Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008527.1 Hibiscus syriacus cultivar Beakdansim tig00111402_pilon, whole genome shotgun sequence
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: 9057482
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 37
Found at i:439867 original size:22 final size:22
Alignment explanation
Indices: 439841--439943 Score: 71
Period size: 22 Copynumber: 4.5 Consensus size: 22
439831 TAATAAATTA
*
439841 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATAAATCCATAT
* *
439863 TTTAAAATAAATCAATTCATACT
1 TTTAAAATAAATAAATCCATA-T
** * ** **
439886 AATAAATTATTTAAAATAAATTAT
1 TTTAAAATAAAT-AAATCCA-TAT
*
439910 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATAAATCCATAT
*
439932 TTTATAATAAAT
1 TTTAAAATAAAT
439944 TATTTTAAAA
Statistics
Matches: 60, Mismatches: 18, Indels: 6
0.71 0.21 0.07
Matches are distributed among these distances:
22 34 0.57
23 12 0.20
24 12 0.20
25 2 0.03
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAATAAATAAATCCATAT
Found at i:439915 original size:15 final size:15
Alignment explanation
Indices: 439886--440003 Score: 139
Period size: 15 Copynumber: 7.5 Consensus size: 15
439876 AATTCATACT
439886 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
439900 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
439915 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
439937 AATAAATTATTTTAA
1 AATAAATTATTTTAA
**
439952 AATAAATTATTTTGT
1 AATAAATTATTTTAA
439967 AATAAATTATTTTAA
1 AATAAATTATTTTAA
439982 AATAAATTATTTTAA
1 AATAAATTATTTTAA
439997 AATAAAT
1 AATAAAT
440004 AACCTTATTA
Statistics
Matches: 90, Mismatches: 6, Indels: 15
0.81 0.05 0.14
Matches are distributed among these distances:
14 9 0.10
15 63 0.70
17 1 0.01
18 3 0.03
19 3 0.03
20 1 0.01
22 10 0.11
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.45
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:439928 original size:69 final size:67
Alignment explanation
Indices: 439832--439988 Score: 219
Period size: 69 Copynumber: 2.3 Consensus size: 67
439822 AATCCATACT
*
439832 AATAAATTA-TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTA-
1 AATAAATTATTTTAAAATAAATCAATCCATATTTTAAAATAAAT-AATT-ATA-AAATAAATTAT
439895 TTTAA
63 TTTAA
* * *
439900 AATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAAATTATTTTAAAATAAATTATTTT
1 AATAAATTATTTTAAAATAAATCAATCCATATTTTAAAATAAATAATTATAAAATAAATTATTTT
**
439965 GT
66 AA
439967 AATAAATTATTTTAAAATAAAT
1 AATAAATTATTTTAAAATAAAT
439989 TATTTTAAAA
Statistics
Matches: 81, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
66 9 0.11
67 27 0.33
68 12 0.15
69 33 0.41
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.42
Consensus pattern (67 bp):
AATAAATTATTTTAAAATAAATCAATCCATATTTTAAAATAAATAATTATAAAATAAATTATTTT
AA
Found at i:441835 original size:22 final size:20
Alignment explanation
Indices: 441798--441837 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
441788 ATATATATAT
*
441798 TAAAAAAATAATCAAACAAC
1 TAAAAAAATAAACAAACAAC
441818 TAAAAAAACGTAAACAAACA
1 TAAAAAAA--TAAACAAACA
441838 TCATTTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
22 9 0.53
ACGTcount: A:0.70, C:0.15, G:0.03, T:0.12
Consensus pattern (20 bp):
TAAAAAAATAAACAAACAAC
Found at i:448404 original size:18 final size:19
Alignment explanation
Indices: 448378--448415 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
448368 TATAGAATGA
*
448378 TATTTAAAATATT-ATTTT
1 TATTAAAAATATTAATTTT
448396 TATTAAAAATATTAATTTT
1 TATTAAAAATATTAATTTT
448415 T
1 T
448416 TCACATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATTAAAAATATTAATTTT
Found at i:451998 original size:131 final size:131
Alignment explanation
Indices: 451759--452045 Score: 339
Period size: 131 Copynumber: 2.2 Consensus size: 131
451749 AATTACGTAT
* *
451759 TGGACAAGTTTTCAATTTCTCGATTTGGAGGTTTGATCTGATTTCCCAGAGCTATGAGGGTTGCA
1 TGGACAAGTTTTCAATTT-TCGATTTGAAGGTTTGATCTGATTTCCCAGAGCTAGGAGGGTTGCA
* * * *
451824 TTATGATAGACTATAGAGTAGTCTGTGGTTCCCAAGTCACTTTAAT-TTGATATTTGCGACCTTG
65 TTATGATAGACTATAGAGTAATCAGGGGTTCCAAAGTCACTTTAATATT-ATATTTGCGACCTTG
451888 TAG
129 TAG
* * *
451891 TGGACAAGTTTTCGATTTTTGATTTGAAGGTTTGATCTGATTTTCCAGAGCTAGGAGGGTTG-AT
1 TGGACAAGTTTTCAATTTTCGATTTGAAGGTTTGATCTGATTTCCCAGAGCTAGGAGGGTTGCAT
* ** * * ** *
451955 T-TG-TGGTGTATTAAGAGTAATCAGCGGGTTCCAAAGTCCCTTTAGTATTATATTTTTGATCTT
66 TATGATAGACTA-T-AGAGTAATCAG-GGGTTCCAAAGTCACTTTAATATTATATTTGCGACCTT
*
452018 GTAT
128 GTAG
452022 TGGACAAGTTTTCAATTTTCGATT
1 TGGACAAGTTTTCAATTTTCGATT
452046 CGGAGGTCGA
Statistics
Matches: 131, Mismatches: 20, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
128 4 0.03
129 3 0.02
130 12 0.09
131 93 0.71
132 19 0.15
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.40
Consensus pattern (131 bp):
TGGACAAGTTTTCAATTTTCGATTTGAAGGTTTGATCTGATTTCCCAGAGCTAGGAGGGTTGCAT
TATGATAGACTATAGAGTAATCAGGGGTTCCAAAGTCACTTTAATATTATATTTGCGACCTTGTA
G
Found at i:453503 original size:2 final size:2
Alignment explanation
Indices: 453492--453521 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
453482 AAATGGTAAT
453492 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
453522 TTTAATTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:456781 original size:14 final size:15
Alignment explanation
Indices: 456755--456783 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
456745 TTGAGGTCAG
456755 AATGAAGAACAGCTC
1 AATGAAGAACAGCTC
456770 AATGAA-AACAGCTC
1 AATGAAGAACAGCTC
456784 CGAATGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.48, C:0.21, G:0.17, T:0.14
Consensus pattern (15 bp):
AATGAAGAACAGCTC
Found at i:459792 original size:29 final size:29
Alignment explanation
Indices: 459758--459825 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
459748 TCTATTTGAT
* *
459758 CACTAAACTTTAAAAGATTCTAATTTTATA
1 CACTAAACTTTAAAAGACTCCAATTTTA-A
* *
459788 -ACTAAACCTTAAAATACTCCAATTTTAA
1 CACTAAACTTTAAAAGACTCCAATTTTAA
459816 CACTAAACTT
1 CACTAAACTT
459826 CCTATATTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
28 1 0.03
29 31 0.97
ACGTcount: A:0.44, C:0.19, G:0.01, T:0.35
Consensus pattern (29 bp):
CACTAAACTTTAAAAGACTCCAATTTTAA
Found at i:461666 original size:43 final size:43
Alignment explanation
Indices: 461614--461697 Score: 168
Period size: 43 Copynumber: 2.0 Consensus size: 43
461604 TGTATACATA
461614 TAACATAGGCATCTACACGCATGAACAAAGTAACACATATATG
1 TAACATAGGCATCTACACGCATGAACAAAGTAACACATATATG
461657 TAACATAGGCATCTACACGCATGAACAAAGTAACACATATA
1 TAACATAGGCATCTACACGCATGAACAAAGTAACACATATA
461698 CAGGCATTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.45, C:0.21, G:0.13, T:0.20
Consensus pattern (43 bp):
TAACATAGGCATCTACACGCATGAACAAAGTAACACATATATG
Found at i:471906 original size:20 final size:19
Alignment explanation
Indices: 471881--471925 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
471871 ATATTTTTAT
* *
471881 TATTTATTTATTTTTAATAA
1 TATTTATATATATTTAAT-A
*
471901 TATTTATATGTATTTAATA
1 TATTTATATATATTTAATA
471920 TATTTA
1 TATTTA
471926 ATAATAATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TATTTATATATATTTAATA
Found at i:471925 original size:29 final size:29
Alignment explanation
Indices: 471866--471931 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
471856 ATTGGGCCTG
* * * *
471866 TAATTATATTTTTATTATTTATTTATTTT
1 TAATAATATTTATATTATTTATATATATT
471895 TAATAATATTTATATGTATTTA-ATATATT
1 TAATAATATTTATAT-TATTTATATATATT
471924 TAATAATA
1 TAATAATA
471932 ATAGTAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 26 0.81
30 6 0.19
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (29 bp):
TAATAATATTTATATTATTTATATATATT
Found at i:471932 original size:3 final size:3
Alignment explanation
Indices: 471924--472027 Score: 199
Period size: 3 Copynumber: 34.7 Consensus size: 3
471914 TTAATATATT
*
471924 TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
471972 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
472020 TAA TAA TA
1 TAA TAA TA
472028 TGGATAAAAA
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 99 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:472594 original size:113 final size:113
Alignment explanation
Indices: 472346--472903 Score: 922
Period size: 113 Copynumber: 5.0 Consensus size: 113
472336 GAATTATGCC
* * *
472346 AAAA-GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
472410 TATGAAC-TTCTCCGGAAAAGATAATCCATCAATTGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
472457 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * **
472522 TATGAACTTTTTCTGGAAAAGCTGATCCATTAAATGATGGATTCATAT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
472570 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
472635 TATGAACTTGCTCTGGAAAAAATGATCCATCAAGTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
472683 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
472748 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
472796 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
472861 TATGAACTTTTTCTGGAAAAGCTGATCCATTAAATGATGGATT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATT
472904 TGAATCTTTG
Statistics
Matches: 418, Mismatches: 27, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
111 4 0.01
112 64 0.15
113 350 0.84
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.38
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
Found at i:473825 original size:83 final size:83
Alignment explanation
Indices: 473613--473981 Score: 636
Period size: 83 Copynumber: 4.5 Consensus size: 83
473603 CCTACTGAAT
** *
473613 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTTTAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATTCAA
*
473678 TGATT-GTTTTGTCAAAT
66 TGATTGGTTTTGTCAAAC
*
473695 CAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATTCAA
473760 TGATTGGTTTTGTCAAAC
66 TGATTGGTTTTGTCAAAC
*
473778 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCACATTCATCTTCCAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTCCAAATTCA
473842 ATGATTGGTTTTGTCAAAC
65 ATGATTGGTTTTGTCAAAC
*
473861 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCACATTCATCTTCCAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTCCAAATTCA
473925 ATGATTGGTTTTGTCAAAC
65 ATGATTGGTTTTGTCAAAC
473944 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
473982 TGATTCTGTC
Statistics
Matches: 278, Mismatches: 7, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
82 66 0.24
83 210 0.76
84 2 0.01
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (83 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATTCAA
TGATTGGTTTTGTCAAAC
Found at i:475184 original size:14 final size:15
Alignment explanation
Indices: 475165--475194 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
475155 TTGACCCCCC
475165 TTTTTTTTTCT-TCT
1 TTTTTTTTTCTCTCT
475179 TTTTTTTTTCTCTCT
1 TTTTTTTTTCTCTCT
475194 T
1 T
475195 CAAGCATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTTTTTCTCTCT
Found at i:487888 original size:27 final size:27
Alignment explanation
Indices: 487841--487894 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
487831 TAATTATATT
* *
487841 TTTATTATTTATTTATTTTTAATAATA
1 TTTATTATTTATATATATTTAATAATA
487868 TTTATGTATTTA-ATATATTTAATAATA
1 TTTAT-TATTTATATATATTTAATAATA
487895 ATAGTAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 18 0.75
28 6 0.25
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (27 bp):
TTTATTATTTATATATATTTAATAATA
Found at i:487895 original size:3 final size:3
Alignment explanation
Indices: 487887--487972 Score: 136
Period size: 3 Copynumber: 28.7 Consensus size: 3
487877 TTAATATATT
* * *
487887 TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TTA TAA TAA TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
487935 TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
487973 TGGATAAAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:492601 original size:12 final size:12
Alignment explanation
Indices: 492584--492627 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
492574 TATACATATG
*
492584 CATGCACGTATA
1 CATGCACGCATA
492596 CATGCACGCATA
1 CATGCACGCATA
492608 CATGCACGCATA
1 CATGCACGCATA
*
492620 CATTCACG
1 CATGCACG
492628 GTTACTAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.20
Consensus pattern (12 bp):
CATGCACGCATA
Found at i:497868 original size:30 final size:30
Alignment explanation
Indices: 497832--497902 Score: 142
Period size: 30 Copynumber: 2.4 Consensus size: 30
497822 TCTGGTTAGG
497832 TTGAAAATCTATTTTGTTGGCTTACAAAGA
1 TTGAAAATCTATTTTGTTGGCTTACAAAGA
497862 TTGAAAATCTATTTTGTTGGCTTACAAAGA
1 TTGAAAATCTATTTTGTTGGCTTACAAAGA
497892 TTGAAAATCTA
1 TTGAAAATCTA
497903 AACTGTCATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.39
Consensus pattern (30 bp):
TTGAAAATCTATTTTGTTGGCTTACAAAGA
Found at i:511374 original size:35 final size:35
Alignment explanation
Indices: 511327--511412 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
511317 AAAACAGTCA
* * *
511327 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
* * * *
511362 TCAATTTTATTCTAAACCCTAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
*
511397 TCAATTAAATTCTAAA
1 TCAATTTAATTCTAAA
511413 ATACTTCAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.41, C:0.21, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
Found at i:511406 original size:21 final size:21
Alignment explanation
Indices: 511381--511423 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
511371 TTCTAAACCC
511381 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
511402 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
511423 T
1 T
511424 TAAGGTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTCTAAAATACTTCAAT
Found at i:511577 original size:15 final size:17
Alignment explanation
Indices: 511546--511577 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
511536 TATTATTGTA
511546 TGAATCATTTATATTTT
1 TGAATCATTTATATTTT
511563 TGAAT-ATTT-TATTTT
1 TGAATCATTTATATTTT
511578 AATAAGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.28, C:0.03, G:0.06, T:0.62
Consensus pattern (17 bp):
TGAATCATTTATATTTT
Found at i:512242 original size:130 final size:130
Alignment explanation
Indices: 512039--512286 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
512029 AATTTTCTTC
* * *
512039 TAATTAGGAGGTGACATGTGTCACCAATAACACATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
* *
512104 CTTGATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * *
512169 TAATTAGGTGGTAACACGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
512234 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
512287 TATATAAATA
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.36
Consensus pattern (130 bp):
TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:512744 original size:35 final size:35
Alignment explanation
Indices: 512690--512757 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
512680 TTAATTTAAG
*
512690 TATTTTGGAATTTAAGGTTTAGAATAAAATTGAAT
1 TATTTTGGAAATTAAGGTTTAGAATAAAATTGAAT
** *
512725 TATTTTGGAAATTGGGGTTTAGAATGAAATTGA
1 TATTTTGGAAATTAAGGTTTAGAATAAAATTGA
512758 TGATTGTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.37, C:0.00, G:0.22, T:0.41
Consensus pattern (35 bp):
TATTTTGGAAATTAAGGTTTAGAATAAAATTGAAT
Found at i:515030 original size:18 final size:18
Alignment explanation
Indices: 515001--515035 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
514991 GAAATTCTAA
515001 TTAAATTATTAATATAATT
1 TTAAATTATTAAT-TAATT
515020 TTAAA-TATTAATTAAT
1 TTAAATTATTAATTAAT
515036 ACGAGAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 7 0.44
19 5 0.31
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTAAATTATTAATTAATT
Found at i:517334 original size:3 final size:3
Alignment explanation
Indices: 517326--517408 Score: 166
Period size: 3 Copynumber: 27.7 Consensus size: 3
517316 TTGTGAGTTG
517326 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
517374 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
517409 GGTAATTTTG
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 80 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:520607 original size:2 final size:2
Alignment explanation
Indices: 520596--520625 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
520586 ATGTAATTGT
520596 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
520626 GTGCAAGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:527514 original size:27 final size:27
Alignment explanation
Indices: 527474--527594 Score: 78
Period size: 27 Copynumber: 4.6 Consensus size: 27
527464 TTGTTAATTC
*
527474 TATATCAAT-AAGAAAACGTGATTCTT
1 TATATAAATAAAGAAAACGTGATTCTT
* *
527500 TTTATAAATAAAGAAATA-GT-A-T-TG
1 TATATAAATAAAGAAA-ACGTGATTCTT
* *
527524 TATATGAGAATAACAGAAAATGTTAATTC--
1 TATAT-A-AATAA-AGAAAACG-TGATTCTT
*
527553 TATATCAAT-AAGAAAACGTGATTCTT
1 TATATAAATAAAGAAAACGTGATTCTT
*
527579 TTTATAAATAAAGAAA
1 TATATAAATAAAGAAA
527595 TAGTATTGTA
Statistics
Matches: 73, Mismatches: 9, Indels: 25
0.68 0.08 0.23
Matches are distributed among these distances:
24 10 0.14
25 9 0.12
26 22 0.30
27 23 0.32
28 2 0.03
29 6 0.08
30 1 0.01
ACGTcount: A:0.48, C:0.07, G:0.12, T:0.34
Consensus pattern (27 bp):
TATATAAATAAAGAAAACGTGATTCTT
Found at i:527558 original size:79 final size:78
Alignment explanation
Indices: 527465--527609 Score: 281
Period size: 79 Copynumber: 1.8 Consensus size: 78
527455 ATTCATATTT
527465 TGTTAATTCTATATCAATAAGAAAACGTGATTCTTTTTATAAATAAAGAAATAGTATTGTATATG
1 TGTTAATTCTATATCAATAAGAAAACGTGATTCTTTTTATAAATAAAGAAATAGTATTGTA-ATG
527530 AGAATAACAGAAAA
65 AGAATAACAGAAAA
527544 TGTTAATTCTATATCAATAAGAAAACGTGATTCTTTTTATAAATAAAGAAATAGTATTGTAATGA
1 TGTTAATTCTATATCAATAAGAAAACGTGATTCTTTTTATAAATAAAGAAATAGTATTGTAATGA
527609 G
66 G
527610 TGTTATCAAA
Statistics
Matches: 66, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
78 5 0.08
79 61 0.92
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (78 bp):
TGTTAATTCTATATCAATAAGAAAACGTGATTCTTTTTATAAATAAAGAAATAGTATTGTAATGA
GAATAACAGAAAA
Found at i:527727 original size:14 final size:15
Alignment explanation
Indices: 527708--527736 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
527698 TCCGTGACAA
527708 TAAAATA-AAAAAAT
1 TAAAATATAAAAAAT
527722 TAAAATATAAAAAAT
1 TAAAATATAAAAAAT
527737 ATCATATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
TAAAATATAAAAAAT
Found at i:530333 original size:23 final size:21
Alignment explanation
Indices: 530302--530348 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
530292 TTATAAATTT
*
530302 ATATAAT-TTTTAAATTAAACA
1 ATATAATATTTTAAACTAAA-A
530323 ATATAATATTTTAAACTAAAA
1 ATATAATATTTTAAACTAAAA
530344 ATATA
1 ATATA
530349 TTAACTTAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (21 bp):
ATATAATATTTTAAACTAAAA
Found at i:530349 original size:23 final size:22
Alignment explanation
Indices: 530301--530349 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
530291 ATTATAAATT
* *
530301 TATATAATTTTTAAATTAAACA
1 TATATAATTTTTAAACTAAAAA
530323 -ATATAATATTTTAAACTAAAAA
1 TATATAAT-TTTTAAACTAAAAA
530345 TATAT
1 TATAT
530350 TAACTTAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 7 0.30
22 12 0.52
23 4 0.17
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (22 bp):
TATATAATTTTTAAACTAAAAA
Found at i:530450 original size:22 final size:23
Alignment explanation
Indices: 530408--530455 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
530398 ATATGAGTCA
* * *
530408 TAATTGTTTATTAAAATAATATT
1 TAATTGTTTATAAAAAAAATAAT
530431 TAATTGTTT-TAAAAAAAATAAT
1 TAATTGTTTATAAAAAAAATAAT
530453 TAA
1 TAA
530456 ATATTATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (23 bp):
TAATTGTTTATAAAAAAAATAAT
Found at i:532887 original size:25 final size:25
Alignment explanation
Indices: 532853--532935 Score: 166
Period size: 25 Copynumber: 3.3 Consensus size: 25
532843 AATGAGACTG
532853 GTTTTAGTTGGTAACCAGTTCTTTT
1 GTTTTAGTTGGTAACCAGTTCTTTT
532878 GTTTTAGTTGGTAACCAGTTCTTTT
1 GTTTTAGTTGGTAACCAGTTCTTTT
532903 GTTTTAGTTGGTAACCAGTTCTTTT
1 GTTTTAGTTGGTAACCAGTTCTTTT
532928 GTTTTAGT
1 GTTTTAGT
532936 GTTCATTAAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 58 1.00
ACGTcount: A:0.16, C:0.11, G:0.20, T:0.53
Consensus pattern (25 bp):
GTTTTAGTTGGTAACCAGTTCTTTT
Found at i:533636 original size:18 final size:18
Alignment explanation
Indices: 533613--533652 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
533603 TGGAACTTGA
533613 TACATTTGTACATATTTT
1 TACATTTGTACATATTTT
*
533631 TACATTTGTAGATATTTT
1 TACATTTGTACATATTTT
533649 TACA
1 TACA
533653 CACTCCTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (18 bp):
TACATTTGTACATATTTT
Found at i:539155 original size:15 final size:15
Alignment explanation
Indices: 539131--539166 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
539121 TCATCTGATT
539131 AGAT-TCGAGTTTAA
1 AGATATCGAGTTTAA
539145 AGATATCGAGTTTAA
1 AGATATCGAGTTTAA
*
539160 AAATATC
1 AGATATC
539167 TATTCTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.33
Consensus pattern (15 bp):
AGATATCGAGTTTAA
Found at i:539805 original size:17 final size:17
Alignment explanation
Indices: 539783--539820 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
539773 TTTTTTGGGC
539783 ATCTTTAAGAAGTTAGG
1 ATCTTTAAGAAGTTAGG
*
539800 ATCTTTAAGAAGTTGGG
1 ATCTTTAAGAAGTTAGG
539817 ATCT
1 ATCT
539821 ATGCTATGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.37
Consensus pattern (17 bp):
ATCTTTAAGAAGTTAGG
Found at i:544041 original size:2 final size:2
Alignment explanation
Indices: 544034--544070 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
544024 ATGTGTTCTA
544034 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
544071 CATTTCAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:544170 original size:37 final size:37
Alignment explanation
Indices: 544089--544438 Score: 307
Period size: 37 Copynumber: 9.3 Consensus size: 37
544079 GAAAAAACTA
* * *
544089 TATATTATGTTTTCGAAAAATGTTTTTCAAAACTATATAA
1 TATA-TATGTTTTC--AAAATGTTTTTTAAAATTATATAT
* * **
544129 TATATATTTTTTTAAAATGTTTTTTAAAATTACCTAT
1 TATATATGTTTTCAAAATGTTTTTTAAAATTATATAT
544166 TATATATGTTTTCAAAAATGTTTTTT-AAATTATATAT
1 TATATATGTTTTC-AAAATGTTTTTTAAAATTATATAT
*
544203 TATATATGTTTTTAAAA-GTATTTTTAAAATTATATAT
1 TATATATGTTTTCAAAATGT-TTTTTAAAATTATATAT
* *
544240 TATATATATTTTCAAAATGTTTTTTTAAAACTATATAT
1 TATATATGTTTTCAAAATG-TTTTTTAAAATTATATAT
* *
544278 TATATATGTTTTCAAAAAAATG-TTTTCAAAACTATATAT
1 TATATATGTTTTC---AAAATGTTTTTTAAAATTATATAT
* * * **
544317 TATATATATATTTAAAAAATG-CTTTTAAAACCATATAT
1 TATATATGT-TTT-CAAAATGTTTTTTAAAATTATATAT
* * * *
544355 TATATTTTTTTTAAAAATCG-TTTTTAAAACTATATAT
1 TATATATGTTTTCAAAAT-GTTTTTTAAAATTATATAT
* * * * *
544392 TATATATATTTTCGAAAA-ATATTCTCAAATTATATAT
1 TATATATGTTTTC-AAAATGTTTTTTAAAATTATATAT
544429 TATATATGTT
1 TATATATGTT
544439 ATATGTATAT
Statistics
Matches: 262, Mismatches: 35, Indels: 29
0.80 0.11 0.09
Matches are distributed among these distances:
35 2 0.01
36 15 0.06
37 128 0.49
38 72 0.27
39 32 0.12
40 7 0.03
41 6 0.02
ACGTcount: A:0.40, C:0.05, G:0.04, T:0.50
Consensus pattern (37 bp):
TATATATGTTTTCAAAATGTTTTTTAAAATTATATAT
Found at i:544189 original size:75 final size:73
Alignment explanation
Indices: 544089--544435 Score: 358
Period size: 74 Copynumber: 4.6 Consensus size: 73
544079 GAAAAAACTA
* *
544089 TATATTATGTTTTCGAAAAATGTTTTTCAAAACTATATAATATATATTTTTTTAAAATGTTTTTT
1 TATA-TATATTTTC-AAAAATGTTTTT-AAAACTATATATTATATATTTTTTTAAAATG-TTTTT
* **
544154 AAAATTACCTAT
62 AAAACTATATAT
* * * * *
544166 TATATATGTTTTCAAAAATGTTTTTTAAATTATATATTATATATGTTTTTAAAAGTATTTTTAAA
1 TATATATATTTTCAAAAATGTTTTTAAAACTATATATTATATATTTTTTTAAAA-TGTTTTTAAA
*
544231 ATTATATAT
65 ACTATATAT
**
544240 TATATATATTTTC-AAAATGTTTTTTTAAAACTATATATTATATATGTTTTCAAAAAAATGTTTT
1 TATATATATTTTCAAAAATG--TTTTTAAAACTATATATTATATAT-TTTT--TTAAAATGTTTT
*
544304 CAAAACTATATAT
61 TAAAACTATATAT
* * *
544317 TATATATATATTTAAAAAATGCTTTTAAAACCATATATTATAT-TTTTTTTAAAAATCGTTTTTA
1 TATATATAT-TTTCAAAAATGTTTTTAAAACTATATATTATATATTTTTTT-AAAAT-GTTTTTA
544381 AAACTATATAT
63 AAACTATATAT
* * * *
544392 TATATATATTTTCGAAAAAT-ATTCTCAAATTATATATTATATAT
1 TATATATATTTTC-AAAAATGTTTTTAAAACTATATATTATATAT
544436 GTTATATGTA
Statistics
Matches: 230, Mismatches: 28, Indels: 26
0.81 0.10 0.09
Matches are distributed among these distances:
73 6 0.03
74 77 0.33
75 72 0.31
76 13 0.06
77 49 0.21
78 7 0.03
79 6 0.03
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.50
Consensus pattern (73 bp):
TATATATATTTTCAAAAATGTTTTTAAAACTATATATTATATATTTTTTTAAAATGTTTTTAAAA
CTATATAT
Found at i:545223 original size:3 final size:3
Alignment explanation
Indices: 545217--545279 Score: 63
Period size: 3 Copynumber: 20.0 Consensus size: 3
545207 ATTTTTGTTT
** *
545217 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA ATA TTA TATA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA T-TA
*
545264 TATA TTA CTA TTA TTA
1 T-TA TTA TTA TTA TTA
545280 AAAAATAATT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
3 40 0.78
4 11 0.22
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:545711 original size:21 final size:21
Alignment explanation
Indices: 545686--545728 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
545676 CCCTGCAAAC
* * *
545686 AAAAATAACAGGGAAGGGAGA
1 AAAAAAAACAGAGAAGAGAGA
545707 AAAAAAAACAGAGAAGAGAGA
1 AAAAAAAACAGAGAAGAGAGA
545728 A
1 A
545729 GAAAGAAAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.65, C:0.05, G:0.28, T:0.02
Consensus pattern (21 bp):
AAAAAAAACAGAGAAGAGAGA
Found at i:546700 original size:3 final size:3
Alignment explanation
Indices: 546692--546721 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
546682 TTTACTTTTA
*
546692 ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
546722 TAGCTATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:546947 original size:119 final size:116
Alignment explanation
Indices: 546812--547050 Score: 293
Period size: 120 Copynumber: 2.0 Consensus size: 116
546802 TTTAATCATT
* * * *
546812 TTTTAATATTTATTTATTTTTCAATAT-TAAG-AAAGGGCAGTCTTAAAACAACTGGATGTCCAT
1 TTTTAATATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGT-CAT
*
546875 TTTCTGATATTTTTAAATAAATAAATATCCTATTTTATAAATTATATATTAATTG
65 TTTCTGATATTTATAAATAAATAAATATCCTA-TTTATAAA-TATATA-TAATTG
* * * ** *
546930 TTTTAATTATTTTTTTATTTTTTAATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCAT
1 TTTTAA-TATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCAT
** *
546995 TTTCTGATATTTATAAATAAATAAATATTTTATTTATAAATATATATAATTT
65 TTTCTGATATTTATAAATAAATAAATATCCTATTTATAAATATATATAATTG
547047 TTTT
1 TTTT
547051 TTTCATAATT
Statistics
Matches: 104, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
117 9 0.09
118 12 0.12
119 27 0.26
120 35 0.34
121 21 0.20
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (116 bp):
TTTTAATATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCATT
TTCTGATATTTATAAATAAATAAATATCCTATTTATAAATATATATAATTG
Found at i:547602 original size:13 final size:14
Alignment explanation
Indices: 547567--547603 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
547557 TTTTTATTAC
547567 TTATTATT-TTTAT
1 TTATTATTATTTAT
*
547580 ATATTATTATTTAT
1 TTATTATTATTTAT
547594 TTATT-TTATT
1 TTATTATTATT
547604 CAAGTATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TTATTATTATTTAT
Found at i:547603 original size:16 final size:16
Alignment explanation
Indices: 547557--547591 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
547547 TCTTTCAAAT
547557 TTTTTAT-TACTTATTA
1 TTTTTATATA-TTATTA
547573 TTTTTATATATTATTA
1 TTTTTATATATTATTA
547589 TTT
1 TTT
547592 ATTTATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.89
17 2 0.11
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTTATATATTATTA
Found at i:549203 original size:27 final size:27
Alignment explanation
Indices: 549167--549226 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
549157 CATTCACATA
549167 TTTACATTTGCATTTACATTTGCATTT
1 TTTACATTTGCATTTACATTTGCATTT
* * *
549194 TTTACGTTTGTATTTACATTTTCA-TT
1 TTTACATTTGCATTTACATTTGCATTT
549220 TTTACAT
1 TTTACAT
549227 AATTACATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.13, G:0.07, T:0.58
Consensus pattern (27 bp):
TTTACATTTGCATTTACATTTGCATTT
Found at i:549220 original size:12 final size:12
Alignment explanation
Indices: 549166--549193 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
549156 ACATTCACAT
549166 ATTTACATTTGC
1 ATTTACATTTGC
549178 ATTTACATTTGC
1 ATTTACATTTGC
549190 ATTT
1 ATTT
549194 TTTACGTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.14, G:0.07, T:0.54
Consensus pattern (12 bp):
ATTTACATTTGC
Found at i:549225 original size:14 final size:14
Alignment explanation
Indices: 549139--549226 Score: 51
Period size: 14 Copynumber: 6.5 Consensus size: 14
549129 TACTATACAA
*
549139 TTTACATTTTTATT
1 TTTACATTTTCATT
* ** *
549153 GTTACATTCACATA
1 TTTACATTTTCATT
*
549167 TTTACATTTGCA--
1 TTTACATTTTCATT
*
549179 TTTACATTTGCATTT
1 TTTACATTTTCA-TT
*
549194 TTTACGTTTGT-A--
1 TTTACATTT-TCATT
549206 TTTACATTTTCATT
1 TTTACATTTTCATT
549220 TTTACAT
1 TTTACAT
549227 AATTACATTT
Statistics
Matches: 56, Mismatches: 11, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
11 1 0.02
12 21 0.38
14 25 0.45
15 9 0.16
ACGTcount: A:0.24, C:0.14, G:0.06, T:0.57
Consensus pattern (14 bp):
TTTACATTTTCATT
Found at i:553484 original size:114 final size:114
Alignment explanation
Indices: 553283--553502 Score: 350
Period size: 114 Copynumber: 1.9 Consensus size: 114
553273 CACGTTCTCG
* * * *
553283 TAGTAGAAATAATGAGACCCAATAGCTTCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTT
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGATTC
* * *
553348 GGTATGAACCCTAAAACTAATCATTAGATTTGAAAGATGAATTTGCTCA
66 GGTAGGAACCCTAAAACCAATCATTAGAATTGAAAGATGAATTTGCTCA
*
553397 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTTC
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGATTC
* *
553462 GGTAGGAACCCTAGAACCAATCATTGGAATTGAAAGATGAA
66 GGTAGGAACCCTAAAACCAATCATTAGAATTGAAAGATGAA
553503 CTGCATGATC
Statistics
Matches: 96, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 96 1.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (114 bp):
TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGATTC
GGTAGGAACCCTAAAACCAATCATTAGAATTGAAAGATGAATTTGCTCA
Found at i:555617 original size:50 final size:50
Alignment explanation
Indices: 555537--555637 Score: 175
Period size: 50 Copynumber: 2.0 Consensus size: 50
555527 TGATTGAGAA
*
555537 ATCTTGGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATATTTTAC
1 ATCTGGGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATATTTTAC
* *
555587 ATCTGGGCAGAAACCACAGGAAATGATGAATGTGTTGTCAAATGTTTTAC
1 ATCTGGGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATATTTTAC
555637 A
1 A
555638 AACCAGTTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (50 bp):
ATCTGGGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATATTTTAC
Found at i:556033 original size:22 final size:22
Alignment explanation
Indices: 556007--556083 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
555997 ATCTACACTC
556007 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
556029 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
* *
556051 TTTAAAGATAATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
556073 TTCAAAGATGA
1 TTCAAAGATGA
556084 AAGCTTTATT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:557005 original size:46 final size:46
Alignment explanation
Indices: 556761--557412 Score: 1083
Period size: 46 Copynumber: 14.0 Consensus size: 46
556751 CTATTTCCCA
556761 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC--AAAAACCTTCGGGT
* *
556809 CATCTGTAAGTCCTTTAGTGCATGATGTTTTCAAAAAACCTTCGGGC
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAAACCTTCGGGT
556856 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC--AAAAACCTTCGGGT
*
556904 CATTTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC--AAAAACCTTCGGGT
556952 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
556998 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC--AAAAACCTTCGGGT
557046 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAAACCTTCGGGT
*
557093 CATCTGTAAGTCCTTCAGTGCATGAT-TTTTCAAAAGCCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
*
557138 TATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
557184 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
557230 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
*
557276 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAGCCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
* * *
557322 TATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAGCCTTAGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
* * *
557367 CATCTTTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGG
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAA-CCTTCGGG
557413 AGCTTTTTGA
Statistics
Matches: 579, Mismatches: 19, Indels: 13
0.95 0.03 0.02
Matches are distributed among these distances:
45 78 0.13
46 239 0.41
47 93 0.16
48 169 0.29
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.35
Consensus pattern (46 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
Found at i:557644 original size:3 final size:3
Alignment explanation
Indices: 557636--557682 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
557626 TTGTTTTTAA
*
557636 TAT TAT TAT TAA TAT TA- TAT ATAT TAT TA- TAT ATAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT -TAT TAT TAT TAT
557681 TA
1 TA
557683 AAAAATAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
2 4 0.11
3 28 0.74
4 6 0.16
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:557647 original size:12 final size:12
Alignment explanation
Indices: 557632--557679 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
557622 ATTTTTGTTT
557632 TTAATATTATTA
1 TTAATATTATTA
557644 TTAATATTA-TA
1 TTAATATTATTA
557655 -T-ATATTATTA
1 TTAATATTATTA
557665 -TATATATTATTA
1 TTA-ATATTATTA
557677 TTA
1 TTA
557680 TTAAAAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
9 6 0.19
10 4 0.12
11 2 0.06
12 18 0.56
13 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TTAATATTATTA
Found at i:557659 original size:21 final size:20
Alignment explanation
Indices: 557635--557682 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 20
557625 TTTGTTTTTA
557635 ATATTATTAT-TAATATTATAT
1 ATATTATTATAT-ATATTAT-T
557656 ATATTATTATATATATTATT
1 ATATTATTATATATATTATT
557676 ATTATTA
1 A-TATTA
557683 AAAAATAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 2 0.08
21 22 0.88
22 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATATTATTATATATATTATT
Found at i:558114 original size:21 final size:21
Alignment explanation
Indices: 558089--558131 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
558079 CCCTGTAAAC
* * *
558089 AAAAACAACAGGGAAGGGAGA
1 AAAAAAAACAGAGAAGAGAGA
558110 AAAAAAAACAGAGAAGAGAGA
1 AAAAAAAACAGAGAAGAGAGA
558131 A
1 A
558132 GAAGAAAGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.65, C:0.07, G:0.28, T:0.00
Consensus pattern (21 bp):
AAAAAAAACAGAGAAGAGAGA
Found at i:559297 original size:120 final size:120
Alignment explanation
Indices: 559180--559412 Score: 303
Period size: 120 Copynumber: 2.0 Consensus size: 120
559170 ATTTTAATCC
* * * *
559180 TGTTTTAA-TATTTATTTATTTTTCAATAT-TAAGAAAGGA-CAATCTTAAAACAACTGGATGTC
1 TGTTTTAATTATTTATTTATTTTTCAATATCGAAGAAAAGAGCAATCTTAAAACAACTAGAAGT-
*
559242 CATTTTCTGATATTTTTAAATAAATAAATATCCTATTTTATAAAT-TATATATTAAT
65 CATTTTCTGATATTTCTAAATAAATAAATATCCTA-TTTATAAATATATATATTAAT
* ** ** *
559298 TGTTTTAATTATTTATTTATTTTTTAATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTC
1 TGTTTTAATTATTTATTTATTTTTCAATATCGAAGAAAAGAGCAATCTTAAAACAACTAGAAGTC
**
559363 ATTTTCTGATATTTCTAAATAAATAAATATTTTATTTATAAATATATATA
66 ATTTTCTGATATTTCTAAATAAATAAATATCCTATTTATAAATATATATA
559413 AATTAATATT
Statistics
Matches: 98, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
118 8 0.08
119 29 0.30
120 46 0.47
121 15 0.15
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.45
Consensus pattern (120 bp):
TGTTTTAATTATTTATTTATTTTTCAATATCGAAGAAAAGAGCAATCTTAAAACAACTAGAAGTC
ATTTTCTGATATTTCTAAATAAATAAATATCCTATTTATAAATATATATATTAAT
Found at i:559309 original size:20 final size:19
Alignment explanation
Indices: 559284--559325 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
559274 CTATTTTATA
559284 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
559304 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
559323 AAT
1 AAT
559326 ATCGAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:559414 original size:29 final size:30
Alignment explanation
Indices: 559381--559438 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
559371 ATATTTCTAA
559381 ATAAATAAATATTTTATTT-ATAAATATAT
1 ATAAATAAATATTTTATTTCATAAATATAT
* * *
559410 ATAAATTAATATTTTTTTTCATAATTATA
1 ATAAATAAATATTTTATTTCATAAATATA
559439 ATTTTGAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (30 bp):
ATAAATAAATATTTTATTTCATAAATATAT
Found at i:561517 original size:62 final size:62
Alignment explanation
Indices: 561444--561570 Score: 204
Period size: 62 Copynumber: 2.0 Consensus size: 62
561434 TGACAACTTA
* *
561444 CTATTCTTATTTGATAATCACATGA-GTCTTGATTATATTTA-AATTTGAATTGAATCAGACTC
1 CTATTCTTATTTGATAATCACAT-ATGTCTTGATTATATTTATAA-TTAAATTGAATCACACTC
561506 CTATTCTTATTTGATAATCACATATGTCTTGATTATATTTATAATTAAATTGAATCACACTC
1 CTATTCTTATTTGATAATCACATATGTCTTGATTATATTTATAATTAAATTGAATCACACTC
561568 CTA
1 CTA
561571 AATAAAGAGT
Statistics
Matches: 61, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
61 1 0.02
62 58 0.95
63 2 0.03
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (62 bp):
CTATTCTTATTTGATAATCACATATGTCTTGATTATATTTATAATTAAATTGAATCACACTC
Found at i:567307 original size:18 final size:18
Alignment explanation
Indices: 567284--567327 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
567274 AACCATAATT
567284 AAATATTGACATGAGCTG
1 AAATATTGACATGAGCTG
567302 AAATATTGACATGAGCTG
1 AAATATTGACATGAGCTG
567320 AAATATTG
1 AAATATTG
567328 GACTATTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.30
Consensus pattern (18 bp):
AAATATTGACATGAGCTG
Found at i:568399 original size:33 final size:32
Alignment explanation
Indices: 568341--568405 Score: 80
Period size: 31 Copynumber: 2.0 Consensus size: 32
568331 ATAAATTTAA
*
568341 TTAAAATATATAGAAATTTATTATTA-TATTT
1 TTAAAATATATAGAAAATTATTATTATTATTT
568372 TTAAAATATATAAAGAATAATTA-TATTATTATTT
1 TTAAAATATAT--AGAA-AATTATTATTATTATTT
568406 CAAATCATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
31 11 0.38
33 9 0.31
34 9 0.31
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (32 bp):
TTAAAATATATAGAAAATTATTATTATTATTT
Found at i:577510 original size:3 final size:3
Alignment explanation
Indices: 577502--577530 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
577492 AACGACTATC
577502 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
577531 GTCTTTCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:577692 original size:2 final size:2
Alignment explanation
Indices: 577685--577720 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
577675 TCGAGACACG
577685 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
577721 GTTCTTGGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:578217 original size:23 final size:23
Alignment explanation
Indices: 578182--578229 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
578172 ATTAAGTACA
*
578182 ATAATATATTAGGTAACGCTTAT
1 ATAATATAATAGGTAACGCTTAT
* *
578205 ATAATGTAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAACGCTTAT
578228 AT
1 AT
578230 TGACATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.38
Consensus pattern (23 bp):
ATAATATAATAGGTAACGCTTAT
Found at i:578645 original size:199 final size:195
Alignment explanation
Indices: 578224--578948 Score: 647
Period size: 199 Copynumber: 3.6 Consensus size: 195
578214 TAGGTAGCGC
* * * * * * * * **
578224 TTATATTGACATATTTTATAATTAAACTGATATATTTATACCGGTAACATTACAAATTTACCTAT
1 TTATGTTGACATATTTTCTCATAAAACCGGTATATTTATA-CTGTTACATTGTAAATTTACCTAT
* * * * *
578289 TATATTATAATTATCGGTTTCAATATTTTTTGGATCGATACAATTT--GAAATGTATCGACACTT
65 TACATTATAATAATCGGTTTCAAT-TTTTTGGGATCGATA-ATTTTAATAAATGTATCGACACTT
* * * * * * *
578352 TATACGTCCACTTCGTTGGGCATTCATTCTGGAAAAAAGTATCGACAGAAACTTAAAAAGTGTCG
128 TATGCGTGCAC-CCGTTTGGCATTCATTCTGGACAAAAGTATCGACACAAA-TTAACAAGTGTCG
578417 ATACA
191 ATACA
* ** * *
578422 TTAT-TTAGACTTATTTTCTCATAAAATTGGTATATTTATATTGGGTACATTGTAAATTTACCTA
1 TTATGTT-GACATATTTTCTCATAAAACCGGTATATTTATACT-GTTACATTGTAAATTTACCTA
* * * *
578486 TCACATTGTAATAATCGGTTTCGATGTTTTTGGGATCGATAATTTTAATAAATGTATCGACACTC
64 TTACATTATAATAATCGGTTTCAAT-TTTTTGGGATCGATAATTTTAATAAATGTATCGACACTT
*
578551 TATGCGTGCACCCGTTTGGCATTCATTATGGACAAAATGTATCGACACAAATTTAACAAGTGTCG
128 TATGCGTGCACCCGTTTGGCATTCATTCTGGACAAAA-GTATCGACACAAA-TTAACAAGTGTCG
*
578616 ATACT
191 ATACA
* ** * * *
578621 TTATGCTCTCCTATTTTCTCATAAAACCAGTATATTTATACCTGTTACATTGTAAATTTACATAT
1 TTATGTTGACATATTTTCTCATAAAACCGGTATATTTATA-CTGTTACATTGTAAATTTACCTAT
* * ** * * * * *
578686 TATA-TACAAATTTAA-AAGTATCAATTTTATTGGGATCAATACTTTTAATAAATGTACCGACAT
65 TACATTA-TAA--TAATCGGTTTCAATTTT-TTGGGATCGATAATTTTAATAAATGTATCGACAC
* * *
578749 TTTATGTGAGCACCTCGTTTGGTCATTCATTCTGGACAATAAGTATCTACACAAATTACACAAGT
126 TTTATGCGTGCACC-CGTTTGG-CATTCATTCTGGACAA-AAGTATCGACACAAATTA-ACAAGT
578814 GTCGATACA
187 GTCGATACA
* * * * * *
578823 TTATGTTGACATGTTTTCTAAT-TAACCGGTATATTTGTACCAGTTACATTGTTAATTTACCTAT
1 TTATGTTGACATATTTTCTCATAAAACCGGTATATTTATA-CTGTTACATTGTAAATTTACCTAT
* * *
578887 TACATTATAATTATTGGTTTCGATATTTTTTGGG-TCGATACTTTTAGA-AAATGTATCGACAC
65 TACATTATAATAATCGGTTTC-A-ATTTTTTGGGATCGATAATTTTA-ATAAATGTATCGACAC
578949 ATATTTAGGT
Statistics
Matches: 426, Mismatches: 81, Indels: 38
0.78 0.15 0.07
Matches are distributed among these distances:
197 6 0.01
198 105 0.25
199 112 0.26
200 76 0.18
201 61 0.14
202 64 0.15
203 2 0.00
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (195 bp):
TTATGTTGACATATTTTCTCATAAAACCGGTATATTTATACTGTTACATTGTAAATTTACCTATT
ACATTATAATAATCGGTTTCAATTTTTTGGGATCGATAATTTTAATAAATGTATCGACACTTTAT
GCGTGCACCCGTTTGGCATTCATTCTGGACAAAAGTATCGACACAAATTAACAAGTGTCGATACA
Found at i:580219 original size:199 final size:200
Alignment explanation
Indices: 579865--580840 Score: 1240
Period size: 200 Copynumber: 4.9 Consensus size: 200
579855 AGATCAGATT
* * * ** * *
579865 ACTTTTTATAAATGTATCGACACTTTATACATGCACCATTTTGGGCATTCATTTTGGACAAAATG
1 ACTTTTTATAAATGTATCGACACTTTATGCGTTCACCATTTTGGAAATTCATTCTGGACAAAAAG
* * * *
579930 TATCGACA-CATAATTAAAAAGTGTCGATAAATTATGTAGACCTATTCTTAAATAAAACCGGTAT
66 TATCGACACCA-ATTTAAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTAT
* ** * *
579994 ATTTACACCTATTACATTAAAAAATTACCTATTACATTATAATTATG-GGTTCGATGTCTCTGGG
130 ATTTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGTGGTTCGATGTCTCTGAG
580058 ATCGAC
195 ATCGAC
* * * * *
580064 ACGTTTTAAAAATGTATTGACACTTTATGCGTTCATCATTTTGGACATTCATTCTGGACAAAAAG
1 ACTTTTTATAAATGTATCGACACTTTATGCGTTCACCATTTTGGAAATTCATTCTGGACAAAAAG
** * *
580129 TATCGACACCAATTTAAATTGTGTCGACACATTATGTAGACCTATTCTAACATAAAACCGGTATA
66 TATCGACACCAATTTAAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTATA
* * * *
580194 TTTATACCGGTTACATTACAAAATTACCTATTTCATTATAATTATGTGTTTCGATATCTCTGGGA
131 TTTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGTGGTTCGATGTCTCTGAGA
580259 TCGAC
196 TCGAC
* * * * * * * *
580264 ACTTTTAAAAAATGTATCGACACTTTATGGGTGCACCCTTTTAGG-TATTCCTTCTGGACAAACA
1 ACTTTTTATAAATGTATCGACACTTTATGCGTTCACCATTTT-GGAAATTCATTCTGGACAAAAA
* ** * * * *
580328 GTATCGACACAAATTCCATAAGTGTCGATACATTATGTAGATCTATTATCTCATAAAACCGGTAT
65 GTATCGACACCAATTTAAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTAT
* ** * ** * *
580393 AGTTATATTGTTTACATTGTAAATTTACCTATTACATTATAATTATG-GGTTTCGATGTTTCTGA
130 ATTTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGTGG-TTCGATGTCTCTGA
*
580457 GATCGAT
194 GATCGAC
*
580464 ATTTTTTATAAATGTATCGACACTTTATGCGTTCACCATTTTGGAAATTCATTCTGGACAAAAAG
1 ACTTTTTATAAATGTATCGACACTTTATGCGTTCACCATTTTGGAAATTCATTCTGGACAAAAAG
*
580529 TATCGACACCAATTTAAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACTGGTATA
66 TATCGACACCAATTTAAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTATA
** * * * * *
580594 TTTATACTAGTTATATTACAAAATTACCTATTACATTATAATTATGTGTTTTGATGTTTTTGAGA
131 TTTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGTGGTTCGATGTCTCTGAGA
*
580659 TCGAT
196 TCGAC
*
580664 ACTTTTTATAAATGTATCGACACTTTATGCGTTCACCATTTTGGAAATTCATTCTGGAAAAAAAA
1 ACTTTTTATAAATGTATCGACACTTTATGCGTTCACCATTTTGGAAATTCATTCTGG-ACAAAAA
* ** * *
580729 GTATCGACACCAATTTAAAAAGTATATATATATTATGTAGACCTATTCTCATATAAAACCGGTAT
65 GTATCGACACCAATTTAAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTAT
* * *
580794 ATTTATATCGGTTATAATACAAAATTACCTATTACATTATAATTATG
130 ATTTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATG
580841 ATTATGAGTT
Statistics
Matches: 672, Mismatches: 98, Indels: 12
0.86 0.13 0.02
Matches are distributed among these distances:
199 154 0.23
200 407 0.61
201 111 0.17
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (200 bp):
ACTTTTTATAAATGTATCGACACTTTATGCGTTCACCATTTTGGAAATTCATTCTGGACAAAAAG
TATCGACACCAATTTAAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTATA
TTTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGTGGTTCGATGTCTCTGAGA
TCGAC
Found at i:581267 original size:19 final size:19
Alignment explanation
Indices: 581243--581291 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
581233 TTATATTCAC
581243 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
581262 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
581281 ATACAAAATTA
1 ATACAAAATTA
581292 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:583153 original size:21 final size:21
Alignment explanation
Indices: 583129--583171 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
583119 CACTTCCCCT
583129 TCTCAAGTGTCTCTTCGACTC
1 TCTCAAGTGTCTCTTCGACTC
*
583150 TCTCAAGTTTCTCTTCGACTC
1 TCTCAAGTGTCTCTTCGACTC
583171 T
1 T
583172 TGATTGTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.33, G:0.12, T:0.42
Consensus pattern (21 bp):
TCTCAAGTGTCTCTTCGACTC
Found at i:583578 original size:22 final size:23
Alignment explanation
Indices: 583550--583604 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
583540 AACCTTCATT
*
583550 TATAATAAAAT-TTATAATTTTA
1 TATAATAAAATACTATAATTTTA
*
583572 TATAATAACTATACTATAATTTTA
1 TATAATAA-AATACTATAATTTTA
583596 TATAA-AAAA
1 TATAATAAAA
583605 CAAAAATGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 9 0.32
23 4 0.14
24 15 0.54
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (23 bp):
TATAATAAAATACTATAATTTTA
Found at i:585843 original size:182 final size:182
Alignment explanation
Indices: 585536--586391 Score: 1302
Period size: 182 Copynumber: 4.7 Consensus size: 182
585526 TACGCGTACT
* *
585536 TATTAAAGTATCGACACTTTCAATATATCCAGTAGCGCTTTACTGGTTTTGTCATTTCGAGACCG
1 TATTAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTGTCATTTCGAGACCG
* * *
585601 GTTTTATCATATTTTTACCTGTTATATCGTTATGGATCGATACATTTTTATAAAGTATCGACACT
66 ATTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACACT
* *
585666 TTATATGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
131 TTATAGGCGCTAAAACTACTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
** * * * * *
585718 TATTAAAGTATCGACACTTTCAATATATCCGGTCTCTCTATAGCGGTTTTGTCATTTAGAGATCG
1 TATTAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTGTCATTTCGAGACCG
* * *
585783 ATTTTGTCATATTTTTACCTGTTATATCTTTATGGATCGATACATTATTATAAAGTATCGACACT
66 ATTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACACT
*
585848 TTATAGGCGCTAAAACTGA-TTCTCTTTTAAATTTACAAAGTGTCGATACTTA
131 TTATAGGCGCTAAAACT-ACTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
* * * * * * *
585900 TATTAAAGTATCAACACTTTCAATATATTCGGTCGCTCTATACCGGTTTTATCATTTGGAGACCG
1 TATTAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTGTCATTTCGAGACCG
* *
585965 ATTTTGTTATATTTTTACCTGTTATATCGTTGTGGATCGATACATTATTATAAAGTATCGACACT
66 ATTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACACT
* *
586030 TTATAGGCGCTAAAACTACTTCTCTTTTAAATTCACAAATTGTCGATTCTTA
131 TTATAGGCGCTAAAACTACTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
* *
586082 TATTAAAGTATCGACACTTTCAATATATCCGATAGCGCTTTACCGGTTTTGTCTTTTCGAGACCG
1 TATTAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTGTCATTTCGAGACCG
*
586147 ATTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATAGACACT
66 ATTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACACT
586212 TTATAGGCGCTAAAACTACTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
131 TTATAGGCGCTAAAACTACTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
* * * *
586264 TATTAAAGTATCGACACTTTTAATATATCCGATATCGCTTTACCGGTTTTGTC-TATTCGTGACC
1 TATTAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTGTCAT-TTCGAGACC
* * * * * *
586328 GGTTTTGTAATATTTTTACCTGTAATATTGATGTGGATCGATACATTTTTATAAAGAATCGACA
65 GATTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACA
586392 TAAACCGATA
Statistics
Matches: 618, Mismatches: 53, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
181 2 0.00
182 616 1.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (182 bp):
TATTAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTGTCATTTCGAGACCG
ATTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACACT
TTATAGGCGCTAAAACTACTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
Found at i:587912 original size:4 final size:4
Alignment explanation
Indices: 587903--587927 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
587893 CATGATGAAC
587903 ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT A
587928 GTAATTAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:593882 original size:21 final size:21
Alignment explanation
Indices: 593834--593885 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
593824 TGAACTATGT
593834 ATTTAATCATCTACTTATTTC
1 ATTTAATCATCTACTTATTTC
** *
593855 ACATAATCATCTACTTATTTT
1 ATTTAATCATCTACTTATTTC
*
593876 TTTTAATCAT
1 ATTTAATCAT
593886 ACAATTATTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.52
Consensus pattern (21 bp):
ATTTAATCATCTACTTATTTC
Found at i:593893 original size:21 final size:23
Alignment explanation
Indices: 593869--593910 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
593859 AATCATCTAC
593869 TTATTTT-TTT-TAATCATACAA
1 TTATTTTGTTTGTAATCATACAA
*
593890 TTATTTTGTTTGTAATTATAC
1 TTATTTTGTTTGTAATCATAC
593911 CAAACATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 3 0.17
23 8 0.44
ACGTcount: A:0.29, C:0.07, G:0.05, T:0.60
Consensus pattern (23 bp):
TTATTTTGTTTGTAATCATACAA
Found at i:600296 original size:15 final size:12
Alignment explanation
Indices: 600262--600287 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
600252 ACCCACAGTT
600262 GTTAAAATAATA
1 GTTAAAATAATA
600274 GTTAAAATAATA
1 GTTAAAATAATA
600286 GT
1 GT
600288 GTAGAAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.35
Consensus pattern (12 bp):
GTTAAAATAATA
Found at i:601575 original size:52 final size:52
Alignment explanation
Indices: 601514--601616 Score: 206
Period size: 52 Copynumber: 2.0 Consensus size: 52
601504 TATTATTGAT
601514 ATAACATAGAGGTGTATGCTTAAATACATCTAATATTTGAAGGATTCTTACA
1 ATAACATAGAGGTGTATGCTTAAATACATCTAATATTTGAAGGATTCTTACA
601566 ATAACATAGAGGTGTATGCTTAAATACATCTAATATTTGAAGGATTCTTAC
1 ATAACATAGAGGTGTATGCTTAAATACATCTAATATTTGAAGGATTCTTAC
601617 TGTGCGTATT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.35
Consensus pattern (52 bp):
ATAACATAGAGGTGTATGCTTAAATACATCTAATATTTGAAGGATTCTTACA
Found at i:607815 original size:12 final size:12
Alignment explanation
Indices: 607800--607826 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
607790 ATAAACTAAT
607800 ATATAAAACACA
1 ATATAAAACACA
607812 ATATAAAACACA
1 ATATAAAACACA
607824 ATA
1 ATA
607827 AGAAAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.67, C:0.15, G:0.00, T:0.19
Consensus pattern (12 bp):
ATATAAAACACA
Found at i:611255 original size:4 final size:4
Alignment explanation
Indices: 611246--611272 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
611236 TATTGTTTCC
611246 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
611273 TCTTCGTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:622658 original size:105 final size:105
Alignment explanation
Indices: 622476--622881 Score: 717
Period size: 105 Copynumber: 3.9 Consensus size: 105
622466 TACCCATAGC
622476 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
622541 GGACCGCTGGTTGTCAACAAACATTTCTCAGATTCAGAGT
66 GGACCGCTGGTTGTCAACAAACATTTCTCAGATTCAGAGT
*
622581 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
*
622646 GGACCGCTGGTTGTCAACAAACATTTCTCAGATCCAGAGT
66 GGACCGCTGGTTGTCAACAAACATTTCTCAGATTCAGAGT
* * *
622686 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGATGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* * *
622751 GGACCGCTGGTTGTCATCAAACATTTCTCCA-ATTTAGAGC
66 GGACCGCTGGTTGTCAACAAACATTTCT-CAGATTCAGAGT
622791 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
622856 GGACCGCTGGTTGTCAACAAA-ATTTC
66 GGACCGCTGGTTGTCAACAAACATTTC
622882 CATGTTTAAA
Statistics
Matches: 288, Mismatches: 12, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
104 5 0.02
105 281 0.98
106 2 0.01
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (105 bp):
CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
GGACCGCTGGTTGTCAACAAACATTTCTCAGATTCAGAGT
Found at i:623005 original size:269 final size:265
Alignment explanation
Indices: 622624--623120 Score: 635
Period size: 269 Copynumber: 1.8 Consensus size: 265
622614 CCAGACAACG
* * * *
622624 CAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATCCAGAGTCAA
1 CAAGTTCAACTTCACAACGAAGGGACCGCTGGCTGTCAACAAACATTTCCCAGATCC--A--CAA
** * *
622689 TTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGATGAAGGGA
62 TTTCAACTTCACAGAAAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACAACGAAGGGA
** * * *
622754 CCGCTGGTTGTCATCAAAC-ATTTCTCCAATTTAGAGCCAATTTCAACTTCACA-ACGAAGGATA
127 CCGCTGACTGTCAACAAACAATTT-T-C-----AGAGCCAAGTTCAACTTCACAGA-AAAGGATA
*
622817 TTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAATTTC
184 TTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAAATTTC
622882 CATGTTTAAAGACAGCA
249 CATGTTTAAAGACAGCA
*
622899 CAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAATTTCCCA-AT-C-CAATTT
1 CAAGTTCAACTTCACAACGAAGGGACCGCTGGCTGTCAACAAAC-ATTTCCCAGATCCACAATTT
* * * *
622961 CAACTTCACAGAAAATGATATTGGACTCGAGACAGCTCAAGTTCAACTTCACAACGAAGGGGCCG
65 CAACTTCACAGAAAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACAACGAAGGGACCG
* *
623026 CTGACTGTCAACAAACAATTTTCAGAGCCAAGTTCAACTTCACAGAAAATGATATTGGACTCGAG
130 CTGACTGTCAACAAACAATTTTCAGAGCCAAGTTCAACTTCACAGAAAAGGATATTGGACTCCAG
* *
623091 ACAGCTCAAGTTCAACTTCACAACGAAGGG
195 ACAACGCAAGTTCAACTTCACAACGAAGGG
623121 GCTGACTGTC
Statistics
Matches: 196, Mismatches: 23, Indels: 18
0.83 0.10 0.08
Matches are distributed among these distances:
263 63 0.32
264 1 0.01
268 1 0.01
269 77 0.39
270 4 0.02
274 1 0.01
275 42 0.21
276 7 0.04
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (265 bp):
CAAGTTCAACTTCACAACGAAGGGACCGCTGGCTGTCAACAAACATTTCCCAGATCCACAATTTC
AACTTCACAGAAAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGC
TGACTGTCAACAAACAATTTTCAGAGCCAAGTTCAACTTCACAGAAAAGGATATTGGACTCCAGA
CAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAAATTTCCATGTTTAAAGA
CAGCA
Found at i:623006 original size:164 final size:166
Alignment explanation
Indices: 622729--623040 Score: 416
Period size: 164 Copynumber: 1.9 Consensus size: 166
622719 CGAGACAACG
* * * *
622729 CAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCATCAAACATTTCTCCAATTTAGAGCCAA
1 CAAGTTCAACTTCACAACGAAGGGACCGCTGGCTGTCAACAAACATTTCTCCAA-TT--A-CCAA
* *
622794 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGA
62 TTTCAACTTCACAACAAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGA
**
622859 CCGCTGGTTGTCAACAAAATTTCCATGTTTAAAGACAGCA
127 CCGCTGACTGTCAACAAAATTTCCATGTTTAAAGACAGCA
*
622899 CAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAATTTC-CCAA-T-CCAATTT
1 CAAGTTCAACTTCACAACGAAGGGACCGCTGGCTGTCAACAAAC-ATTTCTCCAATTACCAATTT
* * * * *
622961 CAACTTCACAGA-AAATGATATTGGACTCGAGACAGCTCAAGTTCAACTTCACAACGAAGGGGCC
65 CAACTTCACA-ACAAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACC
623025 GCTGACTGTCAACAAA
129 GCTGACTGTCAACAAA
623041 CAATTTTCAG
Statistics
Matches: 126, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
164 76 0.60
165 1 0.01
168 1 0.01
170 43 0.34
171 5 0.04
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (166 bp):
CAAGTTCAACTTCACAACGAAGGGACCGCTGGCTGTCAACAAACATTTCTCCAATTACCAATTTC
AACTTCACAACAAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGC
TGACTGTCAACAAAATTTCCATGTTTAAAGACAGCA
Found at i:623062 original size:99 final size:99
Alignment explanation
Indices: 622891--623237 Score: 549
Period size: 99 Copynumber: 3.5 Consensus size: 99
622881 CCATGTTTAA
* * * *
622891 AGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAATTTCCCA-ATC
1 AGACAGCTCAAGTTCAACTTCACAACGAAGGGGCCGCTGACTGTCAACAAACAATTT-TCAGAGC
622955 CAATTTCAACTTCACAGAAAATGATATTGGACTCG
65 CAATTTCAACTTCACAGAAAATGATATTGGACTCG
622990 AGACAGCTCAAGTTCAACTTCACAACGAAGGGGCCGCTGACTGTCAACAAACAATTTTCAGAGCC
1 AGACAGCTCAAGTTCAACTTCACAACGAAGGGGCCGCTGACTGTCAACAAACAATTTTCAGAGCC
*
623055 AAGTTCAACTTCACAGAAAATGATATTGGACTCG
66 AATTTCAACTTCACAGAAAATGATATTGGACTCG
623089 AGACAGCTCAAGTTCAACTTCACAACGAA-GGG--GCTGACTGTCAACAAACAATTTTCAGAGCC
1 AGACAGCTCAAGTTCAACTTCACAACGAAGGGGCCGCTGACTGTCAACAAACAATTTTCAGAGCC
** *
623151 AATTTCAACTTCACAGCGAAGGATATTGGACTCG
66 AATTTCAACTTCACAGAAAATGATATTGGACTCG
* * **
623185 AGACAACGCAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAACA
1 AGACAGCTCAAGTTCAACTTCACAACGAAGGGGCCGCTGACTGTCAACAAACA
623238 CTTTCCAAGT
Statistics
Matches: 231, Mismatches: 13, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
96 87 0.38
97 3 0.01
98 5 0.02
99 136 0.59
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.20
Consensus pattern (99 bp):
AGACAGCTCAAGTTCAACTTCACAACGAAGGGGCCGCTGACTGTCAACAAACAATTTTCAGAGCC
AATTTCAACTTCACAGAAAATGATATTGGACTCG
Found at i:623189 original size:96 final size:98
Alignment explanation
Indices: 622891--623291 Score: 520
Period size: 99 Copynumber: 4.0 Consensus size: 98
622881 CCATGTTTAA
* * * *
622891 AGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAATTTCCCA-ATC
1 AGACAGCTCAAGTTCAACTTCACAACGAAGGGG-CGCTGACTGTCAACAAACAATTT-TCAGAGC
*
622955 CAATTTCAACTTCACAGAAAATGATATTGGACTCG
64 CAATTTCAACTTCACAGAAAAGGATATTGGACTCG
622990 AGACAGCTCAAGTTCAACTTCACAACGAAGGGGCCGCTGACTGTCAACAAACAATTTTCAGAGCC
1 AGACAGCTCAAGTTCAACTTCACAACGAAGGGG-CGCTGACTGTCAACAAACAATTTTCAGAGCC
* *
623055 AAGTTCAACTTCACAGAAAATGATATTGGACTCG
65 AATTTCAACTTCACAGAAAAGGATATTGGACTCG
623089 AGACAGCTCAAGTTCAACTTCACAACGAA-GGG-GCTGACTGTCAACAAACAATTTTCAGAGCCA
1 AGACAGCTCAAGTTCAACTTCACAACGAAGGGGCGCTGACTGTCAACAAACAATTTTCAGAGCCA
**
623152 ATTTCAACTTCACAGCGAAGGATATTGGACTCG
66 ATTTCAACTTCACAGAAAAGGATATTGGACTCG
* * ** *
623185 AGACAACGCAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAACACTTTCCAAGTTT
1 AGACAGCTCAAGTTCAACTTCACAACGAAGGGG-CGCTGACTGTCAAC-AA-A-----CAATTTT
* ** *
623250 CAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGCCTCG
58 CAGAGCCAATTTCAACTTCACAGAAAAGGATATTGGACTCG
623291 A
1 A
623292 AGCAACACAA
Statistics
Matches: 275, Mismatches: 16, Indels: 15
0.90 0.05 0.05
Matches are distributed among these distances:
96 87 0.32
97 3 0.01
98 5 0.02
99 131 0.48
100 2 0.01
101 1 0.00
106 46 0.17
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (98 bp):
AGACAGCTCAAGTTCAACTTCACAACGAAGGGGCGCTGACTGTCAACAAACAATTTTCAGAGCCA
ATTTCAACTTCACAGAAAAGGATATTGGACTCG
Found at i:628931 original size:2 final size:2
Alignment explanation
Indices: 628924--628958 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
628914 ATCAGGTAAT
628924 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
628959 TACTTTTACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:637019 original size:19 final size:19
Alignment explanation
Indices: 636983--637020 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
636973 TATTCATCGA
*
636983 TTATTTTTATTGTTATTTT
1 TTATTTTTATTGTAATTTT
637002 TTATTTTTGATTG-AATTTT
1 TTATTTTT-ATTGTAATTTT
637021 GTTCAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.18, C:0.00, G:0.08, T:0.74
Consensus pattern (19 bp):
TTATTTTTATTGTAATTTT
Found at i:640337 original size:28 final size:28
Alignment explanation
Indices: 640296--640352 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
640286 AACAAAATCA
* *
640296 TGCTTCACTAACCGGCTGCTTTGAATTT
1 TGCTCCACCAACCGGCTGCTTTGAATTT
640324 TGCTCCACCAACCGGCTGCTTTGAATTT
1 TGCTCCACCAACCGGCTGCTTTGAATTT
640352 T
1 T
640353 CAACAATCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.18, C:0.28, G:0.18, T:0.37
Consensus pattern (28 bp):
TGCTCCACCAACCGGCTGCTTTGAATTT
Found at i:642662 original size:438 final size:438
Alignment explanation
Indices: 641847--642715 Score: 1522
Period size: 438 Copynumber: 2.0 Consensus size: 438
641837 ACTTAGCCTT
* *
641847 GCCATTCTTTCCCGATGACTTTCCTAGGCTATTAACAGTCGATTGCTCACATTGGCCATTCGAAT
1 GCCATTCTTTCCCGATGACTTTCCTAGGCTATTAACAGTCGATGGCTCACATTGGCCATTCGAAG
*
641912 AGCTTCCTCTACCATCTCCCCGCTGCACATTTTCCCGGTCTCCCCCACTGTTGCCACTATCCCTG
66 AGCTTCCTCTACCATCTCCCCGCTGCACATTTTCCCGGTCTCCCCCACTGTCGCCACTATCCCTG
*
641977 GGCATGGGCCTGGATGACACATTGCTACTTGGCTTGACTCCTGCAAGCTCAGTCAGCTTTCCAGC
131 GGCATGGGCCTGGACGACACATTGCTACTTGGCTTGACTCCTGCAAGCTCAGTCAGCTTTCCAGC
* *
642042 TACAACTATGGCCTCCGAAAGTCTCTGGGCATCACCTTGCTCTCTCCCGAGCATTGGCCCTGGTT
196 TACAACTATGGCCTCCGAAAGTCTCTGGGCATCACCTTGCTCTCTCCCGAGCATTGCCCCTGGTC
*
642107 TAAGTCCTTCCAAGAAGGTCTTGAGCGCAGCATTCAACTTCTCAATTTTCACATTCCCTTCGTCT
261 TAAGTCCTTCCAAGAAGGTCTTGAGCGCACCATTCAACTTCTCAATTTTCACATTCCCTTCGTCT
*
642172 GCGCCATCTCTCCCACTCGAATCTGGCTTTGTTTGAATCATTTCTGACAATTTCTGTGAACCACC
326 GCGCCATCGCTCCCACTCGAATCTGGCTTTGTTTGAATCATTTCTGACAATTTCTGTGAACCACC
* *
642237 GTGTATTAGAACACATTCGTCGATAAATTCATATCGCCGACGACATTG
391 GTGTATTAGAACACATCCGTCGACAAATTCATATCGCCGACGACATTG
*
642285 GCCATTCTTTCCCGATGACTTTCCTAGGCTATTAACTGTCGATGGCTCACATTGGCCATTCGAAG
1 GCCATTCTTTCCCGATGACTTTCCTAGGCTATTAACAGTCGATGGCTCACATTGGCCATTCGAAG
* * * *
642350 AGCTTCCTCTATCATCTCCCTGCTGCACCTTTTCCCGGTCTCCCCCATTGTCGCCACTATCCCTG
66 AGCTTCCTCTACCATCTCCCCGCTGCACATTTTCCCGGTCTCCCCCACTGTCGCCACTATCCCTG
* *
642415 GGCATGGGCCTGGACGATACATTGCTACTTGGCTTGACTCCTGCAAGCTCAGTCAGCTTTCCGGC
131 GGCATGGGCCTGGACGACACATTGCTACTTGGCTTGACTCCTGCAAGCTCAGTCAGCTTTCCAGC
* **
642480 TATAGTTATGGCCTCCGAAAGTCTCTGGGCATCACCTTGCTCTCTCCCGAGCATTGCCCCTGGTC
196 TACAACTATGGCCTCCGAAAGTCTCTGGGCATCACCTTGCTCTCTCCCGAGCATTGCCCCTGGTC
*
642545 TAAGTCCTTCCAAGAAGGTCTTGAGCGCACCATTCAACTTCTCAATTTTCACATTCCCTTCGTTT
261 TAAGTCCTTCCAAGAAGGTCTTGAGCGCACCATTCAACTTCTCAATTTTCACATTCCCTTCGTCT
* *
642610 GCGCCATCGCTCCCACTCGAATCTGGCTTTGTTTGGATCGTTTCTGACAATTTCTGTGAACCACC
326 GCGCCATCGCTCCCACTCGAATCTGGCTTTGTTTGAATCATTTCTGACAATTTCTGTGAACCACC
*
642675 GTGTATTAGAACACCTCCGTCGACAAATTCATATCGCCGAC
391 GTGTATTAGAACACATCCGTCGACAAATTCATATCGCCGAC
642716 CAAATTTTAC
Statistics
Matches: 407, Mismatches: 24, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
438 407 1.00
ACGTcount: A:0.19, C:0.32, G:0.18, T:0.31
Consensus pattern (438 bp):
GCCATTCTTTCCCGATGACTTTCCTAGGCTATTAACAGTCGATGGCTCACATTGGCCATTCGAAG
AGCTTCCTCTACCATCTCCCCGCTGCACATTTTCCCGGTCTCCCCCACTGTCGCCACTATCCCTG
GGCATGGGCCTGGACGACACATTGCTACTTGGCTTGACTCCTGCAAGCTCAGTCAGCTTTCCAGC
TACAACTATGGCCTCCGAAAGTCTCTGGGCATCACCTTGCTCTCTCCCGAGCATTGCCCCTGGTC
TAAGTCCTTCCAAGAAGGTCTTGAGCGCACCATTCAACTTCTCAATTTTCACATTCCCTTCGTCT
GCGCCATCGCTCCCACTCGAATCTGGCTTTGTTTGAATCATTTCTGACAATTTCTGTGAACCACC
GTGTATTAGAACACATCCGTCGACAAATTCATATCGCCGACGACATTG
Found at i:652491 original size:198 final size:197
Alignment explanation
Indices: 652153--652540 Score: 530
Period size: 198 Copynumber: 2.0 Consensus size: 197
652143 AATCTCTAGG
* *
652153 TCCTAAAACACCACCTGCCAAGGAGAATCCCACTGTCAGAGTAACCTCTCCTGATACACCACCTG
1 TCCTAAAACACCACCTGCCAAGGAGAATCCCACAGTCAGAGTAACCCCTCCTGATACACCACCTG
* * *
652218 TTAAAGAGAATCAAACTATTAGTAACATACCTCCAGAAGTATCTTCATCTTTGAAGGAAGTTTTA
66 TTAAAGAGAATCAAACTATCAATAACATACCTCCAGAAGTATCTTCATCTTTGAAGGAAGTCTTA
* *
652283 ACTGGGTTAATGACAACT-ATAGAAGCACCAATCCCTCCTTCTGCATCTCCTTTGAGTAAATCTC
131 ACTGGGTTAATGACAACTCAT-CAA-CACCAATACCTCCTTCTGCATCTCCTTTGAGTAAATCTC
652347 CACC
194 CACC
* * * *
652351 TCCTAAAATACCACCTGCCAAGGAGGA-CGCCACAGTCAGAGTGACCCCTCCTGCTACACCACCT
1 TCCTAAAACACCACCTGCCAAGGAGAATC-CCACAGTCAGAGTAACCCCTCCTGATACACCACCT
* ** * * *
652415 GTTAAAGAGAATCAAATTATCAATGGCATGCCTCCTGAAGTGTCTTCATCTTTGAAGGAAGTCTT
65 GTTAAAGAGAATCAAACTATCAATAACATACCTCCAGAAGTATCTTCATCTTTGAAGGAAGTCTT
* * *
652480 AGA-TGGGTTAATGACAACTCCATCAACACCGATATCTCTTTCTGCATCTCCTTTGAGTAAA
130 A-ACTGGGTTAATGACAACT-CATCAACACCAATACCTCCTTCTGCATCTCCTTTGAGTAAA
652541 ATTGAAGCTG
Statistics
Matches: 166, Mismatches: 20, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
197 1 0.01
198 160 0.96
199 3 0.02
200 2 0.01
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.26
Consensus pattern (197 bp):
TCCTAAAACACCACCTGCCAAGGAGAATCCCACAGTCAGAGTAACCCCTCCTGATACACCACCTG
TTAAAGAGAATCAAACTATCAATAACATACCTCCAGAAGTATCTTCATCTTTGAAGGAAGTCTTA
ACTGGGTTAATGACAACTCATCAACACCAATACCTCCTTCTGCATCTCCTTTGAGTAAATCTCCA
CC
Found at i:652785 original size:51 final size:51
Alignment explanation
Indices: 652708--652839 Score: 174
Period size: 51 Copynumber: 2.6 Consensus size: 51
652698 CACCCCACCC
* * * *
652708 CCACCATCACACACAGCTGGTACATCATCAGTACCCTTACTAGCGCTAGCA
1 CCACCATCACCCACAGCTGGTACATCATCAGTACCCTCACCAACGCTAGCA
*
652759 CCACCATCACCCACAGCTGGTGCATCATCAGTACCCTCACCAACGCTAGCA
1 CCACCATCACCCACAGCTGGTACATCATCAGTACCCTCACCAACGCTAGCA
* * ** *
652810 GCACCATCACCCCCAATTGGTTCATCATCA
1 CCACCATCACCCACAGCTGGTACATCATCA
652840 TCAACACCCC
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 71 1.00
ACGTcount: A:0.28, C:0.40, G:0.13, T:0.19
Consensus pattern (51 bp):
CCACCATCACCCACAGCTGGTACATCATCAGTACCCTCACCAACGCTAGCA
Found at i:652894 original size:36 final size:36
Alignment explanation
Indices: 652856--653070 Score: 171
Period size: 36 Copynumber: 6.0 Consensus size: 36
652846 CCCCGACACC
* *
652856 CAACCGTTTCATCATCAGCACCCCCACCACCACCCC
1 CAACTGTTTCATCATCAGCACCCCCACCACCACCCA
* * *
652892 CAACTGTTCCATCATCA--A-CACCGCCACCA--C-
1 CAACTGTTTCATCATCAGCACCCCCACCACCACCCA
* *
652922 CAACTGTTTCATCGTCAGCAACGTCCCCATCC-CCACACA
1 CAACTGTTTCATCATCAGC-AC--CCCCA-CCACCACCCA
*
652961 CAACTAG-TTCTTCATCAGCACCCCCACCACCACCCA
1 CAACT-GTTTCATCATCAGCACCCCCACCACCACCCA
* *
652997 TAGCTAG-TTCATCATCAGCACCCCCCCACCACCACCCA
1 CAACT-GTTTCATCATCAGCA--CCCCCACCACCACCCA
* * *
653035 CAACTGGTTCATTATCAGCACCCCCAACACC-CCCA
1 CAACTGTTTCATCATCAGCACCCCCACCACCACCCA
653070 C
1 C
653071 CTCCACCACC
Statistics
Matches: 146, Mismatches: 18, Indels: 31
0.75 0.09 0.16
Matches are distributed among these distances:
30 15 0.10
31 1 0.01
33 10 0.07
34 1 0.01
35 7 0.05
36 59 0.40
37 3 0.02
38 34 0.23
39 15 0.10
40 1 0.01
ACGTcount: A:0.27, C:0.49, G:0.07, T:0.17
Consensus pattern (36 bp):
CAACTGTTTCATCATCAGCACCCCCACCACCACCCA
Found at i:652933 original size:27 final size:28
Alignment explanation
Indices: 652880--652934 Score: 67
Period size: 30 Copynumber: 1.9 Consensus size: 28
652870 TCAGCACCCC
*
652880 CACCACCACCCCCAACTGTTCCATCATCAA
1 CACCACCACCACCAACTGTT-C-TCATCAA
*
652910 CACCGCCACCACCAACTGTT-TCATC
1 CACCACCACCACCAACTGTTCTCATC
652935 GTCAGCAACG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 5 0.22
30 18 0.78
ACGTcount: A:0.27, C:0.49, G:0.05, T:0.18
Consensus pattern (28 bp):
CACCACCACCACCAACTGTTCTCATCAA
Found at i:652950 original size:69 final size:66
Alignment explanation
Indices: 652811--653058 Score: 173
Period size: 69 Copynumber: 3.6 Consensus size: 66
652801 ACGCTAGCAG
* * *
652811 CACCATCACCCCCAATTGGTTCATCATCATCAACACCCCGA-CACCCAACCGTTTCATCATCAGC
1 CACCACCACCCCCAACTAGTTC--CATCATCAACACCCC-ACCA-CCAACCGTTTCATCATCAGC
652875 ACCCC
62 ACCCC
* *
652880 CACCACCACCCCCAACT-GTTCCATCATCAACACCGCCACCACCAACTGTTTCATCGTCAGCAAC
1 CACCACCACCCCCAACTAGTTCCATCATCAACACC-CCACCACCAACCGTTTCATCATCAGC-AC
652944 GTCCC
64 --CCC
* * * * *
652949 CATCC-CCACACACAACTAGTT-CTTCATCAGCACCCCCACCACCACCCATAGCTAGTTCATCAT
1 CA-CCACCACCCCCAACTAGTTCCATCATCAACA-CCCCACCACCAACC---G-T--TTCATCAT
653012 CAGCACCCCCC
58 CAGCA--CCCC
* * * *
653023 CACCACCACCCACAACTGGTT-CATTATCAGCACCCC
1 CACCACCACCCCCAACTAGTTCCATCATCAACACCCC
653059 CAACACCCCC
Statistics
Matches: 147, Mismatches: 15, Indels: 30
0.77 0.08 0.16
Matches are distributed among these distances:
66 32 0.22
67 6 0.04
68 4 0.03
69 49 0.33
70 7 0.05
72 1 0.01
73 7 0.05
74 29 0.20
75 11 0.07
76 1 0.01
ACGTcount: A:0.27, C:0.48, G:0.08, T:0.18
Consensus pattern (66 bp):
CACCACCACCCCCAACTAGTTCCATCATCAACACCCCACCACCAACCGTTTCATCATCAGCACCC
C
Found at i:652987 original size:30 final size:35
Alignment explanation
Indices: 652964--653065 Score: 114
Period size: 38 Copynumber: 2.8 Consensus size: 35
652954 CCACACACAA
*
652964 CTAGTTCTTCATCAGCACCCCCACCACCACCCATAG
1 CTAGTTCATCATCAGCACCCCCACCACCA-CCATAG
* *
653000 CTAGTTCATCATCAGCACCCCCCCACCACCACCCACAA
1 CTAGTTCATCATCAGCA--CCCCCACCACCA-CCATAG
* * *
653038 CTGGTTCATTATCAGCACCCCCAACACC
1 CTAGTTCATCATCAGCACCCCCACCACC
653066 CCCACCTCCA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
36 26 0.45
38 32 0.55
ACGTcount: A:0.26, C:0.48, G:0.08, T:0.18
Consensus pattern (35 bp):
CTAGTTCATCATCAGCACCCCCACCACCACCATAG
Found at i:653031 original size:38 final size:38
Alignment explanation
Indices: 652946--653262 Score: 177
Period size: 48 Copynumber: 8.3 Consensus size: 38
652936 TCAGCAACGT
* *
652946 CCCCATCC-CCACACACAACTAGTTCTTCATCAGCA--C
1 CCCCA-CCACCACCCACAACTAGTTCATCATCAGCACCC
* *
652982 CCCCACCACCACCCATAGCTAGTTCATCATCAGCACCC
1 CCCCACCACCACCCACAACTAGTTCATCATCAGCACCC
* *
653020 CCCCACCACCACCCACAACTGGTTCATTATCAGCACCCCCAACAC
1 CCCCACCACCACCCACAACTAGTTCATCATCAGCA----C--C-C
* *
653065 CCCCACCTCCACCACCCACAACTGGTTCATCATCAGTACCC
1 CCCCA---CCACCACCCACAACTAGTTCATCATCAGCACCC
* *
653106 CCACCATCCCCACTGCCACCCACCACAACTGGTTCATCATCGGCA---
1 CC-CCA---CCA---CCA--C-CCACAACTAGTTCATCATCAGCACCC
*
653151 --CC-CCA-C-CCC-CAACTGGTTCATCATCAGCA-CC
1 CCCCACCACCACCCACAACTAGTTCATCATCAGCACCC
653182 CCCCACCACCA---ACAACTAGTTCATCATCAGCA--C
1 CCCCACCACCACCCACAACTAGTTCATCATCAGCACCC
* *
653215 CCCCACCACCA-CCACCAACTAGTTCATCCTCAGTACCC
1 CCCCACCACCACCCA-CAACTAGTTCATCATCAGCACCC
*
653253 CGCCACCACC
1 CCCCACCACC
653263 TGCTCCTTTT
Statistics
Matches: 229, Mismatches: 19, Indels: 64
0.73 0.06 0.21
Matches are distributed among these distances:
29 19 0.08
30 2 0.01
31 1 0.00
33 14 0.06
34 23 0.10
35 4 0.02
36 46 0.20
38 45 0.20
41 3 0.01
42 11 0.05
44 2 0.01
45 9 0.04
47 1 0.00
48 49 0.21
ACGTcount: A:0.26, C:0.50, G:0.08, T:0.15
Consensus pattern (38 bp):
CCCCACCACCACCCACAACTAGTTCATCATCAGCACCC
Found at i:653080 original size:48 final size:48
Alignment explanation
Indices: 653015--653154 Score: 187
Period size: 48 Copynumber: 2.9 Consensus size: 48
653005 TCATCATCAG
* *
653015 CACCCCC-CCACCACCACCCACAACTGGTTCATTATCAGCACCCCCAA
1 CACCCCCACCTCCACCACCCACAACTGGTTCATCATCAGCACCCCCAA
* *
653062 CACCCCCACCTCCACCACCCACAACTGGTTCATCATCAGTACCCCCAC
1 CACCCCCACCTCCACCACCCACAACTGGTTCATCATCAGCACCCCCAA
* *
653110 CATCCCCA-CTGCCACC-CACCACAACTGGTTCATCATCGGCACCCC
1 CACCCCCACCT-CCACCAC-CCACAACTGGTTCATCATCAGCACCCC
653155 ACCCCCAACT
Statistics
Matches: 83, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
47 10 0.12
48 73 0.88
ACGTcount: A:0.25, C:0.53, G:0.08, T:0.14
Consensus pattern (48 bp):
CACCCCCACCTCCACCACCCACAACTGGTTCATCATCAGCACCCCCAA
Found at i:653165 original size:29 final size:31
Alignment explanation
Indices: 653125--653226 Score: 136
Period size: 29 Copynumber: 3.2 Consensus size: 31
653115 CCACTGCCAC
*
653125 CCACCACAACTGGTTCATCATCGGCACCCCA
1 CCACCACAACTGGTTCATCATCAGCACCCCA
653156 CC-CC-CAACTGGTTCATCATCAGCACCCCCCA
1 CCACCACAACTGGTTCATCATCAGCA--CCCCA
*
653187 CCACCAACAACTAGTTCATCATCAGCACCCCCA
1 CCACC-ACAACTGGTTCATCATCAGCA-CCCCA
653220 CCACCAC
1 CCACCAC
653227 CACCAACTAG
Statistics
Matches: 64, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
29 19 0.30
30 2 0.03
31 9 0.14
32 4 0.06
33 11 0.17
34 19 0.30
ACGTcount: A:0.27, C:0.49, G:0.09, T:0.15
Consensus pattern (31 bp):
CCACCACAACTGGTTCATCATCAGCACCCCA
Found at i:653234 original size:36 final size:35
Alignment explanation
Indices: 653149--653262 Score: 151
Period size: 36 Copynumber: 3.3 Consensus size: 35
653139 TCATCATCGG
* *
653149 CACC-CCACCCCCAACTGGTTCATCATCAGCACCC
1 CACCACCACCACCAACTAGTTCATCATCAGCACCC
*
653183 C-CCACCACCAACAACTAGTTCATCATCAGCACCCC
1 CACCACCACCACCAACTAGTTCATCATCAGCA-CCC
* *
653218 CACCACCACCACCAACTAGTTCATCCTCAGTACCC
1 CACCACCACCACCAACTAGTTCATCATCAGCACCC
*
653253 CGCCACCACC
1 CACCACCACC
653263 TGCTCCTTTT
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
33 2 0.03
34 25 0.36
35 16 0.23
36 27 0.39
ACGTcount: A:0.27, C:0.52, G:0.07, T:0.14
Consensus pattern (35 bp):
CACCACCACCACCAACTAGTTCATCATCAGCACCC
Found at i:663303 original size:18 final size:17
Alignment explanation
Indices: 663280--663313 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
663270 TAAAATTATC
663280 ATATATATTTTT-TTAA
1 ATATATATTTTTATTAA
663296 ATATATATTTTTATTAA
1 ATATATATTTTTATTAA
663313 A
1 A
663314 ATTTTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATATATATTTTTATTAA
Found at i:669275 original size:2 final size:2
Alignment explanation
Indices: 669268--669297 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
669258 CATATTTCAA
669268 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
669298 GTGTGTGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:669302 original size:2 final size:2
Alignment explanation
Indices: 669297--669327 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
669287 TATATATATA
669297 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
669328 ATAACCATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:674224 original size:198 final size:198
Alignment explanation
Indices: 673767--674239 Score: 693
Period size: 199 Copynumber: 2.4 Consensus size: 198
673757 CCATATTGTC
* *
673767 ATAT-AAGTATCGATATTTAAAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATTAATAAT
1 ATATAAAGTATCGATA-CTAAAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATTAACAAT
* * * *
673831 GTAAATGGTAAAAGTCTATCGGTATATTGATAATATGCGTAAATACCAAGTATCGATACTTTTAT
65 GTAAACGGTAAAAGTCTATCAGTATATTCATAATAGGCGTAAATACCAAGTATCGATACTTTTAT
* * *
673896 ATAGGTATGGATACGTTTATTCCAGTATGTTTCTTAAACAATTTGCACATAAAATATATCGATAC
130 ATAGGTATAGATACGTTTATTCCAGTATGCTTCTTAAACAATTTACACATAAAATATATCGATAC
673961 ACAT
195 ACAT
*
673965 ATATAAAGTATCGATACTTAGAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATTAACAAT
1 ATATAAAGTATCGATAC-TAAAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATTAACAAT
*
674030 GTAAACGGTAAAAGTCTATCAGTATATTCATAATAGGCGTAAATATCAAGTATCGATACTTTTAT
65 GTAAACGGTAAAAGTCTATCAGTATATTCATAATAGGCGTAAATACCAAGTATCGATACTTTTAT
* * * *
674095 ATAGGTATAGATACTTTTGTTCGAGTATGCTTC-T-CACAATTTACACGCA-AAAATATATCGAT
130 ATAGGTATAGATACGTTTATTCCAGTATGCTTCTTAAACAATTTACA--CATAAAATATATCGAT
*
674157 ACATAT
193 ACACAT
** *
674163 ATATAAAGTATCGATACTAATAATTTTGAAACCTAATACTTTAAAGTAATAGGTAAATTAACAAT
1 ATATAAAGTATCGATACTAA-AATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATTAACAAT
*
674228 GTACACGGTAAA
65 GTAAACGGTAAA
674240 TTTTTCTACC
Statistics
Matches: 249, Mismatches: 21, Indels: 10
0.89 0.08 0.04
Matches are distributed among these distances:
197 11 0.04
198 92 0.37
199 146 0.59
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (198 bp):
ATATAAAGTATCGATACTAAAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATG
TAAACGGTAAAAGTCTATCAGTATATTCATAATAGGCGTAAATACCAAGTATCGATACTTTTATA
TAGGTATAGATACGTTTATTCCAGTATGCTTCTTAAACAATTTACACATAAAATATATCGATACA
CAT
Found at i:685209 original size:50 final size:52
Alignment explanation
Indices: 685155--685258 Score: 122
Period size: 50 Copynumber: 2.0 Consensus size: 52
685145 ATTTAAAATA
* *
685155 TAATTCAATAATCCGTAATATA-TTTTCCTGTC-AAATCACAACGAATTCAT
1 TAATTCAATAATCCGTAATATACTTCTCCTATCTAAATCACAACGAATTCAT
* ** * * *
685205 TAATTTAATAATCTTTAATGTACTTCTCCTATCTAAATCACGACGAATTTAT
1 TAATTCAATAATCCGTAATATACTTCTCCTATCTAAATCACAACGAATTCAT
685257 TA
1 TA
685259 GTTTCCTATT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
50 18 0.41
51 8 0.18
52 18 0.41
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.39
Consensus pattern (52 bp):
TAATTCAATAATCCGTAATATACTTCTCCTATCTAAATCACAACGAATTCAT
Found at i:686344 original size:196 final size:199
Alignment explanation
Indices: 685984--686402 Score: 594
Period size: 196 Copynumber: 2.1 Consensus size: 199
685974 TATCCGGATG
*
685984 CACATTAGTGTCAGATACATACCCTTATCTATCATGAGTACACAAGTAACATATCTACTACCATC
1 CACATTAGTGTCAGATACATACCCATATCTATCATGAGTA-ACAAGTAACATATCTACTACCATC
* *
686049 ACCATACATACTGCCAATGATTCTACATTCAGCTCAATCGTCACCATACATAAATATAAATACCC
65 ACCATA-ATACTGCCAATGATTCTACAGTCAGCTCAATCGTCACCAAACATAAATATAAATACCC
* *** **
686114 CATATCATGGCATCATACATATATCTGGACATATGCATGCGGATAAATGAAAAGGCTTCAAAATA
129 CATATCATGGCATCATACAAATATCCCAACATATGCATGCAAATAAATGAAAAGGCTTCAAAATA
686179 ATGGAA
194 ATGGAA
* * *
686185 CACGTTAGTGTCAGTTACATACCCATATCTATCATGAGT-ACAAGTAACATATCTGCTTACCATC
1 CACATTAGTGTCAGATACATACCCATATCTATCATGAGTAACAAGTAACATATCTAC-TACCATC
* * * *
686249 ACCAT-A-A-TGCCAATTATTCTACAGTCAGCTCACTCGTCAGCAAACATCAATATAAATACCCC
65 ACCATAATACTGCCAATGATTCTACAGTCAGCTCAATCGTCACCAAACATAAATATAAATACCCC
* * *
686311 ATATCATGGCATCGTACAAATATCCCAACATATGCATTCAAATAAATGAAATGGCTTCAAAATAA
130 ATATCATGGCATCATACAAATATCCCAACATATGCATGCAAATAAATGAAAAGGCTTCAAAATAA
686376 TGGAA
195 TGGAA
* *
686381 CATATTAGTGTCGGATACATAC
1 CACATTAGTGTCAGATACATAC
686403 GTGTATCTAT
Statistics
Matches: 194, Mismatches: 23, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
196 128 0.66
197 1 0.01
198 1 0.01
199 16 0.08
200 12 0.06
201 36 0.19
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (199 bp):
CACATTAGTGTCAGATACATACCCATATCTATCATGAGTAACAAGTAACATATCTACTACCATCA
CCATAATACTGCCAATGATTCTACAGTCAGCTCAATCGTCACCAAACATAAATATAAATACCCCA
TATCATGGCATCATACAAATATCCCAACATATGCATGCAAATAAATGAAAAGGCTTCAAAATAAT
GGAA
Found at i:688146 original size:1 final size:1
Alignment explanation
Indices: 688142--688167 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
688132 TCGCGGATTC
688142 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
688168 GAGGGAAACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:689439 original size:34 final size:34
Alignment explanation
Indices: 689396--689497 Score: 177
Period size: 34 Copynumber: 3.0 Consensus size: 34
689386 TTTAAAATTC
*
689396 AATACTAAAATCAACACACAACCTAAAGTTTAGT
1 AATACTAAAATCATCACACAACCTAAAGTTTAGT
*
689430 AATACTAAAATCATCACACAGCCTAAAGTTTAGT
1 AATACTAAAATCATCACACAACCTAAAGTTTAGT
*
689464 AATACTAAAATCATCCCACAACCTAAAGTTTAGT
1 AATACTAAAATCATCACACAACCTAAAGTTTAGT
689498 CACTAATATG
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 64 1.00
ACGTcount: A:0.46, C:0.22, G:0.07, T:0.25
Consensus pattern (34 bp):
AATACTAAAATCATCACACAACCTAAAGTTTAGT
Found at i:694476 original size:30 final size:30
Alignment explanation
Indices: 694442--694503 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
694432 TAAATTCTAT
* *
694442 TTGGATTCGTACATGATTATACTTCTGTTG
1 TTGGATTCATACATGATTATACTTATGTTG
694472 TTGGATTCATACATGATTATACTTATGTTG
1 TTGGATTCATACATGATTATACTTATGTTG
694502 TT
1 TT
694504 AGACTTTGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.11, G:0.18, T:0.48
Consensus pattern (30 bp):
TTGGATTCATACATGATTATACTTATGTTG
Found at i:696905 original size:19 final size:20
Alignment explanation
Indices: 696881--696928 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
696871 AACGATTTTC
*
696881 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
696900 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
696920 TTTTGAAAA
1 TTTTGAAAA
696929 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:698381 original size:18 final size:18
Alignment explanation
Indices: 698359--698411 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
698349 GATTGTCCAG
*
698359 GGGGTACAGATTCTCCCA
1 GGGGTACAGATTCCCCCA
*
698377 GGGGTACCGATTCCCCCA
1 GGGGTACAGATTCCCCCA
* *
698395 GGGGAAAAGATTCCCCC
1 GGGGTACAGATTCCCCC
698412 CACGCTCCAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.23, C:0.32, G:0.28, T:0.17
Consensus pattern (18 bp):
GGGGTACAGATTCCCCCA
Found at i:699180 original size:103 final size:104
Alignment explanation
Indices: 699067--699269 Score: 381
Period size: 104 Copynumber: 2.0 Consensus size: 104
699057 AAATAACCTC
*
699067 AGTGACCAAAAATCTCAGATAATATACGATTTTGACCAAC-TTTTTTTGGATTTGCGAAAATGAC
1 AGTGACCAAAAATCCCAGATAATATACGATTTTGACCAACTTTTTTTTGGATTTGCGAAAATGAC
*
699131 CAACAAAATTGCAATGCGATCTCTAATTCGCATTGCGAT
66 CAACAAAATCGCAATGCGATCTCTAATTCGCATTGCGAT
699170 AGTGACCAAAAATCCCAGATAATATACGATTTTGACCAACTTTTTTTTGGATTTGCGAAAATGAC
1 AGTGACCAAAAATCCCAGATAATATACGATTTTGACCAACTTTTTTTTGGATTTGCGAAAATGAC
699235 CAACAAAATCGCAATGCGATCTCTAATTCGCATTG
66 CAACAAAATCGCAATGCGATCTCTAATTCGCATTG
699270 TGATCTCTAC
Statistics
Matches: 97, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
103 39 0.40
104 58 0.60
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (104 bp):
AGTGACCAAAAATCCCAGATAATATACGATTTTGACCAACTTTTTTTTGGATTTGCGAAAATGAC
CAACAAAATCGCAATGCGATCTCTAATTCGCATTGCGAT
Found at i:699328 original size:21 final size:21
Alignment explanation
Indices: 699304--699380 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 21
699294 GTTGCATTTT
699304 GCGTTGCGATAGTTGAAAATC
1 GCGTTGCGATAGTTGAAAATC
* ** **
699325 GCGTTGCGAT-TTTCCATTTC
1 GCGTTGCGATAGTTGAAAATC
*
699345 GCGTTGCGATAGTTGAAAATT
1 GCGTTGCGATAGTTGAAAATC
699366 GCGTTTTGCGATAGT
1 GCG--TTGCGATAGT
699381 CTACAGTTGT
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
20 15 0.36
21 17 0.40
23 10 0.24
ACGTcount: A:0.21, C:0.16, G:0.27, T:0.36
Consensus pattern (21 bp):
GCGTTGCGATAGTTGAAAATC
Found at i:699399 original size:22 final size:22
Alignment explanation
Indices: 699371--699440 Score: 83
Period size: 22 Copynumber: 3.3 Consensus size: 22
699361 AAATTGCGTT
699371 TTGCGATAGTCTACAGTTGTCG
1 TTGCGATAGTCTACAGTTGTCG
* * **
699393 TTGCGAT--TTTCCAAAT-TCG
1 TTGCGATAGTCTACAGTTGTCG
699412 TTGCGATAGTCTACAGTTGTCG
1 TTGCGATAGTCTACAGTTGTCG
699434 TTGCGAT
1 TTGCGAT
699441 TTTCCAAATT
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
19 10 0.27
20 5 0.14
21 5 0.14
22 17 0.46
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.39
Consensus pattern (22 bp):
TTGCGATAGTCTACAGTTGTCG
Found at i:699414 original size:19 final size:19
Alignment explanation
Indices: 699390--699455 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
699380 TCTACAGTTG
699390 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
699409 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
699430 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
699450 TCGTTG
1 TCGTTG
699456 TGATAGTTAA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 16 0.44
20 5 0.14
21 5 0.14
22 10 0.28
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:699420 original size:41 final size:41
Alignment explanation
Indices: 699371--699462 Score: 175
Period size: 41 Copynumber: 2.2 Consensus size: 41
699361 AAATTGCGTT
699371 TTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCG
1 TTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCG
699412 TTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCG
1 TTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCG
*
699453 TTGTGATAGT
1 TTGCGATAGT
699463 TAAAAAAAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.40
Consensus pattern (41 bp):
TTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCG
Found at i:699551 original size:6 final size:6
Alignment explanation
Indices: 699540--699571 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
699530 GACACGTATT
699540 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
699572 CGAGACGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.31, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:700231 original size:20 final size:20
Alignment explanation
Indices: 700206--700278 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
700196 ACTGTAGACT
*
700206 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGAAAA
** * **
700226 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGA-AATGAAAA
*
700247 ATCGCAACGTGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
700267 ATCGCAACGCGA
1 ATCGCAACGCGA
700279 TTTTCAACTA
Statistics
Matches: 39, Mismatches: 13, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
20 26 0.67
21 13 0.33
ACGTcount: A:0.40, C:0.23, G:0.21, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:700248 original size:41 final size:41
Alignment explanation
Indices: 700203--700300 Score: 178
Period size: 41 Copynumber: 2.4 Consensus size: 41
700193 ACAACTGTAG
*
700203 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCA
*
700244 ACTATCGCAACGTGAAATGAAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCA
700285 ACTATCGCAACGCGAA
1 ACTATCGCAACGCGAA
700301 TTTGCGATAG
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.19
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCA
Found at i:700252 original size:21 final size:21
Alignment explanation
Indices: 700226--700299 Score: 87
Period size: 21 Copynumber: 3.6 Consensus size: 21
700216 GAAATGGAAA
700226 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
* ** * **
700247 ATCGCAACGTGA-AATGAAAA
1 ATCGCAACGCGATTTTCAACT
700267 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
700288 ATCGCAACGCGA
1 ATCGCAACGCGA
700300 ATTTGCGATA
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 14 0.35
21 26 0.65
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.22
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:708654 original size:14 final size:14
Alignment explanation
Indices: 708635--708664 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
708625 GAAAACATAG
708635 TGAAGATGTTTCTT
1 TGAAGATGTTTCTT
708649 TGAAGATGTTTCTT
1 TGAAGATGTTTCTT
708663 TG
1 TG
708665 GATGACGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.07, G:0.23, T:0.50
Consensus pattern (14 bp):
TGAAGATGTTTCTT
Done.