Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D11
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: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 408745 characters in sequence are not A, C, G, or T
File 92 of 226
Found at i:28862157 original size:32 final size:31
Alignment explanation
Indices: 28862120--28862220 Score: 95
Period size: 32 Copynumber: 3.3 Consensus size: 31
28862110 TTAATATAAT
28862120 ATTTAGTATTTGAACTTAACACTTTTTTTCTA
1 ATTTAGTATTT-AACTTAACACTTTTTTTCTA
** *
28862152 ATTTAGTATTT--CGTT--TTCTTTTTTGCTTA
1 ATTTAGTATTTAAC-TTAACACTTTTTTTC-TA
*
28862181 ATTTAGTATTTAAACTTAACATTTTTTTTCTA
1 ATTTAGTATTT-AACTTAACACTTTTTTTCTA
28862213 ATTT-GTAT
1 ATTTAGTAT
28862221 CCCAAAACAT
Statistics
Matches: 55, Mismatches: 7, Indels: 15
0.71 0.09 0.19
Matches are distributed among these distances:
28 8 0.15
29 14 0.25
30 2 0.04
31 6 0.11
32 18 0.33
33 7 0.13
ACGTcount: A:0.25, C:0.10, G:0.07, T:0.58
Consensus pattern (31 bp):
ATTTAGTATTTAACTTAACACTTTTTTTCTA
Found at i:28862726 original size:7 final size:7
Alignment explanation
Indices: 28862714--28862750 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
28862704 GTTGTTGTAA
28862714 GGTGAAG
1 GGTGAAG
28862721 GGTGAAG
1 GGTGAAG
28862728 GGTGAAG
1 GGTGAAG
*
28862735 GGTGAAA
1 GGTGAAG
28862742 GGTGAAG
1 GGTGAAG
28862749 GG
1 GG
28862751 GGGATCGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.57, T:0.14
Consensus pattern (7 bp):
GGTGAAG
Found at i:28867115 original size:15 final size:15
Alignment explanation
Indices: 28867066--28867107 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
28867056 CTTGAACTTC
*
28867066 ATTATTACTATTACT
1 ATTATTACTATTAAT
*
28867081 ATTATTAATATTAAT
1 ATTATTACTATTAAT
28867096 ATTATTACTATT
1 ATTATTACTATT
28867108 GTTATTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTATTACTATTAAT
Found at i:28877307 original size:381 final size:381
Alignment explanation
Indices: 28876604--28877369 Score: 1397
Period size: 381 Copynumber: 2.0 Consensus size: 381
28876594 TACTCTAGCC
*
28876604 TCCATGATTAAAGTAAACAGACAAGAGGACATGAAACCTATCTGGATAAGCATCTATGAAACCCC
1 TCCATGATTAAAGTAAACAGACAAGAGGACATGAAACCTATCCGGATAAGCATCTATGAAACCCC
*
28876669 AGCTCATTGTTGCAATATCAAGGAAGGGGAAAAGGATGACAGCCCTTGGTATCAAGATATATTAT
66 AGCTCATTGTTGCAATATCAAGGAAGGGGAAAAGGATGACAGCCCTTGGTATCAAGATATATTAC
28876734 GATATTTGAAGAATCGTGAATATCCTAACCAGGCAGCTGAGAATGATAAGAGGACTCTGAGAAGA
131 GATATTTGAAGAATCGTGAATATCCTAACCAGGCAGCTGAGAATGATAAGAGGACTCTGAGAAGA
* * *
28876799 GTAGCCATTGATTATGTTTTAAATGGAGAGATTTTATATAAAAGAGGGAAGGATCAGGTACTGTT
196 CTAGCCATTGATTATATTTTAAATGGAGAGATCTTATATAAAAGAGGGAAGGATCAGGTACTGTT
* *
28876864 AAGATGTGTGGACGCTGTGGAGGCTAAAAAAGTTTTGGAAGAAGTTCATGATGGTATTTGCGGAA
261 AAGATGTGTGGACGCTGTGGAGGCTAAAAAAGTTTTGGAAGAAGTCCATGAGGGTATTTGCGGAA
*
28876929 CGCATGCTAGTGGTTTCTCAATGGCTAGACAGATTATGAGATTCGGGTACTACTGG
326 CGCATGCTAGTGGTTTCACAATGGCTAGACAGATTATGAGATTCGGGTACTACTGG
* * *
28876985 TCCATGATTAAAGTAAACAGACAAGAGGACATGAAACCTATCCGGATGAGCATTTATGAAACCCT
1 TCCATGATTAAAGTAAACAGACAAGAGGACATGAAACCTATCCGGATAAGCATCTATGAAACCCC
*
28877050 AGCTCATTGTTGCAATATCAAGGAAGGGGAAAAGGATGATAGCCCTTGGTATCAAGATATATTAC
66 AGCTCATTGTTGCAATATCAAGGAAGGGGAAAAGGATGACAGCCCTTGGTATCAAGATATATTAC
*
28877115 GATATTTGAAGAATCGTGAATATCCTGACCAGGCAGCTGAGAATGATAAGAGGACTCTGAGAAGA
131 GATATTTGAAGAATCGTGAATATCCTAACCAGGCAGCTGAGAATGATAAGAGGACTCTGAGAAGA
*
28877180 CTAGCCATTGATTATATTTTAGATGGAGAGATCTTATATAAAAGAGGGAAGGATCAGGTACTGTT
196 CTAGCCATTGATTATATTTTAAATGGAGAGATCTTATATAAAAGAGGGAAGGATCAGGTACTGTT
*
28877245 AAGATGTGTGGACGCTGTGGAGGCTAAAAAAGTTTTGGAGGAAGTCCATGAGGGTATTTGCGGAA
261 AAGATGTGTGGACGCTGTGGAGGCTAAAAAAGTTTTGGAAGAAGTCCATGAGGGTATTTGCGGAA
28877310 CGCATGCTAGTGGTTTCACAATGGCTAGACAGATTATGAGATTCGGGTACTACTGG
326 CGCATGCTAGTGGTTTCACAATGGCTAGACAGATTATGAGATTCGGGTACTACTGG
28877366 TCCA
1 TCCA
28877370 CTATAGAAGG
Statistics
Matches: 370, Mismatches: 15, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
381 370 1.00
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.26
Consensus pattern (381 bp):
TCCATGATTAAAGTAAACAGACAAGAGGACATGAAACCTATCCGGATAAGCATCTATGAAACCCC
AGCTCATTGTTGCAATATCAAGGAAGGGGAAAAGGATGACAGCCCTTGGTATCAAGATATATTAC
GATATTTGAAGAATCGTGAATATCCTAACCAGGCAGCTGAGAATGATAAGAGGACTCTGAGAAGA
CTAGCCATTGATTATATTTTAAATGGAGAGATCTTATATAAAAGAGGGAAGGATCAGGTACTGTT
AAGATGTGTGGACGCTGTGGAGGCTAAAAAAGTTTTGGAAGAAGTCCATGAGGGTATTTGCGGAA
CGCATGCTAGTGGTTTCACAATGGCTAGACAGATTATGAGATTCGGGTACTACTGG
Found at i:28879788 original size:132 final size:131
Alignment explanation
Indices: 28879550--28880066 Score: 651
Period size: 132 Copynumber: 3.9 Consensus size: 131
28879540 GCAGATCCTA
* * * * *
28879550 TCTCCCTAAGCAGTAGTGGAGCAAATCGAAGACGACAAATCTTATCTTCCCAAGCTAATAGGGAA
1 TCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACGAATCTTATCTTCCCAAGGTAGTAGGGAA
* *
28879615 GCAGATTTAAGCCACTAATCCTATCTCCCTGTGCAGCAGTGGAGTAGGTTTAAGAATGTAGATCT
66 GCAGATTTAAGCCACTAATCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTAAAGAATGTAGATCT
28879680 GG
131 -G
* * * *
28879682 TCTCCCTAAGTAGTAGTGGAGCAGATCGAAGAC-AGTGAATCTTATCTTCTCAAGGTAGTAGGGA
1 TCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGA-CGAATCTTATCTTCCCAAGGTAGTAGGGA
* *
28879746 AGCAGATTTAAGCCACTAATCCTATCTCCCTGAGCAGTAGTGGAGTAGATTAAAGAATGTAGATC
65 AGCAGATTTAAGCCACTAATCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTAAAGAATGTAGATC
28879811 TTG
130 -TG
** * * * *
28879814 TCTCCCTAAGCAGTAGTGGAATAGATAAAAAAAAATGGCGAATCTTATCTTCCCAAGGTAGTAGG
1 TCTCCCTAAGCAGTAGTGGAGCAGAT---CAAAGACGACGAATCTTATCTTCCCAAGGTAGTAGG
* * * * * * *
28879879 GAAGCAGATTTAAGCCACCAATCCTATTTCCTTGAGCAGGAGTGGAGTAGGTTGAAGATTGCAGA
63 GAAGCAGATTTAAGCCACTAATCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTAAAGAATGTAGA
28879944 TCATG
128 TC-TG
* * *
28879949 TTTCCTTGAGCAGTAGTGGAGCAGATCAAAGACGACGAATCTTATCTTCCCAAGGTAGTAGGGAA
1 TCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACGAATCTTATCTTCCCAAGGTAGTAGGGAA
* * * *
28880014 GCAGATTTAGGTCACT-AGCCTTATCTCTCTGAGCAGCAGTGGAGTAGGTTAAA
66 GCAGATTTAAGCCACTAATCC-TATCTCCCTGAGCAGCAGTGGAGTAGGTTAAA
28880067 AATTACAGAT
Statistics
Matches: 330, Mismatches: 48, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
131 4 0.01
132 215 0.65
133 1 0.00
135 110 0.33
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (131 bp):
TCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACGAATCTTATCTTCCCAAGGTAGTAGGGAA
GCAGATTTAAGCCACTAATCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTAAAGAATGTAGATCT
G
Found at i:28880087 original size:267 final size:267
Alignment explanation
Indices: 28879587--28880090 Score: 696
Period size: 267 Copynumber: 1.9 Consensus size: 267
28879577 GAAGACGACA
* *
28879587 AATCTTATCTTCCCAAGCTAATAGGGAAGCAGATTTAAGCCACTAATCCTATCTCCCTGTGCAGC
1 AATCTTATCTTCCCAAGCTAATAGGGAAGCAGATTTAAGCCACCAATCCTATCTCCCTGAGCAGC
* * * *
28879652 AGTGGAGTAGGTTTAAGAATGTAGATCTGGTCTCCCTAAGTAGTAGTGGAGCAGATCGAAGACAG
66 AGTGGAGTAGGTTGAAGAATGCAGATCTGGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACAG
* * *
28879717 TGAATCTTATCTTCTCAAGGTAGTAGGGAAGCAGATTTAAGCCACTAATCCTATCTCCCTGAGCA
131 CGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACTAAGCCTATCTCCCTGAGCA
* *
28879782 GTAGTGGAGTAGATTAAAGAATGTAGATCTTGTCTCCCTAAGCAGTAGTGGAATAGATAAAAAAA
196 GCAGTGGAGTAGATTAAAGAATGTAGATCTTATCTCCCTAAGCAGTAGTGGAATAGATAAAAAAA
28879847 AATGGCG
261 AATGGCG
* * * * *
28879854 AATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAATCCTATTTCCTTGAGCAGG
1 AATCTTATCTTCCCAAGCTAATAGGGAAGCAGATTTAAGCCACCAATCCTATCTCCCTGAGCAGC
* * * *
28879919 AGTGGAGTAGGTTGAAGATTGCAGATCAT-GTTTCCTTGAGCAGTAGTGGAGCAGATCAAAGAC-
66 AGTGGAGTAGGTTGAAGAATGCAGATC-TGGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACA
* * *
28879982 GACGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAGGTCACT-AGCCTTATCTCTCTGA
130 G-CGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACTAAGCC-TATCTCCCTGA
*
28880046 GCAGCAGTGGAGTAGGTTAAA-AAT-TACAGAT-TCTATCTCCCTAAG
193 GCAGCAGTGGAGTAGATTAAAGAATGT--AGATCT-TATCTCCCTAAG
28880091 TTGCAGTGGA
Statistics
Matches: 207, Mismatches: 24, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
265 1 0.00
266 8 0.04
267 197 0.95
268 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (267 bp):
AATCTTATCTTCCCAAGCTAATAGGGAAGCAGATTTAAGCCACCAATCCTATCTCCCTGAGCAGC
AGTGGAGTAGGTTGAAGAATGCAGATCTGGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACAG
CGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACTAAGCCTATCTCCCTGAGCA
GCAGTGGAGTAGATTAAAGAATGTAGATCTTATCTCCCTAAGCAGTAGTGGAATAGATAAAAAAA
AATGGCG
Found at i:28881422 original size:13 final size:13
Alignment explanation
Indices: 28881400--28881431 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
28881390 GGCGTTTCAA
*
28881400 TTATATTTATAAT
1 TTATACTTATAAT
28881413 TTATACTTATAAT
1 TTATACTTATAAT
28881426 TTATAC
1 TTATAC
28881432 ATATTTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (13 bp):
TTATACTTATAAT
Found at i:28893256 original size:48 final size:49
Alignment explanation
Indices: 28893200--28893292 Score: 127
Period size: 49 Copynumber: 1.9 Consensus size: 49
28893190 GGAGTCCTAA
* * *
28893200 CCAAATGAGT-AG-GAAGAAACAAAGAAAATGATAATCCAGCTATGGCAG
1 CCAAATGAGTGAGAGAA-AAACAAAGAAAATAAAAATCCAACTATGGCAG
*
28893248 CCAAATGAGTGAGAGAAAAACAAAGGAAATAAAAATCCAACTATG
1 CCAAATGAGTGAGAGAAAAACAAAGAAAATAAAAATCCAACTATG
28893293 TTATTAACGC
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
48 10 0.26
49 26 0.67
50 3 0.08
ACGTcount: A:0.52, C:0.14, G:0.20, T:0.14
Consensus pattern (49 bp):
CCAAATGAGTGAGAGAAAAACAAAGAAAATAAAAATCCAACTATGGCAG
Found at i:28900468 original size:15 final size:15
Alignment explanation
Indices: 28900450--28900480 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
28900440 TATTCGATGT
28900450 ATGATCACTCGATTA
1 ATGATCACTCGATTA
28900465 ATGATCACTCGATTA
1 ATGATCACTCGATTA
28900480 A
1 A
28900481 GCCATGAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (15 bp):
ATGATCACTCGATTA
Found at i:28917931 original size:18 final size:18
Alignment explanation
Indices: 28917908--28917952 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
28917898 TTCTCATTTT
*
28917908 CAACAACTTCTTCTT-TAG
1 CAACAACTTCCTCTTCT-G
28917926 CAACAACTTCCTCTTCTG
1 CAACAACTTCCTCTTCTG
28917944 CAACAACTT
1 CAACAACTT
28917953 TTTTCTCAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 24 0.96
19 1 0.04
ACGTcount: A:0.29, C:0.33, G:0.04, T:0.33
Consensus pattern (18 bp):
CAACAACTTCCTCTTCTG
Found at i:28921415 original size:32 final size:32
Alignment explanation
Indices: 28921360--28921559 Score: 222
Period size: 32 Copynumber: 6.3 Consensus size: 32
28921350 GAATGACTAC
* * *
28921360 AAGCCATAAGT-ACAGTAATATGATTGGCACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
* * * *
28921391 AAGCCATAAGTAGTGGTAATATGATTGGCACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
* * * *
28921423 CAGCCATTAGTAATAGTAGTATGATTGGCACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
*
28921455 AAGCCATCAGTAGTAGTAATATGATCGGCACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
* * *
28921487 TAGCCATCAGTAATGGTAATATGATCGGTACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
* ** *
28921519 CAGTAATCAGTAATGGTAATATGATCGGCACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
28921551 AAGCCATCA
1 AAGCCATCA
28921560 ATAACATTGC
Statistics
Matches: 144, Mismatches: 24, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
31 11 0.08
32 133 0.92
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (32 bp):
AAGCCATCAGTAATAGTAATATGATCGGCACA
Found at i:28921451 original size:64 final size:64
Alignment explanation
Indices: 28921360--28921559 Score: 249
Period size: 64 Copynumber: 3.1 Consensus size: 64
28921350 GAATGACTAC
* * * *
28921360 AAGCCATAAGT-ACAGTAATATGATTGGCACAAAGCCATAAGTAGTGGTAATATGATTGGCACA
1 AAGCCATCAGTAATAGTAATATGATTGGCACAAAGCCATCAGTAGTGGTAATATGATCGGCACA
* * * *
28921423 CAGCCATTAGTAATAGTAGTATGATTGGCACAAAGCCATCAGTAGTAGTAATATGATCGGCACA
1 AAGCCATCAGTAATAGTAATATGATTGGCACAAAGCCATCAGTAGTGGTAATATGATCGGCACA
* * * * * ** *
28921487 TAGCCATCAGTAATGGTAATATGATCGGTACACAGTAATCAGTAATGGTAATATGATCGGCACA
1 AAGCCATCAGTAATAGTAATATGATTGGCACAAAGCCATCAGTAGTGGTAATATGATCGGCACA
28921551 AAGCCATCA
1 AAGCCATCA
28921560 ATAACATTGC
Statistics
Matches: 117, Mismatches: 19, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
63 9 0.08
64 108 0.92
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (64 bp):
AAGCCATCAGTAATAGTAATATGATTGGCACAAAGCCATCAGTAGTGGTAATATGATCGGCACA
Found at i:28921542 original size:96 final size:95
Alignment explanation
Indices: 28921360--28921559 Score: 265
Period size: 96 Copynumber: 2.1 Consensus size: 95
28921350 GAATGACTAC
* * * *
28921360 AAGCCATAAGTACAGTAATATGATTGGCACAAAGCCATAAGTAGTGGTAATATGATTGGCACACA
1 AAGCCATCAGTACAGTAATATGATCGGCACAAAGCCATAAGTAATGGTAATATGATCGGCACACA
* * * *
28921425 GCCATTAGTAATAGTAGTATGATTGGCACA
66 GCAATCAGTAATAGTAATATGATCGGCACA
* * * *
28921455 AAGCCATCAGTAGTAGTAATATGATCGGCACATAGCCATCAGTAATGGTAATATGATCGGTACAC
1 AAGCCATCAGTA-CAGTAATATGATCGGCACAAAGCCATAAGTAATGGTAATATGATCGGCACAC
* *
28921520 AGTAATCAGTAATGGTAATATGATCGGCACA
65 AGCAATCAGTAATAGTAATATGATCGGCACA
28921551 AAGCCATCA
1 AAGCCATCA
28921560 ATAACATTGC
Statistics
Matches: 90, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
95 11 0.12
96 79 0.88
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (95 bp):
AAGCCATCAGTACAGTAATATGATCGGCACAAAGCCATAAGTAATGGTAATATGATCGGCACACA
GCAATCAGTAATAGTAATATGATCGGCACA
Found at i:28921617 original size:26 final size:26
Alignment explanation
Indices: 28921569--28921618 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
28921559 AATAACATTG
* *
28921569 CAGCAAAGCTGGCAGCAATAGTATCA
1 CAGCAAAGCTGCCAGCAACAGTATCA
*
28921595 CAGCAAAGCTGCCAGTAACAGTAT
1 CAGCAAAGCTGCCAGCAACAGTAT
28921619 ATGTGGCCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (26 bp):
CAGCAAAGCTGCCAGCAACAGTATCA
Found at i:28921780 original size:24 final size:24
Alignment explanation
Indices: 28921744--28921832 Score: 117
Period size: 24 Copynumber: 3.7 Consensus size: 24
28921734 AAACAGTCAT
28921744 ACAAATCAATCATTTAAATCACAG
1 ACAAATCAATCATTTAAATCACAG
* * * *
28921768 ACAAATCAGTCATTTACATCTCGG
1 ACAAATCAATCATTTAAATCACAG
*
28921792 ACAAATCAATCATTTACATCACAGG
1 ACAAATCAATCATTTAAATCACA-G
28921817 A-AAATCAATCATTTAA
1 ACAAATCAATCATTTAA
28921833 CTCTAAGGGG
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
24 54 0.96
25 2 0.04
ACGTcount: A:0.45, C:0.21, G:0.07, T:0.27
Consensus pattern (24 bp):
ACAAATCAATCATTTAAATCACAG
Found at i:28921868 original size:27 final size:27
Alignment explanation
Indices: 28921825--28922080 Score: 176
Period size: 27 Copynumber: 9.6 Consensus size: 27
28921815 GGAAAATCAA
* * * *
28921825 TCATTTAACTCTA-AGGGGCAAAAAAG
1 TCATTTTACCCTACAGGGGCAATAAGG
*
28921851 TCATTTTACCCTACAGGGG-AATTATGG
1 TCATTTTACCCTACAGGGGCAA-TAAGG
* * * *
28921878 TCATTTTACCCTATAGGGGCATTACGA
1 TCATTTTACCCTACAGGGGCAATAAGG
* *
28921905 TCATTTTACCCTACAGGGGCATTACGG
1 TCATTTTACCCTACAGGGGCAATAAGG
* * * * *
28921932 TCATTTTATCCTATAGGGGTATTACGG
1 TCATTTTACCCTACAGGGGCAATAAGG
* * *
28921959 TCATTTTACCCTACAGGGGCATTACGA
1 TCATTTTACCCTACAGGGGCAATAAGG
* ** * * *
28921986 TCATTTTACCCTAGAGCAGCATTACGA
1 TCATTTTACCCTACAGGGGCAATAAGG
* * * * *
28922013 TCATTCTGCCCTATAGGGGCATTACGG
1 TCATTTTACCCTACAGGGGCAATAAGG
* * * *
28922040 TTATTTTACCCTA-AAGGGCATTATGG
1 TCATTTTACCCTACAGGGGCAATAAGG
28922066 TCATTTTACCCTACA
1 TCATTTTACCCTACA
28922081 AGAGTATTAC
Statistics
Matches: 193, Mismatches: 33, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
26 36 0.19
27 156 0.81
28 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (27 bp):
TCATTTTACCCTACAGGGGCAATAAGG
Found at i:28922097 original size:27 final size:27
Alignment explanation
Indices: 28921851--28922236 Score: 357
Period size: 27 Copynumber: 14.4 Consensus size: 27
28921841 GGCAAAAAAG
* * *
28921851 TCATTTTACCCTACAGGGGAATTATGG
1 TCATTTTACCCTACAGGGGCATTACGA
*
28921878 TCATTTTACCCTATAGGGGCATTACGA
1 TCATTTTACCCTACAGGGGCATTACGA
*
28921905 TCATTTTACCCTACAGGGGCATTACGG
1 TCATTTTACCCTACAGGGGCATTACGA
* * * *
28921932 TCATTTTATCCTATAGGGGTATTACGG
1 TCATTTTACCCTACAGGGGCATTACGA
28921959 TCATTTTACCCTACAGGGGCATTACGA
1 TCATTTTACCCTACAGGGGCATTACGA
* **
28921986 TCATTTTACCCTAGAGCAGCATTACGA
1 TCATTTTACCCTACAGGGGCATTACGA
* * * *
28922013 TCATTCTGCCCTATAGGGGCATTACGG
1 TCATTTTACCCTACAGGGGCATTACGA
* * * *
28922040 TTATTTTACCCTA-AAGGGCATTATGG
1 TCATTTTACCCTACAGGGGCATTACGA
* * *
28922066 TCATTTTACCCTACAAGAGTATTACGA
1 TCATTTTACCCTACAGGGGCATTACGA
* * ***
28922093 TCATTTTAACCTATAGGGGTGCTACGA
1 TCATTTTACCCTACAGGGGCATTACGA
* * * *
28922120 TCATTTTACCTTTCAGAGGCATTACGG
1 TCATTTTACCCTACAGGGGCATTACGA
* * * *
28922147 TAATTTTACCGTACAGGGGCGTTGCGA
1 TCATTTTACCCTACAGGGGCATTACGA
* * *
28922174 TCATTTTA-CCAATC-GAGGGTATTTCGA
1 TCATTTTACCCTA-CAG-GGGCATTACGA
* *
28922201 TCATTTTACCCTTCA-GGGTATTACGA
1 TCATTTTACCCTACAGGGGCATTACGA
28922227 TCATTTTACC
1 TCATTTTACC
28922237 TTTCAAAGGT
Statistics
Matches: 291, Mismatches: 63, Indels: 11
0.80 0.17 0.03
Matches are distributed among these distances:
26 46 0.16
27 243 0.84
28 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (27 bp):
TCATTTTACCCTACAGGGGCATTACGA
Found at i:28922255 original size:27 final size:25
Alignment explanation
Indices: 28922117--28922277 Score: 124
Period size: 27 Copynumber: 6.0 Consensus size: 25
28922107 AGGGGTGCTA
*
28922117 CGATCATTTTACCTTTCAGAGGCATT
1 CGATCATTTTACCTTTCAG-GGTATT
* * * * **
28922143 ACGGTAATTTTACCGTACAGGGGCGTT
1 -CGATCATTTTACCTTTCA-GGGTATT
**
28922170 GCGATCATTTTACCAATCGAGGGTATTT
1 -CGATCATTTTACCTTTC-AGGGTA-TT
*
28922198 CGATCATTTTACCCTTCAGGGTATT
1 CGATCATTTTACCTTTCAGGGTATT
*
28922223 ACGATCATTTTACCTTTCAAAGGTATAT
1 -CGATCATTTTACCTTTC-AGGGTAT-T
*
28922251 CGATCATTTTACCTTTTGAGGGTATT
1 CGATCATTTTACC-TTTCAGGGTATT
28922277 C
1 C
28922278 CAGTAATTTT
Statistics
Matches: 108, Mismatches: 19, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
25 2 0.02
26 24 0.22
27 74 0.69
28 8 0.07
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.38
Consensus pattern (25 bp):
CGATCATTTTACCTTTCAGGGTATT
Found at i:28922346 original size:27 final size:26
Alignment explanation
Indices: 28922289--28922359 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 26
28922279 AGTAATTTTA
* *
28922289 TATTTCAATAATTTTATCCTTTAAGGG
1 TATTTC-ATAATTTTACCCTTGAAGGG
*
28922316 TATTTCGATAATTTTACCCTTCGAA-GT
1 TATTTC-ATAATTTTACCCTT-GAAGGG
28922343 TATTTCAGTAATTTTAC
1 TATTTCA-TAATTTTAC
28922360 AACCTTTTCG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
26 1 0.03
27 35 0.92
28 2 0.05
ACGTcount: A:0.28, C:0.14, G:0.10, T:0.48
Consensus pattern (26 bp):
TATTTCATAATTTTACCCTTGAAGGG
Found at i:28932579 original size:21 final size:21
Alignment explanation
Indices: 28932553--28932595 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
28932543 TCCATTTACC
28932553 TTAATTTTTCCTTCTATTATA
1 TTAATTTTTCCTTCTATTATA
28932574 TTAATTTTTCCTTCTATTATA
1 TTAATTTTTCCTTCTATTATA
28932595 T
1 T
28932596 CCTTTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.14, G:0.00, T:0.63
Consensus pattern (21 bp):
TTAATTTTTCCTTCTATTATA
Found at i:28933601 original size:23 final size:23
Alignment explanation
Indices: 28933571--28933616 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
28933561 GATTGAGGTC
28933571 TGTTCTTTGTAATTTTTATATTT
1 TGTTCTTTGTAATTTTTATATTT
28933594 TGTTCTTTGTAATTTTTATATTT
1 TGTTCTTTGTAATTTTTATATTT
28933617 CTGAGATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.04, G:0.09, T:0.70
Consensus pattern (23 bp):
TGTTCTTTGTAATTTTTATATTT
Found at i:28935271 original size:13 final size:13
Alignment explanation
Indices: 28935253--28935277 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28935243 GTTGATGGTT
28935253 TTGAAGTTATAAG
1 TTGAAGTTATAAG
28935266 TTGAAGTTATAA
1 TTGAAGTTATAA
28935278 TGTATTTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (13 bp):
TTGAAGTTATAAG
Found at i:28938197 original size:50 final size:50
Alignment explanation
Indices: 28938119--28938215 Score: 149
Period size: 50 Copynumber: 1.9 Consensus size: 50
28938109 ACTCACTTGA
* * *
28938119 GACTTCCTTGCCTTATTTGCTTAACTTTTTCTAGACACTGGAGCTTCCAT
1 GACTTCCTCGCCTTATCTGCTTAACTTTTTCTAGACACTAGAGCTTCCAT
* *
28938169 GACTTCCTCGCCTTATCTGCTTAGCTTTTTCTAGACGCTAGAGCTTC
1 GACTTCCTCGCCTTATCTGCTTAACTTTTTCTAGACACTAGAGCTTC
28938216 TATTCTCCCA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.16, C:0.28, G:0.15, T:0.40
Consensus pattern (50 bp):
GACTTCCTCGCCTTATCTGCTTAACTTTTTCTAGACACTAGAGCTTCCAT
Found at i:28942526 original size:5 final size:5
Alignment explanation
Indices: 28942516--28942547 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
28942506 GCGTTCCTTG
28942516 TTATT TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TTATT TT
28942548 TCCTTTACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:28943335 original size:3 final size:3
Alignment explanation
Indices: 28943329--28943392 Score: 119
Period size: 3 Copynumber: 21.3 Consensus size: 3
28943319 AACTAATAAG
*
28943329 TTA TTA TTA TGA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28943377 TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA T
28943393 CTATGTCTTG
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:28943518 original size:17 final size:18
Alignment explanation
Indices: 28943489--28943525 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
28943479 CTTTTTTATT
28943489 TTATATAGATATAAATAC
1 TTATATAGATATAAATAC
*
28943507 TTATAT-GATATATATAC
1 TTATATAGATATAAATAC
28943524 TT
1 TT
28943526 TACACTTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.46
Consensus pattern (18 bp):
TTATATAGATATAAATAC
Found at i:28947526 original size:3 final size:3
Alignment explanation
Indices: 28947518--28947543 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
28947508 AAAGTTTCAA
28947518 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
28947544 AGAGCTCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:28954797 original size:21 final size:21
Alignment explanation
Indices: 28954761--28954807 Score: 85
Period size: 22 Copynumber: 2.2 Consensus size: 21
28954751 GTCAAGAAAT
28954761 ATTTCACTTAAAAAAAAGGGTC
1 ATTTCACTTAAAAAAAAGGG-C
28954783 ATTTCACTTAAAAAAAAGGGC
1 ATTTCACTTAAAAAAAAGGGC
28954804 ATTT
1 ATTT
28954808 AAAAAAAAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.30
Consensus pattern (21 bp):
ATTTCACTTAAAAAAAAGGGC
Found at i:28956220 original size:96 final size:96
Alignment explanation
Indices: 28956056--28957094 Score: 1510
Period size: 96 Copynumber: 10.9 Consensus size: 96
28956046 GTAACCATAG
28956056 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGGAACAGA
1 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGGAACAGA
28956121 TTGAAGCTACAACGGCGAGTCTCACTTCCCC
66 TTGAAGCTACAACGGCGAGTCTCACTTCCCC
*
28956152 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTATTTCCAGGCGATGCAGCGGAACAGA
1 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGGAACAGA
28956217 TTGAAGCTACAACGGCGAGTCTCACTTCCCC
66 TTGAAGCTACAACGGCGAGTCTCACTTCCCC
*
28956248 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTTCAGGCGATGCAGCGGAACAGA
1 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGGAACAGA
*
28956313 TTGAAGTTACAACGGCGAGTCTCACTTCCCC
66 TTGAAGCTACAACGGCGAGTCTCACTTCCCC
*
28956344 ATTGCAATTTAAAAGATCGAAGCCACAACGGTGAATCTTACTTCCAGGCGATGCAGCGGAACAGA
1 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGGAACAGA
* * *
28956409 TTGAAGCTACAACGGTGAGTTTCACTTTCCC
66 TTGAAGCTACAACGGCGAGTCTCACTTCCCC
*
28956440 ATTGCAA--T---AGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGAAACAGA
1 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGGAACAGA
*
28956500 TTGAAGCTACAACGGCGAGTCTCACTTCCTC
66 TTGAAGCTACAACGGCGAGTCTCACTTCCCC
*
28956531 ATTGCAATTTAAAAGATCGAAGCCACAACGGTGAATCTTACTTCCAGGCGATGCAGCGGAACAGA
1 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGGAACAGA
28956596 TTGAAGCTACAACGGCGAGTCTCACTTCCCC
66 TTGAAGCTACAACGGCGAGTCTCACTTCCCC
* *
28956627 ATTGCAATTTAAAAGATCGAAGCCACAACGTCGAATCTTATTTCCAGGCGATGCAGCGGAACAGA
1 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGGAACAGA
28956692 TTGAAGCTACAACGGCGAGTCTCACTTCCCC
66 TTGAAGCTACAACGGCGAGTCTCACTTCCCC
* * *
28956723 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTTCAGACGATGCAGCAGAACAGA
1 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGGAACAGA
28956788 TTGAAGCTACAACGGCGAGTCTCACTTCCCC
66 TTGAAGCTACAACGGCGAGTCTCACTTCCCC
* * * *
28956819 ACTGCAA--T---AGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCAGAATATA
1 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGGAACAGA
*
28956879 TTGAAGCTACAACAGCGAGTCTCACTTCCCCGAC
66 TTGAAGCTACAACGGCGAGTCTCACTT-CCC--C
* * * * * ** * * *
28956913 ATTGCAA-TTAAAAGATTGAAGCCATAACGACGAATCTCATTTCCTTGCGGTGTAGTGGAACAGA
1 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGGAACAGA
* * * *
28956977 TTGAAGCTACGATGGCGAATCTCGCTTCCCC
66 TTGAAGCTACAACGGCGAGTCTCACTTCCCC
* * * * * * * * *
28957008 AATATTGC-AGTCAAATAGATTGAAGCTACAACAGCGAATCTCACAT-CATTGGCGATACAGTGG
1 ---ATTGCAATTTAAA-AGATCGAAGCCACAACGGCGAATCTTACTTCCA--GGCGATGCAGCGG
*
28957071 AACAGATTGAAGCTACAATGGCGA
60 AACAGATTGAAGCTACAACGGCGA
28957095 ACCTTGTTTT
Statistics
Matches: 859, Mismatches: 65, Indels: 34
0.90 0.07 0.04
Matches are distributed among these distances:
91 158 0.18
92 3 0.00
93 1 0.00
94 9 0.01
95 2 0.00
96 555 0.65
97 4 0.00
98 71 0.08
99 24 0.03
100 32 0.04
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (96 bp):
ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGGAACAGA
TTGAAGCTACAACGGCGAGTCTCACTTCCCC
Found at i:28956777 original size:379 final size:379
Alignment explanation
Indices: 28956069--28957094 Score: 1549
Period size: 379 Copynumber: 2.7 Consensus size: 379
28956059 GCAATTTAAA
*
28956069 AGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGGAACAGATTGAAGCTACAAC
1 AGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGAAACAGATTGAAGCTACAAC
*
28956134 GGCGAGTCTCACTTCCCCATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTATTTCCAG
66 GGCGAGTCTCACTTCCACATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTATTTCCAG
28956199 GCGATGCAGCGGAACAGATTGAAGCTACAACGGCGAGTCTCACTTCCCCATTGCAATTTAAAAGA
131 GCGATGCAGCGGAACAGATTGAAGCTACAACGGCGAGTCTCACTTCCCCATTGCAATTTAAAAGA
*
28956264 TCGAAGCCACAACGGCGAATCTTACTTTCAGGCGATGCAGCGGAACAGATTGAAGTTACAACGGC
196 TCGAAGCCACAACGGCGAATCTTACTTTCAGGCGATGCAGCGGAACAGATTGAAGCTACAACGGC
* *
28956329 GAGTCTCACTTCCCCATTGCAATTTAAAAGATCGAAGCCACAACGGTGAATCTTACTTCCAGGCG
261 GAGTCTCACTTCCCCATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCCAGACG
* * * * *
28956394 ATGCAGCGGAACAGATTGAAGCTACAACGGTGAGTTTCACTTTCCCATTGCAAT
326 ATGCAGCAGAACAGATTGAAGCTACAACGGCGAGTCTCACTTCCCCACTGCAAT
28956448 AGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGAAACAGATTGAAGCTACAAC
1 AGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGAAACAGATTGAAGCTACAAC
* * *
28956513 GGCGAGTCTCACTTCCTCATTGCAATTTAAAAGATCGAAGCCACAACGGTGAATCTTACTTCCAG
66 GGCGAGTCTCACTTCCACATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTATTTCCAG
28956578 GCGATGCAGCGGAACAGATTGAAGCTACAACGGCGAGTCTCACTTCCCCATTGCAATTTAAAAGA
131 GCGATGCAGCGGAACAGATTGAAGCTACAACGGCGAGTCTCACTTCCCCATTGCAATTTAAAAGA
*
28956643 TCGAAGCCACAACGTCGAATCTTA-TTTCCAGGCGATGCAGCGGAACAGATTGAAGCTACAACGG
196 TCGAAGCCACAACGGCGAATCTTACTTT-CAGGCGATGCAGCGGAACAGATTGAAGCTACAACGG
*
28956707 CGAGTCTCACTTCCCCATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTTCAGAC
260 CGAGTCTCACTTCCCCATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCCAGAC
28956772 GATGCAGCAGAACAGATTGAAGCTACAACGGCGAGTCTCACTTCCCCACTGCAAT
325 GATGCAGCAGAACAGATTGAAGCTACAACGGCGAGTCTCACTTCCCCACTGCAAT
* *
28956827 AGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGC-AGAATATATTGAAGCTACAA
1 AGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGA-AACAGATTGAAGCTACAA
* * * * *
28956891 CAGCGAGTCTCACTTCCCCGACATTGCAA-TTAAAAGATTGAAGCCATAACGACGAATCTCATTT
65 CGGCGAGTCTCACTT--CC-ACATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTATTT
** * * * * * * * *
28956955 CCTTGCGGTGTAGTGGAACAGATTGAAGCTACGATGGCGAATCTCGCTTCCCCAATATTGC-AGT
127 CCAGGCGATGCAGCGGAACAGATTGAAGCTACAACGGCGAGTCTCACTTCCCC---ATTGCAATT
* * * * * * * *
28957019 CAAATAGATTGAAGCTACAACAGCGAATCTCAC-ATCATTGGCGATACAGTGGAACAGATTGAAG
189 TAAA-AGATCGAAGCCACAACGGCGAATCTTACTTTCA--GGCGATGCAGCGGAACAGATTGAAG
*
28957083 CTACAATGGCGA
251 CTACAACGGCGA
28957095 ACCTTGTTTT
Statistics
Matches: 591, Mismatches: 44, Indels: 18
0.91 0.07 0.03
Matches are distributed among these distances:
378 4 0.01
379 435 0.74
381 75 0.13
382 8 0.01
383 7 0.01
384 28 0.05
385 34 0.06
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.21
Consensus pattern (379 bp):
AGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGAAACAGATTGAAGCTACAAC
GGCGAGTCTCACTTCCACATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTATTTCCAG
GCGATGCAGCGGAACAGATTGAAGCTACAACGGCGAGTCTCACTTCCCCATTGCAATTTAAAAGA
TCGAAGCCACAACGGCGAATCTTACTTTCAGGCGATGCAGCGGAACAGATTGAAGCTACAACGGC
GAGTCTCACTTCCCCATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCCAGACG
ATGCAGCAGAACAGATTGAAGCTACAACGGCGAGTCTCACTTCCCCACTGCAAT
Found at i:28957741 original size:5 final size:5
Alignment explanation
Indices: 28957731--28957757 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
28957721 GCGTTCCTTG
28957731 TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
28957758 TCCTTTACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:28958547 original size:3 final size:3
Alignment explanation
Indices: 28958541--28958574 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
28958531 AACTAATAAG
*
28958541 TTA TTA TTA TGA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
28958575 CTATGTCTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:28958692 original size:17 final size:18
Alignment explanation
Indices: 28958663--28958699 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
28958653 CTTTTTTATT
28958663 TTATATAGATATAAATAC
1 TTATATAGATATAAATAC
*
28958681 TTATAT-GATATATATAC
1 TTATATAGATATAAATAC
28958698 TT
1 TT
28958700 TACACTTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.46
Consensus pattern (18 bp):
TTATATAGATATAAATAC
Found at i:28962551 original size:113 final size:113
Alignment explanation
Indices: 28962216--28962651 Score: 651
Period size: 113 Copynumber: 3.9 Consensus size: 113
28962206 AAAATAAGCA
** * ** * ** *
28962216 TTAGCGGCGTTTTCCAAAAAGCGCCGCAAAAAACCTAAGCCTAACGACGCCGTTTTCAGAGCTTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAAATAAGCCCAACGACGCCGTTTTGTGGGCTTT
*
28962281 TGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGGTCAGGGCT
66 TGGGGATTTAGCGACGTTTTTAAGAAAGCGCCGCTAATGGTCAGGGCT
*
28962329 TTAGCGGCGTTTTTGAGAAAGCGCCGC-AAAAAAA-AAGCCCAACGACGTCGTTTTGTGGGCTTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAAATAAGCCCAACGACGCCGTTTTGTGGGCTTT
*
28962392 TGGGGATTTAACGACGTTTTTAAGAAAGCGCCGCTAATGGTCAGGGCT
66 TGGGGATTTAGCGACGTTTTTAAGAAAGCGCCGCTAATGGTCAGGGCT
* **
28962440 TTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAAAATAAGCCCAACGGTGCCGTTTTGTGGGCTTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAAATAAGCCCAACGACGCCGTTTTGTGGGCTTT
* * * *
28962505 TGGGGATTTAGCGGCGTTTTTAAGAAAGTGCCACTAATGCTCAGGGCT
66 TGGGGATTTAGCGACGTTTTTAAGAAAGCGCCGCTAATGGTCAGGGCT
* *
28962553 TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAAATAAGCCCAACGACGCTGTTTTGTGGGCTTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAAATAAGCCCAACGACGCCGTTTTGTGGGCTTT
* *
28962618 TGGGGATTTAGCAACGTTTTTAAGAAAACGCCGC
66 TGGGGATTTAGCGACGTTTTTAAGAAAGCGCCGC
28962652 AAAAAAACAT
Statistics
Matches: 290, Mismatches: 31, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
111 96 0.33
112 12 0.04
113 182 0.63
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (113 bp):
TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAAATAAGCCCAACGACGCCGTTTTGTGGGCTTT
TGGGGATTTAGCGACGTTTTTAAGAAAGCGCCGCTAATGGTCAGGGCT
Found at i:28962683 original size:73 final size:72
Alignment explanation
Indices: 28962560--28962702 Score: 205
Period size: 73 Copynumber: 2.0 Consensus size: 72
28962550 GCTTTAGCGG
** * * * * * *
28962560 CGTTTTTGGGAAAGCGCCGCAAAAAAAATAAGCCCAACGACGCTGTTTTGTGGGCTTTTGGGGAT
1 CGTTTTTAAGAAAACGCCGCAAAAAAAATAAGCCAAACGACCCCGTTTTGTGAGCTTTCGGGGAT
28962625 TTAGCAA
66 TTAGCAA
28962632 CGTTTTTAAGAAAACGCCGCAAAAAAACATAAGCCAAACGACCCCGTTTTGTGAGCTTTCGGGGA
1 CGTTTTTAAGAAAACGCCGCAAAAAAA-ATAAGCCAAACGACCCCGTTTTGTGAGCTTTCGGGGA
28962697 TTTAGC
65 TTTAGC
28962703 GGCCAAAAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
72 24 0.39
73 38 0.61
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.25
Consensus pattern (72 bp):
CGTTTTTAAGAAAACGCCGCAAAAAAAATAAGCCAAACGACCCCGTTTTGTGAGCTTTCGGGGAT
TTAGCAA
Found at i:28962897 original size:14 final size:14
Alignment explanation
Indices: 28962880--28962910 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
28962870 GGTTTAGAGT
28962880 TTATGGATTAGGGA
1 TTATGGATTAGGGA
*
28962894 TTATGGATTATGGA
1 TTATGGATTAGGGA
28962908 TTA
1 TTA
28962911 GGGGTTGGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (14 bp):
TTATGGATTAGGGA
Found at i:28962952 original size:15 final size:15
Alignment explanation
Indices: 28962908--28962962 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
28962898 GGATTATGGA
*
28962908 TTAGGGGTT-GGGAT
1 TTAGGGGTTAGGGGT
* *
28962922 TTAAGGTTTAGGGG-
1 TTAGGGGTTAGGGGT
*
28962936 TTAGAGGGTTAGTGGT
1 TTAG-GGGTTAGGGGT
28962952 TTAGGGGTTAG
1 TTAGGGGTTAG
28962963 ACGTGCTAGG
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
14 10 0.31
15 18 0.56
16 4 0.12
ACGTcount: A:0.18, C:0.00, G:0.45, T:0.36
Consensus pattern (15 bp):
TTAGGGGTTAGGGGT
Found at i:28963245 original size:15 final size:15
Alignment explanation
Indices: 28963227--28963280 Score: 81
Period size: 15 Copynumber: 3.6 Consensus size: 15
28963217 TGATTTAAGG
*
28963227 TTTAGGGGTTAGGGG
1 TTTAGGGGTTAGGGA
28963242 TTTAGGGGTTAGGGA
1 TTTAGGGGTTAGGGA
* *
28963257 TTTAAGGTTTAGGGA
1 TTTAGGGGTTAGGGA
28963272 TTTAGGGGT
1 TTTAGGGGT
28963281 CGAGTTAAGG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.19, C:0.00, G:0.44, T:0.37
Consensus pattern (15 bp):
TTTAGGGGTTAGGGA
Found at i:28963246 original size:8 final size:8
Alignment explanation
Indices: 28963225--28963280 Score: 64
Period size: 8 Copynumber: 7.4 Consensus size: 8
28963215 TGTGATTTAA
28963225 GGTTTAGG
1 GGTTTAGG
28963233 GG-TTAGG
1 GGTTTAGG
28963240 GGTTTAGG
1 GGTTTAGG
28963248 GG-TTAGG
1 GGTTTAGG
* *
28963255 GATTTA-A
1 GGTTTAGG
28963262 GGTTTAGG
1 GGTTTAGG
*
28963270 GATTTAGG
1 GGTTTAGG
28963278 GGT
1 GGT
28963281 CGAGTTAAGG
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
7 18 0.46
8 21 0.54
ACGTcount: A:0.18, C:0.00, G:0.46, T:0.36
Consensus pattern (8 bp):
GGTTTAGG
Found at i:28963267 original size:7 final size:7
Alignment explanation
Indices: 28963220--28963278 Score: 55
Period size: 7 Copynumber: 8.0 Consensus size: 7
28963210 AGTGTTGTGA
*
28963220 TTTAAGG
1 TTTAGGG
28963227 TTTAGGG
1 TTTAGGG
*
28963234 GTTAGGGG
1 TTTA-GGG
28963242 TTTAGGG
1 TTTAGGG
*
28963249 GTTAGGG
1 TTTAGGG
*
28963256 ATTTAAGG
1 -TTTAGGG
28963264 TTTAGGG
1 TTTAGGG
28963271 ATTTAGGG
1 -TTTAGGG
28963279 GTCGAGTTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
7 24 0.57
8 18 0.43
ACGTcount: A:0.20, C:0.00, G:0.42, T:0.37
Consensus pattern (7 bp):
TTTAGGG
Found at i:28964217 original size:154 final size:151
Alignment explanation
Indices: 28963888--28964274 Score: 624
Period size: 154 Copynumber: 2.6 Consensus size: 151
28963878 GCGGCGTTTT
28963888 TAAAGGTAAGCAATAGCGGCGTTTTTATAAAAAACGCCACAAAATAATTTTACTTTAAAAAAATA
1 TAAAGGTAAGCAATAGCGGCGTTTTTATAAAAAACGCCACAAAATAATTTTAC-TTAAAAAAATA
28963953 GCCCC-TTT----TAGCATAGCATAGCAAAACGGCATAGTTTTGTTCAAAATGAATTTTTTTGCG
65 GCCCCTTTTAGCATAGCATAGCATAGCAAAACGGCATAGTTTTGTTCAAAATGAATTTTTTTGCG
28964013 GCGTTTTTATGAAAAACGCCAC
130 GCGTTTTTATGAAAAACGCCAC
* *
28964035 TAAAGGTAAGCAATAGCGGCGTTTTTATAAAAAACGTCACAAAATAATTTAACGTTAAAAAAATA
1 TAAAGGTAAGCAATAGCGGCGTTTTTATAAAAAACGCCACAAAATAATTTTAC-TTAAAAAAATA
28964100 GCCCCTTTTAGCATAGCATAGCATAGCAAAACGGCATAGTTTTGTTCAAAATGAATTTTTTTTTG
65 GCCCCTTTTAGCATAGCATAGCATAGCAAAACGGCATAGTTTTGTTCAAAATGAA--TTTTTTTG
**
28964165 CGGCGTTTTTATGAAAAACGCTGC
128 CGGCGTTTTTATGAAAAACGCCAC
* * *
28964189 TAAAGGTAAGCAATAGCGACATTTTTATAAAAAACGCCACAAAATAATTTTACTTTAAAAAATAG
1 TAAAGGTAAGCAATAGCGGCGTTTTTATAAAAAACGCCACAAAATAATTTTACTTAAAAAAATAG
*
28964254 -CCATTTTAGCATAGCATAGCA
66 CCCCTTTTAGCATAGCATAGCA
28964275 AAACGGCGTA
Statistics
Matches: 222, Mismatches: 11, Indels: 9
0.92 0.05 0.04
Matches are distributed among these distances:
147 67 0.30
148 3 0.01
152 62 0.28
153 11 0.05
154 79 0.36
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (151 bp):
TAAAGGTAAGCAATAGCGGCGTTTTTATAAAAAACGCCACAAAATAATTTTACTTAAAAAAATAG
CCCCTTTTAGCATAGCATAGCATAGCAAAACGGCATAGTTTTGTTCAAAATGAATTTTTTTGCGG
CGTTTTTATGAAAAACGCCAC
Found at i:28968501 original size:42 final size:42
Alignment explanation
Indices: 28968381--28968503 Score: 156
Period size: 42 Copynumber: 2.9 Consensus size: 42
28968371 TTTGTGAAAG
* * *
28968381 AAGCGTCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGA
1 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTTTGGGA
* ** *
28968423 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTTTTTGT
1 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTTTGGGA
** *
28968465 AAGCGCCGCTAAAGAACATGGTCTTTAGCAGCGTTTTTG
1 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTTTG
28968504 TTTGTAAACG
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.20, C:0.19, G:0.29, T:0.33
Consensus pattern (42 bp):
AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTTTGGGA
Found at i:28975602 original size:46 final size:45
Alignment explanation
Indices: 28975552--28975639 Score: 106
Period size: 46 Copynumber: 1.9 Consensus size: 45
28975542 CCGTATGGGT
* * *
28975552 CACACAGCCTAGGCTAA-TTCGGGTGTGTGGGCTTACATGGGTGAGC
1 CACACAGCCAAGGCTAACTT-GGGCGTGTGGGC-TACACGGGTGAGC
* *
28975598 CACACGGGCAAGGCTAACTTGGGCGTGTGGGCTACACGGGTG
1 CACACAGCCAAGGCTAACTTGGGCGTGTGGGCTACACGGGTG
28975640 CATGGGCCCA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
45 9 0.25
46 25 0.69
47 2 0.06
ACGTcount: A:0.19, C:0.23, G:0.38, T:0.20
Consensus pattern (45 bp):
CACACAGCCAAGGCTAACTTGGGCGTGTGGGCTACACGGGTGAGC
Found at i:28980570 original size:39 final size:39
Alignment explanation
Indices: 28980527--28980661 Score: 198
Period size: 39 Copynumber: 3.4 Consensus size: 39
28980517 CATATTCACT
*
28980527 TTTAAGCATATATCACATTACACATATAATCTCATAACA
1 TTTAAGCATATATCACATTACACATATAATCACATAACA
* * *
28980566 TTTAAAGCATATATCACAATACTCGTATAATCACATAACA
1 TTT-AAGCATATATCACATTACACATATAATCACATAACA
* * *
28980606 TTCAAGCATATACCTCATTACACATATAATCACATAACA
1 TTTAAGCATATATCACATTACACATATAATCACATAACA
28980645 TTTAAGCATATATCACA
1 TTTAAGCATATATCACA
28980662 ATACTCAAAA
Statistics
Matches: 82, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
39 48 0.59
40 34 0.41
ACGTcount: A:0.44, C:0.21, G:0.04, T:0.31
Consensus pattern (39 bp):
TTTAAGCATATATCACATTACACATATAATCACATAACA
Found at i:28986226 original size:27 final size:27
Alignment explanation
Indices: 28986173--28986411 Score: 115
Period size: 27 Copynumber: 9.1 Consensus size: 27
28986163 ACATAAGGCC
* * * *
28986173 ATAACAGTCATTTCATCTTCTAGGGGT
1 ATAACAGTCATTTTACCCTATAGGGGT
*
28986200 ATAACAGTCATTTTACCCTATAAGGGT
1 ATAACAGTCATTTTACCCTATAGGGGT
** * *
28986227 ATTTCGGTTATTTTACCCTATAGGGGT
1 ATAACAGTCATTTTACCCTATAGGGGT
**** *
28986254 ATTTTGGTTATTTTACCCTAT-GAGGG-
1 ATAACAGTCATTTTACCCTATAG-GGGT
* *
28986280 -TAACAATCATTTCATCTCC--TAGGGGT
1 ATAACAGTCATTTTA-C-CCTATAGGGGT
28986306 AT---AGTCATTTTACCCTAT-GGGGT
1 ATAACAGTCATTTTACCCTATAGGGGT
** *
28986329 ATTTC-GATCATTTTACTCTAT-GGAGGT
1 ATAACAG-TCATTTTACCCTATAGG-GGT
**
28986356 ATTTC-GATCATTTTACCCTATAGGGGT
1 ATAACAG-TCATTTTACCCTATAGGGGT
** * *
28986383 ATTTCGGTCATTTTACCCTATGGGGGT
1 ATAACAGTCATTTTACCCTATAGGGGT
28986410 AT
1 AT
28986412 TTTGGTTATT
Statistics
Matches: 174, Mismatches: 23, Indels: 30
0.77 0.10 0.13
Matches are distributed among these distances:
22 2 0.01
23 8 0.05
24 9 0.05
25 12 0.07
26 18 0.10
27 122 0.70
28 3 0.02
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40
Consensus pattern (27 bp):
ATAACAGTCATTTTACCCTATAGGGGT
Found at i:28986383 original size:102 final size:104
Alignment explanation
Indices: 28986174--28986380 Score: 278
Period size: 102 Copynumber: 2.0 Consensus size: 104
28986164 CATAAGGCCA
* * * *
28986174 TAACAGTCATTTCATCTTCTAGGGGTATAACAGTCATTTTACCCTATAAGGGTATTTCGGTTATT
1 TAACAATCATTTCATCTCCTAGGGGTAT-A-AGTCATTTTACCCTATAAGGGTATTTCGATCATT
* * *
28986239 TTACCCTATAGGGGTATTTTGGTTATTTTACCCTATGAGGG
64 TTACCCTATAGGGGTATTTCGATCATTTTACCCTATGAGGG
*
28986280 TAACAATCATTTCATCTCCTAGGGGTAT-AGTCATTTTACCCTAT-GGGGTATTTCGATCATTTT
1 TAACAATCATTTCATCTCCTAGGGGTATAAGTCATTTTACCCTATAAGGGTATTTCGATCATTTT
*
28986343 ACTCTAT-GGAGGTATTTCGATCATTTTACCCTAT-AGGG
66 ACCCTATAGG-GGTATTTCGATCATTTTACCCTATGAGGG
28986381 GTATTTCGGT
Statistics
Matches: 91, Mismatches: 9, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
101 6 0.07
102 43 0.47
103 16 0.18
106 26 0.29
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.40
Consensus pattern (104 bp):
TAACAATCATTTCATCTCCTAGGGGTATAAGTCATTTTACCCTATAAGGGTATTTCGATCATTTT
ACCCTATAGGGGTATTTCGATCATTTTACCCTATGAGGG
Found at i:28986412 original size:27 final size:27
Alignment explanation
Indices: 28986206--28986426 Score: 201
Period size: 27 Copynumber: 8.4 Consensus size: 27
28986196 GGGTATAACA
*
28986206 GTCATTTTACCCTATAAGGGTATTTCG
1 GTCATTTTACCCTATAGGGGTATTTCG
* *
28986233 GTTATTTTACCCTATAGGGGTATTTTG
1 GTCATTTTACCCTATAGGGGTATTTCG
* * *
28986260 GTTATTTTACCCTAT-GAGGGTA--ACA
1 GTCATTTTACCCTATAG-GGGTATTTCG
* * *
28986285 ATCATTTCATCTCC--TAGGGGTA--T-A
1 GTCATTTTA-C-CCTATAGGGGTATTTCG
28986309 GTCATTTTACCCTAT-GGGGTATTTCG
1 GTCATTTTACCCTATAGGGGTATTTCG
* *
28986335 ATCATTTTACTCTAT-GGAGGTATTTCG
1 GTCATTTTACCCTATAGG-GGTATTTCG
*
28986362 ATCATTTTACCCTATAGGGGTATTTCG
1 GTCATTTTACCCTATAGGGGTATTTCG
* *
28986389 GTCATTTTACCCTATGGGGGTATTTTG
1 GTCATTTTACCCTATAGGGGTATTTCG
*
28986416 GTTATTTTACC
1 GTCATTTTACC
28986427 TATTTTGGGG
Statistics
Matches: 163, Mismatches: 20, Indels: 22
0.80 0.10 0.11
Matches are distributed among these distances:
22 2 0.01
23 7 0.04
24 9 0.06
25 13 0.08
26 18 0.11
27 112 0.69
28 2 0.01
ACGTcount: A:0.21, C:0.17, G:0.20, T:0.43
Consensus pattern (27 bp):
GTCATTTTACCCTATAGGGGTATTTCG
Found at i:28998643 original size:5 final size:5
Alignment explanation
Indices: 28998633--28998657 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
28998623 TAATTTCAAT
28998633 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
28998658 GTCCTAAACC
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:29001852 original size:15 final size:16
Alignment explanation
Indices: 29001825--29001863 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
29001815 ATGGGTTAGC
29001825 TAAATCAAGTTCC-CA
1 TAAATCAAGTTCCACA
* *
29001840 TAATTCAATTTCCACA
1 TAAATCAAGTTCCACA
29001856 TAAATCAA
1 TAAATCAA
29001864 AGAAAAATTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.44, C:0.23, G:0.03, T:0.31
Consensus pattern (16 bp):
TAAATCAAGTTCCACA
Found at i:29005855 original size:27 final size:27
Alignment explanation
Indices: 29005825--29006140 Score: 282
Period size: 27 Copynumber: 11.7 Consensus size: 27
29005815 GCAAGGTTCG
*
29005825 CCACAAGGGCTTTTCTTTCATATTTCA
1 CCACAAAGGCTTTTCTTTCATATTTCA
* **
29005852 CCACAAGGGCTTTTCTTTCATATTTTT
1 CCACAAAGGCTTTTCTTTCATATTTCA
*
29005879 CCACAAAGGC-TTTCTTTTCATATTTCG
1 CCACAAAGGCTTTTC-TTTCATATTTCA
* * * *
29005906 CCACAAAAGTTTTTCTTTCATGTTTTA
1 CCACAAAGGCTTTTCTTTCATATTTCA
* ** **
29005933 TCACAAAGAATTTTCTTTCATATTTTG
1 CCACAAAGGCTTTTCTTTCATATTTCA
*
29005960 CTACAAAGG-TTTTCCTTTCATATTTCA
1 CCACAAAGGCTTTT-CTTTCATATTTCA
* *
29005987 CCATAAAGGTTTTTCTTTCATATTTCA
1 CCACAAAGGCTTTTCTTTCATATTTCA
* * *
29006014 CCACAAAGGATTTTCTTTCAAGATTT-T
1 CCACAAAGGCTTTTCTTTC-ATATTTCA
* *
29006041 CCACAAAGACTTTTCTTTCATGTTT-A
1 CCACAAAGGCTTTTCTTTCATATTTCA
* * *
29006067 GCAACAAAAGCTTTTCTTTCATGATTT-T
1 -CCACAAAGGCTTTTCTTTCAT-ATTTCA
* * *
29006095 CCACAAAGGCTTTTCTTTTATTTTTCT
1 CCACAAAGGCTTTTCTTTCATATTTCA
* *
29006122 CCACAAAGGTTTTTATTTC
1 CCACAAAGGCTTTTCTTTC
29006141 CTGTCATGTT
Statistics
Matches: 237, Mismatches: 44, Indels: 16
0.80 0.15 0.05
Matches are distributed among these distances:
26 15 0.06
27 206 0.87
28 16 0.07
ACGTcount: A:0.25, C:0.21, G:0.09, T:0.45
Consensus pattern (27 bp):
CCACAAAGGCTTTTCTTTCATATTTCA
Found at i:29005938 original size:81 final size:81
Alignment explanation
Indices: 29005821--29006130 Score: 331
Period size: 81 Copynumber: 3.8 Consensus size: 81
29005811 CTTTGCAAGG
** * *
29005821 TTCGCCACAAGGGCTTTTCTTTCATATTTCACCACAAGGGCTTTTCTTTCATATTTTTCCACAAA
1 TTCGCCACAAAAGCTTTTCTTTCATATTTCACCACAAAGGATTTTCTTTCATATTTTTCCACAAA
29005886 GGCTTTCTTTTCATAT
66 GGCTTTCTTTTCATAT
* * * * * * *
29005902 TTCGCCACAAAAGTTTTTCTTTCATGTTTTATCACAAAGAATTTTCTTTCATATTTTGCTACAAA
1 TTCGCCACAAAAGCTTTTCTTTCATATTTCACCACAAAGGATTTTCTTTCATATTTTTCCACAAA
* *
29005967 GGTTTTCCTTTCATAT
66 GGCTTTCTTTTCATAT
* * * * *
29005983 TTCACCATAAAGGTTTTTCTTTCATATTTCACCACAAAGGATTTTCTTTCA-AGATTTTCCACAA
1 TTCGCCACAAAAGCTTTTCTTTCATATTTCACCACAAAGGATTTTCTTTCATA-TTTTTCCACAA
* *
29006047 AGACTTT-TCTTTCATGT
65 AGGCTTTCT-TTTCATAT
* * * * *
29006064 TTAGCAACAAAAGCTTTTCTTTCATGATTT-TCCACAAAGGCTTTTCTTTTAT-TTTTCTCCACA
1 TTCGCCACAAAAGCTTTTCTTTCAT-ATTTCACCACAAAGGATTTTCTTTCATATTTT-TCCACA
29006127 AAGG
64 AAGG
29006131 TTTTTATTTC
Statistics
Matches: 186, Mismatches: 38, Indels: 10
0.79 0.16 0.04
Matches are distributed among these distances:
80 4 0.02
81 178 0.96
82 4 0.02
ACGTcount: A:0.25, C:0.21, G:0.10, T:0.44
Consensus pattern (81 bp):
TTCGCCACAAAAGCTTTTCTTTCATATTTCACCACAAAGGATTTTCTTTCATATTTTTCCACAAA
GGCTTTCTTTTCATAT
Found at i:29033772 original size:3 final size:3
Alignment explanation
Indices: 29033766--29033840 Score: 73
Period size: 3 Copynumber: 25.0 Consensus size: 3
29033756 AAAGTAGTAG
* *
29033766 TAA TAA TAA TGA TGA TAA TAA TAA TAA TAA TAA TAA TAA TGAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
* * *
29033811 TAT TAA -AC TAAA TAA TAA TAA TAA AAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
29033841 CACAAAAAGG
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
2 3 0.05
3 53 0.88
4 4 0.07
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:29033784 original size:30 final size:30
Alignment explanation
Indices: 29033718--29033834 Score: 98
Period size: 30 Copynumber: 3.9 Consensus size: 30
29033708 GTATAAGCGA
*
29033718 ATAAT-ATAATAGTAATAGTAAAAAT-ATCG
1 ATAATAATAATAGTAATAGTAATAATAAT-G
*
29033747 ATAATAATGAA-AGTAGTAGTAATAATAATG
1 ATAATAAT-AATAGTAATAGTAATAATAATG
* * *
29033777 ATGATAATAATAATAATAATAATAATAATG
1 ATAATAATAATAGTAATAGTAATAATAATG
* * * *
29033807 AAAATATTAA-ACTAAATAATAATAATAA
1 ATAATAATAATAGT-AATAGTAATAATAA
29033835 AAATAACACA
Statistics
Matches: 73, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
29 9 0.12
30 60 0.82
31 4 0.05
ACGTcount: A:0.59, C:0.02, G:0.09, T:0.31
Consensus pattern (30 bp):
ATAATAATAATAGTAATAGTAATAATAATG
Found at i:29041856 original size:62 final size:62
Alignment explanation
Indices: 29041759--29041884 Score: 243
Period size: 62 Copynumber: 2.0 Consensus size: 62
29041749 CAAAATGCTT
*
29041759 TATACATGTACTAAATAAAAGTGTTCCAAAAGGACTTAGCTAGTCATGCAACATAAGTCCAA
1 TATACATGTACTAAATAAAAGTGTTCCAAAAGGACTTACCTAGTCATGCAACATAAGTCCAA
29041821 TATACATGTACTAAATAAAAGTGTTCCAAAAGGACTTACCTAGTCATGCAACATAAGTCCAA
1 TATACATGTACTAAATAAAAGTGTTCCAAAAGGACTTACCTAGTCATGCAACATAAGTCCAA
29041883 TA
1 TA
29041885 CCATTCATTA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.26
Consensus pattern (62 bp):
TATACATGTACTAAATAAAAGTGTTCCAAAAGGACTTACCTAGTCATGCAACATAAGTCCAA
Found at i:29042241 original size:22 final size:22
Alignment explanation
Indices: 29042207--29042262 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
29042197 AGCCTGATAC
*
29042207 GCACAAAGCCTGAATAACACCA
1 GCACTAAGCCTGAATAACACCA
* *
29042229 GCACTAAGTCTGAATAACACCG
1 GCACTAAGCCTGAATAACACCA
29042251 GCACTAAGCCTG
1 GCACTAAGCCTG
29042263 TAAGGCACAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.30, G:0.18, T:0.14
Consensus pattern (22 bp):
GCACTAAGCCTGAATAACACCA
Found at i:29042289 original size:38 final size:37
Alignment explanation
Indices: 29042229--29042322 Score: 134
Period size: 38 Copynumber: 2.5 Consensus size: 37
29042219 AATAACACCA
* * *
29042229 GCACTAAGTCTGAATAACACCGGCACTAAGCCTGTAAG
1 GCACAAAGCCTGAATAACACCGGCACTAAACCTG-AAG
*
29042267 GCACAAAGCCTGAATAACACCGGCACTAAACCTGCAG
1 GCACAAAGCCTGAATAACACCGGCACTAAACCTGAAG
*
29042304 GCACAAAGCCCGAATAACA
1 GCACAAAGCCTGAATAACA
29042323 ATATAATTTG
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
37 20 0.39
38 31 0.61
ACGTcount: A:0.38, C:0.30, G:0.19, T:0.13
Consensus pattern (37 bp):
GCACAAAGCCTGAATAACACCGGCACTAAACCTGAAG
Found at i:29042300 original size:22 final size:22
Alignment explanation
Indices: 29042207--29042300 Score: 78
Period size: 22 Copynumber: 4.5 Consensus size: 22
29042197 AGCCTGATAC
*
29042207 GCAC-AAAGCCTGAATAACACCA
1 GCACTAAA-CCTGAATAACACCG
**
29042229 GCACTAAGTCTGAATAACACCG
1 GCACTAAACCTGAATAACACCG
*
29042251 GCACTAAGCCTG--T-A-A--G
1 GCACTAAACCTGAATAACACCG
29042267 GCAC-AAAGCCTGAATAACACCG
1 GCACTAAA-CCTGAATAACACCG
29042289 GCACTAAACCTG
1 GCACTAAACCTG
29042301 CAGGCACAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
15 2 0.03
16 9 0.16
18 2 0.03
19 2 0.03
20 2 0.03
22 36 0.62
23 5 0.09
ACGTcount: A:0.38, C:0.30, G:0.18, T:0.14
Consensus pattern (22 bp):
GCACTAAACCTGAATAACACCG
Found at i:29045750 original size:14 final size:15
Alignment explanation
Indices: 29045725--29045769 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
29045715 AAAAGTTTAG
29045725 TGTTGAAAAATTAAA
1 TGTTGAAAAATTAAA
* *
29045740 TGTTGAAAATTTAAG
1 TGTTGAAAAATTAAA
29045755 T-TTGAAAAATTAAA
1 TGTTGAAAAATTAAA
29045769 T
1 T
29045770 AATCATTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (15 bp):
TGTTGAAAAATTAAA
Found at i:29053551 original size:26 final size:26
Alignment explanation
Indices: 29053515--29053612 Score: 126
Period size: 26 Copynumber: 3.7 Consensus size: 26
29053505 GAACACGTCA
29053515 AAAATGGAAGCCTTTGTGGCGTATCT
1 AAAATGGAAGCCTTTGTGGCGTATCT
*
29053541 AAAATGGAAGCCTTTGTGGC-AATCT
1 AAAATGGAAGCCTTTGTGGCGTATCT
* * *
29053566 AGAAAATGGAAGTCTTAGTTGCGTATCT
1 --AAAATGGAAGCCTTTGTGGCGTATCT
*
29053594 AAAATGGAAACCTTTGTGG
1 AAAATGGAAGCCTTTGTGG
29053613 TAATCTAAGA
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
25 4 0.07
26 35 0.58
27 17 0.28
28 4 0.07
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.30
Consensus pattern (26 bp):
AAAATGGAAGCCTTTGTGGCGTATCT
Found at i:29053595 original size:53 final size:54
Alignment explanation
Indices: 29053515--29053635 Score: 181
Period size: 53 Copynumber: 2.3 Consensus size: 54
29053505 GAACACGTCA
* *
29053515 AAAATGGAAGCCTTTGTGGCGTATCTAAAATGGAAGCCTTTGTGGCAATCT-AG
1 AAAATGGAAGCCTTAGTGGCGTATCTAAAATGGAAACCTTTGTGGCAATCTAAG
* * *
29053568 AAAATGGAAGTCTTAGTTGCGTATCTAAAATGGAAACCTTTGTGGTAATCTAAG
1 AAAATGGAAGCCTTAGTGGCGTATCTAAAATGGAAACCTTTGTGGCAATCTAAG
*
29053622 AAAATGAAAGCCTT
1 AAAATGGAAGCCTT
29053636 TGAGGTAATC
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
53 46 0.77
54 14 0.23
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (54 bp):
AAAATGGAAGCCTTAGTGGCGTATCTAAAATGGAAACCTTTGTGGCAATCTAAG
Found at i:29053635 original size:28 final size:27
Alignment explanation
Indices: 29053515--29053668 Score: 149
Period size: 28 Copynumber: 5.7 Consensus size: 27
29053505 GAACACGTCA
29053515 AAAATGGAAGCCTTTGTGGCGT-ATCT--
1 AAAATGGAAGCCTTTGT-G-GTAATCTAG
*
29053541 AAAATGGAAGCCTTTGTGGCAATCTAG
1 AAAATGGAAGCCTTTGTGGTAATCTAG
* *
29053568 AAAATGGAAGTCTTAGTTGCGT-ATCT--
1 AAAATGGAAGCCTTTG-TG-GTAATCTAG
*
29053594 AAAATGGAAACCTTTGTGGTAATCTAAG
1 AAAATGGAAGCCTTTGTGGTAATCT-AG
* *
29053622 AAAATGAAAGCCTTTGAGGTAATCTAAG
1 AAAATGGAAGCCTTTGTGGTAATCT-AG
*
29053650 AAAATGGAAGCCTTCGTGG
1 AAAATGGAAGCCTTTGTGG
29053669 AAAATTTTGT
Statistics
Matches: 106, Mismatches: 13, Indels: 16
0.79 0.10 0.12
Matches are distributed among these distances:
24 3 0.03
25 11 0.10
26 30 0.28
27 14 0.13
28 47 0.44
29 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (27 bp):
AAAATGGAAGCCTTTGTGGTAATCTAG
Found at i:29066475 original size:102 final size:102
Alignment explanation
Indices: 29066359--29066561 Score: 388
Period size: 102 Copynumber: 2.0 Consensus size: 102
29066349 TAACTTCTCA
29066359 CAACATTTTTTTGAGGGTCTTTTACCAAAATATTACAAAAAAATAAAAAAAATATCAAAATAATA
1 CAACATTTTTTTGAGGGTCTTTTACCAAAATATTACAAAAAAATAAAAAAAATATCAAAATAATA
* *
29066424 TTACTTTTTTTATTTACCAAAATAATACCAAAAAAAG
66 TTACTTTTCTTATTTACCAAAATAATACAAAAAAAAG
29066461 CAACATTTTTTTGAGGGTCTTTTACCAAAATATTACAAAAAAATAAAAAAAATATCAAAATAATA
1 CAACATTTTTTTGAGGGTCTTTTACCAAAATATTACAAAAAAATAAAAAAAATATCAAAATAATA
29066526 TTACTTTTCTTATTTACCAAAATAATACAAAAAAAA
66 TTACTTTTCTTATTTACCAAAATAATACAAAAAAAA
29066562 AACAAAAAAG
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
102 99 1.00
ACGTcount: A:0.51, C:0.12, G:0.04, T:0.33
Consensus pattern (102 bp):
CAACATTTTTTTGAGGGTCTTTTACCAAAATATTACAAAAAAATAAAAAAAATATCAAAATAATA
TTACTTTTCTTATTTACCAAAATAATACAAAAAAAAG
Found at i:29066692 original size:11 final size:11
Alignment explanation
Indices: 29066672--29066736 Score: 73
Period size: 11 Copynumber: 6.1 Consensus size: 11
29066662 GCTGGTGGGT
29066672 GGAGAAGGAAA
1 GGAGAAGGAAA
*
29066683 GGAGAGGGAAA
1 GGAGAAGGAAA
29066694 GGAGAA-GAAA
1 GGAGAAGGAAA
*
29066704 GAAAGAAGGAAA
1 G-GAGAAGGAAA
*
29066716 -GAAAAGGAAA
1 GGAGAAGGAAA
29066726 GGAGAA-GAAA
1 GGAGAAGGAAA
29066736 G
1 G
29066737 AAAGAAAAAG
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
10 18 0.40
11 23 0.51
12 4 0.09
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (11 bp):
GGAGAAGGAAA
Found at i:29066707 original size:4 final size:4
Alignment explanation
Indices: 29066698--29066791 Score: 52
Period size: 4 Copynumber: 22.5 Consensus size: 4
29066688 GGGAAAGGAG
*
29066698 AAGA AAGA AAGA AGGA AAGAA AAGGA AAGGA GAAGA AAGA AAG- AA-A
1 AAGA AAGA AAGA AAGA AAG-A AA-GA AA-GA -AAGA AAGA AAGA AAGA
* * *
29066744 AAGA AAGGA GAAG- AAGA AGAGGG AAGG AAGG AA-A AAGA AAGA AAGA
1 AAGA AA-GA -AAGA AAGA A-A-GA AAGA AAGA AAGA AAGA AAGA AAGA
29066790 AA
1 AA
29066792 AAGGTAATTT
Statistics
Matches: 75, Mismatches: 4, Indels: 22
0.74 0.04 0.22
Matches are distributed among these distances:
3 9 0.12
4 43 0.57
5 16 0.21
6 7 0.09
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:29066739 original size:24 final size:24
Alignment explanation
Indices: 29066706--29066792 Score: 97
Period size: 24 Copynumber: 3.6 Consensus size: 24
29066696 AGAAGAAAGA
*
29066706 AAGAAGGAAAGAAAAGGAAAGGAG
1 AAGAAAGAAAGAAAAGGAAAGGAG
*
29066730 AAGAAAGAAAGAAAAAGAAAGGAG
1 AAGAAAGAAAGAAAAGGAAAGGAG
** *
29066754 AAG-AAGAAGAGGGAAGG-AAGGAAA
1 AAGAAAGAA-AGAAAAGGAAAGG-AG
29066778 AAGAAAGAAAGAAAA
1 AAGAAAGAAAGAAAA
29066793 AGGTAATTTT
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
23 9 0.17
24 38 0.73
25 5 0.10
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (24 bp):
AAGAAAGAAAGAAAAGGAAAGGAG
Found at i:29066769 original size:13 final size:13
Alignment explanation
Indices: 29066690--29066761 Score: 51
Period size: 14 Copynumber: 5.2 Consensus size: 13
29066680 AAAGGAGAGG
29066690 GAAAGGAGAAGAAA
1 GAAAGGAGAAG-AA
*
29066704 GAAAGAAGGAAAGAAAA
1 GAAAGGA-G-AAG--AA
29066721 GGAAAGGAGAAGAAA
1 -GAAAGGAGAAG-AA
29066736 GAAA-GA-AA-AA
1 GAAAGGAGAAGAA
29066746 GAAAGGAGAAGAA
1 GAAAGGAGAAGAA
29066759 GAA
1 GAA
29066762 GAGGGAAGGA
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
10 6 0.12
11 2 0.04
12 4 0.08
13 7 0.14
14 10 0.20
15 4 0.08
16 6 0.12
17 4 0.08
18 6 0.12
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (13 bp):
GAAAGGAGAAGAA
Found at i:29067640 original size:8 final size:8
Alignment explanation
Indices: 29067617--29067652 Score: 54
Period size: 8 Copynumber: 4.2 Consensus size: 8
29067607 CATAATGTAC
29067617 TAAAATAAA
1 TAAAAT-AA
29067626 GTAAAATAA
1 -TAAAATAA
29067635 TAAAATAA
1 TAAAATAA
29067643 TAAAATAA
1 TAAAATAA
29067651 TA
1 TA
29067653 TATTTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 18 0.69
9 2 0.08
10 6 0.23
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (8 bp):
TAAAATAA
Found at i:29067963 original size:306 final size:306
Alignment explanation
Indices: 29067120--29068186 Score: 1643
Period size: 306 Copynumber: 3.5 Consensus size: 306
29067110 AAATTGTATT
* * *
29067120 TTTAAAAAACAAACTAAA-TTA-ATAAATTTAAAACATAATGTACTAAAATAATGTAAAATAATA
1 TTTAAAAAACACACTAAATTTATTTAAATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
*
29067183 AAATTAGAAAATA-TGATATTTTTT-AAAGTAATAAAATGCAGAGAAAAAAATACGAACAAAGGG
66 AAATTAGAAAATAGT-ATATTTTTTAAAAGTAATAAAATTC-GAGAAAAAAATACGAACAAAGGG
* * * *
29067246 CAGAAGTAAGGGTTTTTTACTAAATTTAAAAAAATAAATAATTAATTAA-ACCATTTCAAACATA
129 CCGAAATAAGGGTTTTTTACTAAA-TTAAAAAAAT--AGACTTAATTAATA-CATTTCAAACATA
* *
29067310 ATTTACTAAAATAATGTAAAA-AATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAAA
190 ATGTACTAAAATAAAGTAAAATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAAA
* * * *
29067374 TTTGGG-AGAAAATACGAGCAAAGGGTCGAAATAAGGGTTTTTTTAAAATTTA
255 TTCGGGAAAAAAATATGAGCAAAGGG-CGAAATAAGGGTTTTTTTTAAATTTA
29067426 TTTAAAAAACACACTAAATTTATTTAAATTTCAAACATAATGTACT--AA-AA--T--AAT-ATA
1 TTTAAAAAACACACTAAATTTATTTAAATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
29067483 AAATTAGAAAATAGTATATTTTTTAAAAGTAATAAAATTCGAGAAAAAAATACGAACAAAGGGCC
66 AAATTAGAAAATAGTATATTTTTTAAAAGTAATAAAATTCGAGAAAAAAATACGAACAAAGGGCC
* * *
29067548 GAAATAAGGGTTTTTTTTTACTAAATTAAAAAAAACAGACTTAAATAATACATTTTAAACATAAT
131 GAAATAAGGG---TTTTTTACTAAATT-AAAAAAATAGACTTAATTAATACATTTCAAACATAAT
**
29067613 GTACTAAAATAAAGTAAAATAATAAAATAATAAAATAATATATTTTTATTGAAAGTAATAAAATT
192 GTACTAAAATAAAGTAAAATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAAATT
29067678 CGGGAAAAAAATATGAGCAAAGGGCGAAATAAGGGTTTTTTTTTAAATTTA
257 CGGGAAAAAAATATGAGCAAAGGGCGAAATAAGGG-TTTTTTTTAAATTTA
*
29067729 TTTAAAAAATACACTAAATTTATTTAAATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
1 TTTAAAAAACACACTAAATTTATTTAAATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
29067794 AAATTAGAAAATAGTATATTTTTTAAAAGTAATAAAATTC-AG-AAAAAATACGAACAAAGGGCC
66 AAATTAGAAAATAGTATATTTTTTAAAAGTAATAAAATTCGAGAAAAAAATACGAACAAAGGGCC
29067857 GAAATAAGGGTTTTTTTACTAAATTAAAAAAATAGACTTAATTAATACATTTCAAACATAATGTA
131 GAAATAAGGG-TTTTTTACTAAATTAAAAAAATAGACTTAATTAATACATTTCAAACATAATGTA
29067922 CTAAAATAAAGTAAAATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAAATTCGG
195 CTAAAATAAAGTAAAATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAAATTCGG
*
29067987 GAAAAAAATATGAGCAAATGGTCGAAATAAGGG-TTTTTTTAAATTTA
260 GAAAAAAATATGAGCAAA-GGGCGAAATAAGGGTTTTTTTTAAATTTA
*
29068034 TTTAAAAAACACACTAAATTTATTTAAATTTCAAGCATAATGTACTAAAATAATGTAAAATAATA
1 TTTAAAAAACACACTAAATTTATTTAAATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
* *
29068099 AAAGTAGAAAATAGTATATTTTTTAAAAGTAATAAAATTC-AGGAAAAAAATACAAACAAAGGGC
66 AAATTAGAAAATAGTATATTTTTTAAAAGTAATAAAATTCGA-GAAAAAAATACGAACAAAGGGC
29068163 CGAAATAA-GGTTTTTTACTAAATT
130 CGAAATAAGGGTTTTTTACTAAATT
29068187 TTTTTGAAGT
Statistics
Matches: 708, Mismatches: 30, Indels: 47
0.90 0.04 0.06
Matches are distributed among these distances:
300 58 0.08
301 58 0.08
302 60 0.08
303 96 0.14
305 135 0.19
306 142 0.20
307 58 0.08
308 22 0.03
309 31 0.04
310 5 0.01
311 43 0.06
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.31
Consensus pattern (306 bp):
TTTAAAAAACACACTAAATTTATTTAAATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
AAATTAGAAAATAGTATATTTTTTAAAAGTAATAAAATTCGAGAAAAAAATACGAACAAAGGGCC
GAAATAAGGGTTTTTTACTAAATTAAAAAAATAGACTTAATTAATACATTTCAAACATAATGTAC
TAAAATAAAGTAAAATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAAATTCGGG
AAAAAAATATGAGCAAAGGGCGAAATAAGGGTTTTTTTTAAATTTA
Found at i:29071026 original size:43 final size:42
Alignment explanation
Indices: 29070963--29071088 Score: 148
Period size: 43 Copynumber: 2.9 Consensus size: 42
29070953 AGGACTCCGA
29070963 TATGTGTTTTCGTGTAAGACCACGTCTGGGACGTCGGCATCAAC
1 TATGTGTTTTCGTGTAAGACCACGTCTGGGACGT-GGCATC-AC
**
29071007 T-TGTGTTTTCGTGTAAGACC-CTGTCTGGGACAGTGGCATCGG
1 TATGTGTTTTCGTGTAAGACCAC-GTCTGGGAC-GTGGCATCAC
* * *
29071049 TATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 TATGTGTTTTCGTGTAAGACCACGTCTGGGACG-TGGCAT
29071089 TGTACTAGCT
Statistics
Matches: 72, Mismatches: 5, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
42 3 0.04
43 65 0.90
44 4 0.06
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.31
Consensus pattern (42 bp):
TATGTGTTTTCGTGTAAGACCACGTCTGGGACGTGGCATCAC
Found at i:29071759 original size:14 final size:15
Alignment explanation
Indices: 29071735--29071769 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
29071725 TACTTTAATC
29071735 ATGGATTAGTATTT-T
1 ATGG-TTAGTATTTAT
29071750 ATGGTTAGTATTTAT
1 ATGGTTAGTATTTAT
29071765 ATGGT
1 ATGGT
29071770 AATGTATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (15 bp):
ATGGTTAGTATTTAT
Found at i:29072476 original size:47 final size:47
Alignment explanation
Indices: 29072021--29072437 Score: 735
Period size: 47 Copynumber: 8.9 Consensus size: 47
29072011 GAGTAAATGA
*
29072021 ATGTATATGCTGTCAAATTTTGTTGTACAAATGCAGTCCAATTATAT
1 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATAT
*
29072068 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAATCCAATTATAT
1 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATAT
*
29072115 ATGTATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATAT
1 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATAT
* *
29072162 ATGTATATGGTGTCAAATTTTGATGAACAAATGCAGTCCAATTATAT
1 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATAT
*
29072209 ATGTATATGCTGTCAAATTTTGATGTACAAATGTAGTCCAATTATAT
1 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATAT
29072256 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATAT
1 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATAT
*
29072303 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATTT
1 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATAT
* *
29072350 ATGTATATGCTGTCAAATTTCGATGTATAAATGCAGTCCAATTATAT
1 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATAT
* *
29072397 ATGTATATGCTGTCAAATTTTGATGTATAAATGTAGTCCAA
1 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAA
29072438 ATTTTGTATA
Statistics
Matches: 353, Mismatches: 17, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 353 1.00
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (47 bp):
ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATAT
Found at i:29078990 original size:43 final size:42
Alignment explanation
Indices: 29078937--29079065 Score: 154
Period size: 43 Copynumber: 3.0 Consensus size: 42
29078927 CATAGAACTC
*
29078937 CGATATGTGTTTTCGTGTAAGACCACGTCTGGGACGTCGGCAT
1 CGATATGTGTTTTCATGTAAGACCACGTCTGGGACGT-GGCAT
*
29078980 CGA-ATTGTGTTTTCCTGTAAGACC-CTGTCTGGGACAGTGGCAT
1 CGATA-TGTGTTTTCATGTAAGACCAC-GTCTGGGAC-GTGGCAT
* * *
29079023 CGGTATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGATATGTGTTTTCATGTAAGACCACGTCTGGGACG-TGGCAT
29079066 TGTACTAGCT
Statistics
Matches: 75, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
42 3 0.04
43 68 0.91
44 4 0.05
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.30
Consensus pattern (42 bp):
CGATATGTGTTTTCATGTAAGACCACGTCTGGGACGTGGCAT
Found at i:29079736 original size:14 final size:15
Alignment explanation
Indices: 29079712--29079746 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
29079702 TACTTTAATC
29079712 ATGGATTAGTATTT-T
1 ATGG-TTAGTATTTAT
29079727 ATGGTTAGTATTTAT
1 ATGGTTAGTATTTAT
29079742 ATGGT
1 ATGGT
29079747 AATGTATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (15 bp):
ATGGTTAGTATTTAT
Found at i:29080522 original size:47 final size:47
Alignment explanation
Indices: 29080000--29080510 Score: 848
Period size: 47 Copynumber: 10.9 Consensus size: 47
29079990 GAGTAAATGA
*
29080000 ACAAATGCAGTCCAATTATATATGTATATGCTGTC-GATTTTGATGT
1 ACAAATGCAGTCCAATTATATATGTATATGCTGTCAAATTTTGATGT
*
29080046 ATAAATGCAGTCCAATTATATATGTATATGCTGTCAAATTTTGATGT
1 ACAAATGCAGTCCAATTATATATGTATATGCTGTCAAATTTTGATGT
* *
29080093 ATAAATGAAGTCCAATTATATATGTATATGCTGTCAAATTTTGATGT
1 ACAAATGCAGTCCAATTATATATGTATATGCTGTCAAATTTTGATGT
29080140 ACAAATGCAGTCCAATTATATATGTATATGCTGTCAAATTTTGATGT
1 ACAAATGCAGTCCAATTATATATGTATATGCTGTCAAATTTTGATGT
* **
29080187 ATAAATATAGTCCAATTATATATGTATATGCTGTCAAATTTTGATGT
1 ACAAATGCAGTCCAATTATATATGTATATGCTGTCAAATTTTGATGT
*
29080234 ACAAATGCAGTCCAATTATATATGTATATGTTGTCAAATTTTGATGT
1 ACAAATGCAGTCCAATTATATATGTATATGCTGTCAAATTTTGATGT
29080281 ACAAATGCAGTCCAATTATATATGTATATGCTGTCAAATTTTGATGT
1 ACAAATGCAGTCCAATTATATATGTATATGCTGTCAAATTTTGATGT
29080328 ACAAATGCAGTCCAATTATATATGTATATGCTGTCAAATTTTGATGT
1 ACAAATGCAGTCCAATTATATATGTATATGCTGTCAAATTTTGATGT
*
29080375 ACAAATGCAGTCCAATTATTTATGTATATGCTGTCAAATTTTGATGT
1 ACAAATGCAGTCCAATTATATATGTATATGCTGTCAAATTTTGATGT
* *
29080422 ATAAATGCAGTCCAATTATATATGTATATGCTGTCAAATTTTGATGA
1 ACAAATGCAGTCCAATTATATATGTATATGCTGTCAAATTTTGATGT
* * * *
29080469 ATAAATGTAGTCCAAATT-T-TGTATATATGCTGTCCAAATTTT
1 ACAAATGCAGTCC-AATTATATATGTATATGCTGT-CAAATTTT
29080511 AGTGTGAAAA
Statistics
Matches: 442, Mismatches: 20, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
46 46 0.10
47 392 0.89
48 4 0.01
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (47 bp):
ACAAATGCAGTCCAATTATATATGTATATGCTGTCAAATTTTGATGT
Found at i:29082068 original size:12 final size:12
Alignment explanation
Indices: 29082051--29082075 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29082041 GGTGTTCATT
29082051 CGGTTAACCGAC
1 CGGTTAACCGAC
29082063 CGGTTAACCGAC
1 CGGTTAACCGAC
29082075 C
1 C
29082076 CAAAATTGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:29082248 original size:9 final size:9
Alignment explanation
Indices: 29082234--29082299 Score: 71
Period size: 9 Copynumber: 7.2 Consensus size: 9
29082224 TTTGGTTAAA
29082234 AATTACCCG
1 AATTACCCG
29082243 AATTACCCG
1 AATTACCCG
*
29082252 -ATTAACCG
1 AATTACCCG
*
29082260 AATTAACCG
1 AATTACCCG
*
29082269 AATTAACCG
1 AATTACCCG
*
29082278 AAAATTACCCA
1 --AATTACCCG
29082289 AATTACCCG
1 AATTACCCG
29082298 AA
1 AA
29082300 AATTACCCAA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.14
9 36 0.72
11 7 0.14
ACGTcount: A:0.42, C:0.27, G:0.09, T:0.21
Consensus pattern (9 bp):
AATTACCCG
Found at i:29082275 original size:18 final size:18
Alignment explanation
Indices: 29082234--29082279 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
29082224 TTTGGTTAAA
* *
29082234 AATTACCCGAATTACCCG
1 AATTAACCGAATTAACCG
29082252 -ATTAACCGAATTAACCG
1 AATTAACCGAATTAACCG
29082269 AATTAACCGAA
1 AATTAACCGAA
29082280 AATTACCCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 15 0.60
18 10 0.40
ACGTcount: A:0.41, C:0.26, G:0.11, T:0.22
Consensus pattern (18 bp):
AATTAACCGAATTAACCG
Found at i:29082292 original size:20 final size:20
Alignment explanation
Indices: 29082243--29082310 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
29082233 AAATTACCCG
*
29082243 AATTACCC-GATTAACCG--
1 AATTACCCAAATTAACCGAA
* *
29082260 AATTAACCGAATTAACCGAA
1 AATTACCCAAATTAACCGAA
*
29082280 AATTACCCAAATTACCCGAA
1 AATTACCCAAATTAACCGAA
29082300 AATTACCCAAA
1 AATTACCCAAA
29082311 AAGTTCGGTG
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
17 7 0.16
18 8 0.19
20 28 0.65
ACGTcount: A:0.46, C:0.26, G:0.07, T:0.21
Consensus pattern (20 bp):
AATTACCCAAATTAACCGAA
Found at i:29082312 original size:11 final size:10
Alignment explanation
Indices: 29082278--29082311 Score: 52
Period size: 9 Copynumber: 3.4 Consensus size: 10
29082268 GAATTAACCG
29082278 AAAATTACCC
1 AAAATTACCC
29082288 -AAATTACCC
1 AAAATTACCC
29082297 GAAAATTACCC
1 -AAAATTACCC
29082308 AAAA
1 AAAA
29082312 AGTTCGGTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 9 0.41
10 4 0.18
11 9 0.41
ACGTcount: A:0.53, C:0.26, G:0.03, T:0.18
Consensus pattern (10 bp):
AAAATTACCC
Found at i:29084833 original size:26 final size:27
Alignment explanation
Indices: 29084804--29084869 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
29084794 TAACTAACAC
* *
29084804 AATAATAATAA-TA-GTTTTATACTTAA
1 AATAATAATAACTAGGGTTT-TACTAAA
*
29084830 AATAATACTAACTAGGGTTTTACTAAA
1 AATAATAATAACTAGGGTTTTACTAAA
29084857 AATAATAACTAAC
1 AATAATAA-TAAC
29084870 AATAATATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 10 0.30
27 15 0.45
28 8 0.24
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.35
Consensus pattern (27 bp):
AATAATAATAACTAGGGTTTTACTAAA
Found at i:29084907 original size:22 final size:22
Alignment explanation
Indices: 29084863--29084908 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
29084853 TAAAAATAAT
*
29084863 AACTAACAATAATATAATGTAA
1 AACTAACAATAATATAATCTAA
*
29084885 AACTAACAATCATACTAA-CTAA
1 AACTAACAATAATA-TAATCTAA
29084907 AA
1 AA
29084909 TAATAATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.59, C:0.15, G:0.02, T:0.24
Consensus pattern (22 bp):
AACTAACAATAATATAATCTAA
Found at i:29087481 original size:87 final size:89
Alignment explanation
Indices: 29087069--29087525 Score: 482
Period size: 87 Copynumber: 5.0 Consensus size: 89
29087059 GTGTAAAAAA
* * * *
29087069 CCCTCAAAATTCTTCAAAAAAAAAGTAATTAAGCCCCTGCTCTTTTTTTCCACTCAATTGGGTAC
1 CCCTCAAAATTTTTC-AAAAAAAAGCAATTAAGCCAC-GCT-TTTTTTTGCACTCAATTGGGTAC
* * **
29087134 TTGAATTTTCAAAATGCATGAAAAAAA
63 TTGAACTTTCAAAATGCATCAAAAAGG
* *
29087161 CCCT-GAAATTTTTCAAAAAAAAACAATTAAGCC-C-CTACTTTTTTT--ACTCAATTGGGTACT
1 CCCTCAAAATTTTTCAAAAAAAAGCAATTAAGCCACGCT--TTTTTTTGCACTCAATTGGGTACT
*
29087221 TGAGCTTTCAAAATGCATCAAAAAGG
64 TGAACTTTCAAAATGCATCAAAAAGG
** * ** *
29087247 CCCTCAATTTTTTTTCAAAATAAATAAATTAAGCCACTGCTTTTTTTTTGCACTCAATTAGGTAC
1 CCCTCAA-AATTTTTCAAAAAAAAGCAATTAAGCCAC-GC-TTTTTTTTGCACTCAATTGGGTAC
* * *
29087312 TTGAACTTTTAAAATACATAAAAAAAAGG
63 TTGAACTTTCAAAATGCAT--CAAAAAGG
*
29087341 CCATCAAAA-TTTTCAAAAAAAAGCAATTAAGCCCCTACGTACTTTCTTTTTGCACTCAATTGGG
1 CCCTCAAAATTTTTCAAAAAAAAGCAATTAAG--CC-ACG--CTTT-TTTTTGCACTCAATTGGG
*
29087405 TACTTAAACTTTCAAAATGCATCAAAAAGG
60 TACTTGAACTTTCAAAATGCATCAAAAAGG
*
29087435 CCCT-AAAATTTTTTCAAAATAAAGCAATTAAGCC-C-CTTTTTTTTGCACTCAATTGGGTACTT
1 CCCTCAAAA-TTTTTCAAAAAAAAGCAATTAAGCCACGCTTTTTTTTGCACTCAATTGGGTACTT
*
29087497 GAACTGTCAAAATGCATCAAAAAGG
65 GAACTTTCAAAATGCATCAAAAAGG
29087522 CCCT
1 CCCT
29087526 TTGACCGTTA
Statistics
Matches: 311, Mismatches: 35, Indels: 43
0.80 0.09 0.11
Matches are distributed among these distances:
86 40 0.13
87 53 0.17
88 34 0.11
89 2 0.01
90 24 0.08
91 10 0.03
92 53 0.17
93 6 0.02
94 26 0.08
95 26 0.08
96 37 0.12
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.32
Consensus pattern (89 bp):
CCCTCAAAATTTTTCAAAAAAAAGCAATTAAGCCACGCTTTTTTTTGCACTCAATTGGGTACTTG
AACTTTCAAAATGCATCAAAAAGG
Found at i:29087666 original size:10 final size:10
Alignment explanation
Indices: 29087625--29087666 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
29087615 ACATGTGGTA
*
29087625 AAAAATTATA
1 AAAAATTATT
* *
29087635 AAAAATCAAT
1 AAAAATTATT
29087645 AAAAATTA-T
1 AAAAATTATT
29087654 AAAAATTATT
1 AAAAATTATT
29087664 AAA
1 AAA
29087667 TTTAAATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 9 0.33
10 18 0.67
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (10 bp):
AAAAATTATT
Found at i:29087921 original size:18 final size:20
Alignment explanation
Indices: 29087900--29087952 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
29087890 TGGTATGATA
29087900 AATTTTAT-ATTTT-TTACG
1 AATTTTATAATTTTCTTACG
29087918 AATTTTATAATTTTCTTACG
1 AATTTTATAATTTTCTTACG
* *
29087938 ACTTTATAAAATTTT
1 AATTT-TATAATTTT
29087953 ATAATTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 8 0.27
19 5 0.17
20 9 0.30
21 8 0.27
ACGTcount: A:0.32, C:0.08, G:0.04, T:0.57
Consensus pattern (20 bp):
AATTTTATAATTTTCTTACG
Found at i:29087943 original size:19 final size:19
Alignment explanation
Indices: 29087903--29087946 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
29087893 TATGATAAAT
*
29087903 TTTAT-ATTTTTTACGAAT
1 TTTATAATTTTTTACGAAC
29087921 TTTATAATTTTCTTACG-AC
1 TTTATAATTTT-TTACGAAC
29087940 TTTATAA
1 TTTATAA
29087947 AATTTTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 5 0.22
19 13 0.57
20 5 0.22
ACGTcount: A:0.30, C:0.09, G:0.05, T:0.57
Consensus pattern (19 bp):
TTTATAATTTTTTACGAAC
Found at i:29088005 original size:29 final size:27
Alignment explanation
Indices: 29087918--29088010 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 27
29087908 ATTTTTTACG
* * *
29087918 AATTTTATAATTTTCTTACGACTTTATAA
1 AATTTTATAATTTTTTTAC-AATTT-TAT
29087947 AATTTTATAATTTTTTT-CTATATTTCTAT
1 AATTTTATAATTTTTTTAC-A-ATTT-TAT
29087976 ATATTTTATAATTTTTTTACAATTCTTAT
1 A-ATTTTATAATTTTTTTACAATT-TTAT
29088005 AATTTT
1 AATTTT
29088011 TTTACTAATT
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
28 7 0.13
29 29 0.53
30 18 0.33
31 1 0.02
ACGTcount: A:0.31, C:0.08, G:0.01, T:0.60
Consensus pattern (27 bp):
AATTTTATAATTTTTTTACAATTTTAT
Found at i:29088006 original size:20 final size:21
Alignment explanation
Indices: 29087981--29088020 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
29087971 TCTATATATT
29087981 TTATAATTTTTTTAC-AATTC
1 TTATAATTTTTTTACTAATTC
29088001 TTATAATTTTTTTACTAATT
1 TTATAATTTTTTTACTAATT
29088021 TAAATTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.62
Consensus pattern (21 bp):
TTATAATTTTTTTACTAATTC
Found at i:29088183 original size:30 final size:31
Alignment explanation
Indices: 29088118--29088203 Score: 85
Period size: 29 Copynumber: 2.9 Consensus size: 31
29088108 CGACTTTATA
* *
29088118 AAATTTTAT-ATTTTTTTCTATATTTCTATGT
1 AAATTTTATAATTTTTTACTA-ATTTTTATGT
29088149 --ATTTTATAATTTTTTACTAATTTTTA-GT
1 AAATTTTATAATTTTTTACTAATTTTTATGT
*
29088177 AAATTTTA-AATATTTTTA-TATTTTTTA
1 AAATTTTATAAT-TTTTTACTAATTTTTA
29088204 ATTAAAATTT
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
28 2 0.04
29 24 0.50
30 22 0.46
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.64
Consensus pattern (31 bp):
AAATTTTATAATTTTTTACTAATTTTTATGT
Found at i:29088215 original size:30 final size:29
Alignment explanation
Indices: 29088151--29088215 Score: 69
Period size: 30 Copynumber: 2.2 Consensus size: 29
29088141 TTCTATGTAT
*
29088151 TTTATAATTTTTTACTAATTTTTAGTAAAT
1 TTTA-AATTTTTTACTAATTTTTAGTAAAA
* *
29088181 TTTAAATATTTTTA-TATTTTTTAATTAAAA
1 TTTAAAT-TTTTTACTAATTTTT-AGTAAAA
29088211 TTTAA
1 TTTAA
29088216 TAACTTATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (29 bp):
TTTAAATTTTTTACTAATTTTTAGTAAAA
Found at i:29088217 original size:29 final size:29
Alignment explanation
Indices: 29088155--29088217 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
29088145 ATGTATTTTA
*
29088155 TAAT-TTTTTACTAATTTTTAGTAAATTT
1 TAATATTTTTACTAATTTTTAGTAAAATT
* *
29088183 TAAATATTTTTA-TATTTTTTAATTAAAATT
1 T-AATATTTTTACTAATTTTT-AGTAAAATT
29088213 TAATA
1 TAATA
29088218 ACTTATATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
28 1 0.03
29 14 0.48
30 14 0.48
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (29 bp):
TAATATTTTTACTAATTTTTAGTAAAATT
Found at i:29093559 original size:35 final size:35
Alignment explanation
Indices: 29093498--29093564 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
29093488 GAAAAAGGAT
*
29093498 AAAATACAAAAATATGTATGTGTGTATATATTTAC
1 AAAATACAAAAATATGTATGTATGTATATATTTAC
*
29093533 AAAATA-AAAAA-ATGTATAAGTATGTATGTATT
1 AAAATACAAAAATATGTAT--GTATGTATATATT
29093565 GGAAAATCGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 6 0.21
34 5 0.18
35 17 0.61
ACGTcount: A:0.49, C:0.03, G:0.12, T:0.36
Consensus pattern (35 bp):
AAAATACAAAAATATGTATGTATGTATATATTTAC
Found at i:29093933 original size:21 final size:23
Alignment explanation
Indices: 29093900--29093942 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 23
29093890 ATATATATTT
*
29093900 TATATAAAGAAATATGTATATAC
1 TATATAAAGAAATACGTATATAC
*
29093923 TATAT-AA-AAATGCGTATATA
1 TATATAAAGAAATACGTATATA
29093943 AGTTTAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 11 0.61
22 2 0.11
23 5 0.28
ACGTcount: A:0.51, C:0.05, G:0.09, T:0.35
Consensus pattern (23 bp):
TATATAAAGAAATACGTATATAC
Found at i:29096808 original size:17 final size:16
Alignment explanation
Indices: 29096778--29096822 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 16
29096768 ATTTTTTTAA
*
29096778 TTTAAAAGAGTTTTTGTT
1 TTTAAAA-A-TTTTTATT
29096796 TTTCAAAAATTTTTATT
1 TTT-AAAAATTTTTATT
29096813 TTTAAAAATT
1 TTTAAAAATT
29096823 ATAAATTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 7 0.28
17 10 0.40
18 4 0.16
19 4 0.16
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.56
Consensus pattern (16 bp):
TTTAAAAATTTTTATT
Found at i:29102122 original size:6 final size:6
Alignment explanation
Indices: 29102111--29102139 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
29102101 ACATAAGAAA
29102111 TATATG TATATG TATATG TATATG TATAT
1 TATATG TATATG TATATG TATATG TATAT
29102140 TTTTGGCTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (6 bp):
TATATG
Found at i:29103338 original size:31 final size:31
Alignment explanation
Indices: 29103303--29103363 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
29103293 ATTTAAATAT
*
29103303 AAATATAGG-TAAAAATAC-GGTCAACGGGTCA
1 AAATA-AGGATAAAAA-ACGGGTCAACAGGTCA
*
29103334 AAATACGGATAAAAAACGGGTCAACAGGTC
1 AAATAAGGATAAAAAACGGGTCAACAGGTC
29103364 GCGCCTATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.46, C:0.15, G:0.23, T:0.16
Consensus pattern (31 bp):
AAATAAGGATAAAAAACGGGTCAACAGGTCA
Found at i:29103557 original size:11 final size:10
Alignment explanation
Indices: 29103541--29103596 Score: 53
Period size: 11 Copynumber: 5.5 Consensus size: 10
29103531 GTATCAACTG
29103541 GAAAAGAGAAA
1 GAAAAGAG-AA
29103552 GAAAAGAG-A
1 GAAAAGAGAA
*
29103561 GAAAGGAGAA
1 GAAAAGAGAA
*
29103571 GAAGAGAAGAA
1 GAAAAG-AGAA
29103582 GAAGAAGA-AA
1 GAA-AAGAGAA
29103592 GAAAA
1 GAAAA
29103597 AAAAAAGTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 10 0.26
10 10 0.26
11 16 0.42
12 2 0.05
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (10 bp):
GAAAAGAGAA
Found at i:29103577 original size:17 final size:17
Alignment explanation
Indices: 29103550--29103594 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
29103540 GGAAAAGAGA
29103550 AAGAA-AAGAG-AGAAAG
1 AAGAAGAAGAGAAG-AAG
*
29103566 GAGAAGAAGAGAAGAAG
1 AAGAAGAAGAGAAGAAG
29103583 AAGAAGAA-AGAA
1 AAGAAGAAGAGAA
29103595 AAAAAAAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 8 0.32
17 15 0.60
18 2 0.08
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (17 bp):
AAGAAGAAGAGAAGAAG
Found at i:29103881 original size:21 final size:21
Alignment explanation
Indices: 29103855--29103898 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
29103845 TAATTTAAAT
29103855 TTGTAAGACTTCAATATTATA
1 TTGTAAGACTTCAATATTATA
29103876 TTGTAAGACTTCAATATTATA
1 TTGTAAGACTTCAATATTATA
29103897 TT
1 TT
29103899 CGAAATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.45
Consensus pattern (21 bp):
TTGTAAGACTTCAATATTATA
Found at i:29104370 original size:38 final size:39
Alignment explanation
Indices: 29104328--29104405 Score: 131
Period size: 38 Copynumber: 2.0 Consensus size: 39
29104318 TTTTAATCAT
29104328 ATAGTTGCTGTTAACTCATTTAA-TTTTTTTATATCAAC
1 ATAGTTGCTGTTAACTCATTTAAGTTTTTTTATATCAAC
*
29104366 ATAGTTGTTGTTAACTCATTTAATGTTTTTTTATATCAAC
1 ATAGTTGCTGTTAACTCATTTAA-GTTTTTTTATATCAAC
29104406 TTGGGGTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
38 22 0.59
40 15 0.41
ACGTcount: A:0.28, C:0.12, G:0.09, T:0.51
Consensus pattern (39 bp):
ATAGTTGCTGTTAACTCATTTAAGTTTTTTTATATCAAC
Found at i:29104642 original size:58 final size:58
Alignment explanation
Indices: 29104484--29104670 Score: 211
Period size: 58 Copynumber: 3.2 Consensus size: 58
29104474 TACCGAAATG
* *
29104484 ATATGTTTTTTGTAATCGTGCCTATCTGACAGGCGCCAATCAATTTTTTATATTAACAAA
1 ATATATTTTTT-TAATCGTGCCTATCTGACAGGCGCAAATCAATTTTTTATATTAA-AAA
** * * * *
29104544 A-A-A--AATTTAATCGCGCCTATTTGACAGACGCGAATCAATTTTTTATATTAAAAA
1 ATATATTTTTTTAATCGTGCCTATCTGACAGGCGCAAATCAATTTTTTATATTAAAAA
* * *
29104598 ATATATTTTTTTAATCGTGTCTATCCGACAGGCGCAAATTAATTTTTTATATTAAAAA
1 ATATATTTTTTTAATCGTGCCTATCTGACAGGCGCAAATCAATTTTTTATATTAAAAA
*
29104656 ATATTTTTTGTTTAA
1 ATATATTTT-TTTAA
29104671 ATAAAATATT
Statistics
Matches: 105, Mismatches: 17, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
54 4 0.04
55 41 0.39
56 3 0.03
58 50 0.48
59 6 0.06
60 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.41
Consensus pattern (58 bp):
ATATATTTTTTTAATCGTGCCTATCTGACAGGCGCAAATCAATTTTTTATATTAAAAA
Found at i:29104939 original size:16 final size:16
Alignment explanation
Indices: 29104918--29104956 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
29104908 TTAACTCATT
*
29104918 TAATTTTTATATAATG
1 TAATTTTTATATAATA
29104934 TAATTTTTATATAATA
1 TAATTTTTATATAATA
29104950 TAATTTT
1 TAATTTT
29104957 ATTTGATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
TAATTTTTATATAATA
Found at i:29108097 original size:20 final size:20
Alignment explanation
Indices: 29108072--29108109 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29108062 ACTAGATCTG
29108072 TTAAAAAAATTTCAAAATTC
1 TTAAAAAAATTTCAAAATTC
* *
29108092 TTAAAACAATTTCGAAAT
1 TTAAAAAAATTTCAAAAT
29108110 GCAAAAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.34
Consensus pattern (20 bp):
TTAAAAAAATTTCAAAATTC
Found at i:29108602 original size:57 final size:56
Alignment explanation
Indices: 29108519--29108635 Score: 180
Period size: 57 Copynumber: 2.1 Consensus size: 56
29108509 ATATTTTATT
* * * *
29108519 AAAAGAAAAAAATTAATATAAAAAATTTATTGACGCCTGTCAGATAGGCTCGATTA
1 AAAAGAAAAAAATTAATATAAAAAATTCATTGACACCTGTCAGATAGGCGCCATTA
*
29108575 AAAAGAAAAAAAATTAATATAAAAAATTCATTGGCACCTGTCAGATAGGCGCCATTA
1 AAAAG-AAAAAAATTAATATAAAAAATTCATTGACACCTGTCAGATAGGCGCCATTA
29108632 AAAA
1 AAAA
29108636 AAACATACTA
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
56 5 0.09
57 50 0.91
ACGTcount: A:0.50, C:0.12, G:0.14, T:0.24
Consensus pattern (56 bp):
AAAAGAAAAAAATTAATATAAAAAATTCATTGACACCTGTCAGATAGGCGCCATTA
Found at i:29113181 original size:26 final size:26
Alignment explanation
Indices: 29113159--29113225 Score: 65
Period size: 25 Copynumber: 2.8 Consensus size: 26
29113149 TTTTTATGTG
29113159 TTAAAATATA-TATATTAAATTATTA
1 TTAAAATATATTATATTAAATTATTA
* * *
29113184 TTATATTATATTATATTATATTA-TA
1 TTAAAATATATTATATTAAATTATTA
29113209 TT---ATATATTATA-TAAAT
1 TTAAAATATATTATATTAAAT
29113226 AAGTAAAGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
21 4 0.11
22 9 0.25
25 12 0.33
26 11 0.31
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TTAAAATATATTATATTAAATTATTA
Found at i:29113221 original size:5 final size:5
Alignment explanation
Indices: 29113164--29113214 Score: 75
Period size: 5 Copynumber: 9.8 Consensus size: 5
29113154 ATGTGTTAAA
*
29113164 ATATAT ATATT AAATT ATTATT ATATT ATATT ATATT ATATT ATATT ATAT
1 ATAT-T ATATT ATATT A-TATT ATATT ATATT ATATT ATATT ATATT ATAT
29113215 ATTATATAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
5 34 0.81
6 8 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
ATATT
Found at i:29114559 original size:18 final size:19
Alignment explanation
Indices: 29114536--29114574 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
29114526 ATATATAGAT
29114536 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
29114554 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
29114573 AT
1 AT
29114575 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:29114924 original size:39 final size:40
Alignment explanation
Indices: 29114814--29114924 Score: 100
Period size: 38 Copynumber: 2.8 Consensus size: 40
29114804 GACCTCGAGT
* * **
29114814 CGATGAGACACTGGGTGTCACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA-AATATTACTTCGGATAGAGC
** ** * *
29114855 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAG-GC
1 CGATGAGACACTGGGTGTCAAATATTACTTCGGATAGAGC
*
29114893 CGATGAGACACTGGGTGTCAAATATTGCTTCG
1 CGATGAGACACTGGGTGTCAAATATTACTTCG
29114925 AACTATCCGA
Statistics
Matches: 53, Mismatches: 16, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
38 18 0.34
39 18 0.34
40 1 0.02
41 16 0.30
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAAATATTACTTCGGATAGAGC
Found at i:29115092 original size:18 final size:19
Alignment explanation
Indices: 29115071--29115111 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
29115061 AATGAAATGA
29115071 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
29115089 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
29115108 GAAA
1 GAAA
29115112 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:29116599 original size:26 final size:26
Alignment explanation
Indices: 29116563--29116640 Score: 86
Period size: 26 Copynumber: 3.0 Consensus size: 26
29116553 ACTCAGTTCC
29116563 CGAGGCAAAGCCAAAGATCCAGCTCG
1 CGAGGCAAAGCCAAAGATCCAGCTCG
*
29116589 CGAGGCAAAGCCAATGA-CCTAGCTCG
1 CGAGGCAAAGCCAAAGATCC-AGCTCG
* * ** *
29116615 CAAGGCAAGGCCGCAGATCTAGCTCG
1 CGAGGCAAAGCCAAAGATCCAGCTCG
29116641 TAGAAAGGAC
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
25 2 0.05
26 40 0.93
27 1 0.02
ACGTcount: A:0.31, C:0.31, G:0.28, T:0.10
Consensus pattern (26 bp):
CGAGGCAAAGCCAAAGATCCAGCTCG
Found at i:29119619 original size:109 final size:108
Alignment explanation
Indices: 29119413--29119622 Score: 325
Period size: 109 Copynumber: 1.9 Consensus size: 108
29119403 GCTAAACGAC
* *
29119413 AAATGGAAAATGTGTATCAACTTAAATGACAAATAACAGTTTTCCCTACCCTCGATTGATCGATT
1 AAATGGAAAATGTGTATCAACTTAAACGACAAATAACAGTTTTCCCTACCCTCGATTGATCAATT
29119478 AATGGATGCCTCTTCAGGTCACAAGTTCACGAGCTTAAACGGT
66 AATGGATGCCTCTTCAGGTCACAAGTTCACGAGCTTAAACGGT
* * *
29119521 AAAT-GAAGAATGTGTATCGACTTAAACGACAAATGACAGTTTTCCCCTACCCTTGATTGA-CTA
1 AAATGGAA-AATGTGTATCAACTTAAACGACAAATAACAGTTTT-CCCTACCCTCGATTGATC-A
*
29119584 ATTAGTGGATGCCTCTTCAGGTCACAAGTTCACGAGCTT
63 ATTAATGGATGCCTCTTCAGGTCACAAGTTCACGAGCTT
29119623 CATGGATGCT
Statistics
Matches: 93, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
107 3 0.03
108 37 0.40
109 53 0.57
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (108 bp):
AAATGGAAAATGTGTATCAACTTAAACGACAAATAACAGTTTTCCCTACCCTCGATTGATCAATT
AATGGATGCCTCTTCAGGTCACAAGTTCACGAGCTTAAACGGT
Found at i:29122866 original size:70 final size:70
Alignment explanation
Indices: 29122752--29123218 Score: 402
Period size: 70 Copynumber: 6.7 Consensus size: 70
29122742 AACATTTGTG
* ** * *
29122752 TCATACTAAGGCTCGCAGGATAAAAAACCACAGCCTCCGTCACAGTTAGAGAGAGTAAAGCTCCC
1 TCATACTAAGGCTCACAGGATAAAAAACCACAGCCTCCAACACAGTTAGTGAGAGCAAAGCTCCC
*
29122817 AATTA
66 AACTA
* * * *
29122822 TCATATTAAGACTCACAGGATAAAAAACCACAGCCTCCAACACAGTTAGTGAGAACAAAGCTTCC
1 TCATACTAAGGCTCACAGGATAAAAAACCACAGCCTCCAACACAGTTAGTGAGAGCAAAGCTCCC
*
29122887 AACTG
66 AACTA
* **** * * *
29122892 TCATACTAAGGCTCGCAGGATAAAAAATTGTAACCTCTAACATAGTTAGTGAGAGCAAAGCTCCC
1 TCATACTAAGGCTCACAGGATAAAAAACCACAGCCTCCAACACAGTTAGTGAGAGCAAAGCTCCC
*
29122957 AACTG
66 AACTA
* * * * * * * *
29122962 TCATGCTGAGGCTCATAGGACAAAAAACCATAGCCTCAAATACAGTTAGCGAGAGCAAAGCTCCC
1 TCATACTAAGGCTCACAGGATAAAAAACCACAGCCTCCAACACAGTTAGTGAGAGCAAAGCTCCC
*
29123027 AGCTA
66 AACTA
** * * * * *
29123032 TCATACTAAGGCTTGCAAGATAAAAAACTGA-AGCCTCCAATACAGTTACTGAGAGCAAAGATCC
1 TCATACTAAGGCTCACAGGATAAAAAAC-CACAGCCTCCAACACAGTTAGTGAGAGCAAAGCTCC
* *
29123096 TAGCTA
65 CAACTA
* * * * * * * **
29123102 TCATATTAAGGCTCACAAGAT-AAGAACCACAGCCTTCAACATAGTTAGCGAGAGCAAAACT-TA
1 TCATACTAAGGCTCACAGGATAAAAAACCACAGCCTCCAACACAGTTAGTGAGAGCAAAGCTCCC
*
29123165 AAGCTG
66 AA-CTA
*** * * *
29123171 TCATACTAAGGCTTGTAGGAT-AAAAACTACAGCCTTCAACATAGTTAG
1 TCATACTAAGGCTCACAGGATAAAAAACCACAGCCTCCAACACAGTTAG
29123219 CGAAAGTTAA
Statistics
Matches: 320, Mismatches: 74, Indels: 7
0.80 0.18 0.02
Matches are distributed among these distances:
68 2 0.01
69 72 0.22
70 245 0.77
71 1 0.00
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.21
Consensus pattern (70 bp):
TCATACTAAGGCTCACAGGATAAAAAACCACAGCCTCCAACACAGTTAGTGAGAGCAAAGCTCCC
AACTA
Found at i:29123338 original size:58 final size:58
Alignment explanation
Indices: 29123276--29123387 Score: 152
Period size: 58 Copynumber: 1.9 Consensus size: 58
29123266 AGTATAAAAT
* *
29123276 AGCTCACAAATTCACATCCCCAATTGGTTATCTCTCAGAGTTTTCTTAAGTATATGAC
1 AGCTCACAAATTCACATCCCCAATTGGTTATCTCTAAAAGTTTTCTTAAGTATATGAC
* * * * * *
29123334 AGCTCACAGATTCACATCTCTAGTTGGTTATCTTTAAAATTTTTCTTAAGTATA
1 AGCTCACAAATTCACATCCCCAATTGGTTATCTCTAAAAGTTTTCTTAAGTATA
29123388 GTTGGTGATT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
58 46 1.00
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (58 bp):
AGCTCACAAATTCACATCCCCAATTGGTTATCTCTAAAAGTTTTCTTAAGTATATGAC
Found at i:29136958 original size:5 final size:5
Alignment explanation
Indices: 29136948--29136986 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
29136938 AAATATTATC
* * *
29136948 TTTTA TTTTA TTTTA TTTTC TTTGA TTTTA TTTTC TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
29136987 GAAATAATCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.13, C:0.05, G:0.03, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:29136966 original size:15 final size:15
Alignment explanation
Indices: 29136948--29136986 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
29136938 AAATATTATC
*
29136948 TTTTATTTTATTTTA
1 TTTTCTTTTATTTTA
*
29136963 TTTTCTTTGATTTTA
1 TTTTCTTTTATTTTA
29136978 TTTTCTTTT
1 TTTTCTTTT
29136987 GAAATAATCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.13, C:0.05, G:0.03, T:0.79
Consensus pattern (15 bp):
TTTTCTTTTATTTTA
Found at i:29136969 original size:20 final size:20
Alignment explanation
Indices: 29136941--29136986 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
29136931 TCGGGGGAAA
* *
29136941 TATTATCTTTTATTTTATTT
1 TATTTTCTTTGATTTTATTT
29136961 TATTTTCTTTGATTTTATTT
1 TATTTTCTTTGATTTTATTT
*
29136981 TCTTTT
1 TATTTT
29136987 GAAATAATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.07, G:0.02, T:0.76
Consensus pattern (20 bp):
TATTTTCTTTGATTTTATTT
Found at i:29138316 original size:328 final size:324
Alignment explanation
Indices: 29137723--29138378 Score: 1017
Period size: 328 Copynumber: 2.0 Consensus size: 324
29137713 ATTTAATTTC
* *
29137723 TCATTACCATGAGTTCTCCAATTCGTCTAAGTGTATAAATAAAGAGATTTATTTAACTCTAGTCA
1 TCATTACCATGAGTTCTCCAATTCATCTAAGTGTATAAATAAAGAGATTTATTTAACTCTAATCA
* *
29137788 AGGATTACTGTATTGATGAAGGACGTGATCACATGCACGAATATATAAATACATTTATGATAATG
66 AGGATCACTGTATTGATGAAGGACGTAATCACATGCACGAATATATAAATACATTTATGATAATG
* * * *
29137853 ATATTGTTGATGGCGGGCAAGGTTTTTTGATGTTGGTCGATGATGAAGCCATGCAAAGAAATTGG
131 ATATTGTTGATGACGAGCAAGGTTTTTTGATGTTGGTCGACGATGAAGCCACGCAAAGAAATTGG
* * * *
29137918 AAATAATTATACAGACTAGAAAACTGGAAGTAATTAAAAGTTTGTGGGGGGTTTTGTGCTATTCA
196 AAATAACTATACAGACCAAAAAACTGGAAGTAATTAAAAGTTTATGGGGGGTTTTGTGCTATTCA
* **
29137983 TAGATACATGCATCGCATTTTCATGGTTGCT-TATATAGTTAATTGTATTTAGTGCTTTCCCTTT
261 TAGATACATGAATCGCATTTTCATGGTT-CTCTATATAAATAATTGTATTTAGTGCTTTCCCTTT
* * *
29138047 TCATTACCATGAGTTCTCCAATTCATTTAAGTGTATAAATAAAGAGATTTGTTTAATTCTAATCA
1 TCATTACCATGAGTTCTCCAATTCATCTAAGTGTATAAATAAAGAGATTTATTTAACTCTAATCA
* ** *
29138112 ATGATCACTGTATTGATGAAGGACGTAATCACATGCATTAATATATAAATAAATATATATATGAT
66 AGGATCACTGTATTGATGAAGGACGTAATCACATGCACGAATATATAAAT--ACAT-T-TATGAT
* *
29138177 AATGATATTGTTGATGACGAGCAAGGTTTTTTGATGTTGGTTGACGATGAAGCCACGTAAAGAAA
127 AATGATATTGTTGATGACGAGCAAGGTTTTTTGATGTTGGTCGACGATGAAGCCACGCAAAGAAA
*
29138242 TTGGAAATAACTATGCAGACCAAAAAACTGGAAGTAATTAAAAGTTTATGGGGGGTTTTGTGCTA
192 TTGGAAATAACTATACAGACCAAAAAACTGGAAGTAATTAAAAGTTTATGGGGGGTTTTGTGCTA
* *
29138307 TTCATAGATACATGAATTGCATTTTCATGGTTCTCTATATAAATAATTGTATTTAGTGCTTTCCT
257 TTCATAGATACATGAATCGCATTTTCATGGTTCTCTATATAAATAATTGTATTTAGTGCTTTCCC
29138372 TTT
322 TTT
29138375 TCAT
1 TCAT
29138379 ATTTATCAAG
Statistics
Matches: 300, Mismatches: 27, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
324 105 0.35
326 3 0.01
327 3 0.01
328 189 0.63
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (324 bp):
TCATTACCATGAGTTCTCCAATTCATCTAAGTGTATAAATAAAGAGATTTATTTAACTCTAATCA
AGGATCACTGTATTGATGAAGGACGTAATCACATGCACGAATATATAAATACATTTATGATAATG
ATATTGTTGATGACGAGCAAGGTTTTTTGATGTTGGTCGACGATGAAGCCACGCAAAGAAATTGG
AAATAACTATACAGACCAAAAAACTGGAAGTAATTAAAAGTTTATGGGGGGTTTTGTGCTATTCA
TAGATACATGAATCGCATTTTCATGGTTCTCTATATAAATAATTGTATTTAGTGCTTTCCCTTT
Found at i:29139840 original size:13 final size:14
Alignment explanation
Indices: 29139822--29139850 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
29139812 TAAGCATTTC
29139822 TGTTTAGTTA-AAA
1 TGTTTAGTTAGAAA
29139835 TGTTTAGTTAGAAA
1 TGTTTAGTTAGAAA
29139849 TG
1 TG
29139851 AAACTGTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (14 bp):
TGTTTAGTTAGAAA
Found at i:29148474 original size:105 final size:105
Alignment explanation
Indices: 29148293--29148486 Score: 246
Period size: 105 Copynumber: 1.8 Consensus size: 105
29148283 AATGTTTAAA
* * * * **
29148293 TGTAAGACCATAGCTGGGCTATGGCATTTTAATGAAAAGATCGTAACTGGGTTATGGCACCTTGA
1 TGTAAGACCATAGCTGGGATATGGCATTCTAATGAAAAGACCATAACTGGGTTATGGCACCTACA
**
29148358 ACGTAAAACCATGGTTGGACCATGACAGTATAGATACATG
66 ACGTAAAACCATGGCAGGACCATGACAGTATAGATACATG
* * * *
29148398 TGTAAGACTATAGTTGGGATATGGCATTCTGATGATAAGACCATAACTGGGTTATGGCA-CTACA
1 TGTAAGACCATAGCTGGGATATGGCATTCTAATGAAAAGACCATAACTGGGTTATGGCACCTACA
* *
29148462 GATGTAAGACCATGGCAGGACCATG
66 -ACGTAAAACCATGGCAGGACCATG
29148487 GCAATGCATG
Statistics
Matches: 74, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
104 3 0.04
105 71 0.96
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (105 bp):
TGTAAGACCATAGCTGGGATATGGCATTCTAATGAAAAGACCATAACTGGGTTATGGCACCTACA
ACGTAAAACCATGGCAGGACCATGACAGTATAGATACATG
Found at i:29148521 original size:33 final size:34
Alignment explanation
Indices: 29148391--29148522 Score: 96
Period size: 33 Copynumber: 4.0 Consensus size: 34
29148381 GACAGTATAG
* *
29148391 ATACATG-TGTAAGACTATAGTTGGGA-TATGGC-
1 ATACATGATGTAAGACCATAGCT-GGATTATGGCA
* * *
29148423 ATTC-TGATGATAAGACCATAACTGGGTTATGGCA
1 ATACATGATG-TAAGACCATAGCTGGATTATGGCA
* * * **
29148457 CTACA-GATGTAAGACCATGGCAGGACCATGGCA
1 ATACATGATGTAAGACCATAGCTGGATTATGGCA
* *
29148490 ATGCATG-TGTAAGACCATAGTTGGATTATGGCA
1 ATACATGATGTAAGACCATAGCTGGATTATGGCA
29148523 TAAAAAGAAC
Statistics
Matches: 74, Mismatches: 20, Indels: 11
0.70 0.19 0.10
Matches are distributed among these distances:
31 2 0.03
32 7 0.09
33 58 0.78
34 7 0.09
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.27
Consensus pattern (34 bp):
ATACATGATGTAAGACCATAGCTGGATTATGGCA
Found at i:29150122 original size:14 final size:13
Alignment explanation
Indices: 29150098--29150128 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
29150088 AATGTTTAAG
29150098 TATATTTATATTA
1 TATATTTATATTA
29150111 TATATATTATATTA
1 TATAT-TTATATTA
29150125 TATA
1 TATA
29150129 ATAATAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TATATTTATATTA
Done.