Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 89 of 132
Found at i:27279653 original size:15 final size:15
Alignment explanation
Indices: 27279630--27279659 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
27279620 TATACCATTC
27279630 CTTAATTTTCCCAAT
1 CTTAATTTTCCCAAT
*
27279645 CTTAGTTTTCCCAAT
1 CTTAATTTTCCCAAT
27279660 ACATTTTCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.27, G:0.03, T:0.47
Consensus pattern (15 bp):
CTTAATTTTCCCAAT
Found at i:27287118 original size:9 final size:9
Alignment explanation
Indices: 27287100--27287145 Score: 65
Period size: 9 Copynumber: 5.1 Consensus size: 9
27287090 GATTTCACCC
*
27287100 AAAAAGAAG
1 AAAAAAAAG
27287109 AAAAAAAAG
1 AAAAAAAAG
*
27287118 AAAAAAGAG
1 AAAAAAAAG
*
27287127 ACAAAAAAG
1 AAAAAAAAG
27287136 AAAAAAAAG
1 AAAAAAAAG
27287145 A
1 A
27287146 GAGGTCGAGG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:27287132 original size:11 final size:10
Alignment explanation
Indices: 27287100--27287147 Score: 57
Period size: 11 Copynumber: 4.9 Consensus size: 10
27287090 GATTTCACCC
27287100 AAAAAGAAGAA
1 AAAAAG-AGAA
27287111 AAAAA-AG-A
1 AAAAAGAGAA
27287119 AAAAAGAGACA
1 AAAAAGAGA-A
27287130 AAAAAGA-AA
1 AAAAAGAGAA
27287139 AAAAAGAGA
1 AAAAAGAGA
27287148 GGTCGAGGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
8 6 0.18
9 12 0.36
10 2 0.06
11 13 0.39
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (10 bp):
AAAAAGAGAA
Found at i:27287143 original size:20 final size:18
Alignment explanation
Indices: 27287100--27287147 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 18
27287090 GATTTCACCC
*
27287100 AAAAAGAAGAAAAAAAAGA
1 AAAAAG-AGAAAAAAAAAA
27287119 AAAAAGAGACAAAAAAGAAA
1 AAAAAGAGA-AAAAAA-AAA
27287139 AAAAAGAGA
1 AAAAAGAGA
27287148 GGTCGAGGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 3 0.12
19 12 0.46
20 11 0.42
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAAAGAGAAAAAAAAAA
Found at i:27288363 original size:39 final size:39
Alignment explanation
Indices: 27288301--27288448 Score: 197
Period size: 39 Copynumber: 3.8 Consensus size: 39
27288291 ACATCATCAT
* * *
27288301 CCAATCTCTTACCCTGATCATGGGACAGATTGCAGCCAC
1 CCAATCTTTTACCCCGATCATGGGGCAGATTGCAGCCAC
* *
27288340 CCTATCTTTTACCCCAATCATGGGGCAGATTGCAGCCAC
1 CCAATCTTTTACCCCGATCATGGGGCAGATTGCAGCCAC
* * * *
27288379 CCAATCATTTACCCCGATCATGGGGTAGATTGCATCCAT
1 CCAATCTTTTACCCCGATCATGGGGCAGATTGCAGCCAC
* *
27288418 CCAATCTCTTACCCCGATCATGAGGCAGATT
1 CCAATCTTTTACCCCGATCATGGGGCAGATT
27288449 ACAGTCATCT
Statistics
Matches: 94, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 94 1.00
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.26
Consensus pattern (39 bp):
CCAATCTTTTACCCCGATCATGGGGCAGATTGCAGCCAC
Found at i:27288789 original size:85 final size:84
Alignment explanation
Indices: 27288636--27288802 Score: 221
Period size: 84 Copynumber: 2.0 Consensus size: 84
27288626 TTCAAACCCC
* * *
27288636 ATCTTCCTGATGAGATATAGAGAAGTGGGTCGAACCAATAAGTGGTCATCTTTCTGACGAGATGC
1 ATCTTCCTGATGAGATACAGAGAAGTGGATCGAAACAATAAGTGGTCATCTTTCTGACGAGATGC
27288701 AGAGAAGT-GAACCAAATTT
66 AGAGAAGTAG-ACCAAATTT
* * * * *
27288720 ATCTTTCTGCTGAGATACAGAGAAGTGGATTGAAACAATGAGGTGGTCATC-TTCTTGATGAGAT
1 ATCTTCCTGATGAGATACAGAGAAGTGGATCGAAACAAT-AAGTGGTCATCTTTC-TGACGAGAT
27288784 GCAGAGAAGTAGACCAAAT
64 GCAGAGAAGTAGACCAAAT
27288803 CAATAAAGCG
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
84 36 0.50
85 35 0.49
86 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.26
Consensus pattern (84 bp):
ATCTTCCTGATGAGATACAGAGAAGTGGATCGAAACAATAAGTGGTCATCTTTCTGACGAGATGC
AGAGAAGTAGACCAAATTT
Found at i:27288987 original size:85 final size:85
Alignment explanation
Indices: 27288852--27289011 Score: 223
Period size: 85 Copynumber: 1.9 Consensus size: 85
27288842 CATCTTCCTG
* *
27288852 ATGAGATACAAAGAAGTGGGTCAAAGCAATAAAGCGGTCATCTTCCTGATGAAATATAGAGAAGT
1 ATGAGATACAAAGAAGTGGGTCAAAGCAATAAAGCGGTCATCTTCCTGATGAAATACAGAGAAGA
*
27288917 GGACCAAATCGGTCTTCTTA
66 AGACCAAATCGGTCTTCTTA
* * * * * *
27288937 ATGAGATACAGAGAAGTGGATTGAAA-CAATGAGGCGGTCATCTTCCTGATGAGATACAGAGAAG
1 ATGAGATACAAAGAAGTGG-GTCAAAGCAATAAAGCGGTCATCTTCCTGATGAAATACAGAGAAG
27289001 AAGACCAAATC
65 AAGACCAAATC
27289012 AATGAAGCGA
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
85 61 0.94
86 4 0.06
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.21
Consensus pattern (85 bp):
ATGAGATACAAAGAAGTGGGTCAAAGCAATAAAGCGGTCATCTTCCTGATGAAATACAGAGAAGA
AGACCAAATCGGTCTTCTTA
Found at i:27288990 original size:208 final size:208
Alignment explanation
Indices: 27288460--27289131 Score: 906
Period size: 208 Copynumber: 3.2 Consensus size: 208
27288450 CAGTCATCTG
* * * *
27288460 AAGCAATAAAGTGGTCATCTTCTTGACGAGATGCAGAGAAGTGAACCAAATCCATCTTCCTGATG
1 AAGCAATAAAGCGGTCATCTTCCTGACGAGATACAGAGAAGTGAACCAAATCCATCTTCTTGATG
* **
27288525 AGATACAGAGAAATGGATT-AAATCAATGAGGTAATCATCTTCTTGATGAGATACAGAGAAGTAG
66 AGATACAGAGAAGTGGATTGAAA-CAATGAGGTGGTCATCTTCTTGATGAGATACAGAGAAGTAG
* * * *
27288589 ACCAAATCATTGAAGCGCAGCTCAAT--GTAAGTGAAAATTCAAACCCCATCTTCCTGATGAGAT
130 ACCAAATCAATGAAGCGAAGCTCAATACG-AA-TGAGACTTCAAACCCCATCTTCCTGATGAGAT
* *
27288652 ATAGAGAAGTGGGTCG
193 ACAGAGAAGTGGGTCA
* * * * ** *
27288668 AACCAAT-AAGTGGTCATCTTTCTGACGAGATGCAGAGAAGTGAACCAAATTTATCTT-TCTGCT
1 AAGCAATAAAGCGGTCATCTTCCTGACGAGATACAGAGAAGTGAACCAAATCCATCTTCT-TGAT
*
27288731 GAGATACAGAGAAGTGGATTGAAACAATGAGGTGGTCATCTTCTTGATGAGATGCAGAGAAGTAG
65 GAGATACAGAGAAGTGGATTGAAACAATGAGGTGGTCATCTTCTTGATGAGATACAGAGAAGTAG
*
27288796 ACCAAATCAATAAAGCGAAGCTCAATACGAATGAGACTTCAAACCCCATCTTCCTGATGAGATAC
130 ACCAAATCAATGAAGCGAAGCTCAATACGAATGAGACTTCAAACCCCATCTTCCTGATGAGATAC
*
27288861 AAAGAAGTGGGTCA
195 AGAGAAGTGGGTCA
* * * * ** *
27288875 AAGCAATAAAGCGGTCATCTTCCTGATGAAATATAGAGAAGTGGACCAAATCGGTCTTCTTAATG
1 AAGCAATAAAGCGGTCATCTTCCTGACGAGATACAGAGAAGTGAACCAAATCCATCTTCTTGATG
* * *
27288940 AGATACAGAGAAGTGGATTGAAACAATGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAAGA
66 AGATACAGAGAAGTGGATTGAAACAATGAGGTGGTCATCTTCTTGATGAGATACAGAGAAGTAGA
*
27289005 CCAAATCAATGAAGCGAACCTCAATACGAATGAGACTTCAAACCCCATCTTCCTGATGAGATACA
131 CCAAATCAATGAAGCGAAGCTCAATACGAATGAGACTTCAAACCCCATCTTCCTGATGAGATACA
*
27289070 GAGAAGTGGGTTA
196 GAGAAGTGGGTCA
* * * *
27289083 AAACAATGAAA-CGGTCATCTTCCTGATGAGATACAGTGAAGTGGACCAA
1 AAGCAAT-AAAGCGGTCATCTTCCTGACGAGATACAGAGAAGTGAACCAA
27289132 GAGATGCCAC
Statistics
Matches: 413, Mismatches: 44, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
207 178 0.43
208 230 0.56
209 5 0.01
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (208 bp):
AAGCAATAAAGCGGTCATCTTCCTGACGAGATACAGAGAAGTGAACCAAATCCATCTTCTTGATG
AGATACAGAGAAGTGGATTGAAACAATGAGGTGGTCATCTTCTTGATGAGATACAGAGAAGTAGA
CCAAATCAATGAAGCGAAGCTCAATACGAATGAGACTTCAAACCCCATCTTCCTGATGAGATACA
GAGAAGTGGGTCA
Found at i:27289567 original size:17 final size:18
Alignment explanation
Indices: 27289547--27289582 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
27289537 AGAATAAAAT
27289547 TTTAAATTAAAAT-TCTA
1 TTTAAATTAAAATGTCTA
*
27289564 TTTAATTTAAAATGTCTA
1 TTTAAATTAAAATGTCTA
27289582 T
1 T
27289583 AAAAAAAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.50
Consensus pattern (18 bp):
TTTAAATTAAAATGTCTA
Found at i:27290097 original size:14 final size:14
Alignment explanation
Indices: 27290078--27290104 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
27290068 GAAATATATC
27290078 CAAAAAATATAAAT
1 CAAAAAATATAAAT
27290092 CAAAAAATATAAA
1 CAAAAAATATAAA
27290105 AAAGGGAAAG
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:0.74, C:0.07, G:0.00, T:0.19
Consensus pattern (14 bp):
CAAAAAATATAAAT
Found at i:27292450 original size:17 final size:17
Alignment explanation
Indices: 27292403--27292451 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
27292393 ACTACAATGA
* *
27292403 AAAATGCATTAACAAAT
1 AAAATGCAATGACAAAT
*
27292420 AAAATGCAGA-GACAAGT
1 AAAATGCA-ATGACAAAT
27292437 AAAATGCAATGACAA
1 AAAATGCAATGACAA
27292452 CTATATGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 1 0.04
17 26 0.96
ACGTcount: A:0.57, C:0.12, G:0.14, T:0.16
Consensus pattern (17 bp):
AAAATGCAATGACAAAT
Found at i:27313156 original size:11 final size:11
Alignment explanation
Indices: 27313136--27313182 Score: 53
Period size: 12 Copynumber: 4.3 Consensus size: 11
27313126 CAGTCACTTG
27313136 AAAA-AGAAAA
1 AAAAGAGAAAA
*
27313146 AAATGAGAAAA
1 AAAAGAGAAAA
27313157 AGAAAGAGAAAA
1 A-AAAGAGAAAA
27313169 GAAAAGA-AAAA
1 -AAAAGAGAAAA
27313180 AAA
1 AAA
27313183 TTATTGATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
10 6 0.19
11 11 0.34
12 14 0.44
13 1 0.03
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (11 bp):
AAAAGAGAAAA
Found at i:27313157 original size:17 final size:15
Alignment explanation
Indices: 27313135--27313182 Score: 53
Period size: 17 Copynumber: 3.0 Consensus size: 15
27313125 TCAGTCACTT
27313135 GAAAAAGAAAAAAATGA
1 GAAAAAGAAAAAAA--A
27313152 GAAAAAGAAAGAGAAAA
1 GAAAAAGAAA-A-AAAA
27313169 G-AAAAGAAAAAAAA
1 GAAAAAGAAAAAAAA
27313183 TTATTGATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
14 4 0.14
15 1 0.03
16 8 0.28
17 12 0.41
18 1 0.03
19 3 0.10
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (15 bp):
GAAAAAGAAAAAAAA
Found at i:27317302 original size:196 final size:195
Alignment explanation
Indices: 27316957--27317407 Score: 650
Period size: 196 Copynumber: 2.3 Consensus size: 195
27316947 AAACCGACAC
* * * * *
27316957 GATGGCTAAGATACCGCATATGTTTCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGAGTTGA
1 GATGGCT-AGGTACCGCATATGTTGCGAGTCCTCGACAGCTCCTGAGAGCAGCATCGTGAGTCGA
27317022 GAAAATGAGAAATGAATCCAAGAATAGATTATAGGCCCTACGATGGCTGAGATTTATGCATAAGT
65 GAAAATGAGAAATGAATCCAAGAATAGATTATAGGCCCTACGATGGCTGAGATTTATGCATAAGT
* ** * *
27317087 GCATATTTTCGACAGCTCGTGTGAGCAGTATCATTAGGGAACAATTATATGCACAGATATCGTAT
130 GCATATTCTCGACAGCTCGTGTGAGCAACATCATTAGGGAACAATTATACGCACAGATACCGTAT
27317152 A
195 A
* * * *
27317153 GATGGCTGAGGTACTGCAAATGTTGCTAGTCCTCGACAGCTCCTGAGAGCAGCATTGTGAGTCGA
1 GATGGCT-AGGTACCGCATATGTTGCGAGTCCTCGACAGCTCCTGAGAGCAGCATCGTGAGTCGA
* * *
27317218 GAAAATGATAAATGAATCCAAGAATGGATTATATGCCCTACGATGGCTGAGATTTATGCATAAGT
65 GAAAATGAGAAATGAATCCAAGAATAGATTATAGGCCCTACGATGGCTGAGATTTATGCATAAGT
* *
27317283 GCATATTCTCGATAGCTCGTGTGAGCAACATCGTTAGGGAACAATTATACGCACAGATACCGTAT
130 GCATATTCTCGACAGCTCGTGTGAGCAACATCATTAGGGAACAATTATACGCACAGATACCGTAT
*
27317348 C
195 A
* * * * *
27317349 GATGGCTAGGGTACCGCATATGTTGCGAATCCTCGACAACTCTTGTGAGAAGCATCGTG
1 GATGGCTA-GGTACCGCATATGTTGCGAGTCCTCGACAGCTCCTGAGAGCAGCATCGTG
27317408 TATTGGTAAT
Statistics
Matches: 224, Mismatches: 30, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
195 1 0.00
196 223 1.00
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.26
Consensus pattern (195 bp):
GATGGCTAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCCTGAGAGCAGCATCGTGAGTCGAG
AAAATGAGAAATGAATCCAAGAATAGATTATAGGCCCTACGATGGCTGAGATTTATGCATAAGTG
CATATTCTCGACAGCTCGTGTGAGCAACATCATTAGGGAACAATTATACGCACAGATACCGTATA
Found at i:27322738 original size:46 final size:46
Alignment explanation
Indices: 27322671--27322765 Score: 138
Period size: 46 Copynumber: 2.1 Consensus size: 46
27322661 TTCGATGACT
* *
27322671 ATGTGTCATTATGCGTATATGAATCCTTTACGGATAATGAGGTCTG
1 ATGTGTCATCATGCGTATATGAATCCTTTACAGATAATGAGGTCTG
* *
27322717 ATGTGTCATCATGAC-TATATGAATCCTTTGCAGATTATGAGGTCTG
1 ATGTGTCATCATG-CGTATATGAATCCTTTACAGATAATGAGGTCTG
27322763 ATG
1 ATG
27322766 ACTATGTGTC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
46 43 0.98
47 1 0.02
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (46 bp):
ATGTGTCATCATGCGTATATGAATCCTTTACAGATAATGAGGTCTG
Found at i:27322796 original size:52 final size:51
Alignment explanation
Indices: 27322662--27322838 Score: 202
Period size: 52 Copynumber: 3.5 Consensus size: 51
27322652 TGAAAAAGGT
* * *
27322662 TCGATGACTATGTGTCATTATGCGTATATGAATCCTTTACGGATAATGAGG
1 TCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGGATTATGAGG
* * *
27322713 TC--TG---ATGTGTCATCATGACTATATGAATCCTTTGCAGATTATGAGG
1 TCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGGATTATGAGG
* * * *
27322759 TCTGATGACTATGTGTCATCATGAGTATAAGATTCCTTTACGGATTAAGAAG
1 TC-GATGACTATGTGTCATCATGAGTATATGAATCCTTTACGGATTATGAGG
*
27322811 TCCGATGACTATGTGTCATCATAAGTAT
1 T-CGATGACTATGTGTCATCATGAGTAT
27322839 TAAATGAAAT
Statistics
Matches: 105, Mismatches: 14, Indels: 13
0.80 0.11 0.10
Matches are distributed among these distances:
46 38 0.36
49 4 0.04
51 2 0.02
52 60 0.57
53 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (51 bp):
TCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGGATTATGAGG
Found at i:27329785 original size:62 final size:62
Alignment explanation
Indices: 27329688--27329866 Score: 243
Period size: 52 Copynumber: 3.0 Consensus size: 62
27329678 TCCGATGACT
** *
27329688 ATGTGTCATTATGAGTATATAAATCCTTTACGGATTATGAGGTCCGATGACTATGTGTCATC
1 ATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACTATGTGTCATC
* *
27329750 ATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATGAGGTCC----A--A--TGAC-T-
1 ATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACTATGTGTCATC
27329802 ATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACTATGTGTCATC
1 ATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACTATGTGTCATC
27329864 ATG
1 ATG
27329867 AGTATATGAT
Statistics
Matches: 100, Mismatches: 7, Indels: 20
0.79 0.06 0.16
Matches are distributed among these distances:
52 44 0.44
53 1 0.01
54 3 0.03
56 2 0.02
58 2 0.02
60 3 0.03
61 1 0.01
62 44 0.44
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (62 bp):
ATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACTATGTGTCATC
Found at i:27329812 original size:52 final size:52
Alignment explanation
Indices: 27329750--27329983 Score: 283
Period size: 52 Copynumber: 4.3 Consensus size: 52
27329740 ATGTGTCATC
* *
27329750 ATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATGAGGTCCAATGACT
1 ATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACT
27329802 ATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACT
1 ATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACT
* * * *
27329854 ATGTGTCATCATGAGTATATGATTCCTTTACGGATTAAGAGG-CTCGATGACC
1 ATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTC-CGATGACT
* *
27329906 ATGTGTCATCGTGAGTATTAAATGAAATGAATCCCATTACGGATTA-AAGGTCCGATGACT
1 ATGTGTCATCGTGAG---T--AT---ATGAAT-CCTTTACGGATTATGAGGTCCGATGACT
*
27329966 CTGTGTCATCGTGAGTAT
1 ATGTGTCATCGTGAGTAT
27329984 CAAATATGCA
Statistics
Matches: 159, Mismatches: 12, Indels: 19
0.84 0.06 0.10
Matches are distributed among these distances:
51 1 0.01
52 110 0.69
55 3 0.02
57 3 0.02
60 29 0.18
61 13 0.08
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (52 bp):
ATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACT
Found at i:27331822 original size:196 final size:195
Alignment explanation
Indices: 27331404--27331840 Score: 581
Period size: 196 Copynumber: 2.2 Consensus size: 195
27331394 GCTAAGATAC
*
27331404 CGCATATGTTTCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGAGTCGAGAAAATGAGAAATG
1 CGCATATGTTACGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGAGTCGAGAAAATGAGAAATG
* *
27331469 AATCCAAGAATGGATTATAGGCCCTACGATGGCTGAGATTTATGCATAACTGCATATTCTCGATA
66 AATCCAAGAATGGATTATAGGCCCTACGATGGCTGAGATTTATGCATAACTGCATATTCTCCACA
** * * * * *
27331534 GCTCGTGTGAACAGTATTATTAGGGAACAGTTAAATGCACTGATAGCGTATCGATGGTTGGGTTA
131 GCTCGTGTGAACAACATCATTAAGGAACAGTTAAATGCACAGATAGCGTATCGATGGCTGGGGTA
* * * * *
27331599 CTGCATATGCTACAAGTTCTCGACAGCTCGTGTGCGCAGCATCGTGAGTCGAGAAAATGAGTAAT
1 C-GCATATGTTACGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGAGTCGAGAAAATGAGAAAT
* *
27331664 GAATCCAAGAATGGATTATATGCCCTACGATGGCTGAGATTTATGCATAAGTGCATATTCTCCAC
65 GAATCCAAGAATGGATTATAGGCCCTACGATGGCTGAGATTTATGCATAACTGCATATTCTCCAC
* * * * * *
27331729 AGCTTGTGTGAGCAACATCGTTAAGGAATAGTTATATGCACAGAT-GTCGTATTGATGGCTGGGG
130 AGCTCGTGTGAACAACATCATTAAGGAACAGTTAAATGCACAGATAG-CGTATCGATGGCTGGGG
27331793 TA
194 TA
* * **
27331795 TCGCATATGTTACGAGGCCAT-GACAGCTTGTGTGAATAGCATCGTG
1 -CGCATATGTTACGAGTCC-TCGACAGCTCGTGTGAGCAGCATCGTG
27331841 TACTGGTAAT
Statistics
Matches: 207, Mismatches: 31, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
195 2 0.01
196 203 0.98
197 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (195 bp):
CGCATATGTTACGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGAGTCGAGAAAATGAGAAATG
AATCCAAGAATGGATTATAGGCCCTACGATGGCTGAGATTTATGCATAACTGCATATTCTCCACA
GCTCGTGTGAACAACATCATTAAGGAACAGTTAAATGCACAGATAGCGTATCGATGGCTGGGGTA
Found at i:27340440 original size:26 final size:26
Alignment explanation
Indices: 27340397--27340477 Score: 90
Period size: 26 Copynumber: 3.1 Consensus size: 26
27340387 AATTCTGGGC
* * * * *
27340397 ACAATTCTAGACACGTTCATTCAGTG
1 ACAATTCTATATATGTTCATGCAGCG
*
27340423 ATAATTCTATATATGTTCATGCAGCG
1 ACAATTCTATATATGTTCATGCAGCG
* *
27340449 ACAATTCTGTATATGTTCATGCCGCG
1 ACAATTCTATATATGTTCATGCAGCG
27340475 ACA
1 ACA
27340478 TTCCTCAGTA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (26 bp):
ACAATTCTATATATGTTCATGCAGCG
Found at i:27342651 original size:12 final size:12
Alignment explanation
Indices: 27342634--27342662 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
27342624 AAAACCATCG
27342634 TCGATTAGGGTC
1 TCGATTAGGGTC
27342646 TCGATTAGGGTC
1 TCGATTAGGGTC
27342658 TCGAT
1 TCGAT
27342663 ATCCTTCTAT
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:0.17, C:0.17, G:0.31, T:0.34
Consensus pattern (12 bp):
TCGATTAGGGTC
Found at i:27346626 original size:23 final size:23
Alignment explanation
Indices: 27346600--27346952 Score: 492
Period size: 23 Copynumber: 15.4 Consensus size: 23
27346590 CTTATATATA
27346600 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATATGATTTG
* * *
27346623 TGCTCAAATATTAATGTGATTTA
1 TGCTTAAATATTAATATGATTTG
*
27346646 TGCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATATGATTTG
*
27346669 TGCTTAAATATTAATATGATTTA
1 TGCTTAAATATTAATATGATTTG
* *
27346692 TGATTAAATATTAATTTGATTTG
1 TGCTTAAATATTAATATGATTTG
* * *
27346715 TGCTTAAGTATTAATTTGATTTA
1 TGCTTAAATATTAATATGATTTG
27346738 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATATGATTTG
*
27346761 TGCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATATGATTTG
27346784 TGCTTAAATATTAATATGA-TTG
1 TGCTTAAATATTAATATGATTTG
* *
27346806 TGCTCAAATATTAATGTGATTTG
1 TGCTTAAATATTAATATGATTTG
27346829 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATATGATTTG
* *
27346852 TGCTCAAATATTAATATGATTTA
1 TGCTTAAATATTAATATGATTTG
* *
27346875 TGCTTAAATATTAACATGATTTA
1 TGCTTAAATATTAATATGATTTG
* * * *
27346898 TGATTAAATATTAATGTTATTTA
1 TGCTTAAATATTAATATGATTTG
*
27346921 TGCTTAAATATTAATATGATTTA
1 TGCTTAAATATTAATATGATTTG
*
27346944 TGGTTAAAT
1 TGCTTAAAT
27346953 GTGATTTGTT
Statistics
Matches: 295, Mismatches: 34, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
22 20 0.07
23 275 0.93
ACGTcount: A:0.35, C:0.05, G:0.13, T:0.47
Consensus pattern (23 bp):
TGCTTAAATATTAATATGATTTG
Found at i:27347098 original size:35 final size:36
Alignment explanation
Indices: 27347052--27347147 Score: 158
Period size: 36 Copynumber: 2.7 Consensus size: 36
27347042 AAAGTGAATC
*
27347052 TGTGGGTATGTTCTTCATACCATGTGACA-AAAATA
1 TGTGGGTATGTTCTTCATGCCATGTGACAGAAAATA
*
27347087 TGTGGGTATGTTCTTCATGCCATGTGACAGAGAATA
1 TGTGGGTATGTTCTTCATGCCATGTGACAGAAAATA
*
27347123 TGTGGGTATGTTCTTAATGCCATGT
1 TGTGGGTATGTTCTTCATGCCATGT
27347148 AACTGATTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
35 28 0.49
36 29 0.51
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (36 bp):
TGTGGGTATGTTCTTCATGCCATGTGACAGAAAATA
Found at i:27347130 original size:36 final size:35
Alignment explanation
Indices: 27347047--27347147 Score: 157
Period size: 35 Copynumber: 2.9 Consensus size: 35
27347037 TTATGAAAGT
* *
27347047 GAATCTGTGGGTATGTTCTTCATACCATGTGACAA
1 GAATATGTGGGTATGTTCTTCATGCCATGTGACAA
*
27347082 AAATATGTGGGTATGTTCTTCATGCCATGTGACAGA
1 GAATATGTGGGTATGTTCTTCATGCCATGTGACA-A
*
27347118 GAATATGTGGGTATGTTCTTAATGCCATGT
1 GAATATGTGGGTATGTTCTTCATGCCATGT
27347148 AACTGATTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
35 31 0.52
36 29 0.48
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.36
Consensus pattern (35 bp):
GAATATGTGGGTATGTTCTTCATGCCATGTGACAA
Found at i:27348933 original size:22 final size:21
Alignment explanation
Indices: 27348900--27348954 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 21
27348890 TCTTAGTACT
27348900 TCTCCAA-AGGTACCTATACA
1 TCTCCAAGAGGTACCTATACA
* *
27348920 TCTCCCAAGAGGTACCTGTACG
1 TCT-CCAAGAGGTACCTATACA
27348942 TCTCC-AGAGGTAC
1 TCTCCAAGAGGTAC
27348955 ATGTACCTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.35
21 6 0.19
22 14 0.45
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (21 bp):
TCTCCAAGAGGTACCTATACA
Found at i:27348952 original size:20 final size:20
Alignment explanation
Indices: 27348895--27348960 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
27348885 AAATGTCTTA
* *
27348895 GTACTTCTCCAAAGGTACCT
1 GTACATCTCCAGAGGTACCT
*
27348915 ATACATCTCCCAAGAGGTACCT
1 GTACATCT-CC-AGAGGTACCT
* *
27348937 GTACGTCTCCAGAGGTACAT
1 GTACATCTCCAGAGGTACCT
27348957 GTAC
1 GTAC
27348961 CTTTGTTTCA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
20 19 0.50
21 4 0.11
22 15 0.39
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.26
Consensus pattern (20 bp):
GTACATCTCCAGAGGTACCT
Found at i:27349109 original size:22 final size:22
Alignment explanation
Indices: 27349084--27349132 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
27349074 GCCTCAAAAT
*
27349084 TTTTCTAAACTTGATTTT-ATGA
1 TTTTCTAAA-TTGATTTTCAAGA
* *
27349106 TTTTATAAATTTATTTTCAAGA
1 TTTTCTAAATTGATTTTCAAGA
27349128 TTTTC
1 TTTTC
27349133 GTTTCGTTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.57
Consensus pattern (22 bp):
TTTTCTAAATTGATTTTCAAGA
Found at i:27350332 original size:40 final size:41
Alignment explanation
Indices: 27350288--27350387 Score: 114
Period size: 40 Copynumber: 2.5 Consensus size: 41
27350278 GCCTGGAGCT
*
27350288 ATTTTGACTTGTTTGAAAAACATTTTGAAGTG-TTAAAATG
1 ATTTTGACTTGTTTGAAAAACATTTTGAAGTGTTTAAAATA
* * **
27350328 ATTTTGACTTGGTTG-AAATCATTTTGACTTGTTTAAAATA
1 ATTTTGACTTGTTTGAAAAACATTTTGAAGTGTTTAAAATA
* *
27350368 ATTTTAACTTGATTTTAAAA
1 ATTTTGACTTG-TTTGAAAA
27350388 TTATTTCAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
39 13 0.27
40 31 0.63
41 2 0.04
42 3 0.06
ACGTcount: A:0.34, C:0.06, G:0.14, T:0.46
Consensus pattern (41 bp):
ATTTTGACTTGTTTGAAAAACATTTTGAAGTGTTTAAAATA
Found at i:27350351 original size:20 final size:20
Alignment explanation
Indices: 27350288--27350378 Score: 85
Period size: 20 Copynumber: 4.5 Consensus size: 20
27350278 GCCTGGAGCT
* *
27350288 ATTTTGACTTGTTTGAAAAAC
1 ATTTTGACTTGGTT-AAAATC
** *
27350309 ATTTTGAAGT-GTTAAAATG
1 ATTTTGACTTGGTTAAAATC
*
27350328 ATTTTGACTTGGTTGAAATC
1 ATTTTGACTTGGTTAAAATC
* *
27350348 ATTTTGACTTGTTTAAAATA
1 ATTTTGACTTGGTTAAAATC
*
27350368 ATTTTAACTTG
1 ATTTTGACTTG
27350379 ATTTTAAAAT
Statistics
Matches: 56, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
19 12 0.21
20 36 0.64
21 8 0.14
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.46
Consensus pattern (20 bp):
ATTTTGACTTGGTTAAAATC
Found at i:27350387 original size:22 final size:20
Alignment explanation
Indices: 27350320--27350393 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
27350310 TTTTGAAGTG
* * *
27350320 TTAAAATGATTTTGACTTGG
1 TTAAAATAATTTTAACTTGT
* * *
27350340 TTGAAATCATTTTGACTTGT
1 TTAAAATAATTTTAACTTGT
27350360 TTAAAATAATTTTAACTTGATT
1 TTAAAATAATTTTAACTTG--T
*
27350382 TTAAAATTATTT
1 TTAAAATAATTT
27350394 CAAAATTTTC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 33 0.73
22 12 0.27
ACGTcount: A:0.34, C:0.05, G:0.11, T:0.50
Consensus pattern (20 bp):
TTAAAATAATTTTAACTTGT
Found at i:27356419 original size:33 final size:33
Alignment explanation
Indices: 27356381--27356455 Score: 150
Period size: 33 Copynumber: 2.3 Consensus size: 33
27356371 CAGAAGAGGA
27356381 AGAAGAAAAGTGGCAATAACCGCGACCAAAAAG
1 AGAAGAAAAGTGGCAATAACCGCGACCAAAAAG
27356414 AGAAGAAAAGTGGCAATAACCGCGACCAAAAAG
1 AGAAGAAAAGTGGCAATAACCGCGACCAAAAAG
27356447 AGAAGAAAA
1 AGAAGAAAA
27356456 TTGAAAGATG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.55, C:0.16, G:0.24, T:0.05
Consensus pattern (33 bp):
AGAAGAAAAGTGGCAATAACCGCGACCAAAAAG
Found at i:27359320 original size:295 final size:295
Alignment explanation
Indices: 27358784--27359372 Score: 1169
Period size: 295 Copynumber: 2.0 Consensus size: 295
27358774 TGTGCAATGC
*
27358784 TCACAGACTTAGAACTATGGTCCGTGACACGTAGGGATGGATATTGGTTTGTTAGGTTGGACGGA
1 TCACAAACTTAGAACTATGGTCCGTGACACGTAGGGATGGATATTGGTTTGTTAGGTTGGACGGA
27358849 GAAAGTGTGCAAGGTTGGGGGTTACATAATTAAATTTGTATTTGTAACTAAATGTGAGTCTGAAA
66 GAAAGTGTGCAAGGTTGGGGGTTACATAATTAAATTTGTATTTGTAACTAAATGTGAGTCTGAAA
27358914 CAATATCTATAACTGTGACTATACAATCGAACTGTAACTAACACTGTCTAATTGAACTGTATATG
131 CAATATCTATAACTGTGACTATACAATCGAACTGTAACTAACACTGTCTAATTGAACTGTATATG
27358979 TGTTGACTGTGTAATTGGTATCAAATCGATTGAAATTAATGAATCGTAATGGTTACTTCTATAAT
196 TGTTGACTGTGTAATTGGTATCAAATCGATTGAAATTAATGAATCGTAATGGTTACTTCTATAAT
27359044 TTTGTGTATAGAACATGGGAAACTTCATTATATGG
261 TTTGTGTATAGAACATGGGAAACTTCATTATATGG
27359079 TCACAAACTTAGAACTATGGTCCGTGACACGTAGGGATGGATATTGGTTTGTTAGGTTGGACGGA
1 TCACAAACTTAGAACTATGGTCCGTGACACGTAGGGATGGATATTGGTTTGTTAGGTTGGACGGA
27359144 GAAAGTGTGCAAGGTTGGGGGTTACATAATTAAATTTGTATTTGTAACTAAATGTGAGTCTGAAA
66 GAAAGTGTGCAAGGTTGGGGGTTACATAATTAAATTTGTATTTGTAACTAAATGTGAGTCTGAAA
27359209 CAATATCTATAACTGTGACTATACAATCGAACTGTAACTAACACTGTCTAATTGAACTGTATATG
131 CAATATCTATAACTGTGACTATACAATCGAACTGTAACTAACACTGTCTAATTGAACTGTATATG
27359274 TGTTGACTGTGTAATTGGTATCAAATCGATTGAAATTAATGAATCGTAATGGTTACTTCTATAAT
196 TGTTGACTGTGTAATTGGTATCAAATCGATTGAAATTAATGAATCGTAATGGTTACTTCTATAAT
27359339 TTTGTGTATAGAACATGGGAAACTTCATTATATG
261 TTTGTGTATAGAACATGGGAAACTTCATTATATG
27359373 TTGCACTAAC
Statistics
Matches: 293, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
295 293 1.00
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34
Consensus pattern (295 bp):
TCACAAACTTAGAACTATGGTCCGTGACACGTAGGGATGGATATTGGTTTGTTAGGTTGGACGGA
GAAAGTGTGCAAGGTTGGGGGTTACATAATTAAATTTGTATTTGTAACTAAATGTGAGTCTGAAA
CAATATCTATAACTGTGACTATACAATCGAACTGTAACTAACACTGTCTAATTGAACTGTATATG
TGTTGACTGTGTAATTGGTATCAAATCGATTGAAATTAATGAATCGTAATGGTTACTTCTATAAT
TTTGTGTATAGAACATGGGAAACTTCATTATATGG
Found at i:27374921 original size:25 final size:25
Alignment explanation
Indices: 27374892--27374940 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
27374882 ACGATATTTG
*
27374892 TAACTGTGACTGTAC-AATCGAACTA
1 TAACTGAGACT-TACTAATCGAACTA
*
27374917 TAACTGAGACTTTCTAATCGAACT
1 TAACTGAGACTTACTAATCGAACT
27374941 GTATATGTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 19 0.90
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (25 bp):
TAACTGAGACTTACTAATCGAACTA
Found at i:27384833 original size:22 final size:20
Alignment explanation
Indices: 27384800--27384853 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 20
27384790 TATATAAGTA
*
27384800 TATTTTTAATATTTTATTAT
1 TATTTTTAATATTGTATTAT
27384820 TATTATTTGAATATTGTATTAT
1 TATT-TTT-AATATTGTATTAT
*
27384842 T-TTTTTATTATT
1 TATTTTTAATATT
27384854 ATTAATTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 5 0.17
20 7 0.23
21 5 0.17
22 13 0.43
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.69
Consensus pattern (20 bp):
TATTTTTAATATTGTATTAT
Found at i:27384843 original size:30 final size:29
Alignment explanation
Indices: 27384799--27384874 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 29
27384789 ATATATAAGT
* *
27384799 ATATTTTTAATATTTTATTATTATTATTTGA
1 ATATTGTTATTATTTTATTATTATTA-TT-A
*
27384830 ATATTG-TATTATTTTTTTATTATTATTA
1 ATATTGTTATTATTTTATTATTATTATTA
*
27384858 ATTTTGTTATTATTTTA
1 ATATTGTTATTATTTTA
27384875 AAAGTATTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
28 6 0.15
29 11 0.28
30 17 0.44
31 5 0.13
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (29 bp):
ATATTGTTATTATTTTATTATTATTATTA
Found at i:27384867 original size:18 final size:18
Alignment explanation
Indices: 27384836--27384875 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
27384826 TTGAATATTG
*
27384836 TATT-ATTTTTTTATTAT
1 TATTAATTTTGTTATTAT
27384853 TATTAATTTTGTTATTAT
1 TATTAATTTTGTTATTAT
27384871 T-TTAA
1 TATTAA
27384876 AAGTATTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (18 bp):
TATTAATTTTGTTATTAT
Found at i:27387043 original size:13 final size:13
Alignment explanation
Indices: 27387025--27387049 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27387015 ATTTAAAATA
27387025 TTACATAATCAAT
1 TTACATAATCAAT
27387038 TTACATAATCAA
1 TTACATAATCAA
27387050 ATCTAATCAT
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:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (13 bp):
TTACATAATCAAT
Found at i:27387517 original size:40 final size:40
Alignment explanation
Indices: 27387450--27387583 Score: 160
Period size: 40 Copynumber: 3.3 Consensus size: 40
27387440 AGCGGCACTT
** *
27387450 TTAGCGGCGTTTGGACAATAAACGTCGCAAAAGGTGAAGCA
1 TTAGCGGCGTTTTTAC-ATAAACGTCGCAAAAGGTAAAGCA
* *
27387491 ATAGCGGCGTTTTTCCATAAACGTCGCAAAAGGTAAAGCA
1 TTAGCGGCGTTTTTACATAAACGTCGCAAAAGGTAAAGCA
* * * * *
27387531 TTAGCGGCATTTTTACATAAGCGCCGCTAAAGGTCAGAGCA
1 TTAGCGGCGTTTTTACATAAACGTCGCAAAAGGT-AAAGCA
27387572 TTAGCGGCGTTT
1 TTAGCGGCGTTT
27387584 ATGGAAAAGC
Statistics
Matches: 79, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
40 51 0.65
41 28 0.35
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (40 bp):
TTAGCGGCGTTTTTACATAAACGTCGCAAAAGGTAAAGCA
Found at i:27387594 original size:41 final size:40
Alignment explanation
Indices: 27387549--27387788 Score: 318
Period size: 41 Copynumber: 5.9 Consensus size: 40
27387539 ATTTTTACAT
* *
27387549 AAGCGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGGAA
1 AAGCGCCGCTAAAGGTCAGAGTAATAGCGGCGTTTATGG-A
*
27387590 AAGCGCCGCTAAAGGTCAGAGTAATAGCGGCGTTTACGGGA
1 AAGCGCCGCTAAAGGTCAGAGTAATAGCGGCGTTTA-TGGA
* * *
27387631 AAGCGTCGCTAAAGGTCAGAGTAATAGCGGTGTTTACAGGA
1 AAGCGCCGCTAAAGGTCAGAGTAATAGCGGCGTTTA-TGGA
* * *
27387672 AAGCACCGCTAAAGGTCAGAGTAATAGCAGCGTTTATGTGG
1 AAGCGCCGCTAAAGGTCAGAGTAATAGCGGCGTTTATG-GA
* *
27387713 AAGCGCCGCTAAAGGTTAGAGTAATAGCGGTGTTTATGAGA
1 AAGCGCCGCTAAAGGTCAGAGTAATAGCGGCGTTTATG-GA
* *
27387754 AAACACCGCTAAAGGTCAGAGTAATAGCGGCGTTT
1 AAGCGCCGCTAAAGGTCAGAGTAATAGCGGCGTTT
27387789 TTCTATAAAC
Statistics
Matches: 175, Mismatches: 22, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
40 1 0.01
41 172 0.98
42 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.21
Consensus pattern (40 bp):
AAGCGCCGCTAAAGGTCAGAGTAATAGCGGCGTTTATGGA
Found at i:27387641 original size:82 final size:82
Alignment explanation
Indices: 27387549--27387788 Score: 351
Period size: 82 Copynumber: 2.9 Consensus size: 82
27387539 ATTTTTACAT
* * * *
27387549 AAGCGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGGAAAAGCGCCGCTAAAGGTCAGAGTAA
1 AAGCGCCGCTAAAGGTCAGAGTAATAGCGGTGTTTATGGAAAAGCACCGCTAAAGGTCAGAGTAA
27387614 TAGCGGCGTTTACG-GG
66 TAGCGGCGTTTACGTGG
* *
27387630 AAAGCGTCGCTAAAGGTCAGAGTAATAGCGGTGTTTACAGG-AAAGCACCGCTAAAGGTCAGAGT
1 -AAGCGCCGCTAAAGGTCAGAGTAATAGCGGTGTTTA-TGGAAAAGCACCGCTAAAGGTCAGAGT
* *
27387694 AATAGCAGCGTTTATGTGG
64 AATAGCGGCGTTTACGTGG
*
27387713 AAGCGCCGCTAAAGGTTAGAGTAATAGCGGTGTTTATGAGAAAA-CACCGCTAAAGGTCAGAGTA
1 AAGCGCCGCTAAAGGTCAGAGTAATAGCGGTGTTTATG-GAAAAGCACCGCTAAAGGTCAGAGTA
27387777 ATAGCGGCGTTT
65 ATAGCGGCGTTT
27387789 TTCTATAAAC
Statistics
Matches: 142, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
81 1 0.01
82 134 0.94
83 7 0.05
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.21
Consensus pattern (82 bp):
AAGCGCCGCTAAAGGTCAGAGTAATAGCGGTGTTTATGGAAAAGCACCGCTAAAGGTCAGAGTAA
TAGCGGCGTTTACGTGG
Found at i:27389048 original size:20 final size:20
Alignment explanation
Indices: 27389006--27389050 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
27388996 TGAATGTTTC
*
27389006 AAAATCAAATTTAAACCGAA
1 AAAATCAAATTTAAACAGAA
*
27389026 AAAATCAAAATTTAAA-AGCA
1 AAAATC-AAATTTAAACAGAA
27389046 AAAAT
1 AAAAT
27389051 TTATTATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.64, C:0.11, G:0.04, T:0.20
Consensus pattern (20 bp):
AAAATCAAATTTAAACAGAA
Found at i:27389177 original size:41 final size:40
Alignment explanation
Indices: 27389132--27389337 Score: 146
Period size: 41 Copynumber: 5.2 Consensus size: 40
27389122 TTCCCATAAA
*
27389132 CGCCGCTAAAGGTCAGAACATTAGCGACGCTTGTGAGAAAG
1 CGCCGCTAAAGGTCAGAACATTAGCGACGCTTATG-GAAAG
* * *
27389173 CGCCGCTAAAGGT-----C--TAGTG--G-TAAAGGAGAAAG
1 CGCCGCTAAAGGTCAGAACATTAGCGACGCT-TATG-GAAAG
27389205 CGCCGCTAAAGGTCA-AATCATTAGCGACGCTTATGGTAAAG
1 CGCCGCTAAAGGTCAGAA-CATTAGCGACGCTTATGG-AAAG
* * * *
27389246 CGCCGTTAAAGGTCAGAGCACTAGCGACGCTTATGGGAAAA
1 CGCCGCTAAAGGTCAGAACATTAGCGACGCTTAT-GGAAAG
* * * * *
27389287 CGCCTCTAAATGTTAGAGCATTAGTGACGCTTATTGGAAAG
1 CGCCGCTAAAGGTCAGAACATTAGCGACGCTTA-TGGAAAG
*
27389328 CACCGCTAAA
1 CGCCGCTAAA
27389338 AGTTAAACAA
Statistics
Matches: 130, Mismatches: 20, Indels: 30
0.72 0.11 0.17
Matches are distributed among these distances:
31 1 0.01
32 21 0.16
34 4 0.03
36 1 0.01
37 1 0.01
39 4 0.03
40 1 0.01
41 92 0.71
42 5 0.04
ACGTcount: A:0.32, C:0.21, G:0.27, T:0.20
Consensus pattern (40 bp):
CGCCGCTAAAGGTCAGAACATTAGCGACGCTTATGGAAAG
Found at i:27392287 original size:48 final size:48
Alignment explanation
Indices: 27392233--27392401 Score: 152
Period size: 48 Copynumber: 3.4 Consensus size: 48
27392223 TTAAATATTT
*
27392233 AAATATTTAACTAATTAATTATTAAAAATAACCCAAATATTTAATTAA
1 AAATATTTAATTAATTAATTATTAAAAATAACCCAAATATTTAATTAA
* *
27392281 AAATATTTTATTAGTTAATTATATTTAATAATTAAAAACAATCCAAATA--T--TT--
1 AAATA-TTTA--A-TTAATTA-A--T--T-ATTAAAAATAACCCAAATATTTAATTAA
*
27392333 AAATATTTAATTAATTATTTATTAAAAATAACCCAAATATTTAATTAA
1 AAATATTTAATTAATTAATTATTAAAAATAACCCAAATATTTAATTAA
* *
27392381 AAATATTTTATTATTTAATTA
1 AAATATTTAATTAATTAATTA
27392402 CATTTAATTA
Statistics
Matches: 96, Mismatches: 9, Indels: 32
0.70 0.07 0.23
Matches are distributed among these distances:
42 17 0.18
43 1 0.01
44 1 0.01
45 1 0.01
46 2 0.02
48 30 0.31
49 5 0.05
51 5 0.05
52 11 0.11
53 1 0.01
54 2 0.02
55 1 0.01
56 1 0.01
57 1 0.01
58 17 0.18
ACGTcount: A:0.50, C:0.06, G:0.01, T:0.43
Consensus pattern (48 bp):
AAATATTTAATTAATTAATTATTAAAAATAACCCAAATATTTAATTAA
Found at i:27392341 original size:100 final size:100
Alignment explanation
Indices: 27392225--27392409 Score: 334
Period size: 100 Copynumber: 1.9 Consensus size: 100
27392215 ACATTTAATT
27392225 AAATATTTAAATATTTAACTAATTAATTATTAAAAATAACCCAAATATTTAATTAAAAATATTTT
1 AAATATTTAAATATTTAACTAATTAATTATTAAAAATAACCCAAATATTTAATTAAAAATATTTT
*
27392290 ATTAGTTAATTATATTTAATAATTAAAAACAATCC
66 ATTAGTTAATTACATTTAATAATTAAAAACAATCC
* *
27392325 AAATATTTAAATATTTAATTAATTATTTATTAAAAATAACCCAAATATTTAATTAAAAATATTTT
1 AAATATTTAAATATTTAACTAATTAATTATTAAAAATAACCCAAATATTTAATTAAAAATATTTT
*
27392390 ATTATTTAATTACATTTAAT
66 ATTAGTTAATTACATTTAAT
27392410 TAAATATTTA
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
100 81 1.00
ACGTcount: A:0.50, C:0.06, G:0.01, T:0.44
Consensus pattern (100 bp):
AAATATTTAAATATTTAACTAATTAATTATTAAAAATAACCCAAATATTTAATTAAAAATATTTT
ATTAGTTAATTACATTTAATAATTAAAAACAATCC
Found at i:27394164 original size:21 final size:21
Alignment explanation
Indices: 27394134--27394173 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
27394124 TTACAACTTA
*
27394134 AAGCGGAGGCAGCAGCGAGGG
1 AAGCGAAGGCAGCAGCGAGGG
*
27394155 AAGCGAAGGCAGTAGCGAG
1 AAGCGAAGGCAGCAGCGAG
27394174 AGTCGCGAAA
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:0.33, C:0.17, G:0.47, T:0.03
Consensus pattern (21 bp):
AAGCGAAGGCAGCAGCGAGGG
Found at i:27394569 original size:43 final size:43
Alignment explanation
Indices: 27394503--27394602 Score: 128
Period size: 43 Copynumber: 2.3 Consensus size: 43
27394493 AATCAGTTAA
* **
27394503 TTTTAGCAGCGTTTGTGTGAAAAGTGCCGCTAAAGACCATGTT
1 TTTTAGCAGCGTTTGCGCAAAAAGTGCCGCTAAAGACCATGTT
* * *
27394546 TTTTAGCTGCGTTTGCGCAAAAAGTGCCGCTAAAGATCGTGTT
1 TTTTAGCAGCGTTTGCGCAAAAAGTGCCGCTAAAGACCATGTT
* *
27394589 CTTTAGCGGCGTTT
1 TTTTAGCAGCGTTT
27394603 ATAGATAGGC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (43 bp):
TTTTAGCAGCGTTTGCGCAAAAAGTGCCGCTAAAGACCATGTT
Found at i:27394643 original size:42 final size:42
Alignment explanation
Indices: 27394585--27394686 Score: 123
Period size: 42 Copynumber: 2.4 Consensus size: 42
27394575 CTAAAGATCG
* * * * *
27394585 TGTTCTTTAGCGGCGTTTATAGATAGGCGTCGTTACAGACCA
1 TGTTCTTTAGCGGCGTTTATAGAAAAGCGCCGTTAAAAACCA
* * **
27394627 TGTTCTTTAGCAGCGTTTGTTTAAAAGCGCCGTTAAAAACCA
1 TGTTCTTTAGCGGCGTTTATAGAAAAGCGCCGTTAAAAACCA
27394669 TGTTCTTTAGCGGCGTTT
1 TGTTCTTTAGCGGCGTTT
27394687 TTTCTCATAA
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.36
Consensus pattern (42 bp):
TGTTCTTTAGCGGCGTTTATAGAAAAGCGCCGTTAAAAACCA
Found at i:27399780 original size:21 final size:21
Alignment explanation
Indices: 27399741--27399791 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
27399731 TTTTTAGTAC
* *
27399741 TGGTAGAAGCATGATTTGT-T
1 TGGTAGAAGCATCACTTGTGT
*
27399761 TCGGTAGAAGCTTCACTTGTGT
1 T-GGTAGAAGCATCACTTGTGT
27399783 TGGTAGAAG
1 TGGTAGAAG
27399792 TCTGCACTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 1 0.04
21 23 0.88
22 2 0.08
ACGTcount: A:0.24, C:0.10, G:0.31, T:0.35
Consensus pattern (21 bp):
TGGTAGAAGCATCACTTGTGT
Found at i:27405329 original size:19 final size:20
Alignment explanation
Indices: 27405305--27405352 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
27405295 GGGTTTGTAA
*
27405305 AAAGTCAACGGTCAA-AGTT
1 AAAGTCAACGGTCAATAGCT
*
27405324 AAAGTCAACGGTCAATGGCT
1 AAAGTCAACGGTCAATAGCT
27405344 AAAGTCAAC
1 AAAGTCAAC
27405353 ATGTCTGTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.42, C:0.19, G:0.21, T:0.19
Consensus pattern (20 bp):
AAAGTCAACGGTCAATAGCT
Found at i:27406261 original size:36 final size:36
Alignment explanation
Indices: 27406214--27406313 Score: 173
Period size: 36 Copynumber: 2.8 Consensus size: 36
27406204 TAGTAACAGG
*
27406214 CATGACCTTTGGGTCAACAGGGAGTAAGATGAGCAT
1 CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
* *
27406250 CATGACCTTTGGGTCAAAAAGGAGTAAAATGAGCAT
1 CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
27406286 CATGACCTTTGGGTCAACAGGGAGTAAA
1 CATGACCTTTGGGTCAACAGGGAGTAAA
27406314 TCTGATATTG
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 59 1.00
ACGTcount: A:0.34, C:0.16, G:0.28, T:0.22
Consensus pattern (36 bp):
CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
Found at i:27408283 original size:2 final size:2
Alignment explanation
Indices: 27408276--27408304 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
27408266 ATTGAAAAAC
27408276 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
27408305 AATAATTGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27409691 original size:21 final size:21
Alignment explanation
Indices: 27409667--27409721 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
27409657 GAAGCATGAT
*
27409667 TTGTTTCGATAGAAGTTTCAC
1 TTGTATCGATAGAAGTTTCAC
27409688 TTGTATCGATAGAAGTTTCAC
1 TTGTATCGATAGAAGTTTCAC
*
27409709 TTGTATCGGTAGA
1 TTGTATCGATAGA
27409722 TGTCTGCACT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.13, G:0.22, T:0.40
Consensus pattern (21 bp):
TTGTATCGATAGAAGTTTCAC
Found at i:27423718 original size:13 final size:13
Alignment explanation
Indices: 27423700--27423747 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
27423690 ATTTGTAAAA
27423700 AAAGTCAACGGTC
1 AAAGTCAACGGTC
*
27423713 AAAGTCAA-AGTC
1 AAAGTCAACGGTC
*
27423725 AACAGTCAATGGTC
1 AA-AGTCAACGGTC
27423739 AAAGTCAAC
1 AAAGTCAAC
27423748 ATGTCTGTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 5 0.17
13 20 0.67
14 5 0.17
ACGTcount: A:0.44, C:0.21, G:0.19, T:0.17
Consensus pattern (13 bp):
AAAGTCAACGGTC
Found at i:27423761 original size:19 final size:19
Alignment explanation
Indices: 27423700--27423766 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 19
27423690 ATTTGTAAAA
* **
27423700 AAAGTCAACGGTCAAAGTC
1 AAAGTCAACAGTCATGGTC
27423719 AAAGTCAACAGTCAATGGTC
1 AAAGTCAACAGTC-ATGGTC
*
27423739 AAAGTCAACATGTC-TGTTC
1 AAAGTCAACA-GTCATGGTC
27423758 AAAGTCAAC
1 AAAGTCAAC
27423767 GGGTCAGTCA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
19 25 0.60
20 14 0.33
21 3 0.07
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (19 bp):
AAAGTCAACAGTCATGGTC
Found at i:27424659 original size:36 final size:36
Alignment explanation
Indices: 27424612--27424711 Score: 182
Period size: 36 Copynumber: 2.8 Consensus size: 36
27424602 TAGTAACAGG
*
27424612 CATGACCTTTGGGTCAACAGGGAGTAAGATGAGCAT
1 CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
*
27424648 CATGACCTTTGGGTCAACAAGGAGTAAAATGAGCAT
1 CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
27424684 CATGACCTTTGGGTCAACAGGGAGTAAA
1 CATGACCTTTGGGTCAACAGGGAGTAAA
27424712 TCGGATATTG
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 61 1.00
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.22
Consensus pattern (36 bp):
CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
Found at i:27425669 original size:223 final size:223
Alignment explanation
Indices: 27425281--27425730 Score: 882
Period size: 223 Copynumber: 2.0 Consensus size: 223
27425271 CTTAGCTGTC
27425281 TGAAGTTTTTAGTATAGGTAGAAGCGTGGTTTGTTTCGATAGAAGTTTTACTTGTATCAGTAGAA
1 TGAAGTTTTTAGTATAGGTAGAAGCGTGGTTTGTTTCGATAGAAGTTTTACTTGTATCAGTAGAA
27425346 GTCTGCACTGTTTCATGAATTGTTTACTGACTTGACAACTACTGATACTTGTCCAACAAGTACCG
66 GTCTGCACTGTTTCATGAATTGTTTACTGACTTGACAACTACTGATACTTGTCCAACAAGTACCG
*
27425411 GTAAAAGTATCCAAAAATCATTAAAATAACCTTTTTGCCCTTGTTGAGTTATGATTATAATTAAT
131 GTAAAAGTATCCAAAAATCATGAAAATAACCTTTTTGCCCTTGTTGAGTTATGATTATAATTAAT
27425476 TGATGATTTATGACATGATATTAAAAGA
196 TGATGATTTATGACATGATATTAAAAGA
27425504 TGAAGTTTTTAGTATAGGTAGAAGCGTGGTTTGTTTCGATAGAAGTTTTACTTGTATCAGTAGAA
1 TGAAGTTTTTAGTATAGGTAGAAGCGTGGTTTGTTTCGATAGAAGTTTTACTTGTATCAGTAGAA
27425569 GTCTGCACTGTTTCATGAATTGTTTACTGACTTGACAACTACTGATACTTGTCCAACAAGTACCG
66 GTCTGCACTGTTTCATGAATTGTTTACTGACTTGACAACTACTGATACTTGTCCAACAAGTACCG
*
27425634 GTAGAAGTATCCAAAAATCATGAAAATAACCTTTTTGCCCTTGTTGAGTTATGATTATAATTAAT
131 GTAAAAGTATCCAAAAATCATGAAAATAACCTTTTTGCCCTTGTTGAGTTATGATTATAATTAAT
27425699 TGATGATTTATGACATGATATTAAAAGA
196 TGATGATTTATGACATGATATTAAAAGA
27425727 TGAA
1 TGAA
27425731 TAGTGATAAA
Statistics
Matches: 225, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
223 225 1.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.37
Consensus pattern (223 bp):
TGAAGTTTTTAGTATAGGTAGAAGCGTGGTTTGTTTCGATAGAAGTTTTACTTGTATCAGTAGAA
GTCTGCACTGTTTCATGAATTGTTTACTGACTTGACAACTACTGATACTTGTCCAACAAGTACCG
GTAAAAGTATCCAAAAATCATGAAAATAACCTTTTTGCCCTTGTTGAGTTATGATTATAATTAAT
TGATGATTTATGACATGATATTAAAAGA
Found at i:27428275 original size:21 final size:21
Alignment explanation
Indices: 27428251--27428305 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
27428241 GAAGCATGAT
*
27428251 TTGTTTCGATAGAAGTTTCAC
1 TTGTATCGATAGAAGTTTCAC
27428272 TTGTATCGATAGAAGTTTCAC
1 TTGTATCGATAGAAGTTTCAC
*
27428293 TTGTATCGGTAGA
1 TTGTATCGATAGA
27428306 TGTCTGCACT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.13, G:0.22, T:0.40
Consensus pattern (21 bp):
TTGTATCGATAGAAGTTTCAC
Found at i:27448612 original size:20 final size:20
Alignment explanation
Indices: 27448583--27448620 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
27448573 GTCAAAAAAT
*
27448583 GTCAATGGTCAAAGTCAAAG
1 GTCAACGGTCAAAGTCAAAG
27448603 GTCAACGGTCAAAGTCAA
1 GTCAACGGTCAAAGTCAA
27448621 CATGTTTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.18
Consensus pattern (20 bp):
GTCAACGGTCAAAGTCAAAG
Found at i:27451433 original size:2 final size:2
Alignment explanation
Indices: 27451426--27451458 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
27451416 AGTGATTGAA
27451426 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
27451459 TATATAAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:27455688 original size:13 final size:13
Alignment explanation
Indices: 27455670--27455718 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
27455660 ATTTGTAAAA
27455670 AAAGTCAACAGTC
1 AAAGTCAACAGTC
27455683 AAAGTCAA-AGTC
1 AAAGTCAACAGTC
* **
27455695 AACGGTCAATGGTC
1 AA-AGTCAACAGTC
27455709 AAAGTCAACA
1 AAAGTCAACA
27455719 TGTCTGTTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
12 6 0.21
13 18 0.62
14 5 0.17
ACGTcount: A:0.45, C:0.20, G:0.18, T:0.16
Consensus pattern (13 bp):
AAAGTCAACAGTC
Found at i:27469428 original size:21 final size:21
Alignment explanation
Indices: 27469403--27469454 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
27469393 GAAGCTTCAC
27469403 CAAAGAAGGAGAAAGGAAAAA
1 CAAAGAAGGAGAAAGGAAAAA
27469424 CAAAGAAGGAGAAAGGAAAAA
1 CAAAGAAGGAGAAAGGAAAAA
*
27469445 TAAAGAAGGA
1 CAAAGAAGGA
27469455 AGCGAAACAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.65, C:0.04, G:0.29, T:0.02
Consensus pattern (21 bp):
CAAAGAAGGAGAAAGGAAAAA
Found at i:27473215 original size:16 final size:16
Alignment explanation
Indices: 27473194--27473224 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27473184 ATAATGAGAA
27473194 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
27473210 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
27473225 GGATCCACAA
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:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:27476577 original size:19 final size:19
Alignment explanation
Indices: 27476529--27476731 Score: 174
Period size: 19 Copynumber: 10.7 Consensus size: 19
27476519 AAGGAATATA
* * *
27476529 GATACTGGCTAGCAAGAGT
1 GATACTGGCTCGTAAGAGC
* *
27476548 AATACTAGCTCGTAAGAGC
1 GATACTGGCTCGTAAGAGC
* *
27476567 GATATTGGCTCGTAAGATC
1 GATACTGGCTCGTAAGAGC
* *
27476586 GATATTGGCTTGTAAGAGC
1 GATACTGGCTCGTAAGAGC
* *
27476605 GATACTGGCTGGTGAGAGC
1 GATACTGGCTCGTAAGAGC
*
27476624 GATACTGGCTCGTGAGAGC
1 GATACTGGCTCGTAAGAGC
* **
27476643 GATACTGGCTCGTGAGAAT
1 GATACTGGCTCGTAAGAGC
**
27476662 GATACTGGCTCGTCGGAGC
1 GATACTGGCTCGTAAGAGC
* * * * * *
27476681 AATATTAGTTTGCAAGAGC
1 GATACTGGCTCGTAAGAGC
27476700 -AGTACTGGCTCGTAAGAGC
1 GA-TACTGGCTCGTAAGAGC
*
27476719 AATACTGGCTCGT
1 GATACTGGCTCGT
27476732 GCGAGTAATA
Statistics
Matches: 148, Mismatches: 34, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
18 1 0.01
19 146 0.99
20 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.25
Consensus pattern (19 bp):
GATACTGGCTCGTAAGAGC
Found at i:27483876 original size:38 final size:38
Alignment explanation
Indices: 27483770--27483908 Score: 138
Period size: 38 Copynumber: 3.7 Consensus size: 38
27483760 AAGGAATATA
* **
27483770 AATATTGGCTCG-AAGAGCAGTACTGGCTCGCAAGAGA-
1 AATATTGGCTCGTAAGAGCAATACTGGCTCGTGAGA-AC
* ** *
27483807 AATATTAGCTCGTAAGAGGGATACTAGCTCGTGAGAAC
1 AATATTGGCTCGTAAGAGCAATACTGGCTCGTGAGAAC
* *
27483845 AATATTGGCTCGTAATAGCAATACTGGCTCGTGAGATC
1 AATATTGGCTCGTAAGAGCAATACTGGCTCGTGAGAAC
* ** *
27483883 AATACTAACTCGTAAGAGAAATACTG
1 AATATTGGCTCGTAAGAGCAATACTG
27483909 TATTGGCTCG
Statistics
Matches: 82, Mismatches: 18, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
37 12 0.15
38 70 0.85
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (38 bp):
AATATTGGCTCGTAAGAGCAATACTGGCTCGTGAGAAC
Found at i:27483905 original size:19 final size:19
Alignment explanation
Indices: 27483777--27483907 Score: 86
Period size: 19 Copynumber: 6.9 Consensus size: 19
27483767 ATAAATATTG
* * *
27483777 GCTCG-AAGAGCAGTACTG
1 GCTCGTAAGAGAAATACTA
* *
27483795 GCTCGCAAGAGAAATATTA
1 GCTCGTAAGAGAAATACTA
**
27483814 GCTCGTAAGAGGGATACTA
1 GCTCGTAAGAGAAATACTA
* * *
27483833 GCTCGTGAGA-ACAATATTG
1 GCTCGTAAGAGA-AATACTA
* * *
27483852 GCTCGTAATAGCAATACTG
1 GCTCGTAAGAGAAATACTA
* **
27483871 GCTCGTGAGATCAATACTA
1 GCTCGTAAGAGAAATACTA
*
27483890 ACTCGTAAGAGAAATACT
1 GCTCGTAAGAGAAATACT
27483908 GTATTGGCTC
Statistics
Matches: 85, Mismatches: 25, Indels: 5
0.74 0.22 0.04
Matches are distributed among these distances:
18 5 0.06
19 80 0.94
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.23
Consensus pattern (19 bp):
GCTCGTAAGAGAAATACTA
Found at i:27486245 original size:16 final size:16
Alignment explanation
Indices: 27486224--27486255 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
27486214 AGTAATTTTT
*
27486224 ATGTTAAAGGACTAAA
1 ATGTTAAAGGAATAAA
27486240 ATGTTAAAGGAATAAA
1 ATGTTAAAGGAATAAA
27486256 TTTGTAAGGA
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:0.53, C:0.03, G:0.19, T:0.25
Consensus pattern (16 bp):
ATGTTAAAGGAATAAA
Found at i:27502728 original size:15 final size:15
Alignment explanation
Indices: 27502704--27502740 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
27502694 CCAGCAGAAG
*
27502704 GAGAAGGAAGAAAAA
1 GAGAAAGAAGAAAAA
27502719 GAGAAAGAAGAAAAA
1 GAGAAAGAAGAAAAA
27502734 GAAGAAA
1 G-AGAAA
27502741 AGAATGAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (15 bp):
GAGAAAGAAGAAAAA
Found at i:27502735 original size:21 final size:21
Alignment explanation
Indices: 27502711--27502757 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
27502701 AAGGAGAAGG
27502711 AAGAA-AAAGAGAAAGAAGA-AA
1 AAGAAGAAA-AGAAAGAA-ATAA
*
27502732 AAGAAGAAAAGAATGAAATAA
1 AAGAAGAAAAGAAAGAAATAA
27502753 AAGAA
1 AAGAA
27502758 CCTACTGGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 1 0.04
21 19 0.83
22 3 0.13
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.04
Consensus pattern (21 bp):
AAGAAGAAAAGAAAGAAATAA
Found at i:27503847 original size:24 final size:23
Alignment explanation
Indices: 27503813--27503860 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
27503803 TCAATCACTT
* *
27503813 GAAAAATAAAAAAAATGAGAAAAA
1 GAAAAAGAAAAAAAAGGA-AAAAA
*
27503837 GAAAAAGAAAATAAAGGAAAAAA
1 GAAAAAGAAAAAAAAGGAAAAAA
27503860 G
1 G
27503861 TTTTGCTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (23 bp):
GAAAAAGAAAAAAAAGGAAAAAA
Found at i:27505909 original size:3 final size:3
Alignment explanation
Indices: 27505901--27505942 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
27505891 GCTTCGTCTA
* * *
27505901 AAG AAG AAG AAA AAG AAG AAG AAA AAG AAA AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
27505943 GAGACTGAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:27505917 original size:12 final size:12
Alignment explanation
Indices: 27505900--27505942 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
27505890 AGCTTCGTCT
27505900 AAAGAAGAAGAA
1 AAAGAAGAAGAA
27505912 AAAGAAGAAGAA
1 AAAGAAGAAGAA
*
27505924 AAAGAAAAAGAA
1 AAAGAAGAAGAA
*
27505936 GAAGAAG
1 AAAGAAG
27505943 GAGACTGAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AAAGAAGAAGAA
Found at i:27505928 original size:18 final size:18
Alignment explanation
Indices: 27505901--27505941 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
27505891 GCTTCGTCTA
*
27505901 AAGAAGAAGAAAAAGAAG
1 AAGAAAAAGAAAAAGAAG
27505919 AAGAAAAAGAAAAAGAAG
1 AAGAAAAAGAAAAAGAAG
27505937 AAGAA
1 AAGAA
27505942 GGAGACTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (18 bp):
AAGAAAAAGAAAAAGAAG
Found at i:27507186 original size:27 final size:28
Alignment explanation
Indices: 27507148--27507206 Score: 102
Period size: 27 Copynumber: 2.1 Consensus size: 28
27507138 TTAGAAGATA
*
27507148 AACAATAATGAAGTTGATCACTATGT-C
1 AACAATAATGAAGCTGATCACTATGTCC
27507175 AACAATAATGAAGCTGATCACTATGTCC
1 AACAATAATGAAGCTGATCACTATGTCC
27507203 AACA
1 AACA
27507207 TGGAACAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 25 0.83
28 5 0.17
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (28 bp):
AACAATAATGAAGCTGATCACTATGTCC
Found at i:27518851 original size:52 final size:51
Alignment explanation
Indices: 27518760--27518870 Score: 134
Period size: 52 Copynumber: 2.2 Consensus size: 51
27518750 TTTCTTTTTT
** * *
27518760 TTAAAAAAAATCATTATTTTGCTTAAAAATTCAAATTTTTATTTCAAAATAG
1 TTAAAAAAAATCAAAACTTTGCTTAAAAATTCAAATTTTTATTT-AAAATAA
* *
27518812 TTAAAAAAAATCAAAACTTTG-TTAAAAATTTAAATTTTTTCTTTAAAATAA
1 TTAAAAAAAATCAAAACTTTGCTTAAAAATTCAAA-TTTTTATTTAAAATAA
*
27518863 CTAAAAAA
1 TTAAAAAA
27518871 CAGATTTTTA
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
51 25 0.49
52 26 0.51
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (51 bp):
TTAAAAAAAATCAAAACTTTGCTTAAAAATTCAAATTTTTATTTAAAATAA
Found at i:27518908 original size:293 final size:293
Alignment explanation
Indices: 27518321--27519303 Score: 1633
Period size: 285 Copynumber: 3.4 Consensus size: 293
27518311 TGATTAAACA
* * * *
27518321 AAAATCACTACTTTACTTAAAAATCCAAACGTTTATTTCGAAATAGTTAAAAAAATCAAAATTTT
1 AAAATCACTATTTTACCTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
27518386 GTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAAAAATCT
66 GTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACA-ATTTTTATTTTT---AAAAATCT
*
27518451 AAACTTTCTCTTTTTTTAAAGAAAATCATTATTTTGCTTAAAAATCCAAACTTTTATTTCGAAAT
127 AAACTTTCT-TTTTTTTAAAGAAAATCATTATTTTGCTTAAAAATTCAAACTTTTATTTCGAAAT
*
27518516 AGTTAGAAAAAATCAAAACTTTGTTAAAAAATTTAAATTTTTTCTTTAAAATAACTAAAAAACAG
191 AGTTAAAAAAAATCAAAACTTTGTT-AAAAATTTAAATTTTTTCTTTAAAATAACTAAAAAACAG
*
27518581 ATTTTTATTTTTAAAAATATAAACTTTATCTTTTTAAAG
255 ATTTTTATTTTTAAAAATATAAACTTTCTCTTTTTAAAG
*
27518620 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
1 AAAATCACTATTTTACCTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
27518685 GTTAAAAA-TTAAACTTTTTCTTTAAAATAACTAAAAAACATATTTTTATTTTTAAAAATCTAAA
66 GTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACA-ATTTTTATTTTTAAAAATCTAAA
* * *
27518749 CTTTCTTTTTTTTAAAAAAAATCATTATTTTGCTTAAAAATTCAAATTTTTATTTCAAAATAGTT
130 CTTTCTTTTTTTTAAAGAAAATCATTATTTTGCTTAAAAATTCAAACTTTTATTTCGAAATAGTT
27518814 AAAAAAAATCAAAACTTTGTTAAAAATTTAAATTTTTTCTTTAAAATAACTAAAAAACAGATTTT
195 AAAAAAAATCAAAACTTTGTTAAAAATTTAAATTTTTTCTTTAAAATAACTAAAAAACAGATTTT
27518879 TATTTTTAAAAATATAAACTTTCTCTTTTTAAAG
260 TATTTTTAAAAATATAAACTTTCTCTTTTTAAAG
*
27518913 AAAATCACTATTTTACCTAAAAATCCAAACTTTTATGTCGAAATAGTTAAAAAAATCAAAACTTT
1 AAAATCACTATTTTACCTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
* * *
27518978 GTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAATAAATTTTATTTTTAAAAATATAAA-
66 GTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAATTTTTATTTTTAAAAATCTAAAC
* * * *
27519042 ---C---TTTTTAAAGAAAATCACTGTTTTACCTAAAAATTCAAACTTTTATTTCGAAATAGTT-
131 TTTCTTTTTTTTAAAGAAAATCATTATTTTGCTTAAAAATTCAAACTTTTATTTCGAAATAGTTA
* * *
27519100 ACAAAAATCAAAACTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAATAGATTTTT
196 AAAAAAATCAAAACTTTGTTAAAAATTTAAATTTTTTCTTTAAAATAACTAAAAAACAGATTTTT
*
27519165 ATTTTTAAAAATATAAACTTTCTTTTTTTAAAG
261 ATTTTTAAAAATATAAACTTTCTCTTTTTAAAG
27519198 AAAATCACTATTTTACCTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
1 AAAATCACTATTTTACCTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
27519263 GTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACA
66 GTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACA
27519304 GATCAAAGCT
Statistics
Matches: 655, Mismatches: 28, Indels: 16
0.94 0.04 0.02
Matches are distributed among these distances:
285 198 0.30
286 50 0.08
289 1 0.00
293 169 0.26
294 106 0.16
295 17 0.03
298 44 0.07
299 70 0.11
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (293 bp):
AAAATCACTATTTTACCTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
GTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAATTTTTATTTTTAAAAATCTAAAC
TTTCTTTTTTTTAAAGAAAATCATTATTTTGCTTAAAAATTCAAACTTTTATTTCGAAATAGTTA
AAAAAAATCAAAACTTTGTTAAAAATTTAAATTTTTTCTTTAAAATAACTAAAAAACAGATTTTT
ATTTTTAAAAATATAAACTTTCTCTTTTTAAAG
Found at i:27519292 original size:50 final size:50
Alignment explanation
Indices: 27519069--27519301 Score: 119
Period size: 50 Copynumber: 4.7 Consensus size: 50
27519059 CTGTTTTACC
* ** * *
27519069 TAAAAATTCAAACTTTTAT-TTCGAAATAGTTACAAAAATCAAAACTTTGT
1 TAAAAATTTAAACTTTT-TCTTTAAAATAATTAAAAAAATCAAAACTTTGT
* *** *
27519119 TAAAAATTTAAACTTTTTCTTTAAAATAACT-AAAAAAT-AGATTTTTATTTT
1 TAAAAATTTAAACTTTTTCTTTAAAATAATTAAAAAAATCA-A-AACT-TTGT
* * ** * **
27519170 TAAAAATATAAAC--TTTCTTT----T-TTTAAAGAAAATCACTATTTTACC
1 TAAAAATTTAAACTTTTTCTTTAAAATAATTAAA-AAAATCAAAACTTT-GT
** ** *
27519215 TAAAAATCCAAACTTTTAT-TTCGAAATAGTTAAAAAAATCAAAACTTTGT
1 TAAAAATTTAAACTTTT-TCTTTAAAATAATTAAAAAAATCAAAACTTTGT
*
27519265 TAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAA
1 TAAAAATTTAAACTTTTTCTTTAAAATAATTAAAAAA
27519302 CAGATCAAAG
Statistics
Matches: 134, Mismatches: 32, Indels: 34
0.67 0.16 0.17
Matches are distributed among these distances:
44 3 0.02
45 17 0.13
46 5 0.04
47 5 0.04
48 2 0.01
49 16 0.12
50 54 0.40
51 27 0.20
52 5 0.04
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.39
Consensus pattern (50 bp):
TAAAAATTTAAACTTTTTCTTTAAAATAATTAAAAAAATCAAAACTTTGT
Found at i:27519317 original size:146 final size:146
Alignment explanation
Indices: 27518321--27519306 Score: 1574
Period size: 146 Copynumber: 6.7 Consensus size: 146
27518311 TGATTAAACA
* * *
27518321 AAAATCACTACTTTACTTAAAAATCCAAACGTTTATTTCGAAATAGTTAAAAAAATCAAAATTTT
1 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
*
27518386 GTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAAAAATCT
66 GTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTT---AAAAATAT
27518451 AAACTTTCTCTTTTTTTAAAG
128 AAAC-TT-TCTTTTTTTAAAG
* *
27518472 AAAATCATTATTTTGCTTAAAAATCCAAACTTTTATTTCGAAATAGTTAGAAAAAATCAAAACTT
1 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTA-AAAAAATCAAAACTT
*
27518537 TGTTAAAAAATTTAAATTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATATA
65 TGTT-AAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATATA
* *
27518602 AACTTTATCTTTTTAAAG
129 AACTTTCTTTTTTTAAAG
27518620 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
1 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
* *
27518685 GTTAAAAA-TTAAACTTTTTCTTTAAAATAACTAAAAAACATATTTTTATTTTTAAAAATCTAAA
66 GTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATATAAA
*
27518749 CTTTCTTTTTTTTAAAA
131 CTTTC-TTTTTTTAAAG
* * * * *
27518766 AAAATCATTATTTTGCTTAAAAATTCAAATTTTTATTTCAAAATAGTTAAAAAAAATCAAAACTT
1 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTT-AAAAAAATCAAAACTT
*
27518831 TGTTAAAAATTTAAATTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATATAA
65 TGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATATAA
*
27518896 ACTTTCTCTTTTTAAAG
130 ACTTTCTTTTTTTAAAG
* *
27518913 AAAATCACTATTTTACCTAAAAATCCAAACTTTTATGTCGAAATAGTTAAAAAAATCAAAACTTT
1 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
* *
27518978 GTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAATA-AATTTTATTTTTAAAAATATAAA
66 GTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATATAAA
27519042 ----C--TTTTTAAAG
131 CTTTCTTTTTTTAAAG
* * * *
27519052 AAAATCACTGTTTTACCTAAAAATTCAAACTTTTATTTCGAAATAGTTACAAAAATCAAAACTTT
1 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
*
27519117 GTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAATAGATTTTTATTTTTAAAAATATAAA
66 GTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATATAAA
27519182 CTTTCTTTTTTTAAAG
131 CTTTCTTTTTTTAAAG
*
27519198 AAAATCACTATTTTACCTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
1 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
27519263 GTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGAT
66 GTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGAT
27519307 CAAAGCTTTT
Statistics
Matches: 777, Mismatches: 46, Indels: 29
0.91 0.05 0.03
Matches are distributed among these distances:
139 111 0.14
140 22 0.03
141 1 0.00
144 1 0.00
145 79 0.10
146 227 0.29
147 94 0.12
148 116 0.15
149 2 0.00
150 11 0.01
151 45 0.06
152 18 0.02
153 50 0.06
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (146 bp):
AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
GTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATATAAA
CTTTCTTTTTTTAAAG
Found at i:27519777 original size:3 final size:3
Alignment explanation
Indices: 27519769--27519813 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
27519759 AAAAAATTAA
* * *
27519769 AAT AAT AAT AAT AAG AAT AAG AAT AAT AAT AAT GAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
27519814 TTGGGCCCAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:27519855 original size:11 final size:11
Alignment explanation
Indices: 27519839--27519863 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
27519829 TCCAATAAGG
27519839 AAAGAAAAATA
1 AAAGAAAAATA
27519850 AAAGAAAAATA
1 AAAGAAAAATA
27519861 AAA
1 AAA
27519864 ACCTCTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAGAAAAATA
Found at i:27520233 original size:42 final size:42
Alignment explanation
Indices: 27520186--27520624 Score: 542
Period size: 42 Copynumber: 10.5 Consensus size: 42
27520176 TCTACGCCTA
* * * * *
27520186 GGCCTCTAAATGCAATAAAAAGTAAGTGGGCATTCACACTTG
1 GGCCTCTAAATGCAATGAAAAGTAAATGGGCCTCCACACCTG
* * *
27520228 GGCCTCTAAATACAACGAAAAGTAAATGGACCTCCACACCTG
1 GGCCTCTAAATGCAATGAAAAGTAAATGGGCCTCCACACCTG
* * *
27520270 GGCCTCTGAATGCAATGAAAAGTAAATGAGCCTCCACACTTG
1 GGCCTCTAAATGCAATGAAAAGTAAATGGGCCTCCACACCTG
* * * * *
27520312 GGCCTCTAAATGCAAAGAAAAGTAAAAGGACCTCTACACTTG
1 GGCCTCTAAATGCAATGAAAAGTAAATGGGCCTCCACACCTG
27520354 GGCCTCTAAATGCAATGAAAAGTAAATGGGCCTCCACACCTG
1 GGCCTCTAAATGCAATGAAAAGTAAATGGGCCTCCACACCTG
* *
27520396 GGCCTCTAAATGCAATGAAAAGTAAATGGGCCTCCACTCCTA
1 GGCCTCTAAATGCAATGAAAAGTAAATGGGCCTCCACACCTG
* * * *
27520438 GACCTCTGAATGCGAA-GAAAAGTAAATGGACCTCCACACCTA
1 GGCCTCTAAATGC-AATGAAAAGTAAATGGGCCTCCACACCTG
* *
27520480 GGCCTC-ATAATGCAATGAAAAGTAAATGGGCCCCCACACTTG
1 GGCCTCTA-AATGCAATGAAAAGTAAATGGGCCTCCACACCTG
* * * * *
27520522 GGCCTTTGAATGCGATGAAAAGTAAATGGACCTCCACACTTG
1 GGCCTCTAAATGCAATGAAAAGTAAATGGGCCTCCACACCTG
**
27520564 GGCCTCTAAATGTGATGAAAAGTAAATGGG-CTACCACACCTG
1 GGCCTCTAAATGCAATGAAAAGTAAATGGGCCT-CCACACCTG
*
27520606 GGCTTCTAAATGCAATGAA
1 GGCCTCTAAATGCAATGAA
27520625 TGCTTTCCTT
Statistics
Matches: 342, Mismatches: 50, Indels: 10
0.85 0.12 0.02
Matches are distributed among these distances:
41 4 0.01
42 336 0.98
43 2 0.01
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.21
Consensus pattern (42 bp):
GGCCTCTAAATGCAATGAAAAGTAAATGGGCCTCCACACCTG
Found at i:27521046 original size:11 final size:11
Alignment explanation
Indices: 27521026--27521077 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
27521016 TTTCTCTCTC
*
27521026 TTTCTATTTTT
1 TTTCTTTTTTT
27521037 TTTCTTTTTTT
1 TTTCTTTTTTT
27521048 TTTCTTCTTCTTT
1 TTTCTT-TT-TTT
*
27521061 TTT-TGTATTTT
1 TTTCT-TTTTTT
27521072 TTTCTT
1 TTTCTT
27521078 GATTTAAACA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
11 23 0.66
12 5 0.14
13 7 0.20
ACGTcount: A:0.04, C:0.12, G:0.02, T:0.83
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:27521055 original size:14 final size:15
Alignment explanation
Indices: 27521027--27521064 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
27521017 TTCTCTCTCT
*
27521027 TTCTATTTTTT-TTC
1 TTCTTTTTTTTCTTC
27521041 TT-TTTTTTTTCTTC
1 TTCTTTTTTTTCTTC
27521055 TTCTTTTTTT
1 TTCTTTTTTT
27521065 GTATTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 7 0.33
14 7 0.33
15 7 0.33
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (15 bp):
TTCTTTTTTTTCTTC
Found at i:27529374 original size:4 final size:4
Alignment explanation
Indices: 27529367--27529401 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
27529357 ACAAATGAGC
*
27529367 GAAT GAAT GAAT GAAT GAAT GAGT GAAT GAAT GAA
1 GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAA
27529402 ATTGAGGCAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.49, C:0.00, G:0.29, T:0.23
Consensus pattern (4 bp):
GAAT
Found at i:27534184 original size:51 final size:51
Alignment explanation
Indices: 27534129--27534343 Score: 115
Period size: 50 Copynumber: 4.3 Consensus size: 51
27534119 TTTTATTTCG
27534129 AAATAGTTAAAAAAAATCAAAAATTTATTAAAAATTTAAATTTTTTCTTTA
1 AAATAGTTAAAAAAAATCAAAAATTTATTAAAAATTTAAATTTTTTCTTTA
* * **** * * *
27534180 AAATAACTAAAAAACAAAT-TTTTATTTTTTAAAAAATCTAAACTTTTTCTATT-
1 AAAT-AGTTAAAAA-AAATCAAAAATTTATT-AAAAATTTAAATTTTTTCT-TTA
* ** * * **
27534233 ---T--TTAAAGAAAATCACTATTTTGCTTAAAAATTTAAATTTTTAT-TTCG
1 AAATAGTTAAAAAAAATCAAAAATTT-ATTAAAAATTTAAATTTTT-TCTTTA
* * * *
27534280 AAATAGTT-TAAAAAATCAAAACTTTGTTAAAAATTTAAATCTTTTCTTTA
1 AAATAGTTAAAAAAAATCAAAAATTTATTAAAAATTTAAATTTTTTCTTTA
**
27534330 AAATAACTAAAAAA
1 AAATAGTTAAAAAA
27534344 CAGATTTTTA
Statistics
Matches: 118, Mismatches: 31, Indels: 30
0.66 0.17 0.17
Matches are distributed among these distances:
46 5 0.04
47 24 0.20
48 3 0.03
49 1 0.01
50 27 0.23
51 20 0.17
52 15 0.13
53 21 0.18
54 2 0.02
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.41
Consensus pattern (51 bp):
AAATAGTTAAAAAAAATCAAAAATTTATTAAAAATTTAAATTTTTTCTTTA
Found at i:27534687 original size:147 final size:147
Alignment explanation
Indices: 27534089--27535174 Score: 1537
Period size: 147 Copynumber: 7.4 Consensus size: 147
27534079 TGATTAAACA
* * *
27534089 AAAATCACTAGTTTACTTAAAAA-TCAAAACTTTTATTTCGAAATAGTTAAAAAAAATCAAAAAT
1 AAAATCACTATTTTGCTTAAAAATTC-AAACTTTTATTTCGAAATAGTT-AAAAAAATCAAAACT
* * * *
27534153 TTATTAAAAATTTAAATTTTTTCTTTAAAATAACTAAAAAACAAATTTTTATTTTTTAAAAAATC
64 TTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTA-TTTTT-AAAAATA
*
27534218 TAAACTTTTTCTATTTTTAAAG
127 TAAACTTTCTCT-TTTTTAAAG
* * *
27534240 AAAATCACTATTTTGCTTAAAAATTTAAATTTTTATTTCGAAATAGTTTAAAAAATCAAAACTTT
1 AAAATCACTATTTTGCTTAAAAATTCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
27534305 GTTAAAAATTTAAA-TCTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATATAA
66 GTTAAAAATTTAAACT-TTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATATAA
27534369 AC-TT-TCTTTTTTAAA-
130 ACTTTCTCTTTTTTAAAG
* * * *
27534384 AAAA-CCCTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTAAAAAAAAATCAAAACTT
1 AAAATCACTATTTTGCTTAAAAATTCAAACTTTTATTTCGAAATAGT-TAAAAAAATCAAAACTT
* * * *
27534448 TGTTAAAAATTTAAAATTTTTCTTTAAAGTAATTAAAAAACAGATTTTTATTTTTAAAAATCTAA
65 TGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATATAA
27534513 ACTTTC-CTTTTTTAAAG
130 ACTTTCTCTTTTTTAAAG
* * *
27534530 AAAATCACTATTTTGCTTAAAAATTCAAATTTTTATTTTGAAATAGTTTAAAAAATCAAAACTTT
1 AAAATCACTATTTTGCTTAAAAATTCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
* *
27534595 GTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAATAAATTTTTATTTTTAAAAATATAAA
66 GTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATATAAA
27534660 CTTTCTCTTTTTTAAAG
131 CTTTCTCTTTTTTAAAG
* * * *
27534677 AAAATAACTATTTTGCCTAAAAATCCAAACTTTTATTTCGAAATAATTAAAAAAAATCAAAACTT
1 AAAATCACTATTTTGCTTAAAAATTCAAACTTTTATTTCGAAATAGTT-AAAAAAATCAAAACTT
*
27534742 TGTTAAAAATTTAAACTTTTTCTTTAAAATAACT-AAAAACAAATTTTTATTTTTAAAAATATAA
65 TGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATATAA
*
27534806 ACTTTCTCTTTTTTAAAT
130 ACTTTCTCTTTTTTAAAG
* * * *
27534824 AAAATAACTATTTTACCTAAAAA-TCAAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAATTT
1 AAAATCACTATTTTGCTTAAAAATTC-AAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTT
* *
27534888 TGTTAAAAATTTAAAATTTTTCTTTAAAATAACTAAAAAATAGATTTTTATTTTTAAAAATATAA
65 TGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATATAA
27534953 ACTTTCTC-TTTTTAAAG
130 ACTTTCTCTTTTTTAAAG
* ** * * * * * * *
27534970 AAAATCATTATTTACCCTAAAAATCCAAAATTTTATTTCAAAATAATT-AAAAAATAAAAACTTA
1 AAAATCACTATTTTGCTTAAAAATTCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
*
27535034 GTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATCTAAA
66 GTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATATAAA
27535099 CTTTCTCTTTTTTAAAG
131 CTTTCTCTTTTTTAAAG
* *
27535116 AAAATCACTATTTTGCTTTAAAAAAATCAAAGCTTTTATTTCGAAATTGTTTAAAAAAA
1 AAAATCACTATTTTGC-TT-AAAAATTCAAA-CTTTTATTTCGAAATAG-TTAAAAAAA
27535175 AACAAAACAT
Statistics
Matches: 843, Mismatches: 73, Indels: 38
0.88 0.08 0.04
Matches are distributed among these distances:
143 37 0.04
144 81 0.10
145 103 0.12
146 204 0.24
147 219 0.26
148 69 0.08
149 19 0.02
150 62 0.07
151 48 0.06
152 1 0.00
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.41
Consensus pattern (147 bp):
AAAATCACTATTTTGCTTAAAAATTCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
GTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATATAAA
CTTTCTCTTTTTTAAAG
Found at i:27534947 original size:51 final size:50
Alignment explanation
Indices: 27534596--27535108 Score: 164
Period size: 51 Copynumber: 10.5 Consensus size: 50
27534586 CAAAACTTTG
* *
27534596 TTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAATAAATTTTTATTT
1 TTAAAAATCTAAACTTTTTCTTTAAAATAACTAAAAAATAGATTTTTA-TT
* * ** * **
27534647 TTAAAAATATAAACTTTCTCTTT--TTTAA--AGAAAATA-ACTATTTT-GC
1 TTAAAAATCTAAACTTTTTCTTTAAAATAACTAAAAAATAGA-T-TTTTATT
* * ** * *** *
27534693 CTAAAAATCCAAACTTTTAT-TTCGAAATAATTAAAAAAAATCA-AAACTT-TG
1 TTAAAAATCTAAACTTTT-TCTTTAAAATAACT--AAAAAAT-AGATTTTTATT
*
27534744 TTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAACA-A-ATTTTTATTT
1 TTAAAAATCTAAACTTTTTCTTTAAAATAACTAAAAA-ATAGATTTTTA-TT
* * ** * *
27534794 TTAAAAATATAAACTTTCTCTTT--TTTAA--ATAAAATA-ACTATTTTA-C
1 TTAAAAATCTAAACTTTTTCTTTAAAATAACTAAAAAATAGA-T-TTTTATT
* * ** ** ** *
27534840 CTAAAAATCAAAACTTTTAT-TTCGAAATAGTTAAAAAAATCA-AAATTT-TG
1 TTAAAAATCTAAACTTTT-TCTTTAAAATAACT-AAAAAAT-AGATTTTTATT
* *
27534890 TTAAAAATTTAAAATTTTTCTTTAAAATAACTAAAAAATAGATTTTTATTT
1 TTAAAAATCTAAACTTTTTCTTTAAAATAACTAAAAAATAGATTTTTA-TT
* * * * * **
27534941 TTAAAAATATAAACTTTCTCTTT---TTAA--AGAAAAT-CATTATTTACC
1 TTAAAAATCTAAACTTTTTCTTTAAAATAACTAAAAAATAGATT-TTTATT
* * * * * * *** *
27534986 CTAAAAATCCAAAATTTTAT-TTCAAAATAATTAAAAAATAAAAACTTA-G
1 TTAAAAATCTAAACTTTT-TCTTTAAAATAACTAAAAAATAGATTTTTATT
* *
27535035 TTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTT
1 TTAAAAATCTAAACTTTTTCTTTAAAATAACTAAAAAATAGATTTTTA-TT
*
27535086 TTAAAAATCTAAACTTTCTCTTT
1 TTAAAAATCTAAACTTTTTCTTT
27535109 TTTAAAGAAA
Statistics
Matches: 328, Mismatches: 94, Indels: 80
0.65 0.19 0.16
Matches are distributed among these distances:
45 19 0.06
46 50 0.15
47 11 0.03
48 29 0.09
49 55 0.17
50 58 0.18
51 96 0.29
52 8 0.02
53 2 0.01
ACGTcount: A:0.47, C:0.10, G:0.02, T:0.42
Consensus pattern (50 bp):
TTAAAAATCTAAACTTTTTCTTTAAAATAACTAAAAAATAGATTTTTATT
Found at i:27535624 original size:12 final size:12
Alignment explanation
Indices: 27535605--27535635 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
27535595 TTCAAAAATT
27535605 AAAATAAGAATA
1 AAAATAAGAATA
*
27535617 AGAATAAGAATA
1 AAAATAAGAATA
27535629 AAAATAA
1 AAAATAA
27535636 TAATGATGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.16
Consensus pattern (12 bp):
AAAATAAGAATA
Found at i:27535684 original size:11 final size:11
Alignment explanation
Indices: 27535668--27535693 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
27535658 GGCCCATACA
27535668 AAAAGAAAAAT
1 AAAAGAAAAAT
27535679 AAAAGAAAAAT
1 AAAAGAAAAAT
27535690 AAAA
1 AAAA
27535694 ACCTCTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAAGAAAAAT
Found at i:27542344 original size:56 final size:55
Alignment explanation
Indices: 27542244--27542467 Score: 290
Period size: 56 Copynumber: 4.0 Consensus size: 55
27542234 ATGGTCATGA
* * *
27542244 AAATCGAAGACCATATAGTGTAAGACCTAGTCATGGTGACTATGGCATCATATGG
1 AAATTGAATACCATATAGTGTAAGACCTAGTCATGGTGGCTATGGCATCATATGG
* *
27542299 ACAATTGAATACCATATAGTGTAAAACCTAGTCATGGTGGGTATGGCATCATATGAG
1 A-AATTGAATACCATATAGTGTAAGACCTAGTCATGGTGGCTATGGCATCATATG-G
* * * *
27542356 GAATTGAATATCATATAGTGTAAGACCTACTCATGGTAGCTATGGCATCATATAGGG
1 AAATTGAATACCATATAGTGTAAGACCTAGTCATGGTGGCTATGGCATCATAT--GG
* * *
27542413 AAA-TGAAGACCACATAGTGTAAGACCTAGTC-TGGTGGCTATGGCATCATGTGG
1 AAATTGAATACCATATAGTGTAAGACCTAGTCATGGTGGCTATGGCATCATATGG
27542466 AA
1 AA
27542468 GAAGATGAAA
Statistics
Matches: 147, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
53 4 0.03
55 19 0.13
56 119 0.81
57 4 0.03
58 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (55 bp):
AAATTGAATACCATATAGTGTAAGACCTAGTCATGGTGGCTATGGCATCATATGG
Found at i:27542621 original size:29 final size:29
Alignment explanation
Indices: 27542576--27542696 Score: 163
Period size: 29 Copynumber: 4.2 Consensus size: 29
27542566 TAAAAAAGGA
* *
27542576 AGCCTTTGTGGCAGATTCCATTATATGTG
1 AGCCTTTGTGGCTGATTCTATTATATGTG
27542605 AG-CTTTCGTGGCTGATTCTATTATATGTG
1 AGCCTTT-GTGGCTGATTCTATTATATGTG
* * *
27542634 AGCCTTTTTGGTTGATTCTATTATATGTT
1 AGCCTTTGTGGCTGATTCTATTATATGTG
* *
27542663 AGCCTTTGTGGTTGATTCTGTTATATGTG
1 AGCCTTTGTGGCTGATTCTATTATATGTG
27542692 AGCCT
1 AGCCT
27542697 CTATGGCTAT
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
28 4 0.05
29 74 0.90
30 4 0.05
ACGTcount: A:0.17, C:0.14, G:0.23, T:0.45
Consensus pattern (29 bp):
AGCCTTTGTGGCTGATTCTATTATATGTG
Found at i:27543026 original size:18 final size:15
Alignment explanation
Indices: 27542986--27543029 Score: 79
Period size: 15 Copynumber: 2.9 Consensus size: 15
27542976 TTATGTCTCA
27542986 AGTAATGATGATGCT
1 AGTAATGATGATGCT
27543001 AGTAATGATGATGCT
1 AGTAATGATGATGCT
*
27543016 AGTAAGGATGATGC
1 AGTAATGATGATGC
27543030 CAGGGATACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.34, C:0.07, G:0.30, T:0.30
Consensus pattern (15 bp):
AGTAATGATGATGCT
Found at i:27558708 original size:158 final size:158
Alignment explanation
Indices: 27558414--27558891 Score: 595
Period size: 158 Copynumber: 3.0 Consensus size: 158
27558404 CGATTTCGGG
* * * **
27558414 ATTACAGGTTATATAGGTGCTGGTCTTAGATGTCCTACAT-ATGGCTGAGATTCAAAAAACATTA
1 ATTACAGGTTATATGGGTGCTGGTCTTAGATGTCCTAC-TGATGGCTGAGATCCGAAAATTATTA
* * *
27558478 CGGATTCTCCACAGCTTGTGTGAGAAGCATCGTGTAGCCCAACATCTCGACCCACAGCTCGTGTG
65 CGGATTCTCCACAGCTTATGTGAGAAACATCGTGTAGCCCAACATCTCGACCCACAACTCGTGTG
* *
27558543 AGC-AGGCCCATTTCACAGCTCGTCTAAGC
130 A-CTAGGCCCATTTCACAGCTCGTATGAGC
* * * * * *
27558572 ATTACAGGTTATATGGGTGCTAGTCATAGATGTCCTACTGATGGTTGAGATCCGACAATTATAAT
1 ATTACAGGTTATATGGGTGCTGGTCTTAGATGTCCTACTGATGGCTGAGATCCGAAAATTATTAC
* * *
27558637 GGATTCTCCACAACTTTTGTGAGAAACATCGTGTAGCCCAACATCTCGACCCATAACTCGTGTGA
66 GGATTCTCCACAGCTTATGTGAGAAACATCGTGTAGCCCAACATCTCGACCCACAACTCGTGTGA
* *
27558702 CTAGGCCCATTTCACAGCTCGTGTGAGA
131 CTAGGCCCATTTCACAGCTCGTATGAGC
* * * * **
27558730 ATTACAAGTTATATGGGTGCTGGTCTTAAATGTCTTACCGATGGCTGAGATCCGGTAATTATTAC
1 ATTACAGGTTATATGGGTGCTGGTCTTAGATGTCCTACTGATGGCTGAGATCCGAAAATTATTAC
* * * * * * *
27558795 GGATTCTTCAGAGCTCATGTGAGCAACAT--TATAGCCCAACATCTCAACTCACAACTCGTGTGA
66 GGATTCTCCACAGCTTATGTGAGAAACATCGTGTAGCCCAACATCTCGACCCACAACTCGTGTGA
*
27558858 GTAGGCCCATTTCACAGCTCGTATGAGC
131 CTAGGCCCATTTCACAGCTCGTATGAGC
27558886 ATTACA
1 ATTACA
27558892 TGATATGGAA
Statistics
Matches: 275, Mismatches: 43, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
156 61 0.22
157 2 0.01
158 212 0.77
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.28
Consensus pattern (158 bp):
ATTACAGGTTATATGGGTGCTGGTCTTAGATGTCCTACTGATGGCTGAGATCCGAAAATTATTAC
GGATTCTCCACAGCTTATGTGAGAAACATCGTGTAGCCCAACATCTCGACCCACAACTCGTGTGA
CTAGGCCCATTTCACAGCTCGTATGAGC
Found at i:27563259 original size:41 final size:41
Alignment explanation
Indices: 27563214--27563407 Score: 307
Period size: 41 Copynumber: 4.7 Consensus size: 41
27563204 TTAATCGTAT
* * *
27563214 TCTCATTCTCAACTCGAGATATGAGTCTTCCTTAATCAAAA
1 TCTCATTCTCATCTCGAGACATGAGTCTTCCTTATTCAAAA
*
27563255 TCTCATTCTCATTTCGAGACATGAGTCTTCCTTATTCAAAA
1 TCTCATTCTCATCTCGAGACATGAGTCTTCCTTATTCAAAA
*
27563296 TCTCATTCTCATCTCGAGACATGAGTCTTTCTTATTCAAAA
1 TCTCATTCTCATCTCGAGACATGAGTCTTCCTTATTCAAAA
* * *
27563337 TCTTATTCTTATCCCGAGACATGAGTCTTCCTTATTCAAAA
1 TCTCATTCTCATCTCGAGACATGAGTCTTCCTTATTCAAAA
*
27563378 TCTCATTCTCATCTCAAGACATGAGTCTTC
1 TCTCATTCTCATCTCGAGACATGAGTCTTC
27563408 TATTTATACA
Statistics
Matches: 139, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 139 1.00
ACGTcount: A:0.27, C:0.25, G:0.10, T:0.38
Consensus pattern (41 bp):
TCTCATTCTCATCTCGAGACATGAGTCTTCCTTATTCAAAA
Found at i:27563305 original size:82 final size:82
Alignment explanation
Indices: 27563214--27563453 Score: 313
Period size: 82 Copynumber: 2.9 Consensus size: 82
27563204 TTAATCGTAT
* * **
27563214 TCTCATTCTCAACTCGAGATATGAGTCTTCCTTAATCAAAATCTCATTCTCATTTCGAGACATGA
1 TCTCATTCTCATCTCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATCCCGAGACATGA
27563279 GTCTTCCTTATTCAAAA
66 GTCTTCCTTATTCAAAA
* * * *
27563296 TCTCATTCTCATCTCGAGACATGAGTCTTTCTTATTCAAAATCTTATTCTTATCCCGAGACATGA
1 TCTCATTCTCATCTCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATCCCGAGACATGA
27563361 GTCTTCCTTATTCAAAA
66 GTCTTCCTTATTCAAAA
* * * **
27563378 TCTCATTCTCATCTCAAGACATGAGTCTTCTATTTATACAATTTCTCAAGTTC-CA-CCCGAGAC
1 TCTCATTCTCATCTCGAGACATGAGTCTTC-CTTAAT-CAAAATCTC-A-TTCTCATCCCGAGAC
27563441 ATGAGTCTTCCTT
62 ATGAGTCTTCCTT
27563454 TTTATACACC
Statistics
Matches: 137, Mismatches: 17, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
82 102 0.74
83 3 0.02
84 27 0.20
85 2 0.01
86 3 0.02
ACGTcount: A:0.27, C:0.25, G:0.10, T:0.38
Consensus pattern (82 bp):
TCTCATTCTCATCTCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATCCCGAGACATGA
GTCTTCCTTATTCAAAA
Found at i:27564279 original size:20 final size:21
Alignment explanation
Indices: 27564239--27564280 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
27564229 TTTAGACTTT
*
27564239 CATTATTAAGCTTTAATTAAA
1 CATTATTAACCTTTAATTAAA
*
27564260 CATTTTTAACCTTT-ATTAAA
1 CATTATTAACCTTTAATTAAA
27564280 C
1 C
27564281 CTATTTATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.38, C:0.14, G:0.02, T:0.45
Consensus pattern (21 bp):
CATTATTAACCTTTAATTAAA
Found at i:27564287 original size:20 final size:21
Alignment explanation
Indices: 27564244--27564287 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
27564234 ACTTTCATTA
* *
27564244 TTAAGCTTTAATTAAACATTT
1 TTAACCTTTAATTAAACATAT
*
27564265 TTAACCTTT-ATTAAACCTAT
1 TTAACCTTTAATTAAACATAT
27564285 TTA
1 TTA
27564288 TAATCAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.36, C:0.14, G:0.02, T:0.48
Consensus pattern (21 bp):
TTAACCTTTAATTAAACATAT
Found at i:27567147 original size:27 final size:27
Alignment explanation
Indices: 27567117--27567181 Score: 112
Period size: 27 Copynumber: 2.4 Consensus size: 27
27567107 TTACCACCAT
*
27567117 TGCTGCCACAAGATGGAGTTCCTCCAG
1 TGCTGCCACAAGATGAAGTTCCTCCAG
*
27567144 TGCTGTCACAAGATGAAGTTCCTCCAG
1 TGCTGCCACAAGATGAAGTTCCTCCAG
27567171 TGCTGCCACAA
1 TGCTGCCACAA
27567182 ATTATTAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (27 bp):
TGCTGCCACAAGATGAAGTTCCTCCAG
Found at i:27572614 original size:20 final size:21
Alignment explanation
Indices: 27572580--27572618 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
27572570 GTATTTTCTA
*
27572580 TTTACTTTTATTTGTTTCACT
1 TTTACTTTTAGTTGTTTCACT
27572601 TTTACTTTT-GTTGTTTCA
1 TTTACTTTTAGTTGTTTCA
27572619 AATTTCTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.13, C:0.13, G:0.08, T:0.67
Consensus pattern (21 bp):
TTTACTTTTAGTTGTTTCACT
Found at i:27575547 original size:6 final size:6
Alignment explanation
Indices: 27575536--27575582 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
27575526 TCAGTCATTT
**
27575536 GAAAAA GAAAAA TGAGAAAA -AGGAA GAAAAA GAAAAA GAAAAA GAAA
1 GAAAAA GAAAAA -GA-AAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAA
27575583 GAAATTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
5 2 0.06
6 26 0.76
7 2 0.06
8 4 0.12
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (6 bp):
GAAAAA
Found at i:27575569 original size:16 final size:16
Alignment explanation
Indices: 27575536--27575586 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
27575526 TCAGTCATTT
27575536 GAAAAAGAAAAATG--A
1 GAAAAAGAAAAA-GAAA
*
27575551 GAAAAAGGAAGAA-AAA
1 GAAAAA-GAAAAAGAAA
27575567 GAAAAAGAAAAAGAAA
1 GAAAAAGAAAAAGAAA
27575583 GAAA
1 GAAA
27575587 TTTTTTATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
15 11 0.37
16 19 0.63
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (16 bp):
GAAAAAGAAAAAGAAA
Found at i:27582830 original size:158 final size:158
Alignment explanation
Indices: 27582542--27582858 Score: 510
Period size: 158 Copynumber: 2.0 Consensus size: 158
27582532 CGATTTTGGG
* *
27582542 ATTACAGGTTATATGGGTGCTGGTCTTAGATGTCCTACCGATGGCTGAGATCTGACAATTATTGC
1 ATTACAGGTTATATGGGTGCTGGTCTTAGATGTCCTACCGATAGCTGAGATCCGACAATTATTGC
* * *
27582607 GATTTCTCCATAACTCGTGTGAGAAGCATCGTGTAGCCCAACATCTCGACCCACATCTCGTGTGA
66 GATTTCTCCACAACTCGTGTGAGAAGCATCATGTAGCCCAACATCTCGACCCACAGCTCGTGTGA
* *
27582672 GCAGGCTCATTTCACAACTCATGTGAGC
131 GCAGGCCCATTTAACAACTCATGTGAGC
27582700 ATTACAGGTTATATGGGTGCTGGTCTTAGATGTCCTACCGATAGCTGAGATCCGACAATTATTGC
1 ATTACAGGTTATATGGGTGCTGGTCTTAGATGTCCTACCGATAGCTGAGATCCGACAATTATTGC
* * *
27582765 GGA-TTCTCCACAGCTCGTGTGAGCAGCATCATGTAGCCCAACATCTTGACCCACAGCTCGTGTG
66 -GATTTCTCCACAACTCGTGTGAGAAGCATCATGTAGCCCAACATCTCGACCCACAGCTCGTGTG
* *
27582829 AGCAGGCCCATTTAACAGCTTATGTGAGC
130 AGCAGGCCCATTTAACAACTCATGTGAGC
27582858 A
1 A
27582859 GGCGCATTTC
Statistics
Matches: 146, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
158 144 0.99
159 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.28
Consensus pattern (158 bp):
ATTACAGGTTATATGGGTGCTGGTCTTAGATGTCCTACCGATAGCTGAGATCCGACAATTATTGC
GATTTCTCCACAACTCGTGTGAGAAGCATCATGTAGCCCAACATCTCGACCCACAGCTCGTGTGA
GCAGGCCCATTTAACAACTCATGTGAGC
Found at i:27582854 original size:26 final size:26
Alignment explanation
Indices: 27582817--27582887 Score: 97
Period size: 26 Copynumber: 2.7 Consensus size: 26
27582807 ATCTTGACCC
*
27582817 ACAGCTCGTGTGAGCAGGCCCATTTA
1 ACAGCTCATGTGAGCAGGCCCATTTA
* * *
27582843 ACAGCTTATGTGAGCAGGCGCATTTC
1 ACAGCTCATGTGAGCAGGCCCATTTA
*
27582869 ACAGCTCGTGTGAGCAGGC
1 ACAGCTCATGTGAGCAGGC
27582888 ATGTTATATT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.23, C:0.25, G:0.30, T:0.23
Consensus pattern (26 bp):
ACAGCTCATGTGAGCAGGCCCATTTA
Found at i:27583040 original size:183 final size:184
Alignment explanation
Indices: 27582663--27583041 Score: 519
Period size: 183 Copynumber: 2.1 Consensus size: 184
27582653 CGACCCACAT
* *
27582663 CTCGTGTGAGCAGGCTCATTTCACAACTCATGTGAGCATTACAGGTTATATGGGTGCTGGTCTTA
1 CTCGTGTGAGCAGGCGCATTTCACAACTCATGTGAGCATGACAGGTTATATGGGTGCTGGTCTTA
* * *
27582728 GATGTCCTACCGATAGCTGAGATCCGACAATTATTGCGGATTCTCCACAGCTCGTGTGAGCAGCA
66 GATGTCCTACCAATAGCTGAGATCCGACAATTATTACGGATTCTCCACAGCTCATGTGAGCAGCA
* *
27582793 TCATGTAGCCCAACATCTTGACCCACAGCTCGTGTGAGCAGGCCCATTTAACAG
131 TCATGTAGCCCAACATCTCGACCCACAGCTCGTATGAGCAGGCCCATTTAACAG
** * * * * * *
27582847 CTTATGTGAGCAGGCGCATTTCACAGCTCGTGTGAGCA-GGCATGTTATATTGGTGTTGGT-TTG
1 CTCGTGTGAGCAGGCGCATTTCACAACTCATGTGAGCATGACAGGTTATATGGGTGCTGGTCTT-
* * * ** *
27582910 AGATGTTCTACCAATGGTTGAGATTTGGCAATTATTACGGATTCTCCACAGCTCATGTGAGCAGC
65 AGATGTCCTACCAATAGCTGAGATCCGACAATTATTACGGATTCTCCACAGCTCATGTGAGCAGC
* * *
27582975 ATCGTGTAGCCCAACATCTCGACCCACAGCTCGTATGAGCAGGCCCATTTCATAG
130 ATCATGTAGCCCAACATCTCGACCCACAGCTCGTATGAGCAGGCCCATTTAACAG
27583030 CTCGTGTGAGCA
1 CTCGTGTGAGCA
27583042 TTACATGATA
Statistics
Matches: 168, Mismatches: 26, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
182 2 0.01
183 133 0.79
184 33 0.20
ACGTcount: A:0.23, C:0.24, G:0.25, T:0.28
Consensus pattern (184 bp):
CTCGTGTGAGCAGGCGCATTTCACAACTCATGTGAGCATGACAGGTTATATGGGTGCTGGTCTTA
GATGTCCTACCAATAGCTGAGATCCGACAATTATTACGGATTCTCCACAGCTCATGTGAGCAGCA
TCATGTAGCCCAACATCTCGACCCACAGCTCGTATGAGCAGGCCCATTTAACAG
Found at i:27585563 original size:34 final size:34
Alignment explanation
Indices: 27585520--27585586 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
27585510 AACTTCCTGT
27585520 GAAAAAAGTGAGCAAAGAATATGGCTTTAGTAAG
1 GAAAAAAGTGAGCAAAGAATATGGCTTTAGTAAG
*
27585554 GAAAAAAGTGAGCAAAGAATATGGTTTTAGTAA
1 GAAAAAAGTGAGCAAAGAATATGGCTTTAGTAA
27585587 CCGCCCATGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.48, C:0.04, G:0.25, T:0.22
Consensus pattern (34 bp):
GAAAAAAGTGAGCAAAGAATATGGCTTTAGTAAG
Found at i:27588117 original size:205 final size:205
Alignment explanation
Indices: 27587760--27588160 Score: 642
Period size: 205 Copynumber: 2.0 Consensus size: 205
27587750 TATATCTTAG
* *
27587760 AATGGAGATGTTATCAAATTTGTTGTTCAATTTGCTAATGCTAGCTCATCAAATAATACATTGCA
1 AATGGAGATGTAATCAAATTTGTTGTTAAATTTGCTAATGCTAGCTCATCAAATAATACATTGCA
* * *
27587825 ATAATAATATGAGTTACAAATCAAATATCATCTCTACATCATCCAAACCGTTACACTATAGAGAG
66 ATAATAATACGAGTTACAAATCAAATATCATCTCTACATCATCCAAACCATTAAACTATAGAGAG
* *
27587890 GACATTTCATTCCTAACCTATGAAGCACGAACACGCCGGAAATCCCCTCGTACTGGTGTCAACAC
131 GACATTTCATTCCTAACCTATGAAGCACGAACACGCCGCAAATCCCCTCGTACCGGTGTCAACAC
27587955 GTTGTCCGAC
196 GTTGTCCGAC
* ** *
27587965 AATGGAGATGTAATTAGGTTTGTTGTTAAATTTGCTAATGCTAGCTTATCAAATAATACATTGCA
1 AATGGAGATGTAATCAAATTTGTTGTTAAATTTGCTAATGCTAGCTCATCAAATAATACATTGCA
27588030 ATAATAATACGAGTTACAAATCAAA-ATTCATCTCTACATCATCCAAACCATTAAACTATAGAGA
66 ATAATAATACGAGTTACAAATCAAATA-TCATCTCTACATCATCCAAACCATTAAACTATAGAGA
* * * * *
27588094 GGACATTTCATTCCTAGCCTATGAAGCATGGACACGCTGCAAATCCCCTCGTACCGGTGTCGACA
130 GGACATTTCATTCCTAACCTATGAAGCACGAACACGCCGCAAATCCCCTCGTACCGGTGTCAACA
27588159 CG
195 CG
27588161 GTGTTCAACA
Statistics
Matches: 179, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
204 1 0.01
205 178 0.99
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.29
Consensus pattern (205 bp):
AATGGAGATGTAATCAAATTTGTTGTTAAATTTGCTAATGCTAGCTCATCAAATAATACATTGCA
ATAATAATACGAGTTACAAATCAAATATCATCTCTACATCATCCAAACCATTAAACTATAGAGAG
GACATTTCATTCCTAACCTATGAAGCACGAACACGCCGCAAATCCCCTCGTACCGGTGTCAACAC
GTTGTCCGAC
Found at i:27596371 original size:40 final size:40
Alignment explanation
Indices: 27596326--27596428 Score: 179
Period size: 40 Copynumber: 2.6 Consensus size: 40
27596316 GGTATTTTCG
*
27596326 AATAAATGAAAAGGTTGAAAAGGATATTATTCGGAAGGAT
1 AATAAATGAAAAGGTTGAAAAGGATATTATCCGGAAGGAT
*
27596366 AATAAATGAAAAGGTTGAATAGGATATTATCCGGAAGGAT
1 AATAAATGAAAAGGTTGAAAAGGATATTATCCGGAAGGAT
*
27596406 AATAAATGAAAAGGTCGAAAAGG
1 AATAAATGAAAAGGTTGAAAAGG
27596429 TAAATTTATT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 59 1.00
ACGTcount: A:0.49, C:0.04, G:0.25, T:0.22
Consensus pattern (40 bp):
AATAAATGAAAAGGTTGAAAAGGATATTATCCGGAAGGAT
Found at i:27597182 original size:13 final size:13
Alignment explanation
Indices: 27597144--27597227 Score: 62
Period size: 13 Copynumber: 6.5 Consensus size: 13
27597134 AATGTATAGA
*
27597144 ATGAAATGG-TAA
1 ATGAAATGGTTAT
* *
27597156 ATAGAAACGATTAT
1 AT-GAAATGGTTAT
27597170 ATGAAATGGTTAT
1 ATGAAATGGTTAT
*
27597183 AAGAAATGGTTAT
1 ATGAAATGGTTAT
* * * *
27597196 AGGGAATGATTAC
1 ATGAAATGGTTAT
*
27597209 ATGAATTGGTTAT
1 ATGAAATGGTTAT
*
27597222 GTGAAA
1 ATGAAA
27597228 ATATATGTAT
Statistics
Matches: 53, Mismatches: 17, Indels: 3
0.73 0.23 0.04
Matches are distributed among these distances:
12 2 0.04
13 47 0.89
14 4 0.08
ACGTcount: A:0.43, C:0.02, G:0.24, T:0.31
Consensus pattern (13 bp):
ATGAAATGGTTAT
Found at i:27598875 original size:22 final size:22
Alignment explanation
Indices: 27598850--27598893 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
27598840 TGGAAAGTTG
*
27598850 TAATGTAACTCAAATTTGAAAA
1 TAATGTAACTAAAATTTGAAAA
*
27598872 TAATGTAATTAAAATTTGAAAA
1 TAATGTAACTAAAATTTGAAAA
27598894 CTTAAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.52, C:0.05, G:0.09, T:0.34
Consensus pattern (22 bp):
TAATGTAACTAAAATTTGAAAA
Found at i:27598900 original size:14 final size:14
Alignment explanation
Indices: 27598883--27598933 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
27598873 AATGTAATTA
27598883 AAATTTGAAAACTT
1 AAATTTGAAAACTT
* *
27598897 AAATTT-TAAATTT
1 AAATTTGAAAACTT
* *
27598910 GAATTTTAAAACTT
1 AAATTTGAAAACTT
27598924 AAATTTGAAA
1 AAATTTGAAA
27598934 GCTAAAAACT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
13 10 0.34
14 19 0.66
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.41
Consensus pattern (14 bp):
AAATTTGAAAACTT
Found at i:27598908 original size:27 final size:27
Alignment explanation
Indices: 27598878--27598929 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
27598868 AAAATAATGT
27598878 AATTAAAATTTGAAAACTTAAATTTTA
1 AATTAAAATTTGAAAACTTAAATTTTA
** *
27598905 AATTTGAATTTTAAAACTTAAATTT
1 AATTAAAATTTGAAAACTTAAATTT
27598930 GAAAGCTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (27 bp):
AATTAAAATTTGAAAACTTAAATTTTA
Found at i:27598939 original size:20 final size:20
Alignment explanation
Indices: 27598883--27598940 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
27598873 AATGTAATTA
**
27598883 AAATTTGAAAACTTAAATTTT
1 AAATTTGAAAAC-TAAAACTT
***
27598904 AAATTTGAATTTTAAAACTT
1 AAATTTGAAAACTAAAACTT
*
27598924 AAATTTGAAAGCTAAAA
1 AAATTTGAAAACTAAAA
27598941 ACTGTGGAGA
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 20 0.69
21 9 0.31
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (20 bp):
AAATTTGAAAACTAAAACTT
Found at i:27599196 original size:22 final size:22
Alignment explanation
Indices: 27599166--27599230 Score: 103
Period size: 22 Copynumber: 3.0 Consensus size: 22
27599156 AGAGAATCTT
*
27599166 GTCAGAGAATCTCACTATTCAC
1 GTCAGAGAATCTCACTGTTCAC
*
27599188 GTCAAAGAATCTCACTGTTCAC
1 GTCAGAGAATCTCACTGTTCAC
*
27599210 ATCAGAGAATCTCACTGTTCA
1 GTCAGAGAATCTCACTGTTCA
27599231 TTTTATTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.28
Consensus pattern (22 bp):
GTCAGAGAATCTCACTGTTCAC
Found at i:27606306 original size:3 final size:3
Alignment explanation
Indices: 27606300--27606334 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
27606290 AACTCAGTAG
27606300 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
27606335 CATTAATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:27617953 original size:21 final size:21
Alignment explanation
Indices: 27617909--27617946 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
27617899 TCATTTGTAA
27617909 TAAATTATTAATAATATTATT
1 TAAATTATTAATAATATTATT
27617930 TAAATTA-TAAT-ATATTA
1 TAAATTATTAATAATATTA
27617947 ATATTAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 4 0.24
21 7 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TAAATTATTAATAATATTATT
Found at i:27619229 original size:70 final size:71
Alignment explanation
Indices: 27619086--27619233 Score: 212
Period size: 70 Copynumber: 2.1 Consensus size: 71
27619076 GTTCCATTTT
* * * *
27619086 TCCA-ATTTAAATTGAAAGTAAGCAGAAACCTTGAAATCTTGATCTGTTCTCTTATTTTGTAGGG
1 TCCATATTTAAATTGAAAGTAAGAAAAAACCTTGAAATATTGATCTGTTCTCTTATTCTGTAGGG
*
27619150 TTTTAA
66 TTCTAA
*
27619156 TCCATATTTAAATTGATAA-TAAGAAAAAATCTTGAAATATTGATCT-TTCTCTTATTCTGTAGG
1 TCCATATTTAAATTGA-AAGTAAGAAAAAACCTTGAAATATTGATCTGTTCTCTTATTCTGTAGG
27619219 GTTCTAA
65 GTTCTAA
27619226 TCCATATT
1 TCCATATT
27619234 AGTAATTAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
70 34 0.49
71 34 0.49
72 2 0.03
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (71 bp):
TCCATATTTAAATTGAAAGTAAGAAAAAACCTTGAAATATTGATCTGTTCTCTTATTCTGTAGGG
TTCTAA
Found at i:27623496 original size:31 final size:32
Alignment explanation
Indices: 27623456--27623515 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 32
27623446 CAGATCAATG
*
27623456 ACTTGAATAAAAACTTTCGAATA-TTTTAGTA
1 ACTTAAATAAAAACTTTCGAATAGTTTTAGTA
27623487 ACTTAAATAAAAACTTTCGAATAGTTTTA
1 ACTTAAATAAAAACTTTCGAATAGTTTTA
27623516 TGACCCAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 22 0.81
32 5 0.19
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.38
Consensus pattern (32 bp):
ACTTAAATAAAAACTTTCGAATAGTTTTAGTA
Found at i:27624126 original size:90 final size:90
Alignment explanation
Indices: 27624010--27624188 Score: 349
Period size: 90 Copynumber: 2.0 Consensus size: 90
27624000 TGAGTAACTT
27624010 AAATTCTACCTAAACAAGTGGTTTTTCAAAATCCCTTCTAGGTCCCATAGTAAAATAAAAATCAA
1 AAATTCTACCTAAACAAGTGGTTTTTCAAAATCCCTTCTAGGTCCCATAGTAAAATAAAAATCAA
27624075 TAATTTTAAAATATAACTTTTATTC
66 TAATTTTAAAATATAACTTTTATTC
*
27624100 AAATTCTACCTAAACAAGTGGTTTTTCAAAATCCCTTCTAGGTCCCATTGTAAAATAAAAATCAA
1 AAATTCTACCTAAACAAGTGGTTTTTCAAAATCCCTTCTAGGTCCCATAGTAAAATAAAAATCAA
27624165 TAATTTTAAAATATAACTTTTATT
66 TAATTTTAAAATATAACTTTTATT
27624189 TAATTTCAAT
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 88 1.00
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.36
Consensus pattern (90 bp):
AAATTCTACCTAAACAAGTGGTTTTTCAAAATCCCTTCTAGGTCCCATAGTAAAATAAAAATCAA
TAATTTTAAAATATAACTTTTATTC
Found at i:27624202 original size:24 final size:24
Alignment explanation
Indices: 27624165--27624211 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
27624155 TAAAAATCAA
*
27624165 TAATTTTAAAATATA-ACTTTTATT
1 TAATTTCAAAATATATA-TTTTATT
*
27624189 TAATTTCAATATATATATTTTAT
1 TAATTTCAAAATATATATTTTAT
27624212 ATTTTATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 19 0.95
25 1 0.05
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.55
Consensus pattern (24 bp):
TAATTTCAAAATATATATTTTATT
Found at i:27624234 original size:19 final size:20
Alignment explanation
Indices: 27624210--27624250 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
27624200 TATATATTTT
27624210 ATATTT-TATATTATTTA-AA
1 ATATTTATATATT-TTTACAA
27624229 ATATTTATATATTTTTACAA
1 ATATTTATATATTTTTACAA
27624249 AT
1 AT
27624251 CTAATGATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
ATATTTATATATTTTTACAA
Found at i:27636785 original size:30 final size:30
Alignment explanation
Indices: 27636750--27636899 Score: 133
Period size: 30 Copynumber: 5.0 Consensus size: 30
27636740 CATTAAAACC
* * *
27636750 GGGTCAATTTTGAATTTTTAGAAACTTTAGA
1 GGGTCAAATTAGAATTTTTGGAAA-TTTAGA
* * *
27636781 -GGTCAAATCAGAATTTTTGGAAAGTTCGA
1 GGGTCAAATTAGAATTTTTGGAAATTTAGA
* * * *
27636810 GAGTCAAATCAAAATTTTTAGAAAGTTTA-A
1 GGGTCAAATTAGAATTTTTGGAAA-TTTAGA
* * *
27636840 GGGTCAAATTTGAATTTTTGGAAAATTCGA
1 GGGTCAAATTAGAATTTTTGGAAATTTAGA
*
27636870 GGGTCAAATTCGAATTTTTGGAAAATTTAG
1 GGGTCAAATTAGAATTTTTGG-AAATTTAG
27636900 GGTTTAGGAT
Statistics
Matches: 94, Mismatches: 21, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
29 6 0.06
30 80 0.85
31 8 0.09
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (30 bp):
GGGTCAAATTAGAATTTTTGGAAATTTAGA
Done.