Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 62 of 322
Found at i:19744452 original size:54 final size:56
Alignment explanation
Indices: 19744162--19744484 Score: 267
Period size: 54 Copynumber: 6.0 Consensus size: 56
19744152 GTAATTCCAC
** * * ** * *
19744162 CCTACAGGGGT-TTTTAGTAATTCTACCTTATAGGGGTATTTTAGTAA--TTCTAC
1 CCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTTTATAA
* * *
19744215 CCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTTGGTAA--TTCTAC
1 CCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTTTATAA
* * * * *
19744269 CCTACAAGGGTATTTCGGTTATTCTACCCTACAGGGGTAATTCGATAA--TTCTAA
1 CCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTTTATAA
* * * * *
19744323 CCTACAGGGGTATTCCGGTAATTCTACCCTATAGGGGTATTCCGGTAA--TTCTAC
1 CCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTTTATAA
* * *
19744377 CCTATAGGGGTATTCCAGTAATTCTACCCTACAGGGGTATTTCGGTAATTTTATAA
1 CCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTTTATAA
* * * ** *
19744433 GCC-A-A-GGGCATTTTGGTAATTTTA-CAAACAAGGGGTATTTTGGTAATTTTAT
1 -CCTACAGGGGTATTTCGGTAATTCTACCCTAC-AGGGGTATTTCGGTAATTTTAT
19744485 TGATCGAGGG
Statistics
Matches: 232, Mismatches: 33, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
53 14 0.06
54 210 0.91
55 1 0.00
56 5 0.02
57 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (56 bp):
CCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTTTATAA
Found at i:19744495 original size:27 final size:27
Alignment explanation
Indices: 19744411--19744815 Score: 197
Period size: 27 Copynumber: 15.1 Consensus size: 27
19744401 TACCCTACAG
** *
19744411 GGGTATTTCGGTAATTTTATAAGCCAA
1 GGGTATTTCGGTAATTTTATAAATCGA
* * * *
19744438 GGGCATTTTGGTAATTTTACAAA-CAA
1 GGGTATTTCGGTAATTTTATAAATCGA
* **
19744464 GGGGTATTTTGGTAATTTTATTGATCGA
1 -GGGTATTTCGGTAATTTTATAAATCGA
* **
19744492 GGGTATTTCAGTAATTTTGCAAA-CTGA
1 GGGTATTTCGGTAATTTTATAAATC-GA
*
19744519 GGGTATTTCGGTAATTTTACAAATCGA
1 GGGTATTTCGGTAATTTTATAAATCGA
* * *
19744546 GGATATTTGGGTAATTTTATAAATCGG
1 GGGTATTTCGGTAATTTTATAAATCGA
* * *
19744573 GGGTACTTT-GGTAATTTTACAACT-GG
1 GGGTA-TTTCGGTAATTTTATAAATCGA
* * *
19744599 GGGTATTTCAGTAATTTCAT-AATTGA
1 GGGTATTTCGGTAATTTTATAAATCGA
** *
19744625 GGGTAAAAT-GGTAATTTTGTAAA-CTGA
1 GGGT-ATTTCGGTAATTTTATAAATC-GA
** *
19744652 GGGTAAAAT-GGTAATTTTGTAAATCGA
1 GGGT-ATTTCGGTAATTTTATAAATCGA
** * * * *
19744679 GGGTAAAAT-AGTAACTCTGTAAATCGA
1 GGGT-ATTTCGGTAATTTTATAAATCGA
** *
19744706 GGGTAAAAT-GGTAATTCTATAAATCGA
1 GGGT-ATTTCGGTAATTTTATAAATCGA
** *
19744733 GGGTAAAAT-GGTAATTTTGTAAATCGA
1 GGGT-ATTTCGGTAATTTTATAAATCGA
** * *
19744760 GGGTGA-AACGGTAATTCTGTAAATCGA
1 GGGT-ATTTCGGTAATTTTATAAATCGA
* *
19744787 GGGTACTTT-GGTAATTTTACAAATTGA
1 GGGTA-TTTCGGTAATTTTATAAATCGA
19744814 GG
1 GG
19744816 ACATTTTAGT
Statistics
Matches: 312, Mismatches: 52, Indels: 28
0.80 0.13 0.07
Matches are distributed among these distances:
25 5 0.02
26 34 0.11
27 266 0.85
28 7 0.02
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (27 bp):
GGGTATTTCGGTAATTTTATAAATCGA
Found at i:19744802 original size:81 final size:81
Alignment explanation
Indices: 19744623--19744791 Score: 268
Period size: 81 Copynumber: 2.1 Consensus size: 81
19744613 TTTCATAATT
* * *
19744623 GAGGGTAAAATGGTAATTTTGTAAACTGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAAAT
1 GAGGGTAAAATGGTAATTCTATAAACTGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAAAC
19744688 AGTAACTCTGTAAATC
66 AGTAACTCTGTAAATC
*
19744704 GAGGGTAAAATGGTAATTCTATAAA-TCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTGAAA
1 GAGGGTAAAATGGTAATTCTATAAACT-GAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAAA
* *
19744768 CGGTAATTCTGTAAATC
65 CAGTAACTCTGTAAATC
19744785 GAGGGTA
1 GAGGGTA
19744792 CTTTGGTAAT
Statistics
Matches: 81, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
80 1 0.01
81 80 0.99
ACGTcount: A:0.37, C:0.07, G:0.27, T:0.30
Consensus pattern (81 bp):
GAGGGTAAAATGGTAATTCTATAAACTGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAAAC
AGTAACTCTGTAAATC
Found at i:19744804 original size:54 final size:54
Alignment explanation
Indices: 19744623--19744791 Score: 259
Period size: 54 Copynumber: 3.1 Consensus size: 54
19744613 TTTCATAATT
*
19744623 GAGGGTAAAATGGTAATTTTGTAAA-CTGAGGGTAAAATGGTAATTTTGTAAATC
1 GAGGGTAAAATGGTAATTTTGTAAATC-GAGGGTAAAATGGTAATTCTGTAAATC
* * * *
19744677 GAGGGTAAAATAGTAACTCTGTAAATCGAGGGTAAAATGGTAATTCTATAAATC
1 GAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTGTAAATC
* *
19744731 GAGGGTAAAATGGTAATTTTGTAAATCGAGGGTGAAACGGTAATTCTGTAAATC
1 GAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTGTAAATC
19744785 GAGGGTA
1 GAGGGTA
19744792 CTTTGGTAAT
Statistics
Matches: 103, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
54 102 0.99
55 1 0.01
ACGTcount: A:0.37, C:0.07, G:0.27, T:0.30
Consensus pattern (54 bp):
GAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTGTAAATC
Found at i:19746458 original size:26 final size:26
Alignment explanation
Indices: 19746429--19746480 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
19746419 ACTTTTATTA
*
19746429 AGGGACT-TTTTATGAAAATGTGAAAT
1 AGGGACTAATTTATG-AAATGTGAAAT
*
19746455 AGGGACTAATTTGTGAAATGTGAAAT
1 AGGGACTAATTTATGAAATGTGAAAT
19746481 TTATGAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.33
Consensus pattern (26 bp):
AGGGACTAATTTATGAAATGTGAAAT
Found at i:19750463 original size:42 final size:42
Alignment explanation
Indices: 19750355--19750464 Score: 107
Period size: 42 Copynumber: 2.6 Consensus size: 42
19750345 CGAGATTCTG
* * *
19750355 TATATGACCATATCTGGGATATGGCATCAGTATGTGATTTCG
1 TATAAGACCATATCTGGGATATGGCACCAGTATGTGATTTCA
* * * *
19750397 TATAAGACCATGTCAGGGACATGGCGCC-GATATGAT-ATTTCA
1 TATAAGACCATATCTGGGATATGGCACCAG-TATG-TGATTTCA
* *
19750439 TGTAAGACCATATCTGGGGTATGGCA
1 TATAAGACCATATCTGGGATATGGCA
19750465 TTAATACGGT
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
41 1 0.02
42 51 0.96
43 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.30
Consensus pattern (42 bp):
TATAAGACCATATCTGGGATATGGCACCAGTATGTGATTTCA
Found at i:19760923 original size:55 final size:54
Alignment explanation
Indices: 19760809--19760995 Score: 193
Period size: 55 Copynumber: 3.5 Consensus size: 54
19760799 AACTTACCAT
* * * * *
19760809 TGCCATGTCTTGACATGGTCTTAC-GTGGT-ATCCTTGCTTTAT-GAACTCACCAA
1 TGCCATGCCTTGGCATGGTCTTACAG-GATGA-CCTTGCCTTATAGAACTCATCAA
*
19760862 TGCCATGCCTTGGCATGGTCTTACAGGA-GACCTTTGTCTTATAGTAACTCATCAA
1 TGCCATGCCTTGGCATGGTCTTACAGGATGACC-TTGCCTTATAG-AACTCATCAA
* * * * ** *
19760917 TTCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTATAGAACTTATCAA
1 TGCCATGCCTTGGCATGGTCTTACAGGATGACCTTGCCTTATAGAACTCATCAA
19760971 TGCCATGCCTTGGCATGGTCTTACA
1 TGCCATGCCTTGGCATGGTCTTACA
19760996 TGATATCCTT
Statistics
Matches: 111, Mismatches: 17, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
52 2 0.02
53 31 0.28
54 33 0.30
55 43 0.39
56 2 0.02
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (54 bp):
TGCCATGCCTTGGCATGGTCTTACAGGATGACCTTGCCTTATAGAACTCATCAA
Found at i:19761100 original size:47 final size:47
Alignment explanation
Indices: 19760984--19761120 Score: 184
Period size: 47 Copynumber: 2.9 Consensus size: 47
19760974 CATGCCTTGG
* * * *
19760984 CATGGTCTTACATGATATCCTTATCTAAACAAATGCCATGTTCAAAA
1 CATGGTCTTACATGGTATCCTTGTCTTAACAAATGCCATATTCAAAA
* *
19761031 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATATTCCAAA
1 CATGGTCTTACATGGTATCCTTGTCTTAACAAATGCCATATTCAAAA
* *
19761078 CATGGTCGTACATGGTATCCTTGTCTTAGTACCAATGCCATAT
1 CATGGTCTTACATGGTATCCTTGTCTTA--ACAAATGCCATAT
19761121 CTTGATGTGG
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
47 68 0.86
49 11 0.14
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (47 bp):
CATGGTCTTACATGGTATCCTTGTCTTAACAAATGCCATATTCAAAA
Found at i:19775755 original size:45 final size:45
Alignment explanation
Indices: 19775691--19775823 Score: 212
Period size: 45 Copynumber: 3.0 Consensus size: 45
19775681 CAGGATTCTA
19775691 ATATGTGTTTTCGTGTAAGACCATGTCTGGGACGTTGGCATTGAT
1 ATATGTGTTTTCGTGTAAGACCATGTCTGGGACGTTGGCATTGAT
*
19775736 ATATGTGTTTTTGTGTAAGACCATGTCTGGGACGTTGGCATTGAT
1 ATATGTGTTTTCGTGTAAGACCATGTCTGGGACGTTGGCATTGAT
* * * * *
19775781 CTATGTGGTTACGTGTAAGACCATGTCTGGAACATTGGCATTG
1 ATATGTGTTTTCGTGTAAGACCATGTCTGGGACGTTGGCATTG
19775824 TATTTGATTC
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 81 1.00
ACGTcount: A:0.21, C:0.14, G:0.29, T:0.37
Consensus pattern (45 bp):
ATATGTGTTTTCGTGTAAGACCATGTCTGGGACGTTGGCATTGAT
Found at i:19785394 original size:37 final size:37
Alignment explanation
Indices: 19785344--19785495 Score: 250
Period size: 37 Copynumber: 4.1 Consensus size: 37
19785334 ACCTTTAGCT
* * *
19785344 CGGACGTAATCTCCACACGAAGTTATCGGGTCTTACC
1 CGGACATAATCTCCACACGTAGTCATCGGGTCTTACC
*
19785381 CGGACAAAATCTCCACACGTAGTCATCGGGTCTTACC
1 CGGACATAATCTCCACACGTAGTCATCGGGTCTTACC
*
19785418 CGGACATAACCTCCACACGTAGTCATCGGGTCTTACC
1 CGGACATAATCTCCACACGTAGTCATCGGGTCTTACC
*
19785455 CGGACATAATCTCCACACGTAGTCATCGGGTCTCACC
1 CGGACATAATCTCCACACGTAGTCATCGGGTCTTACC
19785492 CGGA
1 CGGA
19785496 ATATATTTCC
Statistics
Matches: 107, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 107 1.00
ACGTcount: A:0.25, C:0.33, G:0.20, T:0.22
Consensus pattern (37 bp):
CGGACATAATCTCCACACGTAGTCATCGGGTCTTACC
Found at i:19785710 original size:47 final size:48
Alignment explanation
Indices: 19785658--19785868 Score: 252
Period size: 47 Copynumber: 4.5 Consensus size: 48
19785648 TTTCACACTA
* ** ** * *
19785658 GCCATTCGGCTTTACT-GTATATATGCATTTTCATATTCAGCACATTG
1 GCCATTCGGCCTTACTCACATATATGCATGCTCACATTCATCACATTG
*
19785705 GCCATTCGGCCTTA-TCACACATATGCATGCTCACATTCATCACATTG
1 GCCATTCGGCCTTACTCACATATATGCATGCTCACATTCATCACATTG
* * *
19785752 GCCATTCGGTCTTA-TCACATATATGCATGCTCACATTTATCACATAG
1 GCCATTCGGCCTTACTCACATATATGCATGCTCACATTCATCACATTG
* * * *
19785799 GCCATTCGGCC-TAATCACATATATGCATGTTCATATTCACCACATTG
1 GCCATTCGGCCTTACTCACATATATGCATGCTCACATTCATCACATTG
19785846 GCCATTCGGCCTTAC-CACATATA
1 GCCATTCGGCCTTACTCACATATA
19785869 CATATCTCAT
Statistics
Matches: 142, Mismatches: 19, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
46 3 0.02
47 137 0.96
48 2 0.01
ACGTcount: A:0.26, C:0.27, G:0.13, T:0.33
Consensus pattern (48 bp):
GCCATTCGGCCTTACTCACATATATGCATGCTCACATTCATCACATTG
Found at i:19785909 original size:48 final size:48
Alignment explanation
Indices: 19785839--19786310 Score: 610
Period size: 48 Copynumber: 9.5 Consensus size: 48
19785829 TCATATTCAC
* * * *
19785839 CACATTGGCCATTCGGCCTTACCACATATACATATCTCATATATATTT
1 CACATTAGCCATTCGGCTTTACCACATATACATATCACACATATATTT
*
19785887 CACATTAACCATTCGGCTTTACCACATATACATATCACACATATATTT
1 CACATTAGCCATTCGGCTTTACCACATATACATATCACACATATATTT
19785935 CACATTAGCCATTCGGCTTTACCACATATACATATCACACATATATTT
1 CACATTAGCCATTCGGCTTTACCACATATACATATCACACATATATTT
19785983 CACATTAGCCATTCGGCTTTACCACATATACATATC-CACATATACATATCT
1 CACATTAGCCATTCGGCTTTACCACATATACATATCACACATAT--AT-T-T
*
19786034 CATACATATTTCA-CATTCGCCATTCGGCTTCACCACATATACATATCACACATATATTT
1 C--AC--A-TT-AGC------CATTCGGCTTTACCACATATACATATCACACATATATTT
* * *
19786093 CACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTT
1 CACATTAGCCATTCGGCTTTACCACATATACATATCACACATATATTT
* *
19786141 TACATTCA-CCATTCGGCTTTACCACATATACATATAACACATATATTT
1 CACATT-AGCCATTCGGCTTTACCACATATACATATCACACATATATTT
* * *
19786189 CACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTT
1 CACATTAGCCATTCGGCTTTACCACATATACATATCACACATATATTT
*
19786237 CACATTCGCCATTCGG-TTTCACCACATATACATATCACACATATATTT
1 CACATTAGCCATTCGGCTTT-ACCACATATACATATCACACATATATTT
*
19786285 CACATTAGCCATTCGGCTTCACCACA
1 CACATTAGCCATTCGGCTTTACCACA
19786311 CACATATATA
Statistics
Matches: 375, Mismatches: 27, Indels: 44
0.84 0.06 0.10
Matches are distributed among these distances:
47 11 0.03
48 304 0.81
49 5 0.01
50 1 0.00
51 2 0.01
53 3 0.01
54 3 0.01
55 2 0.01
56 3 0.01
57 3 0.01
59 2 0.01
60 1 0.00
61 2 0.01
62 26 0.07
63 7 0.02
ACGTcount: A:0.32, C:0.28, G:0.06, T:0.33
Consensus pattern (48 bp):
CACATTAGCCATTCGGCTTTACCACATATACATATCACACATATATTT
Found at i:19786023 original size:14 final size:14
Alignment explanation
Indices: 19786004--19786032 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
19785994 TTCGGCTTTA
19786004 CCACATATACATAT
1 CCACATATACATAT
19786018 CCACATATACATAT
1 CCACATATACATAT
19786032 C
1 C
19786033 TCATACATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.31, G:0.00, T:0.28
Consensus pattern (14 bp):
CCACATATACATAT
Found at i:19786025 original size:62 final size:62
Alignment explanation
Indices: 19785956--19786089 Score: 214
Period size: 62 Copynumber: 2.1 Consensus size: 62
19785946 TTCGGCTTTA
* *
19785956 CCACATATACATATCACACATATATTTCACATTAGCCATTCGGCTTTACCACATATACATAT
1 CCACATATACATATCACACACATATTTCACATTAGCCATTCGGCTTCACCACATATACATAT
* * *
19786018 CCACATATACATATCTCATACATATTTCACATTCGCCATTCGGCTTCACCACATATACATAT
1 CCACATATACATATCACACACATATTTCACATTAGCCATTCGGCTTCACCACATATACATAT
19786080 CACACATATA
1 C-CACATATA
19786090 TTTCACATTA
Statistics
Matches: 66, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
62 58 0.88
63 8 0.12
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.31
Consensus pattern (62 bp):
CCACATATACATATCACACACATATTTCACATTAGCCATTCGGCTTCACCACATATACATAT
Found at i:19790935 original size:44 final size:44
Alignment explanation
Indices: 19790887--19791035 Score: 139
Period size: 43 Copynumber: 3.5 Consensus size: 44
19790877 TGTGATTTCC
19790887 TGTAAGACCACGTCTGGGACATTGGCATCGAT-TTGAGATTTACG
1 TGTAAGACCACGTCTGGGACATTGGCATCGATATT-AGATTTACG
* * * * *
19790931 TGTAAGACCATGTCTGAGACATCGGCATC-ATATTTGATTT-TG
1 TGTAAGACCACGTCTGGGACATTGGCATCGATATTAGATTTACG
* * * * *
19790973 TGTAAGAACC-TGTATGGGATAGTT-GCGTCGATATTAGA-TTACA
1 TGTAAG-ACCACGTCTGGGACA-TTGGCATCGATATTAGATTTACG
19791016 TGTAAGACCACGTCTGGGAC
1 TGTAAGACCACGTCTGGGAC
19791036 GTCGGCATTG
Statistics
Matches: 83, Mismatches: 16, Indels: 13
0.74 0.14 0.12
Matches are distributed among these distances:
42 24 0.29
43 31 0.37
44 28 0.34
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.31
Consensus pattern (44 bp):
TGTAAGACCACGTCTGGGACATTGGCATCGATATTAGATTTACG
Found at i:19795347 original size:26 final size:26
Alignment explanation
Indices: 19795318--19795372 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
19795308 CATCCTTGCA
19795318 ATTACTTAAACTAAACCTATAGGATT
1 ATTACTTAAACTAAACCTATAGGATT
19795344 ATTACTTAAACTAAACCTATAGGATT
1 ATTACTTAAACTAAACCTATAGGATT
19795370 ATT
1 ATT
19795373 GAAGATCCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.36
Consensus pattern (26 bp):
ATTACTTAAACTAAACCTATAGGATT
Found at i:19810768 original size:18 final size:18
Alignment explanation
Indices: 19810742--19810783 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
19810732 AAAAGTCGTG
19810742 GCCCATGTGGGCCCACAT-
1 GCCCATGT-GGCCCACATA
*
19810760 GCCCGTGTGGCCCACATA
1 GCCCATGTGGCCCACATA
19810778 GCCCAT
1 GCCCAT
19810784 ACTGGCCTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.17, C:0.40, G:0.26, T:0.17
Consensus pattern (18 bp):
GCCCATGTGGCCCACATA
Found at i:19817749 original size:45 final size:45
Alignment explanation
Indices: 19817699--19817785 Score: 156
Period size: 45 Copynumber: 1.9 Consensus size: 45
19817689 CCAAAACATG
*
19817699 TGTCACATATATCACGAACTCAGACCATAACTCAATGAGTTCGGA
1 TGTCACATATATCACGAACTCAGACCACAACTCAATGAGTTCGGA
*
19817744 TGTCACATATATCATGAACTCAGACCACAACTCAATGAGTTC
1 TGTCACATATATCACGAACTCAGACCACAACTCAATGAGTTC
19817786 AAATTACATA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (45 bp):
TGTCACATATATCACGAACTCAGACCACAACTCAATGAGTTCGGA
Found at i:19825492 original size:36 final size:37
Alignment explanation
Indices: 19825386--19825493 Score: 182
Period size: 37 Copynumber: 2.9 Consensus size: 37
19825376 AGCTCAGACG
* *
19825386 AAATCTCCACACGAAGTCATCGGGTCTTACCCGGATA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
19825423 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
19825460 TAATCTCCACACGTAGTCATC-GGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
19825494 ATATATTTCC
Statistics
Matches: 68, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
36 13 0.19
37 55 0.81
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:19825778 original size:47 final size:47
Alignment explanation
Indices: 19825712--19825944 Score: 317
Period size: 47 Copynumber: 5.0 Consensus size: 47
19825702 TTTCGGATTA
* * *
19825712 GCCATTCGG-CTTCACCACATATATACACT-TTCACGTTCATCACATTG
1 GCCATTCGGCCTT-ATCACATATATGCA-TGTTCACATTCATCACATTG
* *
19825759 GCCATTCTGCCTTATCACATATATGCATGGTCACATTCATCACATTG
1 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
* *
19825806 GCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTG
1 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
* *
19825853 GCCATTTGGCCTTATCACATATATGCATGTTCATATTCATCACATTG
1 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
* * * *
19825900 GTCATTCGGCCTTATCACACATATACATATTCACATTCATCACAT
1 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACAT
19825945 AAAATCCTAA
Statistics
Matches: 166, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
46 1 0.01
47 162 0.98
48 3 0.02
ACGTcount: A:0.27, C:0.29, G:0.11, T:0.33
Consensus pattern (47 bp):
GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
Found at i:19829286 original size:19 final size:20
Alignment explanation
Indices: 19829240--19829292 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
19829230 AATGGCTAAT
*
19829240 ATGAAAGTTGTTTTATGAATG
1 ATGAAAGTT-TTTCATGAATG
*
19829261 CAAGAAAGTTTTTCATGAATG
1 -ATGAAAGTTTTTCATGAATG
*
19829282 -TGAAAATTTTT
1 ATGAAAGTTTTT
19829293 GGCACGGTCG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 9 0.33
21 10 0.37
22 8 0.30
ACGTcount: A:0.36, C:0.04, G:0.19, T:0.42
Consensus pattern (20 bp):
ATGAAAGTTTTTCATGAATG
Found at i:19832124 original size:31 final size:31
Alignment explanation
Indices: 19832086--19832149 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
19832076 AGATGAATGG
19832086 CAATGATACAAGATCTCAGCAATCTTACTTT
1 CAATGATACAAGATCTCAGCAATCTTACTTT
19832117 CAATGATACAAGATCTCAGCAATCTTACTTT
1 CAATGATACAAGATCTCAGCAATCTTACTTT
19832148 CA
1 CA
19832150 GCTACACAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.36, C:0.23, G:0.09, T:0.31
Consensus pattern (31 bp):
CAATGATACAAGATCTCAGCAATCTTACTTT
Found at i:19841178 original size:15 final size:17
Alignment explanation
Indices: 19841143--19841182 Score: 57
Period size: 15 Copynumber: 2.4 Consensus size: 17
19841133 TTTCAAAATT
19841143 ATTTTCAAATAAAATCTC
1 ATTTT-AAATAAAATCTC
19841161 ATTTTAAA-AAAATC-C
1 ATTTTAAATAAAATCTC
19841176 ATTTTAA
1 ATTTTAA
19841183 CCAAATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.36
16 6 0.27
17 3 0.14
18 5 0.23
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.40
Consensus pattern (17 bp):
ATTTTAAATAAAATCTC
Found at i:19842298 original size:20 final size:21
Alignment explanation
Indices: 19842269--19842308 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
19842259 TTTTGAGCAA
19842269 TTTAAATTTT-TTTATTTTCT
1 TTTAAATTTTCTTTATTTTCT
* *
19842289 TTTAACTTTTCTTTTTTTTC
1 TTTAAATTTTCTTTATTTTC
19842309 CCTTTATTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTAAATTTTCTTTATTTTCT
Found at i:19851797 original size:40 final size:40
Alignment explanation
Indices: 19851720--19852700 Score: 1808
Period size: 40 Copynumber: 24.6 Consensus size: 40
19851710 AAACCAAGTA
* * * *
19851720 CCTTCGGAATTTAG-CCGGATATAGCT-ACTTGCTCAAATG
1 CCTTCGGGATTTAGCCCGGTTATAG-TAACTCGCACAAATG
*
19851759 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
19851799 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
19851839 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
19851879 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
19851919 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
19851959 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
19851999 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
19852039 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
19852079 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
19852119 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
19852159 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
19852199 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
19852239 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
19852279 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
19852319 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
19852359 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
19852399 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
19852439 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
19852479 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
19852519 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
19852559 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
* *
19852599 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
* * * *
19852639 CCTTCGGG-CTTAGCCCGG-AATTAGTCACTAGCACAAATG
1 CCTTCGGGATTTAGCCCGGTTA-TAGTAACTCGCACAAATG
*
19852678 CCTTCGGGACTTAGCCCGGTTAT
1 CCTTCGGGATTTAGCCCGGTTAT
19852701 CATCCGAATA
Statistics
Matches: 925, Mismatches: 12, Indels: 9
0.98 0.01 0.01
Matches are distributed among these distances:
38 1 0.00
39 47 0.05
40 876 0.95
41 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (40 bp):
CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
Found at i:19855691 original size:46 final size:46
Alignment explanation
Indices: 19855584--19855693 Score: 175
Period size: 46 Copynumber: 2.4 Consensus size: 46
19855574 GCAAACTCGA
* * **
19855584 ACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTTGG
1 ACTCAACTCAACGAGTTCGGGCATTCGCATCCATAAGTGAACTCAG
19855630 ACTCAACTCAACGAGTTCGGGCATTCGCATCCATAAGTGAACTCAG
1 ACTCAACTCAACGAGTTCGGGCATTCGCATCCATAAGTGAACTCAG
*
19855676 ACTCAAGTCAACGAGTTC
1 ACTCAACTCAACGAGTTC
19855694 AGATGCCCAA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 59 1.00
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
ACTCAACTCAACGAGTTCGGGCATTCGCATCCATAAGTGAACTCAG
Found at i:19864706 original size:24 final size:24
Alignment explanation
Indices: 19864674--19864723 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
19864664 ATTATTTAAT
19864674 AATATCAAATAATCAAAGATTCTC
1 AATATCAAATAATCAAAGATTCTC
*
19864698 AATATCAAATAATCAACGATTCTC
1 AATATCAAATAATCAAAGATTCTC
19864722 AA
1 AA
19864724 CATAACCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.18, G:0.04, T:0.28
Consensus pattern (24 bp):
AATATCAAATAATCAAAGATTCTC
Found at i:19868062 original size:24 final size:24
Alignment explanation
Indices: 19868030--19868118 Score: 92
Period size: 24 Copynumber: 3.7 Consensus size: 24
19868020 TCTTACTTAT
19868030 TCGCACACATAGTGCCACGTTTTC
1 TCGCACACATAGTGCCACGTTTTC
* * **
19868054 TCGCACACATAGTACCATGTAATC
1 TCGCACACATAGTGCCACGTTTTC
*
19868078 TCACACACATAGTGCCACTTAGTTTT-
1 TCGCACACATAGTGCCAC---GTTTTC
19868104 T-GCACACATAGTGCC
1 TCGCACACATAGTGCC
19868119 GCATAACCTT
Statistics
Matches: 52, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
24 35 0.67
25 13 0.25
26 1 0.02
27 3 0.06
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.28
Consensus pattern (24 bp):
TCGCACACATAGTGCCACGTTTTC
Found at i:19870342 original size:8 final size:8
Alignment explanation
Indices: 19870329--19870353 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
19870319 CTCGAGAATG
19870329 CAACATAT
1 CAACATAT
19870337 CAACATAT
1 CAACATAT
19870345 CAACATAT
1 CAACATAT
19870353 C
1 C
19870354 TTCGAGTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (8 bp):
CAACATAT
Found at i:19875669 original size:24 final size:24
Alignment explanation
Indices: 19875636--19875747 Score: 89
Period size: 24 Copynumber: 4.6 Consensus size: 24
19875626 TCTTTCTTAT
* **
19875636 TCGCATACATAGTGCCACATTTTC
1 TCGCACACATAGTGCCACATAATC
**
19875660 TCGCACACATAGTGCCATGTAATC
1 TCGCACACATAGTGCCACATAATC
* * * *
19875684 TCACACACATAGTGCCACTTAGTTT
1 TCGCACACATAGTGCCACATA-ATC
* * * *
19875709 TTGTACACATAGTGCCGCATAACC
1 TCGCACACATAGTGCCACATAATC
*
19875733 TTGCACACATAGTGC
1 TCGCACACATAGTGC
19875748 TGAAATTTCT
Statistics
Matches: 68, Mismatches: 19, Indels: 2
0.76 0.21 0.02
Matches are distributed among these distances:
24 51 0.75
25 17 0.25
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.29
Consensus pattern (24 bp):
TCGCACACATAGTGCCACATAATC
Found at i:19876831 original size:20 final size:21
Alignment explanation
Indices: 19876799--19876837 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
19876789 TAATTTCTTC
19876799 TTTTATTTCTATT-TTTATTT
1 TTTTATTTCTATTATTTATTT
19876819 TTTTA-TTCATATTATTTAT
1 TTTTATTTC-TATTATTTAT
19876838 GATATTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.18
20 9 0.53
21 5 0.29
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTATTTCTATTATTTATTT
Found at i:19881592 original size:19 final size:18
Alignment explanation
Indices: 19881563--19881599 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
19881553 GTATATATTT
19881563 TAAATTTATTTAGGTAGA
1 TAAATTTATTTAGGTAGA
*
19881581 TAAATCTTATTTGGGTAGA
1 TAAAT-TTATTTAGGTAGA
19881600 AAAGTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.35, C:0.03, G:0.19, T:0.43
Consensus pattern (18 bp):
TAAATTTATTTAGGTAGA
Found at i:19881609 original size:19 final size:19
Alignment explanation
Indices: 19881563--19881610 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
19881553 GTATATATTT
19881563 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
* *
19881581 TAAATCTTATTTGGGTAGA
1 TAAATTTTATTTAGGTAGA
19881600 -AAAGTTTTATT
1 TAAA-TTTTATT
19881611 CATATTCTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.35, C:0.02, G:0.17, T:0.46
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:19881672 original size:43 final size:43
Alignment explanation
Indices: 19881624--19881716 Score: 152
Period size: 43 Copynumber: 2.2 Consensus size: 43
19881614 ATTCTAGAAA
19881624 TATTTT-TATTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC
1 TATTTTCT-TTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC
* *
19881667 TATTTTCTTTTTATGTTTTAGTAGTTTATTAGAATAAGGGAAC
1 TATTTTCTTTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC
19881710 TATTTTC
1 TATTTTC
19881717 CTAATTAGGA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
43 46 0.98
44 1 0.02
ACGTcount: A:0.28, C:0.06, G:0.14, T:0.52
Consensus pattern (43 bp):
TATTTTCTTTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC
Found at i:19884908 original size:40 final size:40
Alignment explanation
Indices: 19884853--19884932 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
19884843 GGGCTGTAAA
19884853 TGGGTGTTCACAACCAAATTCAAACCAGATGGATCTTTAG
1 TGGGTGTTCACAACCAAATTCAAACCAGATGGATCTTTAG
*
19884893 TGGGTGTTCACAACCAATTTCAAACCAGATGGATCTTTAG
1 TGGGTGTTCACAACCAAATTCAAACCAGATGGATCTTTAG
19884933 ATAGATACAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (40 bp):
TGGGTGTTCACAACCAAATTCAAACCAGATGGATCTTTAG
Found at i:19886366 original size:19 final size:19
Alignment explanation
Indices: 19886320--19886367 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
19886310 GTATATATTT
19886320 TAAA-TTTATTTAAGTAGA
1 TAAATTTTATTTAAGTAGA
* *
19886338 TAAATCTTATTTAGGTAGA
1 TAAATTTTATTTAAGTAGA
*
19886357 TAAGTTTTATT
1 TAAATTTTATT
19886368 CATATTCTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAAGTAGA
Found at i:19886429 original size:43 final size:43
Alignment explanation
Indices: 19886381--19886473 Score: 152
Period size: 43 Copynumber: 2.2 Consensus size: 43
19886371 ATTCTAGAAA
19886381 TATTTT-TATTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC
1 TATTTTCT-TTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC
* *
19886424 TATTTTCTTTTTATGTTTTAGTAGTTTATTAGAATAAGGGAAC
1 TATTTTCTTTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC
19886467 TATTTTC
1 TATTTTC
19886474 CTAATTAGGA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
43 46 0.98
44 1 0.02
ACGTcount: A:0.28, C:0.06, G:0.14, T:0.52
Consensus pattern (43 bp):
TATTTTCTTTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC
Found at i:19888537 original size:3 final size:3
Alignment explanation
Indices: 19888529--19888614 Score: 104
Period size: 3 Copynumber: 28.7 Consensus size: 3
19888519 AGTGGATCAT
*
19888529 ATG ATG ATG ATG ATG ATTG -TG ATG GTG ATG ATG ATTG -TG ATG ATG
1 ATG ATG ATG ATG ATG A-TG ATG ATG ATG ATG ATG A-TG ATG ATG ATG
* * *
19888574 ATG ATG ATG AGG ATG AGG ATG AGG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
19888615 ACCAATAATG
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
2 4 0.06
3 63 0.89
4 4 0.06
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:19899005 original size:40 final size:40
Alignment explanation
Indices: 19898807--19898991 Score: 352
Period size: 40 Copynumber: 4.6 Consensus size: 40
19898797 GTGATTAATT
*
19898807 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTATGTCCCGAAGGCATTTGTGCGAGTTACTATAA
19898847 CCGGGCTATGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTATGTCCCGAAGGCATTTGTGCGAGTTACTATAA
19898887 CCGGGCTATGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTATGTCCCGAAGGCATTTGTGCGAGTTACTATAA
19898927 CCGGGCTATGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTATGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
19898967 CCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTATGTCCCGAAGGCATTTG
19898992 AGCAAGTAGC
Statistics
Matches: 143, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 143 1.00
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTATGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:19900552 original size:18 final size:18
Alignment explanation
Indices: 19900531--19900569 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
19900521 GATTGAGAGT
* *
19900531 GAAAAGGAATGTGAAACA
1 GAAAAGAAATGTGAAAAA
*
19900549 GAAAAGAAATTTGAAAAA
1 GAAAAGAAATGTGAAAAA
19900567 GAA
1 GAA
19900570 GTTGAAGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.23, T:0.13
Consensus pattern (18 bp):
GAAAAGAAATGTGAAAAA
Found at i:19904333 original size:4 final size:4
Alignment explanation
Indices: 19904324--19904357 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
19904314 TATTTTTATT
19904324 TTTA TTTA TTTA TTTA TTTA TTTTA TTTA GTTTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA -TTTA
19904358 AATTTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:19905475 original size:40 final size:40
Alignment explanation
Indices: 19905420--19905623 Score: 286
Period size: 40 Copynumber: 5.1 Consensus size: 40
19905410 TGGATGATAA
* * *
19905420 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
*
19905460 CCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
19905500 CCGGGTTAAGTCCTGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
19905540 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTACAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
19905580 CCGGGCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
19905620 CCGG
1 CCGG
19905624 TTAAATATTG
Statistics
Matches: 148, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
39 3 0.02
40 145 0.98
ACGTcount: A:0.22, C:0.23, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:19908608 original size:37 final size:37
Alignment explanation
Indices: 19908561--19908631 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
19908551 TTCCCCCCCT
*
19908561 CCATTGCCGTGAGTTAAAGAAAAGAAAGGAGAAACCC
1 CCATTGCCGTGAGCTAAAGAAAAGAAAGGAGAAACCC
* **
19908598 CCATTGCCGTGAGCTCAAGTGAAGAAAGGAGAAA
1 CCATTGCCGTGAGCTAAAGAAAAGAAAGGAGAAA
19908632 AGTTTGTGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.41, C:0.18, G:0.27, T:0.14
Consensus pattern (37 bp):
CCATTGCCGTGAGCTAAAGAAAAGAAAGGAGAAACCC
Found at i:19909914 original size:79 final size:81
Alignment explanation
Indices: 19909778--19909962 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
19909768 TTGAACGATG
*
19909778 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
19909842 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
19909857 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
19909919 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
19909937 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
19909963 AACGAGGAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:19909976 original size:40 final size:40
Alignment explanation
Indices: 19909779--19909962 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
19909769 TGAACGATGT
* * * *
19909779 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
19909819 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
19909859 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
19909897 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
19909938 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
19909963 AACGAGGAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:19909984 original size:79 final size:79
Alignment explanation
Indices: 19909779--19909995 Score: 201
Period size: 79 Copynumber: 2.7 Consensus size: 79
19909769 TGAACGATGT
** * * * **
19909779 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAG-CCCGAAGGCATTTGAAC-GAGTGACTAAATCCGGGTTAA-ATCCCGAAGGCATT
*
19909842 TGTGCGAGATACTAATT
63 TGTGCGAGATACTAATA
** * *
19909859 CCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGT
1 CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTTGT
*
19909924 GCGAGTTACT-ATAA
66 GCGAGATACTAAT-A
* * *
19909938 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-CTAAATCCGGGTTAAATCCCGAAGG
19909996 TACGTGATTT
Statistics
Matches: 116, Mismatches: 16, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
78 3 0.03
79 71 0.61
80 42 0.36
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (79 bp):
CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTTGT
GCGAGATACTAATA
Found at i:19913162 original size:65 final size:65
Alignment explanation
Indices: 19913075--19913203 Score: 215
Period size: 65 Copynumber: 2.0 Consensus size: 65
19913065 GGCTATTATC
*
19913075 AGTTGCGAATTCGAGAATCGGACATACCCAAAACTGCCTTCAGGACGAGATAT-GATCACTACGA
1 AGTTGCGAATTCGAGAATCGGACATACCCAAAACTGCCTTCAGAACGAGATATCG-TCACTACGA
19913139 G
65 G
* *
19913140 AGTTGCGAATTTGAGATTCGGACATACCCAAAACTGCCTTCAGAACGAGATATCGTCACTACGA
1 AGTTGCGAATTCGAGAATCGGACATACCCAAAACTGCCTTCAGAACGAGATATCGTCACTACGA
19913204 ATTCTTAGTG
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
65 59 0.98
66 1 0.02
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.22
Consensus pattern (65 bp):
AGTTGCGAATTCGAGAATCGGACATACCCAAAACTGCCTTCAGAACGAGATATCGTCACTACGAG
Found at i:19917337 original size:39 final size:40
Alignment explanation
Indices: 19917242--19917464 Score: 273
Period size: 39 Copynumber: 5.7 Consensus size: 40
19917232 TTGAATGATG
*
19917242 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
19917280 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
19917321 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
19917360 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
19917399 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
19917438 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
19917465 AACGAGGAGC
Statistics
Matches: 166, Mismatches: 10, Indels: 15
0.87 0.05 0.08
Matches are distributed among these distances:
39 93 0.56
40 61 0.37
41 11 0.07
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:19917428 original size:79 final size:81
Alignment explanation
Indices: 19917242--19917464 Score: 282
Period size: 79 Copynumber: 2.8 Consensus size: 81
19917232 TTGAATGATG
* * *
19917242 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATATCCGGACTAAGATCCGAAGGCA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATATCCGGGCTAAGACCCGAAGGCA
*
19917303 TTTGTGCGAGATACTAAT
64 TTTGTGCGAGATACTAAA
19917321 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT-TCCGGGCTAAG-CCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATATCCGGGCTAAGACCCGAAGGCATT
*
19917383 TGTGCGAGTTACTAAA
66 TGTGCGAGATACTAAA
* * * * *
19917399 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATATCCGGGCTAAGACCCGAAGGCATT
19917463 TG
66 TG
19917465 AACGAGGAGC
Statistics
Matches: 128, Mismatches: 9, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
78 46 0.36
79 56 0.44
80 25 0.20
81 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATATCCGGGCTAAGACCCGAAGGCATT
TGTGCGAGATACTAAA
Found at i:19917486 original size:79 final size:79
Alignment explanation
Indices: 19917242--19917497 Score: 224
Period size: 79 Copynumber: 3.3 Consensus size: 79
19917232 TTGAATGATG
* * * *
19917242 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATATCCGGACTAAGATCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA-CCGGGCTAAG-CCCGAAGGCA
** *
19917303 TTTGTGCGAGAT-ACTAAT
62 TTTGAACGAG-TGACTAAA
* *
19917321 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
** *
19917385 TGCGAGTTACTAAA
66 AACGAGTGACTAAA
* *
19917399 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATT
*
19917463 TGAACGAG-GAGCTATA
64 TGAACGAGTGA-CTAAA
* *
19917479 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
19917498 TACGTGATTT
Statistics
Matches: 153, Mismatches: 15, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
77 1 0.01
78 45 0.29
79 70 0.46
80 36 0.24
81 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
AACGAGTGACTAAA
Found at i:19922499 original size:19 final size:19
Alignment explanation
Indices: 19922475--19922515 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
19922465 TTATATCAAT
19922475 ATTCCTACCAATAATGTGA
1 ATTCCTACCAATAATGTGA
19922494 ATTCCTACCAATAATGTGA
1 ATTCCTACCAATAATGTGA
19922513 ATT
1 ATT
19922516 TTATTGAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.34
Consensus pattern (19 bp):
ATTCCTACCAATAATGTGA
Found at i:19927075 original size:27 final size:27
Alignment explanation
Indices: 19926996--19927065 Score: 140
Period size: 27 Copynumber: 2.6 Consensus size: 27
19926986 CAGTTCACAA
19926996 AAACCAACTGGCGAACCTTAGCTCACC
1 AAACCAACTGGCGAACCTTAGCTCACC
19927023 AAACCAACTGGCGAACCTTAGCTCACC
1 AAACCAACTGGCGAACCTTAGCTCACC
19927050 AAACCAACTGGCGAAC
1 AAACCAACTGGCGAAC
19927066 TCCAGCTCAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.36, C:0.36, G:0.16, T:0.13
Consensus pattern (27 bp):
AAACCAACTGGCGAACCTTAGCTCACC
Found at i:19929937 original size:49 final size:49
Alignment explanation
Indices: 19929716--19930907 Score: 2210
Period size: 49 Copynumber: 24.6 Consensus size: 49
19929706 CCCTTCGGGA
* * * * *
19929716 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
19929763 CCTGTCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
19929810 CTCATCAC--ATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19929857 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19929904 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19929953 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19930002 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19930051 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19930100 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19930149 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19930198 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19930247 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19930296 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19930345 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19930394 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19930443 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19930492 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19930541 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19930590 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19930639 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19930688 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19930737 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
19930786 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19930835 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19930882 CTTATCACATATATATACA--TTCACAT
1 CTTATCACATATATATACACTTTCACAT
19930908 CACAATTATC
Statistics
Matches: 1124, Mismatches: 15, Indels: 12
0.98 0.01 0.01
Matches are distributed among these distances:
46 1 0.00
47 186 0.17
49 937 0.83
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:19934359 original size:64 final size:64
Alignment explanation
Indices: 19934258--19934390 Score: 241
Period size: 64 Copynumber: 2.1 Consensus size: 64
19934248 AGCTCCTAAG
*
19934258 TTTTCAAGGAGGCTTTTAGTTTGAATCCCCTTACTCCCATATTTTTATTAAATTTTTGCACACT
1 TTTTCAAGGAGGCTTTTAGTTTGAATCCCCTTACTCCCATATTTTTATTAAATTTCTGCACACT
19934322 TTTTCAAGGAGG-TCTTTAGTTTGAATCCCCTTACTCCCATATTTTTATTAAATTTCTGCACACT
1 TTTTCAAGGAGGCT-TTTAGTTTGAATCCCCTTACTCCCATATTTTTATTAAATTTCTGCACACT
19934386 TTTTC
1 TTTTC
19934391 TACATTAACT
Statistics
Matches: 67, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
63 1 0.01
64 66 0.99
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.46
Consensus pattern (64 bp):
TTTTCAAGGAGGCTTTTAGTTTGAATCCCCTTACTCCCATATTTTTATTAAATTTCTGCACACT
Found at i:19936939 original size:19 final size:19
Alignment explanation
Indices: 19936915--19936953 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
19936905 AACTTAGACC
*
19936915 ATTAGAAAAATGTTTTCAA
1 ATTAGAAAAATGGTTTCAA
19936934 ATTAGAAAAATGGTTTCAA
1 ATTAGAAAAATGGTTTCAA
19936953 A
1 A
19936954 AAACTTCATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.49, C:0.05, G:0.13, T:0.33
Consensus pattern (19 bp):
ATTAGAAAAATGGTTTCAA
Found at i:19940880 original size:40 final size:40
Alignment explanation
Indices: 19940822--19941050 Score: 343
Period size: 40 Copynumber: 5.7 Consensus size: 40
19940812 AGCATTTGAA
*
19940822 TGATATATTCGGGCTAAGACCCGAAGGCATTTGTGCGAAT
1 TGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAAT
* *
19940862 TGATATATCCGGGATAAGACCCGAAGGCATTTGTGCGAAC
1 TGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAAT
* *
19940902 TGATATATCCGGGCTAAGACCCGATGGCGTTTGTGCGAAT
1 TGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAAT
*
19940942 TGATATATCCGGGCTAAGACCCGAAGGCAATTGTGC-AAGT
1 TGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAA-T
* *
19940982 TGATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGT
1 TGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAAT
* * *
19941022 TGCTATACCCGGGTTAAGACCCGAAGGCA
1 TGATATATCCGGGCTAAGACCCGAAGGCA
19941051 ATTGAGCTTG
Statistics
Matches: 171, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
39 2 0.01
40 168 0.98
41 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (40 bp):
TGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAAT
Found at i:19946403 original size:93 final size:93
Alignment explanation
Indices: 19946291--19946461 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
19946281 GCCCCTAAGT
*
19946291 GAACTCGGACTCAACTCAACAAGCTC-GAGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACAAGCTCGGA-CATTCGCATCCATAAGTGAACTCGGACTCAACTCA
19946355 ACGAGTTCGGATGCCTAGTTACATCTCAC
65 ACGAGTTCGGATGCCTAGTTACATCTCAC
* * *
19946384 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAGGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
19946449 CGAGTTCGGATGC
66 CGAGTTCGGATGC
19946462 TCAACCATCC
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
93 71 0.97
94 2 0.03
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:19946457 original size:46 final size:46
Alignment explanation
Indices: 19946288--19946458 Score: 192
Period size: 46 Copynumber: 3.7 Consensus size: 46
19946278 CCCGCCCCTA
* * *
19946288 AGTGAACTCGGACTCAACTCAACAAGCTC-GAGCGTTCGCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTCGCATCCAT
*
19946333 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-T
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGA-G-C-A-TTCGCATCCAT
*
19946381 CA-CGAACTCGGACTCAACTCAACGAGTTCGGA-CATTCGCATCCAT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTCGCATCCAT
19946426 AGGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 A-GTGAACTCGGACTCAACTCAACGAGTTCGGA
19946459 TGCTCAACCA
Statistics
Matches: 107, Mismatches: 8, Indels: 20
0.79 0.06 0.15
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 3 0.03
45 1 0.01
46 56 0.52
47 31 0.29
48 3 0.03
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTCGCATCCAT
Found at i:19946919 original size:30 final size:30
Alignment explanation
Indices: 19946885--19946944 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
19946875 ATTTAATACG
19946885 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
19946915 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
19946945 GGCTCGAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:19950114 original size:48 final size:48
Alignment explanation
Indices: 19950050--19950157 Score: 182
Period size: 48 Copynumber: 2.2 Consensus size: 48
19950040 ATACTCAGGA
*
19950050 ATCTCGCACACTAAGTGCGAATATCATAGCCCGAAGCCAACTCAATGT
1 ATCTCGCACACTAAGTGCCAATATCATAGCCCGAAGCCAACTCAATGT
*
19950098 ATCTCGCAC-CTGAAGTGCCAATATCATGGCCCGAAGCCAACTCAATGT
1 ATCTCGCACACT-AAGTGCCAATATCATAGCCCGAAGCCAACTCAATGT
19950146 ATCTCGCACACT
1 ATCTCGCACACT
19950158 CAATGTATCT
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
47 2 0.04
48 52 0.93
49 2 0.04
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.21
Consensus pattern (48 bp):
ATCTCGCACACTAAGTGCCAATATCATAGCCCGAAGCCAACTCAATGT
Found at i:19950160 original size:18 final size:18
Alignment explanation
Indices: 19950137--19950172 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
19950127 CCCGAAGCCA
19950137 ACTCAATGTATCTCGCAC
1 ACTCAATGTATCTCGCAC
*
19950155 ACTCAATGTATCTTGCAC
1 ACTCAATGTATCTCGCAC
19950173 CCAAAGTGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.31, G:0.11, T:0.31
Consensus pattern (18 bp):
ACTCAATGTATCTCGCAC
Found at i:19950195 original size:66 final size:66
Alignment explanation
Indices: 19950089--19950220 Score: 210
Period size: 66 Copynumber: 2.0 Consensus size: 66
19950079 CCCGAAGCCA
** * *
19950089 ACTCAATGTATCTCGCACCTGAAGTGCCAATATCATGGCCCGAAGCCAACTCAATGTATCTCGCA
1 ACTCAATGTATCTCGCACCCAAAGTGCCAATATCATGGCCCAAAGCCAACTCAAGGTATCTCGCA
19950154 C
66 C
* *
19950155 ACTCAATGTATCTTGCACCCAAAGTGCCAATATCATGGCCCAAAGCCAACTCAAGGTATCTTGCA
1 ACTCAATGTATCTCGCACCCAAAGTGCCAATATCATGGCCCAAAGCCAACTCAAGGTATCTCGCA
19950220 C
66 C
19950221 CCGAACTGTC
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.30, C:0.31, G:0.16, T:0.23
Consensus pattern (66 bp):
ACTCAATGTATCTCGCACCCAAAGTGCCAATATCATGGCCCAAAGCCAACTCAAGGTATCTCGCA
C
Found at i:19950214 original size:48 final size:48
Alignment explanation
Indices: 19950155--19950262 Score: 153
Period size: 48 Copynumber: 2.2 Consensus size: 48
19950145 TATCTCGCAC
*
19950155 ACTCAATGTATCTTGCACCCAAAGTGCCAATATCATGGCCCAAAGCCA
1 ACTCAATGTATCTTGCACCCAAACTGCCAATATCATGGCCCAAAGCCA
* * * * * *
19950203 ACTCAAGGTATCTTGCACCCGAACTGTCAATATTATGGCTCGAAGCCA
1 ACTCAATGTATCTTGCACCCAAACTGCCAATATCATGGCCCAAAGCCA
19950251 ACTCAATGTATC
1 ACTCAATGTATC
19950263 CCCTAATGAG
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (48 bp):
ACTCAATGTATCTTGCACCCAAACTGCCAATATCATGGCCCAAAGCCA
Found at i:19953917 original size:19 final size:19
Alignment explanation
Indices: 19953890--19953941 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
19953880 AATAAATTAC
19953890 TCATCTTAGTTAATTGAGT
1 TCATCTTAGTTAATTGAGT
* *
19953909 TCATTTTAGTTAATTGATT
1 TCATCTTAGTTAATTGAGT
19953928 TCATCTTAGTTAAT
1 TCATCTTAGTTAAT
19953942 AACTCATCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.27, C:0.10, G:0.12, T:0.52
Consensus pattern (19 bp):
TCATCTTAGTTAATTGAGT
Found at i:19953950 original size:17 final size:18
Alignment explanation
Indices: 19953928--19953961 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
19953918 TTAATTGATT
19953928 TCATCTTAG-TTAATAAC
1 TCATCTTAGATTAATAAC
19953945 TCATCTTAGATTAATAA
1 TCATCTTAGATTAATAA
19953962 ATGAGTTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41
Consensus pattern (18 bp):
TCATCTTAGATTAATAAC
Found at i:19958549 original size:19 final size:19
Alignment explanation
Indices: 19958520--19958571 Score: 88
Period size: 19 Copynumber: 2.7 Consensus size: 19
19958510 AATAAATTAG
19958520 TCATCTTAGTTAATTGAGT
1 TCATCTTAGTTAATTGAGT
19958539 TCAAT-TTAGTTAATTGAGT
1 TC-ATCTTAGTTAATTGAGT
19958558 TCATCTTAGTTAAT
1 TCATCTTAGTTAAT
19958572 AACTCATCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
18 2 0.06
19 27 0.87
20 2 0.06
ACGTcount: A:0.29, C:0.10, G:0.13, T:0.48
Consensus pattern (19 bp):
TCATCTTAGTTAATTGAGT
Found at i:19958580 original size:17 final size:18
Alignment explanation
Indices: 19958558--19958591 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
19958548 TTAATTGAGT
19958558 TCATCTTAG-TTAATAAC
1 TCATCTTAGATTAATAAC
19958575 TCATCTTAGATTAATAA
1 TCATCTTAGATTAATAA
19958592 ATGAGTTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41
Consensus pattern (18 bp):
TCATCTTAGATTAATAAC
Found at i:19958841 original size:10 final size:10
Alignment explanation
Indices: 19958817--19958854 Score: 67
Period size: 10 Copynumber: 3.7 Consensus size: 10
19958807 ATGTGTTTGA
19958817 GTTTAATTAGT
1 GTTTAATT-GT
19958828 GTTTAATTGT
1 GTTTAATTGT
19958838 GTTTAATTGT
1 GTTTAATTGT
19958848 GTTTAAT
1 GTTTAAT
19958855 AAGTTCATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 19 0.70
11 8 0.30
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (10 bp):
GTTTAATTGT
Found at i:19962528 original size:152 final size:152
Alignment explanation
Indices: 19962252--19962563 Score: 597
Period size: 152 Copynumber: 2.1 Consensus size: 152
19962242 ATTGGGTCGT
19962252 GTGGGCCCTATGGGCATGTGGGCCCTACGCGGGTGAACTACAGGGGTGTGTGAAATTTATTCCGC
1 GTGGGCCCTATGGGCATGTGGGCCCTACGCGGGTGAACTACAGGGGTGTGTGAAATTTATTCCGC
19962317 CAGGCTGTATAATCCACATGGCCAAGGTTATTTTAGACCGTATGGGCAACGGGGCGTGTGGGCCC
66 CAGGCTGTATAATCCACATGGCCAAGGTTATTTTAGACCGTATGGGCAACGGGGCGTGTGGGCCC
19962382 ACGTAGGCCAACAATATAGGTC
131 ACGTAGGCCAACAATATAGGTC
*
19962404 GTGGGCCCTATGGGCATGTGGGCCCTACGCGGGTGAACTACAGGGGTGTGTGAAATTTATTGCGC
1 GTGGGCCCTATGGGCATGTGGGCCCTACGCGGGTGAACTACAGGGGTGTGTGAAATTTATTCCGC
*
19962469 CAGGCTGTATAATCCACATGGCCAAGGTTATTTTAGACCGTGTGGGCAACGGGGCGTGTGGGCCC
66 CAGGCTGTATAATCCACATGGCCAAGGTTATTTTAGACCGTATGGGCAACGGGGCGTGTGGGCCC
19962534 ACGTAGGCCAACAATATAGGTC
131 ACGTAGGCCAACAATATAGGTC
*
19962556 GTGCGCCC
1 GTGGGCCC
19962564 ATTTTTACTA
Statistics
Matches: 157, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
152 157 1.00
ACGTcount: A:0.21, C:0.23, G:0.34, T:0.23
Consensus pattern (152 bp):
GTGGGCCCTATGGGCATGTGGGCCCTACGCGGGTGAACTACAGGGGTGTGTGAAATTTATTCCGC
CAGGCTGTATAATCCACATGGCCAAGGTTATTTTAGACCGTATGGGCAACGGGGCGTGTGGGCCC
ACGTAGGCCAACAATATAGGTC
Found at i:19974196 original size:48 final size:48
Alignment explanation
Indices: 19974123--19974390 Score: 237
Period size: 48 Copynumber: 5.6 Consensus size: 48
19974113 AATAGTAGGG
* * *
19974123 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGGCCACATATCGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCACATATCGA
* *
19974171 TGCCAATGCCATGTTCCAGACATGGTCTTACATAGGATCACACATATCGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-C-CACATATCGA
* * * * *
19974221 AGCCGAT---A-G-CCCAG-CTAAGGTCTTACATGATGTA-CTCATATCGA
1 TGCCAATGCCATGTCCCAGAC-ATGGTCTTACATG--GGACCACATATCGA
* * *
19974265 TGCCAATGCCATGTCCCAGACATGGTCTTATATGGGATCACATAACGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCACATATCGA
* * *
19974313 TTG-CAATGCCATGTCCTAGACATAGTCTTACATGGGACCATATATCGA
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCACATATCGA
* * * **
19974361 TGCCGATGCAATATCCCAGTTATGGTCTTA
1 TGCCAATGCCATGTCCCAGACATGGTCTTA
19974391 TACGGGATCT
Statistics
Matches: 174, Mismatches: 32, Indels: 28
0.74 0.14 0.12
Matches are distributed among these distances:
44 15 0.09
45 15 0.09
46 1 0.01
47 8 0.05
48 100 0.57
49 19 0.11
50 16 0.09
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (48 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCACATATCGA
Found at i:19978419 original size:27 final size:27
Alignment explanation
Indices: 19978351--19978448 Score: 101
Period size: 27 Copynumber: 3.6 Consensus size: 27
19978341 CCTCGAATTA
* *
19978351 TAAAATTACTAAAATAACCC-CGGTTTG
1 TAAAATTACCAAAAT-ACCCTCAGTTTG
* * *
19978378 TAAAATTATCGAAATACCCTCAATTTG
1 TAAAATTACCAAAATACCCTCAGTTTG
* *
19978405 TAAAATTACCAAAATACCCT-TGTAGTG
1 TAAAATTACCAAAATACCCTCAGT-TTG
19978432 TAAAATTACCAAAATAC
1 TAAAATTACCAAAATAC
19978449 TCTTGTATGA
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
26 5 0.08
27 54 0.92
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.30
Consensus pattern (27 bp):
TAAAATTACCAAAATACCCTCAGTTTG
Found at i:19978453 original size:27 final size:27
Alignment explanation
Indices: 19978403--19978455 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
19978393 ACCCTCAATT
19978403 TGTAAAATTACCAAAATACCCTTGTAG
1 TGTAAAATTACCAAAATACCCTTGTAG
*
19978430 TGTAAAATTACCAAAATACTCTTGTA
1 TGTAAAATTACCAAAATACCCTTGTA
19978456 TGACTATGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.32
Consensus pattern (27 bp):
TGTAAAATTACCAAAATACCCTTGTAG
Found at i:19978871 original size:28 final size:27
Alignment explanation
Indices: 19978835--19978899 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 27
19978825 ATTACACTGT
* * *
19978835 ACTGATACTGTATTGGGCTTAGGCTCAC
1 ACTG-TACTGTATAGGGCTAAGGCCCAC
*
19978863 ACTGTTACTGTATAGGGCTAAGGCCCAG
1 ACTG-TACTGTATAGGGCTAAGGCCCAC
19978891 ACTGTACTG
1 ACTGTACTG
19978900 ATACTTATAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 5 0.16
28 27 0.84
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (27 bp):
ACTGTACTGTATAGGGCTAAGGCCCAC
Found at i:19978913 original size:32 final size:33
Alignment explanation
Indices: 19978863--19978927 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
19978853 TTAGGCTCAC
* * *
19978863 ACTGTTACTGTATAGGGCTAAGGCCCAGACTGT
1 ACTGATACTGTATAGGGCTAAAGCCCAAACTGT
19978896 ACTGATACT-TATAGGGCTAAAGCCCAAACTGT
1 ACTGATACTGTATAGGGCTAAAGCCCAAACTGT
19978928 TTTGCATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 21 0.72
33 8 0.28
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (33 bp):
ACTGATACTGTATAGGGCTAAAGCCCAAACTGT
Found at i:19980659 original size:6 final size:6
Alignment explanation
Indices: 19980629--19980815 Score: 143
Period size: 6 Copynumber: 30.3 Consensus size: 6
19980619 AAGAAACATT
* *
19980629 ATCAGA A-CTAGA ATCAAA ATAAGA ATCAGA ATCAGA ATCAGA ATCAG-
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA
* * * * *
19980676 GTGACAGA ATCAAA ATTAGA ATCAGA ATCAAA ATTAGGTA A-CAGA ATCAGA
1 AT--CAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA
* *
19980727 ATCAGT ATCAGGTA AT-AGA ATCAGA ATCAGA ATCAGA ATTAGGTA A-CAGA
1 ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA
*
19980777 ATCAGA ATCAGT ATCAGGTA A-CAGA ATCAGA ATCAGA AT
1 ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA AT
19980816 GTGAATGCAA
Statistics
Matches: 144, Mismatches: 20, Indels: 34
0.73 0.10 0.17
Matches are distributed among these distances:
5 11 0.08
6 113 0.78
7 12 0.08
8 8 0.06
ACGTcount: A:0.49, C:0.13, G:0.18, T:0.20
Consensus pattern (6 bp):
ATCAGA
Found at i:19980697 original size:31 final size:31
Alignment explanation
Indices: 19980650--19980815 Score: 170
Period size: 31 Copynumber: 5.5 Consensus size: 31
19980640 AATCAAAATA
*
19980650 AGAATCAGAATCAGAATCAGAATCAGGTGAC
1 AGAATCAGAATCAGAATCAGAATCAGGTAAC
* * * *
19980681 AGAATCAAAATTAGAATCAGAATCA--AAATT
1 AGAATCAGAATCAGAATCAGAATCAGGTAA-C
* *
19980711 AGGTAA-CAGAATCAGAATCAGTATCAGGTAAT
1 A-G-AATCAGAATCAGAATCAGAATCAGGTAAC
*
19980743 AGAATCAGAATCAGAATCAGAATTAGGTAAC
1 AGAATCAGAATCAGAATCAGAATCAGGTAAC
19980774 AGAATCAGAATCAG--T----ATCAGGTAAC
1 AGAATCAGAATCAGAATCAGAATCAGGTAAC
19980799 AGAATCAGAATCAGAAT
1 AGAATCAGAATCAGAAT
19980816 GTGAATGCAA
Statistics
Matches: 114, Mismatches: 13, Indels: 20
0.78 0.09 0.14
Matches are distributed among these distances:
25 23 0.20
27 1 0.01
29 2 0.02
30 3 0.03
31 79 0.69
32 4 0.04
33 2 0.02
ACGTcount: A:0.48, C:0.13, G:0.19, T:0.20
Consensus pattern (31 bp):
AGAATCAGAATCAGAATCAGAATCAGGTAAC
Found at i:19980721 original size:25 final size:25
Alignment explanation
Indices: 19980693--19980815 Score: 147
Period size: 25 Copynumber: 4.7 Consensus size: 25
19980683 AATCAAAATT
* *
19980693 AGAATCAGAATCAAAATTAGGTAAC
1 AGAATCAGAATCAGAATCAGGTAAC
*
19980718 AGAATCAGAATCAGTATCAGGTAATAGAATC
1 AGAATCAGAATCAGAATCAGG---T--AA-C
*
19980749 AGAATCAGAATCAGAATTAGGTAAC
1 AGAATCAGAATCAGAATCAGGTAAC
*
19980774 AGAATCAGAATCAGTATCAGGTAAC
1 AGAATCAGAATCAGAATCAGGTAAC
19980799 AGAATCAGAATCAGAAT
1 AGAATCAGAATCAGAAT
19980816 GTGAATGCAA
Statistics
Matches: 84, Mismatches: 8, Indels: 12
0.81 0.08 0.12
Matches are distributed among these distances:
25 58 0.69
26 2 0.02
28 2 0.02
30 2 0.02
31 20 0.24
ACGTcount: A:0.48, C:0.13, G:0.19, T:0.20
Consensus pattern (25 bp):
AGAATCAGAATCAGAATCAGGTAAC
Found at i:19980730 original size:43 final size:42
Alignment explanation
Indices: 19980629--19980709 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 42
19980619 AAGAAACATT
*
19980629 ATCAGA-ACTAGAATCAAAATAAGAATCAGAATCAGAATCAGA
1 ATCAGATAC-AGAATCAAAATAAGAATCAGAATCAAAATCAGA
* *
19980671 ATCAGGTGACAGAATCAAAATTAGAATCAGAATCAAAAT
1 ATCAGAT-ACAGAATCAAAATAAGAATCAGAATCAAAAT
19980710 TAGGTAACAG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
42 5 0.15
43 27 0.79
44 2 0.06
ACGTcount: A:0.53, C:0.14, G:0.15, T:0.19
Consensus pattern (42 bp):
ATCAGATACAGAATCAAAATAAGAATCAGAATCAAAATCAGA
Found at i:19981261 original size:27 final size:27
Alignment explanation
Indices: 19981231--19981445 Score: 222
Period size: 27 Copynumber: 8.0 Consensus size: 27
19981221 GGGGTAAAAT
* *
19981231 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTTTACCCTACAAGGGTATTTC
* *
19981258 GGTAATTCTACCTTAC-AGGAGTATTTC
1 GGTAATTTTACCCTACAAGG-GTATTTC
* * *
19981285 AGTAATTTTATCCTACAGGGGTATTTC
1 GGTAATTTTACCCTACAAGGGTATTTC
*
19981312 GGT-ATTTCTACCCTATAAGGGTATTTC
1 GGTAATTT-TACCCTACAAGGGTATTTC
* * *
19981339 GGTAATTCTACCCTACAGGGGTATTTT
1 GGTAATTTTACCCTACAAGGGTATTTC
* * *
19981366 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTTTACCCTACAAGGGTATTTC
* *
19981393 AGT-ATTTCTACCCTACAGGGGTATTTC
1 GGTAATTT-TACCCTACAAGGGTATTTC
19981420 GGT-ATTTCTACCCTACAAGGGTATTT
1 GGTAATTT-TACCCTACAAGGGTATTT
19981446 TGACATTTCT
Statistics
Matches: 161, Mismatches: 22, Indels: 10
0.83 0.11 0.05
Matches are distributed among these distances:
26 10 0.06
27 146 0.91
28 5 0.03
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (27 bp):
GGTAATTTTACCCTACAAGGGTATTTC
Found at i:19981294 original size:54 final size:53
Alignment explanation
Indices: 19981232--19981445 Score: 268
Period size: 54 Copynumber: 4.0 Consensus size: 53
19981222 GGGTAAAATG
* * * *
19981232 GTAATTTTACCCCACAAGGGTATCTCGGTAATTCTACCTTACAGGAGTATTTCA
1 GTAATTTTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGG-GTATTTCA
* * * *
19981286 GTAATTTTATCCTACAGGGGTATTTCGGTATTTCTACCCTATAAGGGTATTTCG
1 GTAATTTTACCCTACAGGGGTATTTCGGTAATTCTACCCTA-CAGGGTATTTCA
* **
19981340 GTAATTCTACCCTACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCA
1 GTAATTTTACCCTACAGGGGTATTTCGGTAATTCTACCCTACA-GGGTATTTCA
*
19981394 GT-ATTTCTACCCTACAGGGGTATTTCGGTATTTCTACCCTACAAGGGTATTT
1 GTAATTT-TACCCTACAGGGGTATTTCGGTAATTCTACCCTAC-AGGGTATTT
19981446 TGACATTTCT
Statistics
Matches: 137, Mismatches: 19, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
53 4 0.03
54 129 0.94
55 4 0.03
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (53 bp):
GTAATTTTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGTATTTCA
Found at i:19981446 original size:81 final size:81
Alignment explanation
Indices: 19981235--19981446 Score: 302
Period size: 81 Copynumber: 2.6 Consensus size: 81
19981225 TAAAATGGTA
* * * * * *
19981235 ATTT-TACCCCACAAGGGTATCTCGGTAATTCTACCTTAC-AGGAGTATTTCAGTAATTTTATCC
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAAGG-GTATTTTAGTAATTCTACCC
*
19981298 TACAGGGGTATTTCGGT
65 TACAGGGGTATTTCAGT
* *
19981315 ATTTCTACCCTATAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTTAGTAATTCTACCCT
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTTAGTAATTCTACCCT
19981380 ACAGGGGTATTTCAGT
66 ACAGGGGTATTTCAGT
* *
19981396 ATTTCTACCCTACAGGGGTATTTCGGTATTTCTACCCTACAAGGGTATTTT
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTT
19981447 GACATTTCTA
Statistics
Matches: 117, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
80 4 0.03
81 111 0.95
82 2 0.02
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.37
Consensus pattern (81 bp):
ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTTAGTAATTCTACCCT
ACAGGGGTATTTCAGT
Found at i:19981453 original size:27 final size:27
Alignment explanation
Indices: 19981235--19981473 Score: 209
Period size: 27 Copynumber: 8.9 Consensus size: 27
19981225 TAAAATGGTA
* * * *
19981235 ATTT-TACCCCACAAGGGTATCTCGGT
1 ATTTCTACCCTACAGGGGTATTTCGAT
* * *
19981261 AATTCTACCTTACAGGAGTATTTC-AGT
1 ATTTCTACCCTACAGGGGTATTTCGA-T
* *
19981288 AATTT-TATCCTACAGGGGTATTTCGGT
1 -ATTTCTACCCTACAGGGGTATTTCGAT
* * *
19981315 ATTTCTACCCTATAAGGGTATTTCGGT
1 ATTTCTACCCTACAGGGGTATTTCGAT
* *
19981342 AATTCTACCCTACAGGGGTATTT-TAGT
1 ATTTCTACCCTACAGGGGTATTTCGA-T
*
19981369 AATTCTACCCTACAGGGGTATTTC-AGT
1 ATTTCTACCCTACAGGGGTATTTCGA-T
*
19981396 ATTTCTACCCTACAGGGGTATTTCGGT
1 ATTTCTACCCTACAGGGGTATTTCGAT
* * *
19981423 ATTTCTACCCTACAAGGGTATTTTGAC
1 ATTTCTACCCTACAGGGGTATTTCGAT
** *
19981450 ATTTCTACTGTACAAGGGTATTTC
1 ATTTCTACCCTACAGGGGTATTTC
19981474 AATAATTTTG
Statistics
Matches: 176, Mismatches: 29, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
26 7 0.04
27 166 0.94
28 3 0.02
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.37
Consensus pattern (27 bp):
ATTTCTACCCTACAGGGGTATTTCGAT
Found at i:19981456 original size:81 final size:81
Alignment explanation
Indices: 19981235--19981474 Score: 292
Period size: 81 Copynumber: 3.0 Consensus size: 81
19981225 TAAAATGGTA
* * * * *
19981235 ATTT-TACCCCACAAGGGTATCTCGGTAATTCTACCTTAC-AGGAGTATTTCAGTAATTT-TATC
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAAGG-GTATTT-TGTAATTTCTACC
*
19981297 CTACAGGGGTATTTCGGT
64 CTACAGGGGTATTTCAGT
* *
19981315 ATTTCTACCCTATAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTTAGTAA-TTCTACCC
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTT-GTAATTTCTACCC
19981379 TACAGGGGTATTTCAGT
65 TACAGGGGTATTTCAGT
* * **
19981396 ATTTCTACCCTACAGGGGTATTTCGGTATTTCTACCCTACAAGGGTATTTTG-ACATTTCTACTG
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTTGTA-ATTTCTACCC
*
19981460 TACAAGGGTATTTCA
65 TACAGGGGTATTTCA
19981475 ATAATTTTGT
Statistics
Matches: 139, Mismatches: 15, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
79 1 0.01
80 8 0.06
81 128 0.92
82 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (81 bp):
ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTTGTAATTTCTACCCT
ACAGGGGTATTTCAGT
Found at i:19981549 original size:27 final size:26
Alignment explanation
Indices: 19981519--19981695 Score: 131
Period size: 27 Copynumber: 6.5 Consensus size: 26
19981509 TATAAATCAG
*
19981519 GGGTACTTTGGTAATTTTACAAGTCGA
1 GGGTATTTTGGTAATTTTACAA-TCGA
*** *
19981546 GGGTATTTCAATAATTTTACAGTTCGA
1 GGGTATTTTGGTAATTTTACA-ATCGA
* ** *
19981573 GGGCATTTCAGTAATTTCACAAATC-A
1 GGGTATTTTGGTAATTTTAC-AATCGA
* *
19981599 GGGGTATTTTGGTAATTTTACAAACTA
1 -GGGTATTTTGGTAATTTTACAATCGA
* * *
19981626 GGAGTATTTTGATAATTTTACAAACCA
1 GG-GTATTTTGGTAATTTTACAATCGA
* *
19981653 GGGGTATTTTGGTAATTTTACAAACTA
1 -GGGTATTTTGGTAATTTTACAATCGA
19981680 GGGGTATTTTTGGTAA
1 -GGGTA-TTTTGGTAA
19981696 GTGATGAGAA
Statistics
Matches: 125, Mismatches: 18, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
26 6 0.05
27 107 0.86
28 12 0.10
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.38
Consensus pattern (26 bp):
GGGTATTTTGGTAATTTTACAATCGA
Found at i:19981572 original size:81 final size:80
Alignment explanation
Indices: 19981464--19981648 Score: 203
Period size: 81 Copynumber: 2.3 Consensus size: 80
19981454 CTACTGTACA
** * *
19981464 AGGGTATTTCAATAATTTTGTAATTCGAGGGTAAAAT-GGTAA-TTCTATAAATCAGGGGTACTT
1 AGGGTATTTCAATAATTTTACAATTCGAGGG-AAAATCAGTAATTTC-ACAAATCAGGGGTACTT
*
19981527 TGGTAATTTTACAAGTCG
64 TGGTAATTTTACAA-ACG
* * ** *
19981545 AGGGTATTTCAATAATTTTACAGTTCGAGGGCATTTCAGTAATTTCACAAATCAGGGGTATTTTG
1 AGGGTATTTCAATAATTTTACAATTCGAGGGAAAATCAGTAATTTCACAAATCAGGGGTACTTTG
*
19981610 GTAATTTTACAAACT
66 GTAATTTTACAAACG
**
19981625 AGGAGTATTTTGATAATTTTACAA
1 AGG-GTATTTCAATAATTTTACAA
19981649 ACCAGGGGTA
Statistics
Matches: 87, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
80 6 0.07
81 78 0.90
82 3 0.03
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (80 bp):
AGGGTATTTCAATAATTTTACAATTCGAGGGAAAATCAGTAATTTCACAAATCAGGGGTACTTTG
GTAATTTTACAAACG
Found at i:19981615 original size:54 final size:54
Alignment explanation
Indices: 19981570--19981677 Score: 148
Period size: 54 Copynumber: 2.0 Consensus size: 54
19981560 TTTTACAGTT
*
19981570 CGAGG-GCATTTCAG-TAATTTCACAAATCAGGGGTATTTTGGTAATTTTACAAA
1 CGAGGAGCATTT-AGATAATTTCACAAACCAGGGGTATTTTGGTAATTTTACAAA
* * * *
19981623 CTAGGAGTATTTTGATAATTTTACAAACCAGGGGTATTTTGGTAATTTTACAAA
1 CGAGGAGCATTTAGATAATTTCACAAACCAGGGGTATTTTGGTAATTTTACAAA
19981677 C
1 C
19981678 TAGGGGTATT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
53 5 0.10
54 43 0.90
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.36
Consensus pattern (54 bp):
CGAGGAGCATTTAGATAATTTCACAAACCAGGGGTATTTTGGTAATTTTACAAA
Found at i:19981668 original size:81 final size:81
Alignment explanation
Indices: 19981512--19981695 Score: 203
Period size: 81 Copynumber: 2.3 Consensus size: 81
19981502 GTAATTCTAT
* * ***
19981512 AAATCAGGGGTACTTTGGTAATTTTACAAGTCGAGGGTATTTCAATAATTTTACAGTTCGAGGGC
1 AAATCAGGGGTATTTTGGTAATTTTACAAGACGAGGGTATTTCAATAATTTTACAAACCGAGGGC
19981577 ATTTCAGTAATTTCAC
66 ATTTCAGTAATTTCAC
* **
19981593 AAATCAGGGGTATTTTGGTAATTTTACAA-ACTAGGAGTATTTTGATAATTTTACAAACC-AGGG
1 AAATCAGGGGTATTTTGGTAATTTTACAAGACGAGG-GTATTTCAATAATTTTACAAACCGA-GG
* ** *
19981656 GTATTTTGGTAATTTTAC
64 GCATTTCAGTAATTTCAC
19981674 AAA-CTAGGGGTATTTTTGGTAA
1 AAATC-AGGGGTA-TTTTGGTAA
19981696 GTGATGAGAA
Statistics
Matches: 87, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
80 6 0.07
81 72 0.83
82 9 0.10
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (81 bp):
AAATCAGGGGTATTTTGGTAATTTTACAAGACGAGGGTATTTCAATAATTTTACAAACCGAGGGC
ATTTCAGTAATTTCAC
Found at i:19981678 original size:54 final size:54
Alignment explanation
Indices: 19981584--19981689 Score: 185
Period size: 54 Copynumber: 2.0 Consensus size: 54
19981574 GGCATTTCAG
*
19981584 TAATTTCACAAATCAGGGGTATTTTGGTAATTTTACAAACTAGGAGTATTTTGA
1 TAATTTCACAAACCAGGGGTATTTTGGTAATTTTACAAACTAGGAGTATTTTGA
* *
19981638 TAATTTTACAAACCAGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTT
1 TAATTTCACAAACCAGGGGTATTTTGGTAATTTTACAAACTAGGAGTATTTT
19981690 TGGTAAGTGA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (54 bp):
TAATTTCACAAACCAGGGGTATTTTGGTAATTTTACAAACTAGGAGTATTTTGA
Found at i:19985814 original size:27 final size:27
Alignment explanation
Indices: 19985746--19985843 Score: 101
Period size: 27 Copynumber: 3.6 Consensus size: 27
19985736 CCTCGAATTA
* *
19985746 TAAAATTACTAAAATAACCC-CGGTTTG
1 TAAAATTACCAAAAT-ACCCTCAGTTTG
* * *
19985773 TAAAATTATCGAAATACCCTCAATTTG
1 TAAAATTACCAAAATACCCTCAGTTTG
* *
19985800 TAAAATTACCAAAATACCCT-TGTAGTG
1 TAAAATTACCAAAATACCCTCAGT-TTG
19985827 TAAAATTACCAAAATAC
1 TAAAATTACCAAAATAC
19985844 TCTTGTATGA
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
26 5 0.08
27 54 0.92
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.30
Consensus pattern (27 bp):
TAAAATTACCAAAATACCCTCAGTTTG
Found at i:19985848 original size:27 final size:27
Alignment explanation
Indices: 19985798--19985850 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
19985788 ACCCTCAATT
19985798 TGTAAAATTACCAAAATACCCTTGTAG
1 TGTAAAATTACCAAAATACCCTTGTAG
*
19985825 TGTAAAATTACCAAAATACTCTTGTA
1 TGTAAAATTACCAAAATACCCTTGTA
19985851 TGACTATGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.32
Consensus pattern (27 bp):
TGTAAAATTACCAAAATACCCTTGTAG
Found at i:19986266 original size:28 final size:27
Alignment explanation
Indices: 19986230--19986294 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 27
19986220 ATTACACTGT
* * *
19986230 ACTGATACTGTATTGGGCTTAGGCTCAC
1 ACTG-TACTGTATAGGGCTAAGGCCCAC
*
19986258 ACTGTTACTGTATAGGGCTAAGGCCCAG
1 ACTG-TACTGTATAGGGCTAAGGCCCAC
19986286 ACTGTACTG
1 ACTGTACTG
19986295 ATACTTATAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 5 0.16
28 27 0.84
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (27 bp):
ACTGTACTGTATAGGGCTAAGGCCCAC
Found at i:19986308 original size:32 final size:33
Alignment explanation
Indices: 19986258--19986322 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
19986248 TTAGGCTCAC
* * *
19986258 ACTGTTACTGTATAGGGCTAAGGCCCAGACTGT
1 ACTGATACTGTATAGGGCTAAAGCCCAAACTGT
19986291 ACTGATACT-TATAGGGCTAAAGCCCAAACTGT
1 ACTGATACTGTATAGGGCTAAAGCCCAAACTGT
19986323 TTTGCATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 21 0.72
33 8 0.28
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (33 bp):
ACTGATACTGTATAGGGCTAAAGCCCAAACTGT
Found at i:19988039 original size:12 final size:12
Alignment explanation
Indices: 19988024--19988938 Score: 222
Period size: 12 Copynumber: 73.7 Consensus size: 12
19988014 AAGAAACATT
19988024 ATCAGAACT-AGA
1 ATCAGAA-TAAGA
*
19988036 ATCAAAATAAGA
1 ATCAGAATAAGA
*
19988048 ATCAGAATCAGA
1 ATCAGAATAAGA
*
19988060 ATCAGAATCAG-
1 ATCAGAATAAGA
*
19988071 GTGACAGAATCAA-A
1 AT--CAGAAT-AAGA
* *
19988085 ATTAGAATCAGA
1 ATCAGAATAAGA
* *
19988097 ATCAAAATTAGGTA
1 ATCAGAA-TAAG-A
*
19988111 A-CAGAATCAGA
1 ATCAGAATAAGA
* *
19988122 ATCAGTATCAGGTA
1 ATCAGAAT-AAG-A
*
19988136 AT-AGAATCAGA
1 ATCAGAATAAGA
*
19988147 ATCAGAATCAGA
1 ATCAGAATAAGA
* *
19988159 ATTAGGTAA-CAGA
1 ATCA-G-AATAAGA
* *
19988172 ATCAGAATCAGT
1 ATCAGAATAAGA
19988184 ATCAGGTAAT-AGA
1 ATCA-G-AATAAGA
*
19988197 ATCAGAATCAGA
1 ATCAGAATAAGA
*
19988209 ATCAGAATTAGGTA
1 ATCAGAA-TAAG-A
*
19988223 A-CAGAATCAGA
1 ATCAGAATAAGA
* *
19988234 ATCAGTATCAGGTA
1 ATCAGAAT-AAG-A
*
19988248 AT-AGAATCAGA
1 ATCAGAATAAGA
*
19988259 ATCAGAATCAGA
1 ATCAGAATAAGA
* *
19988271 ATTAGGTAA-CAGA
1 ATCA-G-AATAAGA
* *
19988284 ATCAGAATCAGT
1 ATCAGAATAAGA
19988296 ATCAGGTAAT-AGA
1 ATCA-G-AATAAGA
*
19988309 ATCAGAATCAGA
1 ATCAGAATAAGA
*
19988321 ATCAGAATTAGGTA
1 ATCAGAA-TAAG-A
*
19988335 A-CAGAATCAGA
1 ATCAGAATAAGA
* *
19988346 ATCAGTATCAGGTA
1 ATCAGAAT-AAG-A
*
19988360 AT-AGAATCAGA
1 ATCAGAATAAGA
*
19988371 ATCAGAATCAGA
1 ATCAGAATAAGA
* *
19988383 ATTAGGTAA-CAGA
1 ATCA-G-AATAAGA
* *
19988396 ATCAGAATCAGT
1 ATCAGAATAAGA
19988408 ATCAGGTAAT-AGA
1 ATCA-G-AATAAGA
*
19988421 ATCAGAATCAGA
1 ATCAGAATAAGA
*
19988433 ATCAGAATTAGGTA
1 ATCAGAA-TAAG-A
*
19988447 A-CAGAATCAGA
1 ATCAGAATAAGA
* *
19988458 ATCAGTATCAGGTA
1 ATCAGAAT-AAG-A
*
19988472 AT-AGAATCAGA
1 ATCAGAATAAGA
*
19988483 ATCAGAATCAGA
1 ATCAGAATAAGA
* *
19988495 ATTAGGTAA-CAGA
1 ATCA-G-AATAAGA
* *
19988508 ATCAGAATCAGT
1 ATCAGAATAAGA
19988520 ATCAGGTAAT-AGA
1 ATCA-G-AATAAGA
*
19988533 ATCAGAATCAGA
1 ATCAGAATAAGA
*
19988545 ATCAGAATTAGGTA
1 ATCAGAA-TAAG-A
*
19988559 A-CAGAATCAGA
1 ATCAGAATAAGA
* *
19988570 ATCAGTATCAGGTA
1 ATCAGAAT-AAG-A
*
19988584 AT-AGAATCAGA
1 ATCAGAATAAGA
*
19988595 ATCAGAATCAGA
1 ATCAGAATAAGA
* *
19988607 ATTAGGTAA-CAGA
1 ATCA-G-AATAAGA
* *
19988620 ATCAGAATCAGT
1 ATCAGAATAAGA
19988632 ATCAGGTAAT-AGA
1 ATCA-G-AATAAGA
*
19988645 ATCAGAATCAGA
1 ATCAGAATAAGA
*
19988657 ATCAGAATTAGGTA
1 ATCAGAA-TAAG-A
*
19988671 A-CAGAATCAGA
1 ATCAGAATAAGA
* *
19988682 ATCAGTATCAGGTA
1 ATCAGAAT-AAG-A
*
19988696 AT-AGAATCAGA
1 ATCAGAATAAGA
*
19988707 ATCAGAATCAGA
1 ATCAGAATAAGA
* *
19988719 ATTAGGTAA-CAGA
1 ATCA-G-AATAAGA
* *
19988732 ATCAGAATCAGT
1 ATCAGAATAAGA
19988744 ATCAGGTAAT-AGA
1 ATCA-G-AATAAGA
*
19988757 ATCAGAATCAGA
1 ATCAGAATAAGA
*
19988769 ATCAGAATTAGGTA
1 ATCAGAA-TAAG-A
*
19988783 A-CAGAATCAGA
1 ATCAGAATAAGA
* *
19988794 ATCAGTATCAGGTA
1 ATCAGAAT-AAG-A
*
19988808 AT-AGAATCAGA
1 ATCAGAATAAGA
*
19988819 ATCAGAATCAGA
1 ATCAGAATAAGA
* *
19988831 ATTAGGTAA-CAGA
1 ATCA-G-AATAAGA
* *
19988844 ATCAGAATCAGT
1 ATCAGAATAAGA
19988856 ATCAGGTAAT-AGA
1 ATCA-G-AATAAGA
*
19988869 ATCAGAATCAGA
1 ATCAGAATAAGA
*
19988881 ATCAGAATTAGGTA
1 ATCAGAA-TAAG-A
*
19988895 A-CAGAATCAGA
1 ATCAGAATAAGA
* *
19988906 ATCAGTATCAGGTA
1 ATCAGAAT-AAG-A
*
19988920 A-CAGAATCAGA
1 ATCAGAATAAGA
19988931 ATCAGAAT
1 ATCAGAAT
19988939 GTGAATGCAA
Statistics
Matches: 688, Mismatches: 119, Indels: 192
0.69 0.12 0.19
Matches are distributed among these distances:
11 77 0.11
12 328 0.48
13 207 0.30
14 76 0.11
ACGTcount: A:0.47, C:0.13, G:0.19, T:0.21
Consensus pattern (12 bp):
ATCAGAATAAGA
Found at i:19988122 original size:56 final size:56
Alignment explanation
Indices: 19988088--19988938 Score: 1684
Period size: 56 Copynumber: 15.2 Consensus size: 56
19988078 AATCAAAATT
*
19988088 AGAATCAGAATCAAAATTAGGTAACAGAATCAGAATCAGTATCAGGTAATAGAATC
1 AGAATCAGAATCAGAATTAGGTAACAGAATCAGAATCAGTATCAGGTAATAGAATC
19988144 AGAATCAGAATCAGAATTAGGTAACAGAATCAGAATCAGTATCAGGTAATAGAATC
1 AGAATCAGAATCAGAATTAGGTAACAGAATCAGAATCAGTATCAGGTAATAGAATC
19988200 AGAATCAGAATCAGAATTAGGTAACAGAATCAGAATCAGTATCAGGTAATAGAATC
1 AGAATCAGAATCAGAATTAGGTAACAGAATCAGAATCAGTATCAGGTAATAGAATC
19988256 AGAATCAGAATCAGAATTAGGTAACAGAATCAGAATCAGTATCAGGTAATAGAATC
1 AGAATCAGAATCAGAATTAGGTAACAGAATCAGAATCAGTATCAGGTAATAGAATC
19988312 AGAATCAGAATCAGAATTAGGTAACAGAATCAGAATCAGTATCAGGTAATAGAATC
1 AGAATCAGAATCAGAATTAGGTAACAGAATCAGAATCAGTATCAGGTAATAGAATC
19988368 AGAATCAGAATCAGAATTAGGTAACAGAATCAGAATCAGTATCAGGTAATAGAATC
1 AGAATCAGAATCAGAATTAGGTAACAGAATCAGAATCAGTATCAGGTAATAGAATC
19988424 AGAATCAGAATCAGAATTAGGTAACAGAATCAGAATCAGTATCAGGTAATAGAATC
1 AGAATCAGAATCAGAATTAGGTAACAGAATCAGAATCAGTATCAGGTAATAGAATC
19988480 AGAATCAGAATCAGAATTAGGTAACAGAATCAGAATCAGTATCAGGTAATAGAATC
1 AGAATCAGAATCAGAATTAGGTAACAGAATCAGAATCAGTATCAGGTAATAGAATC
19988536 AGAATCAGAATCAGAATTAGGTAACAGAATCAGAATCAGTATCAGGTAATAGAATC
1 AGAATCAGAATCAGAATTAGGTAACAGAATCAGAATCAGTATCAGGTAATAGAATC
19988592 AGAATCAGAATCAGAATTAGGTAACAGAATCAGAATCAGTATCAGGTAATAGAATC
1 AGAATCAGAATCAGAATTAGGTAACAGAATCAGAATCAGTATCAGGTAATAGAATC
19988648 AGAATCAGAATCAGAATTAGGTAACAGAATCAGAATCAGTATCAGGTAATAGAATC
1 AGAATCAGAATCAGAATTAGGTAACAGAATCAGAATCAGTATCAGGTAATAGAATC
19988704 AGAATCAGAATCAGAATTAGGTAACAGAATCAGAATCAGTATCAGGTAATAGAATC
1 AGAATCAGAATCAGAATTAGGTAACAGAATCAGAATCAGTATCAGGTAATAGAATC
19988760 AGAATCAGAATCAGAATTAGGTAACAGAATCAGAATCAGTATCAGGTAATAGAATC
1 AGAATCAGAATCAGAATTAGGTAACAGAATCAGAATCAGTATCAGGTAATAGAATC
19988816 AGAATCAGAATCAGAATTAGGTAACAGAATCAGAATCAGTATCAGGTAATAGAATC
1 AGAATCAGAATCAGAATTAGGTAACAGAATCAGAATCAGTATCAGGTAATAGAATC
*
19988872 AGAATCAGAATCAGAATTAGGTAACAGAATCAGAATCAGTATCAGGTAACAGAATC
1 AGAATCAGAATCAGAATTAGGTAACAGAATCAGAATCAGTATCAGGTAATAGAATC
19988928 AGAATCAGAAT
1 AGAATCAGAAT
19988939 GTGAATGCAA
Statistics
Matches: 793, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 793 1.00
ACGTcount: A:0.47, C:0.13, G:0.20, T:0.21
Consensus pattern (56 bp):
AGAATCAGAATCAGAATTAGGTAACAGAATCAGAATCAGTATCAGGTAATAGAATC
Found at i:19989384 original size:27 final size:27
Alignment explanation
Indices: 19989354--19990432 Score: 1206
Period size: 27 Copynumber: 40.0 Consensus size: 27
19989344 GGGGTAAAAT
* * *
19989354 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTTTACCCTACAGGGGTATTTC
* * *
19989381 GGTAATTCTACCTTACAGGAGTATTTC
1 GGTAATTTTACCCTACAGGGGTATTTC
* *
19989408 AGTAATTTTATCCTACAGGGGTATTTC
1 GGTAATTTTACCCTACAGGGGTATTTC
* *
19989435 GGT-ATTTCTACCCTATAAGGGTATTTC
1 GGTAATTT-TACCCTACAGGGGTATTTC
* *
19989462 GGTAATTCTACCCTACAGGGGTATTTT
1 GGTAATTTTACCCTACAGGGGTATTTC
* *
19989489 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTTTACCCTACAGGGGTATTTC
*
19989516 AGT-ATTTCTACCCTACAGGGGTATTTC
1 GGTAATTT-TACCCTACAGGGGTATTTC
* *
19989543 GGT-ATTTCTACCCTATAAGGGTATTTC
1 GGTAATTT-TACCCTACAGGGGTATTTC
* *
19989570 GGTAATTCTACCCTACAGGGGTATTTT
1 GGTAATTTTACCCTACAGGGGTATTTC
* *
19989597 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTTTACCCTACAGGGGTATTTC
*
19989624 AGT-ATTTCTACCCTACAGGGGTATTTC
1 GGTAATTT-TACCCTACAGGGGTATTTC
* *
19989651 GGT-ATTTCTACCCTATAAGGGTATTTC
1 GGTAATTT-TACCCTACAGGGGTATTTC
* *
19989678 GGTAATTCTACCCTACAGGGGTATTTT
1 GGTAATTTTACCCTACAGGGGTATTTC
* *
19989705 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTTTACCCTACAGGGGTATTTC
*
19989732 AGT-ATTTCTACCCTACAGGGGTATTTC
1 GGTAATTT-TACCCTACAGGGGTATTTC
* *
19989759 GGT-ATTTCTACCCTATAAGGGTATTTC
1 GGTAATTT-TACCCTACAGGGGTATTTC
* *
19989786 GGTAATTCTACCCTACAGGGGTATTTT
1 GGTAATTTTACCCTACAGGGGTATTTC
* *
19989813 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTTTACCCTACAGGGGTATTTC
*
19989840 AGT-ATTTCTACCCTACAGGGGTATTTC
1 GGTAATTT-TACCCTACAGGGGTATTTC
* *
19989867 GGT-ATTTCTACCCTATAAGGGTATTTC
1 GGTAATTT-TACCCTACAGGGGTATTTC
* *
19989894 GGTAATTCTACCCTACAGGGGTATTTT
1 GGTAATTTTACCCTACAGGGGTATTTC
* *
19989921 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTTTACCCTACAGGGGTATTTC
*
19989948 AGT-ATTTCTACCCTACAGGGGTATTTC
1 GGTAATTT-TACCCTACAGGGGTATTTC
* *
19989975 GGT-ATTTCTACCCTATAAGGGTATTTC
1 GGTAATTT-TACCCTACAGGGGTATTTC
* *
19990002 GGTAATTCTACCCTACAGGGGTATTTT
1 GGTAATTTTACCCTACAGGGGTATTTC
* *
19990029 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTTTACCCTACAGGGGTATTTC
*
19990056 AGT-ATTTCTACCCTACAGGGGTATTTC
1 GGTAATTT-TACCCTACAGGGGTATTTC
* *
19990083 GGT-ATTTCTACCCTATAAGGGTATTTC
1 GGTAATTT-TACCCTACAGGGGTATTTC
* *
19990110 GGTAATTCTACCCTACAGGGGTATTTT
1 GGTAATTTTACCCTACAGGGGTATTTC
* *
19990137 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTTTACCCTACAGGGGTATTTC
*
19990164 AGT-ATTTCTACCCTACAGGGGTATTTC
1 GGTAATTT-TACCCTACAGGGGTATTTC
* *
19990191 GGT-ATTTCTACCCTATAAGGGTATTTC
1 GGTAATTT-TACCCTACAGGGGTATTTC
* *
19990218 GGTAATTCTACCCTACAGGGGTATTTT
1 GGTAATTTTACCCTACAGGGGTATTTC
* *
19990245 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTTTACCCTACAGGGGTATTTC
*
19990272 AGT-ATTTCTACCCTACAGGGGTATTTC
1 GGTAATTT-TACCCTACAGGGGTATTTC
* *
19990299 GGT-ATTTCTACCCTATAAGGGTATTTC
1 GGTAATTT-TACCCTACAGGGGTATTTC
* *
19990326 GGTAATTCTACCCTACAGGGGTATTTT
1 GGTAATTTTACCCTACAGGGGTATTTC
* *
19990353 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTTTACCCTACAGGGGTATTTC
*
19990380 AGT-ATTTCTACCCTACAGGGGTATTTC
1 GGTAATTT-TACCCTACAGGGGTATTTC
*
19990407 GGT-ATTTCTACCCTACAAGGGTATTT
1 GGTAATTT-TACCCTACAGGGGTATTT
19990433 TGACATTTCT
Statistics
Matches: 929, Mismatches: 104, Indels: 38
0.87 0.10 0.04
Matches are distributed among these distances:
26 31 0.03
27 871 0.94
28 27 0.03
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.37
Consensus pattern (27 bp):
GGTAATTTTACCCTACAGGGGTATTTC
Found at i:19990497 original size:108 final size:108
Alignment explanation
Indices: 19989354--19990432 Score: 2052
Period size: 108 Copynumber: 10.0 Consensus size: 108
19989344 GGGGTAAAAT
* * * * ** * *
19989354 GGTAATTTTACCCCACAAGGGTATCTCGGTAATTCTACCTTACAGGAGTATTTCAGTAATTT-TA
1 GGTAATTCTACCCTACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCAGT-ATTTCTA
*
19989418 TCCTACAGGGGTATTTCGGTATTTCTACCCTATAAGGGTATTTC
65 CCCTACAGGGGTATTTCGGTATTTCTACCCTATAAGGGTATTTC
19989462 GGTAATTCTACCCTACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCAGTATTTCTAC
1 GGTAATTCTACCCTACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCAGTATTTCTAC
19989527 CCTACAGGGGTATTTCGGTATTTCTACCCTATAAGGGTATTTC
66 CCTACAGGGGTATTTCGGTATTTCTACCCTATAAGGGTATTTC
19989570 GGTAATTCTACCCTACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCAGTATTTCTAC
1 GGTAATTCTACCCTACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCAGTATTTCTAC
19989635 CCTACAGGGGTATTTCGGTATTTCTACCCTATAAGGGTATTTC
66 CCTACAGGGGTATTTCGGTATTTCTACCCTATAAGGGTATTTC
19989678 GGTAATTCTACCCTACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCAGTATTTCTAC
1 GGTAATTCTACCCTACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCAGTATTTCTAC
19989743 CCTACAGGGGTATTTCGGTATTTCTACCCTATAAGGGTATTTC
66 CCTACAGGGGTATTTCGGTATTTCTACCCTATAAGGGTATTTC
19989786 GGTAATTCTACCCTACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCAGTATTTCTAC
1 GGTAATTCTACCCTACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCAGTATTTCTAC
19989851 CCTACAGGGGTATTTCGGTATTTCTACCCTATAAGGGTATTTC
66 CCTACAGGGGTATTTCGGTATTTCTACCCTATAAGGGTATTTC
19989894 GGTAATTCTACCCTACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCAGTATTTCTAC
1 GGTAATTCTACCCTACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCAGTATTTCTAC
19989959 CCTACAGGGGTATTTCGGTATTTCTACCCTATAAGGGTATTTC
66 CCTACAGGGGTATTTCGGTATTTCTACCCTATAAGGGTATTTC
19990002 GGTAATTCTACCCTACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCAGTATTTCTAC
1 GGTAATTCTACCCTACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCAGTATTTCTAC
19990067 CCTACAGGGGTATTTCGGTATTTCTACCCTATAAGGGTATTTC
66 CCTACAGGGGTATTTCGGTATTTCTACCCTATAAGGGTATTTC
19990110 GGTAATTCTACCCTACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCAGTATTTCTAC
1 GGTAATTCTACCCTACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCAGTATTTCTAC
19990175 CCTACAGGGGTATTTCGGTATTTCTACCCTATAAGGGTATTTC
66 CCTACAGGGGTATTTCGGTATTTCTACCCTATAAGGGTATTTC
19990218 GGTAATTCTACCCTACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCAGTATTTCTAC
1 GGTAATTCTACCCTACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCAGTATTTCTAC
19990283 CCTACAGGGGTATTTCGGTATTTCTACCCTATAAGGGTATTTC
66 CCTACAGGGGTATTTCGGTATTTCTACCCTATAAGGGTATTTC
19990326 GGTAATTCTACCCTACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCAGTATTTCTAC
1 GGTAATTCTACCCTACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCAGTATTTCTAC
*
19990391 CCTACAGGGGTATTTCGGTATTTCTACCCTACAAGGGTATTT
66 CCTACAGGGGTATTTCGGTATTTCTACCCTATAAGGGTATTT
19990433 TGACATTTCT
Statistics
Matches: 960, Mismatches: 10, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
107 4 0.00
108 956 1.00
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.37
Consensus pattern (108 bp):
GGTAATTCTACCCTACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCAGTATTTCTAC
CCTACAGGGGTATTTCGGTATTTCTACCCTATAAGGGTATTTC
Found at i:19990559 original size:81 final size:80
Alignment explanation
Indices: 19990451--19990716 Score: 207
Period size: 81 Copynumber: 3.3 Consensus size: 80
19990441 CTACTGTACA
** * *
19990451 AGGGTATTTCAATAATTTTGTAATTCGAGGGTAAAAT-GGTAA-TTCTATAAATCAGGGGTACTT
1 AGGGTATTTCAATAATTTTACAATTCGAGGG-AAAATCAGTAATTTC-ACAAATCAGGGGTACTT
*
19990514 TGGTAATTTTACAAGTCG
64 TGGTAATTTTACAA-ACG
* * ** *
19990532 AGGGTATTTCAATAATTTTACAGTTCGAGGGCATTTCAGTAATTTCACAAATCAGGGGTATTTTG
1 AGGGTATTTCAATAATTTTACAATTCGAGGGAAAATCAGTAATTTCACAAATCAGGGGTACTTTG
*
19990597 GTAATTTTACAAACT
66 GTAATTTTACAAACG
** * * * ** ** * *
19990612 AGGAGTATTTTGATAATTTTACAA-ACCAGGGGTATTTTGGTAATTTTACAAA-CTAGGGGTATT
1 AGG-GTATTTCAATAATTTTACAATTCGA-GGGAAAATCAGTAATTTCACAAATC-AGGGGTACT
* *
19990675 TTGGTAATTTTATAAACCA
63 TTGGTAATTTTACAAA-CG
* *
19990694 AGGGTATTTTAGTAATTTTACAA
1 AGGGTATTTCAATAATTTTACAA
19990717 ACCAAGGGTA
Statistics
Matches: 155, Mismatches: 24, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
80 9 0.06
81 139 0.90
82 7 0.05
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.38
Consensus pattern (80 bp):
AGGGTATTTCAATAATTTTACAATTCGAGGGAAAATCAGTAATTTCACAAATCAGGGGTACTTTG
GTAATTTTACAAACG
Found at i:19991717 original size:54 final size:54
Alignment explanation
Indices: 19990587--19991710 Score: 1699
Period size: 54 Copynumber: 20.8 Consensus size: 54
19990577 CACAAATCAG
* * * *
19990587 GGGTATTTTGGTAATTTTACAAACTAGGAGTATTTTGATAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAA
19990641 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAA
1 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAA
* * * * *
19990695 GGGTATTTTAGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTGTAAACTAA
1 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAA
19990749 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAA
1 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAA
* * * * *
19990803 GGGTATTTTAGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTGTAAACTAA
1 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAA
* *
19990857 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTGATTTTATAAACTAA
1 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAA
* * * *
19990911 GGGTATTTTAGTAATTTTACAAATTATGGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAA
* *
19990965 GGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTGATTTTATAAACCAA
1 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAA
* * * *
19991019 GGGTATTTTAGTAATTTTACAAATTATGGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAA
* *
19991073 GGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTGATTTTATAAACCAA
1 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAA
* * * *
19991127 GGGTATTTTAGTAATTTTACAAATTATGGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAA
* *
19991181 GGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTGATTTTATAAACCAA
1 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAA
* * * *
19991235 GGGTATTTTAGTAATTTTACAAATTATGGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAA
*
19991289 GGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACCAA
1 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAA
* * * * *
19991343 GGGTATTTTAGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTGTAAACTAA
1 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAA
19991397 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAA
1 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAA
* * * * *
19991451 GGGTATTTTAGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTGTAAACTAA
1 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAA
* *
19991505 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTGATTTTATAAACTAA
1 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAA
* * * *
19991559 GGGTATTTTAGTAATTTTACAAATTATGGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAA
* *
19991613 GGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTGATTTTATAAACCAA
1 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAA
* * * *
19991667 GGGTATTTTAGTAATTTTACAAACCAGAGTTATTTTGGTAATTT
1 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTT
19991711 GGTAAACTAA
Statistics
Matches: 964, Mismatches: 106, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 964 1.00
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.41
Consensus pattern (54 bp):
GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAA
Found at i:19991720 original size:216 final size:217
Alignment explanation
Indices: 19990587--19991717 Score: 1905
Period size: 216 Copynumber: 5.2 Consensus size: 217
19990577 CACAAATCAG
* * * * ** *
19990587 GGGTATTTTGGTAATTTTACAAACTAGGA-GTATTTTGATAATTTTACAAACCAGGGGTATTTTG
1 GGGTATTTTAGTAATTTTACAAACCATGAGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTG
*
19990651 GTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTAGTAATTTTACA
66 GTAATTTTACAAACTAGGGGTATTTTGGTGATTTTATAAACCAAGGGTATTTTAGTAATTTTACA
** * * *
19990716 AACCAAGGGTATTTTGGTAATTTTGTAAACTAAGGGTATTTTGGTAATTTTACAAACTAGGGGTA
131 AATTATGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTGGTAATTTTACAAACCAGGGGTA
*
19990781 TTTTGGTAATTTTATAAACCAA
196 TTTTGGTGATTTTATAAACCAA
* *
19990803 GGGTATTTTAGTAATTTTACAAACCAAG-GGTATTTTGGTAATTTTGTAAACTAAGGGTATTTTG
1 GGGTATTTTAGTAATTTTACAAACCATGAGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTG
*
19990867 GTAATTTTACAAACTAGGGGTATTTTGGTGATTTTATAAACTAAGGGTATTTTAGTAATTTTACA
66 GTAATTTTACAAACTAGGGGTATTTTGGTGATTTTATAAACCAAGGGTATTTTAGTAATTTTACA
19990932 AATTATGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTGGTAATTTTACAAACCAGGGGTA
131 AATTATGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTGGTAATTTTACAAACCAGGGGTA
19990997 TTTTGGTGATTTTATAAACCAA
196 TTTTGGTGATTTTATAAACCAA
**
19991019 GGGTATTTTAGTAATTTTACAAATTATG-GGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTG
1 GGGTATTTTAGTAATTTTACAAACCATGAGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTG
*
19991083 GTAATTTTACAAACCAGGGGTATTTTGGTGATTTTATAAACCAAGGGTATTTTAGTAATTTTACA
66 GTAATTTTACAAACTAGGGGTATTTTGGTGATTTTATAAACCAAGGGTATTTTAGTAATTTTACA
19991148 AATTATGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTGGTAATTTTACAAACCAGGGGTA
131 AATTATGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTGGTAATTTTACAAACCAGGGGTA
19991213 TTTTGGTGATTTTATAAACCAA
196 TTTTGGTGATTTTATAAACCAA
**
19991235 GGGTATTTTAGTAATTTTACAAATTATG-GGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTG
1 GGGTATTTTAGTAATTTTACAAACCATGAGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTG
* *
19991299 GTAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTAGTAATTTTACA
66 GTAATTTTACAAACTAGGGGTATTTTGGTGATTTTATAAACCAAGGGTATTTTAGTAATTTTACA
** * * *
19991364 AACCAAGGGTATTTTGGTAATTTTGTAAACTAAGGGTATTTTGGTAATTTTACAAACTAGGGGTA
131 AATTATGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTGGTAATTTTACAAACCAGGGGTA
*
19991429 TTTTGGTAATTTTATAAACCAA
196 TTTTGGTGATTTTATAAACCAA
* *
19991451 GGGTATTTTAGTAATTTTACAAACCAAG-GGTATTTTGGTAATTTTGTAAACTAAGGGTATTTTG
1 GGGTATTTTAGTAATTTTACAAACCATGAGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTG
*
19991515 GTAATTTTACAAACTAGGGGTATTTTGGTGATTTTATAAACTAAGGGTATTTTAGTAATTTTACA
66 GTAATTTTACAAACTAGGGGTATTTTGGTGATTTTATAAACCAAGGGTATTTTAGTAATTTTACA
19991580 AATTATGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTGGTAATTTTACAAACCAGGGGTA
131 AATTATGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTGGTAATTTTACAAACCAGGGGTA
19991645 TTTTGGTGATTTTATAAACCAA
196 TTTTGGTGATTTTATAAACCAA
* *
19991667 GGGTATTTTAGTAATTTTACAAACCA-GAGTTATTTTGGTAATTTGGTAAAC
1 GGGTATTTTAGTAATTTTACAAACCATGAGGTATTTTGGTAATTTTGTAAAC
19991718 TAAAGTATTC
Statistics
Matches: 869, Mismatches: 44, Indels: 4
0.95 0.05 0.00
Matches are distributed among these distances:
215 1 0.00
216 868 1.00
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.41
Consensus pattern (217 bp):
GGGTATTTTAGTAATTTTACAAACCATGAGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTG
GTAATTTTACAAACTAGGGGTATTTTGGTGATTTTATAAACCAAGGGTATTTTAGTAATTTTACA
AATTATGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTGGTAATTTTACAAACCAGGGGTA
TTTTGGTGATTTTATAAACCAA
Found at i:20000586 original size:27 final size:26
Alignment explanation
Indices: 20000551--20000662 Score: 134
Period size: 27 Copynumber: 4.2 Consensus size: 26
20000541 AGCATGGCTG
* *
20000551 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
20000577 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
*
20000605 CCGGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
** *
20000632 CCAGATTAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
20000659 CCAG
1 CCAG
20000663 GACGCTTCCT
Statistics
Matches: 75, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
26 6 0.08
27 53 0.71
28 16 0.21
ACGTcount: A:0.36, C:0.22, G:0.25, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:20000645 original size:54 final size:54
Alignment explanation
Indices: 20000554--20000660 Score: 153
Period size: 54 Copynumber: 2.0 Consensus size: 54
20000544 ATGGCTGCCA
*
20000554 GAACAGATAATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCACCG
1 GAACAGATAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCACCG
* * * *
20000608 GAACAGATATATGTGGCAGAGCCACCAGAT-TAGATAATTGTGGCATAGCCACC
1 GAACAGATA-ATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCACC
20000661 AGGACGCTTC
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
54 29 0.62
55 18 0.38
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.18
Consensus pattern (54 bp):
GAACAGATAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCACCG
Found at i:20000830 original size:28 final size:26
Alignment explanation
Indices: 20000768--20000830 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 26
20000758 AAAGTAACCC
* *
20000768 TAGGGGTATAATGGTAATTTTGCACC
1 TAGGGGTATAATGGTAATTTTCCACA
20000794 TAGGGGTATAACT-GTAATTTTCCATACA
1 TAGGGGTATAA-TGGTAATTTTCC--ACA
20000822 TAGGGGTAT
1 TAGGGGTAT
20000831 TCAAGTAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 20 0.62
27 1 0.03
28 11 0.34
ACGTcount: A:0.29, C:0.11, G:0.25, T:0.35
Consensus pattern (26 bp):
TAGGGGTATAATGGTAATTTTCCACA
Found at i:20004687 original size:56 final size:57
Alignment explanation
Indices: 20004575--20004690 Score: 162
Period size: 56 Copynumber: 2.1 Consensus size: 57
20004565 GTTTTATTTA
* * *
20004575 ACTTAGTGTATTTACTTTTTAGAGGTTTTCCATCAGCGCATGAGAAGAGGCATTCCT
1 ACTTAGTGTATTTACTTTTTACAGGTCTTCAATCAGCGCATGAGAAGAGGCATTCCT
* * * *
20004632 ACTTAGTGTATTTAGTTTTTACAGG-CTTCAATCAGTGTATGAGAAGAGGCGTTCCT
1 ACTTAGTGTATTTACTTTTTACAGGTCTTCAATCAGCGCATGAGAAGAGGCATTCCT
20004688 ACT
1 ACT
20004691 AACATAAAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
56 29 0.56
57 23 0.44
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (57 bp):
ACTTAGTGTATTTACTTTTTACAGGTCTTCAATCAGCGCATGAGAAGAGGCATTCCT
Found at i:20007874 original size:31 final size:31
Alignment explanation
Indices: 20007834--20007899 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
20007824 AACCCTTCCT
*
20007834 GCATTAAATCCAACCAAAAACA-ACAAATATA
1 GCATGAAATCCAACCAAAAACAGA-AAATATA
*
20007865 GCATGAAATCCAACCAAAAACAGAAAATGTA
1 GCATGAAATCCAACCAAAAACAGAAAATATA
20007896 GCAT
1 GCAT
20007900 AAAAAATACA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 31 0.97
32 1 0.03
ACGTcount: A:0.55, C:0.21, G:0.09, T:0.15
Consensus pattern (31 bp):
GCATGAAATCCAACCAAAAACAGAAAATATA
Found at i:20008179 original size:21 final size:21
Alignment explanation
Indices: 20008155--20008230 Score: 84
Period size: 21 Copynumber: 3.6 Consensus size: 21
20008145 ACTACCATCG
*
20008155 CTGCTGCCTCTGCCTCTCTCA
1 CTGCTGCCTCTGCCTCCCTCA
20008176 CTGCTGCCGT-TGCCTCCCTCA
1 CTGCTGCC-TCTGCCTCCCTCA
* *
20008197 CTGCTG-TTGCTGCCTCCCTCT
1 CTGCTGCCT-CTGCCTCCCTCA
*
20008218 CTACTGCCTCTGC
1 CTGCTGCCTCTGC
20008231 TCTAAGTTGT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
19 1 0.02
21 43 0.93
22 2 0.04
ACGTcount: A:0.04, C:0.46, G:0.17, T:0.33
Consensus pattern (21 bp):
CTGCTGCCTCTGCCTCCCTCA
Found at i:20008662 original size:13 final size:14
Alignment explanation
Indices: 20008636--20008664 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
20008626 ACTAACGATG
20008636 AATTAAACCATTAT
1 AATTAAACCATTAT
20008650 AATTAAA-CATTAT
1 AATTAAACCATTAT
20008663 AA
1 AA
20008665 ATATTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACCATTAT
Found at i:20013793 original size:9 final size:9
Alignment explanation
Indices: 20013772--20013938 Score: 55
Period size: 9 Copynumber: 19.0 Consensus size: 9
20013762 TATGTATTAC
*
20013772 GTAAGTTAA
1 GTAAGTTAT
20013781 GTAAGCTT-T
1 GTAAG-TTAT
20013790 GTAAGTTAT
1 GTAAGTTAT
20013799 GTAAGTTAT
1 GTAAGTTAT
* *
20013808 GTTA-TGAT
1 GTAAGTTAT
* *
20013816 ATACATTTAT
1 GTA-AGTTAT
*
20013826 ATAAAG-TAT
1 GT-AAGTTAT
20013835 GTAAGTTAT
1 GTAAGTTAT
* *
20013844 GATATGATAT
1 G-TAAGTTAT
* *
20013854 AT-ATTTAT
1 GTAAGTTAT
*
20013862 AT-A-TTAT
1 GTAAGTTAT
*
20013869 GTAAGTTGT
1 GTAAGTTAT
20013878 GTAAGTTAT
1 GTAAGTTAT
* *
20013887 GATATGATAT
1 G-TAAGTTAT
* *
20013897 AT-ATTTAT
1 GTAAGTTAT
*
20013905 GT-A-TTTT
1 GTAAGTTAT
*
20013912 GTAAGGTAT
1 GTAAGTTAT
*
20013921 ATAAGTTAT
1 GTAAGTTAT
20013930 GTAAGTTAT
1 GTAAGTTAT
20013939 TATATGATAT
Statistics
Matches: 116, Mismatches: 30, Indels: 24
0.68 0.18 0.14
Matches are distributed among these distances:
7 10 0.09
8 22 0.19
9 63 0.54
10 20 0.17
11 1 0.01
ACGTcount: A:0.35, C:0.01, G:0.17, T:0.46
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:20013843 original size:36 final size:36
Alignment explanation
Indices: 20013796--20013864 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
20013786 CTTTGTAAGT
*
20013796 TATGTAAGTTATGTTATGATATACATTTATATAAAG
1 TATGTAAGTTATGATATGATATACATTTATATAAAG
*
20013832 TATGTAAGTTATGATATGATATATATTTATATA
1 TATGTAAGTTATGATATGATATACATTTATATA
20013865 TTATGTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.39, C:0.01, G:0.13, T:0.46
Consensus pattern (36 bp):
TATGTAAGTTATGATATGATATACATTTATATAAAG
Found at i:20013875 original size:34 final size:35
Alignment explanation
Indices: 20013795--20013875 Score: 119
Period size: 36 Copynumber: 2.3 Consensus size: 35
20013785 GCTTTGTAAG
*
20013795 TTATGTAAGTTATGTTATGATATACATTTATATAAA
1 TTATGTAAGTTATGATATGATATACATTTATAT-AA
* *
20013831 GTATGTAAGTTATGATATGATATATATTTATAT-A
1 TTATGTAAGTTATGATATGATATACATTTATATAA
20013865 TTATGTAAGTT
1 TTATGTAAGTT
20013876 GTGTAAGTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
34 11 0.27
36 30 0.73
ACGTcount: A:0.37, C:0.01, G:0.14, T:0.48
Consensus pattern (35 bp):
TTATGTAAGTTATGATATGATATACATTTATATAA
Found at i:20013887 original size:43 final size:43
Alignment explanation
Indices: 20013822--20013930 Score: 155
Period size: 43 Copynumber: 2.5 Consensus size: 43
20013812 TGATATACAT
* *
20013822 TTATATAAAGTATGTAAGTTATGATATGATATATATTTATATA
1 TTATGTAAGGTATGTAAGTTATGATATGATATATATTTATATA
* * *
20013865 TTATGTAAGTTGTGTAAGTTATGATATGATATATATTTATGTA
1 TTATGTAAGGTATGTAAGTTATGATATGATATATATTTATATA
* *
20013908 TTTTGTAAGGTATATAAGTTATG
1 TTATGTAAGGTATGTAAGTTATG
20013931 TAAGTTATTA
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.36, C:0.00, G:0.17, T:0.48
Consensus pattern (43 bp):
TTATGTAAGGTATGTAAGTTATGATATGATATATATTTATATA
Found at i:20013943 original size:43 final size:43
Alignment explanation
Indices: 20013831--20013953 Score: 140
Period size: 43 Copynumber: 2.8 Consensus size: 43
20013821 TTTATATAAA
* *
20013831 GTATGTAAGTTATGATATGATATATATTTATATATTATGTAAG
1 GTATGTAAGTTATGATAAGATATATATTTATATATTTTGTAAG
* * * *
20013874 TTGTGTAAGTTATGATATGATATATATTTATGTATTTTGTAAG
1 GTATGTAAGTTATGATAAGATATATATTTATATATTTTGTAAG
* * *
20013917 GTATATAAGTTATG-TAAGTTATTATATGATATATATT
1 GTATGTAAGTTATGATAAGATA-TATAT-TTATATATT
20013954 GAACATTAAG
Statistics
Matches: 67, Mismatches: 11, Indels: 3
0.83 0.14 0.04
Matches are distributed among these distances:
42 5 0.07
43 55 0.82
44 7 0.10
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (43 bp):
GTATGTAAGTTATGATAAGATATATATTTATATATTTTGTAAG
Found at i:20014015 original size:11 final size:11
Alignment explanation
Indices: 20013999--20014030 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
20013989 AATATTTTAA
20013999 TTAAATAAATT
1 TTAAATAAATT
20014010 TTAAATAAATT
1 TTAAATAAATT
*
20014021 TTAAAAAAAT
1 TTAAATAAAT
20014031 CACATGAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
TTAAATAAATT
Found at i:20016623 original size:19 final size:19
Alignment explanation
Indices: 20016599--20016635 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
20016589 GCAGGTCGTC
20016599 CACTCGGAGTCTTCAATGG
1 CACTCGGAGTCTTCAATGG
20016618 CACTCGGAGTCTTCAATG
1 CACTCGGAGTCTTCAATG
20016636 ACAGAAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (19 bp):
CACTCGGAGTCTTCAATGG
Found at i:20016689 original size:20 final size:20
Alignment explanation
Indices: 20016666--20016709 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
20016656 TTGATTCGGA
*
20016666 GAAATATTTAGGGATTAGGG
1 GAAATAGTTAGGGATTAGGG
*
20016686 GAAA-AGTTAGGGATTTGGG
1 GAAATAGTTAGGGATTAGGG
20016705 GAAAT
1 GAAAT
20016710 TTGGGTGGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.27
Consensus pattern (20 bp):
GAAATAGTTAGGGATTAGGG
Found at i:20017823 original size:14 final size:15
Alignment explanation
Indices: 20017788--20017825 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
20017778 TGAAATTTAT
20017788 TTTTAGGGTTTACAA
1 TTTTAGGGTTTACAA
*
20017803 TTTTAGGGTTTATAA
1 TTTTAGGGTTTACAA
20017818 -TTTAGGGT
1 TTTTAGGGT
20017826 ATAAGGGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.24, C:0.03, G:0.24, T:0.50
Consensus pattern (15 bp):
TTTTAGGGTTTACAA
Found at i:20018017 original size:108 final size:108
Alignment explanation
Indices: 20017887--20018300 Score: 801
Period size: 108 Copynumber: 3.8 Consensus size: 108
20017877 GTTTTATAGC
20017887 TCATGGGTTATGATTTAGGGGTTAGGCTTCATATTTTAGGGTTTAAGGTAGTTTAGGGTTTTAGG
1 TCATGGGTTATGATTTAGGGGTTAGGCTTCATATTTTAGGGTTTAAGGTAGTTTAGGGTTTTAGG
20017952 ATTAGGCTTTAGAGTTTATGGTTTAAAAAGTTTAGAGTTTAGG
66 ATTAGGCTTTAGAGTTTATGGTTTAAAAAGTTTAGAGTTTAGG
20017995 TCATGGGTTATGATTTAGGGGTTAGGCTTCATATTTTAGGGTTTAAGGTAGTTTAGGGTTTTAGG
1 TCATGGGTTATGATTTAGGGGTTAGGCTTCATATTTTAGGGTTTAAGGTAGTTTAGGGTTTTAGG
20018060 ATTAGGCTTTAGAGTTTATGGTTTAAAAAGTTTAGAGTTTAGG
66 ATTAGGCTTTAGAGTTTATGGTTTAAAAAGTTTAGAGTTTAGG
20018103 TCATGGGTTATGATTTAGGGGTTAGGCTTCATATTTTAGGGTTTAAGGTAGTTTAGGGTTTTAGG
1 TCATGGGTTATGATTTAGGGGTTAGGCTTCATATTTTAGGGTTTAAGGTAGTTTAGGGTTTTAGG
20018168 ATTAGGCTTTAGAGTTTATGGTTTAAAAAGTTTAGAGTTTAGG
66 ATTAGGCTTTAGAGTTTATGGTTTAAAAAGTTTAGAGTTTAGG
* *
20018211 TCATGGGTTATGATTTAGGGGTTAGGCTTCATATTTTAGGGTTTAAGGTAGTTTAAGGTTTTGGG
1 TCATGGGTTATGATTTAGGGGTTAGGCTTCATATTTTAGGGTTTAAGGTAGTTTAGGGTTTTAGG
*
20018276 ATTAGGCTTTAGAGTTTAGGGTTTA
66 ATTAGGCTTTAGAGTTTATGGTTTA
20018301 GGGGCTAAAA
Statistics
Matches: 303, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
108 303 1.00
ACGTcount: A:0.23, C:0.04, G:0.30, T:0.43
Consensus pattern (108 bp):
TCATGGGTTATGATTTAGGGGTTAGGCTTCATATTTTAGGGTTTAAGGTAGTTTAGGGTTTTAGG
ATTAGGCTTTAGAGTTTATGGTTTAAAAAGTTTAGAGTTTAGG
Found at i:20018956 original size:80 final size:82
Alignment explanation
Indices: 20018872--20019029 Score: 209
Period size: 80 Copynumber: 2.0 Consensus size: 82
20018862 ATTTTTGACA
* *
20018872 AAAACACCACTATTTCTCTAT-TTTTTA-CGACGTTTTGGAT-AAAATG-CACTATTT-CTCAGT
1 AAAACACCACTATTACT-T-TGTTTTTAGCGACGTTTTGGATAAAAAAGCCACT-TTTGCTCAGT
*
20018932 TTTTTGCGGCGTTTTGGTTG
63 TTTTAGCGGCGTTTTGGTTG
* *
20018952 AAAACGCCACTATTACTTTGTTTTTAGCGGCGTTTTGGATAAAAAAGCCACTTTTGCTCAGTTTT
1 AAAACACCACTATTACTTTGTTTTTAGCGACGTTTTGGATAAAAAAGCCACTTTTGCTCAGTTTT
20019017 TAGCGGCGTTTTG
66 TAGCGGCGTTTTG
20019030 TTTTAAACCC
Statistics
Matches: 68, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
78 1 0.01
79 7 0.10
80 27 0.40
81 8 0.12
82 25 0.37
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41
Consensus pattern (82 bp):
AAAACACCACTATTACTTTGTTTTTAGCGACGTTTTGGATAAAAAAGCCACTTTTGCTCAGTTTT
TAGCGGCGTTTTGGTTG
Found at i:20018975 original size:41 final size:40
Alignment explanation
Indices: 20018790--20019029 Score: 184
Period size: 41 Copynumber: 5.9 Consensus size: 40
20018780 CGCTTTTATA
** * * *
20018790 AAAACGCCACTATAGCTCAACTTTTT-GTGGCG-TTTGGAAC
1 AAAACGCCACTATTTCTC-AGTTTTTAGCGGCGTTTTGG-AT
* * * * * *
20018830 AAAAGCGCCACTATATCTAAGTTTTTGGCGGCATTTTTGACA
1 AAAA-CGCCACTATTTCTCAGTTTTTAGCGGCGTTTTGGA-T
* * *
20018872 AAAACACCACTATTTCTCTATTTTTTA-CGACGTTTTGGAT
1 AAAACGCCACTATTTCTC-AGTTTTTAGCGGCGTTTTGGAT
* * *
20018912 AAAATG-CACTATTTCTCAGTTTTTTGCGGCGTTTTGGTT
1 AAAACGCCACTATTTCTCAGTTTTTAGCGGCGTTTTGGAT
* **
20018951 GAAAACGCCACTATTACTTTGTTTTTAGCGGCGTTTTGGAT
1 -AAAACGCCACTATTTCTCAGTTTTTAGCGGCGTTTTGGAT
*
20018992 AAAAAAGCCACT-TTTGCTCAGTTTTTAGCGGCGTTTTG
1 -AAAACGCCACTATTT-CTCAGTTTTTAGCGGCGTTTTG
20019030 TTTTAAACCC
Statistics
Matches: 158, Mismatches: 33, Indels: 17
0.76 0.16 0.08
Matches are distributed among these distances:
38 6 0.04
39 22 0.14
40 21 0.13
41 95 0.60
42 14 0.09
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.38
Consensus pattern (40 bp):
AAAACGCCACTATTTCTCAGTTTTTAGCGGCGTTTTGGAT
Found at i:20019475 original size:27 final size:26
Alignment explanation
Indices: 20019444--20019768 Score: 328
Period size: 27 Copynumber: 12.0 Consensus size: 26
20019434 TACATCGCAT
*
20019444 AGGGCAAAACAGTCATCTTACCATATA
1 AGGGCAAAACAGTCAT-TTACCACATA
*
20019471 AGGGCAAAACAATCATCTTACCACATA
1 AGGGCAAAACAGTCAT-TTACCACATA
20019498 AGGGCAAAACAGTCATCTTACCACATA
1 AGGGCAAAACAGTCAT-TTACCACATA
*
20019525 AAGGCAAAACAGTCATCTTACCACATA
1 AGGGCAAAACAGTCAT-TTACCACATA
* ** * *
20019552 ACGATAAAATTA-TCATTTCACCATATA
1 AGGGCAAAA-CAGTCATTT-ACCACATA
20019579 AGGGCAAAACAGTCATTTCACCACATA
1 AGGGCAAAACAGTCATTT-ACCACATA
* *
20019606 AGGGCAAAATATTCATTTCACCACATA
1 AGGGCAAAACAGTCATTT-ACCACATA
* * *
20019633 AAGGCAAAATAGTCATTTTACCACTTA
1 AGGGCAAAACAGTCA-TTTACCACATA
* * *
20019660 AGTGTAAAACAGTCATTTTACCATATA
1 AGGGCAAAACAGTCA-TTTACCACATA
*
20019687 AGGGCAAAACAGTTATTTCACCACATA
1 AGGGCAAAACAGTCATTT-ACCACATA
* *
20019714 AGGGTAAAACAGTTATTTTACCACATA
1 AGGGCAAAACAGTCA-TTTACCACATA
* * *
20019741 AGGGTAAAACAATCATTTTACCATATA
1 AGGGCAAAACAGTCA-TTTACCACATA
20019768 A
1 A
20019769 AGGGTCTAGG
Statistics
Matches: 259, Mismatches: 33, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
26 6 0.02
27 246 0.95
28 7 0.03
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.25
Consensus pattern (26 bp):
AGGGCAAAACAGTCATTTACCACATA
Found at i:20019581 original size:81 final size:81
Alignment explanation
Indices: 20019446--20019771 Score: 361
Period size: 81 Copynumber: 4.0 Consensus size: 81
20019436 CATCGCATAG
* * * *
20019446 GGCAAAACAGTCATCTT-ACCATATAAGGGCAAAACAATCATCTTACCACATAAGGGCAAAACAG
1 GGCAAAACAGTCAT-TTCACCACATAAGGGCAAAATAGTCATTTTACCACATAAGGGCAAAACAG
*
20019510 TCATCTTACCACATAAA
65 TCATTTTACCACATAAA
* ** * *
20019527 GGCAAAACAGTCATCTT-ACCACATAACGATAAAATTA-TCATTTCACCATATAAGGGCAAAACA
1 GGCAAAACAGTCAT-TTCACCACATAAGGGCAAAA-TAGTCATTTTACCACATAAGGGCAAAACA
* *
20019590 GTCATTTCACCACATAAG
64 GTCATTTTACCACATAAA
* * * * * *
20019608 GGCAAAATATTCATTTCACCACATAAAGGCAAAATAGTCATTTTACCACTTAAGTGTAAAACAGT
1 GGCAAAACAGTCATTTCACCACATAAGGGCAAAATAGTCATTTTACCACATAAGGGCAAAACAGT
* *
20019673 CATTTTACCATATAAG
66 CATTTTACCACATAAA
* * * * * *
20019689 GGCAAAACAGTTATTTCACCACATAAGGGTAAAACAGTTATTTTACCACATAAGGGTAAAACAAT
1 GGCAAAACAGTCATTTCACCACATAAGGGCAAAATAGTCATTTTACCACATAAGGGCAAAACAGT
*
20019754 CATTTTACCATATAAA
66 CATTTTACCACATAAA
20019770 GG
1 GG
20019772 GTCTAGGTAA
Statistics
Matches: 208, Mismatches: 34, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
80 4 0.02
81 203 0.98
82 1 0.00
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.25
Consensus pattern (81 bp):
GGCAAAACAGTCATTTCACCACATAAGGGCAAAATAGTCATTTTACCACATAAGGGCAAAACAGT
CATTTTACCACATAAA
Done.