Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr6
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: 44797108
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 921406 characters in sequence are not A, C, G, or T
File 3 of 144
Found at i:435637 original size:51 final size:46
Alignment explanation
Indices: 435612--436176 Score: 560
Period size: 46 Copynumber: 11.8 Consensus size: 46
435602 ACAGTGGAAC
* * *
435612 AGATTAAAGCTGAAAGCAGTGAATCTTATTTACC-TAGCGTTGCAGT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTT-CCTTGGCGTTGCAGT
* *
435658 AGATTAAAGCTGAAGGCAGTGAATCTTATTTCCTTGGCATTGCAGT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTTGGCGTTGCAGT
* *
435704 GGAACATATTAAAGCTGAAGGCAACGAATCTTATTTCCTTGGCGTTGCAGT
1 -----AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTTGGCGTTGCAGT
*
435755 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTTAGCGTTGCAGT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTTGGCGTTGCAGT
* * * * * *
435801 GGAACATATTAAAGCTGAAGACAACAAATCTTATTTCCCTGGCATTGCAGT
1 -----AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTTGGCGTTGCAGT
* * * *
435852 AGATTAAAGTTGAAGGCAGTGAATCTTATTTCCTTAGCATTGCAGTGGAAT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTTGGCGTTGCA---G--T
*
435903 AGATTAAAGCTGAAGGCAGCGAATCTTATTT-CTCTAGCGTTGCAGT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCT-TGGCGTTGCAGT
* * * *
435949 AGATTAAAGTTGAAGGCAGTG-ATCTTGTTTCCTTGCCGTTGCAGT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTTGGCGTTGCAGT
* * *
435994 GGAACAGATTAAAGCTGAAGGCAGGGAATCTTATTTCCCTGGTGTTGCAGT
1 -----AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTTGGCGTTGCAGT
* * * * *
436045 AGATTAAAGCTGAAGGCAACGAATCTTATCTCCTTAGTGTTGTAGTGGAAT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTT-G-G-CGT--TGCAGT
* * *
436096 AGATTAAAGCTGAACGCAGCGAATCTTATTTCCCTGGCGTTACAGT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTTGGCGTTGCAGT
436142 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTT
436177 AGTGTTGTAG
Statistics
Matches: 435, Mismatches: 55, Indels: 58
0.79 0.10 0.11
Matches are distributed among these distances:
45 20 0.05
46 208 0.48
47 1 0.00
48 4 0.01
49 5 0.01
50 22 0.05
51 175 0.40
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (46 bp):
AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTTGGCGTTGCAGT
Found at i:435696 original size:97 final size:97
Alignment explanation
Indices: 435578--436207 Score: 868
Period size: 97 Copynumber: 6.5 Consensus size: 97
435568 AAGTCATTAT
* * * *
435578 AGTGAATCTTATTTCCTTGGCATTACAGTGGAACAGATTAAAGCTGAAAGCAGTGAATCTTATTT
1 AGTGAATCTTATTTCCTTAGCATTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATTT
* *
435643 ACCTAGCGTTGCAGTAGATTAAAGCTGAAGGC
66 CCCTGGCGTTGCAGTAGATTAAAGCTGAAGGC
* * *
435675 AGTGAATCTTATTTCCTTGGCATTGCAGTGGAACATATTAAAGCTGAAGGCAACGAATCTTATTT
1 AGTGAATCTTATTTCCTTAGCATTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATTT
*
435740 CCTTGGCGTTGCAGTAGATTAAAGCTGAAGGC
66 CCCTGGCGTTGCAGTAGATTAAAGCTGAAGGC
* * * * * *
435772 AGCGAATCTTATTTCCTTAGCGTTGCAGTGGAACATATTAAAGCTGAAGACAACAAATCTTATTT
1 AGTGAATCTTATTTCCTTAGCATTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATTT
* *
435837 CCCTGGCATTGCAGTAGATTAAAGTTGAAGGC
66 CCCTGGCGTTGCAGTAGATTAAAGCTGAAGGC
*
435869 AGTGAATCTTATTTCCTTAGCATTGCAGTGGAATAGATTAAAGCTGAAGGCAGCGAATCTTATTT
1 AGTGAATCTTATTTCCTTAGCATTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATTT
* * *
435934 CTCTAGCGTTGCAGTAGATTAAAGTTGAAGGC
66 CCCTGGCGTTGCAGTAGATTAAAGCTGAAGGC
* * *
435966 AGTG-ATCTTGTTTCCTT-GCCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGGGAATCTTATT
1 AGTGAATCTTATTTCCTTAG-CATTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATT
*
436029 TCCCTGGTGTTGCAGTAGATTAAAGCTGAAGGC
65 TCCCTGGCGTTGCAGTAGATTAAAGCTGAAGGC
** * ** * * *
436062 AACGAATCTTATCTCCTTAGTGTTGTAGTGGAATAGATTAAAGCTGAACGCAGCGAATCTTATTT
1 AGTGAATCTTATTTCCTTAGCATTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATTT
*
436127 CCCTGGCGTTACAGTAGATTAAAGCTGAAGGC
66 CCCTGGCGTTGCAGTAGATTAAAGCTGAAGGC
* ** * * *
436159 AGCGAATCTTATTTCCTTAGTGTTGTAGTGGAATAGATTGAAGCTGAAG
1 AGTGAATCTTATTTCCTTAGCATTGCAGTGGAACAGATTAAAGCTGAAG
436208 TGGAACATCT
Statistics
Matches: 481, Mismatches: 49, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
95 1 0.00
96 84 0.17
97 395 0.82
98 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.31
Consensus pattern (97 bp):
AGTGAATCTTATTTCCTTAGCATTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATTT
CCCTGGCGTTGCAGTAGATTAAAGCTGAAGGC
Found at i:436307 original size:118 final size:118
Alignment explanation
Indices: 436088--436346 Score: 367
Period size: 118 Copynumber: 2.2 Consensus size: 118
436078 TTAGTGTTGT
* *
436088 AGTGGAATAGATTAAAGCTGAACGCAGCGAATCTTATTTCCCTGGCGTTACAGTAGATTAAAGCT
1 AGTGGAACAGATTAAAGCTGAACGCAGCGAATCTTATTTCCCTGGCATTACAGTAGATTAAAGCT
* * *
436153 GAAGGCAGCGAATCTTATTTCCTTAGTGTTGTAGTGGAATAGATTGAAGCTGA
66 GAAGGCAGCGAATCTTATTTCCTTAGCGTTGCAGTGGAATAGATTAAAGCTGA
** * * **
436206 AGTGGAACATCTTAAAGCTGAAGGCAGCGAATCTTATTTCTCTGGCATTGTAGTAGATTAAAGCT
1 AGTGGAACAGATTAAAGCTGAACGCAGCGAATCTTATTTCCCTGGCATTACAGTAGATTAAAGCT
* * *
436271 GAAGGTAGTGAATCTTTTTTTCC-TAGCGTTGCAGTGGAATAGATTAAAGCTGA
66 GAAGGCAGCGAATC-TTATTTCCTTAGCGTTGCAGTGGAATAGATTAAAGCTGA
*
436324 AGTGGAACAGATTAAAGCGGAAC
1 AGTGGAACAGATTAAAGCTGAAC
436347 AGATTAAAGC
Statistics
Matches: 122, Mismatches: 18, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
118 115 0.94
119 7 0.06
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.29
Consensus pattern (118 bp):
AGTGGAACAGATTAAAGCTGAACGCAGCGAATCTTATTTCCCTGGCATTACAGTAGATTAAAGCT
GAAGGCAGCGAATCTTATTTCCTTAGCGTTGCAGTGGAATAGATTAAAGCTGA
Found at i:436347 original size:15 final size:15
Alignment explanation
Indices: 436327--436356 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
436317 AAGCTGAAGT
436327 GGAACAGATTAAAGC
1 GGAACAGATTAAAGC
436342 GGAACAGATTAAAGC
1 GGAACAGATTAAAGC
436357 TGAAGGCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.27, T:0.13
Consensus pattern (15 bp):
GGAACAGATTAAAGC
Found at i:436634 original size:15 final size:16
Alignment explanation
Indices: 436603--436638 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
436593 CCGGGCCCAT
436603 TAAAACCAAATTAAAA
1 TAAAACCAAATTAAAA
*
436619 TAAAACTAAA-TAAAA
1 TAAAACCAAATTAAAA
436634 TAAAA
1 TAAAA
436639 TAATGTCTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.19
Consensus pattern (16 bp):
TAAAACCAAATTAAAA
Found at i:437866 original size:23 final size:22
Alignment explanation
Indices: 437840--437965 Score: 94
Period size: 23 Copynumber: 5.5 Consensus size: 22
437830 ATGCTTAAGT
437840 TTAATATATTTTTAAATTTATCA
1 TTAATAT-TTTTTAAATTTATCA
* *
437863 TTAATACTATTTT-AATTTATAA
1 TTAATA-TTTTTTAAATTTATCA
* *
437885 TATATTATTATTTTAAATTTATTA
1 T-TAATATT-TTTTAAATTTATCA
* *
437909 TTAACATTATTTTAAGTTTATCA
1 TTAATATT-TTTTAAATTTATCA
*
437932 TGT-ATTTTTATTTAAATTTATCA
1 T-TAATATTT-TTTAAATTTATCA
*
437955 TGTATTATTTT
1 T-TAATATTTT
437966 ATATATTTTT
Statistics
Matches: 82, Mismatches: 14, Indels: 14
0.75 0.13 0.13
Matches are distributed among these distances:
22 11 0.13
23 56 0.68
24 15 0.18
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (22 bp):
TTAATATTTTTTAAATTTATCA
Found at i:437890 original size:17 final size:18
Alignment explanation
Indices: 437864--437912 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
437854 AATTTATCAT
437864 TAATACTATT-TTAATTTA
1 TAATA-TATTATTAATTTA
*
437882 TAATATATTATTATTTTA
1 TAATATATTATTAATTTA
*
437900 -AATTTATTATTAA
1 TAATATATTATTAA
437913 CATTATTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (18 bp):
TAATATATTATTAATTTA
Found at i:437899 original size:46 final size:47
Alignment explanation
Indices: 437849--437955 Score: 146
Period size: 46 Copynumber: 2.3 Consensus size: 47
437839 TTTAATATAT
*
437849 TTTTAAATTTATCATTAATACTATTTTAA-TTTATAATATATTATTA
1 TTTTAAATTTATCATTAACACTATTTTAAGTTTATAATATATTATTA
* * * * *
437895 TTTTAAATTTATTATTAACATTATTTTAAGTTTATCATGTATTTTTA
1 TTTTAAATTTATCATTAACACTATTTTAAGTTTATAATATATTATTA
437942 -TTTAAATTTATCAT
1 TTTTAAATTTATCAT
437956 GTATTATTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
46 39 0.74
47 14 0.26
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.58
Consensus pattern (47 bp):
TTTTAAATTTATCATTAACACTATTTTAAGTTTATAATATATTATTA
Found at i:437973 original size:23 final size:23
Alignment explanation
Indices: 437925--437970 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
437915 TTATTTTAAG
*
437925 TTTATCATGTATTTTTATTTAAA
1 TTTATCATGTATTTTTATATAAA
437948 TTTATCATGTATTATTTTATATA
1 TTTATCATGTA-T-TTTTATATA
437971 TTTTTATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 11 0.55
24 1 0.05
25 8 0.40
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.61
Consensus pattern (23 bp):
TTTATCATGTATTTTTATATAAA
Found at i:438360 original size:21 final size:22
Alignment explanation
Indices: 438328--438369 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
438318 ATTAATATAT
438328 ATATTATTATTT-TTATTTTAC
1 ATATTATTATTTGTTATTTTAC
*
438349 ATATT-TTGATTTGTTTTTTTA
1 ATATTATT-ATTTGTTATTTTA
438370 TATACAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 2 0.11
21 9 0.50
22 7 0.39
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.69
Consensus pattern (22 bp):
ATATTATTATTTGTTATTTTAC
Found at i:440805 original size:21 final size:20
Alignment explanation
Indices: 440775--440823 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
440765 ATAAAAGTTT
440775 ATAATTTTTTATAGTTTTAA
1 ATAATTTTTTATAGTTTTAA
* *
440795 ATAATTGTTTTTTATTTTTAA
1 ATAATT-TTTTATAGTTTTAA
440816 AT-ATTTTT
1 ATAATTTTT
440824 AAATTTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 3 0.12
20 9 0.35
21 14 0.54
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (20 bp):
ATAATTTTTTATAGTTTTAA
Found at i:456783 original size:29 final size:29
Alignment explanation
Indices: 456738--456795 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
456728 CATGGAGCAG
*
456738 CCAGAGGGTTTTGTTGCACAAGGGAAAGA
1 CCAGAGGGTTTTATTGCACAAGGGAAAGA
456767 CCAGAGGGTTTTATTGCACAAGGGAAAGA
1 CCAGAGGGTTTTATTGCACAAGGGAAAGA
456796 GGACTATGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.33, C:0.14, G:0.33, T:0.21
Consensus pattern (29 bp):
CCAGAGGGTTTTATTGCACAAGGGAAAGA
Found at i:460410 original size:18 final size:19
Alignment explanation
Indices: 460389--460426 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
460379 GTCTTTTACC
*
460389 AAAATATTA-CAAAAAAAT
1 AAAATAATATCAAAAAAAT
*
460407 AAAATAATATCAAAATAAT
1 AAAATAATATCAAAAAAAT
460426 A
1 A
460427 TTATTTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAATAATATCAAAAAAAT
Found at i:460468 original size:5 final size:5
Alignment explanation
Indices: 460458--460483 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
460448 TAATACTAAA
460458 AAAAC AAAAC AAAAC AAAAC AAAAC A
1 AAAAC AAAAC AAAAC AAAAC AAAAC A
460484 GTAGAAACCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:460542 original size:27 final size:27
Alignment explanation
Indices: 460497--460594 Score: 115
Period size: 27 Copynumber: 3.6 Consensus size: 27
460487 GAAACCTGGA
*
460497 TGCCACAGGCGGCACCAAAGGTGCTTG
1 TGCCAGAGGCGGCACCAAAGGTGCTTG
** *
460524 TGGTAGAGGCGGCATCAAAGGTGCTTG
1 TGCCAGAGGCGGCACCAAAGGTGCTTG
* ***
460551 TGCCAGAGGCGGCACCAAAGGCGCCAC
1 TGCCAGAGGCGGCACCAAAGGTGCTTG
*
460578 TGCCACAGGCGGCACCA
1 TGCCAGAGGCGGCACCA
460595 CTTGTATTAT
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 59 1.00
ACGTcount: A:0.23, C:0.30, G:0.35, T:0.12
Consensus pattern (27 bp):
TGCCAGAGGCGGCACCAAAGGTGCTTG
Found at i:460639 original size:3 final size:3
Alignment explanation
Indices: 460631--460661 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
460621 CAGCTAAAGG
460631 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
460662 AAGCAATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:464046 original size:30 final size:30
Alignment explanation
Indices: 464010--464088 Score: 90
Period size: 30 Copynumber: 2.7 Consensus size: 30
464000 ATGATGTCAG
464010 CTTGTGTGAGCAACTCTATTATAATGCCAA
1 CTTGTGTGAGCAACTCTATTATAATGCCAA
* * * *
464040 CTTGTGTAAGCAACCCTGA-TATACTGTCAA
1 CTTGTGTGAGCAACTCT-ATTATAATGCCAA
*
464070 CTTGTGTGAGTAACT-TATT
1 CTTGTGTGAGCAACTCTATT
464089 CCCGAGTATC
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
28 1 0.03
29 2 0.05
30 36 0.90
31 1 0.03
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (30 bp):
CTTGTGTGAGCAACTCTATTATAATGCCAA
Found at i:466714 original size:15 final size:14
Alignment explanation
Indices: 466686--466751 Score: 53
Period size: 15 Copynumber: 4.6 Consensus size: 14
466676 AATAAAAGAG
*
466686 AAAACATATAAAATT
1 AAAA-ATATTAAATT
466701 AATAAATATTAAATT
1 AA-AAATATTAAATT
*
466716 -AAAATAATACAATT
1 AAAAATATTA-AATT
* *
466730 AAAAAAATTAAAAT
1 AAAAATATTAAATT
*
466744 AATAATAT
1 AAAAATAT
466752 AAGTGGATCT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
13 7 0.17
14 14 0.34
15 18 0.44
16 2 0.05
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (14 bp):
AAAAATATTAAATT
Found at i:467775 original size:27 final size:27
Alignment explanation
Indices: 467737--467882 Score: 211
Period size: 27 Copynumber: 5.4 Consensus size: 27
467727 TGGTGGTTTG
* *
467737 GGTGGACTTGGAGGAACCGGAGGATTC
1 GGTGGACTTGGAGGAACCGGTGGAGTC
467764 GGTGGACTTGGAGGAACCGGTGGAGTC
1 GGTGGACTTGGAGGAACCGGTGGAGTC
**
467791 GGTGGACTTGGAGGTCCCGGTGGAGTC
1 GGTGGACTTGGAGGAACCGGTGGAGTC
* * *
467818 GGTGGATTTGGAGGTACCGGTGGAGCC
1 GGTGGACTTGGAGGAACCGGTGGAGTC
*
467845 GATGGACTTGGAGGAACCGGTGGAGTC
1 GGTGGACTTGGAGGAACCGGTGGAGTC
*
467872 GGTGGATTTGG
1 GGTGGACTTGG
467883 TGGTGCTGGT
Statistics
Matches: 106, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 106 1.00
ACGTcount: A:0.17, C:0.14, G:0.47, T:0.21
Consensus pattern (27 bp):
GGTGGACTTGGAGGAACCGGTGGAGTC
Found at i:467908 original size:12 final size:12
Alignment explanation
Indices: 467893--467953 Score: 50
Period size: 12 Copynumber: 5.1 Consensus size: 12
467883 TGGTGCTGGT
* *
467893 GGTGGTGTAGGG
1 GGTGGAGTAGGA
467905 GGTGGAGTAGGA
1 GGTGGAGTAGGA
** * *
467917 GGTGCTGTTGGC
1 GGTGGAGTAGGA
*
467929 GGTGGAGTTGGA
1 GGTGGAGTAGGA
*
467941 GGTGGAGCAGGA
1 GGTGGAGTAGGA
467953 G
1 G
467954 CAGGAGCTGG
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.15, C:0.05, G:0.59, T:0.21
Consensus pattern (12 bp):
GGTGGAGTAGGA
Found at i:467920 original size:24 final size:24
Alignment explanation
Indices: 467893--467945 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
467883 TGGTGCTGGT
*
467893 GGTGGTGTAGGGGGTGGAGTAGGA
1 GGTGGTGTAGGCGGTGGAGTAGGA
* * *
467917 GGTGCTGTTGGCGGTGGAGTTGGA
1 GGTGGTGTAGGCGGTGGAGTAGGA
467941 GGTGG
1 GGTGG
467946 AGCAGGAGCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.11, C:0.04, G:0.60, T:0.25
Consensus pattern (24 bp):
GGTGGTGTAGGCGGTGGAGTAGGA
Found at i:468077 original size:15 final size:16
Alignment explanation
Indices: 468057--468090 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
468047 AATCGTCTTC
468057 TTTGTTTAGTT-ATGT
1 TTTGTTTAGTTAATGT
*
468072 TTTGTTTTGTTAATGT
1 TTTGTTTAGTTAATGT
468088 TTT
1 TTT
468091 TTCTAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.12, C:0.00, G:0.18, T:0.71
Consensus pattern (16 bp):
TTTGTTTAGTTAATGT
Found at i:476636 original size:21 final size:21
Alignment explanation
Indices: 476610--476669 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
476600 CGAGAGGAGG
476610 AAGAAGAAAGAAGAAAAAAGA
1 AAGAAGAAAGAAGAAAAAAGA
* *
476631 AAGAAGAGA-AAGAGAAAGAGA
1 AAGAAGAAAGAAGA-AAAAAGA
476652 AAGAAG-AAGAAGAAAAAA
1 AAGAAGAAAGAAGAAAAAA
476670 AAACAGACGG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
20 9 0.27
21 24 0.73
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (21 bp):
AAGAAGAAAGAAGAAAAAAGA
Found at i:476888 original size:13 final size:13
Alignment explanation
Indices: 476872--476905 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
476862 CCAACGCAAA
476872 AGCAGGCCAGCCC
1 AGCAGGCCAGCCC
476885 AGCAGGCCAGCCC
1 AGCAGGCCAGCCC
476898 AGCAGGCC
1 AGCAGGCC
476906 CAGTACGCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.24, C:0.44, G:0.32, T:0.00
Consensus pattern (13 bp):
AGCAGGCCAGCCC
Found at i:476939 original size:8 final size:8
Alignment explanation
Indices: 476927--476994 Score: 63
Period size: 8 Copynumber: 9.0 Consensus size: 8
476917 ACAGCCCAGC
476927 AAAAAAA-
1 AAAAAAAG
*
476934 AGAAAAAG
1 AAAAAAAG
*
476942 -AAAAGAG
1 AAAAAAAG
*
476949 AAGAAAAG
1 AAAAAAAG
476957 AAAAAAAG
1 AAAAAAAG
*
476965 AAAGAAAG
1 AAAAAAAG
476973 -AAAAAAG
1 AAAAAAAG
*
476980 -GAAAAAG
1 AAAAAAAG
476987 AAAAAAAG
1 AAAAAAAG
476995 GGGGCTCAAG
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
7 23 0.48
8 25 0.52
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:476954 original size:16 final size:14
Alignment explanation
Indices: 476928--476994 Score: 82
Period size: 14 Copynumber: 4.6 Consensus size: 14
476918 CAGCCCAGCA
476928 AAAAAAAGAAAAAG
1 AAAAAAAGAAAAAG
476942 AAAAGAGAAG-AAAAG
1 AAAA-A-AAGAAAAAG
476957 AAAAAAAGAAAGAAAG
1 AAAAAAAG-AA-AAAG
*
476973 AAAAAAGGAAAAAG
1 AAAAAAAGAAAAAG
476987 AAAAAAAG
1 AAAAAAAG
476995 GGGGCTCAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
13 3 0.07
14 16 0.35
15 13 0.28
16 14 0.30
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAAAAAG
Found at i:476994 original size:22 final size:21
Alignment explanation
Indices: 476929--476994 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 21
476919 AGCCCAGCAA
476929 AAAAAAGAAAAAGAAAAGAGAAG
1 AAAAAAGAAAAAGAAAA-A-AAG
*
476952 AAAAGAA-AAAAAGAAAGAAAG
1 AAAA-AAGAAAAAGAAAAAAAG
476973 AAAAAAGGAAAAAGAAAAAAAG
1 AAAAAA-GAAAAAGAAAAAAAG
476995 GGGGCTCAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
20 2 0.05
21 7 0.18
22 14 0.37
23 13 0.34
24 2 0.05
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (21 bp):
AAAAAAGAAAAAGAAAAAAAG
Found at i:477516 original size:18 final size:17
Alignment explanation
Indices: 477475--477523 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
477465 TTAAAAATAA
477475 TCGTGTTTCAAAAATTT
1 TCGTGTTTCAAAAATTT
* **
477492 TCATGTTTTTAAAATTT
1 TCGTGTTTCAAAAATTT
477509 CTCGTGTTTCAAAAA
1 -TCGTGTTTCAAAAA
477524 ACAATAATAA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
17 14 0.56
18 11 0.44
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.47
Consensus pattern (17 bp):
TCGTGTTTCAAAAATTT
Found at i:477594 original size:17 final size:17
Alignment explanation
Indices: 477574--477711 Score: 116
Period size: 17 Copynumber: 7.9 Consensus size: 17
477564 AGAAAAAAAC
477574 TTCGTGTTTCAAAAATT
1 TTCGTGTTTCAAAAATT
*
477591 TTCGTATTTCCAAAAATT
1 TTCGTGTTT-CAAAAATT
* *
477609 TTCATGTTTCAAAAAAAAT
1 TTCGTGTTTC--AAAAATT
*
477628 CTCGTGTTTTCAAAAATT
1 TTCGTG-TTTCAAAAATT
* *
477646 TTCGTGTTTTAGAAATT
1 TTCGTGTTTCAAAAATT
**
477663 TTCGTGTTTTTAAAATT
1 TTCGTGTTTCAAAAATT
* * *
477680 CTCGTATTGC-AAAATT
1 TTCGTGTTTCAAAAATT
*
477696 TCCGTGTTTTCAAAAA
1 TTCGTG-TTTCAAAAA
477712 AAATTTCGTG
Statistics
Matches: 95, Mismatches: 20, Indels: 11
0.75 0.16 0.09
Matches are distributed among these distances:
16 9 0.09
17 42 0.44
18 30 0.32
19 10 0.11
20 4 0.04
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.45
Consensus pattern (17 bp):
TTCGTGTTTCAAAAATT
Found at i:477604 original size:18 final size:18
Alignment explanation
Indices: 477574--477671 Score: 101
Period size: 18 Copynumber: 5.5 Consensus size: 18
477564 AGAAAAAAAC
477574 TTCGTGTTT-CAAAAATT
1 TTCGTGTTTCCAAAAATT
*
477591 TTCGTATTTCCAAAAATT
1 TTCGTGTTTCCAAAAATT
* * *
477609 TTCATGTTTCAAAAAAAAT
1 TTCGTGTTTC-CAAAAATT
* *
477628 CTCGTGTTTTCAAAAATT
1 TTCGTGTTTCCAAAAATT
* *
477646 TTCGTGTTT-TAGAAATT
1 TTCGTGTTTCCAAAAATT
477663 TTCGTGTTT
1 TTCGTGTTT
477672 TTAAAATTCT
Statistics
Matches: 66, Mismatches: 13, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
17 23 0.35
18 30 0.45
19 13 0.20
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.47
Consensus pattern (18 bp):
TTCGTGTTTCCAAAAATT
Found at i:477673 original size:18 final size:17
Alignment explanation
Indices: 477629--477746 Score: 71
Period size: 17 Copynumber: 6.8 Consensus size: 17
477619 AAAAAAAATC
*
477629 TCGTGTTTTCAAAAATTT
1 TCGTGTTTT-TAAAATTT
477647 TCGTG-TTTTAGAAATTT
1 TCGTGTTTTTA-AAATTT
*
477664 TCGTGTTTTTAAAATTC
1 TCGTGTTTTTAAAATTT
* **
477681 TCGT-ATTGCAAAATTT
1 TCGTGTTTTTAAAATTT
* * *
477697 CCGTGTTTTCAAAAAAAATT
1 TCGTGTTTT---TAAAATTT
*
477717 TCGTG-TTTTAAAATTC
1 TCGTGTTTTTAAAATTT
* *
477733 TCATTTTTTTAAAA
1 TCGTGTTTTTAAAA
477747 AAAATCTCGT
Statistics
Matches: 76, Mismatches: 17, Indels: 15
0.70 0.16 0.14
Matches are distributed among these distances:
16 20 0.26
17 33 0.43
18 10 0.13
19 3 0.04
20 10 0.13
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.48
Consensus pattern (17 bp):
TCGTGTTTTTAAAATTT
Found at i:477721 original size:20 final size:20
Alignment explanation
Indices: 477690--477729 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
477680 CTCGTATTGC
477690 AAAATTTCCGTGTTTTCAAAA
1 AAAATTTCCGTGTTTT-AAAA
477711 AAAATTT-CGTGTTTTAAAA
1 AAAATTTCCGTGTTTTAAAA
477730 TTCTCATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.21
20 8 0.42
21 7 0.37
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (20 bp):
AAAATTTCCGTGTTTTAAAA
Found at i:477729 original size:17 final size:17
Alignment explanation
Indices: 477567--477729 Score: 80
Period size: 17 Copynumber: 9.2 Consensus size: 17
477557 ATTTTAAAGA
* *
477567 AAAAAACTTCGTGTTTC
1 AAAAAATTTCGTGTTTT
* * *
477584 AAAAATTTTCGTATTTCC
1 AAAAAATTTCGTGTTT-T
* * *
477602 AAAAATTTTCATGTTTCAA
1 AAAAAATTTCGTGTTT--T
*
477621 AAAAAATCTCGTGTTTT
1 AAAAAATTTCGTGTTTT
*
477638 CAAAAATTTTCGTGTTTT
1 -AAAAAATTTCGTGTTTT
* *
477656 AGAAATTTTCGTGTTTT
1 AAAAAATTTCGTGTTTT
* *
477673 -TAAAA-TTC-TCGTATT
1 AAAAAATTTCGT-GTTTT
**
477688 GCAAAATTTCCGTGTTTT
1 AAAAAATTT-CGTGTTTT
477706 CAAAAAAAATTTCGTGTTTT
1 ---AAAAAATTTCGTGTTTT
477726 AAAA
1 AAAA
477730 TTCTCATTTT
Statistics
Matches: 114, Mismatches: 21, Indels: 22
0.73 0.13 0.14
Matches are distributed among these distances:
14 1 0.01
15 7 0.06
16 7 0.06
17 35 0.31
18 35 0.31
19 14 0.12
20 8 0.07
21 7 0.06
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.43
Consensus pattern (17 bp):
AAAAAATTTCGTGTTTT
Found at i:480423 original size:34 final size:35
Alignment explanation
Indices: 480339--480478 Score: 120
Period size: 37 Copynumber: 3.9 Consensus size: 35
480329 GAGAATTTTG
* * *
480339 AAACACGGAAAATTTTTTGAAAACACGGAAATTTTTG
1 AAACAC-GAAAA-TTTTTGAAAACACGAAAATTTCTA
* * * *
480376 CAATACGAGAA-TTTTAAAAACACGAAAATTTCTA
1 AAACACGAAAATTTTTGAAAACACGAAAATTTCTA
** * *
480410 AAACACGAAAATTTTTGAAAACACGAGATTTTTTTTG
1 AAACACGAAAATTTTTGAAAACACGA-A-AATTTCTA
* *
480447 AAACACGAAAATTTTTGGAAATACGAAAATTT
1 AAACACGAAAATTTTTGAAAACACGAAAATTT
480479 TTGAAGAACG
Statistics
Matches: 81, Mismatches: 19, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
34 27 0.33
35 16 0.20
36 6 0.07
37 32 0.40
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (35 bp):
AAACACGAAAATTTTTGAAAACACGAAAATTTCTA
Found at i:480490 original size:17 final size:17
Alignment explanation
Indices: 480334--480483 Score: 138
Period size: 17 Copynumber: 8.4 Consensus size: 17
480324 AAAATGAGAA
480334 TTTTGAAACACGGAAAATT
1 TTTTGAAACAC-GAAAA-T
*
480353 TTTTGAAAACACGGAAAT
1 TTTTG-AAACACGAAAAT
* * *
480371 TTTTGCAATACGAGAAT
1 TTTTGAAACACGAAAAT
**
480388 TTTAAAAACACGAAAAT
1 TTTTGAAACACGAAAAT
* *
480405 TTCTAAAACACGAAAAT
1 TTTTGAAACACGAAAAT
**
480422 TTTTGAAAACACGAGATTTT
1 TTTTG-AAACACGA-A-AAT
480442 TTTTGAAACACGAAAAT
1 TTTTGAAACACGAAAAT
*
480459 TTTTGGAAATACGAAAAT
1 TTTT-GAAACACGAAAAT
480477 TTTTGAA
1 TTTTGAA
480484 GAACGAAGTT
Statistics
Matches: 107, Mismatches: 19, Indels: 12
0.78 0.14 0.09
Matches are distributed among these distances:
17 46 0.43
18 31 0.29
19 18 0.17
20 12 0.11
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (17 bp):
TTTTGAAACACGAAAAT
Found at i:480567 original size:18 final size:17
Alignment explanation
Indices: 480540--480588 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 17
480530 TTATTATTAT
480540 TTTTTGAAACACGAGAAA
1 TTTTTGAAACACGA-AAA
*
480558 -TTTTGAAAACATGAAAA
1 TTTTTG-AAACACGAAAA
480575 TTTTTGAAACACGA
1 TTTTTGAAACACGA
480589 TTAATTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (17 bp):
TTTTTGAAACACGAAAA
Found at i:480594 original size:18 final size:17
Alignment explanation
Indices: 480540--480597 Score: 62
Period size: 18 Copynumber: 3.3 Consensus size: 17
480530 TTATTATTAT
*
480540 TTTTTGAAACACGAGAA
1 TTTTTGAAACACGATAA
* * *
480557 ATTTTGAAAACATGAAAA
1 TTTTTG-AAACACGATAA
480575 TTTTTGAAACACGATTAA
1 TTTTTGAAACACGA-TAA
480593 TTTTT
1 TTTTT
480598 TTTAAAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
17 12 0.36
18 21 0.64
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (17 bp):
TTTTTGAAACACGATAA
Found at i:481092 original size:13 final size:14
Alignment explanation
Indices: 481074--481113 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 14
481064 TGAGCCCCCC
481074 TTTTTTCTTTCTTT
1 TTTTTTCTTTCTTT
481088 TTTTTTCTTCTCTTT
1 TTTTTTCTT-TCTTT
481103 TCTTTTTCTTT
1 T-TTTTTCTTT
481114 TTCTGCTGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.38
15 7 0.29
16 8 0.33
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTTTCTTTCTTT
Found at i:481407 original size:24 final size:26
Alignment explanation
Indices: 481380--481438 Score: 86
Period size: 24 Copynumber: 2.3 Consensus size: 26
481370 TTTTTCTCTT
*
481380 TTTTTCTTTTTGTTC-TTC-TTTTTC
1 TTTTTCTTTTTCTTCTTTCTTTTTTC
481404 TTTTTCTTTTTCTTCTTTCTTTTTTC
1 TTTTTCTTTTTCTTCTTTCTTTTTTC
481430 TTCTTTCTT
1 TT-TTTCTT
481439 CTTCCTCCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
24 14 0.45
25 3 0.10
26 8 0.26
27 6 0.19
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.80
Consensus pattern (26 bp):
TTTTTCTTTTTCTTCTTTCTTTTTTC
Found at i:481416 original size:21 final size:20
Alignment explanation
Indices: 481361--481441 Score: 87
Period size: 21 Copynumber: 4.0 Consensus size: 20
481351 CCGTCTGTTA
*
481361 TTTTTTATT-TTTTTC-TCT
1 TTTTTTTTTCTTTTTCTTCT
*
481379 TTTTTTCTTT-TTGTTCTTCT
1 TTTTTT-TTTCTTTTTCTTCT
481399 TTTTCTTTTTCTTTTTCTTCT
1 TTTT-TTTTTCTTTTTCTTCT
*
481420 TTCTTTTTTCTTCTTTCTTCT
1 TTTTTTTTTCTT-TTTCTTCT
481441 T
1 T
481442 CCTCCTTCTC
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
18 6 0.11
19 7 0.13
20 18 0.33
21 23 0.43
ACGTcount: A:0.01, C:0.17, G:0.01, T:0.80
Consensus pattern (20 bp):
TTTTTTTTTCTTTTTCTTCT
Found at i:481440 original size:24 final size:22
Alignment explanation
Indices: 481368--481442 Score: 84
Period size: 22 Copynumber: 3.4 Consensus size: 22
481358 TTATTTTTTA
*
481368 TTTTT-TTCTCTTTTTTTCTT-
1 TTTTTCTTCTTTTTTTTTCTTC
*
481388 TTTGTTCTTCTTTTTCTTT-TTC
1 TTT-TTCTTCTTTTTTTTTCTTC
481410 TTTTTCTTCTTTCTTTTTTCTTC
1 TTTTTCTTCTTT-TTTTTTCTTC
481433 TTTCTTCTTC
1 TTT-TTCTTC
481443 CTCCTTCTCT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
20 3 0.07
21 13 0.28
22 18 0.39
23 6 0.13
24 6 0.13
ACGTcount: A:0.00, C:0.20, G:0.01, T:0.79
Consensus pattern (22 bp):
TTTTTCTTCTTTTTTTTTCTTC
Found at i:481441 original size:7 final size:6
Alignment explanation
Indices: 481380--481438 Score: 73
Period size: 6 Copynumber: 9.3 Consensus size: 6
481370 TTTTTCTCTT
* *
481380 TTTTTC TTTTTG TTCTTC TTTTTC TTTTTC TTTTTC TTCTTTC TTTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TT-TTTC -TTTTTC
481430 TTCTTTC TT
1 TT-TTTC TT
481439 CTTCCTCCTT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
6 30 0.65
7 14 0.30
8 2 0.04
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:481697 original size:17 final size:18
Alignment explanation
Indices: 481641--481697 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 18
481631 GCGGTGGTTG
*
481641 CGGTGGCGGTGGTTGCGCGA
1 CGGTGGCGGT-GATG-GCGA
* *
481661 CGGTGGTGGTGATGTC-A
1 CGGTGGCGGTGATGGCGA
481678 CGGTGGCGGTG-TGGCGA
1 CGGTGGCGGTGATGGCGA
481695 CGG
1 CGG
481698 GGATGGTTGC
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
16 3 0.10
17 15 0.48
18 1 0.03
19 3 0.10
20 9 0.29
ACGTcount: A:0.07, C:0.18, G:0.54, T:0.21
Consensus pattern (18 bp):
CGGTGGCGGTGATGGCGA
Found at i:482063 original size:30 final size:30
Alignment explanation
Indices: 482029--482105 Score: 109
Period size: 30 Copynumber: 2.6 Consensus size: 30
482019 GAAGTTTATG
**
482029 GGTCAAAATGTAATTTTAGGAAAGTTAAGA
1 GGTCAAAATGTAATTTTAAAAAAGTTAAGA
** *
482059 GGTCAAAACATAATTTTAAAAAAGTTAAGG
1 GGTCAAAATGTAATTTTAAAAAAGTTAAGA
482089 GGTCAAAATGTAATTTT
1 GGTCAAAATGTAATTTT
482106 TTATTATTGT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.44, C:0.05, G:0.19, T:0.31
Consensus pattern (30 bp):
GGTCAAAATGTAATTTTAAAAAAGTTAAGA
Found at i:482063 original size:59 final size:60
Alignment explanation
Indices: 481968--482105 Score: 145
Period size: 59 Copynumber: 2.3 Consensus size: 60
481958 AGCAAAACTC
* * * * * ** * *
481968 TGGGTCCAAGTGTAATTTTGAGAAAATTTAGGGGTCAAAATATAA-CTTCGAGAAGTTTA
1 TGGGTCAAAATGTAATTTTGAGAAAATTAAGAGGTCAAAACATAATCTTAAAAAAGTTAA
* *
482027 TGGGTCAAAATGTAATTTT-AGGAAAGTTAAGAGGTCAAAACATAATTTTAAAAAAGTTAA
1 TGGGTCAAAATGTAATTTTGA-GAAAATTAAGAGGTCAAAACATAATCTTAAAAAAGTTAA
*
482087 GGGGTCAAAATGTAATTTT
1 TGGGTCAAAATGTAATTTT
482106 TTATTATTGT
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
58 1 0.02
59 37 0.57
60 27 0.42
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.32
Consensus pattern (60 bp):
TGGGTCAAAATGTAATTTTGAGAAAATTAAGAGGTCAAAACATAATCTTAAAAAAGTTAA
Found at i:484361 original size:111 final size:114
Alignment explanation
Indices: 484202--484422 Score: 283
Period size: 112 Copynumber: 2.0 Consensus size: 114
484192 CACGAAATCT
* * *
484202 CTTAACCAAAACGCTGTGTTTTCGTCTTGATGTATCTTAAAAATAGTGGCG-TT-TACGCG-AAA
1 CTTAACCAAAACGCAGAGTTTTCGTCTTGAAGTATCTTAAAAATAGTGGCGCTTATA-G-GAAAA
*
484264 CGCCGTTAAAGGACAGT-ATAGTGGCGCTTT-CTGGAAACGCCGCAAAATAG
64 CGCCGTTAAAGGACAGTAATAGCGGCGCTTTAC-GGAAACGCCGCAAAATAG
* * *
484314 CTTAACCAAAACGCAGAG-TTTGGTCTTGAAGTATCTTAGAATTAGTGGCGCTTATAGGAAAACG
1 CTTAACCAAAACGCAGAGTTTTCGTCTTGAAGTATCTTAAAAATAGTGGCGCTTATAGGAAAACG
* * *
484378 CCGTTGAAGTACAGTAATAGCGGCGCTTTACGGAAGCGCCGCAAA
66 CCGTTAAAGGACAGTAATAGCGGCGCTTTACGGAAACGCCGCAAA
484423 CTATCTGAAG
Statistics
Matches: 94, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
111 29 0.31
112 37 0.39
113 27 0.29
114 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.26
Consensus pattern (114 bp):
CTTAACCAAAACGCAGAGTTTTCGTCTTGAAGTATCTTAAAAATAGTGGCGCTTATAGGAAAACG
CCGTTAAAGGACAGTAATAGCGGCGCTTTACGGAAACGCCGCAAAATAG
Found at i:484513 original size:114 final size:114
Alignment explanation
Indices: 484196--484937 Score: 501
Period size: 115 Copynumber: 6.5 Consensus size: 114
484186 ATGCGCCACG
* * * * * * *
484196 AAATCTCTTAACCAAAACGC-TGTGTTTTCGTCTTGATGTAT-CTTAAAAATAGTGGCGTTTACG
1 AAATATCTGAACCAAAACGCAT-CGTTTTGGTCTTGATGTATAC-TAGAATTAGTGGCGCTTACG
* * * * * *
484259 CG-AAACGCCGTTAAAGGACAGT-ATAGTGGCGCTT-TCTGGAAACGCCGCA
64 -GTAAACGCCGCTAAAGAATAGTAATAGCGGCGCTTGTATGGAAGCGCCGCA
* * ** * *
484308 AAATAGCTTAACCAAAACGCAGAG-TTTGGTCTTGAAGTAT-CTTAGAATTAGTGGCGCTTATAG
1 AAATATCTGAACCAAAACGCATCGTTTTGGTCTTGATGTATAC-TAGAATTAGTGGCGCTTA-CG
* * * * * *
484371 GAAAACGCCGTTGAAGTACAGTAATAGCGGCGCTT-TACGGAAGCGCCGCA
64 GTAAACGCCGCTAAAGAATAGTAATAGCGGCGCTTGTATGGAAGCGCCGCA
* * * ** * * *
484421 AACTATCTGAAGCGAAACATATCGTTTTGGTCTTGATTTATACTAGAACTAGTGGCGCATACGGT
1 AAATATCTGAACCAAAACGCATCGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTACGGT
* * * * **
484486 CAAACACCGCTAAAAAATAGTATTAGCGGCGATTTGTA-GCTAGCGCCGCA
66 -AAACGCCGCTAAAGAATAGTAATAGCGGCG-CTTGTATGGAAGCGCCGCA
* * * * * * * *
484536 AAATATCTTAACAAAAACGTAGCGTTTTGATCTTAATGTATA-TAAAATTAGTGGCACTTACGGT
1 AAATATCTGAACCAAAACGCATCGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTACGGT
* * *
484600 AAACCGCCGCTAAAGAATATTAATAGCGGCACTT-TTTGAGAAGCGCCGCA
66 AAA-CGCCGCTAAAGAATAGTAATAGCGGCGCTTGTATG-GAAGCGCCGCA
* ** * * *
484650 AAATATCTTAACCAAAACGCATAATTTTGGCCTCGATGTATAGTAGAATTAGTGGCGCTTA--GT
1 AAATATCTGAACCAAAACGCATCGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTACGGT
* * * * ** * *
484713 GAAACGCCGTTAAAGCATAGTATTAGCGGCGCTTGGATAAAAGCGCCACC
66 -AAACGCCGCTAAAGAATAGTAATAGCGGCGCTTGTATGGAAGCGCCGCA
* * * * ** *
484763 AAGTATCTGAACCAAAACGCATCGTTTTGGTCTTGATGTATACTTGATTTAGTGGCGATTTTGAT
1 AAATATCTGAACCAAAACGCATCGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTACGGT
* * * *
484828 AAAACGCCGCTAAAGCATAGTATTAGCGGCGATTTGT-T-GATAGCGCCGCG
66 -AAACGCCGCTAAAGAATAGTAATAGCGGCG-CTTGTATGGA-AGCGCCGCA
* * * * * *
484878 ACATACCAT-AAACAAAACGCAAT-GTTTTGGTCTTAATTTATACTAAAATTAGTGGCGCTT
1 AAATATC-TGAACCAAAACGC-ATCGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTT
484938 TGTTGAAAGC
Statistics
Matches: 494, Mismatches: 115, Indels: 39
0.76 0.18 0.06
Matches are distributed among these distances:
111 32 0.06
112 39 0.08
113 131 0.27
114 140 0.28
115 144 0.29
116 8 0.02
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.28
Consensus pattern (114 bp):
AAATATCTGAACCAAAACGCATCGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTACGGT
AAACGCCGCTAAAGAATAGTAATAGCGGCGCTTGTATGGAAGCGCCGCA
Found at i:484776 original size:113 final size:115
Alignment explanation
Indices: 484571--484858 Score: 298
Period size: 113 Copynumber: 2.5 Consensus size: 115
484561 TTTGATCTTA
* * * * * * *
484571 ATGTATA-TAAAATTAGTGGC-ACTTACGGTAAACCGCCGCTAAAGAATATTAATAGCGGCACTT
1 ATGTATACTAGAATTAGTGGCGACTTA-GATAAAACGCCGCTAAAGCATAGTATTAGCGGCGCTT
** * * * * *
484634 -TTTGAGAAGCGCCGCAAAATATCTTAACCAAAACGCATAATTTTGGCCTCG
65 GGAT-AAAAGCGCCACCAAGTATCTGAACCAAAACGCATAATTTTGGCCTCG
* * *
484685 ATGTATAGTAGAATTAGTGGCG-CTTAG-TGAAACGCCGTTAAAGCATAGTATTAGCGGCGCTTG
1 ATGTATACTAGAATTAGTGGCGACTTAGATAAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTG
** * *
484748 GATAAAAGCGCCACCAAGTATCTGAACCAAAACGCATCGTTTTGGTCTTG
66 GATAAAAGCGCCACCAAGTATCTGAACCAAAACGCATAATTTTGGCCTCG
* * * *
484798 ATGTATACTTGATTTAGTGGCGATTTTGATAAAACGCCGCTAAAGCATAGTATTAGCGGCG
1 ATGTATACTAGAATTAGTGGCGACTTAGATAAAACGCCGCTAAAGCATAGTATTAGCGGCG
484859 ATTTGTTGAT
Statistics
Matches: 143, Mismatches: 26, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
113 85 0.59
114 12 0.08
115 46 0.32
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.27
Consensus pattern (115 bp):
ATGTATACTAGAATTAGTGGCGACTTAGATAAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTG
GATAAAAGCGCCACCAAGTATCTGAACCAAAACGCATAATTTTGGCCTCG
Found at i:485112 original size:7 final size:7
Alignment explanation
Indices: 485102--485216 Score: 65
Period size: 7 Copynumber: 16.0 Consensus size: 7
485092 AAAGTTTAAA
485102 GTTTAGG
1 GTTTAGG
*
485109 GTTTACG
1 GTTTAGG
* *
485116 ATGTA-G
1 GTTTAGG
485122 GTTTAGG
1 GTTTAGG
485129 G-TTAGGG
1 GTTTA-GG
485136 TGTTTAGG
1 -GTTTAGG
485144 G-TTAGG
1 GTTTAGG
485150 GTATTAGGG
1 GT-TTA-GG
*
485159 TGTTTTGG
1 -GTTTAGG
*
485167 GTTTAAG
1 GTTTAGG
485174 GTTTAGG
1 GTTTAGG
*
485181 AGTCTAGG
1 -GTTTAGG
* *
485189 GTATAAG
1 GTTTAGG
*
485196 GTTTAAG
1 GTTTAGG
*
485203 GTTTGGG
1 GTTTAGG
485210 GTTTAGG
1 GTTTAGG
485217 CTACTTTAGT
Statistics
Matches: 83, Mismatches: 16, Indels: 18
0.71 0.14 0.15
Matches are distributed among these distances:
6 13 0.16
7 47 0.57
8 14 0.17
9 7 0.08
10 2 0.02
ACGTcount: A:0.18, C:0.02, G:0.40, T:0.40
Consensus pattern (7 bp):
GTTTAGG
Found at i:485142 original size:15 final size:15
Alignment explanation
Indices: 485122--485151 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
485112 TACGATGTAG
485122 GTTTAGGGTTAGGGT
1 GTTTAGGGTTAGGGT
485137 GTTTAGGGTTAGGGT
1 GTTTAGGGTTAGGGT
485152 ATTAGGGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.00, G:0.47, T:0.40
Consensus pattern (15 bp):
GTTTAGGGTTAGGGT
Found at i:485158 original size:14 final size:15
Alignment explanation
Indices: 485124--485159 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
485114 CGATGTAGGT
*
485124 TTAGGGTTAGGGTGT
1 TTAGGGTTAGGGTGA
485139 TTAGGGTTAGGGT-A
1 TTAGGGTTAGGGTGA
485153 TTAGGGT
1 TTAGGGT
485160 GTTTTGGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.17, C:0.00, G:0.44, T:0.39
Consensus pattern (15 bp):
TTAGGGTTAGGGTGA
Found at i:486364 original size:22 final size:22
Alignment explanation
Indices: 486338--486384 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
486328 ACTATTCCGA
*
486338 TTAAATATGTAAGGCGTTTCTG
1 TTAAATAGGTAAGGCGTTTCTG
486360 TTAAATAGGTAAGGCGTTTCTG
1 TTAAATAGGTAAGGCGTTTCTG
486382 TTA
1 TTA
486385 TTACAGCCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.28, C:0.09, G:0.23, T:0.40
Consensus pattern (22 bp):
TTAAATAGGTAAGGCGTTTCTG
Found at i:486551 original size:44 final size:44
Alignment explanation
Indices: 486487--486608 Score: 235
Period size: 44 Copynumber: 2.8 Consensus size: 44
486477 TTGTGGTATC
486487 AATTTACTATTCCGATTTAGATTATAGCACATGAGAGGGTGGCAA
1 AATTTA-TATTCCGATTTAGATTATAGCACATGAGAGGGTGGCAA
486532 AATTTATATTCCGATTTAGATTATAGCACATGAGAGGGTGGCAA
1 AATTTATATTCCGATTTAGATTATAGCACATGAGAGGGTGGCAA
486576 AATTTATATTCCGATTTAGATTATAGCACATGA
1 AATTTATATTCCGATTTAGATTATAGCACATGA
486609 ATTGGAAGGG
Statistics
Matches: 77, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
44 71 0.92
45 6 0.08
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (44 bp):
AATTTATATTCCGATTTAGATTATAGCACATGAGAGGGTGGCAA
Found at i:486810 original size:36 final size:35
Alignment explanation
Indices: 486768--486883 Score: 96
Period size: 36 Copynumber: 3.3 Consensus size: 35
486758 GTTGTTATGT
486768 TCTGAAATATGCCTTGGATTTGAAATAATTTCTGAG
1 TCTGAAATATG-CTTGGATTTGAAATAATTTCTGAG
** * * *
486804 TCTGAAATAAT--TTGTTTTTG--ATTATGTTGTTATG
1 TCTGAAAT-ATGCTTGGATTTGAAATAAT-TTCTGA-G
*
486838 TTCTGAAATATGCTTTGGATTTGAAATAATTTTTGAG
1 -TCTGAAATATGC-TTGGATTTGAAATAATTTCTGAG
486875 TCTGAAATA
1 TCTGAAATA
486884 ATTTGTTTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 18
0.69 0.11 0.20
Matches are distributed among these distances:
32 4 0.07
33 4 0.07
34 10 0.16
35 8 0.13
36 17 0.28
37 10 0.16
38 4 0.07
39 4 0.07
ACGTcount: A:0.29, C:0.07, G:0.18, T:0.46
Consensus pattern (35 bp):
TCTGAAATATGCTTGGATTTGAAATAATTTCTGAG
Found at i:486834 original size:71 final size:71
Alignment explanation
Indices: 486735--486915 Score: 344
Period size: 71 Copynumber: 2.5 Consensus size: 71
486725 TGAGTGGATT
486735 TGAAATAATTTGTTTTTGATTATGTTGTTATGTTCTGAAATATGCCTTGGATTTGAAATAATTTC
1 TGAAATAATTTGTTTTTGATTATGTTGTTATGTTCTGAAATATGCCTTGGATTTGAAATAATTTC
486800 TGAGTC
66 TGAGTC
* *
486806 TGAAATAATTTGTTTTTGATTATGTTGTTATGTTCTGAAATATGCTTTGGATTTGAAATAATTTT
1 TGAAATAATTTGTTTTTGATTATGTTGTTATGTTCTGAAATATGCCTTGGATTTGAAATAATTTC
486871 TGAGTC
66 TGAGTC
486877 TGAAATAATTTGTTTTTGATTATGTTGTTATGTTCTGAA
1 TGAAATAATTTGTTTTTGATTATGTTGTTATGTTCTGAA
486916 NNNNNNNNNN
Statistics
Matches: 108, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
71 108 1.00
ACGTcount: A:0.27, C:0.05, G:0.18, T:0.50
Consensus pattern (71 bp):
TGAAATAATTTGTTTTTGATTATGTTGTTATGTTCTGAAATATGCCTTGGATTTGAAATAATTTC
TGAGTC
Found at i:489545 original size:132 final size:132
Alignment explanation
Indices: 489330--489997 Score: 1133
Period size: 132 Copynumber: 5.1 Consensus size: 132
489320 GTAATCTTCA
* * * * * ** *
489330 ATCTACTTCATGCCAATACATG-AGGCAAGATCTACTTTCTTCGATCTACTTTACCACCAGTATG
1 ATCTACTTCACGTCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATG
489394 GGAAGACAAGATCTGTATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATATT
66 GGAAGACAAGATCTGTATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATATT
489459 CG
131 CG
489461 ATCTACTTCACGTCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATG
1 ATCTACTTCACGTCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATG
* *
489526 GGAAGACAAGATCTGTATCTTGGATCCACTTCCTATCAATATAGGAAGATGGGACCTGCTATCTT
66 GGAAGACAAGATCTGTATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATATT
489591 CG
131 CG
489593 ATCTACTTCACG-CTAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATAT
1 ATCTACTTCACGTC-AATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATAT
*
489657 GGGAAGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATAT
65 GGGAAGACAAGATCTGTATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATAT
489722 TCG
130 TCG
*
489725 ATCTACTTCACGTCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATG
1 ATCTACTTCACGTCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATG
489790 GGAAGACAAGATCTGTATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATATT
66 GGAAGACAAGATCTGTATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATATT
489855 CG
131 CG
489857 ATCTACTTCACGTCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATG
1 ATCTACTTCACGTCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATG
** * * * * * *
489922 GGAAGACAAGATCTGCGTCGTCGATCCACTTCCTACCAATATAGGAAGATAGGATCAGCTATCTT
66 GGAAGACAAGATCTGTATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATATT
489987 CG
131 CG
489989 ATCTACTTC
1 ATCTACTTC
489998 TTGCCCCGGG
Statistics
Matches: 510, Mismatches: 24, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
131 21 0.04
132 488 0.96
133 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (132 bp):
ATCTACTTCACGTCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATG
GGAAGACAAGATCTGTATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATATT
CG
Found at i:490215 original size:95 final size:95
Alignment explanation
Indices: 490110--490303 Score: 370
Period size: 95 Copynumber: 2.0 Consensus size: 95
490100 AAGATCTGCA
*
490110 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTTAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
490175 TAGTCAGGGAGGTAAAATCTGCCATCTTTG
66 TAGTCAGGGAGGTAAAATCTGCCATCTTTG
490205 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
*
490270 TGGTCAGGGAGGTAAAATCTGCCATCTTTG
66 TAGTCAGGGAGGTAAAATCTGCCATCTTTG
490300 ATCT
1 ATCT
490304 GCTTCGCTAC
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
95 97 1.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (95 bp):
ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
TAGTCAGGGAGGTAAAATCTGCCATCTTTG
Found at i:490412 original size:229 final size:229
Alignment explanation
Indices: 490005--490437 Score: 715
Period size: 229 Copynumber: 1.9 Consensus size: 229
489995 TTCTTGCCCC
490005 GGGAGATAGAACTATCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAAAATCTACCATCTTC
1 GGGAGATAGAACTATCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAAAATCTACCATCTTC
* * *
490070 GATCTGCTTTGCTGCCAAATACAGAAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAA
66 GATCTGCTTCGCTACCAAATACAGAAAGGCAAGATCGGCAATCTTCAATCTATTCCACTGCCAAA
* *
490135 TACAGGGAGATAGAGTTATCGGCTTTAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCAT
131 TACAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCAT
490200 CTTT-GATCTTCAATCTATTCCACTGCCAAATACA
196 -TTTCGATCTTCAATCTATTCCACTGCCAAATACA
** * ** * *
490234 GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTT
1 GGGAGATAGAACTATCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAAAATCTACCATCTTC
*
490299 GATCTGCTTCGCTACCAAATACAGGAAGGCAAGATCGGCAATCTTCAATCTATTCCACTGCCAAA
66 GATCTGCTTCGCTACCAAATACAGAAAGGCAAGATCGGCAATCTTCAATCTATTCCACTGCCAAA
* *
490364 TACAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTTGTCAGGGAGGTAAAATCTGTCAT
131 TACAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCAT
490429 TTTCGATCT
196 TTTCGATCT
490438 GCTTCGCTGC
Statistics
Matches: 188, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
228 3 0.02
229 185 0.98
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (229 bp):
GGGAGATAGAACTATCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAAAATCTACCATCTTC
GATCTGCTTCGCTACCAAATACAGAAAGGCAAGATCGGCAATCTTCAATCTATTCCACTGCCAAA
TACAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCAT
TTTCGATCTTCAATCTATTCCACTGCCAAATACA
Found at i:490480 original size:134 final size:134
Alignment explanation
Indices: 490205--490468 Score: 458
Period size: 134 Copynumber: 2.0 Consensus size: 134
490195 GCCATCTTTG
*
490205 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTG
* *
490270 TGGTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCTACCAAATACAGGAAGGCAAGATC
66 TGGTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCTACCAAATACAGAAAAGCAAGATC
490335 GGCA
131 GGCA
490339 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTG
* * *
490404 TTGTCAGGGAGGTAAAATCTGTCAT-TTTCGATCTGCTTCGCTGCCAAATACAGAAAAGCAAGAT
66 TGGTCAGGGAGGTAAAATCTGCCATCTTT-GATCTGCTTCGCTACCAAATACAGAAAAGCAAGAT
490468 C
130 C
490469 TGATATCTTC
Statistics
Matches: 123, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
133 3 0.02
134 120 0.98
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (134 bp):
ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTG
TGGTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCTACCAAATACAGAAAAGCAAGATC
GGCA
Found at i:490562 original size:86 final size:86
Alignment explanation
Indices: 490461--490691 Score: 372
Period size: 86 Copynumber: 2.7 Consensus size: 86
490451 ATACAGAAAA
490461 GCAAGATCTGATATCTTCAACCAGCTCTGCTACAAACGAGAGTGGCAAGGTTTGTCTTCGATCTG
1 GCAAGATCTGATATCTTCAACCAGCTCTGCTACAAACGAGAGTGGCAAGGTTTGTCTTCGATCTG
490526 CTTCACCGTCAATGCAGGAAG
66 CTTCACCGTCAATGCAGGAAG
* * *
490547 GCAAGATCTGCTATCTTTAACCAGCTCTACTACAAACGAGAGTGGCAAGGTTTGTCTTCGATCTG
1 GCAAGATCTGATATCTTCAACCAGCTCTGCTACAAACGAGAGTGGCAAGGTTTGTCTTCGATCTG
* *
490612 CTTCGCTGTCAATGCAGGAAG
66 CTTCACCGTCAATGCAGGAAG
* * * * *
490633 GCAAGATCTGATAACTTCAACCAGCTCTGCTACGACCGAGAGAGGCAAGGTTTATCTTC
1 GCAAGATCTGATATCTTCAACCAGCTCTGCTACAAACGAGAGTGGCAAGGTTTGTCTTC
490692 AATTTTTACT
Statistics
Matches: 132, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
86 132 1.00
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (86 bp):
GCAAGATCTGATATCTTCAACCAGCTCTGCTACAAACGAGAGTGGCAAGGTTTGTCTTCGATCTG
CTTCACCGTCAATGCAGGAAG
Found at i:507983 original size:18 final size:18
Alignment explanation
Indices: 507962--507998 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
507952 TGAATTTTCG
*
507962 AATTCGAATAACTCAAAT
1 AATTCGAATAAATCAAAT
507980 AATTCGAATAAATCAAAT
1 AATTCGAATAAATCAAAT
507998 A
1 A
507999 TCAAACTCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.14, G:0.05, T:0.27
Consensus pattern (18 bp):
AATTCGAATAAATCAAAT
Found at i:508076 original size:18 final size:19
Alignment explanation
Indices: 508053--508092 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
508043 TTCTTTTCAT
**
508053 TTCCCC-CAAAAGTTTTAC
1 TTCCCCTCAAAAAATTTAC
508071 TTCCCCTCAAAAAATTTAC
1 TTCCCCTCAAAAAATTTAC
508090 TTC
1 TTC
508093 TCTTCAAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.30, C:0.33, G:0.03, T:0.35
Consensus pattern (19 bp):
TTCCCCTCAAAAAATTTAC
Found at i:508248 original size:17 final size:17
Alignment explanation
Indices: 508192--508250 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
508182 TTATGTCTAC
508192 TATTTATATTATTGAAT
1 TATTTATATTATTGAAT
* *
508209 TAAATTTCACATT-TT-ATAC
1 T--ATTT-ATATTATTGA-AT
508228 TATTTATATTATTGAAT
1 TATTTATATTATTGAAT
508245 TATTTA
1 TATTTA
508251 ATCATACTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
16 4 0.12
17 14 0.44
18 2 0.06
19 8 0.25
20 4 0.12
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (17 bp):
TATTTATATTATTGAAT
Found at i:513096 original size:39 final size:39
Alignment explanation
Indices: 513042--513218 Score: 121
Period size: 39 Copynumber: 4.5 Consensus size: 39
513032 CTCTGGGGTT
513042 AACTGAGATTTTTCTTCAGTGCA-TTTTATCGGTGCCAGC
1 AACTGAGATTTTTCTTCAGTGCACTTTTAT-GGTGCCAGC
* * * *
513081 AACTGAGATTTTTCTTCA--GCAAGTTCTATAGGCGTCAGC
1 AACTGAGATTTTTCTTCAGTGC-ACTTTTAT-GGTGCCAGC
* * * * *
513120 GAGTGAGATTTTTCTTCTGTGTACTCTTT-TAGTGCCAGC
1 AACTGAGATTTTTCTTCAGTGCACT-TTTATGGTGCCAGC
* * * * *
513159 AACTGGGATTTTTCTTCAATGTACTCTTT-TGGTGTCATC
1 AACTGAGATTTTTCTTCAGTGCACT-TTTATGGTGCCAGC
* * *
513198 AGCTGAGGTTTCTCTTCAGTG
1 AACTGAGATTTTTCTTCAGTG
513219 TACTGAACAG
Statistics
Matches: 107, Mismatches: 26, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
37 2 0.02
38 1 0.01
39 98 0.92
40 3 0.03
41 3 0.03
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (39 bp):
AACTGAGATTTTTCTTCAGTGCACTTTTATGGTGCCAGC
Found at i:528777 original size:12 final size:12
Alignment explanation
Indices: 528760--528793 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
528750 TTGCACTTGT
* *
528760 AATTTTGTGAGA
1 AATTTTCTGAAA
528772 AATTTTCTGAAA
1 AATTTTCTGAAA
528784 AATTTTCTGA
1 AATTTTCTGA
528794 TTCGAAGCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (12 bp):
AATTTTCTGAAA
Found at i:529458 original size:9 final size:9
Alignment explanation
Indices: 529444--529469 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
529434 CTTTTGGAAG
529444 CTCTATTTA
1 CTCTATTTA
529453 CTCTATTTA
1 CTCTATTTA
529462 CTCTATTT
1 CTCTATTT
529470 CAAAATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.19, C:0.23, G:0.00, T:0.58
Consensus pattern (9 bp):
CTCTATTTA
Found at i:536208 original size:19 final size:19
Alignment explanation
Indices: 536180--536224 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
536170 TGTTAATTTC
*
536180 ATGAATTATATAATGTA-TG
1 ATGAAATATAT-ATGTATTG
*
536199 ATGAAATATATATTTATTG
1 ATGAAATATATATGTATTG
536218 ATGAAAT
1 ATGAAAT
536225 GAGAATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.42
Consensus pattern (19 bp):
ATGAAATATATATGTATTG
Found at i:536381 original size:46 final size:46
Alignment explanation
Indices: 536305--536506 Score: 347
Period size: 46 Copynumber: 4.5 Consensus size: 46
536295 TGATAAGTGA
*
536305 CAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
536351 CAAGTGACAAAGTGATAAGTGGTAGTTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
536397 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
536443 CAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
536488 C-AGGGAC-AAGTGATAAGTG
1 CAAGTGACAAAGTGATAAGTG
536507 ATCATACGTA
Statistics
Matches: 151, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
43 12 0.08
44 5 0.03
45 19 0.13
46 115 0.76
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.29
Consensus pattern (46 bp):
CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
Found at i:538461 original size:6 final size:6
Alignment explanation
Indices: 538450--538475 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
538440 ATAATTCAGC
538450 CTCCTA CTCCTA CTCCTA CTCCTA CT
1 CTCCTA CTCCTA CTCCTA CTCCTA CT
538476 AAAGATTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.50, G:0.00, T:0.35
Consensus pattern (6 bp):
CTCCTA
Found at i:553113 original size:26 final size:26
Alignment explanation
Indices: 553081--553168 Score: 122
Period size: 26 Copynumber: 3.4 Consensus size: 26
553071 TTTTACTCTA
*
553081 GTAAAATTTTGATGATTTTACCCCTG
1 GTAAAATTTTAATGATTTTACCCCTG
*
553107 GTAAAATTTTAATGATTTTACCCTTG
1 GTAAAATTTTAATGATTTTACCCCTG
* * *
553133 TTAAAATTTTAACGATTTTACCCCTA
1 GTAAAATTTTAATGATTTTACCCCTG
*
553159 ATAAAATTTT
1 GTAAAATTTT
553169 GAGAAATTTC
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (26 bp):
GTAAAATTTTAATGATTTTACCCCTG
Found at i:556442 original size:13 final size:13
Alignment explanation
Indices: 556426--556451 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
556416 ACTTTACGCA
556426 AACAAATGGTTTT
1 AACAAATGGTTTT
556439 AACAAATGGTTTT
1 AACAAATGGTTTT
556452 TGGAAACACG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (13 bp):
AACAAATGGTTTT
Found at i:567168 original size:42 final size:41
Alignment explanation
Indices: 567014--567169 Score: 158
Period size: 42 Copynumber: 3.7 Consensus size: 41
567004 TATGTTATCG
*
567014 TGTAAGACCACGTCTGGGACGTTGGCATCGAT-TTGAGATTTA
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATT--GATTCA
* * * *
567056 TGTATAAGACCATGTCTGGGACATCGGCATC-ATATTTGATTTCG
1 TG--TAAGACCACGTCTGGGACGTTGGCATCGATA-TTGA-TTCA
567100 TGTAAGACC-CTGTCTGGGACAG-TGGCATCGATATTGATTACA
1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATTGATT-CA
567142 TGTAAGACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
567170 TGTACGATTT
Statistics
Matches: 94, Mismatches: 9, Indels: 22
0.75 0.07 0.18
Matches are distributed among these distances:
41 3 0.03
42 53 0.56
43 8 0.09
44 28 0.30
45 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (41 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGATATTGATTCA
Found at i:572651 original size:11 final size:11
Alignment explanation
Indices: 572635--572661 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
572625 ATCAGATCCT
572635 TCAAATCGTCC
1 TCAAATCGTCC
572646 TCAAATCGTCC
1 TCAAATCGTCC
572657 TCAAA
1 TCAAA
572662 GTGGACGCGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.33, G:0.07, T:0.26
Consensus pattern (11 bp):
TCAAATCGTCC
Found at i:577329 original size:23 final size:22
Alignment explanation
Indices: 577286--577329 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
577276 TTCTAAGTCG
577286 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
577309 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
577330 TTTGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:577431 original size:45 final size:45
Alignment explanation
Indices: 577376--577462 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
577366 CAGATACTCG
* *
577376 GTGGAGTCAACACATAGCAACCACCTTATTAATCAATGATGTCGA
1 GTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTCGA
*
577421 GTGGAATCAACACATAGCAACCACTTTACTAATCAATGATGT
1 GTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGT
577463 TCGGTTCACA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (45 bp):
GTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTCGA
Found at i:577531 original size:50 final size:50
Alignment explanation
Indices: 577462--577657 Score: 207
Period size: 50 Copynumber: 3.9 Consensus size: 50
577452 ATCAATGATG
* * * *
577462 TTCGGTTCACATAGTAGCCTGAACATAGT-CTACACATGTTACCATTACCA
1 TTCGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCA-TACCA
* * * * * * *
577512 TTCGATACACGTAGTAGCCTTCACATAGTACTACATACGTGATCGAAACTA
1 TTCGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGA-CCATACCA
* * * *
577563 TCCGGTACGCATAGTAGCCTGCACATAGTACTACACATGTGACC-TATCA
1 TTCGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCATACCA
*
577612 TTCCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA
1 TT-CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCA
577658 CCACTTTCAC
Statistics
Matches: 116, Mismatches: 26, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
49 3 0.03
50 64 0.55
51 47 0.41
52 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (50 bp):
TTCGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCATACCA
Found at i:577622 original size:101 final size:100
Alignment explanation
Indices: 577471--577654 Score: 280
Period size: 101 Copynumber: 1.8 Consensus size: 100
577461 GTTCGGTTCA
* *
577471 CATAGTAGCCTGAACATAGTCTACACATGTTACCATTACCATTCGATACACGTAGTAGCCTTCAC
1 CATAGTAGCCTGAACATAGTCTACACATGTGACCA-TACCATTCGATACACGTAGTAGCCTGCAC
*
577536 ATAGTACTACATACGTGATCGAAACTATCCGGTACG
65 ATAGTACTACACACGTGATCGAAACTATCCGGTACG
* * *
577572 CATAGTAGCCTGCACATAGTACTACACATGTGACC-TATCATTCCGGTACACGTAGTAGCCTGCA
1 CATAGTAGCCTGAACATAGT-CTACACATGTGACCATACCATT-CGATACACGTAGTAGCCTGCA
577636 CATAGTACTACACACGTGA
64 CATAGTACTACACACGTGA
577655 CCACCACTTT
Statistics
Matches: 75, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
100 6 0.08
101 56 0.75
102 13 0.17
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.26
Consensus pattern (100 bp):
CATAGTAGCCTGAACATAGTCTACACATGTGACCATACCATTCGATACACGTAGTAGCCTGCACA
TAGTACTACACACGTGATCGAAACTATCCGGTACG
Found at i:585906 original size:39 final size:39
Alignment explanation
Indices: 585842--586031 Score: 265
Period size: 39 Copynumber: 4.9 Consensus size: 39
585832 CAGCTTGTTA
* * * * *
585842 GGCACAAAGCCTACTAAGCATTTAGCCAGAATAATCACC
1 GGCACAAAGCCTGCTAGGCACTTAGCCTGAATAATCACT
*
585881 GGCACAAAGCCTGTTAGGCACTTAGCCTGAATAATCACT
1 GGCACAAAGCCTGCTAGGCACTTAGCCTGAATAATCACT
* *
585920 GGCACAATA-CCTGCTAGGCACTTAGCCTGAACATTCACT
1 GGCACAA-AGCCTGCTAGGCACTTAGCCTGAATAATCACT
585959 GGCACAAAGCCTGCTAGGCACTTAGCCTGAATAATCACT
1 GGCACAAAGCCTGCTAGGCACTTAGCCTGAATAATCACT
** *
585998 GATACAAAGCCTGCTAGGCACTTAGCCCGAATAA
1 GGCACAAAGCCTGCTAGGCACTTAGCCTGAATAA
586032 GCACCGTATT
Statistics
Matches: 135, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
38 1 0.01
39 133 0.99
40 1 0.01
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.21
Consensus pattern (39 bp):
GGCACAAAGCCTGCTAGGCACTTAGCCTGAATAATCACT
Found at i:591107 original size:25 final size:25
Alignment explanation
Indices: 591059--591107 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
591049 CTAAGTTAAT
* *
591059 TAGATTTTAAGTGGGAAAGTAAAAA
1 TAGAGTTTAAGTAGGAAAGTAAAAA
591084 TAGAGTTTAAGTAGGAGAAG-AAAA
1 TAGAGTTTAAGTAGGA-AAGTAAAA
591108 TCCAAAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (25 bp):
TAGAGTTTAAGTAGGAAAGTAAAAA
Found at i:591642 original size:26 final size:27
Alignment explanation
Indices: 591613--591685 Score: 69
Period size: 26 Copynumber: 2.7 Consensus size: 27
591603 CGATTACAAG
591613 TGGAATATAAGATTACCT-TGTTTGGT
1 TGGAATATAAGATTACCTGTGTTTGGT
* * *
591639 TGGAATGTAAAATT-CATGTGTTTGGT
1 TGGAATATAAGATTACCTGTGTTTGGT
*
591665 TGACAAAATATAAGATTACCT
1 TG---GAATATAAGATTACCT
591686 AAAAGTAAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
25 2 0.06
26 22 0.63
29 9 0.26
30 2 0.06
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.38
Consensus pattern (27 bp):
TGGAATATAAGATTACCTGTGTTTGGT
Found at i:596326 original size:28 final size:29
Alignment explanation
Indices: 596294--596352 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
596284 TACAGTCAGT
596294 TGTTCTTACTCTC-AAAGAGACATTAACA
1 TGTTCTTACTCTCGAAAGAGACATTAACA
*
596322 TGTTCTTACTCTCGAAAGAGATATTAACA
1 TGTTCTTACTCTCGAAAGAGACATTAACA
596351 TG
1 TG
596353 ATTTAGGGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 13 0.45
29 16 0.55
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.34
Consensus pattern (29 bp):
TGTTCTTACTCTCGAAAGAGACATTAACA
Found at i:605779 original size:25 final size:25
Alignment explanation
Indices: 605735--605870 Score: 100
Period size: 25 Copynumber: 5.4 Consensus size: 25
605725 GGCAATCACA
* * *
605735 AGCTTCTCATTATTTAGCTCTCATG
1 AGCTTCCCATTATATGGCTCTCATG
*
605760 AGCTTCCCGATTA-ATGGCTCTCTTG
1 AGCTTCCC-ATTATATGGCTCTCATG
* * * * *
605785 AGCTTCTCAATATTTGGCTCGCAAG
1 AGCTTCCCATTATATGGCTCTCATG
* *
605810 AGCTTCCCGTTAT-TCAGCTCAT-ATG
1 AGCTTCCCATTATAT-GGCTC-TCATG
*
605835 AGCTTCCCATTATATGGCTCGGCA-G
1 AGCTTCCCATTATATGGCTC-TCATG
605860 AGCTTCCCATT
1 AGCTTCCCATT
605871 TACATGAATT
Statistics
Matches: 85, Mismatches: 20, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
24 4 0.05
25 75 0.88
26 6 0.07
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.35
Consensus pattern (25 bp):
AGCTTCCCATTATATGGCTCTCATG
Found at i:605837 original size:50 final size:50
Alignment explanation
Indices: 605735--605867 Score: 137
Period size: 50 Copynumber: 2.7 Consensus size: 50
605725 GGCAATCACA
* * * * *
605735 AGCTTCTCATTATTTAGCTCTCATGAGCTTCCCGATTAATGGCTCTCTTG
1 AGCTTCTCATTATTTGGCTCGCAAGAGCTTCCCGATTAATAGCTCTCATG
* *
605785 AGCTTCTCAATATTTGGCTCGCAAGAGCTTCCCG-TTATTCAGCTCAT-ATG
1 AGCTTCTCATTATTTGGCTCGCAAGAGCTTCCCGATTAAT-AGCTC-TCATG
* *
605835 AGCTTCCCATTATATGGCTCGGC-AGAGCTTCCC
1 AGCTTCTCATTATTTGGCTC-GCAAGAGCTTCCC
605868 ATTTACATGA
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
49 4 0.06
50 63 0.90
51 3 0.04
ACGTcount: A:0.20, C:0.28, G:0.18, T:0.35
Consensus pattern (50 bp):
AGCTTCTCATTATTTGGCTCGCAAGAGCTTCCCGATTAATAGCTCTCATG
Found at i:607260 original size:16 final size:17
Alignment explanation
Indices: 607239--607272 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
607229 GATTTGTTTC
607239 TGATATG-AATGTTTGT
1 TGATATGAAATGTTTGT
607255 TGATATGAAATGTTTGT
1 TGATATGAAATGTTTGT
607272 T
1 T
607273 ATTTGATCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (17 bp):
TGATATGAAATGTTTGT
Found at i:612854 original size:25 final size:25
Alignment explanation
Indices: 612826--612899 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 25
612816 CCGATATTTG
612826 GCTCGCAAGAGCTTCCCGTTATACA
1 GCTCGCAAGAGCTTCCCGTTATACA
* * * **
612851 GCTCACATGAGCTTCTCGTTATATG
1 GCTCGCAAGAGCTTCCCGTTATACA
* *
612876 GCTCGGAAGAGCTTTCCGTT-TACA
1 GCTCGCAAGAGCTTCCCGTTATACA
612900 TGCTTATATA
Statistics
Matches: 37, Mismatches: 12, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
24 2 0.05
25 35 0.95
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.30
Consensus pattern (25 bp):
GCTCGCAAGAGCTTCCCGTTATACA
Found at i:612956 original size:39 final size:38
Alignment explanation
Indices: 612880--612956 Score: 82
Period size: 39 Copynumber: 2.0 Consensus size: 38
612870 TATATGGCTC
* * **
612880 GGAAGAGCTTTCCGTTTACATGCTTATATAAGTATACA
1 GGAAGAGCTTCCCATTTACATGCTTATATAACCATACA
* * *
612918 NGGAAGAGCTTCCCATTTATATGTTTGTATAACCATACA
1 -GGAAGAGCTTCCCATTTACATGCTTATATAACCATACA
612957 TGTACATGAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (38 bp):
GGAAGAGCTTCCCATTTACATGCTTATATAACCATACA
Found at i:617704 original size:22 final size:22
Alignment explanation
Indices: 617679--617729 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
617669 GGTAAGACAA
617679 AGAACAGATT-AGATACAGATGC
1 AGAACA-ATTCAGATACAGATGC
*
617701 AGAACAATTCATATACAGATGC
1 AGAACAATTCAGATACAGATGC
*
617723 AAAACAA
1 AGAACAA
617730 ATCAAAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 3 0.12
22 23 0.88
ACGTcount: A:0.51, C:0.16, G:0.16, T:0.18
Consensus pattern (22 bp):
AGAACAATTCAGATACAGATGC
Found at i:618996 original size:17 final size:17
Alignment explanation
Indices: 618970--619009 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
618960 CACACAAGGA
618970 AAGAAAAAGAAAAAAAG
1 AAGAAAAAGAAAAAAAG
* * *
618987 AAGAAGAAGAGAAAAAT
1 AAGAAAAAGAAAAAAAG
619004 AAGAAA
1 AAGAAA
619010 GGAAAAGAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.03
Consensus pattern (17 bp):
AAGAAAAAGAAAAAAAG
Found at i:630624 original size:56 final size:56
Alignment explanation
Indices: 630557--630669 Score: 199
Period size: 56 Copynumber: 2.0 Consensus size: 56
630547 AAGCAATTAA
*
630557 ATCTTTGTCCTCGCCAAATTGAAGTTTGGTTTCAGAATAGAGGGAAAAAGGGAAAG
1 ATCTTTGTCCTCGCCAAATTGAAGTTTGGTTTCAGAATAGAGGGAAAAAGAGAAAG
* *
630613 ATCTTTGTCCTCGCCAAATTGAAGTTTGGTTTTAGAATAGAGGGGAAAAGAGAAAG
1 ATCTTTGTCCTCGCCAAATTGAAGTTTGGTTTCAGAATAGAGGGAAAAAGAGAAAG
630669 A
1 A
630670 GAAAAGAAGA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.35, C:0.12, G:0.27, T:0.27
Consensus pattern (56 bp):
ATCTTTGTCCTCGCCAAATTGAAGTTTGGTTTCAGAATAGAGGGAAAAAGAGAAAG
Found at i:631903 original size:18 final size:19
Alignment explanation
Indices: 631859--631904 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
631849 TCACAATCGC
*
631859 CATATTTCAAGTCATGCAAA
1 CATA-TTCAATTCATGCAAA
631879 -A-ATTCAATTCATG-AAA
1 CATATTCAATTCATGCAAA
631895 CATATTCAAT
1 CATATTCAAT
631905 AAGCACACCA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
16 3 0.13
17 11 0.48
18 8 0.35
19 1 0.04
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (19 bp):
CATATTCAATTCATGCAAA
Found at i:635600 original size:21 final size:20
Alignment explanation
Indices: 635570--635608 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
635560 ATAAAAAAAC
635570 TATATCATTTTTATGAATAAG
1 TATATCATTTTTAT-AATAAG
*
635591 TATATTATTTTTATAATA
1 TATATCATTTTTATAATA
635609 TATAGCACGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (20 bp):
TATATCATTTTTATAATAAG
Found at i:637297 original size:10 final size:9
Alignment explanation
Indices: 637269--637295 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
637259 TATTTTAGTT
637269 TTTTAAAAA
1 TTTTAAAAA
637278 TTTTAAAAA
1 TTTTAAAAA
637287 TTTTAAAAA
1 TTTTAAAAA
637296 ATAAACTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:637323 original size:27 final size:27
Alignment explanation
Indices: 637275--637351 Score: 68
Period size: 28 Copynumber: 2.8 Consensus size: 27
637265 AGTTTTTTAA
* *
637275 AAATTTTAAAAATT-TTAAAAAATAAACT
1 AAATTATAAAAATTATT-TAAAAT-AACT
*
637303 -AATTATAAAAATTATTTAAAATTACT
1 AAATTATAAAAATTATTTAAAATAACT
* *
637329 GAAATTATTAAACTTATTTAAAA
1 -AAATTATAAAAATTATTTAAAA
637352 AGTACAAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
26 3 0.07
27 17 0.41
28 21 0.51
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (27 bp):
AAATTATAAAAATTATTTAAAATAACT
Found at i:637361 original size:28 final size:27
Alignment explanation
Indices: 637311--637375 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 27
637301 CTAATTATAA
* *
637311 AAATTATTTAAAATTACTGAAATTATT
1 AAATTATTTAAAAGTACTAAAATTATT
637338 AAACTTATTTAAAAAGTAC-AAAATTA-T
1 AAA-TTATTT-AAAAGTACTAAAATTATT
637365 AAATT-TTTAAA
1 AAATTATTTAAA
637376 TATTTTTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
24 3 0.09
25 3 0.09
26 2 0.06
27 7 0.21
28 12 0.35
29 7 0.21
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (27 bp):
AAATTATTTAAAAGTACTAAAATTATT
Found at i:637403 original size:19 final size:18
Alignment explanation
Indices: 637357--637405 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
637347 TAAAAAGTAC
*
637357 AAAATTA-TAAATTTTTA
1 AAAATTATTAATTTTTTA
* *
637374 AATATTTTTAATTTTTTA
1 AAAATTATTAATTTTTTA
637392 AAAATTAATTAATT
1 AAAATT-ATTAATT
637406 GCTAACGTGA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 5 0.20
18 14 0.56
19 6 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AAAATTATTAATTTTTTA
Found at i:638822 original size:14 final size:14
Alignment explanation
Indices: 638803--638829 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
638793 AAGACCATGT
638803 TCTTTAGCGGCGCG
1 TCTTTAGCGGCGCG
638817 TCTTTAGCGGCGC
1 TCTTTAGCGGCGC
638830 TTAGAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.30, G:0.33, T:0.30
Consensus pattern (14 bp):
TCTTTAGCGGCGCG
Found at i:638894 original size:42 final size:42
Alignment explanation
Indices: 638817--638942 Score: 198
Period size: 42 Copynumber: 3.0 Consensus size: 42
638807 TAGCGGCGCG
*
638817 TCTTTAGCGGCGCTTAGAAAAAAAACGCCTCTAAAGACCATGT
1 TCTTTAGCGGCGCTTAG-AAAAAAACGCCGCTAAAGACCATGT
*
638860 TCTTTAGCGGCACTTAGAAAAAAACGCCGCTAAAGACCATGT
1 TCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGACCATGT
* * *
638902 ACTTTAGCGGCGCTTAGAAAAAAACACCGCTAAAGAACATG
1 TCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGACCATG
638943 AAAAATAGTG
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
42 61 0.79
43 16 0.21
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (42 bp):
TCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGACCATGT
Found at i:639345 original size:21 final size:21
Alignment explanation
Indices: 639320--639369 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
639310 TTTTGGCTTG
*
639320 CTCTGCTTCTCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* *
639341 TTCTGCTTCCCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
639362 CTCTGCTT
1 CTCTGCTT
639370 TAAGTTGTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.02, C:0.44, G:0.18, T:0.36
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:644896 original size:7 final size:7
Alignment explanation
Indices: 644886--644922 Score: 56
Period size: 7 Copynumber: 5.0 Consensus size: 7
644876 TGATATATTT
644886 TTATGTA
1 TTATGTA
644893 TTATGTAA
1 TTATGT-A
644901 GTTATGTA
1 -TTATGTA
644909 TTATGTA
1 TTATGTA
644916 TTATGTA
1 TTATGTA
644923 AGTACTGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 20 0.71
8 2 0.07
9 6 0.21
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.54
Consensus pattern (7 bp):
TTATGTA
Found at i:644907 original size:9 final size:9
Alignment explanation
Indices: 644893--645559 Score: 590
Period size: 9 Copynumber: 75.2 Consensus size: 9
644883 TTTTTATGTA
644893 TTATGTAAG
1 TTATGTAAG
644902 TTATGT-A-
1 TTATGTAAG
644909 TTATGT-A-
1 TTATGTAAG
644916 TTATGTAAG
1 TTATGTAAG
644925 -TACTGTAAG
1 TTA-TGTAAG
*
644934 TAATGTAAG
1 TTATGTAAG
*
644943 TAATGTAAG
1 TTATGTAAG
644952 TTATGTAAG
1 TTATGTAAG
* * *
644961 -AAAGTTA-
1 TTATGTAAG
644968 TTATGTAAG
1 TTATGTAAG
*
644977 TTGTGTATA-
1 TTATGTA-AG
*
644986 ATAT-TAA-
1 TTATGTAAG
*
644993 TTATGTGAG
1 TTATGTAAG
**
645002 TCGTGT-A-
1 TTATGTAAG
*
645009 TAATGTAAG
1 TTATGTAAG
*
645018 TTAAG-AAGG
1 TTATGTAA-G
645027 TTATGT-A-
1 TTATGTAAG
*
645034 TAATGTAAG
1 TTATGTAAG
645043 TTATGTAAG
1 TTATGTAAG
* * *
645052 TAATTTAAT
1 TTATGTAAG
645061 TTATGTAAG
1 TTATGTAAG
645070 TTATGTAAG
1 TTATGTAAG
* *
645079 TTATTTAAT
1 TTATGTAAG
*
645088 TTATGCAAG
1 TTATGTAAG
645097 TTATGTAAG
1 TTATGTAAG
* *
645106 TTATTTAAT
1 TTATGTAAG
* *
645115 TTGTGTAGG
1 TTATGTAAG
*
645124 TTATGTGAG
1 TTATGTAAG
645133 TTATGTAAG
1 TTATGTAAG
* *
645142 TTATTTAAT
1 TTATGTAAG
645151 TTATGTAAG
1 TTATGTAAG
645160 TTATGTAAG
1 TTATGTAAG
* *
645169 TTATTTAAT
1 TTATGTAAG
*
645178 TTATGCAAG
1 TTATGTAAG
645187 TTATGTAAG
1 TTATGTAAG
* *
645196 TTATTTAAT
1 TTATGTAAG
* *
645205 TTGTGTAGG
1 TTATGTAAG
*
645214 TTATGTGAG
1 TTATGTAAG
645223 TTATGTAAG
1 TTATGTAAG
* *
645232 TTATTTAAT
1 TTATGTAAG
645241 TTATGTAAG
1 TTATGTAAG
645250 TTATGTAAG
1 TTATGTAAG
* *
645259 TTATTTAAT
1 TTATGTAAG
*
645268 TTATGTAGG
1 TTATGTAAG
645277 TTATGTAAG
1 TTATGTAAG
645286 TTATGTAAG
1 TTATGTAAG
* *
645295 TTATTTAAT
1 TTATGTAAG
* *
645304 TTGTGTAGG
1 TTATGTAAG
645313 TTATGTAAG
1 TTATGTAAG
645322 TTATGTAAG
1 TTATGTAAG
*
645331 TTATTTAAG
1 TTATGTAAG
* *
645340 TTATTTAAT
1 TTATGTAAG
645349 TTATGTAAG
1 TTATGTAAG
645358 TTATGTAAG
1 TTATGTAAG
* *
645367 TTATTTAAT
1 TTATGTAAG
*
645376 TTATGTTAG
1 TTATGTAAG
645385 TTATGTAAG
1 TTATGTAAG
* *
645394 TTATTTAAT
1 TTATGTAAG
*
645403 TTATGTAGG
1 TTATGTAAG
645412 TTATGTAAG
1 TTATGTAAG
* * * *
645421 TCCACGGAAT
1 T-TATGTAAG
645431 TTATGTAAG
1 TTATGTAAG
645440 TTATGTAAG
1 TTATGTAAG
* *
645449 TTATTTAAT
1 TTATGTAAG
645458 TTATGTAAG
1 TTATGTAAG
645467 TTATGTAAG
1 TTATGTAAG
* *
645476 TTATTTAAT
1 TTATGTAAG
*
645485 TTATGCAAG
1 TTATGTAAG
645494 TTTATGTAAG
1 -TTATGTAAG
645504 TTATGTAAG
1 TTATGTAAG
* *
645513 TTATTTAAT
1 TTATGTAAG
645522 TTATGTAAG
1 TTATGTAAG
645531 TTATGTAAG
1 TTATGTAAG
* *
645540 TTATTTAAT
1 TTATGTAAG
*
645549 TTATGTCAG
1 TTATGTAAG
645558 TT
1 TT
645560 TCTATATATG
Statistics
Matches: 516, Mismatches: 125, Indels: 34
0.76 0.19 0.05
Matches are distributed among these distances:
7 26 0.05
8 21 0.04
9 454 0.88
10 15 0.03
ACGTcount: A:0.32, C:0.01, G:0.18, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:645684 original size:8 final size:7
Alignment explanation
Indices: 645666--645703 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
645656 ATAATATAAG
645666 TTATGTA
1 TTATGTA
645673 TTATGTTA
1 TTATG-TA
645681 TTATGTA
1 TTATGTA
645688 TTATGTA
1 TTATGTA
645695 --ATGTA
1 TTATGTA
645700 TTAT
1 TTAT
645704 CAGATTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
5 5 0.18
7 16 0.57
8 7 0.25
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (7 bp):
TTATGTA
Found at i:645684 original size:27 final size:26
Alignment explanation
Indices: 645651--645723 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 26
645641 AAGTTATGCA
*
645651 AGATTATAATATAAGTTATGTATTATG
1 AGATTAT-ATATAAGTTATGTATTATC
** * * *
645678 TTATTATGTATTATGTAATGTATTATC
1 AGATTATATA-TAAGTTATGTATTATC
645705 AGATTATATATAAGTTATG
1 AGATTATATATAAGTTATG
645724 AAAGTTATTA
Statistics
Matches: 34, Mismatches: 11, Indels: 3
0.71 0.23 0.06
Matches are distributed among these distances:
26 9 0.26
27 25 0.74
ACGTcount: A:0.37, C:0.01, G:0.14, T:0.48
Consensus pattern (26 bp):
AGATTATATATAAGTTATGTATTATC
Found at i:645716 original size:53 final size:52
Alignment explanation
Indices: 645651--645821 Score: 175
Period size: 53 Copynumber: 3.4 Consensus size: 52
645641 AAGTTATGCA
645651 AGATTATAATATAAGTTATGTATTATGTTATTATGTATTATGTAATGTATTATC
1 AGATTAT-ATATAAGTTATGTATTATGTTATTATGTATTATGTAAT-TATTATC
*
645705 AGATTATATATAAGTTATG-A--AAGTTATTATGTA--A-G---TTA-TA-C
1 AGATTATATATAAGTTATGTATTATGTTATTATGTATTATGTAATTATTATC
* *
645746 AAGCTTATATATAAGTTATGTATTATGTTATTATGTATTATGTAATTTATTATG
1 -AGATTATATATAAGTTATGTATTATGTTATTATGTATTATGTAA-TTATTATC
** *
645800 TTATTATATATACGTTATGTAT
1 AGATTATATATAAGTTATGTAT
645822 GCTGTAAAAT
Statistics
Matches: 96, Mismatches: 8, Indels: 27
0.73 0.06 0.21
Matches are distributed among these distances:
41 1 0.01
42 20 0.21
43 3 0.03
44 1 0.01
45 12 0.12
47 2 0.02
48 2 0.02
50 12 0.12
52 4 0.04
53 32 0.33
54 7 0.07
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.49
Consensus pattern (52 bp):
AGATTATATATAAGTTATGTATTATGTTATTATGTATTATGTAATTATTATC
Found at i:645740 original size:21 final size:22
Alignment explanation
Indices: 645715--645800 Score: 67
Period size: 21 Copynumber: 4.0 Consensus size: 22
645705 AGATTATATA
645715 TAAGTTATGA-AAGTTATTATG
1 TAAGTTATGATAAGTTATTATG
* *
645736 TAAGTTAT-ACAAGCTTA-TATA
1 TAAGTTATGATAAG-TTATTATG
*
645757 TAAGTTATGTATTATGTTATTATG
1 TAAGTTATG-A-TAAGTTATTATG
*
645781 T-A-TTATG-TAATTTATTATG
1 TAAGTTATGATAAGTTATTATG
645800 T
1 T
645801 TATTATATAT
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
19 11 0.21
20 1 0.02
21 22 0.42
22 8 0.15
23 5 0.09
24 6 0.11
ACGTcount: A:0.35, C:0.02, G:0.14, T:0.49
Consensus pattern (22 bp):
TAAGTTATGATAAGTTATTATG
Found at i:645779 original size:8 final size:7
Alignment explanation
Indices: 645761--645806 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
645751 TATATATAAG
645761 TTATGTA
1 TTATGTA
645768 TTATGTTA
1 TTATG-TA
645776 TTATGTA
1 TTATGTA
645783 TTATGTA
1 TTATGTA
*
645790 --ATTTA
1 TTATGTA
645795 TTATGTTA
1 TTATG-TA
645803 TTAT
1 TTAT
645807 ATATACGTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
5 4 0.12
7 16 0.48
8 13 0.39
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (7 bp):
TTATGTA
Found at i:645781 original size:15 final size:15
Alignment explanation
Indices: 645761--645806 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
645751 TATATATAAG
645761 TTATGTATTATGTTA
1 TTATGTATTATGTTA
645776 TTATGTATTATG-TA
1 TTATGTATTATGTTA
*
645790 --ATTTATTATGTTA
1 TTATGTATTATGTTA
645803 TTAT
1 TTAT
645807 ATATACGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 9 0.33
13 2 0.07
14 2 0.07
15 14 0.52
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (15 bp):
TTATGTATTATGTTA
Found at i:645806 original size:95 final size:96
Alignment explanation
Indices: 645619--645818 Score: 312
Period size: 95 Copynumber: 2.1 Consensus size: 96
645609 AGTGGTGTAT
* * *
645619 TAAGCTATGGAAGTTATTATGTAAGTTATGCAAGATTATAATATAAGTTATGTATTATGTTATTA
1 TAAGTTATGAAAGTTATTATGTAAGTTATACAAGATTATAATATAAGTTATGTATTATGTTATTA
645684 TGTATTATGTAATGTATTATCAGATTATATA
66 TGTATTATGTAATGTATTATCAGATTATATA
*
645715 TAAGTTATGAAAGTTATTATGTAAGTTATACAAGCTTAT-ATATAAGTTATGTATTATGTTATTA
1 TAAGTTATGAAAGTTATTATGTAAGTTATACAAGATTATAATATAAGTTATGTATTATGTTATTA
* ***
645779 TGTATTATGTAATTTATTATGTTATTATATA
66 TGTATTATGTAATGTATTATCAGATTATATA
*
645810 TACGTTATG
1 TAAGTTATG
645819 TATGCTGTAA
Statistics
Matches: 95, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
95 60 0.63
96 35 0.37
ACGTcount: A:0.35, C:0.03, G:0.14, T:0.47
Consensus pattern (96 bp):
TAAGTTATGAAAGTTATTATGTAAGTTATACAAGATTATAATATAAGTTATGTATTATGTTATTA
TGTATTATGTAATGTATTATCAGATTATATA
Found at i:645948 original size:19 final size:20
Alignment explanation
Indices: 645912--645953 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
645902 TTATATAAAT
*
645912 AAAATATTTAAATTTTTA-A
1 AAAATATATAAATTTTTACA
645931 AAAATATAT-AATTATTTACA
1 AAAATATATAAATT-TTTACA
645951 AAA
1 AAA
645954 CGTGTAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 4 0.20
19 12 0.60
20 4 0.20
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAATATATAAATTTTTACA
Found at i:646031 original size:61 final size:61
Alignment explanation
Indices: 645940--646087 Score: 176
Period size: 61 Copynumber: 2.4 Consensus size: 61
645930 AAAAATATAT
* * * *
645940 AATTATTTACAAAACGTGTAAAATTGATACTTA-TAAA-TTTTATTAATAATAAATCTAGAAC
1 AATTATTTACAAAACTTATAAATTTAATAC-TACTAAATTTTTA-TAATAATAAATCTAGAAC
* * * *
646001 ACATT-TTTAGAAAACTTATAAATTTAATACTACTAAATTTTTATACTAATAAATTTAGAAT
1 A-ATTATTTACAAAACTTATAAATTTAATACTACTAAATTTTTATAATAATAAATCTAGAAC
646062 AATTATTTACAAAACTTATAAATTTA
1 AATTATTTACAAAACTTATAAATTTA
646088 GAAAACTTAT
Statistics
Matches: 74, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
60 5 0.07
61 61 0.82
62 8 0.11
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (61 bp):
AATTATTTACAAAACTTATAAATTTAATACTACTAAATTTTTATAATAATAAATCTAGAAC
Found at i:646039 original size:15 final size:15
Alignment explanation
Indices: 646018--646057 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
646008 TAGAAAACTT
646018 ATAAATTTAATACTA
1 ATAAATTTAATACTA
* *
646033 CTAAATTTTTATACTA
1 ATAAA-TTTAATACTA
646049 ATAAATTTA
1 ATAAATTTA
646058 GAATAATTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAAATTTAATACTA
Found at i:646092 original size:17 final size:17
Alignment explanation
Indices: 646066--646098 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
646056 TAGAATAATT
646066 ATTTACAAAACTTATAA
1 ATTTACAAAACTTATAA
*
646083 ATTTAGAAAACTTATA
1 ATTTACAAAACTTATA
646099 TAGAAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (17 bp):
ATTTACAAAACTTATAA
Found at i:647413 original size:52 final size:52
Alignment explanation
Indices: 647352--647456 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 52
647342 TCTGTACCTT
*
647352 CAGCAGGATGAAGAAAAGTGAAAACGTTGAAGACCGATGAAACCAATGAAAC
1 CAGCAGGATGAAGAAAACTGAAAACGTTGAAGACCGATGAAACCAATGAAAC
* *
647404 CAGCAGGATGAAGAAATCTGAAACCGTTGAAGACCGATGAAACCAATGAAAC
1 CAGCAGGATGAAGAAAACTGAAAACGTTGAAGACCGATGAAACCAATGAAAC
647456 C
1 C
647457 GTTCACACCA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.12
Consensus pattern (52 bp):
CAGCAGGATGAAGAAAACTGAAAACGTTGAAGACCGATGAAACCAATGAAAC
Found at i:647821 original size:20 final size:20
Alignment explanation
Indices: 647796--647835 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
647786 AATAGATGAA
647796 GAAAGGATGAGGGGAAATCG
1 GAAAGGATGAGGGGAAATCG
647816 GAAAGGATGAGGGGAAATCG
1 GAAAGGATGAGGGGAAATCG
647836 AAGAAAGACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.45, T:0.10
Consensus pattern (20 bp):
GAAAGGATGAGGGGAAATCG
Found at i:647850 original size:22 final size:19
Alignment explanation
Indices: 647796--647874 Score: 63
Period size: 20 Copynumber: 4.0 Consensus size: 19
647786 AATAGATGAA
647796 GAAAGGATGAGGGGAAATCG
1 GAAA-GATGAGGGGAAATCG
647816 GAAAGGATGAGGGGAAATCG
1 GAAA-GATGAGGGGAAATCG
* * *
647836 AAGAAAGACTTA-GGG-ATTTG
1 --GAAAGA-TGAGGGGAAATCG
*
647856 GAAGGATGAGGGGAAATCG
1 GAAAGATGAGGGGAAATCG
647875 CAGAAAGACT
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
17 2 0.04
18 8 0.17
19 3 0.06
20 23 0.49
21 5 0.11
22 6 0.13
ACGTcount: A:0.39, C:0.05, G:0.42, T:0.14
Consensus pattern (19 bp):
GAAAGATGAGGGGAAATCG
Found at i:647864 original size:39 final size:39
Alignment explanation
Indices: 647818--647895 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
647808 GGAAATCGGA
647818 AAGGATGAGGGGAAATCGAAGAAAGACTTAGGGATTTGG
1 AAGGATGAGGGGAAATCGAAGAAAGACTTAGGGATTTGG
* *
647857 AAGGATGAGGGGAAATCGCAGAAAGACTTAGGGGTTTGG
1 AAGGATGAGGGGAAATCGAAGAAAGACTTAGGGATTTGG
647896 CTGAAAAGGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.36, C:0.06, G:0.40, T:0.18
Consensus pattern (39 bp):
AAGGATGAGGGGAAATCGAAGAAAGACTTAGGGATTTGG
Found at i:648503 original size:70 final size:70
Alignment explanation
Indices: 648409--648547 Score: 242
Period size: 70 Copynumber: 2.0 Consensus size: 70
648399 GGAATATAGT
* *
648409 GAAAGCAGAACGAAGCCGTTTTGCAAATTTATTTGCGGTGTTTTTAAAATAAACGCCTCTAAAGC
1 GAAAGCAGAACGAAGCCGTTTTGCAAATTTATTTGCGGCGTTTTTAAAATAAACGCCGCTAAAGC
648474 CTACA
66 CTACA
* *
648479 GAAAGTAGAACGAAGCCGTTTTGCAAATTTATTTGCGGCGTTTTTAAGATAAACGCCGCTAAAGC
1 GAAAGCAGAACGAAGCCGTTTTGCAAATTTATTTGCGGCGTTTTTAAAATAAACGCCGCTAAAGC
648544 CTAC
66 CTAC
648548 CTATTGCGGC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 65 1.00
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (70 bp):
GAAAGCAGAACGAAGCCGTTTTGCAAATTTATTTGCGGCGTTTTTAAAATAAACGCCGCTAAAGC
CTACA
Found at i:651270 original size:115 final size:113
Alignment explanation
Indices: 651067--651275 Score: 260
Period size: 115 Copynumber: 1.8 Consensus size: 113
651057 CCCACGAACT
* * * ** *
651067 CTAATCTACCTCAAGACCAAACGGTGCATTTTGGTTAAGATATTGGCGGCGCTTTTTGTAATACG
1 CTAATATACCTCAAAACCAAACGCTGCATTTTGGTTAAGATATTGGCGGCGCTTCATATAATACG
* *
651132 CCGCTAATACTGTTCTTTAGCGGCGTTTTCTCGTAAACGCCACTAATA
66 CCACTAATACTGTTCTTTAGCGGCATTTTCTCGTAAACGCCACTAATA
* * *
651180 CTAATATACCTCAAAACCAAACGCTGCGTTTTGGTTAAGGTATTTTTGCGGCGCTTACATATAA-
1 CTAATATACCTCAAAACCAAACGCTGCATTTTGGTTAA-G-ATATTGGCGGCGCTT-CATATAAT
*
651244 ACGCCACTAATGA-TGTTCTTTTGCGGCATTTT
63 ACGCCACTAAT-ACTGTTCTTTAGCGGCATTTT
651276 TTAGAAAATG
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
113 34 0.43
114 1 0.01
115 40 0.50
116 5 0.06
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (113 bp):
CTAATATACCTCAAAACCAAACGCTGCATTTTGGTTAAGATATTGGCGGCGCTTCATATAATACG
CCACTAATACTGTTCTTTAGCGGCATTTTCTCGTAAACGCCACTAATA
Found at i:655688 original size:12 final size:12
Alignment explanation
Indices: 655664--655737 Score: 71
Period size: 12 Copynumber: 5.9 Consensus size: 12
655654 AGGAATGTCC
*
655664 AAAAAA-AAGAG
1 AAAAAAGAAAAG
655675 AAAAAAGAAAAG
1 AAAAAAGAAAAG
*
655687 AAAAAAGAATAGAA
1 AAAAAAGAA-A-AG
655701 AAAAAAGAAAAG
1 AAAAAAGAAAAG
655713 AAGAAAAAGAAAA-
1 -A-AAAAAGAAAAG
655726 AGAAAAAGAAAA
1 A-AAAAAGAAAA
655738 AGGAGAGGCC
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
11 6 0.11
12 26 0.47
13 3 0.05
14 20 0.36
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.01
Consensus pattern (12 bp):
AAAAAAGAAAAG
Found at i:655691 original size:6 final size:6
Alignment explanation
Indices: 655676--655739 Score: 67
Period size: 6 Copynumber: 10.0 Consensus size: 6
655666 AAAAAAGAGA
*
655676 AAAAAG -AAAAG AAAAAAG AATAGAAA AAAAAG AAAAGAAG AAAAAG AAAAAG
1 AAAAAG AAAAAG -AAAAAG AA-A-AAG AAAAAG -AAA-AAG AAAAAG AAAAAG
655728 AAAAAG AAAAAG
1 AAAAAG AAAAAG
655740 GAGAGGCCAA
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
5 5 0.10
6 25 0.50
7 13 0.26
8 7 0.14
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:655711 original size:26 final size:26
Alignment explanation
Indices: 655675--655737 Score: 85
Period size: 26 Copynumber: 2.4 Consensus size: 26
655665 AAAAAAAGAG
655675 AAAAAAGAAAAG-A-AAAAAGAATAGAA
1 AAAAAAGAAAAGAAGAAAAAGAA-A-AA
655701 AAAAAAGAAAAGAAGAAAAAGAAAAA
1 AAAAAAGAAAAGAAGAAAAAGAAAAA
*
655727 GAAAAAGAAAA
1 AAAAAAGAAAA
655738 AGGAGAGGCC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
26 24 0.71
27 2 0.06
28 8 0.24
ACGTcount: A:0.83, C:0.00, G:0.16, T:0.02
Consensus pattern (26 bp):
AAAAAAGAAAAGAAGAAAAAGAAAAA
Done.