Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 108 of 193
Found at i:34629814 original size:27 final size:26
Alignment explanation
Indices: 34629784--34629835 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
34629774 TTCAATAATG
* *
34629784 TTAACAAATAAACTTGAATTTTAAAAT
1 TTAAAAAAT-AACTTGAAATTTAAAAT
*
34629811 TTAAAAAATAAGTTGAAATTTAAAA
1 TTAAAAAATAACTTGAAATTTAAAA
34629836 AAATATATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.35
Consensus pattern (26 bp):
TTAAAAAATAACTTGAAATTTAAAAT
Found at i:34640033 original size:44 final size:44
Alignment explanation
Indices: 34639984--34640070 Score: 149
Period size: 44 Copynumber: 2.0 Consensus size: 44
34639974 TTAGTCCACG
*
34639984 AACACCAATTCAATTG-AAGATTTACTCAAAAATCATTTGTATAC
1 AACACCAATTCAATTGAAAG-TTTACTCAAAAATCACTTGTATAC
34640028 AACACCAATTCAATTGAAAGTTTACTCAAAAATCACTTGTATA
1 AACACCAATTCAATTGAAAGTTTACTCAAAAATCACTTGTATA
34640071 TGTATTAGTA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
44 38 0.93
45 3 0.07
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.31
Consensus pattern (44 bp):
AACACCAATTCAATTGAAAGTTTACTCAAAAATCACTTGTATAC
Found at i:34641253 original size:24 final size:24
Alignment explanation
Indices: 34641213--34641262 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
34641203 GTAACACGAT
* **
34641213 TTTAATTTGAAATATTTTTTTCAA
1 TTTAACTTGAAATATTTCATTCAA
34641237 TTTAACTTGAACA-ATTTCATTCAA
1 TTTAACTTGAA-ATATTTCATTCAA
34641261 TT
1 TT
34641263 CGACTCGGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 21 0.95
25 1 0.05
ACGTcount: A:0.34, C:0.10, G:0.04, T:0.52
Consensus pattern (24 bp):
TTTAACTTGAAATATTTCATTCAA
Found at i:34650040 original size:6 final size:6
Alignment explanation
Indices: 34650031--34650143 Score: 181
Period size: 6 Copynumber: 18.8 Consensus size: 6
34650021 CAATATACAT
*
34650031 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATAGAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
* * * *
34650079 ATAGAC ATAGAC ATAGAC ATAGAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
34650127 ATATAC ATATAC ATATA
1 ATATAC ATATAC ATATA
34650144 ACCTACCATT
Statistics
Matches: 105, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 105 1.00
ACGTcount: A:0.50, C:0.16, G:0.04, T:0.29
Consensus pattern (6 bp):
ATATAC
Found at i:34659834 original size:14 final size:14
Alignment explanation
Indices: 34659800--34659836 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
34659790 ATAATTTTTA
34659800 TATTGAATTTGAAT
1 TATTGAATTTGAAT
34659814 TGA-TGAATTTGAAT
1 T-ATTGAATTTGAAT
34659828 TATTGAATT
1 TATTGAATT
34659837 AAAAGTTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 1 0.05
14 19 0.90
15 1 0.05
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
TATTGAATTTGAAT
Found at i:34663417 original size:26 final size:26
Alignment explanation
Indices: 34663388--34663438 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
34663378 GAATTTTATT
34663388 AAAAAATTAATA-AAAATATAAAAAAC
1 AAAAAA-TAATATAAAATATAAAAAAC
* *
34663414 AAAAAATATTATAAAATATAGAAAA
1 AAAAAATAATATAAAATATAAAAAA
34663439 TAGTTTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (26 bp):
AAAAAATAATATAAAATATAAAAAAC
Found at i:34664275 original size:21 final size:21
Alignment explanation
Indices: 34664249--34664288 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
34664239 TGGTGTAGAC
*
34664249 TTCTACTAATACAAGTGACAG
1 TTCTACCAATACAAGTGACAG
*
34664270 TTCTACCGATACAAGTGAC
1 TTCTACCAATACAAGTGAC
34664289 TCTTTTACTG
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:0.35, C:0.23, G:0.15, T:0.28
Consensus pattern (21 bp):
TTCTACCAATACAAGTGACAG
Found at i:34666369 original size:33 final size:33
Alignment explanation
Indices: 34666322--34666391 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
34666312 ATTTAAAATT
*
34666322 TCATTACCAACTTTTAATACGATGCTAACGAAG
1 TCATCACCAACTTTTAATACGATGCTAACGAAG
34666355 TCATCACCAACTTTTAATACGATGCTAACGAAG
1 TCATCACCAACTTTTAATACGATGCTAACGAAG
34666388 TCAT
1 TCAT
34666392 AAATGTTTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.30
Consensus pattern (33 bp):
TCATCACCAACTTTTAATACGATGCTAACGAAG
Found at i:34667272 original size:55 final size:54
Alignment explanation
Indices: 34667146--34667304 Score: 178
Period size: 55 Copynumber: 2.9 Consensus size: 54
34667136 TGAAATAACC
* * * * * *
34667146 TTACGCTCTAATCGAGATGTAAGCA-ACCAGAGCTATACTCGAGCTATAATAGCT
1 TTACGCTCTAATCGAGACGTAAGCAGTCCAAAGCTCTAC-CGAGCTATAAGAGCA
* *
34667200 TTATGCTCTAATCGAGACGTAAGCATGTCCAAAGCTCTACCAAGCTATAAGAGCA
1 TTACGCTCTAATCGAGACGTAAGCA-GTCCAAAGCTCTACCGAGCTATAAGAGCA
* *
34667255 TTACGCTCTAATTGAGACGTAAGCAGAT-CGAAGCTCTACCCGAGCTATAA
1 TTACGCTCTAATCGAGACGTAAGCAG-TCCAAAGCTCTA-CCGAGCTATAA
34667305 ATGGATCAAG
Statistics
Matches: 89, Mismatches: 12, Indels: 7
0.82 0.11 0.06
Matches are distributed among these distances:
54 33 0.37
55 46 0.52
56 10 0.11
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (54 bp):
TTACGCTCTAATCGAGACGTAAGCAGTCCAAAGCTCTACCGAGCTATAAGAGCA
Found at i:34668749 original size:22 final size:22
Alignment explanation
Indices: 34668722--34668782 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
34668712 TCATTAATTG
34668722 CTACTAACCAACTAACTACTAA
1 CTACTAACCAACTAACTACTAA
* * *
34668744 CTACTAACAAACTAACTAGTAT
1 CTACTAACCAACTAACTACTAA
34668766 C-ACTAA-CAATCTAACTA
1 CTACTAACCAA-CTAACTA
34668783 ACTGCTATCA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 2 0.06
21 12 0.35
22 20 0.59
ACGTcount: A:0.46, C:0.28, G:0.02, T:0.25
Consensus pattern (22 bp):
CTACTAACCAACTAACTACTAA
Found at i:34670498 original size:84 final size:84
Alignment explanation
Indices: 34670357--34670524 Score: 266
Period size: 84 Copynumber: 2.0 Consensus size: 84
34670347 GACTTCTTCT
* *
34670357 GAAATCATATAGAATCTAGTTATTATGAAACCTGAGTATATAGATCTTGAAATAAAGTGGTGTGA
1 GAAATCATATAAAATCTAGTTATTATGAAACCTAAGTATATAGATCTTGAAATAAAGTGGTGTGA
34670422 AATTCATCTGAAAGATCTA
66 AATTCATCTGAAAGATCTA
* * * *
34670441 GAAATCATATAAAATCTGAGTTATTGTG-AACCTAAGTATCTGGATCTTGAAATAAAGTTGTGTG
1 GAAATCATATAAAATCT-AGTTATTATGAAACCTAAGTATATAGATCTTGAAATAAAGTGGTGTG
34670505 AAATTCATCTGAAAGATCTA
65 AAATTCATCTGAAAGATCTA
34670525 TGTGGTATAC
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
84 68 0.88
85 9 0.12
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (84 bp):
GAAATCATATAAAATCTAGTTATTATGAAACCTAAGTATATAGATCTTGAAATAAAGTGGTGTGA
AATTCATCTGAAAGATCTA
Found at i:34674772 original size:30 final size:30
Alignment explanation
Indices: 34674736--34674797 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
34674726 CTTCTTGCAC
34674736 TATCATAAGATAAGCATGATTAACAGATGG
1 TATCATAAGATAAGCATGATTAACAGATGG
34674766 TATCATAAGATAAGCATGATTAACAGATGG
1 TATCATAAGATAAGCATGATTAACAGATGG
34674796 TA
1 TA
34674798 ACAGACTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.44, C:0.10, G:0.19, T:0.27
Consensus pattern (30 bp):
TATCATAAGATAAGCATGATTAACAGATGG
Found at i:34677005 original size:44 final size:45
Alignment explanation
Indices: 34676944--34677088 Score: 127
Period size: 44 Copynumber: 3.2 Consensus size: 45
34676934 AAAAACACAT
* * * *
34676944 AAAAATAACATC-CAAACAACCAAAATAACAATCAAAATAGCAGC
1 AAAAATAACAGCAAAAACAACAAAAATAACAATCAAAATAGCAAC
* * *
34676988 AAAACTAACAGC-AAAACAA-AAACAAAAACAATAAAAATAGCAAC
1 AAAAATAACAGCAAAAACAACAAA-AATAACAATCAAAATAGCAAC
* * * *
34677032 AAAAATAACATCAAAAATAACAAAAATAACAGCATCAAAACAGTAA-
1 AAAAATAACAGCAAAAACAACAAAAATAACA--ATCAAAATAGCAAC
34677078 AAAAAGTAACA
1 AAAAA-TAACA
34677089 AAACAACAAT
Statistics
Matches: 81, Mismatches: 14, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
43 2 0.02
44 44 0.54
45 12 0.15
46 8 0.10
47 15 0.19
ACGTcount: A:0.67, C:0.18, G:0.05, T:0.10
Consensus pattern (45 bp):
AAAAATAACAGCAAAAACAACAAAAATAACAATCAAAATAGCAAC
Found at i:34677067 original size:24 final size:25
Alignment explanation
Indices: 34677029--34677088 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 25
34677019 TAAAAATAGC
34677029 AACAAAAAT-A-ACATCAAAA-A-T
1 AACAAAAATAACACATCAAAACAGT
34677050 AACAAAAATAACAGCATCAAAACAGT
1 AACAAAAATAACA-CATCAAAACAGT
34677076 AA-AAAAAGTAACA
1 AACAAAAA-TAACA
34677089 AAACAACAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
21 9 0.27
22 1 0.03
23 1 0.03
24 8 0.24
25 6 0.18
26 8 0.24
ACGTcount: A:0.68, C:0.15, G:0.05, T:0.12
Consensus pattern (25 bp):
AACAAAAATAACACATCAAAACAGT
Found at i:34677096 original size:23 final size:22
Alignment explanation
Indices: 34677070--34677118 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
34677060 ACAGCATCAA
*
34677070 AACAGTAAAAAAAGTAACAAAAC
1 AACAATAAAAAAAGTAA-AAAAC
* * *
34677093 AACAATCAAAACAGTAAAAAAT
1 AACAATAAAAAAAGTAAAAAAC
34677115 AACA
1 AACA
34677119 CCAAAACAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.69, C:0.14, G:0.06, T:0.10
Consensus pattern (22 bp):
AACAATAAAAAAAGTAAAAAAC
Found at i:34677101 original size:56 final size:53
Alignment explanation
Indices: 34677012--34677153 Score: 146
Period size: 56 Copynumber: 2.6 Consensus size: 53
34677002 AACAAAAACA
* * *
34677012 AAAACAATAAAAATAGCAACAAAAATAAC-ATCAAAA-A-TAACAAAAATAACAGCATC
1 AAAACAGTAAAAAAAGCAAC-AAAACAACAATCAAAACAGT-A-AAAAATAACA-C--C
*
34677068 AAAACAGTAAAAAAAGTAACAAAACAACAATCAAAACAGTAAAAAATAACACC
1 AAAACAGTAAAAAAAGCAACAAAACAACAATCAAAACAGTAAAAAATAACACC
*
34677121 AAAACAGTAAAAAAACAGCACCAAAACAACAAT
1 AAAACAGT-AAAAAA-AGCAACAAAACAACAAT
34677154 ATAATTTTTT
Statistics
Matches: 75, Mismatches: 6, Indels: 11
0.82 0.07 0.12
Matches are distributed among these distances:
53 9 0.12
54 6 0.08
55 23 0.31
56 34 0.45
57 2 0.03
58 1 0.01
ACGTcount: A:0.68, C:0.18, G:0.05, T:0.10
Consensus pattern (53 bp):
AAAACAGTAAAAAAAGCAACAAAACAACAATCAAAACAGTAAAAAATAACACC
Found at i:34677113 original size:22 final size:21
Alignment explanation
Indices: 34677077--34677148 Score: 81
Period size: 22 Copynumber: 3.3 Consensus size: 21
34677067 CAAAACAGTA
* *
34677077 AAAAAAGTAACAAAACAACAATC
1 AAAACAGTAA-AAAACAAC-ACC
*
34677100 AAAACAGTAAAAAATAACACC
1 AAAACAGTAAAAAACAACACC
*
34677121 AAAACAGTAAAAAAACAGCACC
1 AAAACAGT-AAAAAACAACACC
34677143 AAAACA
1 AAAACA
34677149 ACAATATAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
21 10 0.23
22 24 0.56
23 9 0.21
ACGTcount: A:0.68, C:0.19, G:0.06, T:0.07
Consensus pattern (21 bp):
AAAACAGTAAAAAACAACACC
Found at i:34677439 original size:18 final size:19
Alignment explanation
Indices: 34677405--34677443 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
34677395 TTTTAAAAAC
34677405 TTTATATTTTATAATAATT
1 TTTATATTTTATAATAATT
*
34677424 TTTATA-TTTCTAATAATT
1 TTTATATTTTATAATAATT
34677442 TT
1 TT
34677444 AAAATGTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTATATTTTATAATAATT
Found at i:34677514 original size:16 final size:16
Alignment explanation
Indices: 34677493--34677525 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
34677483 TTTTTATAAA
34677493 ATTTTAATA-ATTTTAT
1 ATTTT-ATACATTTTAT
34677509 ATTTTATACATTTTAT
1 ATTTTATACATTTTAT
34677525 A
1 A
34677526 CATTTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.19
16 13 0.81
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTTATACATTTTAT
Found at i:34688609 original size:16 final size:16
Alignment explanation
Indices: 34688573--34688614 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
34688563 GAAGAATAGA
34688573 AAGAAGGAAAGAAGAG
1 AAGAAGGAAAGAAGAG
*
34688589 GAGAAGG-AAGAAGAAG
1 AAGAAGGAAAGAAG-AG
34688605 AAGAA-GAAAG
1 AAGAAGGAAAG
34688615 TATAGCCTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (16 bp):
AAGAAGGAAAGAAGAG
Found at i:34689043 original size:19 final size:19
Alignment explanation
Indices: 34688997--34689051 Score: 58
Period size: 19 Copynumber: 2.7 Consensus size: 19
34688987 GTTAGTTGCA
34688997 TGCATTTGTTTTAATTGTCAT
1 TGCATTT-TTTT-ATTGTCAT
*
34689018 TGTATTTTTTTATTGTC-T
1 TGCATTTTTTTATTGTCAT
34689036 CTGCATTTTATTTATT
1 -TGCATTTT-TTTATT
34689052 TTAGCATTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
18 1 0.03
19 13 0.43
20 10 0.33
21 6 0.20
ACGTcount: A:0.16, C:0.09, G:0.11, T:0.64
Consensus pattern (19 bp):
TGCATTTTTTTATTGTCAT
Found at i:34694998 original size:37 final size:37
Alignment explanation
Indices: 34694906--34695061 Score: 138
Period size: 37 Copynumber: 4.1 Consensus size: 37
34694896 CAGTTTTGGT
* * *
34694906 GCAATCTGA-AAGTGCTCATGTGACGACAGATTTTTTGGGC
1 GCAATC-GAGAAGTGCTCATGCGACGAC--A-TGTTTGGAC
* *
34694946 GCAATCTAGAGGTGCTCATGCGACGACATGTTTGGAC
1 GCAATCGAGAAGTGCTCATGCGACGACATGTTTGGAC
* *
34694983 GCAATCGAGAAGTGCTTATGCGGCGACATGTTT-GAGC
1 GCAATCGAGAAGTGCTCATGCGACGACATGTTTGGA-C
* ** *
34695020 GCAATCTAGAAGTGCTCAT-TTAGCGACATGTTTGGGC
1 GCAATCGAGAAGTGCTCATGCGA-CGACATGTTTGGAC
34695057 GCAAT
1 GCAAT
34695062 TCTGGATTAA
Statistics
Matches: 97, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
36 2 0.02
37 70 0.72
38 2 0.02
39 1 0.01
40 22 0.23
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (37 bp):
GCAATCGAGAAGTGCTCATGCGACGACATGTTTGGAC
Found at i:34696256 original size:17 final size:17
Alignment explanation
Indices: 34696212--34696258 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
34696202 GATAATGTAG
34696212 ATGCAGCGACAATAAAA
1 ATGCAGCGACAATAAAA
**
34696229 ATGCAATGACAATAAAA
1 ATGCAGCGACAATAAAA
*
34696246 ATGCAGGGACAAT
1 ATGCAGCGACAAT
34696259 TATACTACAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.51, C:0.15, G:0.19, T:0.15
Consensus pattern (17 bp):
ATGCAGCGACAATAAAA
Found at i:34699245 original size:26 final size:26
Alignment explanation
Indices: 34699216--34699270 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
34699206 CAGCTGTAAG
* *
34699216 ATGCACCGATAATTCTGGACACGTTC
1 ATGCACCAACAATTCTGGACACGTTC
* * *
34699242 ATGCAGCAACAATTCTGTACATGTTC
1 ATGCACCAACAATTCTGGACACGTTC
34699268 ATG
1 ATG
34699271 TAGCGACATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (26 bp):
ATGCACCAACAATTCTGGACACGTTC
Found at i:34699331 original size:35 final size:36
Alignment explanation
Indices: 34699272--34699353 Score: 98
Period size: 38 Copynumber: 2.3 Consensus size: 36
34699262 ATGTTCATGT
*
34699272 AGCGACA-TTCTTGGGTGCATTT-GAATACTTATGC
1 AGCGACAGTTCTTGGATGCATTTAGAATACTTATGC
*
34699306 AGCGACAGTTC-TGGATGCAATTTGAAGAATATTTATGC
1 AGCGACAGTTCTTGGATGC-ATTT--AGAATACTTATGC
34699344 AGCGACAGTT
1 AGCGACAGTT
34699354 TTGTGCAATC
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
34 13 0.32
35 7 0.17
38 21 0.51
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (36 bp):
AGCGACAGTTCTTGGATGCATTTAGAATACTTATGC
Found at i:34699441 original size:37 final size:37
Alignment explanation
Indices: 34699358--34699507 Score: 185
Period size: 37 Copynumber: 4.0 Consensus size: 37
34699348 ACAGTTTTGT
* * *
34699358 GCAATCTGGAAGTGCTCATGTGGCGACAGTTTTTTTGGGT
1 GCAATCTAGAAGTGCTCATGTGGCGACA---TGTTTGGGC
34699398 GCAATCTA-AAGGTGCTCATGTGGCGACATGTTTGGGC
1 GCAATCTAGAA-GTGCTCATGTGGCGACATGTTTGGGC
* *
34699435 GCAATCTAGAAGTGCTCATGAGGTGACATGTTTGGGC
1 GCAATCTAGAAGTGCTCATGTGGCGACATGTTTGGGC
* **
34699472 ACAATCTAGAAGTGCTCATGCAGCGACATGTTTGGG
1 GCAATCTAGAAGTGCTCATGTGGCGACATGTTTGGG
34699508 TACAATTCCG
Statistics
Matches: 99, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
37 71 0.72
38 2 0.02
39 2 0.02
40 24 0.24
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (37 bp):
GCAATCTAGAAGTGCTCATGTGGCGACATGTTTGGGC
Found at i:34699488 original size:74 final size:75
Alignment explanation
Indices: 34699340--34699507 Score: 191
Period size: 74 Copynumber: 2.3 Consensus size: 75
34699330 AAGAATATTT
* * * * * **
34699340 ATGCAGCGACA-GTTT-TGTGCAATCTGGAAGTGCTCATGTGGCGACAGTTTTTTTGGGTGCAAT
1 ATGCAGCGACATGTTTGGGCGCAATCTAGAAGTGCTCATGAGGCGACA--TTGTTTGGGCACAAT
34699403 CTAAAGGTGCTC
64 CTAAAGGTGCTC
** *
34699415 ATGTGGCGACATGTTTGGGCGCAATCTAGAAGTGCTCATGAGGTGACA-TGTTTGGGCACAATCT
1 ATGCAGCGACATGTTTGGGCGCAATCTAGAAGTGCTCATGAGGCGACATTGTTTGGGCACAATCT
34699479 AGAA-GTGCTC
66 A-AAGGTGCTC
34699489 ATGCAGCGACATGTTTGGG
1 ATGCAGCGACATGTTTGGG
34699508 TACAATTCCG
Statistics
Matches: 78, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
74 37 0.47
75 11 0.14
76 4 0.05
77 26 0.33
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (75 bp):
ATGCAGCGACATGTTTGGGCGCAATCTAGAAGTGCTCATGAGGCGACATTGTTTGGGCACAATCT
AAAGGTGCTC
Found at i:34699513 original size:37 final size:37
Alignment explanation
Indices: 34699340--34699513 Score: 167
Period size: 37 Copynumber: 4.7 Consensus size: 37
34699330 AAGAATATTT
* *
34699340 ATGCAGCGACA-GTTT-TGTGCAATCTGGAAGTGCTC
1 ATGCAGCGACATGTTTGGGTGCAATCTAGAAGTGCTC
** *
34699375 ATGTGGCGACAGTTTTTTTGGGTGCAATCTA-AAGGTGCTC
1 ATGCAGCGACA---TGTTTGGGTGCAATCTAGAA-GTGCTC
** *
34699415 ATGTGGCGACATGTTTGGGCGCAATCTAGAAGTGCTC
1 ATGCAGCGACATGTTTGGGTGCAATCTAGAAGTGCTC
* **
34699452 ATG-AGGTGACATGTTTGGGCACAATCTAGAAGTGCTC
1 ATGCA-GCGACATGTTTGGGTGCAATCTAGAAGTGCTC
*
34699489 ATGCAGCGACATGTTTGGGTACAAT
1 ATGCAGCGACATGTTTGGGTGCAAT
34699514 TCCGGATTAA
Statistics
Matches: 118, Mismatches: 12, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
35 9 0.08
37 75 0.64
38 3 0.03
39 5 0.04
40 26 0.22
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (37 bp):
ATGCAGCGACATGTTTGGGTGCAATCTAGAAGTGCTC
Found at i:34702200 original size:48 final size:50
Alignment explanation
Indices: 34702130--34702228 Score: 175
Period size: 48 Copynumber: 2.0 Consensus size: 50
34702120 TGACTATTCA
34702130 AACAACAATGGCTCTAATAATGTCAAAT-GGAAGATTTTTTT-TAAGGCC
1 AACAACAATGGCTCTAATAATGTCAAATGGGAAGATTTTTTTATAAGGCC
*
34702178 AACAACAATGGCTTTAATAATGTCAAATGGGAAGATTTTTTTATAAGGCC
1 AACAACAATGGCTCTAATAATGTCAAATGGGAAGATTTTTTTATAAGGCC
34702228 A
1 A
34702229 CTGTTGGATA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
48 27 0.56
49 13 0.27
50 8 0.17
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.31
Consensus pattern (50 bp):
AACAACAATGGCTCTAATAATGTCAAATGGGAAGATTTTTTTATAAGGCC
Found at i:34707288 original size:24 final size:23
Alignment explanation
Indices: 34707236--34707289 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
34707226 CCATGAAATT
*
34707236 ATATTTATTTTAATTGACTTATTG
1 ATATTGATTTTAATTGA-TTATTG
*
34707260 TTATTGATTTTAATATG-TTATTG
1 ATATTGATTTTAAT-TGATTATTG
34707283 AATATTG
1 -ATATTG
34707290 TTGTTCACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
23 6 0.24
24 17 0.68
25 2 0.08
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (23 bp):
ATATTGATTTTAATTGATTATTG
Found at i:34722647 original size:59 final size:59
Alignment explanation
Indices: 34722609--34723008 Score: 489
Period size: 59 Copynumber: 6.8 Consensus size: 59
34722599 AGAATTTTGA
* * * *
34722609 GGTTAAAATGTAATTTT-GGAAAAGTTTAAGGGTAAAAATGTAATTATGGGAAAGTTT-AG
1 GGTTAAAATGTGATTTTAGG-AAAGTTTGAGGGTTAAAATGTAATTTTGGG-AAGTTTAAG
* * * *
34722668 GGTTAAAATGTGATTTTAGGAAAATTTG-GGATTAAAATGTAATTTTGGAAAGGTTAAG
1 GGTTAAAATGTGATTTTAGGAAAGTTTGAGGGTTAAAATGTAATTTTGGGAAGTTTAAG
* * *
34722726 GGTTTAAAATGTGATTTT-GGGAAGTTT-AGGGGTTAAAATGTGATTTTGGGAAAGTTT-GG
1 GG-TTAAAATGTGATTTTAGGAAAGTTTGA-GGGTTAAAATGTAATTTTGGG-AAGTTTAAG
34722785 GGTTAAAATGTGATTTTAGGAAAGTTTGAGGGTTAAAATGTAATTTT-GGAAGTTTAAG
1 GGTTAAAATGTGATTTTAGGAAAGTTTGAGGGTTAAAATGTAATTTTGGGAAGTTTAAG
34722843 GGTTAAAATGTGATTTTAGGAAAGTTTTGAGGGTTAAAATGTAATTTTGGGAAGTTTAA-
1 GGTTAAAATGTGATTTTAGGAAAG-TTTGAGGGTTAAAATGTAATTTTGGGAAGTTTAAG
* * *
34722902 GGTTAAAATGTGATTTTAGGAAAGTTTGAGGGTTAAAATGTGATTTTAGGAAAGTTTGAG
1 GGTTAAAATGTGATTTTAGGAAAGTTTGAGGGTTAAAATGTAATTTT-GGGAAGTTTAAG
* * * *
34722962 GGTTGAAATGTAATTTT--GAAAGGTTCGAGGGTT-AAATATAATTTTGG
1 GGTTAAAATGTGATTTTAGGAAA-GTTTGAGGGTTAAAATGTAATTTTGG
34723009 AATAGTTTGG
Statistics
Matches: 301, Mismatches: 26, Indels: 30
0.84 0.07 0.08
Matches are distributed among these distances:
57 13 0.04
58 106 0.35
59 149 0.50
60 33 0.11
ACGTcount: A:0.34, C:0.00, G:0.28, T:0.37
Consensus pattern (59 bp):
GGTTAAAATGTGATTTTAGGAAAGTTTGAGGGTTAAAATGTAATTTTGGGAAGTTTAAG
Found at i:34722685 original size:88 final size:87
Alignment explanation
Indices: 34722604--34723008 Score: 516
Period size: 88 Copynumber: 4.6 Consensus size: 87
34722594 TTTAGAGAAT
* *
34722604 TTTGAGGTTAAAATGTAATTTTGGAAAAGTTTAAGGGTAAAAATGTAATTATGGGAAAGTTT-AG
1 TTTGAGGTTAAAATGTAATTTTGG-AAAGTTTAAGGGTTAAAATGTAATTTTGGG-AAGTTTAAG
*
34722668 GGTTAAAATGTGATTTTAGGAAAA
64 GGTTAAAATGTGATTTTAGGAAAG
* * *
34722692 TTTG-GGATTAAAATGTAATTTTGGAAAGGTTAAGGGTTTAAAATGTGATTTTGGGAAGTTTAGG
1 TTTGAGG-TTAAAATGTAATTTTGGAAAGTTTAAGGG-TTAAAATGTAATTTTGGGAAGTTTAAG
*
34722756 GGTTAAAATGTGATTTTGGGAAAG
64 GGTTAAAATGTGATTTTAGGAAAG
* * *
34722780 TTTGGGGTTAAAATGTGATTTTAGGAAAGTTTGAGGGTTAAAATGTAATTTT-GGAAGTTTAAGG
1 TTTGAGGTTAAAATGTAATTTT-GGAAAGTTTAAGGGTTAAAATGTAATTTTGGGAAGTTTAAGG
34722844 GTTAAAATGTGATTTTAGGAAAG
65 GTTAAAATGTGATTTTAGGAAAG
* * * *
34722867 TTTTGAGGGTTAAAATGTAATTTTGGGAAGTTTAA-GGTTAAAATGTGATTTTAGGAAAGTTTGA
1 -TTTGA-GGTTAAAATGTAATTTTGGAAAGTTTAAGGGTTAAAATGTAATTTT-GGGAAGTTTAA
34722931 GGGTTAAAATGTGATTTTAGGAAAG
63 GGGTTAAAATGTGATTTTAGGAAAG
* ** *
34722956 TTTGAGGGTTGAAATGTAATTTT-GAAAGGTTCGAGGGTT-AAATATAATTTTGG
1 TTTGA-GGTTAAAATGTAATTTTGGAAA-GTTTAAGGGTTAAAATGTAATTTTGG
34723009 AATAGTTTGG
Statistics
Matches: 280, Mismatches: 26, Indels: 23
0.85 0.08 0.07
Matches are distributed among these distances:
87 73 0.26
88 140 0.50
89 67 0.24
ACGTcount: A:0.34, C:0.00, G:0.28, T:0.38
Consensus pattern (87 bp):
TTTGAGGTTAAAATGTAATTTTGGAAAGTTTAAGGGTTAAAATGTAATTTTGGGAAGTTTAAGGG
TTAAAATGTGATTTTAGGAAAG
Found at i:34722979 original size:147 final size:144
Alignment explanation
Indices: 34722607--34723059 Score: 538
Period size: 147 Copynumber: 3.1 Consensus size: 144
34722597 AGAGAATTTT
* * * * * *
34722607 GAGGTTAAAATGTAATTTTGGAAAAGTTTAAGGGTAAAAATGTAATTATGGGAAAGTTT-AGGGT
1 GAGGTTAAAATGTGATTTTGG-AAAGTTTGAGGGTTAAAATGTGATTTTAGGAAAGTTTGAGGGT
* * * *
34722671 TAAAATGTGATTTTAGGAAAATTT-GGGATTAAAATGTAATTTTGGAAAGGTTAAGGGTTTAAAA
65 TAAAATGTAATTTT-GG-AAGTTTAGGG-TTAAAATGTAATTTTGGAAAGTTTGAGGG-TTAAAA
*
34722735 TGTGATTTTGGGAAGTTTA
126 TGTAATTTTGGGAAGTTTA
*
34722754 GGGGTTAAAATGTGATTTTGGGAAAGTTTG-GGGTTAAAATGTGATTTTAGGAAAGTTTGAGGGT
1 GAGGTTAAAATGTGATTTT-GGAAAGTTTGAGGGTTAAAATGTGATTTTAGGAAAGTTTGAGGGT
*
34722818 TAAAATGTAATTTTGGAAGTTTAAGGGTTAAAATGTGATTTTAGGAAAGTTTTGAGGGTTAAAAT
65 TAAAATGTAATTTTGGAAGTTT-AGGGTTAAAATGTAATTTT-GGAAAG-TTTGAGGGTTAAAAT
34722883 GTAATTTTGGGAAGTTTA
127 GTAATTTTGGGAAGTTTA
34722901 -AGGTTAAAATGTGATTTTAGGAAAGTTTGAGGGTTAAAATGTGATTTTAGGAAAGTTTGAGGGT
1 GAGGTTAAAATGTGATTTT-GGAAAGTTTGAGGGTTAAAATGTGATTTTAGGAAAGTTTGAGGGT
* * * * * *
34722965 TGAAATGTAATTTTGAAAGGTTCGAGGGTT-AAATATAATTTTGGAATAGTTTGGGGAGTCAAAA
65 TAAAATGTAATTTTGGAA-GTT-TAGGGTTAAAATGTAATTTTGGAA-AGTTTGAGG-GTTAAAA
*
34723029 TATAATTTTGGAGAAGTTTA
126 TGTAATTTTGG-GAAGTTTA
* *
34723049 GGGGTCAAAAT
1 GAGGTTAAAAT
34723060 ATTGTTTCTA
Statistics
Matches: 268, Mismatches: 25, Indels: 24
0.85 0.08 0.08
Matches are distributed among these distances:
145 5 0.02
146 77 0.29
147 153 0.57
148 25 0.09
149 8 0.03
ACGTcount: A:0.35, C:0.01, G:0.28, T:0.36
Consensus pattern (144 bp):
GAGGTTAAAATGTGATTTTGGAAAGTTTGAGGGTTAAAATGTGATTTTAGGAAAGTTTGAGGGTT
AAAATGTAATTTTGGAAGTTTAGGGTTAAAATGTAATTTTGGAAAGTTTGAGGGTTAAAATGTAA
TTTTGGGAAGTTTA
Found at i:34722983 original size:117 final size:118
Alignment explanation
Indices: 34722609--34723016 Score: 544
Period size: 117 Copynumber: 3.5 Consensus size: 118
34722599 AGAATTTTGA
* * *
34722609 GGTTAAAATGTAATTTTGGAAAAG-TTTAAGGGTAAAAATGTAATTATGGGAAAGTTTAGGGTTA
1 GGTTAAAATGTAATTTTGG-AAAGTTTTGAGGGTTAAAATGTAATTTTGGGAAAGTTTAGGGTTA
* * *
34722673 AAATGTGATTTTAGGAAAATTTG-GGATTAAAATGTAATTTTGGAAAGGTTAAG
65 AAATGTGATTTTAGGAAAGTTTGAGGGTTAAAATGTAATTTTGGAAAGTTTAAG
* * * * *
34722726 GGTTTAAAATGTGATTTTGGGAAGTTTAG-GGGTTAAAATGTGATTTTGGGAAAGTTTGGGGTTA
1 GG-TTAAAATGTAATTTTGGAAAGTTTTGAGGGTTAAAATGTAATTTTGGGAAAGTTTAGGGTTA
34722790 AAATGTGATTTTAGGAAAGTTTGAGGGTTAAAATGTAATTTTGG-AAGTTTAAG
65 AAATGTGATTTTAGGAAAGTTTGAGGGTTAAAATGTAATTTTGGAAAGTTTAAG
* *
34722843 GGTTAAAATGTGATTTTAGGAAAGTTTTGAGGGTTAAAATGTAATTTTGGG-AAGTTTAAGGTTA
1 GGTTAAAATGTAATTTT-GGAAAGTTTTGAGGGTTAAAATGTAATTTTGGGAAAGTTTAGGGTTA
* *
34722907 AAATGTGATTTTAGGAAAGTTTGAGGGTTAAAATGTGATTTTAGGAAAGTTTGAG
65 AAATGTGATTTTAGGAAAGTTTGAGGGTTAAAATGTAATTTT-GGAAAGTTTAAG
* * * *
34722962 GGTTGAAATGTAATTTT-GAAAGGTTCGAGGGTT-AAATATAATTTT-GGAATAGTTT
1 GGTTAAAATGTAATTTTGGAAAGTTTTGAGGGTTAAAATGTAATTTTGGGAA-AGTTT
34723017 GGGGAGTCAA
Statistics
Matches: 259, Mismatches: 23, Indels: 18
0.86 0.08 0.06
Matches are distributed among these distances:
115 2 0.01
116 27 0.10
117 148 0.57
118 59 0.23
119 23 0.09
ACGTcount: A:0.34, C:0.00, G:0.28, T:0.38
Consensus pattern (118 bp):
GGTTAAAATGTAATTTTGGAAAGTTTTGAGGGTTAAAATGTAATTTTGGGAAAGTTTAGGGTTAA
AATGTGATTTTAGGAAAGTTTGAGGGTTAAAATGTAATTTTGGAAAGTTTAAG
Found at i:34723033 original size:31 final size:30
Alignment explanation
Indices: 34722613--34723061 Score: 179
Period size: 30 Copynumber: 15.2 Consensus size: 30
34722603 TTTTGAGGTT
* * * *
34722613 AAAATGTAATTTTGGAAAAGTTTAAGGGTA
1 AAAATATAATTTTGGAGAAGTTTAGGGGTC
* * *
34722643 AAAATGTAATTATGG-GAAAGTTTA-GGGTT
1 AAAATATAATTTTGGAG-AAGTTTAGGGGTC
* * * * *
34722672 AAAATGTGATTTTAGGA-AAATTT-GGGATT
1 AAAATATAATTTT-GGAGAAGTTTAGGGGTC
* * * *
34722701 AAAATGTAATTTTGGA-AAGGTTAAGGGTTT
1 AAAATATAATTTTGGAGAA-GTTTAGGGGTC
* * *
34722731 AAAATGTGATTTTGG-GAAGTTTAGGGGTT
1 AAAATATAATTTTGGAGAAGTTTAGGGGTC
* * *
34722760 AAAATGTGATTTTGG-GAAAGTTT-GGGGTT
1 AAAATATAATTTTGGAG-AAGTTTAGGGGTC
* * *
34722789 AAAATGTGATTTTAGGA-AAGTTT-GAGGGTT
1 AAAATATAATTTT-GGAGAAGTTTAG-GGGTC
* * *
34722819 AAAATGTAATTTT-G-GAAGTTTAAGGGTT
1 AAAATATAATTTTGGAGAAGTTTAGGGGTC
* * * *
34722847 AAAATGTGATTTTAGGA-AAGTTTTGAGGGTT
1 AAAATATAATTTT-GGAGAAGTTTAG-GGGTC
* * *
34722878 AAAATGTAATTTTGG-GAAGTTTA-AGGTT
1 AAAATATAATTTTGGAGAAGTTTAGGGGTC
* * *
34722906 AAAATGTGATTTTAGGA-AAGTTT-GAGGGTT
1 AAAATATAATTTT-GGAGAAGTTTAG-GGGTC
* * *
34722936 AAAATGTGATTTTAGGA-AAGTTT-GAGGGTT
1 AAAATATAATTTT-GGAGAAGTTTAG-GGGTC
* * * *
34722966 GAAATGTAATTTT-GA-AAGGTTCGAGGGT-
1 AAAATATAATTTTGGAGAAGTTTAG-GGGTC
* *
34722994 TAAATATAATTTTGGA-ATAGTTTGGGGAGTC
1 AAAATATAATTTTGGAGA-AGTTTAGGG-GTC
34723025 AAAATATAATTTTGGAGAAGTTTAGGGGTC
1 AAAATATAATTTTGGAGAAGTTTAGGGGTC
34723055 AAAATAT
1 AAAATAT
34723062 TGTTTCTAAA
Statistics
Matches: 358, Mismatches: 33, Indels: 56
0.80 0.07 0.13
Matches are distributed among these distances:
28 63 0.18
29 108 0.30
30 146 0.41
31 40 0.11
32 1 0.00
ACGTcount: A:0.35, C:0.01, G:0.28, T:0.37
Consensus pattern (30 bp):
AAAATATAATTTTGGAGAAGTTTAGGGGTC
Found at i:34725785 original size:209 final size:214
Alignment explanation
Indices: 34725382--34725799 Score: 490
Period size: 209 Copynumber: 2.0 Consensus size: 214
34725372 TATCGCTTTA
* * * * *
34725382 TTTCGCTCACATTGAGCTTCGCTTCATCGATTTGGTCTTTTTCTCTGTATCTCTTCAGGAAGATG
1 TTTCACTCACATTGAGCTTCGCTTCATCGATTTGATCTTCTTCTCTGTACCTCTTCAAGAAGATG
* * * * * * *
34725447 ATCGCATCACTTGTTTTAATTCGCTTCTCTGTATCTCATTAGGAAAACGGATTTGGTCCACTTCT
66 ACCGCATCACTTATTTCAATCCACTTCTCTGTATCTCATCAGGAAAACAGATTTGG--CAC-TCT
* * * ** *
34725512 CACTTCTCTATATCTCATCAGGAAGACGGCCGCTTTATTGTTTTGACCCACTTCTCAGTATCTCA
128 CACTTCTCTACATCTCATCAAGAAGACGACCGCTTTATTACTTTAACCCACTTCTCAGTATCTCA
* *
34725577 TTAGGAAGATGAGGGTTCGAAG
193 TCAAGAAGATGAGGGTTCGAAG
* *
34725599 TTTCACTCACATTGAGCTTTGCTTCATTGATTTGAT-TTACTTCTCTGTACCT-TATCAAGAAGA
1 TTTCACTCACATTGAGCTTCGCTTCATCGATTTGATCTT-CTTCTCTGTACCTCT-TCAAGAAGA
* *
34725662 TGACCGCCTCA-TTATTTCAATCCACTTCTCTGTATCTCATCAGGAAGACAGATTT-G-A-TC-C
64 TGACCGCATCACTTATTTCAATCCACTTCTCTGTATCTCATCAGGAAAACAGATTTGGCACTCTC
* * * *
34725722 ACTTCTCTGCATCTCGTCAAGAAGATGACCGCTTTATTACTTTAACCCACTTCTCTGTATCTCAT
129 ACTTCTCTACATCTCATCAAGAAGACGACCGCTTTATTACTTTAACCCACTTCTCAGTATCTCAT
34725787 CAAGAAGATGAGG
194 CAAGAAGATGAGG
34725800 TTTGATTTGC
Statistics
Matches: 171, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
209 67 0.39
210 2 0.01
212 1 0.01
215 1 0.01
216 40 0.23
217 60 0.35
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.37
Consensus pattern (214 bp):
TTTCACTCACATTGAGCTTCGCTTCATCGATTTGATCTTCTTCTCTGTACCTCTTCAAGAAGATG
ACCGCATCACTTATTTCAATCCACTTCTCTGTATCTCATCAGGAAAACAGATTTGGCACTCTCAC
TTCTCTACATCTCATCAAGAAGACGACCGCTTTATTACTTTAACCCACTTCTCAGTATCTCATCA
AGAAGATGAGGGTTCGAAG
Found at i:34725947 original size:39 final size:39
Alignment explanation
Indices: 34725885--34725995 Score: 145
Period size: 39 Copynumber: 2.8 Consensus size: 39
34725875 AAGATTGGAT
* *
34725885 GATGGCTGCAATTTGCCCCATGATCGGGGTAAGAA-AT-T
1 GATGGCTGCAATCTGCCCCATGATCGGGGTAA-AAGATCA
* * *
34725923 GTATGGATGCAATCTGCTCTATGATCGGGGTAAAAGATCA
1 G-ATGGCTGCAATCTGCCCCATGATCGGGGTAAAAGATCA
34725963 GATGGCTGCAATCTGCCCCATGATCGGGGTAAA
1 GATGGCTGCAATCTGCCCCATGATCGGGGTAAA
34725996 GGTTGGATGC
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
38 3 0.05
39 58 0.94
40 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (39 bp):
GATGGCTGCAATCTGCCCCATGATCGGGGTAAAAGATCA
Found at i:34726055 original size:41 final size:41
Alignment explanation
Indices: 34725988--34726244 Score: 280
Period size: 41 Copynumber: 6.4 Consensus size: 41
34725978 CCCCATGATC
* *
34725988 GGGGT-AAAGGTTGG-ATGCTTCAATCTGCCCCTCTTGATTA
1 GGGGTAAAAGATTGGAAT-CTTCAATCTGCCCCTCTTGACTA
* * * *
34726028 GGGGTAAAAGATTGGAATCTTTAATCTGCTCCACTTGATTA
1 GGGGTAAAAGATTGGAATCTTCAATCTGCCCCTCTTGACTA
*
34726069 GGGGT-AAATATTGGAATCTTCAATCT-----TCTTGACTA
1 GGGGTAAAAGATTGGAATCTTCAATCTGCCCCTCTTGACTA
* *
34726104 GGGGTAAAAGAATGGAATCTTCAATCTGCCTCTCTTGACTA
1 GGGGTAAAAGATTGGAATCTTCAATCTGCCCCTCTTGACTA
* *
34726145 GGGGTAAAAGATTAGAATCTGT-AATCTGCCCCTCTTGATTA
1 GGGGTAAAAGATTGGAATCT-TCAATCTGCCCCTCTTGACTA
* * * *
34726186 GAGCTAAAAGACTGGAATCTTCAATCTGCCTCTCTTGACTA
1 GGGGTAAAAGATTGGAATCTTCAATCTGCCCCTCTTGACTA
* *
34726227 GGGGTAAAAAATAGGAAT
1 GGGGTAAAAGATTGGAAT
34726245 GACTGTAGTT
Statistics
Matches: 182, Mismatches: 25, Indels: 19
0.81 0.11 0.08
Matches are distributed among these distances:
35 12 0.07
36 19 0.10
40 25 0.14
41 123 0.68
42 3 0.02
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (41 bp):
GGGGTAAAAGATTGGAATCTTCAATCTGCCCCTCTTGACTA
Found at i:34726126 original size:117 final size:121
Alignment explanation
Indices: 34726005--34726244 Score: 328
Period size: 117 Copynumber: 2.0 Consensus size: 121
34725995 AGGTTGGATG
* * * *
34726005 CTTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGAATCTTTAATCTGCTCCACTTGATTAG
1 CTTCAATCTGCCCCTCTTGACTAGGGGTAAAAGATTAGAATCTGTAATCTGCCCCACTTGATTAG
* * * *
34726070 GGGT-AAATATTGGAATCTTCAA-T-CT-TCTTGACTAGGGGTAAAAGAAT-GGAAT
66 AGCTAAAAGACTGGAATCTTCAACTCCTCTCTTGACTAGGGGTAAAA-AATAGGAAT
* *
34726122 CTTCAATCTGCCTCTCTTGACTAGGGGTAAAAGATTAGAATCTGTAATCTGCCCCTCTTGATTAG
1 CTTCAATCTGCCCCTCTTGACTAGGGGTAAAAGATTAGAATCTGTAATCTGCCCCACTTGATTAG
34726187 AGCTAAAAGACTGGAATCTTCAATCTGCCTCTCTTGACTAGGGGTAAAAAATAGGAAT
66 AGCTAAAAGACTGGAATCTTCAA-CT-CCTCTCTTGACTAGGGGTAAAAAATAGGAAT
34726245 GACTGTAGTT
Statistics
Matches: 106, Mismatches: 10, Indels: 8
0.85 0.08 0.06
Matches are distributed among these distances:
117 61 0.58
118 16 0.15
120 1 0.01
122 5 0.05
123 23 0.22
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (121 bp):
CTTCAATCTGCCCCTCTTGACTAGGGGTAAAAGATTAGAATCTGTAATCTGCCCCACTTGATTAG
AGCTAAAAGACTGGAATCTTCAACTCCTCTCTTGACTAGGGGTAAAAAATAGGAAT
Found at i:34726587 original size:54 final size:55
Alignment explanation
Indices: 34726502--34726611 Score: 134
Period size: 54 Copynumber: 2.0 Consensus size: 55
34726492 TGTCTTTGCG
* * * * * *
34726502 ACCTCAACCTTTTCCTTCAACTCTTCATGGTATCGGGTTCGCCATTGCGGCCTCA
1 ACCTCAACCTTTCCCATCAACTCTTCATGGTACCAGATTCACCATTGCGGCCTCA
*
34726557 ACCTCAACCTTTCCCATC-ACAT-TTCATGGTACCAGATTCACCGTTGCGGCCTCA
1 ACCTCAACCTTTCCCATCAAC-TCTTCATGGTACCAGATTCACCATTGCGGCCTCA
34726611 A
1 A
34726612 TCTTTCCCAT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
54 30 0.64
55 17 0.36
ACGTcount: A:0.20, C:0.35, G:0.15, T:0.30
Consensus pattern (55 bp):
ACCTCAACCTTTCCCATCAACTCTTCATGGTACCAGATTCACCATTGCGGCCTCA
Found at i:34726706 original size:99 final size:98
Alignment explanation
Indices: 34726558--34726880 Score: 373
Period size: 98 Copynumber: 3.3 Consensus size: 98
34726548 GCGGCCTCAA
* * * *
34726558 CCTCAACCTTTCCCATCACAT-TTCATGGTACCAGATTCACCGTTGCGGCCTCAATCTTTCCCAT
1 CCTCAACCTTTCCCTTCAAATCTTCATGGTACCAG-TTCACCGTTACGGCCTCAACCTTTCCCAT
* * *
34726622 CACATCTTCTGAGGTACTGGGTTTGCCGTCACGG
65 CACATCTTCTGAGGTACTGGGTTCGACGTCGCGG
* *
34726656 CCTCAACCTTTCCCTTCAAATCTTCATGGTACCAAGTTCTCCATTACGGCCTCAACCTTTCCCAT
1 CCTCAACCTTTCCCTTCAAATCTTCATGGTACC-AGTTCACCGTTACGGCCTCAACCTTTCCCAT
* *
34726721 CACATCTTTTGAGGTACCGGGTTCGACGTCGCGG
65 CACATCTTCTGAGGTACTGGGTTCGACGTCGCGG
** ** * *
34726755 GTTCAACC-TTCCCTTCAAATCTTCATGGTACTGGGTTCGCTGTTACGGCCTCAACCTTTCCCAT
1 CCTCAACCTTTCCCTTCAAATCTTCATGGTAC-CAGTTCACCGTTACGGCCTCAACCTTTCCCAT
* * * * * *
34726819 CCCATCTTCTAAGGTATTGTGTTC-ATCGTTGCAG
65 CACATCTTCTGAGGTACTGGGTTCGA-CGTCGCGG
*
34726853 CCTCAACCTTTCCCTTTAAATCTTCATG
1 CCTCAACCTTTCCCTTCAAATCTTCATG
34726881 TTTTCTTAGC
Statistics
Matches: 191, Mismatches: 29, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
97 1 0.01
98 99 0.52
99 89 0.47
100 2 0.01
ACGTcount: A:0.19, C:0.33, G:0.16, T:0.33
Consensus pattern (98 bp):
CCTCAACCTTTCCCTTCAAATCTTCATGGTACCAGTTCACCGTTACGGCCTCAACCTTTCCCATC
ACATCTTCTGAGGTACTGGGTTCGACGTCGCGG
Found at i:34727837 original size:23 final size:22
Alignment explanation
Indices: 34727795--34727861 Score: 64
Period size: 24 Copynumber: 3.0 Consensus size: 22
34727785 CTCGACCTCT
**
34727795 CCTTTTCT-TTTTCCTTTTTTC
1 CCTTTTCTCTTTTTTTTTTTTC
*
34727816 CCTTTTCTCTTTTTTTTATTTTT
1 CCTTTTCTCTTTTTTTT-TTTTC
*
34727839 CTTTTTCTTCTTTTTTTCTTTTT
1 CCTTTTC-TCTTTTTTT-TTTTT
34727862 TTATTTATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
21 8 0.21
22 6 0.16
23 10 0.26
24 13 0.34
25 1 0.03
ACGTcount: A:0.01, C:0.21, G:0.00, T:0.78
Consensus pattern (22 bp):
CCTTTTCTCTTTTTTTTTTTTC
Found at i:34727838 original size:17 final size:16
Alignment explanation
Indices: 34727818--34727876 Score: 66
Period size: 17 Copynumber: 3.4 Consensus size: 16
34727808 CTTTTTTCCC
34727818 TTTTCTCTTTTTTTTAT
1 TTTTCT-TTTTTTTTAT
34727835 TTTTCTTTTTCTTCTT-T
1 TTTTCTTTTT-TT-TTAT
34727852 TTTTCTTTTTTTATTTAT
1 TTTTC-TTTTTT-TTTAT
34727870 TTTTCTT
1 TTTTCTT
34727877 CATCGAATCC
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
16 4 0.11
17 19 0.51
18 14 0.38
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTCTTTTTTTTTAT
Found at i:34727861 original size:24 final size:24
Alignment explanation
Indices: 34727802--34727862 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
34727792 TCTCCTTTTC
*
34727802 TTTTTCCTTTTTTCCCTTTTCTCT
1 TTTTTTCTTTTTTCCCTTTTCTCT
*
34727826 TTTTTT-TATTTTT-CTTTTTCTTCT
1 TTTTTTCT-TTTTTCCCTTTTC-TCT
34727850 TTTTTTCTTTTTT
1 TTTTTTCTTTTTT
34727863 TATTTATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 7 0.22
24 24 0.75
25 1 0.03
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (24 bp):
TTTTTTCTTTTTTCCCTTTTCTCT
Found at i:34732668 original size:19 final size:19
Alignment explanation
Indices: 34732644--34732717 Score: 56
Period size: 19 Copynumber: 4.3 Consensus size: 19
34732634 AGTTTCGAAG
34732644 AATTTTAGGGTTAAAATGT
1 AATTTTAGGGTTAAAATGT
34732663 AATTTT--GG--AAAA-G-
1 AATTTTAGGGTTAAAATGT
* *
34732676 --TTTAAGGGTAAAAATGT
1 AATTTTAGGGTTAAAATGT
* *
34732693 AATTATAGGATTAAAATGT
1 AATTTTAGGGTTAAAATGT
34732712 AATTTT
1 AATTTT
34732718 GGAAAGGTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 16
0.65 0.10 0.25
Matches are distributed among these distances:
11 3 0.07
13 2 0.05
14 1 0.02
15 8 0.20
16 1 0.02
17 2 0.05
19 24 0.59
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.39
Consensus pattern (19 bp):
AATTTTAGGGTTAAAATGT
Found at i:34732710 original size:49 final size:49
Alignment explanation
Indices: 34732644--34732741 Score: 151
Period size: 49 Copynumber: 2.0 Consensus size: 49
34732634 AGTTTCGAAG
* * *
34732644 AATTTTAGGGTTAAAATGTAATTTTGGAAAAGTTTAAGGGTAAAAATGT
1 AATTATAGGATTAAAATGTAATTTTGGAAAAGTTAAAGGGTAAAAATGT
* *
34732693 AATTATAGGATTAAAATGTAATTTTGGAAAGGTTAAAGGGTCAAAATGT
1 AATTATAGGATTAAAATGTAATTTTGGAAAAGTTAAAGGGTAAAAATGT
34732742 GATTTTGGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.42, C:0.01, G:0.22, T:0.35
Consensus pattern (49 bp):
AATTATAGGATTAAAATGTAATTTTGGAAAAGTTAAAGGGTAAAAATGT
Found at i:34732739 original size:30 final size:30
Alignment explanation
Indices: 34732713--34732846 Score: 169
Period size: 30 Copynumber: 4.5 Consensus size: 30
34732703 TTAAAATGTA
* *
34732713 ATTTTGGAAAGGTTAAAGGGTCAAAATGTG
1 ATTTTGGAAAAGTTAAAGGGTCAAAATATG
34732743 ATTTTGGAAAAGTTAAAGGGTCAAAATATG
1 ATTTTGGAAAAGTTAAAGGGTCAAAATATG
* * * * * * *
34732773 ATTTTGAAAAAATCAAGGGGTTAAAATCTT
1 ATTTTGGAAAAGTTAAAGGGTCAAAATATG
* *
34732803 ATTTTGGGAAAGTTTAAGGGTCAAAATATG
1 ATTTTGGAAAAGTTAAAGGGTCAAAATATG
34732833 ATTTTGGAAAAGTT
1 ATTTTGGAAAAGTT
34732847 CAAAATGTGA
Statistics
Matches: 85, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 85 1.00
ACGTcount: A:0.40, C:0.04, G:0.24, T:0.33
Consensus pattern (30 bp):
ATTTTGGAAAAGTTAAAGGGTCAAAATATG
Found at i:34732866 original size:21 final size:22
Alignment explanation
Indices: 34732823--34732867 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
34732813 AGTTTAAGGG
34732823 TCAAAATATGATTTTGGAAAAGT
1 TCAAAATATGATTTT-GAAAAGT
*
34732846 TCAAAATGTGATTTT-AAAAGT
1 TCAAAATATGATTTTGAAAAGT
34732867 T
1 T
34732868 TGGAGGTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.33
23 14 0.67
ACGTcount: A:0.42, C:0.04, G:0.16, T:0.38
Consensus pattern (22 bp):
TCAAAATATGATTTTGAAAAGT
Found at i:34733009 original size:30 final size:28
Alignment explanation
Indices: 34732848--34733013 Score: 199
Period size: 30 Copynumber: 5.6 Consensus size: 28
34732838 GGAAAAGTTC
34732848 AAAATGTGATTTTA-AAAGTTTGGAGGTT
1 AAAATGTGATTTTAGAAAGTTTGG-GGTT
*
34732876 AAAATGTGATTTTGGATAAGTTTGGGGTTT
1 AAAATGTGATTTTAGA-AAGTTTGGGG-TT
* * *
34732906 AAAATGTGATTTTGGGAAAATTTAAGGGTT
1 AAAATGTGATTTT-AGAAAGTTT-GGGGTT
*
34732936 AAAATGTGATTTTGGGAAAGTTTGAGGGTT
1 AAAATGTGATTTT-AGAAAGTTTG-GGGTT
34732966 AAAATGTGATTTTAAGAAAGTTTTGGGGTT
1 AAAATGTGATTTT-AGAAAG-TTTGGGGTT
34732996 AAAATGTGATTTTAGAAA
1 AAAATGTGATTTTAGAAA
34733014 ATGTGATTTT
Statistics
Matches: 124, Mismatches: 7, Indels: 13
0.86 0.05 0.09
Matches are distributed among these distances:
28 13 0.10
29 8 0.06
30 93 0.75
31 10 0.08
ACGTcount: A:0.34, C:0.00, G:0.27, T:0.39
Consensus pattern (28 bp):
AAAATGTGATTTTAGAAAGTTTGGGGTT
Found at i:34733016 original size:15 final size:15
Alignment explanation
Indices: 34732996--34733029 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
34732986 TTTTGGGGTT
34732996 AAAATGTGATTTTAG
1 AAAATGTGATTTTAG
34733011 AAAATGTGATTTTAG
1 AAAATGTGATTTTAG
34733026 AAAA
1 AAAA
34733030 GTTTGGGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (15 bp):
AAAATGTGATTTTAG
Found at i:34733017 original size:45 final size:45
Alignment explanation
Indices: 34732966--34733053 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
34732956 TTTGAGGGTT
34732966 AAAATGTGATTTTA-AGAAAGTTTTGGGG-TTAAAATGTGATTTTAG
1 AAAATGTGATTTTAGA-AAAG-TTTGGGGTTTAAAATGTGATTTTAG
34733011 AAAATGTGATTTTAGAAAAGTTTGGGGTTTAAAATGTGATTTT
1 AAAATGTGATTTTAGAAAAGTTTGGGGTTTAAAATGTGATTTT
34733054 GGGAAAATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
44 7 0.17
45 33 0.80
46 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.24, T:0.41
Consensus pattern (45 bp):
AAAATGTGATTTTAGAAAAGTTTGGGGTTTAAAATGTGATTTTAG
Found at i:34733034 original size:75 final size:75
Alignment explanation
Indices: 34732936--34733082 Score: 215
Period size: 75 Copynumber: 2.0 Consensus size: 75
34732926 TTTAAGGGTT
* * * **
34732936 AAAATGTGATTTTGGGAAAGTTTGAGGG-TTAAAATGTGATTTTAAGAAAGTTTTGGGGTTAAAA
1 AAAATGTGATTTTAGAAAAGTTTG-GGGTTTAAAATGTGATTTTAAGAAAATTTAAGGGTTAAAA
34733000 TGTGATTTTAG
65 TGTGATTTTAG
**
34733011 AAAATGTGATTTTAGAAAAGTTTGGGGTTTAAAATGTGATTTTGGGAAAATTTAAGGGTTAAAAT
1 AAAATGTGATTTTAGAAAAGTTTGGGGTTTAAAATGTGATTTTAAGAAAATTTAAGGGTTAAAAT
34733076 GTGATTT
66 GTGATTT
34733083 GGGAAAGTTT
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
74 3 0.05
75 61 0.95
ACGTcount: A:0.35, C:0.00, G:0.27, T:0.39
Consensus pattern (75 bp):
AAAATGTGATTTTAGAAAAGTTTGGGGTTTAAAATGTGATTTTAAGAAAATTTAAGGGTTAAAAT
GTGATTTTAG
Found at i:34733045 original size:105 final size:105
Alignment explanation
Indices: 34732906--34733118 Score: 308
Period size: 105 Copynumber: 2.0 Consensus size: 105
34732896 TTTGGGGTTT
* * *
34732906 AAAATGTGATTTTGGGAAAATTTAAGGGTTAAAATGTGATTTTGGGAAAGTTTGAGGGTTAAAAT
1 AAAATGTGATTTTGAGAAAATTTAAGGGTTAAAATGTGATTTTGGGAAAATTTAAGGGTTAAAAT
34732971 GTGATTTTAAGAAAGTTTTG-GGGTTAAAATGTGATTTT-AG
66 GTGA-TTTAAGAAAG-TTTGAGGGTTAAAATGTGATTTTAAG
*
34733011 AAAATGTGATTTT-AGAAAAGTTT-GGGGTTTAAAATGTGATTTTGGGAAAATTTAAGGGTTAAA
1 AAAATGTGATTTTGAGAAAA-TTTAAGGG-TTAAAATGTGATTTTGGGAAAATTTAAGGGTTAAA
**
34733074 ATGTGATTTGGGAAAGTTTGAGGGTTAAAATGTGATTTTAAG
64 ATGTGATTTAAGAAAGTTTGAGGGTTAAAATGTGATTTTAAG
34733116 AAA
1 AAA
34733119 GTTTTGAGGT
Statistics
Matches: 98, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
103 4 0.04
104 34 0.35
105 60 0.61
ACGTcount: A:0.36, C:0.00, G:0.27, T:0.37
Consensus pattern (105 bp):
AAAATGTGATTTTGAGAAAATTTAAGGGTTAAAATGTGATTTTGGGAAAATTTAAGGGTTAAAAT
GTGATTTAAGAAAGTTTGAGGGTTAAAATGTGATTTTAAG
Found at i:34733097 original size:29 final size:30
Alignment explanation
Indices: 34733011--34733143 Score: 166
Period size: 30 Copynumber: 4.5 Consensus size: 30
34733001 GTGATTTTAG
*
34733011 AAAATGTGATTTTAGAAAAGTTTG-GGGTTT
1 AAAATGTGATTTTAGGAAAGTTTGAGGG-TT
* * *
34733041 AAAATGTGATTTTGGGAAAATTTAAGGGTT
1 AAAATGTGATTTTAGGAAAGTTTGAGGGTT
*
34733071 AAAATGTGA-TTTGGGAAAGTTTGAGGGTT
1 AAAATGTGATTTTAGGAAAGTTTGAGGGTT
*
34733100 AAAATGTGATTTTAAGAAAGTTTTGA-GGTT
1 AAAATGTGATTTTAGGAAAG-TTTGAGGGTT
34733130 -AAATGTGATTTTAG
1 AAAATGTGATTTTAG
34733144 AAAAAATTTG
Statistics
Matches: 91, Mismatches: 9, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
29 40 0.44
30 43 0.47
31 8 0.09
ACGTcount: A:0.35, C:0.00, G:0.27, T:0.38
Consensus pattern (30 bp):
AAAATGTGATTTTAGGAAAGTTTGAGGGTT
Found at i:34733130 original size:59 final size:59
Alignment explanation
Indices: 34733011--34733147 Score: 163
Period size: 59 Copynumber: 2.3 Consensus size: 59
34733001 GTGATTTTAG
**
34733011 AAAATGTGATTTTAGAAAAGTTTGGGGTTTAAAATGTGATTTTGGGAAAATTTAAGGGTT
1 AAAATGTGA-TTTAGAAAAGTTTGGGGTTTAAAATGTGATTTTAAGAAAATTTAAGGGTT
* * * *
34733071 AAAATGTGATTTGGGAAAGTTTGAGGG-TTAAAATGTGATTTTAAGAAAGTTT-TGAGGTT
1 AAAATGTGATTTAGAAAAGTTTG-GGGTTTAAAATGTGATTTTAAGAAAATTTAAG-GGTT
34733130 -AAATGTGATTTTAGAAAA
1 AAAATGTGA-TTTAGAAAA
34733148 AATTTGAGGA
Statistics
Matches: 66, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
58 9 0.14
59 45 0.68
60 12 0.18
ACGTcount: A:0.36, C:0.00, G:0.26, T:0.37
Consensus pattern (59 bp):
AAAATGTGATTTAGAAAAGTTTGGGGTTTAAAATGTGATTTTAAGAAAATTTAAGGGTT
Found at i:34733150 original size:135 final size:135
Alignment explanation
Indices: 34732876--34733147 Score: 503
Period size: 135 Copynumber: 2.0 Consensus size: 135
34732866 TTTGGAGGTT
* *
34732876 AAAATGTGATTTTGGATAAGTTTGGGGTTTAAAATGTGATTTTGGGAAAATTTAAGGGTTAAAAT
1 AAAATGTGATTTTAGAAAAGTTTGGGGTTTAAAATGTGATTTTGGGAAAATTTAAGGGTTAAAAT
*
34732941 GTGATTTTGGGAAAGTTTGAGGGTTAAAATGTGATTTTAAGAAAGTTTTGGGGTTAAAATGTGAT
66 GTGATTTTGGGAAAGTTTGAGGGTTAAAATGTGATTTTAAGAAAGTTTTGAGGTTAAAATGTGAT
34733006 TTTAG
131 TTTAG
34733011 AAAATGTGATTTTAGAAAAGTTTGGGGTTTAAAATGTGATTTTGGGAAAATTTAAGGGTTAAAAT
1 AAAATGTGATTTTAGAAAAGTTTGGGGTTTAAAATGTGATTTTGGGAAAATTTAAGGGTTAAAAT
34733076 GTGA-TTTGGGAAAGTTTGAGGGTTAAAATGTGATTTTAAGAAAGTTTTGAGGTT-AAATGTGAT
66 GTGATTTTGGGAAAGTTTGAGGGTTAAAATGTGATTTTAAGAAAGTTTTGAGGTTAAAATGTGAT
34733139 TTTAG
131 TTTAG
34733144 AAAA
1 AAAA
34733148 AATTTGAGGA
Statistics
Matches: 134, Mismatches: 3, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
133 18 0.13
134 49 0.37
135 67 0.50
ACGTcount: A:0.35, C:0.00, G:0.27, T:0.38
Consensus pattern (135 bp):
AAAATGTGATTTTAGAAAAGTTTGGGGTTTAAAATGTGATTTTGGGAAAATTTAAGGGTTAAAAT
GTGATTTTGGGAAAGTTTGAGGGTTAAAATGTGATTTTAAGAAAGTTTTGAGGTTAAAATGTGAT
TTTAG
Found at i:34733153 original size:29 final size:30
Alignment explanation
Indices: 34733011--34733156 Score: 124
Period size: 29 Copynumber: 4.9 Consensus size: 30
34733001 GTGATTTTAG
* *
34733011 AAAATGTGATTTTAG-AAAAGTTTGGGGTTT
1 AAAATGTGATTTTAGAAAAAATTTGAGG-TT
** *
34733041 AAAATGTGATTTT-GGGAAAATTTAAGGGTT
1 AAAATGTGATTTTAGAAAAAATTTGA-GGTT
** *
34733071 AAAATGTGA-TTT-GGGAAAGTTTGAGGGTT
1 AAAATGTGATTTTAGAAAAAATTTGA-GGTT
**
34733100 AAAATGTGATTTTA-AGAAAGTTTTGAGGTT
1 AAAATGTGATTTTAGA-AAAAATTTGAGGTT
34733130 -AAATGTGATTTTAGAAAAAATTTGAGG
1 AAAATGTGATTTTAGAAAAAATTTGAGG
34733157 ATCTCAGGGG
Statistics
Matches: 98, Mismatches: 12, Indels: 13
0.80 0.10 0.11
Matches are distributed among these distances:
29 51 0.52
30 38 0.39
31 9 0.09
ACGTcount: A:0.36, C:0.00, G:0.27, T:0.37
Consensus pattern (30 bp):
AAAATGTGATTTTAGAAAAAATTTGAGGTT
Found at i:34735761 original size:12 final size:14
Alignment explanation
Indices: 34735740--34735780 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 14
34735730 CACAAAATCT
*
34735740 TCTTCATTTTCTT-
1 TCTTCCTTTTCTTC
34735753 T-TTCCTTTTCTTC
1 TCTTCCTTTTCTTC
34735766 TCTTCCTTCTTCTTC
1 TCTTCCTT-TTCTTC
34735781 AACACCCATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 10 0.42
13 2 0.08
14 6 0.25
15 6 0.25
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (14 bp):
TCTTCCTTTTCTTC
Found at i:34752589 original size:18 final size:18
Alignment explanation
Indices: 34752566--34752608 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
34752556 GAATAATTTT
34752566 TTAATTAAATAAATTTAA-
1 TTAATTAAA-AAATTTAAC
*
34752584 TTAATTAAAAATTTTAAC
1 TTAATTAAAAAATTTAAC
34752602 TTAATTA
1 TTAATTA
34752609 CAACTGAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAC
Found at i:34753402 original size:17 final size:17
Alignment explanation
Indices: 34753361--34753402 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
34753351 TTTTTGAACT
34753361 AACTAATAAAATTATAAA
1 AACTAA-AAAATTATAAA
*
34753379 ATA-TAAAAACTTATAAA
1 A-ACTAAAAAATTATAAA
34753396 AACTAAA
1 AACTAAA
34753403 TTATGTTAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
16 1 0.05
17 15 0.71
18 4 0.19
19 1 0.05
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (17 bp):
AACTAAAAAATTATAAA
Found at i:34754311 original size:110 final size:109
Alignment explanation
Indices: 34754119--34754320 Score: 255
Period size: 110 Copynumber: 1.8 Consensus size: 109
34754109 ACACAATGCT
* * *
34754119 TAGAATTATCCATATCTCTTCTCCAACCCATAAATAAAAAGATAATATATTTCAGCACACTCAAT
1 TAGAATTATCCATATCTCTTCTCCAACCCATAAATAAAAAGATAATACATTTCACCACACTCAAC
* *
34754184 CCCACATTCTGCTACATTGGCAACAATGCCTATGATATAATATC
66 CCCACATTCTCCTACATTAGCAACAATGCCTATGATATAATATC
* * * * * * *
34754228 TAGAATTATCCATAGGTCTC-TCTCCAACCCATAAATAAGAGGATAATGCGTTTTACCGCATTCA
1 TAGAATTATCCATA--TCTCTTCTCCAACCCATAAATAAAAAGATAATACATTTCACCACACTCA
34754292 ACCCCACA-TCTTCCTACATTAGCAACAAT
64 ACCCCACATTC-TCCTACATTAGCAACAAT
34754321 ACCCATGTCA
Statistics
Matches: 78, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
109 16 0.21
110 58 0.74
111 4 0.05
ACGTcount: A:0.36, C:0.26, G:0.09, T:0.29
Consensus pattern (109 bp):
TAGAATTATCCATATCTCTTCTCCAACCCATAAATAAAAAGATAATACATTTCACCACACTCAAC
CCCACATTCTCCTACATTAGCAACAATGCCTATGATATAATATC
Found at i:34755016 original size:28 final size:31
Alignment explanation
Indices: 34754983--34755058 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 31
34754973 TAAAATGAGG
* *
34754983 TTTTAGGTTCCTTAAAA-TTTG-AAAAAAAA
1 TTTTAGGTCCCTTAAAAGTTGGTAAAAAAAA
* *
34755012 -TTTAGATCCCGTAAAAGTTGGTAAAAAAAA
1 TTTTAGGTCCCTTAAAAGTTGGTAAAAAAAA
34755042 TTTTAGG-CCCTTAAAAG
1 TTTTAGGTCCCTTAAAAG
34755059 CTAAAAAGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
28 13 0.34
29 3 0.08
30 17 0.45
31 5 0.13
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (31 bp):
TTTTAGGTCCCTTAAAAGTTGGTAAAAAAAA
Found at i:34755057 original size:30 final size:29
Alignment explanation
Indices: 34754983--34755102 Score: 81
Period size: 30 Copynumber: 4.2 Consensus size: 29
34754973 TAAAATGAGG
* *
34754983 TTTTAGGTTCCTTAAAA-TTTGAAAAAAAA
1 TTTTAGG-CCCTTAAAAGTTGGAAAAAAAA
* *
34755012 -TTTAGATCCCGTAAAAGTTGGTAAAAAAAA
1 TTTTAG-GCCCTTAAAAGTTGG-AAAAAAAA
* *
34755042 TTTTAGGCCCTTAAAAGCT--AAAAAGAA
1 TTTTAGGCCCTTAAAAGTTGGAAAAAAAA
* *
34755069 --TTGGGCCCTTGAAAAGTTGGAAAACAATA
1 TTTTAGGCCCTT-AAAAGTTGGAAAA-AAAA
34755098 TTTTA
1 TTTTA
34755103 AACCCATTTC
Statistics
Matches: 68, Mismatches: 13, Indels: 18
0.69 0.13 0.18
Matches are distributed among these distances:
25 9 0.13
26 6 0.09
27 7 0.10
28 16 0.24
29 5 0.07
30 18 0.26
31 7 0.10
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (29 bp):
TTTTAGGCCCTTAAAAGTTGGAAAAAAAA
Found at i:34762615 original size:20 final size:21
Alignment explanation
Indices: 34762575--34762615 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
34762565 AGTTGTCTTC
34762575 TATGTCGCGACACAAGCCTAG
1 TATGTCGCGACACAAGCCTAG
*
34762596 TATGTCGCGACA-ATGCCTAG
1 TATGTCGCGACACAAGCCTAG
34762616 AAAACACACC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.22
Consensus pattern (21 bp):
TATGTCGCGACACAAGCCTAG
Found at i:34780786 original size:25 final size:24
Alignment explanation
Indices: 34780697--34780804 Score: 137
Period size: 24 Copynumber: 4.5 Consensus size: 24
34780687 ATGCTGGTTA
*
34780697 AACTCTATCTGGGCTCGAATGAGCT
1 AACT-TATCTGGGCTCGTATGAGCT
*
34780722 AACTTATCTGGGCTCGTAAGAGCT
1 AACTTATCTGGGCTCGTATGAGCT
*
34780746 AACTTATCTGAGCTCGTATGAGCT
1 AACTTATCTGGGCTCGTATGAGCT
* *
34780770 AATTTTGTCTGGGCTCGTATGAGCT
1 AA-CTTATCTGGGCTCGTATGAGCT
*
34780795 AAATT-TCTGG
1 AACTTATCTGG
34780805 AGACTCAGCA
Statistics
Matches: 74, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.07
24 44 0.59
25 25 0.34
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (24 bp):
AACTTATCTGGGCTCGTATGAGCT
Found at i:34784316 original size:24 final size:24
Alignment explanation
Indices: 34784284--34784331 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
34784274 TAAGTAAGTT
34784284 TACCAGGTTTTGAGAAAAAAATTA
1 TACCAGGTTTTGAGAAAAAAATTA
34784308 TACCAGGTTTTGAGAAAAAAATTA
1 TACCAGGTTTTGAGAAAAAAATTA
34784332 GGAGTTAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.08, G:0.17, T:0.29
Consensus pattern (24 bp):
TACCAGGTTTTGAGAAAAAAATTA
Found at i:34796063 original size:192 final size:193
Alignment explanation
Indices: 34795729--34796169 Score: 627
Period size: 192 Copynumber: 2.3 Consensus size: 193
34795719 AACCAATACT
* * * *
34795729 CGATGTTGCTCACACGAGCTGTCGAGAACTCGCAATATATGCGGTACCCTAGCCATCTGTACAGT
1 CGATGCTGCTCACACGAGCTGTCGAGGACTCGTAATATATGCGGTACCCTAACCATCTGTACAGT
*
34795794 ATCTACCTGTAAACTGTCCCCCTAACGATGTTGCTCACACGAGCTGTCGAGAATATGCATTCAAC
66 ATCTACCTGTAAACTGTCCCCCTAACAATGTTGCTCACACGAGCTGTCGAGAATATGCATTCAAC
* * *
34795859 CATAAATCCCAGCCATCGTAAGGTATATAATCCATTTAGGATTTCATATCTTTTTTCGACTCA
131 CATAAATCCCAGCCATCGTAAGGTATATAATCCATTTAGGATTTCATATCTCTTTCCAACTCA
* * *
34795922 CGATGCTGCTCACACGAGCTGTCGAGGACTAGTAACATATGCGGTACCCTAACCAT-TGGTACGG
1 CGATGCTGCTCACACGAGCTGTCGAGGACTCGTAATATATGCGGTACCCTAACCATCT-GTACAG
*** *
34795986 TATCTGTTTGTAAACTGT-CCCTTAACAATGTTGCTCACACGAGCTGTCGAGAATATGCATTCAA
65 TATCTACCTGTAAACTGTCCCCCTAACAATGTTGCTCACACGAGCTGTCGAGAATATGCATTCAA
* * * * *
34796050 GCATAAATCCCAGCCATCGTAGGGTCTATAATCCATTTATGATTTCATATCTCTTTCCAACTTA
130 CCATAAATCCCAGCCATCGTAAGGTATATAATCCATTTAGGATTTCATATCTCTTTCCAACTCA
* * ** *
34796114 TGACGCTGCTCACACGAGCTGTTAAGGACTCGTAATATATGCAGTACCC-AACCATC
1 CGATGCTGCTCACACGAGCTGTCGAGGACTCGTAATATATGCGGTACCCTAACCATC
34796170 GCGTCAGTTT
Statistics
Matches: 219, Mismatches: 27, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
191 6 0.03
192 143 0.65
193 70 0.32
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (193 bp):
CGATGCTGCTCACACGAGCTGTCGAGGACTCGTAATATATGCGGTACCCTAACCATCTGTACAGT
ATCTACCTGTAAACTGTCCCCCTAACAATGTTGCTCACACGAGCTGTCGAGAATATGCATTCAAC
CATAAATCCCAGCCATCGTAAGGTATATAATCCATTTAGGATTTCATATCTCTTTCCAACTCA
Found at i:34804891 original size:17 final size:16
Alignment explanation
Indices: 34804866--34804897 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
34804856 TTGGTTGAGA
34804866 AAATTATTTAATTAAG
1 AAATTATTTAATTAAG
34804882 AAATTAATTTAATTAA
1 AAATT-ATTTAATTAA
34804898 TTTAATTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (16 bp):
AAATTATTTAATTAAG
Found at i:34806806 original size:32 final size:32
Alignment explanation
Indices: 34806760--34806820 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
34806750 GGACCTAAAT
**
34806760 TTTATCTCGAGATTCATGGGTTTTCAAAAAAC
1 TTTATCTCGAGATTCATGACTTTTCAAAAAAC
* * *
34806792 TTTATCTTGGGATTCTTGACTTTTCAAAA
1 TTTATCTCGAGATTCATGACTTTTCAAAA
34806821 TTCAATCTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.43
Consensus pattern (32 bp):
TTTATCTCGAGATTCATGACTTTTCAAAAAAC
Found at i:34808552 original size:5 final size:5
Alignment explanation
Indices: 34808542--34808566 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
34808532 CCCAGTAGAC
34808542 CTCAA CTCAA CTCAA CTCAA CTCAA
1 CTCAA CTCAA CTCAA CTCAA CTCAA
34808567 GGTACTCTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (5 bp):
CTCAA
Found at i:34815119 original size:24 final size:24
Alignment explanation
Indices: 34815091--34815138 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
34815081 AAATTCGTAA
34815091 GCAAAATAAATTATGCTAATAAAT
1 GCAAAATAAATTATGCTAATAAAT
*
34815115 GCAAAATATATTATGCTAATAAAT
1 GCAAAATAAATTATGCTAATAAAT
34815139 ACTAAATCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.31
Consensus pattern (24 bp):
GCAAAATAAATTATGCTAATAAAT
Found at i:34815145 original size:24 final size:24
Alignment explanation
Indices: 34815092--34815145 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
34815082 AATTCGTAAG
*
34815092 CAAAATAAATTATGCTAATAAATG
1 CAAAATAAATTATGCTAATAAATA
*
34815116 CAAAATATATTATGCTAATAAATA
1 CAAAATAAATTATGCTAATAAATA
*
34815140 CTAAAT
1 CAAAAT
34815146 CTTTTAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.54, C:0.09, G:0.06, T:0.31
Consensus pattern (24 bp):
CAAAATAAATTATGCTAATAAATA
Found at i:34816091 original size:14 final size:13
Alignment explanation
Indices: 34816067--34816096 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
34816057 TGGTTGGTAC
34816067 ATAATTATATTAT
1 ATAATTATATTAT
34816080 ATAATATATATTAT
1 ATAAT-TATATTAT
34816094 ATA
1 ATA
34816097 TGCTATGCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
ATAATTATATTAT
Found at i:34833168 original size:20 final size:21
Alignment explanation
Indices: 34833145--34833194 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
34833135 ATTAATATAA
*
34833145 TTAATATTTTAA-TAATAATT
1 TTAATATTTTAAGAAATAATT
34833165 TTAA-ATTTTAAGAAATAATT
1 TTAATATTTTAAGAAATAATT
34833185 TT-ATATTTTA
1 TTAATATTTTA
34833195 TTTAAAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 8 0.30
20 19 0.70
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
TTAATATTTTAAGAAATAATT
Found at i:34835145 original size:13 final size:13
Alignment explanation
Indices: 34835127--34835159 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
34835117 GCTTATTTTT
34835127 TTATATTTATATA
1 TTATATTTATATA
*
34835140 TTATATTTATTTA
1 TTATATTTATATA
34835153 TT-TATTT
1 TTATATTT
34835160 CTAATGCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTATATTTATATA
Found at i:34835307 original size:3 final size:3
Alignment explanation
Indices: 34835299--34835327 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
34835289 ATTGCCTTTA
34835299 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
34835328 AATAGTCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:34840599 original size:51 final size:51
Alignment explanation
Indices: 34840541--34840668 Score: 143
Period size: 50 Copynumber: 2.5 Consensus size: 51
34840531 GCAGCGGGTT
* * **
34840541 AGAATGAAATTACAAACAACAAATCTTATCTCCCCGAAGATGTAGTGGAGTA
1 AGAATGAAATTACAAACATCAAATCTTATATCCCCGAAGATACAGTGGA-TA
* * * * *
34840593 AG-ATGAAACTAC-AACATCAAATCCTATATCCCTGAAGTTACAGTGGATC
1 AGAATGAAATTACAAACATCAAATCTTATATCCCCGAAGATACAGTGGATA
*
34840642 AGAATGAAATTTCAAACATCAAATCTT
1 AGAATGAAATTACAAACATCAAATCTT
34840669 TATTTCTTTG
Statistics
Matches: 62, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
49 3 0.05
50 36 0.58
51 21 0.34
52 2 0.03
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (51 bp):
AGAATGAAATTACAAACATCAAATCTTATATCCCCGAAGATACAGTGGATA
Found at i:34840638 original size:50 final size:50
Alignment explanation
Indices: 34840555--34841338 Score: 404
Period size: 50 Copynumber: 15.7 Consensus size: 50
34840545 TGAAATTACA
* * * * * *
34840555 AACAACAAATCTTATCTCCCCGAAGATGTAGTGGAGTAAGATGAAACTAC
1 AACATCAAATCTTATATCCCTGAAGTTGCAGTGGAGTAAGATGAAGCTAC
* * * ** *
34840605 AACATCAAATCCTATATCCCTGAAGTTACAGTGGA-TCAGAATGAAATTTC
1 AACATCAAATCTTATATCCCTGAAGTTGCAGTGGAGTAAG-ATGAAGCTAC
* ** *** *
34840655 AAACATCAAATCTTTATTTCTTTGAAGTTGCAGCAAAGCAAGATGAAGCTAC
1 -AACATCAAATC-TTATATCCCTGAAGTTGCAGTGGAGTAAGATGAAGCTAC
* *
34840707 AACATCAAATCTTATATCCCTTAAGTTGCAGTGGA-TCAGATTGAAGCTAC
1 AACATCAAATCTTATATCCCTGAAGTTGCAGTGGAGTAAGA-TGAAGCTAC
* * * * * * *
34840757 AGA-AGCAAATCTTATCTCCTTGAAGTTACAGTGGAGCAAGATGAATCTAT
1 A-ACATCAAATCTTATATCCCTGAAGTTGCAGTGGAGTAAGATGAAGCTAC
* * * *
34840807 AACA-CAAATCCTATATCCCTAAAGTTGCAATGGA-TCAGATTGAAGCTAC
1 AACATCAAATCTTATATCCCTGAAGTTGCAGTGGAGTAAGA-TGAAGCTAC
* * * * * * * * *
34840856 AAAAGCAAATCTTATCTCCCTAAAGATGTAGTAGAGCAAGATGAAGTTAC
1 AACATCAAATCTTATATCCCTGAAGTTGCAGTGGAGTAAGATGAAGCTAC
*** * * ** * * *
34840906 GGTATCAAATCTTATATCCCTGAAGTTACAATGGAACAA-ATTAAAACTAT
1 AACATCAAATCTTATATCCCTGAAGTTGCAGTGGAGTAAGA-TGAAGCTAC
** * ** *
34840956 AGTAGCAAATCTT-TATCTCTCTGAAGTTGCAGCAGAGCAAGATGAAGCTAC
1 AACATCAAATCTTATATC-C-CTGAAGTTGCAGTGGAGTAAGATGAAGCTAC
* * * * ** *
34841007 AACATCAAATCTTACA-CCCTTGAAATTGTAGAGG-GTCGGATTGAAGTTAC
1 AACATCAAATCTTATATCCC-TGAAGTTGCAGTGGAGTAAGA-TGAAGCTAC
* * * * *
34841057 ATA-AGCAAGTCTTATCTCCCTGAAGATGTAGTGGAGTAAGATGAAGCTAC
1 A-ACATCAAATCTTATATCCCTGAAGTTGCAGTGGAGTAAGATGAAGCTAC
* * *
34841107 AACATCAAATCTTATATCCCTGAAGTTACAG-GGA-TTAGATTAAGACTAC
1 AACATCAAATCTTATATCCCTGAAGTTGCAGTGGAGTAAGATGAAG-CTAC
** * * *
34841156 AGTAGT-AAATCTT-TATCTCTCTGAAATTGCAGTAGAGCAAGATGAAGCTAC
1 AACA-TCAAATCTTATATC-C-CTGAAGTTGCAGTGGAGTAAGATGAAGCTAC
* * * * ** ** *
34841207 AAAATCAAGTCATATA-CCTTTGAAGTTATAGTGG-GTCGGATTGAAGCTGC
1 AACATCAAATCTTATATCC-CTGAAGTTGCAGTGGAGTAAGA-TGAAGCTAC
* * * *
34841257 AAAAGCATATC-TATCA-CCCTGAAGATGCAGTGGAGTAAGATGAAG--A-
1 AACATCAAATCTTAT-ATCCCTGAAGTTGCAGTGGAGTAAGATGAAGCTAC
* * *
34841303 AGACATCAAATCCTATATCCCTGAAGTAGTAGTGGA
1 A-ACATCAAATCTTATATCCCTGAAGTTGCAGTGGA
34841339 TTGGATTAAA
Statistics
Matches: 544, Mismatches: 154, Indels: 74
0.70 0.20 0.10
Matches are distributed among these distances:
46 1 0.00
47 8 0.01
48 33 0.06
49 90 0.17
50 293 0.54
51 83 0.15
52 34 0.06
53 2 0.00
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (50 bp):
AACATCAAATCTTATATCCCTGAAGTTGCAGTGGAGTAAGATGAAGCTAC
Found at i:34840963 original size:100 final size:100
Alignment explanation
Indices: 34840560--34841378 Score: 634
Period size: 100 Copynumber: 8.2 Consensus size: 100
34840550 TTACAAACAA
* * * * * * *
34840560 CAAATCTTATCTCCCCGAAGATGTAGTGGAGTAAGATGAAACTACAACATCAAATCCTATATCCC
1 CAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAAGATGAAGCTACAACATCAAATCTTATATCCC
* * * ** * ** *
34840625 TGAAGTTACAGTGGATCAGAATGAAATTTCAAACAT
66 TGAAGTTGCAATGGATCAGATTGAAGCTAC-AGTAG
* ** * *
34840661 CAAATCTTTATTTCTTTGAAGTTGCAGCAAAGCAAGATGAAGCTACAACATCAAATCTTATATCC
1 CAAATC-TTATCTCCCTGAAGTTGCAGTAGAGCAAGATGAAGCTACAACATCAAATCTTATATCC
* * *
34840726 CTTAAGTTGCAGTGGATCAGATTGAAGCTACAGAAG
65 CTGAAGTTGCAATGGATCAGATTGAAGCTACAGTAG
* * * * * *
34840762 CAAATCTTATCTCCTTGAAGTTACAGTGGAGCAAGATGAATCTATAACA-CAAATCCTATATCCC
1 CAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAAGATGAAGCTACAACATCAAATCTTATATCCC
* **
34840826 TAAAGTTGCAATGGATCAGATTGAAGCTACAAAAG
66 TGAAGTTGCAATGGATCAGATTGAAGCTACAGTAG
* * * * ***
34840861 CAAATCTTATCTCCCTAAAGATGTAGTAGAGCAAGATGAAGTTACGGTATCAAATCTTATATCCC
1 CAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAAGATGAAGCTACAACATCAAATCTTATATCCC
* * * * * *
34840926 TGAAGTTACAATGGAACAAATTAAAACTATAGTAG
66 TGAAGTTGCAATGGATCAGATTGAAGCTACAGTAG
* * *
34840961 CAAATCTTTATCTCTCTGAAGTTGCAGCAGAGCAAGATGAAGCTACAACATCAAATCTTACA-CC
1 CAAATC-TTATCTCCCTGAAGTTGCAGTAGAGCAAGATGAAGCTACAACATCAAATCTTATATCC
* * * * *
34841025 CTTGAAATTGTAGA-GGGTCGGATTGAAGTTACA-TAAG
65 C-TGAAGTTGCA-ATGGATCAGATTGAAGCTACAGT-AG
* * * * *
34841062 CAAGTCTTATCTCCCTGAAGATGTAGTGGAGTAAGATGAAGCTACAACATCAAATCTTATATCCC
1 CAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAAGATGAAGCTACAACATCAAATCTTATATCCC
* * *
34841127 TGAAGTTAC-AGGGATTAGATT-AAGACTACAGTAG
66 TGAAGTTGCAATGGATCAGATTGAAG-CTACAGTAG
* * * * * *
34841161 TAAATCTTTATCTCTCTGAAATTGCAGTAGAGCAAGATGAAGCTACAAAATCAAGTCATATA-CC
1 CAAATC-TTATCTCCCTGAAGTTGCAGTAGAGCAAGATGAAGCTACAACATCAAATCTTATATCC
* ** * * * * **
34841225 TTTGAAGTTATAGTGGGTCGGATTGAAGCTGCAAAAG
65 -CTGAAGTTGCAATGGATCAGATTGAAGCTACAGTAG
* * * * * *
34841262 CATATC-TATCACCCTGAAGATGCAGTGGAGTAAGATGAAG--A-AGACATCAAATCCTATATCC
1 CAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAAGATGAAGCTACA-ACATCAAATCTTATATCC
* * * ** * *
34841323 CTGAAGTAGTAGTGGATTGGATTAAAGCTACATTAG
65 CTGAAGTTGCAATGGATCAGATTGAAGCTACAGTAG
** *
34841359 CAAGCCCTATCTCCCTGAAG
1 CAAATCTTATCTCCCTGAAG
34841379 ATAGAGTGGA
Statistics
Matches: 565, Mismatches: 136, Indels: 37
0.77 0.18 0.05
Matches are distributed among these distances:
96 1 0.00
97 43 0.08
98 18 0.03
99 130 0.23
100 194 0.34
101 104 0.18
102 75 0.13
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (100 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAAGATGAAGCTACAACATCAAATCTTATATCCC
TGAAGTTGCAATGGATCAGATTGAAGCTACAGTAG
Found at i:34841168 original size:300 final size:301
Alignment explanation
Indices: 34840551--34841214 Score: 773
Period size: 300 Copynumber: 2.2 Consensus size: 301
34840541 AGAATGAAAT
* ** * * *
34840551 TACAAACAACAAATCTTATCTCCCCGAAGATGTAGTGGAGTAAGATGAAACTACAACATCAAATC
1 TACAAA-AGCAAATCTTATCTCCCTAAAGATGTAGTAGAGCAAGATGAAGCTACAACATCAAATC
* * ** * * *
34840616 CTATATCCCTGAAGTTACAGTGGATCAGAATGAAATTTCAAACATCAAATCTTTATTTCTTTGAA
65 CTATATCCCTGAAGTTACAATGGAACAGAATGAAAACTCAAACAGCAAATCTTTATCTCTCTGAA
* * *
34840681 GTTGCAGCAAAGCAAGATGAAGCTACAACATCAAATCTTATATCCCTTAAGTTGCAGTGGATCAG
130 GTTGCAGCAAAGCAAGATGAAGCTACAACATCAAATCTTACATCCCTTAAATTGCAGAGGATCAG
* * * *
34840746 ATTGAAGCTACAGAAGCAAATCTTATCTCCTTGAAGTTACAGTGGAGCAAGATGAATCTATAACA
195 ATTGAAGCTACAGAAGCAAATCTTATCTCCCTGAAGATACAGTGGAGCAAGATGAAGCTACAACA
* *
34840811 CAAATCCTATATCCCTAAAGTTGCAATGGATCAGATTGAAGC
260 CAAATCCTATATCCCTAAAGTTACAAGGGATCAGATTGAAGC
* *** *
34840853 TACAAAAGCAAATCTTATCTCCCTAAAGATGTAGTAGAGCAAGATGAAGTTACGGTATCAAATCT
1 TACAAAAGCAAATCTTATCTCCCTAAAGATGTAGTAGAGCAAGATGAAGCTACAACATCAAATCC
* **
34840918 TATATCCCTGAAGTTACAATGGAACA-AATTAAAACT-ATAGTAGCAAATCTTTATCTCTCTGAA
66 TATATCCCTGAAGTTACAATGGAACAGAATGAAAACTCA-AACAGCAAATCTTTATCTCTCTGAA
* * * *
34840981 GTTGCAGCAGAGCAAGATGAAGCTACAACATCAAATCTTACA-CCCTTGAAATTGTAGAGGGTCG
130 GTTGCAGCAAAGCAAGATGAAGCTACAACATCAAATCTTACATCCCTT-AAATTGCAGAGGATCA
* * * ** *
34841045 GATTGAAGTTACATAAGCAAGTCTTATCTCCCTGAAGATGTAGTGGAGTAAGATGAAGCTACAAC
194 GATTGAAGCTACAGAAGCAAATCTTATCTCCCTGAAGATACAGTGGAGCAAGATGAAGCTACAAC
* * *
34841110 ATCAAATCTTATATCCCTGAAGTTAC-AGGGATTAGATT-AAGAC
259 A-CAAATCCTATATCCCTAAAGTTACAAGGGATCAGATTGAAG-C
** * * * * *
34841153 TACAGTAGTAAATCTTTATCTCTCTGAAA-TTGCAGTAGAGCAAGATGAAGCTACAAAATCAA
1 TACAAAAGCAAATC-TTATCTCCCT-AAAGATGTAGTAGAGCAAGATGAAGCTACAACATCAA
34841215 GTCATATACC
Statistics
Matches: 303, Mismatches: 53, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
299 9 0.03
300 156 0.51
301 129 0.43
302 9 0.03
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (301 bp):
TACAAAAGCAAATCTTATCTCCCTAAAGATGTAGTAGAGCAAGATGAAGCTACAACATCAAATCC
TATATCCCTGAAGTTACAATGGAACAGAATGAAAACTCAAACAGCAAATCTTTATCTCTCTGAAG
TTGCAGCAAAGCAAGATGAAGCTACAACATCAAATCTTACATCCCTTAAATTGCAGAGGATCAGA
TTGAAGCTACAGAAGCAAATCTTATCTCCCTGAAGATACAGTGGAGCAAGATGAAGCTACAACAC
AAATCCTATATCCCTAAAGTTACAAGGGATCAGATTGAAGC
Found at i:34841418 original size:50 final size:49
Alignment explanation
Indices: 34841311--34841436 Score: 130
Period size: 50 Copynumber: 2.5 Consensus size: 49
34841301 GAAGACATCA
* * *
34841311 AATCCTATATCCCTGAAGTAGTAGTGGATTGGATTAAAGCTACATTAGC
1 AATCCTATCTCCCTGAAGTAGTAGTGGATAGGATTAAAGCTACAATAGC
* *
34841360 AAGCCCTATCTCCCTGAAGATAG-AGTGGAGTAGGA-TAAAGCTACAATATC
1 AA-TCCTATCTCCCTGAAG-TAGTAGTGGA-TAGGATTAAAGCTACAATAGC
* * *
34841410 GAATCCTATCTTCCTCAAGTTGTAGTG
1 -AATCCTATCTCCCTGAAGTAGTAGTG
34841437 AAGCAAATAA
Statistics
Matches: 63, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
49 4 0.06
50 50 0.79
51 9 0.14
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.29
Consensus pattern (49 bp):
AATCCTATCTCCCTGAAGTAGTAGTGGATAGGATTAAAGCTACAATAGC
Found at i:34843256 original size:94 final size:95
Alignment explanation
Indices: 34843155--34843354 Score: 257
Period size: 94 Copynumber: 2.1 Consensus size: 95
34843145 TTTTATTCAT
* **
34843155 TTTATTATTTATTTATTT-TTGCTA-CTCTTATTTTCTGATATTTACATTTTCT-CCC-ATTAAA
1 TTTATTATTTATTTATTTCTAGC-ACCT-TTATTTTCAAATATTTACATTTT-TACCCTATTAAA
*
34843216 TTTCATTTAAATTTCAATTTAG-TCCTTTCTTAA
63 TTTCATTTAAATTTCAATTTAGCTCCTTGCTT-A
*
34843249 TTTATTATTTATTTATTTCTAGCACCTTTATTTTCAAATATTTACATTTTTACCCTTTTAAATTT
1 TTTATTATTTATTTATTTCTAGCACCTTTATTTTCAAATATTTACATTTTTACCCTATTAAATTT
* *
34843314 CTTTTAAGTTTCAATTTAGCTCCTTGCTTA
66 CATTTAAATTTCAATTTAGCTCCTTGCTTA
34843344 TTTATTTATTT
1 TTTA-TTATTT
34843355 CTAGCACTTT
Statistics
Matches: 93, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
93 1 0.01
94 43 0.46
95 35 0.38
96 14 0.15
ACGTcount: A:0.24, C:0.14, G:0.04, T:0.58
Consensus pattern (95 bp):
TTTATTATTTATTTATTTCTAGCACCTTTATTTTCAAATATTTACATTTTTACCCTATTAAATTT
CATTTAAATTTCAATTTAGCTCCTTGCTTA
Found at i:34843506 original size:3 final size:3
Alignment explanation
Indices: 34843498--34843532 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
34843488 GTTGCATTTA
*
34843498 ATT ATT ATT ATT ATT ATT ATT ATT ATA ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
34843533 AGTCAAATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:34850351 original size:27 final size:27
Alignment explanation
Indices: 34850321--34850377 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
34850311 ACCGTTAAAG
*
34850321 TTAGTTTACAATGATACCAAAGTCATT
1 TTAGTTTACAATGATACAAAAGTCATT
34850348 TTAGTTTACAATGATACAAAAGTCATT
1 TTAGTTTACAATGATACAAAAGTCATT
34850375 TTA
1 TTA
34850378 TCGATATCTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.39
Consensus pattern (27 bp):
TTAGTTTACAATGATACAAAAGTCATT
Found at i:34854583 original size:43 final size:43
Alignment explanation
Indices: 34854522--34854736 Score: 322
Period size: 43 Copynumber: 5.0 Consensus size: 43
34854512 TTGGTGACTC
34854522 TAAATGGAAGACTTATGTCTCGGTTAGAGCATAAGATTAATTA
1 TAAATGGAAGACTTATGTCTCGGTTAGAGCATAAGATTAATTA
* **
34854565 TAAATAGAAGACTTATGTCTCAATTAGAGCATAAGATTAATTA
1 TAAATGGAAGACTTATGTCTCGGTTAGAGCATAAGATTAATTA
* *
34854608 TAAATGGAAGACTTATATCTCGATTAGAGCATAAGATTAATTA
1 TAAATGGAAGACTTATGTCTCGGTTAGAGCATAAGATTAATTA
* * *
34854651 TAAATGGAAGACTTATGTCTCGGGTAGAGCATAAGATTATTTG
1 TAAATGGAAGACTTATGTCTCGGTTAGAGCATAAGATTAATTA
* * *
34854694 TAAATGGAAGAACTTATGACTCGGTTAGAGCGTAAGGTTAATT
1 TAAATGGAAG-ACTTATGTCTCGGTTAGAGCATAAGATTAATT
34854737 CAGCTCAAAA
Statistics
Matches: 155, Mismatches: 16, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
43 128 0.83
44 27 0.17
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.32
Consensus pattern (43 bp):
TAAATGGAAGACTTATGTCTCGGTTAGAGCATAAGATTAATTA
Found at i:34862028 original size:36 final size:36
Alignment explanation
Indices: 34861925--34862246 Score: 421
Period size: 36 Copynumber: 9.0 Consensus size: 36
34861915 TACTTCGATG
* * *
34861925 GATTGCTTATGTCTCGGTTAGAGCATAATACTATGT
1 GATTGCTTACGTCTCGGTTAGAGCGTAATGCTATGT
** * * *
34861961 GATTATTTACGTATCGGTT-TAGCGTAATGATATGT
1 GATTGCTTACGTCTCGGTTAGAGCGTAATGCTATGT
** *
34861996 GATTGCTTACGTCTCAATTAGAGCGTAATGATATGT
1 GATTGCTTACGTCTCGGTTAGAGCGTAATGCTATGT
*
34862032 GATTGCTTACGTCTCAGTTAGAGCGTAATGCTATGT
1 GATTGCTTACGTCTCGGTTAGAGCGTAATGCTATGT
*
34862068 GATTGCTTACGTCTCGGTTAAAGCGTAATGCTATGT
1 GATTGCTTACGTCTCGGTTAGAGCGTAATGCTATGT
* * *
34862104 GATTGTTTATGTCTCGGTTAGAGCATAATGCTATGT
1 GATTGCTTACGTCTCGGTTAGAGCGTAATGCTATGT
* * * * *
34862140 GATTGTTTATGTCTCAGTTAGAGCATAATGTTATGT
1 GATTGCTTACGTCTCGGTTAGAGCGTAATGCTATGT
* *
34862176 GATTGCTTACGTCTCGATTAGAGCATAATGCTATGT
1 GATTGCTTACGTCTCGGTTAGAGCGTAATGCTATGT
*
34862212 GATTGCTTACGTCTCGGTTAAAGCGTAATGCTATG
1 GATTGCTTACGTCTCGGTTAGAGCGTAATGCTATG
34862247 AATAGCTCGG
Statistics
Matches: 253, Mismatches: 32, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
35 26 0.10
36 227 0.90
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.39
Consensus pattern (36 bp):
GATTGCTTACGTCTCGGTTAGAGCGTAATGCTATGT
Found at i:34873345 original size:39 final size:39
Alignment explanation
Indices: 34873287--34873451 Score: 240
Period size: 39 Copynumber: 4.2 Consensus size: 39
34873277 GATATTTATA
* * *
34873287 GCCAGTTCAATATTGTATTGTAGTGTTTATAATGTCACT
1 GCCAGTTCAATATTGTATTGCAGTGTTTACAGTGTCACT
* * * *
34873326 GTCGGTTCAGTATTGTATTGCAATGTTTACAGTGTCACT
1 GCCAGTTCAATATTGTATTGCAGTGTTTACAGTGTCACT
* *
34873365 GCCAGTTCAATATTATATTGCAGTGTTTACAGTATCACT
1 GCCAGTTCAATATTGTATTGCAGTGTTTACAGTGTCACT
34873404 GCCAGTTCAATATTGTATTGCAGTGTTTACAGTGTCACT
1 GCCAGTTCAATATTGTATTGCAGTGTTTACAGTGTCACT
*
34873443 GCCATTTCA
1 GCCAGTTCA
34873452 GTAATTTGAT
Statistics
Matches: 110, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 110 1.00
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.40
Consensus pattern (39 bp):
GCCAGTTCAATATTGTATTGCAGTGTTTACAGTGTCACT
Found at i:34873942 original size:133 final size:134
Alignment explanation
Indices: 34873719--34873960 Score: 378
Period size: 133 Copynumber: 1.8 Consensus size: 134
34873709 TGTGTCCAGG
* *
34873719 CCGTGTAACTCACTATTTCTGTACTTTCAAAACAGTATGGGCACACGATCTGACATACGCCTGTG
1 CCGTGTAACTCACTATTTCTGTACTTTCAAAACAGTATGGGCACACGATCTGACACACGCCCGTG
** * *
34873784 GCGTAACCTGTGTGTCTCCTGTAGCTTATTTATGTGGCACACGGTTTGGCCCATGCCTATTTGTT
66 GCGTAACCCATGTATCTCCTATAGCTTATTTATGTGGCACACGGTTTGGCCCATGCCTATTTGTT
34873849 CAGC
131 CAGC
* * *
34873853 CCGTGTAACTCACTATTTCTGTACTTT-TAAACAGTATGGGCACACGGTCTGGCACACGCCCGTG
1 CCGTGTAACTCACTATTTCTGTACTTTCAAAACAGTATGGGCACACGATCTGACACACGCCCGTG
* *
34873917 GCGTAACCCATGTATCTCTTATAGCTTATTTATGTGGCATACGG
66 GCGTAACCCATGTATCTCCTATAGCTTATTTATGTGGCACACGG
34873961 CCTGGCCACA
Statistics
Matches: 97, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
133 70 0.72
134 27 0.28
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.32
Consensus pattern (134 bp):
CCGTGTAACTCACTATTTCTGTACTTTCAAAACAGTATGGGCACACGATCTGACACACGCCCGTG
GCGTAACCCATGTATCTCCTATAGCTTATTTATGTGGCACACGGTTTGGCCCATGCCTATTTGTT
CAGC
Found at i:34876972 original size:71 final size:71
Alignment explanation
Indices: 34876856--34876999 Score: 288
Period size: 71 Copynumber: 2.0 Consensus size: 71
34876846 ACCGGCTGTC
34876856 AAGTTTAAGAAATTTCTAAATATCATTTAGTAAGTTAGCACCAATTATAATAAGATTTCATAAGA
1 AAGTTTAAGAAATTTCTAAATATCATTTAGTAAGTTAGCACCAATTATAATAAGATTTCATAAGA
34876921 AACTAT
66 AACTAT
34876927 AAGTTTAAGAAATTTCTAAATATCATTTAGTAAGTTAGCACCAATTATAATAAGATTTCATAAGA
1 AAGTTTAAGAAATTTCTAAATATCATTTAGTAAGTTAGCACCAATTATAATAAGATTTCATAAGA
34876992 AACTAT
66 AACTAT
34876998 AA
1 AA
34877000 CGACAATAGC
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 73 1.00
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.35
Consensus pattern (71 bp):
AAGTTTAAGAAATTTCTAAATATCATTTAGTAAGTTAGCACCAATTATAATAAGATTTCATAAGA
AACTAT
Found at i:34877169 original size:39 final size:39
Alignment explanation
Indices: 34877130--34877368 Score: 173
Period size: 39 Copynumber: 6.2 Consensus size: 39
34877120 TATAGCATTA
* * *
34877130 CAGTGTTTATAGTGTCACCATCAATTCAGTACTGTATTA
1 CAGTGTTTATAGTGTCACTATCAATTCAGTATTGTATTG
* * * * * * *
34877169 CGGTATTTACAGTGTTATTGT-AAGTTCAGTATTATATTG
1 CAGTGTTTATAGTGTCACTATCAA-TTCAGTATTGTATTG
* * * **
34877208 TAGTGTTTACAATGTCACTATCGGTTCAGTATTGTATTG
1 CAGTGTTTATAGTGTCACTATCAATTCAGTATTGTATTG
* ** *
34877247 CAATGTTTATAGTGTCACTGCCAGTTCAGTATTGTATTG
1 CAGTGTTTATAGTGTCACTATCAATTCAGTATTGTATTG
* * *
34877286 CAGTGTTTATAGTGTCACTGTCAGTTTAGTATTGTA--G
1 CAGTGTTTATAGTGTCACTATCAATTCAGTATTGTATTG
* * ** * * *
34877323 -TGT-TTTTTAGTGTCACTGCCAGTTTAGTATTATATTG
1 CAGTGTTTATAGTGTCACTATCAATTCAGTATTGTATTG
34877360 CAGTGTTTA
1 CAGTGTTTA
34877369 CAGTATCATT
Statistics
Matches: 158, Mismatches: 36, Indels: 12
0.77 0.17 0.06
Matches are distributed among these distances:
35 28 0.18
36 2 0.01
37 2 0.01
38 4 0.03
39 122 0.77
ACGTcount: A:0.23, C:0.13, G:0.20, T:0.44
Consensus pattern (39 bp):
CAGTGTTTATAGTGTCACTATCAATTCAGTATTGTATTG
Found at i:34877236 original size:78 final size:78
Alignment explanation
Indices: 34877130--34877368 Score: 207
Period size: 78 Copynumber: 3.1 Consensus size: 78
34877120 TATAGCATTA
* ** * * *
34877130 CAGTGTTTATAGTGTCACCATCAATTCAGTACTGTATTACGGTATTTACAGTGTTATTGTAAGTT
1 CAGTGTTTATAGTGTCACTATCAATTCAGTACTGTATTACAATATTTACAGTGTCACTGCAAGTT
34877195 CAGTATTATATTG
66 CAGTATTATATTG
* * * ** * * * * *
34877208 TAGTGTTTACAATGTCACTATCGGTTCAGTATTGTATTGCAATGTTTATAGTGTCACTGCCAGTT
1 CAGTGTTTATAGTGTCACTATCAATTCAGTACTGTATTACAATATTTACAGTGTCACTGCAAGTT
*
34877273 CAGTATTGTATTG
66 CAGTATTATATTG
* * * * * * ** *
34877286 CAGTGTTTATAGTGTCACTGTCAGTTTAGTATTGTAGT---GT-TTTTTAGTGTCACTGCCAGTT
1 CAGTGTTTATAGTGTCACTATCAATTCAGTACTGTATTACAATATTTACAGTGTCACTGCAAGTT
*
34877347 TAGTATTATATTG
66 CAGTATTATATTG
34877360 CAGTGTTTA
1 CAGTGTTTA
34877369 CAGTATCATT
Statistics
Matches: 133, Mismatches: 28, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
74 40 0.30
75 1 0.01
78 92 0.69
ACGTcount: A:0.23, C:0.13, G:0.20, T:0.44
Consensus pattern (78 bp):
CAGTGTTTATAGTGTCACTATCAATTCAGTACTGTATTACAATATTTACAGTGTCACTGCAAGTT
CAGTATTATATTG
Found at i:34877300 original size:117 final size:117
Alignment explanation
Indices: 34877090--34877318 Score: 260
Period size: 117 Copynumber: 2.0 Consensus size: 117
34877080 ATAGCATCTG
* * *
34877090 GTAGTGTTTACAATGTCACCACCCGCTCATTATAGCATTACAGTGTTTATAGTGTCACCATCAAT
1 GTAGTGTTTACAATGTCACCACCCGCTCAGTATAGCATTACAATGTTTATAGTGTCACCACCAAT
* * *
34877155 TCAGTACTGTATTACGGTATTTACAGTGTTATTGTAAGTTCAGTATTATATT
66 TCAGTACTGTATTACAGTATTTACAGTGTCACTGTAAGTTCAGTATTATATT
* * * * * * * ** *
34877207 GTAGTGTTTACAATGTCACTATCGGTTCAGTATTGTATTGCAATGTTTATAGTGTCACTGCCAGT
1 GTAGTGTTTACAATGTCACCACCCGCTCAGTATAGCATTACAATGTTTATAGTGTCACCACCAAT
* * * * * *
34877272 TCAGTATTGTATTGCAGTGTTTATAGTGTCACTGTCAGTTTAGTATT
66 TCAGTACTGTATTACAGTATTTACAGTGTCACTGTAAGTTCAGTATT
34877319 GTAGTGTTTT
Statistics
Matches: 90, Mismatches: 22, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
117 90 1.00
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.41
Consensus pattern (117 bp):
GTAGTGTTTACAATGTCACCACCCGCTCAGTATAGCATTACAATGTTTATAGTGTCACCACCAAT
TCAGTACTGTATTACAGTATTTACAGTGTCACTGTAAGTTCAGTATTATATT
Found at i:34877346 original size:35 final size:38
Alignment explanation
Indices: 34877235--34877390 Score: 174
Period size: 39 Copynumber: 4.1 Consensus size: 38
34877225 CTATCGGTTC
* *
34877235 AGTATTGTATTGCAATGTTTATAGTGTCACTGCCAGTTC
1 AGTATTGTA-TGCAGTGTTTATAGTGTCACTGCCAGTTT
*
34877274 AGTATTGTATTGCAGTGTTTATAGTGTCACTGTCAGTTT
1 AGTATTGTA-TGCAGTGTTTATAGTGTCACTGCCAGTTT
* *
34877313 AGTATTGTA-G-TGT-TTTTTAGTGTCACTGCCAGTTT
1 AGTATTGTATGCAGTGTTTATAGTGTCACTGCCAGTTT
* * * * *
34877348 AGTATTATATTGCAGTGTTTACAGTATCATTGCCAGTTC
1 AGTATTGTA-TGCAGTGTTTATAGTGTCACTGCCAGTTT
34877387 AGTA
1 AGTA
34877391 ATTTGATAAC
Statistics
Matches: 100, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
35 28 0.28
36 2 0.02
37 2 0.02
38 2 0.02
39 66 0.66
ACGTcount: A:0.22, C:0.13, G:0.21, T:0.44
Consensus pattern (38 bp):
AGTATTGTATGCAGTGTTTATAGTGTCACTGCCAGTTT
Found at i:34877360 original size:74 final size:76
Alignment explanation
Indices: 34877191--34877370 Score: 238
Period size: 78 Copynumber: 2.4 Consensus size: 76
34877181 TGTTATTGTA
* * *
34877191 AGTTCAGTATTATATTGTAGTGTTTACAATGTCACTATCGGTTCAGTATTGTATTGCAATGTTTA
1 AGTTCAGTATTATATTGCAGTGTTTACAATGTCACTATCAGTTCAGTATTGTAGTG--ATGTTTA
34877256 TAGTGTCACTGCC
64 TAGTGTCACTGCC
* * * * * *
34877269 AGTTCAGTATTGTATTGCAGTGTTTATAGTGTCACTGTCAGTTTAGTATTGTAGTG-T-TTTTTA
1 AGTTCAGTATTATATTGCAGTGTTTACAATGTCACTATCAGTTCAGTATTGTAGTGATGTTTATA
34877332 GTGTCACTGCC
66 GTGTCACTGCC
*
34877343 AGTTTAGTATTATATTGCAGTGTTTACA
1 AGTTCAGTATTATATTGCAGTGTTTACA
34877371 GTATCATTGC
Statistics
Matches: 90, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
74 41 0.46
75 1 0.01
78 48 0.53
ACGTcount: A:0.23, C:0.12, G:0.21, T:0.44
Consensus pattern (76 bp):
AGTTCAGTATTATATTGCAGTGTTTACAATGTCACTATCAGTTCAGTATTGTAGTGATGTTTATA
GTGTCACTGCC
Found at i:34885756 original size:29 final size:29
Alignment explanation
Indices: 34885714--34885769 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
34885704 CTTCTATCGA
34885714 TACCTATTGGACAAGTATCGATAGAAGAG
1 TACCTATTGGACAAGTATCGATAGAAGAG
34885743 TACCTATTGGACAAGTATCGATAGAAG
1 TACCTATTGGACAAGTATCGATAGAAG
34885770 TTAAGTCAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.25
Consensus pattern (29 bp):
TACCTATTGGACAAGTATCGATAGAAGAG
Found at i:34886595 original size:25 final size:25
Alignment explanation
Indices: 34886567--34886742 Score: 139
Period size: 25 Copynumber: 7.3 Consensus size: 25
34886557 AGTTTAGCTT
*
34886567 TTACGAGCCAAACAGAATATTACTC
1 TTACGAGCCAAACAGAATATTGCTC
** * **
34886592 TTACGAGCCAGGCATAATATCACTC
1 TTACGAGCCAAACAGAATATTGCTC
* * *
34886617 TTATGAGCCAGACAGAATGTTGCTC
1 TTACGAGCCAAACAGAATATTGCTC
*
34886642 TTACGAGCCAAACAGAATATCGCTC
1 TTACGAGCCAAACAGAATATTGCTC
* *
34886667 TT---A--C-AATAGAATGTTGCTC
1 TTACGAGCCAAACAGAATATTGCTC
* * *
34886686 TTCCGAGCCAAATAGAATGTTGCTC
1 TTACGAGCCAAACAGAATATTGCTC
* * *
34886711 TTGCGAGCCAGACAGAATATTTCTC
1 TTACGAGCCAAACAGAATATTGCTC
*
34886736 TTCCGAG
1 TTACGAG
34886743 TTTGATTCTA
Statistics
Matches: 122, Mismatches: 23, Indels: 12
0.78 0.15 0.08
Matches are distributed among these distances:
19 14 0.11
20 1 0.01
22 2 0.02
24 1 0.01
25 104 0.85
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (25 bp):
TTACGAGCCAAACAGAATATTGCTC
Found at i:34887449 original size:3 final size:3
Alignment explanation
Indices: 34887441--34887484 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
34887431 TTGTCCGTGT
*
34887441 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA AAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
34887485 GAAAGATGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:34892344 original size:18 final size:20
Alignment explanation
Indices: 34892309--34892352 Score: 65
Period size: 18 Copynumber: 2.3 Consensus size: 20
34892299 AATTACAAAA
*
34892309 AAAAATCAAAAATAATTTTT
1 AAAAATCAAAAATAATTTAT
34892329 AAAAAT-AAAAAT-ATTTAT
1 AAAAATCAAAAATAATTTAT
34892347 AAAAAT
1 AAAAAT
34892353 TCCAATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.48
19 6 0.26
20 6 0.26
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAAATCAAAAATAATTTAT
Found at i:34895455 original size:10 final size:10
Alignment explanation
Indices: 34895440--34895469 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
34895430 CAGATCTAAA
34895440 AGATCTTATT
1 AGATCTTATT
34895450 AGATCTTATT
1 AGATCTTATT
34895460 AGATCTTATT
1 AGATCTTATT
34895470 CTAAATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (10 bp):
AGATCTTATT
Found at i:34896286 original size:30 final size:30
Alignment explanation
Indices: 34896106--34896442 Score: 159
Period size: 30 Copynumber: 11.5 Consensus size: 30
34896096 AAAGGTCTCT
34896106 AAAC-TTTCCAAAAATCATATTTTAACCCTC
1 AAACTTTTCC-AAAATCATATTTTAACCCTC
* * * * * *
34896136 AAACTTTTTCATTTCAATTACATTGTCACCCTC
1 AAACTTTTCCA---AAATCATATTTTAACCCTC
* * * * *
34896169 GAATTTTTCCAAAATTACATTTTCATCCCT-
1 AAACTTTTCCAAAATCATATTTT-AACCCTC
* * *
34896199 AAACTTTTCTAAAATCACATTTTGACCCT-
1 AAACTTTTCCAAAATCATATTTTAACCCTC
* * *
34896228 AAAATTTTCCAAAGT--TA----CACCCTC
1 AAACTTTTCCAAAATCATATTTTAACCCTC
*
34896252 AAACTTTTCCAAAATCATATTTTAACCCTA
1 AAACTTTTCCAAAATCATATTTTAACCCTC
* *
34896282 AAACTTCT-CAAAATCATACTTTAACCCCTC
1 AAACTTTTCCAAAATCATATTTTAA-CCCTC
*
34896312 AAACTTTCCCAAAATCATATTTTAACCC-C
1 AAACTTTTCCAAAATCATATTTTAACCCTC
* * *
34896341 AACAAC-TTCCCAAAA-CAATATTTTGACCCCC
1 -A-AACTTTTCCAAAATC-ATATTTTAACCCTC
* * *
34896372 AAAC-TTTCCTAAAATTACATTTTGA-CCTC
1 AAACTTTTCC-AAAATCATATTTTAACCCTC
* * * * * *
34896401 AAATTTTTTCGATATTACATTTTAACCCT-
1 AAACTTTTCCAAAATCATATTTTAACCCTC
*
34896430 AAA-TTCTCCAAAA
1 AAACTTTTCCAAAA
34896443 CTTCATTTTT
Statistics
Matches: 237, Mismatches: 48, Indels: 46
0.72 0.15 0.14
Matches are distributed among these distances:
23 5 0.02
24 13 0.05
26 2 0.01
27 1 0.00
28 6 0.03
29 61 0.26
30 100 0.42
31 27 0.11
33 22 0.09
ACGTcount: A:0.36, C:0.27, G:0.02, T:0.35
Consensus pattern (30 bp):
AAACTTTTCCAAAATCATATTTTAACCCTC
Found at i:34896320 original size:83 final size:83
Alignment explanation
Indices: 34896162--34896320 Score: 187
Period size: 83 Copynumber: 1.9 Consensus size: 83
34896152 ATTACATTGT
* * * * * * *
34896162 CACCCTCGAATTTTTCCAAAATTACATTTTCATCCCTAAACTTTTCTAAAATCACATTTTGACCC
1 CACCCTCAAACTTTTCCAAAATCACATTTTCAACCCTAAACTTCTCTAAAATCACACTTTAACCC
*
34896227 TAAAATTTTCCAAAGTTA
66 TAAAACTTTCCAAAGTTA
* *
34896245 CACCCTCAAACTTTTCCAAAATCATATTTT-AACCCTAAAACTTCTC-AAAATCATACTTTAACC
1 CACCCTCAAACTTTTCCAAAATCACATTTTCAACCCT-AAACTTCTCTAAAATCACACTTTAA-C
*
34896308 CCTCAAACTTTCC
64 CCTAAAACTTTCC
34896321 CAAAATCATA
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
82 17 0.27
83 46 0.73
ACGTcount: A:0.35, C:0.29, G:0.02, T:0.35
Consensus pattern (83 bp):
CACCCTCAAACTTTTCCAAAATCACATTTTCAACCCTAAACTTCTCTAAAATCACACTTTAACCC
TAAAACTTTCCAAAGTTA
Found at i:34896324 original size:60 final size:61
Alignment explanation
Indices: 34896247--34896386 Score: 196
Period size: 60 Copynumber: 2.3 Consensus size: 61
34896237 CAAAGTTACA
* * *
34896247 CCCTCAAACTTTTCCAAAATCATATTTTAACCCTAA-AACTTCTCAAAATC-ATACTTTAAC
1 CCCTCAAACTTTCCCAAAATCATATTTTAACCCCAACAACTTCCCAAAA-CAATACTTTAAC
* *
34896307 CCCTCAAACTTTCCCAAAATCATATTTTAACCCCAACAACTTCCCAAAACAATATTTTGAC
1 CCCTCAAACTTTCCCAAAATCATATTTTAACCCCAACAACTTCCCAAAACAATACTTTAAC
*
34896368 CCC-CAAACTTTCCTAAAAT
1 CCCTCAAACTTTCCCAAAAT
34896387 TACATTTTGA
Statistics
Matches: 72, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
60 50 0.69
61 22 0.31
ACGTcount: A:0.38, C:0.31, G:0.01, T:0.30
Consensus pattern (61 bp):
CCCTCAAACTTTCCCAAAATCATATTTTAACCCCAACAACTTCCCAAAACAATACTTTAAC
Found at i:34906028 original size:42 final size:42
Alignment explanation
Indices: 34905969--34906048 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
34905959 ATTTTGCCTG
* * *
34905969 AAAAAAAGGATTGAGATGAAAACCCTCAAAGGGCGTCTCGAT
1 AAAAAAAAGATCGAGATGAAAACCCGCAAAGGGCGTCTCGAT
34906011 AAAAAAAAGATCGAGATGAAAACCCGCAAAGGGCGTCT
1 AAAAAAAAGATCGAGATGAAAACCCGCAAAGGGCGTCT
34906049 TGAAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.45, C:0.17, G:0.24, T:0.14
Consensus pattern (42 bp):
AAAAAAAAGATCGAGATGAAAACCCGCAAAGGGCGTCTCGAT
Found at i:34908475 original size:30 final size:30
Alignment explanation
Indices: 34908441--34908780 Score: 196
Period size: 30 Copynumber: 11.6 Consensus size: 30
34908431 GAACTTTCTA
*
34908441 AAAATCATATTTTAACCCTTAAACTTTTCC
1 AAAATCATATTTTAACCCCTAAACTTTTCC
* * * * ** * * *
34908471 AAAATTATATTATCATCATTGAATTTTTCT
1 AAAATCATATTTTAACCCCTAAACTTTTCC
* * * * *
34908501 AAAATTACATTTTCATCCCTAAACTTTTCA
1 AAAATCATATTTTAACCCCTAAACTTTTCC
* *
34908531 AAAATCATATTTTGACCCCT-AATTTTTCC
1 AAAATCATATTTTAACCCCTAAACTTTTCC
* *
34908560 AAAGT--TA----CA-CCCTCAAACTTTTCC
1 AAAATCATATTTTAACCCCT-AAACTTTTCC
* * *
34908584 AAAATCACATTTTAACCCCAAAACTTTCCC
1 AAAATCATATTTTAACCCCTAAACTTTTCC
* * * *
34908614 AAAATCATATATTCACCCCCAAACTTTTCT
1 AAAATCATATTTTAACCCCTAAACTTTTCC
* * * *
34908644 AAAATCACATTTTGACCCCCAAAC-TTCCC
1 AAAATCATATTTTAACCCCTAAACTTTTCC
* * * * * *
34908673 CAAATCATACTTTGACACTTAAACTTTCCC
1 AAAATCATATTTTAACCCCTAAACTTTTCC
* * *
34908703 AAAAGCATATTTTAACCCCAAAAACTTTCCC
1 AAAATCATATTTTAACCCC-TAAACTTTTCC
* *
34908734 AAAACCATATTTTAACCCCCAAAC-TTTCC
1 AAAATCATATTTTAACCCCTAAACTTTTCC
* *
34908763 TAAAATTACATTTTAACC
1 -AAAATCATATTTTAACC
34908781 TCGAGTTTTT
Statistics
Matches: 239, Mismatches: 59, Indels: 24
0.74 0.18 0.07
Matches are distributed among these distances:
22 4 0.02
23 1 0.00
24 12 0.05
26 1 0.00
27 2 0.01
29 36 0.15
30 152 0.64
31 31 0.13
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.34
Consensus pattern (30 bp):
AAAATCATATTTTAACCCCTAAACTTTTCC
Found at i:34908662 original size:60 final size:59
Alignment explanation
Indices: 34908567--34908780 Score: 232
Period size: 59 Copynumber: 3.6 Consensus size: 59
34908557 TCCAAAGTTA
* *
34908567 CACCCTCAAACTTTTCCAAAATCACATTTTAACCCCAAAACTTTCCCAAAATCATATATT
1 CACCCCCAAACTTTCCCAAAATCACATTTTAACCCCAAAACTTTCCCAAAATCATAT-TT
* * * * *
34908627 CACCCCCAAACTTTTCTAAAATCACATTTTGACCCCCAAAC-TTCCCCAAATCATACTTT
1 CACCCCCAAACTTTCCCAAAATCACATTTTAACCCCAAAACTTTCCCAAAATCATA-TTT
* * ** * * *
34908686 GACACTTAAACTTTCCCAAAAGCATATTTTAACCCCAAAAACTTTCCCAAAACCATATTTT
1 CACCCCCAAACTTTCCCAAAATCACATTTTAACCCC-AAAACTTTCCCAAAATCATA-TTT
* * *
34908747 AACCCCCAAACTTTCCTAAAATTACATTTTAACC
1 CACCCCCAAACTTTCCCAAAATCACATTTTAACC
34908781 TCGAGTTTTT
Statistics
Matches: 125, Mismatches: 26, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
59 42 0.34
60 42 0.34
61 41 0.33
ACGTcount: A:0.37, C:0.32, G:0.01, T:0.29
Consensus pattern (59 bp):
CACCCCCAAACTTTCCCAAAATCACATTTTAACCCCAAAACTTTCCCAAAATCATATTT
Found at i:34908729 original size:31 final size:30
Alignment explanation
Indices: 34908568--34908780 Score: 212
Period size: 30 Copynumber: 7.1 Consensus size: 30
34908558 CCAAAGTTAC
* * *
34908568 ACCCTCAAACTTTTCCAAAATCACATTTTA
1 ACCCCCAAACTTTCCCAAAATCATATTTTA
* * *
34908598 ACCCCAAAACTTTCCCAAAATCATATATTC
1 ACCCCCAAACTTTCCCAAAATCATATTTTA
* * * *
34908628 ACCCCCAAACTTTTCTAAAATCACATTTTG
1 ACCCCCAAACTTTCCCAAAATCATATTTTA
* * *
34908658 ACCCCCAAAC-TTCCCCAAATCATACTTTG
1 ACCCCCAAACTTTCCCAAAATCATATTTTA
* ** *
34908687 ACACTTAAACTTTCCCAAAAGCATATTTTA
1 ACCCCCAAACTTTCCCAAAATCATATTTTA
* *
34908717 ACCCCAAAAACTTTCCCAAAACCATATTTTA
1 ACCCC-CAAACTTTCCCAAAATCATATTTTA
* * *
34908748 ACCCCCAAACTTTCCTAAAATTACATTTTA
1 ACCCCCAAACTTTCCCAAAATCATATTTTA
34908778 ACC
1 ACC
34908781 TCGAGTTTTT
Statistics
Matches: 148, Mismatches: 33, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
29 21 0.14
30 99 0.67
31 28 0.19
ACGTcount: A:0.37, C:0.32, G:0.01, T:0.30
Consensus pattern (30 bp):
ACCCCCAAACTTTCCCAAAATCATATTTTA
Found at i:34908988 original size:25 final size:25
Alignment explanation
Indices: 34908960--34909019 Score: 59
Period size: 25 Copynumber: 2.4 Consensus size: 25
34908950 CATATTTCGG
* * *
34908960 ATTTTATTTTATGCTTAATTTTTGT
1 ATTTTATTTTATACTTAATTGTTCT
*
34908985 A-TTTATTTATCTACTTAATTGTTCT
1 ATTTTATTT-TATACTTAATTGTTCT
*
34909010 ATTTAATTTT
1 ATTTTATTTT
34909020 GCCATTAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
24 7 0.25
25 15 0.54
26 6 0.21
ACGTcount: A:0.23, C:0.07, G:0.05, T:0.65
Consensus pattern (25 bp):
ATTTTATTTTATACTTAATTGTTCT
Found at i:34911309 original size:20 final size:21
Alignment explanation
Indices: 34911274--34911312 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
34911264 TTATTATTTA
*
34911274 TTTATTTATTTTTTATTGTTG
1 TTTATTTATATTTTATTGTTG
34911295 TTTATTT-TATTTTATTGT
1 TTTATTTATATTTTATTGT
34911313 GTAGTATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (21 bp):
TTTATTTATATTTTATTGTTG
Found at i:34913514 original size:28 final size:28
Alignment explanation
Indices: 34913474--34913542 Score: 111
Period size: 28 Copynumber: 2.5 Consensus size: 28
34913464 CTTAGCAAAT
*
34913474 ACTCTATATTCTGGCTCGTAAGAGAGTA
1 ACTCTGTATTCTGGCTCGTAAGAGAGTA
*
34913502 ACTCTGTATTCTGGCTCGTAAGAGTGTA
1 ACTCTGTATTCTGGCTCGTAAGAGAGTA
*
34913530 ACTCTGTACTCTG
1 ACTCTGTATTCTG
34913543 TCTTTTATGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (28 bp):
ACTCTGTATTCTGGCTCGTAAGAGAGTA
Found at i:34916120 original size:46 final size:46
Alignment explanation
Indices: 34916053--34916147 Score: 172
Period size: 46 Copynumber: 2.1 Consensus size: 46
34916043 CTTGCTTAGG
34916053 ATATGGGAAGCTGTAGGATATGCCCCTTTGTTGGTGCTAAGGTAGT
1 ATATGGGAAGCTGTAGGATATGCCCCTTTGTTGGTGCTAAGGTAGT
* *
34916099 ATATGGGGAGCTGTAGGATATGCCCTTTTGTTGGTGCTAAGGTAGT
1 ATATGGGAAGCTGTAGGATATGCCCCTTTGTTGGTGCTAAGGTAGT
34916145 ATA
1 ATA
34916148 GATCGAGACA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.22, C:0.12, G:0.33, T:0.34
Consensus pattern (46 bp):
ATATGGGAAGCTGTAGGATATGCCCCTTTGTTGGTGCTAAGGTAGT
Found at i:34922654 original size:20 final size:20
Alignment explanation
Indices: 34922629--34922737 Score: 71
Period size: 20 Copynumber: 5.5 Consensus size: 20
34922619 TGTTTGCTAT
*
34922629 TTTTTTATCAATATTTTCCA
1 TTTTTTACCAATATTTTCCA
*
34922649 TTTTTTA-CAA-ATGTTTGCA
1 TTTTTTACCAATAT-TTTCCA
* * * *
34922668 ATTTTGACCAATGTTTGCCA
1 TTTTTTACCAATATTTTCCA
** * *
34922688 TTTTTTATTAATGTTTGCCA
1 TTTTTTACCAATATTTTCCA
*
34922708 TTTTTTACCAACATTTGT-CA
1 TTTTTTACCAATATTT-TCCA
*
34922728 TTTTTGACCA
1 TTTTTTACCA
34922738 GTGATTGCTA
Statistics
Matches: 69, Mismatches: 16, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
18 2 0.03
19 13 0.19
20 53 0.77
21 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (20 bp):
TTTTTTACCAATATTTTCCA
Found at i:34922672 original size:19 final size:19
Alignment explanation
Indices: 34922650--34922712 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
34922640 TATTTTCCAT
34922650 TTTTTACAAATGTTTGCAA
1 TTTTTACAAATGTTTGCAA
* * *
34922669 TTTTGACCAATGTTTGCCAT
1 TTTTTACAAATGTTTG-CAA
** *
34922689 TTTTTATTAATGTTTGCCA
1 TTTTTACAAATGTTTGCAA
34922708 TTTTT
1 TTTTT
34922713 TACCAACATT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
19 20 0.57
20 15 0.43
ACGTcount: A:0.22, C:0.13, G:0.11, T:0.54
Consensus pattern (19 bp):
TTTTTACAAATGTTTGCAA
Found at i:34922680 original size:60 final size:60
Alignment explanation
Indices: 34922599--34922752 Score: 175
Period size: 60 Copynumber: 2.5 Consensus size: 60
34922589 CTTTTGCTCA
* * *
34922599 ATTTAGCAATTCTTGATCAATGTTTGCTATTTTTTTATCAATATTTTCCATTTTTTACAAAT
1 ATTT-GCAATT-TTGACCAATGTTTGCTATTTTTTTATCAATATTTGCCATTTTTTACAAAC
* * * * *
34922661 GTTTGCAATTTTGACCAATGTTTGCCA-TTTTTTATTAATGTTTGCCATTTTTTACCAAC
1 ATTTGCAATTTTGACCAATGTTTGCTATTTTTTTATCAATATTTGCCATTTTTTACAAAC
* * *
34922720 ATTTGTCATTTTTGACCAGTGATTGCTATTTTT
1 ATTTG-CAATTTTGACCAATGTTTGCTATTTTT
34922753 AATCTTTTCA
Statistics
Matches: 77, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
59 31 0.40
60 33 0.43
61 10 0.13
62 3 0.04
ACGTcount: A:0.23, C:0.14, G:0.10, T:0.52
Consensus pattern (60 bp):
ATTTGCAATTTTGACCAATGTTTGCTATTTTTTTATCAATATTTGCCATTTTTTACAAAC
Found at i:34922701 original size:39 final size:39
Alignment explanation
Indices: 34922637--34922732 Score: 111
Period size: 39 Copynumber: 2.4 Consensus size: 39
34922627 ATTTTTTTAT
*
34922637 CAATATTTTCCATTTTTTACAAATGTTTGCAATTTTGAC
1 CAATATTTGCCATTTTTTACAAATGTTTGCAATTTTGAC
* ** * *
34922676 CAATGTTTGCCATTTTTTATTAATGTTTGCCATTTTTTAC
1 CAATATTTGCCATTTTTTACAAATGTTTG-CAATTTTGAC
* *
34922716 CAACATTTGTCATTTTT
1 CAATATTTGCCATTTTT
34922733 GACCAGTGAT
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
39 25 0.53
40 22 0.47
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (39 bp):
CAATATTTGCCATTTTTTACAAATGTTTGCAATTTTGAC
Found at i:34923818 original size:193 final size:195
Alignment explanation
Indices: 34923393--34923835 Score: 495
Period size: 199 Copynumber: 2.3 Consensus size: 195
34923383 TAAAGTTACG
* * *
34923393 ACATCAAATCCTATAT-TCCTGAAGTTCCAATGGATCAGATTGAAGCTACAAAAATAAATCTTTA
1 ACATCAAATCCTATATCT-CTGAAGTTACAGTGGATCAGATTGAAGCTACAAAAACAAATCTTTA
* * * * *
34923457 TCTCTCTGAAGTTGTAGTAAAGCAGGACGAAGCTATAAAACCAAATCCTATCCCTAAAGTTGCAG
65 TCTCTCTAAAGTTGCAGTAAAGCAGGACAAAGCTACAAAACCAAATCCTATCCCTAAAGTTACAG
* *
34923522 TGGGTCGAATTGAAGCTATAGAAGCAAATTTTTATCTCCCGAAGTTGTAGTGGAGCAAGATGAGG
130 TGGGTCG-A--GAA-CTATAGAAGCAAATATTTATCTCCCGAAGTTGCAGTGGAGCAAGATGAGG
*
34923587 TCACG
191 TCACA
* * * * * * *
34923592 ACATTAAATCCTATATC-CTTAAAGTTGCAGTGGATCGGATTGAAGGTACGAAAGCAAATCTTTA
1 ACATCAAATCCTATATCTC-TGAAGTTACAGTGGATCAGATTGAAGCTACAAAAACAAATCTTTA
* * * *
34923656 TCTCTTTAAAGTTGCAGTAAAGTAGGATAAAGCTACAAAACCAAATCTTATACCCCTAAAGTTAC
65 TCTCTCTAAAGTTGCAGTAAAGCAGGACAAAGCTACAAAACCAAATCCTAT--CCCTAAAGTTAC
* *
34923721 ATTGGGTCG-G-A-T-TA-AAGCAAATATTTATCTCCATGAAGTTGCAGTGGAGCAAGATGAGGT
128 AGTGGGTCGAGAACTATAGAAGCAAATATTTATCTCC-CGAAGTTGCAGTGGAGCAAGATGAGGT
* *
34923781 TATA
192 CACA
* * *
34923785 ACCTCGAATCCTATATCTCTGAAGTTACAGTGGATCAGATTGAAACTACAA
1 ACATCAAATCCTATATCTCTGAAGTTACAGTGGATCAGATTGAAGCTACAA
34923836 GTCCTATCTC
Statistics
Matches: 204, Mismatches: 34, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
192 17 0.08
193 68 0.33
194 2 0.01
196 1 0.00
197 1 0.00
198 1 0.00
199 95 0.47
201 19 0.09
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (195 bp):
ACATCAAATCCTATATCTCTGAAGTTACAGTGGATCAGATTGAAGCTACAAAAACAAATCTTTAT
CTCTCTAAAGTTGCAGTAAAGCAGGACAAAGCTACAAAACCAAATCCTATCCCTAAAGTTACAGT
GGGTCGAGAACTATAGAAGCAAATATTTATCTCCCGAAGTTGCAGTGGAGCAAGATGAGGTCACA
Found at i:34925352 original size:21 final size:20
Alignment explanation
Indices: 34925310--34925352 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
34925300 TTAATTTTAA
*
34925310 TTTATTTTAATTTTTACCAT
1 TTTATTTTAATTTTTACAAT
*
34925330 TTTATTTTATTTTCTTACAAT
1 TTTATTTTAATTT-TTACAAT
34925351 TT
1 TT
34925353 AATCCCCGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTATTTTAATTTTTACAAT
Found at i:34925688 original size:14 final size:13
Alignment explanation
Indices: 34925657--34925702 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 13
34925647 TTATCATTTG
34925657 TATTGCATTTATT
1 TATTGCATTTATT
34925670 ATATTCGCATTTATT
1 -TATT-GCATTTATT
*
34925685 TATTGTTATTTATT
1 TATTG-CATTTATT
34925699 TATT
1 TATT
34925703 TATCTTATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 1 0.03
14 19 0.66
15 9 0.31
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.63
Consensus pattern (13 bp):
TATTGCATTTATT
Found at i:34927292 original size:17 final size:17
Alignment explanation
Indices: 34927265--34927312 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 17
34927255 GTTATAATTG
34927265 TTTTGTTTGTTATTTTAA
1 TTTT-TTTGTTATTTTAA
34927283 TTTTTTTGTTA----AA
1 TTTTTTTGTTATTTTAA
*
34927296 TTTTGTTGTTATTTTAA
1 TTTTTTTGTTATTTTAA
34927313 AGTTATTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 9
0.71 0.03 0.26
Matches are distributed among these distances:
13 12 0.48
17 9 0.36
18 4 0.16
ACGTcount: A:0.19, C:0.00, G:0.10, T:0.71
Consensus pattern (17 bp):
TTTTTTTGTTATTTTAA
Found at i:34929099 original size:43 final size:43
Alignment explanation
Indices: 34929034--34929133 Score: 168
Period size: 43 Copynumber: 2.3 Consensus size: 43
34929024 TGCTATTCCT
34929034 TGACATGTTATTAAATTATATTACTTGACCCGTGTTAATATCT-
1 TGACATGTTATTAAATTATATTACTTGACCCGTGTTAATAT-TG
34929077 TGGA-ATGTTATTAAATTATATTACTTGACCCGTGTTAATATTG
1 T-GACATGTTATTAAATTATATTACTTGACCCGTGTTAATATTG
34929120 TGACATGTTATTAA
1 TGACATGTTATTAA
34929134 TTGTGCAGTT
Statistics
Matches: 54, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
42 3 0.06
43 49 0.91
44 2 0.04
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44
Consensus pattern (43 bp):
TGACATGTTATTAAATTATATTACTTGACCCGTGTTAATATTG
Found at i:34929534 original size:28 final size:28
Alignment explanation
Indices: 34929482--34929536 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
34929472 ACTCGACTTG
* **
34929482 GGTTTAGGATTAAGGTTTTTTGGTTTAA
1 GGTTTAGGATTAAGGATTTAAGGTTTAA
*
34929510 GGTTTAGGATTTAGGATTTAAGGTTTA
1 GGTTTAGGATTAAGGATTTAAGGTTTA
34929537 GTCTAATAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (28 bp):
GGTTTAGGATTAAGGATTTAAGGTTTAA
Done.