACATGTGTAGTACTAAGTGTAGGCTACTACGCGTACCAGATAG
* * * *
88308343 TT-GGTCACATATGTAGTACTAAGTGTAGGTTACTATGCGTACCAAATAG
1 TTAGGTCACATGTGTAGTACTAAGTGTAGGCTACTACGCGTACCAGATAG
88308392 CTTCGGTTAC
Statistics
Matches: 156, Mismatches: 41, Indels: 7
0.76 0.20 0.03
Matches are distributed among these distances:
49 38 0.24
50 79 0.51
51 38 0.24
52 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (50 bp):
TTAGGTCACATGTGTAGTACTAAGTGTAGGCTACTACGCGTACCAGATAG
Found at i:88308610 original size:16 final size:15
Alignment explanation
Indices: 88308589--88308618 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
88308579 GAATGGAGTA
88308589 AGTGAAATTATGTAAG
1 AGTGAAATT-TGTAAG
88308605 AGTGAAATTTGTAA
1 AGTGAAATTTGTAA
88308619 TAAAACAGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.33
Consensus pattern (15 bp):
AGTGAAATTTGTAAG
Found at i:88310685 original size:24 final size:24
Alignment explanation
Indices: 88310664--88310743 Score: 106
Period size: 24 Copynumber: 3.3 Consensus size: 24
88310654 AAGATTTAGT
*
88310664 ATTTATTAGTATAATATATTTAAC
1 ATTTATTAGCATAATATATTTAAC
* *
88310688 ATTTATTAACATAATATTTTTAAC
1 ATTTATTAGCATAATATATTTAAC
* *
88310712 ATTTATTAGCATATTATATTTGAC
1 ATTTATTAGCATAATATATTTAAC
*
88310736 ATTGATTA
1 ATTTATTA
88310744 AAATAAGGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.39, C:0.06, G:0.05, T:0.50
Consensus pattern (24 bp):
ATTTATTAGCATAATATATTTAAC
Found at i:88317676 original size:31 final size:30
Alignment explanation
Indices: 88317641--88317718 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 30
88317631 AATATAAAAC
88317641 TGGTACTTGAA-TTTATTTACTT-ATCATAGAT
1 TGGTACTTGAAGTTT-TTT--TTAATCATAGAT
* *
88317672 TGGTACTTAAAGTTTTTTTTAATCCTAGAT
1 TGGTACTTGAAGTTTTTTTTAATCATAGAT
*
88317702 TGGTACTTGAACTTTTT
1 TGGTACTTGAAGTTTTT
88317719 CTCCGTCAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 2 0.05
30 23 0.56
31 13 0.32
32 3 0.07
ACGTcount: A:0.26, C:0.10, G:0.14, T:0.50
Consensus pattern (30 bp):
TGGTACTTGAAGTTTTTTTTAATCATAGAT
Found at i:88319335 original size:19 final size:19
Alignment explanation
Indices: 88319311--88319359 Score: 70
Period size: 17 Copynumber: 2.8 Consensus size: 19
88319301 AGAAGAAAGG
88319311 AATATCAGAAAAAAATGGA
1 AATATCAGAAAAAAATGGA
88319330 AATATCAG--AAAAATGGA
1 AATATCAGAAAAAAATGGA
88319347 AATA--AGAAAAAAA
1 AATATCAGAAAAAAA
88319360 ATAGAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 2 0.07
17 18 0.64
19 8 0.29
ACGTcount: A:0.67, C:0.04, G:0.14, T:0.14
Consensus pattern (19 bp):
AATATCAGAAAAAAATGGA
Found at i:88319359 original size:17 final size:17
Alignment explanation
Indices: 88319317--88319369 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
88319307 AAGGAATATC
88319317 AGAAAAAAATGGAAATA
1 AGAAAAAAATGGAAATA
** *
88319334 TCAGAAAAATGGAAATA
1 AGAAAAAAATGGAAATA
*
88319351 AGAAAAAAAATAGAAATA
1 AG-AAAAAAATGGAAATA
88319369 A
1 A
88319370 TTTTTAAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
17 14 0.50
18 14 0.50
ACGTcount: A:0.70, C:0.02, G:0.15, T:0.13
Consensus pattern (17 bp):
AGAAAAAAATGGAAATA
Found at i:88319360 original size:18 final size:18
Alignment explanation
Indices: 88319319--88319369 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
88319309 GGAATATCAG
**
88319319 AAAAAAATGGAAAT-ATC
1 AAAAAAATGGAAATAAGA
*
88319336 AGAAAAATGGAAATAAGA
1 AAAAAAATGGAAATAAGA
*
88319354 AAAAAAATAGAAATAA
1 AAAAAAATGGAAATAA
88319370 TTTTTAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.71, C:0.02, G:0.14, T:0.14
Consensus pattern (18 bp):
AAAAAAATGGAAATAAGA
Found at i:88319392 original size:22 final size:21
Alignment explanation
Indices: 88319367--88319408 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
88319357 AAAATAGAAA
88319367 TAATTTTTAAAAATATTTTTAT
1 TAATTTTT-AAAATATTTTTAT
*
88319389 TAATTTTTAATATATTTTTA
1 TAATTTTTAAAATATTTTTA
88319409 GATAATGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TAATTTTTAAAATATTTTTAT
Found at i:88319414 original size:22 final size:22
Alignment explanation
Indices: 88319365--88319414 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
88319355 AAAAAATAGA
88319365 AATAATTTTTAAAAATATTTTT
1 AATAATTTTTAAAAATATTTTT
* *
88319387 ATTAATTTTT-AATATATTTTT
1 AATAATTTTTAAAAATATTTTT
88319408 AGATAAT
1 A-ATAAT
88319415 GAAATCATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
AATAATTTTTAAAAATATTTTT
Found at i:88322007 original size:3 final size:3
Alignment explanation
Indices: 88321999--88322028 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
88321989 ACCTAATCTC
*
88321999 CTT CTT CTT CTT CTT CTT CTT CTT CAT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
88322029 TATTTACATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.63
Consensus pattern (3 bp):
CTT
Found at i:88327065 original size:27 final size:27
Alignment explanation
Indices: 88327035--88327091 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
88327025 AATTCACTTT
88327035 TCAATTTCCAA-TCAATACTA-ATTTCAA
1 TCAA-TTCCAATTCAATAC-ACATTTCAA
88327062 TCAATTCCAATTCAATACACATTTCAA
1 TCAATTCCAATTCAATACACATTTCAA
88327089 TCA
1 TCA
88327092 TTCATATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.40, C:0.25, G:0.00, T:0.35
Consensus pattern (27 bp):
TCAATTCCAATTCAATACACATTTCAA
Found at i:88327073 original size:16 final size:16
Alignment explanation
Indices: 88327036--88327077 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
88327026 ATTCACTTTT
88327036 CAATTTCCAATCAATAC
1 CAATTT-CAATCAATAC
* *
88327053 TAATTTCAATCAATTC
1 CAATTTCAATCAATAC
88327069 CAA-TTCAAT
1 CAATTTCAAT
88327078 ACACATTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 6 0.27
16 11 0.50
17 5 0.23
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (16 bp):
CAATTTCAATCAATAC
Found at i:88327813 original size:17 final size:15
Alignment explanation
Indices: 88327781--88327816 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 15
88327771 AACCCTAATT
88327781 TTTCCCTTTTCTTTC
1 TTTCCCTTTTCTTTC
88327796 TTTCCCTTTTTCCTTTC
1 TTTCCC-TTTT-CTTTC
88327813 TTTC
1 TTTC
88327817 TTTCTCCCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.32
16 4 0.21
17 9 0.47
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTCCCTTTTCTTTC
Found at i:88327833 original size:21 final size:21
Alignment explanation
Indices: 88327787--88327844 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 21
88327777 AATTTTTCCC
*
88327787 TTTTCTTTC-TT-TCCCTTTT
1 TTTTCTTTCTTTCTCCCTTAT
88327806 TCCTTTCTTTCTTTCTCCCTTAT
1 T--TTTCTTTCTTTCTCCCTTAT
88327829 TTTTCGTTTCTATTCT
1 TTTTC-TTTCT-TTCT
88327845 GTTCTTCTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
19 1 0.03
21 12 0.38
22 7 0.22
23 12 0.38
ACGTcount: A:0.03, C:0.28, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTTCTTTCTTTCTCCCTTAT
Found at i:88327915 original size:16 final size:16
Alignment explanation
Indices: 88327894--88327932 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
88327884 AGTTTATGTT
*
88327894 TATTATATTAATATAA
1 TATTATATTAACATAA
88327910 TATTATATTAACATAA
1 TATTATATTAACATAA
88327926 TAATTAT
1 T-ATTAT
88327933 TAGTTCTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (16 bp):
TATTATATTAACATAA
Found at i:88329666 original size:13 final size:13
Alignment explanation
Indices: 88329648--88329673 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
88329638 CTGTGCATTC
88329648 TTAGTTTAGATAA
1 TTAGTTTAGATAA
88329661 TTAGTTTAGATAA
1 TTAGTTTAGATAA
88329674 AACAAATCCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (13 bp):
TTAGTTTAGATAA
Found at i:88341636 original size:16 final size:16
Alignment explanation
Indices: 88341615--88341645 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
88341605 CTATGCATAC
*
88341615 AAAATATAAAAGACAG
1 AAAATACAAAAGACAG
88341631 AAAATACAAAAGACA
1 AAAATACAAAAGACA
88341646 TAATAGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.10, G:0.10, T:0.10
Consensus pattern (16 bp):
AAAATACAAAAGACAG
Found at i:88350339 original size:15 final size:15
Alignment explanation
Indices: 88350319--88350348 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
88350309 AATACATAGT
88350319 CCTCTGTCCTATGAC
1 CCTCTGTCCTATGAC
88350334 CCTCTGTCCTATGAC
1 CCTCTGTCCTATGAC
88350349 TACATTAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.40, G:0.13, T:0.33
Consensus pattern (15 bp):
CCTCTGTCCTATGAC
Found at i:88355738 original size:50 final size:50
Alignment explanation
Indices: 88355663--88356006 Score: 375
Period size: 50 Copynumber: 6.9 Consensus size: 50
88355653 ATCGAAGCTC
* * * *
88355663 TCTGGTACCCATAGTAGCCTACACTTAGTACTACACATGTGACCTATCAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAA
* * * *
88355713 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACATACGTGACTTAACCA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAA
** * * *
88355763 TCTAATGCACGTAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAA
* * * *
88355813 TCTGGTACACGTAATAGCCTGCACTTAGTACTACACACGTGACTTAACCA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAA
* * * * ** *
88355863 TCTGATACATGTATTAGCCTACACTTAGTACTACACACGTGATCGAAGTTAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGA-CCTA-TCAA
* * * ** *
88355915 -CGGGTACGCATAGTAGCCTGCACTTAGTACTACACGTGCGACCTATCAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAA
* *
88355964 TCTGGTACACGTAGTAGTCTGCACTTAGTATTACACACGTGAC
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGAC
88356007 TCACAACGAA
Statistics
Matches: 235, Mismatches: 56, Indels: 6
0.79 0.19 0.02
Matches are distributed among these distances:
49 3 0.01
50 198 0.84
51 33 0.14
52 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.27
Consensus pattern (50 bp):
TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAA
Found at i:88356383 original size:19 final size:20
Alignment explanation
Indices: 88356355--88356401 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
88356345 AAGAACAGGT
88356355 TATATCATCAAAATACTCACA
1 TATAT-ATCAAAATACTCACA
* *
88356376 TA-ATATCAAATTATTCACA
1 TATATATCAAAATACTCACA
88356395 TATATAT
1 TATATAT
88356402 ACTTAAAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 15 0.65
20 6 0.26
21 2 0.09
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.36
Consensus pattern (20 bp):
TATATATCAAAATACTCACA
Found at i:88357987 original size:24 final size:23
Alignment explanation
Indices: 88357941--88357987 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
88357931 TAAACCCGAC
* *
88357941 ATGGCGTGTAGGGATGGTCGAAG
1 ATGGAGTGTAGGGATGGGCGAAG
*
88357964 ATGGAGTGTAGAGGATGGGGGAAG
1 ATGGAGTGTAG-GGATGGGCGAAG
88357988 GATATTTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.26, C:0.04, G:0.51, T:0.19
Consensus pattern (23 bp):
ATGGAGTGTAGGGATGGGCGAAG
Found at i:88361293 original size:16 final size:16
Alignment explanation
Indices: 88361274--88361305 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
88361264 AATTGTTTTA
88361274 TTACAAAATTTCACTT
1 TTACAAAATTTCACTT
*
88361290 TTACATAATTTCACTT
1 TTACAAAATTTCACTT
88361306 ACTCTATTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.19, G:0.00, T:0.47
Consensus pattern (16 bp):
TTACAAAATTTCACTT
Found at i:88361581 original size:50 final size:50
Alignment explanation
Indices: 88361505--88361899 Score: 353
Period size: 50 Copynumber: 7.9 Consensus size: 50
88361495 ATCGAAGCTC
* * * *
88361505 TCTGGTACCCATAGTAGCCTACACTTAGTACTACACATGCGACCTATCAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
* * * * * *
88361555 TCTGGTACACGTAGTAGCCTGAACTTAGTACTATACACGTGACTTAACCA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
* * * ** *
88361605 TCTGATACATGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGA-CCTA-TCAA
* * * ** *
88361657 -CGGGTACGCATAGTAGCCTGCACTTAGTACTGTACATGCGACCTATCAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
* * * * * *
88361706 TCTGGTACACGTAGCAACCTGCACTTAGTACTACACACGTGACTTAACCA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
* * * ** *
88361756 TCTGATACACGTATTAGCCTACACTTAGTACTACACATGTGATCGAAGTTAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGA-CCTA-TCAA
* *** * *
88361808 -CGGGTGGGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
* * *
88361857 TCTAGTACACGTAGTAGCCTGCACTTAGAACTACACAAGTGAC
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGAC
88361900 TCACAACAAA
Statistics
Matches: 264, Mismatches: 75, Indels: 12
0.75 0.21 0.03
Matches are distributed among these distances:
49 6 0.02
50 188 0.71
51 68 0.26
52 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (50 bp):
TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
Found at i:88361709 original size:101 final size:101
Alignment explanation
Indices: 88361566--88361747 Score: 265
Period size: 101 Copynumber: 1.8 Consensus size: 101
88361556 CTGGTACACG
* * * * * *
88361566 TAGTAGCCTGAACTTAGTACTATACACGTGACTTAACCATCTGATACATGTAGTAGCCTGCACTT
1 TAGTAGCCTGAACTTAGTACTATACACGCGACCTAACAATCTGATACACGTAGCAACCTGCACTT
88361631 AGTACTACACACGTGATCGAAGTTAACGGGTACGCA
66 AGTACTACACACGTGATCGAAGTTAACGGGTACGCA
* * * * *
88361667 TAGTAGCCTGCACTTAGTACTGTACATGCGACCTATCAATCTGGTACACGTAGCAACCTGCACTT
1 TAGTAGCCTGAACTTAGTACTATACACGCGACCTAACAATCTGATACACGTAGCAACCTGCACTT
88361732 AGTACTACACACGTGA
66 AGTACTACACACGTGA
88361748 CTTAACCATC
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
101 70 1.00
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (101 bp):
TAGTAGCCTGAACTTAGTACTATACACGCGACCTAACAATCTGATACACGTAGCAACCTGCACTT
AGTACTACACACGTGATCGAAGTTAACGGGTACGCA
Found at i:88361774 original size:151 final size:151
Alignment explanation
Indices: 88361508--88361900 Score: 633
Period size: 151 Copynumber: 2.6 Consensus size: 151
88361498 GAAGCTCTCT
* *
88361508 GGTACCCATAGTAGCCTACACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGTAGC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGTAGC
* * * *
88361573 CTGAACTTAGTACTATACACGTGACTTAACCATCTGATACATGTAGTAGCCTGCACTTAGTACTA
66 CTGCACTTAGTACTACACACGTGACTTAACCATCTGATACACGTAGTAGCCTACACTTAGTACTA
88361638 CACACGTGATCGAAGTTAACG
131 CACACGTGATCGAAGTTAACG
** * *
88361659 GGTACGCATAGTAGCCTGCACTTAGTACTGTACATGCGACCTATCAATCTGGTACACGTAGCAAC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGTAGC
*
88361724 CTGCACTTAGTACTACACACGTGACTTAACCATCTGATACACGTATTAGCCTACACTTAGTACTA
66 CTGCACTTAGTACTACACACGTGACTTAACCATCTGATACACGTAGTAGCCTACACTTAGTACTA
*
88361789 CACATGTGATCGAAGTTAACG
131 CACACGTGATCGAAGTTAACG
** *
88361810 GGTGGGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTAGTACACGTAGTAGC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGTAGC
* *
88361875 CTGCACTTAGAACTACACAAGTGACT
66 CTGCACTTAGTACTACACACGTGACT
88361901 CACAACAAAT
Statistics
Matches: 221, Mismatches: 21, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
151 221 1.00
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (151 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGTAGC
CTGCACTTAGTACTACACACGTGACTTAACCATCTGATACACGTAGTAGCCTACACTTAGTACTA
CACACGTGATCGAAGTTAACG
Found at i:88362276 original size:19 final size:20
Alignment explanation
Indices: 88362248--88362294 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
88362238 AAGAACATGT
88362248 TATATCATCAAAATAATCACA
1 TATAT-ATCAAAATAATCACA
* *
88362269 TA-ATATCAAATTATTCACA
1 TATATATCAAAATAATCACA
88362288 TATATAT
1 TATATAT
88362295 ACTTACAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 15 0.65
20 6 0.26
21 2 0.09
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (20 bp):
TATATATCAAAATAATCACA
Found at i:88365022 original size:31 final size:33
Alignment explanation
Indices: 88364987--88365059 Score: 109
Period size: 32 Copynumber: 2.3 Consensus size: 33
88364977 CGTTTTTAGG
88364987 AATTTTAA-T-GTTTTTATGATCCTTGTAGTTT
1 AATTTTAACTAGTTTTTATGATCCTTGTAGTTT
*
88365018 AA-TTTAACTAGTTTTTGTGATCCTTGTAGTTT
1 AATTTTAACTAGTTTTTATGATCCTTGTAGTTT
88365050 AA-TTTAACTA
1 AATTTTAACTA
88365060 ACTCGGGTGT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
30 5 0.13
31 3 0.08
32 31 0.79
ACGTcount: A:0.26, C:0.08, G:0.12, T:0.53
Consensus pattern (33 bp):
AATTTTAACTAGTTTTTATGATCCTTGTAGTTT
Found at i:88365032 original size:32 final size:32
Alignment explanation
Indices: 88364996--88365059 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
88364986 GAATTTTAAT
88364996 GTTTTTATGATCCTTGTAGTTTAATTTAACTA
1 GTTTTTATGATCCTTGTAGTTTAATTTAACTA
*
88365028 GTTTTTGTGATCCTTGTAGTTTAATTTAACTA
1 GTTTTTATGATCCTTGTAGTTTAATTTAACTA
88365060 ACTCGGGTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.23, C:0.09, G:0.14, T:0.53
Consensus pattern (32 bp):
GTTTTTATGATCCTTGTAGTTTAATTTAACTA
Found at i:88377210 original size:23 final size:23
Alignment explanation
Indices: 88377179--88377222 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
88377169 GAATTACTTT
*
88377179 AATATTGCATTGTTATTTATGTA
1 AATAATGCATTGTTATTTATGTA
88377202 AATAATGCATTGTTATTTATG
1 AATAATGCATTGTTATTTATG
88377223 CTTTAATTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.32, C:0.05, G:0.14, T:0.50
Consensus pattern (23 bp):
AATAATGCATTGTTATTTATGTA
Found at i:88381119 original size:21 final size:21
Alignment explanation
Indices: 88381078--88381120 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
88381068 GCTGATTTTT
* *
88381078 TTTTTCTTTTTGTTTTGATTC
1 TTTTTCTTTTAGGTTTGATTC
88381099 TTTTTCTTTTCAGGTTT-ATTC
1 TTTTTCTTTT-AGGTTTGATTC
88381120 T
1 T
88381121 GTTAAATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.07, C:0.12, G:0.09, T:0.72
Consensus pattern (21 bp):
TTTTTCTTTTAGGTTTGATTC
Found at i:88386730 original size:20 final size:20
Alignment explanation
Indices: 88386687--88386735 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
88386677 TATTAATTAC
*
88386687 AAATATTTAATGATTATATTT
1 AAATATTTAA-GAATATATTT
88386708 AAATATTTAA-AATATAGTTT
1 AAATATTTAAGAATATA-TTT
88386728 AAATATTT
1 AAATATTT
88386736 TAATTAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 5 0.19
20 11 0.42
21 10 0.38
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (20 bp):
AAATATTTAAGAATATATTT
Found at i:88386801 original size:24 final size:22
Alignment explanation
Indices: 88386661--88386801 Score: 69
Period size: 24 Copynumber: 6.3 Consensus size: 22
88386651 CCTCTAATAA
* *
88386661 TATAATATTTTTAAAA-TATTAAT
1 TATAA-ATATTTAAAATTA-TATT
* *
88386684 TACAAATATTTAATGATTATA-T
1 TATAAATATTTAA-AATTATATT
*
88386706 T-TAAATATTTAAAA-TATAGT
1 TATAAATATTTAAAATTATATT
* *
88386726 T-TAAATATTT-TAATTAAATTT
1 TATAAATATTTAAAATTATA-TT
* * *
88386747 TATAAATAATTAACATTTATTACT
1 TATAAATATTTAA-AATTA-TATT
*
88386771 TAAAAATATTTAAAATTTATATT
1 TATAAATATTTAAAA-TTATATT
88386794 TCATAAAT
1 T-ATAAAT
88386802 TAAAATATTA
Statistics
Matches: 89, Mismatches: 18, Indels: 21
0.70 0.14 0.16
Matches are distributed among these distances:
19 6 0.07
20 15 0.17
21 12 0.13
22 17 0.19
23 12 0.13
24 26 0.29
25 1 0.01
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (22 bp):
TATAAATATTTAAAATTATATT
Found at i:88391158 original size:220 final size:220
Alignment explanation
Indices: 88390776--88391216 Score: 828
Period size: 220 Copynumber: 2.0 Consensus size: 220
88390766 TATGGCTTTG
*
88390776 TAACACCCCTAACACGTATCCATCGTCGAAACAGGGTTACAGAGTGTTACCAGTACATACAGAAC
1 TAACACCCCTAACACGTATCCATCGCCGAAACAGGGTTACAGAGTGTTACCAGTACATACAGAAC
88390841 ATTTACAGATTAATCGAAACATTACTATTCACTTTTTGAAATCATATATATAACGACCTTTATTT
66 ATTTACAGATTAATCGAAACATTACTATTCACTTTTTGAAATCATATATATAACGACCTTTATTT
*
88390906 GGGCCCTCGAAGCCCAACATGAAGGTTAAAATCAAGTTGGAGCTCAACTGATTTCTCATAAAATT
131 GGGCCCTCAAAGCCCAACATGAAGGTTAAAATCAAGTTGGAGCTCAACTGATTTCTCATAAAATT
88390971 TTTCACTTAATTTTTTAATTTTTTT
196 TTTCACTTAATTTTTTAATTTTTTT
* *
88390996 TAACACCCCTAACCCGTATCCTTCGCCGAAACAGGGTTACAGAGTGTTACCAGTACATACAGAAC
1 TAACACCCCTAACACGTATCCATCGCCGAAACAGGGTTACAGAGTGTTACCAGTACATACAGAAC
88391061 ATTTACAGATTAATCGAAACATTACTATTCACTTTTTGAAATCATATATATAACGACCTTTATTT
66 ATTTACAGATTAATCGAAACATTACTATTCACTTTTTGAAATCATATATATAACGACCTTTATTT
88391126 GGGCCCTCAAAGCCCAACATGAAGGTTAAAATCAAGTTGGAGCTCAACTGATTTCTCATAAAATT
131 GGGCCCTCAAAGCCCAACATGAAGGTTAAAATCAAGTTGGAGCTCAACTGATTTCTCATAAAATT
**
88391191 TTTTGCTTAATTTTTTAATTTTTTT
196 TTTCACTTAATTTTTTAATTTTTTT
88391216 T
1 T
88391217 TAAATTTTAC
Statistics
Matches: 215, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
220 215 1.00
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (220 bp):
TAACACCCCTAACACGTATCCATCGCCGAAACAGGGTTACAGAGTGTTACCAGTACATACAGAAC
ATTTACAGATTAATCGAAACATTACTATTCACTTTTTGAAATCATATATATAACGACCTTTATTT
GGGCCCTCAAAGCCCAACATGAAGGTTAAAATCAAGTTGGAGCTCAACTGATTTCTCATAAAATT
TTTCACTTAATTTTTTAATTTTTTT
Found at i:88393442 original size:18 final size:18
Alignment explanation
Indices: 88393419--88393457 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
88393409 TTCTTTTAAG
88393419 TTAGTGCTTGGCCTATAA
1 TTAGTGCTTGGCCTATAA
88393437 TTAGTGCTTGGCCTATAA
1 TTAGTGCTTGGCCTATAA
88393455 TTA
1 TTA
88393458 TTATTTGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.41
Consensus pattern (18 bp):
TTAGTGCTTGGCCTATAA
Found at i:88396963 original size:30 final size:29
Alignment explanation
Indices: 88396916--88396977 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 29
88396906 ACTTGTTTTA
88396916 TTGTTAATTTTTTATTATTTTAGAGGCAT
1 TTGTTAATTTTTTATTATTTTAGAGGCAT
*
88396945 TTGTTAATTTTGTTATTATTTTAGAGGTAT
1 TTGTTAATTTT-TTATTATTTTAGAGGCAT
88396975 TTG
1 TTG
88396978 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 11 0.35
30 20 0.65
ACGTcount: A:0.23, C:0.02, G:0.16, T:0.60
Consensus pattern (29 bp):
TTGTTAATTTTTTATTATTTTAGAGGCAT
Found at i:88399435 original size:56 final size:56
Alignment explanation
Indices: 88399370--88399489 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
88399360 ACAAGGGATG
88399370 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
88399426 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
88399482 ATGGGCAA
1 ATGGGCAA
88399490 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:88401401 original size:47 final size:47
Alignment explanation
Indices: 88401346--88401519 Score: 267
Period size: 47 Copynumber: 3.7 Consensus size: 47
88401336 ATTTAGGATT
88401346 CGATGTGATGAATGTGAAAGTGTATATATGTGAAAAGGCCTAATGGC
1 CGATGTGATGAATGTGAAAGTGTATATATGTGAAAAGGCCTAATGGC
*
88401393 CGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGC
1 CGATGTGATGAATGTGAAAGTGTATATATGTGAAAAGGCCTAATGGC
* * * *
88401440 CGATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGC
1 CGATGTGATGAATGTGAAAGTGTATATATGTGAAAAGGCCTAATGGC
* * * *
88401487 CAACGTGATGGATGTGAAAGTGTATAAATGTGA
1 CGATGTGATGAATGTGAAAGTGTATATATGTGA
88401520 TAAGTCCCGA
Statistics
Matches: 118, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 118 1.00
ACGTcount: A:0.32, C:0.09, G:0.32, T:0.28
Consensus pattern (47 bp):
CGATGTGATGAATGTGAAAGTGTATATATGTGAAAAGGCCTAATGGC
Found at i:88401698 original size:37 final size:37
Alignment explanation
Indices: 88401642--88401720 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
88401632 CCGAGCTCTA
* * *
88401642 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
88401679 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
88401716 AAGAC
1 AAGAC
88401721 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:88404210 original size:46 final size:45
Alignment explanation
Indices: 88404077--88404297 Score: 173
Period size: 46 Copynumber: 4.8 Consensus size: 45
88404067 ACATATTTTT
*
88404077 GCCGATGCCATGTCCCAGACATGGTCTTACACT-GAC-ACATCTCGTA-
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAG-CTTCATCTCG-AG
* *
88404123 GCCGATGCATGTCCCAGACATATCTTACAC-AGGCTTACGTCTCGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTA-GCTT-CATCTCGAG
* * * *
88404169 GCCGATGCATGTCCTAGACATGTCTTACACTAGCATTCGTCTCAAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGC-TTCATCTCGAG
** * * * * *
88404215 ATCGATGCCATGTCCTAGACATGGTCTTACATTGGCTCTCATAAT-GTG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCT-TCAT-CTCGAG
*
88404263 GCCGATGCATGTCCCAGACATGTCTTACAGTAGCT
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCT
88404298 CACAACAAGT
Statistics
Matches: 143, Mismatches: 21, Indels: 22
0.77 0.11 0.12
Matches are distributed among these distances:
44 9 0.06
45 16 0.11
46 67 0.47
47 31 0.22
48 19 0.13
49 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.28
Consensus pattern (45 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCTTCATCTCGAG
Found at i:88412617 original size:37 final size:37
Alignment explanation
Indices: 88412461--88412654 Score: 162
Period size: 37 Copynumber: 5.2 Consensus size: 37
88412451 TCGGTAGTTC
** *
88412461 AGTATACTCAGTAGATAATGCTCGATTGAGCCTT-ATTTT
1 AGTATA-TCAGTAGATTTTGCTCGTTTGAG-CTTCA-TTT
* * * * *
88412500 AGTATATCTGTATATCTCGCTCAG-TTGAGCTCTC-TTC
1 AGTATATCAGTAGATTTTGCTC-GTTTGAGCT-TCATTT
* * *
88412537 AGCATATCTGTAGATTTTGCTCGTTTGAGCTTCATTC
1 AGTATATCAGTAGATTTTGCTCGTTTGAGCTTCATTT
*
88412574 AGTATATCAGTAGATTTTGCTCATTTGAGCTTCATTT
1 AGTATATCAGTAGATTTTGCTCGTTTGAGCTTCATTT
* * * *
88412611 AATATATCGGTA-AGGTTTGCTTGTTTGAGCTTCATTT
1 AGTATATCAGTAGA-TTTTGCTCGTTTGAGCTTCATTT
88412648 AGTATAT
1 AGTATAT
88412655 GATGTCATAT
Statistics
Matches: 129, Mismatches: 20, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
36 4 0.03
37 101 0.78
38 17 0.13
39 7 0.05
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (37 bp):
AGTATATCAGTAGATTTTGCTCGTTTGAGCTTCATTT
Found at i:88414646 original size:50 final size:50
Alignment explanation
Indices: 88414529--88414822 Score: 236
Period size: 50 Copynumber: 5.8 Consensus size: 50
88414519 TTCGCCCCTG
* * * * *
88414529 CATGTGTAGTACTATGTGCAAGCTACTATGTGT-TTAAGAAAGTTTTAGGTCA
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACT-AGATAG--TTAGGTCA
** *
88414581 TGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGATAGTTAGGTCG
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGATAGTTAGGTCA
* * * * * * * *
88414631 CATGTGTAGTACTAAGTTCAGGCTATTATGCGTACCT-GACAACTTCGATCA
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CTAGA-TAGTTAGGTCA
* * * * *
88414682 CGTATGTAGTACTAAGTGCGGGCTACTACATGTA-TCAGATGGTTAGGTCA
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACT-AGATAGTTAGGTCA
* ** * *
88414732 CGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATTGTT-GGTCG
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGATAGTTAGGTCA
* * **
88414781 CATGTGTAGTACTAAATGCAGGCTACTATGCATACTAGATAG
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGATAG
88414823 CTTCGGTTAC
Statistics
Matches: 189, Mismatches: 47, Indels: 15
0.75 0.19 0.06
Matches are distributed among these distances:
49 39 0.21
50 80 0.42
51 36 0.19
52 33 0.17
53 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (50 bp):
CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGATAGTTAGGTCA
Found at i:88414767 original size:101 final size:101
Alignment explanation
Indices: 88414585--88414767 Score: 269
Period size: 101 Copynumber: 1.8 Consensus size: 101
88414575 AGGTCATGTG
* * *
88414585 TGTAGTACTAAGTGCAGGCTACTACGTGTACTAGATAGTTAGGTCGCATGTGTAGTACTAAGTTC
1 TGTAGTACTAAGTGCAGGCTACTACATGTACTAGATAGTTAGGTCACATGTGTAGTACTAAGTGC
* *
88414650 AGGCTATTATGCGTACCTGACAACTTCGATCACGTA
66 AGGCTACTACGCGTACCTGACAACTTCGATCACGTA
* * *
88414686 TGTAGTACTAAGTGCGGGCTACTACATGTA-TCAGATGGTTAGGTCACGTGTGTAGTACTAAGTG
1 TGTAGTACTAAGTGCAGGCTACTACATGTACT-AGATAGTTAGGTCACATGTGTAGTACTAAGTG
*
88414750 CAGGCTACTACGTGTACC
65 CAGGCTACTACGCGTACC
88414768 GGATTGTTGG
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
100 1 0.01
101 71 0.99
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.30
Consensus pattern (101 bp):
TGTAGTACTAAGTGCAGGCTACTACATGTACTAGATAGTTAGGTCACATGTGTAGTACTAAGTGC
AGGCTACTACGCGTACCTGACAACTTCGATCACGTA
Found at i:88416980 original size:25 final size:25
Alignment explanation
Indices: 88416951--88417000 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
88416941 ATGGATCCAC
88416951 CATGCAATGTTGCCAATATAACCAA
1 CATGCAATGTTGCCAATATAACCAA
88416976 CATGCAATGTTGCCAATATAACCAA
1 CATGCAATGTTGCCAATATAACCAA
88417001 TTATACATGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.24, G:0.12, T:0.24
Consensus pattern (25 bp):
CATGCAATGTTGCCAATATAACCAA
Found at i:88433287 original size:22 final size:23
Alignment explanation
Indices: 88433235--88433287 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
88433225 TCAACATTAT
* * *
88433235 GGACTAAATCAAACCAAATTACG
1 GGACAAAATCAAACAAAAATACG
*
88433258 GGACAAAATCAAACAAAAATAGG
1 GGACAAAATCAAACAAAAATACG
88433281 GGA-AAAA
1 GGACAAAA
88433288 GTTAAAAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 4 0.15
23 22 0.85
ACGTcount: A:0.57, C:0.15, G:0.17, T:0.11
Consensus pattern (23 bp):
GGACAAAATCAAACAAAAATACG
Found at i:88434704 original size:17 final size:17
Alignment explanation
Indices: 88434684--88434717 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
88434674 CATTTAAGTT
88434684 ATTGAATCATTCAAAAA
1 ATTGAATCATTCAAAAA
*
88434701 ATTGAATTATTCAAAAA
1 ATTGAATCATTCAAAAA
88434718 TTTTTTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.09, G:0.06, T:0.32
Consensus pattern (17 bp):
ATTGAATCATTCAAAAA
Found at i:88437091 original size:20 final size:20
Alignment explanation
Indices: 88437062--88437100 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
88437052 GTAATAATAA
88437062 TAAATAAAAT-GAAAACAAAT
1 TAAATAAAATAG-AAACAAAT
*
88437082 TAAATGAAATAGAAACAAA
1 TAAATAAAATAGAAACAAA
88437101 GTGGAAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.69, C:0.05, G:0.08, T:0.18
Consensus pattern (20 bp):
TAAATAAAATAGAAACAAAT
Found at i:88445388 original size:16 final size:16
Alignment explanation
Indices: 88445367--88445399 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
88445357 TAGCATAAAT
88445367 AACAGT-CTTCTGAGAC
1 AACAGTCCTT-TGAGAC
88445383 AACAGTCCTTTGAGAC
1 AACAGTCCTTTGAGAC
88445399 A
1 A
88445400 TTTCTGCCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (16 bp):
AACAGTCCTTTGAGAC
Found at i:88447975 original size:10 final size:10
Alignment explanation
Indices: 88447960--88447986 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
88447950 CGACCAAAAC
88447960 AAAAAAAATT
1 AAAAAAAATT
88447970 AAAAAAAATT
1 AAAAAAAATT
88447980 AAAAAAA
1 AAAAAAA
88447987 CTCAATTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAAAATT
Found at i:88454697 original size:17 final size:18
Alignment explanation
Indices: 88454675--88454708 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
88454665 CAGATTATTA
88454675 AAATTACTAAAA-ATTTG
1 AAATTACTAAAATATTTG
*
88454692 AAATTATTAAAATATTT
1 AAATTACTAAAATATTT
88454709 ACATTAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (18 bp):
AAATTACTAAAATATTTG
Found at i:88467536 original size:3 final size:3
Alignment explanation
Indices: 88467528--88467570 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
88467518 AGAGAGCAAA
88467528 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
88467571 GCATCAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:88476359 original size:27 final size:27
Alignment explanation
Indices: 88476317--88476377 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
88476307 CCATGACCGG
88476317 TACCTAAGTCAAAAATTCCTCCATCAT
1 TACCTAAGTCAAAAATTCCTCCATCAT
* * * *
88476344 TATCTAAGTTAGAAATTCTTCCATCAT
1 TACCTAAGTCAAAAATTCCTCCATCAT
88476371 TACCTAA
1 TACCTAA
88476378 ACAAACGCGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (27 bp):
TACCTAAGTCAAAAATTCCTCCATCAT
Found at i:88476531 original size:4 final size:4
Alignment explanation
Indices: 88476518--88476563 Score: 55
Period size: 4 Copynumber: 12.2 Consensus size: 4
88476508 GTATTGTTCA
88476518 CTTT -TTT CTTT CTTT CTTT CTTT CTCTT -TTT C-TT C-TT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CT-TT CTTT CTTT CTTT CTTT CTTT
88476563 C
1 C
88476564 CCACTATATA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
3 11 0.29
4 25 0.66
5 2 0.05
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
CTTT
Found at i:88480147 original size:16 final size:17
Alignment explanation
Indices: 88480116--88480148 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
88480106 TTCATAACTA
88480116 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
88480133 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
88480149 GCTACATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:88480496 original size:46 final size:46
Alignment explanation
Indices: 88480429--88480931 Score: 695
Period size: 46 Copynumber: 11.0 Consensus size: 46
88480419 TTATCTTTGA
* * * * *
88480429 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATAT
* * *** *
88480475 CAGGTTGTCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
* ** * ** ***
88480521 TACATTGCCATGGTATCTTTCAAACATGGTCTTATTCA-TTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
88480566 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
88480612 CCTGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
88480658 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
* * *
88480704 CCTGTTGTCATGGTCTCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
88480750 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
* *
88480796 CCTGTTGCCATGGTGTCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
88480842 CATGTTGCCATGGTGTCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
* *
88480888 CATGTTGCCATGGTGTCTTTCAACCATAGTCTTACACATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
88480932 TTTAGAAAGC
Statistics
Matches: 411, Mismatches: 44, Indels: 4
0.90 0.10 0.01
Matches are distributed among these distances:
45 41 0.10
46 370 0.90
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.41
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
Found at i:88487640 original size:44 final size:44
Alignment explanation
Indices: 88487522--88487822 Score: 195
Period size: 44 Copynumber: 6.8 Consensus size: 44
88487512 GAATTTTCGT
* * *
88487522 TTCAATCTGCTCCACTACTGCTTAAGGAGATATGAGCTGTA--ATC
1 TTCAATCTGCTCCACTACTGCTTAGGGAGATAAG-GCT-CACCATC
** * ** *
88487566 TTCAGCCTACTCCACTGTTG-TTCAGGGAGATAAGGCTCACCGTC
1 TTCAATCTGCTCCACTACTGCTT-AGGGAGATAAGGCTCACCATC
* * *
88487610 TTCAATCTGCTCTACTACTGCTTAGAGAGATAAGATCTGCA--ATC
1 TTCAATCTGCTCCACTACTGCTTAGGGAGATAAG-GCT-CACCATC
* ** * ****
88487654 ATCAGCCTGCTCCACTACCGCTTAGGGAGATAAGGCT-AGTGGC
1 TTCAATCTGCTCCACTACTGCTTAGGGAGATAAGGCTCACCATC
* * * * * *
88487697 TTAAATCTGCTCCAGTGCTGCTGTATGGAGATAAGGTTCGCCATC
1 TTCAATCTGCTCCACTACTGCT-TAGGGAGATAAGGCTCACCATC
* * *
88487742 TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTA--ATC
1 TTCAATCTGCTCCACTACTGCTTAGGGAGATAAG-GCT-CACCATC
* *
88487786 TTCAATCTGCTCCGCTATTGCTTAGGGAGATAAGGCT
1 TTCAATCTGCTCCACTACTGCTTAGGGAGATAAGGCT
88487823 AGTGGCTTTA
Statistics
Matches: 191, Mismatches: 54, Indels: 25
0.71 0.20 0.09
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 25 0.13
44 138 0.72
45 24 0.13
46 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (44 bp):
TTCAATCTGCTCCACTACTGCTTAGGGAGATAAGGCTCACCATC
Found at i:88487765 original size:132 final size:132
Alignment explanation
Indices: 88487591--88488172 Score: 695
Period size: 132 Copynumber: 4.4 Consensus size: 132
88487581 TGTTGTTCAG
* * * * *
88487591 GGAGATAAGGCTCACCGTCTTCAATCTGCTCTACTACTGCTTAGAGAGATAAGATCTGCAATCAT
1 GGAGATAAGGTTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGAGAGATAAGATCTGCAATCTT
* * * * * **
88487656 CAGCCTGCTCCACTACCGCTTAGGGAGATAAGGCTAGTGGCTTAAATCTGCTCCAGTGCTGCTGT
66 CAGCCTGCTCCGCTACTGCTTAGGGAGATAAGGCTAGTGGCTTTAATCTGCTCCATTGCCGCTAC
88487721 AT
131 AT
* * *
88487723 GGAGATAAGGTTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTT
1 GGAGATAAGGTTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGAGAGATAAGATCTGCAATCTT
** * *
88487788 CAATCTGCTCCGCTATTGCTTAGGGAGATAAGGCTAGTGGCTTTAATCTGCTCCATTGCCACTAC
66 CAGCCTGCTCCGCTACTGCTTAGGGAGATAAGGCTAGTGGCTTTAATCTGCTCCATTGCCGCTAC
88487853 AT
131 AT
* * * * *
88487855 GGAGATAATGTTCGCCGTCTTTGGTCTGCTCCACCACTGCTTAG-GAAGATAAGA-CATGTAATC
1 GGAGATAAGGTTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGAG-AGATAAGATC-TGCAATC
* * * * *
88487918 TTCAGCATGCTCCGCTATTGCTTAGAGAGATAAGGCTAGTGGCTTTAATCTGCTCCATTGCTGAT
64 TTCAGCCTGCTCCGCTACTGCTTAGGGAGATAAGGCTAGTGGCTTTAATCTGCTCCATTGCCGCT
88487983 ACAT
129 ACAT
* * ** * *
88487987 AGAGATAAGATTCGCTATCTTCGATCTACTCCACTACTGCTTA-AGGAGATAAGATTTGCAATCT
1 GGAGATAAGGTTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGA-GAGATAAGATCTGCAATCT
** * * *
88488051 TCAGCCTATTCCGCTACTGCTT-GGAAAGATAAGGCTAGTGGCTTTAATCTGCTCTATTACCGCT
65 TCAGCCTGCTCCGCTACTGCTTAGG-GAGATAAGGCTAGTGGCTTTAATCTGCTCCATTGCCGCT
88488115 ACAT
129 ACAT
* * * * *
88488119 GGAGATAAGATTCGCCGTCTTTGGTCTGCTCCACTACTGCTTAGGGATATAAGA
1 GGAGATAAGGTTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGAGAGATAAGA
88488173 CCTGTGAATT
Statistics
Matches: 383, Mismatches: 60, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
131 3 0.01
132 379 0.99
133 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (132 bp):
GGAGATAAGGTTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGAGAGATAAGATCTGCAATCTT
CAGCCTGCTCCGCTACTGCTTAGGGAGATAAGGCTAGTGGCTTTAATCTGCTCCATTGCCGCTAC
AT
Found at i:88487815 original size:88 final size:88
Alignment explanation
Indices: 88487522--88487820 Score: 234
Period size: 88 Copynumber: 3.4 Consensus size: 88
88487512 GAATTTTCGT
* * * * * * * ***
88487522 TTCAATCTGCTCCACTACTGCTTAAGGAGAT-ATGAGCTGTAATCTTCAGCCTACTCCACTGTTG
1 TTCAATCTGCTCCGCTACTGCTTAGGGAGATAAGGATCTGCAATCATCAGCCTGCTCCACTACCG
***
88487586 -TTCAGGGAGATAAGGCTCACCGTC
66 CTT-AGGGAGATAAGGCT-AGTATC
** *
88487610 TTCAATCTGCTCTACTACTGCTTAGAGAGATAA-GATCTGCAATCATCAGCCTGCTCCACTACCG
1 TTCAATCTGCTCCGCTACTGCTTAGGGAGATAAGGATCTGCAATCATCAGCCTGCTCCACTACCG
**
88487674 CTTAGGGAGATAAGGCTAGTGGC
66 CTTAGGGAGATAAGGCTAGTATC
* * * * * * *
88487697 TTAAATCTGCTCCAG-TGCTGCTGTATGGAGATAAGGTTC-GCCATCTTC-GATCTGCTCCACTA
1 TTCAATCTGCTCC-GCTACTGCT-TAGGGAGATAAGGATCTGCAATCATCAG-CCTGCTCCACTA
* *
88487759 CTGCTTAGGGAGATAAGATCT-GTAATC
63 CCGCTTAGGGAGATAAG-GCTAGT-ATC
*
88487786 TTCAATCTGCTCCGCTATTGCTTAGGGAGATAAGG
1 TTCAATCTGCTCCGCTACTGCTTAGGGAGATAAGG
88487821 CTAGTGGCTT
Statistics
Matches: 171, Mismatches: 31, Indels: 18
0.78 0.14 0.08
Matches are distributed among these distances:
87 21 0.12
88 124 0.73
89 26 0.15
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.29
Consensus pattern (88 bp):
TTCAATCTGCTCCGCTACTGCTTAGGGAGATAAGGATCTGCAATCATCAGCCTGCTCCACTACCG
CTTAGGGAGATAAGGCTAGTATC
Found at i:88488068 original size:44 final size:44
Alignment explanation
Indices: 88487988--88488072 Score: 109
Period size: 44 Copynumber: 1.9 Consensus size: 44
88487978 CTGATACATA
* *
88487988 GAGATAAGATTCGCTATCTTCGATCTACTCCACTACTGCTTAAG
1 GAGATAAGATTCGCAATCTTCGACCTACTCCACTACTGCTTAAG
* * *
88488032 GAGATAAGATTTGCAATCTTC-AGCCTATTCCGCTACTGCTT
1 GAGATAAGATTCGCAATCTTCGA-CCTACTCCACTACTGCTT
88488073 GGAAAGATAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 1 0.03
44 34 0.97
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (44 bp):
GAGATAAGATTCGCAATCTTCGACCTACTCCACTACTGCTTAAG
Found at i:88498275 original size:19 final size:20
Alignment explanation
Indices: 88498238--88498275 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
88498228 TTATTTTGCG
*
88498238 TCACACTAATGCTGGTGTAA
1 TCACACTAATGCTGATGTAA
*
88498258 TCACA-TAATTCTGATGTA
1 TCACACTAATGCTGATGTA
88498276 TACCCCTCGG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (20 bp):
TCACACTAATGCTGATGTAA
Found at i:88506492 original size:21 final size:21
Alignment explanation
Indices: 88506455--88506520 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
88506445 CTAAAATATA
*
88506455 AAATC-TAAACTCGAGACCCT
1 AAATCTTAAACTCAAGACCCT
* *
88506475 AAATCTTAAACCCAAGACTCT
1 AAATCTTAAACTCAAGACCCT
*
88506496 AAACCCTTAAACTCAAG-CCCT
1 AAA-TCTTAAACTCAAGACCCT
88506517 AAAT
1 AAAT
88506521 ATGAGAGTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
20 5 0.14
21 21 0.57
22 11 0.30
ACGTcount: A:0.42, C:0.30, G:0.06, T:0.21
Consensus pattern (21 bp):
AAATCTTAAACTCAAGACCCT
Found at i:88520838 original size:25 final size:25
Alignment explanation
Indices: 88520804--88520859 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
88520794 AGACACACCA
88520804 TAGCTCGCAAGAGCGTCTCCTTATT
1 TAGCTCGCAAGAGCGTCTCCTTATT
88520829 TAGCTCGCAAGAGCGTCTCCTTATT
1 TAGCTCGCAAGAGCGTCTCCTTATT
88520854 TAGCTC
1 TAGCTC
88520860 TTATGAACAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.20, C:0.29, G:0.20, T:0.32
Consensus pattern (25 bp):
TAGCTCGCAAGAGCGTCTCCTTATT
Found at i:88520922 original size:25 final size:25
Alignment explanation
Indices: 88520869--88521033 Score: 113
Period size: 25 Copynumber: 6.6 Consensus size: 25
88520859 CTTATGAACA
* ** *
88520869 TCCCGTTATATGGCTCTCACAAGCC
1 TCCCGATATATGGCTCTCATGAGCT
*
88520894 TCCCGATATCTGGCTCTCATGAGCT
1 TCCCGATATATGGCTCTCATGAGCT
* *
88520919 TCCCCAT-TAATGGCTCTCTTGAGCT
1 TCCCGATAT-ATGGCTCTCATGAGCT
*
88520944 TCCCG-TTTATGGCTCGT-ATGAGCT
1 TCCCGATATATGGCTC-TCATGAGCT
* * ** *
88520968 TCCTGATATTTGGCTAGCAAGAGCT
1 TCCCGATATATGGCTCTCATGAGCT
* *
88520993 TCCCGTTATATAGCT-TGCATGAGCT
1 TCCCGATATATGGCTCT-CATGAGCT
** *
88521018 TCTTGTTATATGGCTC
1 TCCCGATATATGGCTC
88521034 GGAAGAGCTC
Statistics
Matches: 108, Mismatches: 25, Indels: 13
0.74 0.17 0.09
Matches are distributed among these distances:
24 19 0.18
25 89 0.82
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.35
Consensus pattern (25 bp):
TCCCGATATATGGCTCTCATGAGCT
Found at i:88521032 original size:50 final size:49
Alignment explanation
Indices: 88520939--88521051 Score: 136
Period size: 50 Copynumber: 2.3 Consensus size: 49
88520929 TGGCTCTCTT
* * *
88520939 GAGCTTCCCGTTTATGGCTCGTATGAGCTTCCTGATATTTGGCTAGCAA
1 GAGCTTCCCGTTTATAGCTCGCATGAGCTTCCTGATATATGGCTAGCAA
* * * * *
88520988 GAGCTTCCCGTTATATAGCTTGCATGAGCTTCTTGTTATATGGCTCGGAA
1 GAGCTTCCCGTT-TATAGCTCGCATGAGCTTCCTGATATATGGCTAGCAA
*
88521038 GAGCTCCCCGTTTA
1 GAGCTTCCCGTTTA
88521052 CATGCTTATA
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
49 14 0.26
50 40 0.74
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.35
Consensus pattern (49 bp):
GAGCTTCCCGTTTATAGCTCGCATGAGCTTCCTGATATATGGCTAGCAA
Found at i:88524203 original size:9 final size:9
Alignment explanation
Indices: 88524189--88524256 Score: 57
Period size: 9 Copynumber: 7.6 Consensus size: 9
88524179 ATAAGTATAA
88524189 AATTAACCG
1 AATTAACCG
*
88524198 AATTAACTG
1 AATTAACCG
* *
88524207 TATTAATCG
1 AATTAACCG
*
88524216 AATTAACAG
1 AATTAACCG
*
88524225 AATT-ACCTA
1 AATTAACC-G
* *
88524234 AATTACCCA
1 AATTAACCG
88524243 AATTAACCG
1 AATTAACCG
88524252 AATTA
1 AATTA
88524257 TTTGTATAAA
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
8 2 0.04
9 41 0.91
10 2 0.04
ACGTcount: A:0.46, C:0.18, G:0.07, T:0.29
Consensus pattern (9 bp):
AATTAACCG
Found at i:88524219 original size:27 final size:27
Alignment explanation
Indices: 88524188--88524256 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 27
88524178 AATAAGTATA
** *
88524188 AAATTAACCGAATTAACTGTATTAATC
1 AAATTAACCGAATTAACTAAATTAACC
* * * *
88524215 GAATTAACAGAATTACCTAAATTACCC
1 AAATTAACCGAATTAACTAAATTAACC
88524242 AAATTAACCGAATTA
1 AAATTAACCGAATTA
88524257 TTTGTATAAA
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.29
Consensus pattern (27 bp):
AAATTAACCGAATTAACTAAATTAACC
Found at i:88524292 original size:5 final size:6
Alignment explanation
Indices: 88524277--88524317 Score: 64
Period size: 6 Copynumber: 6.5 Consensus size: 6
88524267 ATTATATGTT
88524277 TTTTTA TTTTTA TTTTTA TTTTTAAA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTT--A TTTTTA TTTTTA TTT
88524318 ATTAAATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 27 0.82
8 6 0.18
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTA
Found at i:88524305 original size:14 final size:13
Alignment explanation
Indices: 88524277--88524314 Score: 60
Period size: 14 Copynumber: 2.9 Consensus size: 13
88524267 ATTATATGTT
88524277 TTTTTATTTTT-A
1 TTTTTATTTTTAA
88524289 TTTTTATTTTTAAA
1 TTTTTATTTTT-AA
88524303 TTTTTATTTTTA
1 TTTTTATTTTTA
88524315 TTTATTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 11 0.46
13 1 0.04
14 12 0.50
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTATTTTTAA
Found at i:88524307 original size:21 final size:21
Alignment explanation
Indices: 88524282--88524325 Score: 81
Period size: 20 Copynumber: 2.1 Consensus size: 21
88524272 ATGTTTTTTT
88524282 ATTTTTATTTTTATTT-TTAA
1 ATTTTTATTTTTATTTATTAA
88524302 ATTTTTATTTTTATTTATTAA
1 ATTTTTATTTTTATTTATTAA
88524323 ATT
1 ATT
88524326 ATTTGTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (21 bp):
ATTTTTATTTTTATTTATTAA
Found at i:88524358 original size:13 final size:13
Alignment explanation
Indices: 88524342--88524366 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
88524332 AATTTTTATG
88524342 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
88524355 ATTGGGTTGGGT
1 ATTGGGTTGGGT
88524367 TGGGTACTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:88524366 original size:18 final size:18
Alignment explanation
Indices: 88524343--88524380 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
88524333 ATTTTTATGA
88524343 TTGGGTTGGGTAATTGGG
1 TTGGGTTGGGTAATTGGG
*
88524361 TTGGGTTGGGTACTTGGG
1 TTGGGTTGGGTAATTGGG
88524379 TT
1 TT
88524381 TCGAACCGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.08, C:0.03, G:0.47, T:0.42
Consensus pattern (18 bp):
TTGGGTTGGGTAATTGGG
Found at i:88537370 original size:16 final size:17
Alignment explanation
Indices: 88537344--88537379 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
88537334 ATATACAAAA
88537344 AAATATTTAATTTTTAT
1 AAATATTTAATTTTTAT
*
88537361 AAAT-TTTAATTTTTTT
1 AAATATTTAATTTTTAT
88537377 AAA
1 AAA
88537380 ATTGTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
AAATATTTAATTTTTAT
Found at i:88537416 original size:88 final size:87
Alignment explanation
Indices: 88537303--88537474 Score: 317
Period size: 87 Copynumber: 2.0 Consensus size: 87
88537293 CATCATTGTG
88537303 TATGCCATATCATTAATTAATGAATTTTTAAATATACAAAAAAATATTTAATTTTTATAAATTTT
1 TATGCCATATCATTAATTAATGAATTTTTAAATATA-AAAAAAATATTTAATTTTTATAAATTTT
*
88537368 AATTTTTTTAAAATTGTTTTTAT
65 AATTTTTTTAAAATTATTTTTAT
*
88537391 TATGCCATATCATTAATTAATGAATTTTTAAATATATAAAAAATATTTAATTTTTATAAATTTTA
1 TATGCCATATCATTAATTAATGAATTTTTAAATATAAAAAAAATATTTAATTTTTATAAATTTTA
88537456 ATTTTTTTAAAATTATTTT
66 ATTTTTTTAAAATTATTTT
88537475 AAATTTTTAA
Statistics
Matches: 82, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
87 46 0.56
88 36 0.44
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.52
Consensus pattern (87 bp):
TATGCCATATCATTAATTAATGAATTTTTAAATATAAAAAAAATATTTAATTTTTATAAATTTTA
ATTTTTTTAAAATTATTTTTAT
Found at i:88537450 original size:20 final size:20
Alignment explanation
Indices: 88537425--88537495 Score: 57
Period size: 21 Copynumber: 3.8 Consensus size: 20
88537415 TTTTTAAATA
88537425 TATAAAAAATATTTAATTTT
1 TATAAAAAATATTTAATTTT
88537445 TAT---AAAT-TTTAATTTT
1 TATAAAAAATATTTAATTTT
* *
88537461 T-TTAAAATTATTTTAAATTTT
1 TATAAAAAATA-TTT-AATTTT
88537482 TA-AAAAAA-ATTTAA
1 TATAAAAAATATTTAA
88537496 AAATTAATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 16
0.68 0.05 0.27
Matches are distributed among these distances:
15 1 0.02
16 10 0.24
17 4 0.10
18 5 0.12
19 3 0.07
20 7 0.17
21 11 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TATAAAAAATATTTAATTTT
Found at i:88537457 original size:16 final size:17
Alignment explanation
Indices: 88537431--88537466 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
88537421 AATATATAAA
88537431 AAATATTTAATTTTTAT
1 AAATATTTAATTTTTAT
*
88537448 AAAT-TTTAATTTTTTT
1 AAATATTTAATTTTTAT
88537464 AAA
1 AAA
88537467 ATTATTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
AAATATTTAATTTTTAT
Found at i:88538979 original size:24 final size:24
Alignment explanation
Indices: 88538931--88538979 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
88538921 TGCCTTTGTA
**
88538931 AGTAGTTGTAGATATGGGAACTCT
1 AGTAGTTGTAGATATGAAAACTCT
* *
88538955 AGTAGTTGTATATATGAAAATTCT
1 AGTAGTTGTAGATATGAAAACTCT
88538979 A
1 A
88538980 CTGTTCAGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.35, C:0.06, G:0.22, T:0.37
Consensus pattern (24 bp):
AGTAGTTGTAGATATGAAAACTCT
Found at i:88542252 original size:55 final size:55
Alignment explanation
Indices: 88542192--88542299 Score: 198
Period size: 55 Copynumber: 2.0 Consensus size: 55
88542182 AAGAATGAAG
*
88542192 TTTTGGATTGTGCTTTTTGGAATATAGCAATCTTATAAAACACTGTTATGAAGAA
1 TTTTGGATTGTGCTTTATGGAATATAGCAATCTTATAAAACACTGTTATGAAGAA
*
88542247 TTTTGGATTGTGCTTTATGGAATATAGCATTCTTATAAAACACTGTTATGAAG
1 TTTTGGATTGTGCTTTATGGAATATAGCAATCTTATAAAACACTGTTATGAAG
88542300 TTTATTTTAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (55 bp):
TTTTGGATTGTGCTTTATGGAATATAGCAATCTTATAAAACACTGTTATGAAGAA
Found at i:88562157 original size:26 final size:26
Alignment explanation
Indices: 88562128--88562180 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
88562118 TTTACAGTTT
88562128 TACCCCTAGGAGATAAATT-ACCAAAA
1 TACCCCTAGG-GATAAATTGACCAAAA
* * *
88562154 TACCTCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCAAAA
88562180 T
1 T
88562181 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.26
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCAAAA
Found at i:88563385 original size:30 final size:29
Alignment explanation
Indices: 88563358--88563416 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
88563348 AACTTTTACA
*
88563358 AGATTAAATCAAAATTTTATTATTTTTAAGG
1 AGATAAAAT-AAAATTTTATTATTTTTAA-G
* *
88563389 AGATAAAATACAATTTTATTATTATTAA
1 AGATAAAATAAAATTTTATTATTTTTAA
88563417 TTTAAATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (29 bp):
AGATAAAATAAAATTTTATTATTTTTAAG
Found at i:88566583 original size:2 final size:2
Alignment explanation
Indices: 88566576--88566605 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
88566566 ACTTTGTTCC
*
88566576 CT CT CT CT CT CT CT CT TT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
88566606 GACTTTCTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:88566599 original size:18 final size:18
Alignment explanation
Indices: 88566576--88566615 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
88566566 ACTTTGTTCC
*
88566576 CTCTCTCTCTCTCTCTTT
1 CTCTCTCTCTCTCACTTT
*
88566594 CTCTCTCTCTCTGACTTT
1 CTCTCTCTCTCTCACTTT
88566612 CTCT
1 CTCT
88566616 TTTTCCTCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.03, C:0.42, G:0.03, T:0.53
Consensus pattern (18 bp):
CTCTCTCTCTCTCACTTT
Found at i:88566793 original size:24 final size:23
Alignment explanation
Indices: 88566766--88566812 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
88566756 CTCTTCTGGG
88566766 TTTGCTTTTGTT-TTCTATGTTGTT
1 TTTGCTTTT-TTCTTCT-TGTTGTT
88566790 TTTGCTTTTTTCTTCTTGTTGTT
1 TTTGCTTTTTTCTTCTTGTTGTT
88566813 ATGTTATCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.02, C:0.11, G:0.15, T:0.72
Consensus pattern (23 bp):
TTTGCTTTTTTCTTCTTGTTGTT
Found at i:88578377 original size:19 final size:19
Alignment explanation
Indices: 88578353--88578390 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
88578343 AATTCTTCAG
88578353 TTACTTTCATGGATTCAAC
1 TTACTTTCATGGATTCAAC
88578372 TTACTTTCATGGATTCAAC
1 TTACTTTCATGGATTCAAC
88578391 ATTGGAGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.42
Consensus pattern (19 bp):
TTACTTTCATGGATTCAAC
Found at i:88578577 original size:15 final size:16
Alignment explanation
Indices: 88578550--88578579 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
88578540 TTATCACTAA
88578550 AAAGAATAAAAAAAGG
1 AAAGAATAAAAAAAGG
88578566 AAAGAA-AAAAAAAG
1 AAAGAATAAAAAAAG
88578580 AAGTTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (16 bp):
AAAGAATAAAAAAAGG
Found at i:88580104 original size:38 final size:40
Alignment explanation
Indices: 88580031--88580114 Score: 127
Period size: 38 Copynumber: 2.1 Consensus size: 40
88580021 TATATTTTAG
*
88580031 TAGTAGTTTATTTATGTTAAAAGTTTATTTTGTATTAAGGT
1 TAGTAGTTTATTTATGTT-AAAGTTTATTTAGTATTAAGGT
*
88580072 TAGTA-TTTATTTTTGTT-AAGTTTATTTAGTATTAAGGT
1 TAGTAGTTTATTTATGTTAAAGTTTATTTAGTATTAAGGT
88580110 TAGTA
1 TAGTA
88580115 CTAATTATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
38 25 0.61
40 11 0.27
41 5 0.12
ACGTcount: A:0.29, C:0.00, G:0.17, T:0.55
Consensus pattern (40 bp):
TAGTAGTTTATTTATGTTAAAGTTTATTTAGTATTAAGGT
Found at i:88580111 original size:22 final size:22
Alignment explanation
Indices: 88580051--88580111 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 22
88580041 TTTATGTTAA
*
88580051 AAGTTTATTTTGTATTAAGGTT
1 AAGTTTATTTAGTATTAAGGTT
**
88580073 -AG--TATTTA-T-TT-TTGTT
1 AAGTTTATTTAGTATTAAGGTT
88580089 AAGTTTATTTAGTATTAAGGTT
1 AAGTTTATTTAGTATTAAGGTT
88580111 A
1 A
88580112 GTACTAATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 12
0.62 0.11 0.27
Matches are distributed among these distances:
16 3 0.11
17 4 0.14
18 1 0.04
19 11 0.39
20 1 0.04
21 4 0.14
22 4 0.14
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (22 bp):
AAGTTTATTTAGTATTAAGGTT
Found at i:88587565 original size:94 final size:95
Alignment explanation
Indices: 88587399--88587622 Score: 292
Period size: 94 Copynumber: 2.3 Consensus size: 95
88587389 TTTGTGTACC
88587399 AGTGTAAGACATGTCTAGGACATGCATCGGCCATATTATGAGAGCCAGTGTAAGACCATGTCTGG
1 AGTGTAAGACATGTCTAGGACATGCATCGGCCATATTATGAGAGCCAGTGTAAGACCATGTCTGG
* **
88587464 GAGATGGCATCAGCATTGATA-CGAGAGCT
66 GACATGGCATCAGCACAGATAGCGAGAGCT
* * *
88587493 AGTGTAAGACATGTCTAGGACATGCATCGGCACGTA-TA-GAGGTGCCAGTGTAAGGCCATGTCT
1 AGTGTAAGACATGTCTAGGACATGCATCGGC-CATATTATGA-GAGCCAGTGTAAGACCATGTCT
* *
88587556 GGGACATGGCATCGGCACAGATATGTGAGAGCT
64 GGGACATGGCATCAGCACAGATA-GCGAGAGCT
* *
88587589 AGTGTAAGACCATGTCTGGGACATGGCGTCGGCC
1 AGTGTAAGA-CATGTCTAGGACAT-GCATCGGCC
88587623 TCGATGTCAA
Statistics
Matches: 114, Mismatches: 10, Indels: 9
0.86 0.08 0.07
Matches are distributed among these distances:
93 2 0.02
94 72 0.63
95 3 0.03
96 16 0.14
97 14 0.12
98 7 0.06
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.22
Consensus pattern (95 bp):
AGTGTAAGACATGTCTAGGACATGCATCGGCCATATTATGAGAGCCAGTGTAAGACCATGTCTGG
GACATGGCATCAGCACAGATAGCGAGAGCT
Found at i:88587602 original size:50 final size:49
Alignment explanation
Indices: 88587397--88587621 Score: 234
Period size: 47 Copynumber: 4.7 Consensus size: 49
88587387 TATTTGTGTA
* *
88587397 CCAGTGTAAGA-CATGTCTAGGACAT-GCATCGGC-CATAT-TATGAGAG
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGATAT-TGAGAG
* * ** *
88587443 CCAGTGTAAGACCATGTCTGGGAGATGGCATCAGCATTGATA-CGAGAG
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGATATTGAGAG
* * * *
88587491 CTAGTGTAAGA-CATGTCTAGGACAT-GCATCGGCAC-G-TATAGAGGTG
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGATATTGA-GAG
*
88587537 CCAGTGTAAGGCCATGTCTGGGACATGGCATCGGCACAGATATGTGAGAG
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGATAT-TGAGAG
* *
88587587 CTAGTGTAAGACCATGTCTGGGACATGGCGTCGGC
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGC
88587622 CTCGATGTCA
Statistics
Matches: 146, Mismatches: 22, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
44 2 0.01
45 3 0.02
46 30 0.21
47 37 0.25
48 32 0.22
49 3 0.02
50 37 0.25
51 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.22
Consensus pattern (49 bp):
CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGATATTGAGAG
Found at i:88588892 original size:21 final size:21
Alignment explanation
Indices: 88588868--88588913 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
88588858 CCATACCGGT
*
88588868 GTGTTGCCCTTTTACACGGGC
1 GTGTTGCCCTCTTACACGGGC
*
88588889 GTGTTGCCCTCTTACACGGGT
1 GTGTTGCCCTCTTACACGGGC
88588910 GTGT
1 GTGT
88588914 GCCTTGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.09, C:0.26, G:0.30, T:0.35
Consensus pattern (21 bp):
GTGTTGCCCTCTTACACGGGC
Found at i:88589757 original size:45 final size:45
Alignment explanation
Indices: 88589693--88589792 Score: 173
Period size: 45 Copynumber: 2.2 Consensus size: 45
88589683 TAGTATAGAA
*
88589693 AAGTCTGTAAGAGTTTGGAATCATCGTGTAACCCGAAGAAACAAG
1 AAGTCTGTAAGAGTCTGGAATCATCGTGTAACCCGAAGAAACAAG
* *
88589738 AAGTCTGTAAGAGTCTGGAATCATTGTGTAACCTGAAGAAACAAG
1 AAGTCTGTAAGAGTCTGGAATCATCGTGTAACCCGAAGAAACAAG
88589783 AAGTCTGTAA
1 AAGTCTGTAA
88589793 CCACTACGAA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.24
Consensus pattern (45 bp):
AAGTCTGTAAGAGTCTGGAATCATCGTGTAACCCGAAGAAACAAG
Found at i:88597190 original size:48 final size:48
Alignment explanation
Indices: 88597133--88597354 Score: 185
Period size: 48 Copynumber: 4.6 Consensus size: 48
88597123 TCTCAATGCT
* *
88597133 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCC
1 GATGTCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTAGCC
* * * * * * *
88597181 GACGTCATGTCGCAGACATGGTCTTACACTAGCACACATATTG-ACGCT
1 GATGTCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTA-GCC
* * * * ** * **
88597229 AATGTCATGTCCCAGATATGATCTTACACTGGCTCTCACAACATTGTT
1 GATGTCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTAGCC
* * * * * *
88597277 GATGCCATTTTCCAAATATGGTCTTACACTGGCTCTCATATTGTAGCC
1 GATGTCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTAGCC
* * *
88597325 GGTGTCATGTCCTAGACATGGTTTTACACT
1 GATGTCATGTCCCAGACATGGTCTTACACT
88597355 AGCGCATATA
Statistics
Matches: 128, Mismatches: 44, Indels: 4
0.73 0.25 0.02
Matches are distributed among these distances:
48 128 1.00
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (48 bp):
GATGTCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTAGCC
Found at i:88598976 original size:30 final size:30
Alignment explanation
Indices: 88598941--88599000 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
88598931 GTGGACTTAA
88598941 TTTTCCTTTCTTACCGAATCTGAGGACTTT
1 TTTTCCTTTCTTACCGAATCTGAGGACTTT
88598971 TTTTCCTTTCTTACCGAATCTGAGGACTTT
1 TTTTCCTTTCTTACCGAATCTGAGGACTTT
88599001 CTTCTTCGGG
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:0.17, C:0.23, G:0.13, T:0.47
Consensus pattern (30 bp):
TTTTCCTTTCTTACCGAATCTGAGGACTTT
Found at i:88604761 original size:48 final size:48
Alignment explanation
Indices: 88604702--88605019 Score: 255
Period size: 48 Copynumber: 6.6 Consensus size: 48
88604692 GTGAATTACC
* * *
88604702 GATGCCATGTCCCAGATATGGTCTTACACTGGCTCACATGTCGAGGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCGAGGCT
* * * * ***
88604750 GATGCCGTGTCCCAGACATGGTCTTACACTAGCTCTCGTCTC-AATTT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCGAGGCT
* * * * * *
88604797 CGATACCATGTCCCAAATATGGTCTTACACTGGCTCTTATAAT-GTGGCC
1 -GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCAT-ATCGAGGCT
* * * * * * *
88604846 GATGCCATGTCTCAAACATGGTCTTACACTAGCACACATATCGACGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCGAGGCT
* * * * * *
88604894 GATGTCATGTCCTAGACATGGTCTTACACTGACTCTCACAAC-ATTGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCGA-GGCT
* * * **
88604942 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATTGTTGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCGAGGCT
* * *
88604990 GACGCCATGTCTCAGATATGGTCTTACACT
1 GATGCCATGTCCCAGACATGGTCTTACACT
88605020 AGGTTCAACT
Statistics
Matches: 207, Mismatches: 57, Indels: 12
0.75 0.21 0.04
Matches are distributed among these distances:
47 5 0.02
48 201 0.97
49 1 0.00
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (48 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCGAGGCT
Found at i:88604903 original size:96 final size:96
Alignment explanation
Indices: 88604700--88605019 Score: 284
Period size: 96 Copynumber: 3.3 Consensus size: 96
88604690 GGGTGAATTA
* * * * *
88604700 CCGATGCCATGTCCCAGATATGGTCTTACACTGGCTCACAT-GTCGAGGCTGATGCCGTGTCCCA
1 CCGATGCCATGTCCCAGATATGGTCTTACACTGGCTCTCATAAT-GTGGCTGATGCCATGTCTCA
* * * * * **
88604764 GACATGGTCTTACACTAGCTCTCGTCTCAATT
65 AACATGGTCTTACACTAGCACACATATCAACG
* * * * *
88604796 TCGATACCATGTCCCAAATATGGTCTTACACTGGCTCTTATAATGTGGCCGATGCCATGTCTCAA
1 CCGATGCCATGTCCCAGATATGGTCTTACACTGGCTCTCATAATGTGGCTGATGCCATGTCTCAA
*
88604861 ACATGGTCTTACACTAGCACACATATCGACG
66 ACATGGTCTTACACTAGCACACATATCAACG
* * * * * ** *
88604892 CCGATGTCATGTCCTAGACATGGTCTTACACTGACTCTCACAACATTGCTGATGCCATGT-TCCA
1 CCGATGCCATGTCCCAGATATGGTCTTACACTGGCTCTCATAATGTGGCTGATGCCATGTCT-CA
* * * ****
88604956 AACATGGTCTTACACTGGCTCTCATATTGTTG
65 AACATGGTCTTACACTAGCACACATATCAACG
* * *
88604988 CTGACGCCATGTCTCAGATATGGTCTTACACT
1 CCGATGCCATGTCCCAGATATGGTCTTACACT
88605020 AGGTTCAACT
Statistics
Matches: 179, Mismatches: 43, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
95 1 0.01
96 177 0.99
97 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (96 bp):
CCGATGCCATGTCCCAGATATGGTCTTACACTGGCTCTCATAATGTGGCTGATGCCATGTCTCAA
ACATGGTCTTACACTAGCACACATATCAACG
Found at i:88604963 original size:144 final size:144
Alignment explanation
Indices: 88604700--88605021 Score: 398
Period size: 144 Copynumber: 2.2 Consensus size: 144
88604690 GGGTGAATTA
* * * * * * *
88604700 CCGATGCCATGTCCCAGATATGGTCTTACACTGGCTCACATGTCGAGGCTGATGCCGTGTCCCAG
1 CCGATGCCATGTCTCAGATATGGTCTTACACTAGCACACATATCGACGCCGATGCCATGTCCCAG
* * * *
88604765 ACATGGTCTTACACTAGCTCTCGTCTCAATTTCGATACCATGTCCCAAATATGGTCTTACACTGG
66 ACATGGTCTTACACTAGCTCTCGACACAATTGCGATACCATGTCCCAAACATGGTCTTACACTGG
*
88604830 CTCTTATAATGTGG
131 CTCTCATAATGTGG
* * * *
88604844 CCGATGCCATGTCTCAAACATGGTCTTACACTAGCACACATATCGACGCCGATGTCATGTCCTAG
1 CCGATGCCATGTCTCAGATATGGTCTTACACTAGCACACATATCGACGCCGATGCCATGTCCCAG
* *
88604909 ACATGGTCTTACACT-GACTCTC-ACA-ACATTGCTGATGCCATGTTCCAAACATGGTCTTACAC
66 ACATGGTCTTACACTAG-CTCTCGACACA-ATTGC-GATACCATGTCCCAAACATGGTCTTACAC
* *
88604971 TGGCTCTCATATTGTTG
128 TGGCTCTCATAATGTGG
* *
88604988 CTGACGCCATGTCTCAGATATGGTCTTACACTAG
1 CCGATGCCATGTCTCAGATATGGTCTTACACTAG
88605022 GTTCAACTGG
Statistics
Matches: 151, Mismatches: 24, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
142 1 0.01
143 6 0.04
144 144 0.95
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (144 bp):
CCGATGCCATGTCTCAGATATGGTCTTACACTAGCACACATATCGACGCCGATGCCATGTCCCAG
ACATGGTCTTACACTAGCTCTCGACACAATTGCGATACCATGTCCCAAACATGGTCTTACACTGG
CTCTCATAATGTGG
Found at i:88607276 original size:14 final size:15
Alignment explanation
Indices: 88607245--88607277 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
88607235 TATTTTTGTT
88607245 TTAT-TTTATTTAAG
1 TTATATTTATTTAAG
88607259 TTATATTTATTTAA-
1 TTATATTTATTTAAG
88607273 TTATA
1 TTATA
88607278 AAATTTCCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (15 bp):
TTATATTTATTTAAG
Found at i:88611765 original size:155 final size:156
Alignment explanation
Indices: 88611483--88611945 Score: 894
Period size: 155 Copynumber: 3.0 Consensus size: 156
88611473 TGGATGGTAA
88611483 GTTGTGACAATCTTATGCTTCACTTCATGTTTGTTGAGCAACCATTTCAACCCAAAAGAAACTCT
1 GTTGTGACAATCTTATGCTTCACTTCATGTTTGTTGAGCAACCATTTCAACCCAAAAGAAACTCT
88611548 ACTTACTTGTGAATTACGGATTAAACCATGAAGATATACATATGAAAATGAAACAATTGCTATGA
66 ACTTACTTGTGAATTACGGATTAAACCATGAAGATATACATATGAAAATGAAACAATTGCTATGA
88611613 ATTCGATTCTCATCATGACCATTA-G
131 ATTCGATTCTCATCATGACCATTACG
88611638 GTTGTGACAATCTTATGCTTCACTTCATGTTTGTTGAGCAACCATTTCAACCCAAAAGAAACTCT
1 GTTGTGACAATCTTATGCTTCACTTCATGTTTGTTGAGCAACCATTTCAACCCAAAAGAAACTCT
88611703 ACTTACTTGTGAATTACGGATTAAACCATGAAGATATACATATGAAAATGAAACAATTGCTATGA
66 ACTTACTTGTGAATTACGGATTAAACCATGAAGATATACATATGAAAATGAAACAATTGCTATGA
88611768 ATTCGATTCTCATCATGACCATTACG
131 ATTCGATTCTCATCATGACCATTACG
*
88611794 G-TCTGACAATCTTATGCTTCACTTCATGTTTGTTGAGCAACCATTTCAACCCAAAAGAAACTCT
1 GTTGTGACAATCTTATGCTTCACTTCATGTTTGTTGAGCAACCATTTCAACCCAAAAGAAACTCT
*
88611858 ACTTACTTGTGAATTACGGATTAAACCATTAAGATATACATATGAAAATGAAACAATTGCTATGA
66 ACTTACTTGTGAATTACGGATTAAACCATGAAGATATACATATGAAAATGAAACAATTGCTATGA
88611923 ATTCGATTCTCATCATGACCATT
131 ATTCGATTCTCATCATGACCATT
88611946 CTTGCAACCC
Statistics
Matches: 305, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
155 303 0.99
156 2 0.01
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (156 bp):
GTTGTGACAATCTTATGCTTCACTTCATGTTTGTTGAGCAACCATTTCAACCCAAAAGAAACTCT
ACTTACTTGTGAATTACGGATTAAACCATGAAGATATACATATGAAAATGAAACAATTGCTATGA
ATTCGATTCTCATCATGACCATTACG
Found at i:88613932 original size:25 final size:22
Alignment explanation
Indices: 88613879--88613934 Score: 58
Period size: 25 Copynumber: 2.4 Consensus size: 22
88613869 GATGAGATTG
88613879 ATTTTTTATAAATTTGATATTA
1 ATTTTTTATAAATTTGATATTA
* *
88613901 TTATTTTTAGCTAAATTTTGCTATTA
1 AT-TTTTTA--TAAA-TTTGATATTA
88613927 ATTTTTTA
1 ATTTTTTA
88613935 AAAAAATCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
22 1 0.04
23 6 0.22
25 10 0.37
26 10 0.37
ACGTcount: A:0.30, C:0.04, G:0.05, T:0.61
Consensus pattern (22 bp):
ATTTTTTATAAATTTGATATTA
Found at i:88620892 original size:16 final size:16
Alignment explanation
Indices: 88620856--88620891 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
88620846 AGAGGGGAAA
88620856 GAAAATTAAAAGGATT
1 GAAAATTAAAAGGATT
*
88620872 GAAAATTAGAAGGA-T
1 GAAAATTAAAAGGATT
88620887 GAAAA
1 GAAAA
88620892 ACATAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.58, C:0.00, G:0.22, T:0.19
Consensus pattern (16 bp):
GAAAATTAAAAGGATT
Found at i:88622282 original size:22 final size:22
Alignment explanation
Indices: 88622257--88622298 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
88622247 AAACAAGGAT
* * *
88622257 TAAATAAATATGATTATTTTAA
1 TAAAAAAATATAAATATTTTAA
88622279 TAAAAAAATATAAATATTTT
1 TAAAAAAATATAAATATTTT
88622299 TTATTGGGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TAAAAAAATATAAATATTTTAA
Found at i:88622503 original size:22 final size:22
Alignment explanation
Indices: 88622463--88622507 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
88622453 AAAATATTAA
*
88622463 TTAATTAATTAATTGATTAAAT
1 TTAATTAATTAATTAATTAAAT
**
88622485 TTAATTAATTTCTTAATTAAAT
1 TTAATTAATTAATTAATTAAAT
88622507 T
1 T
88622508 ATTTTCTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
TTAATTAATTAATTAATTAAAT
Found at i:88624340 original size:16 final size:16
Alignment explanation
Indices: 88624292--88624343 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
88624282 CTTAGAAGAA
*
88624292 AATATATATACACAA-
1 AATATATATACATAAT
*
88624307 AATA-ATATAAAATCAAT
1 AATATATAT-ACAT-AAT
88624324 AATATATATACATAAT
1 AATATATATACATAAT
88624340 AATA
1 AATA
88624344 AAAAATATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
14 4 0.13
15 6 0.20
16 9 0.30
17 7 0.23
18 4 0.13
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (16 bp):
AATATATATACATAAT
Done.