Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 181 of 211
Found at i:56098153 original size:68 final size:68
Alignment explanation
Indices: 56098080--56098253 Score: 206
Period size: 68 Copynumber: 2.6 Consensus size: 68
56098070 TAACCCAGTA
* * *
56098080 ATGGTCTTATC-ATCAAAATGCCATAGCCTAGCTATGGTCTTACATATAAGCACTGCCATGGTCC
1 ATGGTCTTA-CGATCAAAATGCCATAACCCAGCTATGGTCTTACATATAAACACTGCCATGGTCC
56098144 AACC
65 AACC
* * * *
56098148 ATGGTCTTACGTTCATAGTGCCATAACCCAGTTATGGTCTTACATATAAACACTGCCATGGTCCA
1 ATGGTCTTACGATCAAAATGCCATAACCCAGCTATGGTCTTACATATAAACACTGCCATGGTCCA
56098213 ACC
66 ACC
** * * * * *
56098216 ACAGTCTTACGTTTATAGTGCCATAACCCAGTTATGGT
1 ATGGTCTTACGATCAAAATGCCATAACCCAGCTATGGT
56098254 GTTATCCGTC
Statistics
Matches: 95, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
67 1 0.01
68 94 0.99
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (68 bp):
ATGGTCTTACGATCAAAATGCCATAACCCAGCTATGGTCTTACATATAAACACTGCCATGGTCCA
ACC
Found at i:56103766 original size:27 final size:26
Alignment explanation
Indices: 56103735--56103896 Score: 166
Period size: 27 Copynumber: 6.0 Consensus size: 26
56103725 AACAAATTAT
*
56103735 CAAAATAACCCGAAAAGGTAAAATGAC
1 CAAAATACCCCG-AAAGGTAAAATGAC
* *
56103762 CAAAATACCCCTGAAGGGTATAATGAC
1 CAAAATACCCC-GAAAGGTAAAATGAC
*
56103789 CAAAATACCCTCGAAAGGTAAAATAAC
1 CAAAATACCC-CGAAAGGTAAAATGAC
*
56103816 CAAAATACCCTC-AAAGGGTATAATGAC
1 CAAAATACCC-CGAAA-GGTAAAATGAC
*
56103843 CAAAATACCCCCGAAAGGTAATATGAC
1 CAAAATA-CCCCGAAAGGTAAAATGAC
* *
56103870 CAAAACACCCTC-ATAGGGTAAAATGAC
1 CAAAATACCC-CGA-AAGGTAAAATGAC
56103897 TGATATACCA
Statistics
Matches: 115, Mismatches: 13, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
26 7 0.06
27 100 0.87
28 8 0.07
ACGTcount: A:0.47, C:0.23, G:0.15, T:0.15
Consensus pattern (26 bp):
CAAAATACCCCGAAAGGTAAAATGAC
Found at i:56103905 original size:54 final size:53
Alignment explanation
Indices: 56103735--56103896 Score: 218
Period size: 54 Copynumber: 3.0 Consensus size: 53
56103725 AACAAATTAT
* *
56103735 CAAAATA-ACCCGAAAAGGTAAAATGACCAAAATACCCCTGAAGGGTATAATGAC
1 CAAAATACCCCCG-AAAGGTAAAATGACCAAAATA-CCCTCAAGGGTATAATGAC
* *
56103789 CAAAATACCCTCGAAAGGTAAAATAACCAAAATACCCTCAAAGGGTATAATGAC
1 CAAAATACCCCCGAAAGGTAAAATGACCAAAATACCCTC-AAGGGTATAATGAC
* * *
56103843 CAAAATACCCCCGAAAGGTAATATGACCAAAACACCCTCATAGGGTAAAATGAC
1 CAAAATACCCCCGAAAGGTAAAATGACCAAAATACCCTCA-AGGGTATAATGAC
56103897 TGATATACCA
Statistics
Matches: 96, Mismatches: 9, Indels: 6
0.86 0.08 0.05
Matches are distributed among these distances:
53 5 0.05
54 88 0.92
55 3 0.03
ACGTcount: A:0.47, C:0.23, G:0.15, T:0.15
Consensus pattern (53 bp):
CAAAATACCCCCGAAAGGTAAAATGACCAAAATACCCTCAAGGGTATAATGAC
Found at i:56104263 original size:28 final size:28
Alignment explanation
Indices: 56104225--56104307 Score: 130
Period size: 28 Copynumber: 3.0 Consensus size: 28
56104215 ATTGTAATGT
* *
56104225 TTACTATATTGGGCTAAGGCCCATATTG
1 TTACTGTATTGGGCTAAGGCCCATACTG
*
56104253 TTACTGTATTGGGCTAAGGCCCACACTG
1 TTACTGTATTGGGCTAAGGCCCATACTG
*
56104281 TTACTGTAATGGGCTAAGGCCCATACT
1 TTACTGTATTGGGCTAAGGCCCATACT
56104308 ATACTAATAC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 50 1.00
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (28 bp):
TTACTGTATTGGGCTAAGGCCCATACTG
Found at i:56106763 original size:9 final size:9
Alignment explanation
Indices: 56106749--56106869 Score: 132
Period size: 9 Copynumber: 14.3 Consensus size: 9
56106739 TAAGGGATAT
56106749 TTATGTAAG
1 TTATGTAAG
56106758 TTATGTAAG
1 TTATGTAAG
56106767 TTATGT-A-
1 TTATGTAAG
* *
56106774 TTAAGTAAA
1 TTATGTAAG
56106783 TTATGTAAG
1 TTATGTAAG
56106792 TTATGT-A-
1 TTATGTAAG
*
56106799 TTATGTAAA
1 TTATGTAAG
56106808 TTATGTAAG
1 TTATGTAAG
56106817 TTATGT-A-
1 TTATGTAAG
* *
56106824 TTAAGTAGG
1 TTATGTAAG
56106833 TTATGTAAG
1 TTATGTAAG
*
56106842 TTATGT--C
1 TTATGTAAG
56106849 TTATGTAAG
1 TTATGTAAG
56106858 TTATGTAAG
1 TTATGTAAG
56106867 TTA
1 TTA
56106870 AGGTATAGTA
Statistics
Matches: 94, Mismatches: 10, Indels: 16
0.78 0.08 0.13
Matches are distributed among these distances:
7 22 0.23
8 5 0.05
9 67 0.71
ACGTcount: A:0.34, C:0.01, G:0.19, T:0.46
Consensus pattern (9 bp):
TTATGTAAG
Found at i:56106781 original size:25 final size:25
Alignment explanation
Indices: 56106753--56106869 Score: 180
Period size: 25 Copynumber: 4.7 Consensus size: 25
56106743 GGATATTTAT
56106753 GTAAGTTATGTAAGTTATGTATTAA
1 GTAAGTTATGTAAGTTATGTATTAA
* *
56106778 GTAAATTATGTAAGTTATGTATTAT
1 GTAAGTTATGTAAGTTATGTATTAA
*
56106803 GTAAATTATGTAAGTTATGTATTAA
1 GTAAGTTATGTAAGTTATGTATTAA
* * *
56106828 GTAGGTTATGTAAGTTATGTCTTAT
1 GTAAGTTATGTAAGTTATGTATTAA
56106853 GTAAGTTATGTAAGTTA
1 GTAAGTTATGTAAGTTA
56106870 AGGTATAGTA
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 84 1.00
ACGTcount: A:0.34, C:0.01, G:0.20, T:0.45
Consensus pattern (25 bp):
GTAAGTTATGTAAGTTATGTATTAA
Found at i:56106812 original size:50 final size:50
Alignment explanation
Indices: 56106749--56107071 Score: 222
Period size: 50 Copynumber: 6.4 Consensus size: 50
56106739 TAAGGGATAT
56106749 TTATGTAAGTTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTA
1 TTATGTAAGTTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTA
* ** *
56106799 TTATGTAAATTATGTAAGTTATGTATTAAGTAGGTTATGTAAGTTATGTC
1 TTATGTAAGTTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTA
* *
56106849 TTATGTAAGTTATGTAAGTTAAGGTATAGTATATATCACGGTAACTTATATAAGTTATGTA
1 TTATGTAAGTTATGTAAG-T----TAT-GTAT-TA--A--GTAAATTATGTAAGTTATGTA
* * * ** * * *
56106910 -T-T-TAACTTATTTGAGTTCCA-CCACATAAGGGATATTTATGTAAGTTATGTA
1 TTATGTAAGTTATGTAAGTT--ATGTA-TTAA-GTA-AATTATGTAAGTTATGTA
* *
56106961 TTAAGTAAATTATGTAAG---T-TA-T-A-T--ATTATGTAAGTTATGTA
1 TTATGTAAGTTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTA
* * ** *
56107002 TTAAGTAGGTTATGTAAGTTATGTATTAAGTAGGTTATGTAAGTTATGTC
1 TTATGTAAGTTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTA
56107052 TTATGTAAGTTATGTAAGTT
1 TTATGTAAGTTATGTAAGTT
56107072 TTTGTTTTTG
Statistics
Matches: 214, Mismatches: 31, Indels: 56
0.71 0.10 0.19
Matches are distributed among these distances:
41 32 0.15
44 1 0.00
45 2 0.01
46 2 0.01
47 2 0.01
48 1 0.00
49 1 0.00
50 99 0.46
51 18 0.08
52 1 0.00
53 4 0.02
54 10 0.05
55 4 0.02
56 4 0.02
57 3 0.01
58 10 0.05
59 2 0.01
60 1 0.00
61 17 0.08
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.44
Consensus pattern (50 bp):
TTATGTAAGTTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTA
Found at i:56106852 original size:16 final size:17
Alignment explanation
Indices: 56106749--56106869 Score: 110
Period size: 16 Copynumber: 7.2 Consensus size: 17
56106739 TAAGGGATAT
56106749 TTATGTAAGTTATGTAAG
1 TTATGTAAGTTATGT-AG
* *
56106767 TTATGT-A-TTAAGTAAA
1 TTATGTAAGTTATGT-AG
56106783 TTATGTAAGTTATGTA-
1 TTATGTAAGTTATGTAG
*
56106799 TTATGTAAATTATGTAAG
1 TTATGTAAGTTATGT-AG
*
56106817 TTATGT-A-TTAAGTAGG
1 TTATGTAAGTTATGTA-G
*
56106833 TTATGTAAGTTATGT-C
1 TTATGTAAGTTATGTAG
56106849 TTATGTAAGTTATGTAAG
1 TTATGTAAGTTATGT-AG
56106867 TTA
1 TTA
56106870 AGGTATAGTA
Statistics
Matches: 86, Mismatches: 8, Indels: 18
0.77 0.07 0.16
Matches are distributed among these distances:
15 1 0.01
16 54 0.63
17 6 0.07
18 25 0.29
ACGTcount: A:0.34, C:0.01, G:0.19, T:0.46
Consensus pattern (17 bp):
TTATGTAAGTTATGTAG
Found at i:56106973 original size:25 final size:25
Alignment explanation
Indices: 56106945--56107001 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
56106935 TAAGGGATAT
*
56106945 TTATGTAAGTTATGTATTAAGTAAA
1 TTATGTAAGTTATATATTAAGTAAA
* *
56106970 TTATGTAAGTTATATATTATGTAAG
1 TTATGTAAGTTATATATTAAGTAAA
56106995 TTATGTA
1 TTATGTA
56107002 TTAAGTAGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (25 bp):
TTATGTAAGTTATATATTAAGTAAA
Found at i:56106988 original size:16 final size:16
Alignment explanation
Indices: 56106969--56107067 Score: 103
Period size: 16 Copynumber: 6.1 Consensus size: 16
56106959 TATTAAGTAA
*
56106969 ATTATGTAAGTTATAT
1 ATTATGTAAGTTATGT
56106985 ATTATGTAAGTTATGT
1 ATTATGTAAGTTATGT
* *
56107001 ATTAAGTAGGTTATGT
1 ATTATGTAAGTTATGT
*
56107017 AAGTTATGT-A-TTAAGT
1 -A-TTATGTAAGTTATGT
56107033 AGGTTATGTAAGTTATGT
1 A--TTATGTAAGTTATGT
*
56107051 CTTATGTAAGTTATGT
1 ATTATGTAAGTTATGT
56107067 A
1 A
56107068 AGTTTTTGTT
Statistics
Matches: 69, Mismatches: 9, Indels: 10
0.78 0.10 0.11
Matches are distributed among these distances:
15 1 0.01
16 56 0.81
17 2 0.03
18 10 0.14
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.46
Consensus pattern (16 bp):
ATTATGTAAGTTATGT
Found at i:56106999 original size:41 final size:41
Alignment explanation
Indices: 56106941--56107042 Score: 152
Period size: 41 Copynumber: 2.5 Consensus size: 41
56106931 CACATAAGGG
56106941 ATAT-TTATGTAAGTTATGTATTAAGTAAATTATGTAAGTT
1 ATATATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTT
**
56106981 ATATATTATGTAAGTTATGTATTAAGTAGGTTATGTAAGTT
1 ATATATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTT
* * *
56107022 ATGTATTAAGTAGGTTATGTA
1 ATATATTATGTAAGTTATGTA
56107043 AGTTATGTCT
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
40 4 0.07
41 52 0.93
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (41 bp):
ATATATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTT
Found at i:56107001 original size:196 final size:199
Alignment explanation
Indices: 56106656--56107071 Score: 634
Period size: 196 Copynumber: 2.1 Consensus size: 199
56106646 GTAATTAAGG
*
56106656 TATGTAAGTTAT-T-ATTTAAGGTATAGTATACATCACGGTAACTTATATAAGTTATGCATTTAA
1 TATGTAAGTTATGTAAGTTAAGGTATAGTATACATCACGGTAACTTATATAAGTTATGCATTTAA
*
56106719 CTTATTTGAGTTCCACCACATAAGGGATATTTATGTAAGTTATGTAAGTTATGTATTAAGTAAAT
66 CTTATTTGAGTTCCACCACATAAGGGATATTTATGTAAGTTATGTAAGTTAAGTATTAAGTAAAT
*
56106784 TATGTAAGTTATGTATTATG-TAA-A-TTATGTAAGTTATGTATTAAGTAGGTTATGTAAGTTAT
131 TATATAAGTTATGTATTATGTTAAGAGTTATGTAAGTTATGTATTAAGTAGGTTATGTAAGTTAT
56106846 GTCT
196 GTCT
* *
56106850 TATGTAAGTTATGTAAGTTAAGGTATAGTATATATCACGGTAACTTATATAAGTTATGTATTTAA
1 TATGTAAGTTATGTAAGTTAAGGTATAGTATACATCACGGTAACTTATATAAGTTATGCATTTAA
*
56106915 CTTATTTGAGTTCCACCACATAAGGGATATTTATGTAAGTTATGT-A-TTAAGTAAATTATGTAA
66 CTTATTTGAGTTCCACCACATAAGGGATATTTATGTAAGTTATGTAAGTTAAGT--ATTAAGTAA
*
56106978 GTTATAT-A-TTATGTAAGTTATGTATTAAGTAGGTTATGTAAGTTATGTATTAAGTAGGTTATG
129 ATTATATAAGTTATGT-A-TTATG--TTAAG-A-GTTATGTAAGTTATGTATTAAGTAGGTTATG
56107041 TAAGTTATGTCT
188 TAAGTTATGTCT
56107053 TATGTAAGTTATGTAAGTT
1 TATGTAAGTTATGTAAGTT
56107072 TTTGTTTTTG
Statistics
Matches: 202, Mismatches: 7, Indels: 17
0.89 0.03 0.08
Matches are distributed among these distances:
194 23 0.11
195 4 0.02
196 110 0.54
199 3 0.01
201 1 0.00
203 61 0.30
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43
Consensus pattern (199 bp):
TATGTAAGTTATGTAAGTTAAGGTATAGTATACATCACGGTAACTTATATAAGTTATGCATTTAA
CTTATTTGAGTTCCACCACATAAGGGATATTTATGTAAGTTATGTAAGTTAAGTATTAAGTAAAT
TATATAAGTTATGTATTATGTTAAGAGTTATGTAAGTTATGTATTAAGTAGGTTATGTAAGTTAT
GTCT
Found at i:56107014 original size:25 final size:25
Alignment explanation
Indices: 56106986--56107071 Score: 145
Period size: 25 Copynumber: 3.4 Consensus size: 25
56106976 AAGTTATATA
56106986 TTATGTAAGTTATGTATTAAGTAGG
1 TTATGTAAGTTATGTATTAAGTAGG
56107011 TTATGTAAGTTATGTATTAAGTAGG
1 TTATGTAAGTTATGTATTAAGTAGG
* * *
56107036 TTATGTAAGTTATGTCTTATGTAAG
1 TTATGTAAGTTATGTATTAAGTAGG
56107061 TTATGTAAGTT
1 TTATGTAAGTT
56107072 TTTGTTTTTG
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 58 1.00
ACGTcount: A:0.30, C:0.01, G:0.22, T:0.47
Consensus pattern (25 bp):
TTATGTAAGTTATGTATTAAGTAGG
Found at i:56107056 original size:41 final size:40
Alignment explanation
Indices: 56106949--56107067 Score: 141
Period size: 41 Copynumber: 2.9 Consensus size: 40
56106939 GGATATTTAT
* * *
56106949 GTAAGTTATGTATTAAGTAAATTATGTAAGTTATATATTAT
1 GTAAGTTATGTATTAAGT-ACTTATGTAAGTTATGTATTAA
*
56106990 GTAAGTTATGTATTAAGTAGGTTATGTAAGTTATGTATTAA
1 GTAAGTTATGTATTAAGTA-CTTATGTAAGTTATGTATTAA
* *
56107031 GTAGGTTATGTAAGTTATGT-CTTATGTAAGTTATGTA
1 GTAAGTTATGT-A-TTAAGTACTTATGTAAGTTATGTA
56107068 AGTTTTTGTT
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
40 1 0.01
41 62 0.90
42 1 0.01
43 5 0.07
ACGTcount: A:0.34, C:0.01, G:0.20, T:0.45
Consensus pattern (40 bp):
GTAAGTTATGTATTAAGTACTTATGTAAGTTATGTATTAA
Found at i:56107155 original size:24 final size:24
Alignment explanation
Indices: 56107123--56107171 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
56107113 TTGTGTATTG
*
56107123 TTATATAAGTTAGTATGTAGGTTA
1 TTATATAAGTCAGTATGTAGGTTA
* * *
56107147 TTATGTAAGTCATTATGTTGGTTA
1 TTATATAAGTCAGTATGTAGGTTA
56107171 T
1 T
56107172 GTAAGTTGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.29, C:0.02, G:0.20, T:0.49
Consensus pattern (24 bp):
TTATATAAGTCAGTATGTAGGTTA
Found at i:56107393 original size:9 final size:9
Alignment explanation
Indices: 56107379--56107435 Score: 57
Period size: 9 Copynumber: 6.7 Consensus size: 9
56107369 ATTATAAATT
*
56107379 TAAATTTTG
1 TAAATTATG
56107388 TAAATTATG
1 TAAATTATG
56107397 --AATTATG
1 TAAATTATG
56107404 TAAATTATG
1 TAAATTATG
* *
56107413 TAAAATACG
1 TAAATTATG
*
56107422 TAAGTTATG
1 TAAATTATG
56107431 -AAATT
1 TAAATT
56107436 TGAACTTTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
7 7 0.18
8 4 0.10
9 28 0.72
ACGTcount: A:0.44, C:0.02, G:0.12, T:0.42
Consensus pattern (9 bp):
TAAATTATG
Found at i:56107405 original size:16 final size:16
Alignment explanation
Indices: 56107354--56107412 Score: 61
Period size: 16 Copynumber: 3.9 Consensus size: 16
56107344 TATTAATAAG
* *
56107354 TTATGTAAGTTATGTA
1 TTATGTAAATTATGAA
*
56107370 TTA--TAAATT-TAAA
1 TTATGTAAATTATGAA
*
56107383 TTTTGTAAATTATGAA
1 TTATGTAAATTATGAA
56107399 TTATGTAAATTATG
1 TTATGTAAATTATG
56107413 TAAAATACGT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
13 4 0.12
14 5 0.15
15 6 0.18
16 19 0.56
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (16 bp):
TTATGTAAATTATGAA
Found at i:56108981 original size:6 final size:6
Alignment explanation
Indices: 56108970--56109028 Score: 75
Period size: 6 Copynumber: 9.3 Consensus size: 6
56108960 ACACATGTTA
56108970 AATAAC AATAAC AAATAAC AAATAAC AATAAC AATAAC AATGAGA- AATAAC
1 AATAAC AATAAC -AATAAC -AATAAC AATAAC AATAAC AAT-A-AC AATAAC
56109021 AATAAC AA
1 AATAAC AA
56109029 ATAAACAGTT
Statistics
Matches: 49, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
5 1 0.02
6 30 0.61
7 17 0.35
8 1 0.02
ACGTcount: A:0.68, C:0.14, G:0.03, T:0.15
Consensus pattern (6 bp):
AATAAC
Found at i:56108987 original size:13 final size:13
Alignment explanation
Indices: 56108970--56109032 Score: 85
Period size: 13 Copynumber: 4.9 Consensus size: 13
56108960 ACACATGTTA
56108970 AATAAC-AATAAC
1 AATAACAAATAAC
56108982 AAATAACAAATAAC
1 -AATAACAAATAAC
56108996 AATAAC-AATAAC
1 AATAACAAATAAC
* *
56109008 AATGAGAAATAAC
1 AATAACAAATAAC
56109021 AATAACAAATAA
1 AATAACAAATAA
56109033 ACAGTTCTAC
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
12 10 0.23
13 28 0.64
14 6 0.14
ACGTcount: A:0.68, C:0.13, G:0.03, T:0.16
Consensus pattern (13 bp):
AATAACAAATAAC
Found at i:56121442 original size:18 final size:18
Alignment explanation
Indices: 56121419--56121456 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
56121409 TTCAATTAAG
*
56121419 TCTTTCATT-AAGTGTTTT
1 TCTTTC-TTCAAGTATTTT
56121437 TCTTTCTTCAAGTATTTT
1 TCTTTCTTCAAGTATTTT
56121455 TC
1 TC
56121457 ATCTAGTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.16, C:0.16, G:0.08, T:0.61
Consensus pattern (18 bp):
TCTTTCTTCAAGTATTTT
Found at i:56121539 original size:12 final size:12
Alignment explanation
Indices: 56121451--56121573 Score: 68
Period size: 12 Copynumber: 9.8 Consensus size: 12
56121441 TCTTCAAGTA
*
56121451 TTTTTCATCTAG
1 TTTTTCATCAAG
*
56121463 TTCTTTTATCAAG
1 TT-TTTCATCAAG
*
56121476 TTTTTAATTACCAAG
1 TTTTTCA-T--CAAG
* *
56121491 TTTTTTATCACG
1 TTTTTCATCAAG
* *
56121503 TTTTGCAGCAAG
1 TTTTTCATCAAG
* *
56121515 TTCTTT-TTAAAG
1 TT-TTTCATCAAG
56121527 TTTTTCATCAAG
1 TTTTTCATCAAG
* *
56121539 TCTTTTCATAAAA
1 T-TTTTCATCAAG
*
56121552 TTTTCCATCAAG
1 TTTTTCATCAAG
*
56121564 TTTTTAATCA
1 TTTTTCATCA
56121574 TTTCGTTTTT
Statistics
Matches: 82, Mismatches: 22, Indels: 14
0.69 0.19 0.12
Matches are distributed among these distances:
11 3 0.04
12 45 0.55
13 23 0.28
14 1 0.01
15 10 0.12
ACGTcount: A:0.26, C:0.15, G:0.08, T:0.50
Consensus pattern (12 bp):
TTTTTCATCAAG
Found at i:56121550 original size:25 final size:24
Alignment explanation
Indices: 56121522--56121568 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
56121512 AAGTTCTTTT
* *
56121522 TAAAGTTTTTCATCAAGTCTTTTCA
1 TAAAATTTTCCATCAAGT-TTTTCA
56121547 TAAAATTTTCCATCAAGTTTTT
1 TAAAATTTTCCATCAAGTTTTT
56121569 AATCATTTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.30, C:0.15, G:0.06, T:0.49
Consensus pattern (24 bp):
TAAAATTTTCCATCAAGTTTTTCA
Found at i:56125535 original size:46 final size:47
Alignment explanation
Indices: 56125385--56125562 Score: 315
Period size: 47 Copynumber: 3.8 Consensus size: 47
56125375 TACTATAACG
*
56125385 CAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTTCAACACT
1 CAGTATGGTTTTCTTTATTGAAATACCATACCTACTTTTTCAACACT
56125432 CAGTATGGTTTTCTTTATTGAAATACCATACCTACTTTTTCAACACT
1 CAGTATGGTTTTCTTTATTGAAATACCATACCTACTTTTTCAACACT
56125479 CAGTATGGTTTTCTTTATTGAAATACCATACCTAC-TTTTC-ACAACT
1 CAGTATGGTTTTCTTTATTGAAATACCATACCTACTTTTTCAAC-ACT
*
56125525 CAGTATGGTTTTCTTTATTGAAATACCATGCCTACTTT
1 CAGTATGGTTTTCTTTATTGAAATACCATACCTACTTT
56125563 ACACACTTTG
Statistics
Matches: 127, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
45 2 0.02
46 42 0.33
47 83 0.65
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.42
Consensus pattern (47 bp):
CAGTATGGTTTTCTTTATTGAAATACCATACCTACTTTTTCAACACT
Found at i:56125553 original size:93 final size:94
Alignment explanation
Indices: 56125385--56125562 Score: 315
Period size: 93 Copynumber: 1.9 Consensus size: 94
56125375 TACTATAACG
56125385 CAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTTCAACACTCAGTATGGTTTTCTTTAT
1 CAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTTCAACACTCAGTATGGTTTTCTTTAT
56125450 TGAAATACCATACCTACTTTTTCAACACT
66 TGAAATACCATACCTACTTTTTCAACACT
*
56125479 CAGTATGGTTTTCTTTATTGAAATACCATACCTAC-TTTTC-ACAACTCAGTATGGTTTTCTTTA
1 CAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTTCAAC-ACTCAGTATGGTTTTCTTTA
*
56125542 TTGAAATACCATGCCTACTTT
65 TTGAAATACCATACCTACTTT
56125563 ACACACTTTG
Statistics
Matches: 81, Mismatches: 2, Indels: 3
0.94 0.02 0.03
Matches are distributed among these distances:
92 2 0.02
93 45 0.56
94 34 0.42
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.42
Consensus pattern (94 bp):
CAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTTCAACACTCAGTATGGTTTTCTTTAT
TGAAATACCATACCTACTTTTTCAACACT
Found at i:56127312 original size:23 final size:22
Alignment explanation
Indices: 56127286--56127330 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
56127276 ATCATCATAT
56127286 ACTTCCAACATGCATTCATAGAA
1 ACTTCCAAC-TGCATTCATAGAA
* * *
56127309 ACTTTCAACTTCTTTCATAGAA
1 ACTTCCAACTGCATTCATAGAA
56127331 TCAAAAACTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.33
Consensus pattern (22 bp):
ACTTCCAACTGCATTCATAGAA
Found at i:56129053 original size:6 final size:6
Alignment explanation
Indices: 56129038--56129088 Score: 52
Period size: 6 Copynumber: 8.3 Consensus size: 6
56129028 AATTTTCCTA
*
56129038 TTATTAT TTATTT TTACTATT TTA-TT TTA-TT TTATTT TCATTT TTATTT
1 TTATT-T TTATTT TTA-T-TT TTATTT TTATTT TTATTT TTATTT TTATTT
56129087 TT
1 TT
56129089 GCAAGAAAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
5 10 0.26
6 18 0.46
7 6 0.15
8 5 0.13
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (6 bp):
TTATTT
Found at i:56129057 original size:19 final size:19
Alignment explanation
Indices: 56129030--56129070 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
56129020 AAAAAATTAA
*
56129030 TTTTCCTATTATTA-TTTAT
1 TTTTACTATT-TTATTTTAT
56129049 TTTTACTATTTTATTTTAT
1 TTTTACTATTTTATTTTAT
56129068 TTT
1 TTT
56129071 ATTTTCATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTACTATTTTATTTTAT
Found at i:56130469 original size:18 final size:18
Alignment explanation
Indices: 56130446--56130483 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
56130436 TTCAATTAAG
*
56130446 TCTTTCATT-AAGTGTTTT
1 TCTTTC-TTCAAGTATTTT
56130464 TCTTTCTTCAAGTATTTT
1 TCTTTCTTCAAGTATTTT
56130482 TC
1 TC
56130484 ATCTAGTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.16, C:0.16, G:0.08, T:0.61
Consensus pattern (18 bp):
TCTTTCTTCAAGTATTTT
Found at i:56130532 original size:13 final size:13
Alignment explanation
Indices: 56130471--56130534 Score: 65
Period size: 13 Copynumber: 4.7 Consensus size: 13
56130461 TTTTCTTTCT
*
56130471 TCAAGTATTTTTCA
1 TCAAGT-TTTTTTA
* *
56130485 TCTAGTTCTTTTA
1 TCAAGTTTTTTTA
56130498 TCAAGTTTTTAATTA
1 TCAAGTTTTT--TTA
*
56130513 CCAAGTTTTTTTA
1 TCAAGTTTTTTTA
56130526 TCAAGTTTT
1 TCAAGTTTT
56130535 GCAGCAAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
13 24 0.59
14 5 0.12
15 12 0.29
ACGTcount: A:0.25, C:0.12, G:0.08, T:0.55
Consensus pattern (13 bp):
TCAAGTTTTTTTA
Found at i:56130574 original size:13 final size:12
Alignment explanation
Indices: 56130478--56130601 Score: 61
Period size: 12 Copynumber: 9.8 Consensus size: 12
56130468 TCTTCAAGTA
*
56130478 TTTTTCATCTAG
1 TTTTTCATCAAG
*
56130490 TTCTTTTATCAAG
1 TT-TTTCATCAAG
*
56130503 TTTTTAATTACCAAG
1 TTTTTCA-T--CAAG
*
56130518 TTTTTTTATCAAG
1 -TTTTTCATCAAG
* *
56130531 TTTTGCAGCAAG
1 TTTTTCATCAAG
* *
56130543 TTCTTT-TTAAAG
1 TT-TTTCATCAAG
56130555 TTTTTCATCAAG
1 TTTTTCATCAAG
* *
56130567 TCTTTTCATAAAA
1 T-TTTTCATCAAG
**
56130580 TTTCCCATCAAG
1 TTTTTCATCAAG
*
56130592 TTTTTAATCA
1 TTTTTCATCA
56130602 TTTCGTTTTT
Statistics
Matches: 82, Mismatches: 22, Indels: 16
0.68 0.18 0.13
Matches are distributed among these distances:
11 3 0.04
12 41 0.50
13 27 0.33
15 5 0.06
16 6 0.07
ACGTcount: A:0.27, C:0.15, G:0.08, T:0.50
Consensus pattern (12 bp):
TTTTTCATCAAG
Found at i:56130578 original size:25 final size:24
Alignment explanation
Indices: 56130478--56130597 Score: 73
Period size: 25 Copynumber: 4.8 Consensus size: 24
56130468 TCTTCAAGTA
* *
56130478 TTTTTCATCTAGTTCTTTTATCAAG
1 TTTTTCATCAAG-TCTTTTATAAAG
* * *
56130503 TTTTTAATTACCAAGTTTTTTTATCAAG
1 TTTTTCA-T--CAAG-TCTTTTATAAAG
* *
56130531 TTTTGCAGCAAGTTCTTTT-TAAAG
1 TTTTTCATCAAG-TCTTTTATAAAG
*
56130555 TTTTTCATCAAGTCTTTTCATAAAA
1 TTTTTCATCAAGTCTTTT-ATAAAG
**
56130580 TTTCCCATCAAGT-TTTTA
1 TTTTTCATCAAGTCTTTTA
56130598 ATCATTTCGT
Statistics
Matches: 77, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
23 7 0.09
24 18 0.23
25 31 0.40
26 1 0.01
28 20 0.26
ACGTcount: A:0.26, C:0.15, G:0.08, T:0.51
Consensus pattern (24 bp):
TTTTTCATCAAGTCTTTTATAAAG
Found at i:56132692 original size:39 final size:39
Alignment explanation
Indices: 56132507--56132706 Score: 224
Period size: 39 Copynumber: 5.1 Consensus size: 39
56132497 ACTTCCAATA
* * * *
56132507 CACCGGCACACAGCCTGCTAGGCA-TAAAGGCC-GAAAAAT
1 CACCGGCACAAAGCCTACTAGGCACT-TA-GCCTGAATAAT
* *
56132546 CACCGGCACAAAGCCTGCTAGGCACTTAGCCCGAATAAT
1 CACCGGCACAAAGCCTACTAGGCACTTAGCCTGAATAAT
* *
56132585 CACCGGCACAAAGCTTGCTAGGCACTTAGCCTGAATAAT
1 CACCGGCACAAAGCCTACTAGGCACTTAGCCTGAATAAT
* ** *
56132624 CACCAGCACAAAATCTACTAAGCACTTAGCCTGAATAAT
1 CACCGGCACAAAGCCTACTAGGCACTTAGCCTGAATAAT
* * * *
56132663 CACTGGCATAAAGCCTACTAGGCATTTAGCTTGAATAAT
1 CACCGGCACAAAGCCTACTAGGCACTTAGCCTGAATAAT
56132702 CACCG
1 CACCG
56132707 TGTTTCTATT
Statistics
Matches: 139, Mismatches: 20, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
38 3 0.02
39 135 0.97
40 1 0.01
ACGTcount: A:0.34, C:0.29, G:0.18, T:0.18
Consensus pattern (39 bp):
CACCGGCACAAAGCCTACTAGGCACTTAGCCTGAATAAT
Found at i:56138929 original size:24 final size:24
Alignment explanation
Indices: 56138902--56139042 Score: 165
Period size: 24 Copynumber: 5.9 Consensus size: 24
56138892 TCCAGGTGGA
* * * *
56138902 ATGCCTGGGGGTTTTCCCGGAGGT
1 ATGCCTGGAGGTATGCCTGGAGGT
*
56138926 ATGCCCGGAGGTATGCCTGGAGGT
1 ATGCCTGGAGGTATGCCTGGAGGT
*
56138950 ATGCCCGGAGGTATGCCTGGAGGT
1 ATGCCTGGAGGTATGCCTGGAGGT
*
56138974 ATGCCTGGAGGCATGCCTGGAGGT
1 ATGCCTGGAGGTATGCCTGGAGGT
* * *
56138998 ATGCCTGGAGGCATGCCTGGTGGC
1 ATGCCTGGAGGTATGCCTGGAGGT
* * *
56139022 ATGCCGGGTGGCATGCCTGGA
1 ATGCCTGGAGGTATGCCTGGA
56139043 AATGTTGATT
Statistics
Matches: 105, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 105 1.00
ACGTcount: A:0.14, C:0.22, G:0.42, T:0.22
Consensus pattern (24 bp):
ATGCCTGGAGGTATGCCTGGAGGT
Found at i:56138934 original size:12 final size:12
Alignment explanation
Indices: 56138920--56139042 Score: 165
Period size: 12 Copynumber: 10.2 Consensus size: 12
56138910 GGGTTTTCCC
*
56138920 GGAGGTATGCCC
1 GGAGGTATGCCT
56138932 GGAGGTATGCCT
1 GGAGGTATGCCT
*
56138944 GGAGGTATGCCC
1 GGAGGTATGCCT
56138956 GGAGGTATGCCT
1 GGAGGTATGCCT
56138968 GGAGGTATGCCT
1 GGAGGTATGCCT
*
56138980 GGAGGCATGCCT
1 GGAGGTATGCCT
56138992 GGAGGTATGCCT
1 GGAGGTATGCCT
*
56139004 GGAGGCATGCCT
1 GGAGGTATGCCT
* * *
56139016 GGTGGCATGCCG
1 GGAGGTATGCCT
* *
56139028 GGTGGCATGCCT
1 GGAGGTATGCCT
56139040 GGA
1 GGA
56139043 AATGTTGATT
Statistics
Matches: 101, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 101 1.00
ACGTcount: A:0.15, C:0.21, G:0.43, T:0.20
Consensus pattern (12 bp):
GGAGGTATGCCT
Found at i:56138942 original size:36 final size:36
Alignment explanation
Indices: 56138902--56139042 Score: 174
Period size: 36 Copynumber: 3.9 Consensus size: 36
56138892 TCCAGGTGGA
* * * *
56138902 ATGCCTGGGGGTTTTCCCGGAGGTATGCCCGGAGGT
1 ATGCCTGGAGGTATGCCCGGAGGTATGCCTGGAGGT
56138938 ATGCCTGGAGGTATGCCCGGAGGTATGCCTGGAGGT
1 ATGCCTGGAGGTATGCCCGGAGGTATGCCTGGAGGT
* * *
56138974 ATGCCTGGAGGCATGCCTGGAGGTATGCCTGGAGGC
1 ATGCCTGGAGGTATGCCCGGAGGTATGCCTGGAGGT
* * * * *
56139010 ATGCCTGGTGGCATGCCGGGTGGCATGCCTGGA
1 ATGCCTGGAGGTATGCCCGGAGGTATGCCTGGA
56139043 AATGTTGATT
Statistics
Matches: 94, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 94 1.00
ACGTcount: A:0.14, C:0.22, G:0.42, T:0.22
Consensus pattern (36 bp):
ATGCCTGGAGGTATGCCCGGAGGTATGCCTGGAGGT
Found at i:56140964 original size:29 final size:28
Alignment explanation
Indices: 56140901--56140964 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 28
56140891 AATAAAAGCC
*
56140901 CATTTTTTTAATAATTACGGAAATTGGT
1 CATTTTTTTAATAATTACGGAAATGGGT
** *
56140929 CGGTTTTTTAATTATTTACCGG-AATGGGT
1 CATTTTTTTAA-TAATTA-CGGAAATGGGT
56140958 CATTTTT
1 CATTTTT
56140965 CGCAAAATCG
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
28 9 0.32
29 16 0.57
30 3 0.11
ACGTcount: A:0.25, C:0.09, G:0.17, T:0.48
Consensus pattern (28 bp):
CATTTTTTTAATAATTACGGAAATGGGT
Found at i:56141213 original size:22 final size:21
Alignment explanation
Indices: 56141170--56141246 Score: 109
Period size: 22 Copynumber: 3.6 Consensus size: 21
56141160 TTTCACAAAC
*
56141170 AAATTCTCTCAATTTCTTCAA
1 AAATTCTCTCAATTCCTTCAA
56141191 AAATTCTCTCAATTCCCTTCAA
1 AAATTCTCTCAATT-CCTTCAA
* *
56141213 AAATTTTCTCAATTTCCTTCCA
1 AAATTCTCTCAA-TTCCTTCAA
56141235 AAATTCTCTCAA
1 AAATTCTCTCAA
56141247 ACTCTCAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
21 14 0.28
22 34 0.68
23 2 0.04
ACGTcount: A:0.32, C:0.27, G:0.00, T:0.40
Consensus pattern (21 bp):
AAATTCTCTCAATTCCTTCAA
Found at i:56141253 original size:30 final size:30
Alignment explanation
Indices: 56141219--56141276 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
56141209 TCAAAAATTT
* *
56141219 TCTCAATTTCCTTCCAAAATTCTCTCAAAC
1 TCTCAAATTCCTTCCAAAATACTCTCAAAC
56141249 TCTCAAATTCCTTCCAAAATACTCTCAA
1 TCTCAAATTCCTTCCAAAATACTCTCAA
56141277 TTTCCTTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.34
Consensus pattern (30 bp):
TCTCAAATTCCTTCCAAAATACTCTCAAAC
Found at i:56141253 original size:52 final size:51
Alignment explanation
Indices: 56141196--56141298 Score: 136
Period size: 52 Copynumber: 2.0 Consensus size: 51
56141186 TTCAAAAATT
** * *
56141196 CTCTC-AATTCCCTTCAAAAATTTTCTCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAAATT-CCTTCAAAAATACTCTCAATTTCCTTCAAAAAATCTC-CAAA
*
56141248 CTCTCAAATTCCTTCCAAAATACTCTCAATTTCCTTCAAAAAATCTCCAAA
1 CTCTCAAATTCCTTCAAAAATACTCTCAATTTCCTTCAAAAAATCTCCAAA
56141299 TCCATAGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
51 4 0.09
52 37 0.82
53 4 0.09
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.35
Consensus pattern (51 bp):
CTCTCAAATTCCTTCAAAAATACTCTCAATTTCCTTCAAAAAATCTCCAAA
Found at i:56141287 original size:21 final size:22
Alignment explanation
Indices: 56141247--56141289 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
56141237 ATTCTCTCAA
56141247 ACTCTCAAATTCCTTCCAAAAT
1 ACTCTCAAATTCCTTCCAAAAT
* *
56141269 ACTCTCAATTTCCTTCAAAAA
1 ACTCTCAAATTCCTTCCAAAA
56141290 ATCTCCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.37, C:0.30, G:0.00, T:0.33
Consensus pattern (22 bp):
ACTCTCAAATTCCTTCCAAAAT
Found at i:56141515 original size:14 final size:15
Alignment explanation
Indices: 56141486--56141519 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
56141476 AAATTTTAAA
56141486 TTTTATTTAAGATAT
1 TTTTATTTAAGATAT
*
56141501 TTTTATTTATG-TAT
1 TTTTATTTAAGATAT
56141515 TTTTA
1 TTTTA
56141520 GATATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTATTTAAGATAT
Found at i:56143694 original size:28 final size:28
Alignment explanation
Indices: 56143658--56144017 Score: 447
Period size: 28 Copynumber: 13.5 Consensus size: 28
56143648 ACATTATTTG
56143658 ATTAAAAACCCTAACCTAACCTAATTGA
1 ATTAAAAACCCTAACCTAACCTAATTGA
56143686 ATTAAAAA--C---CCTAACCTAATTGA
1 ATTAAAAACCCTAACCTAACCTAATTGA
* * *
56143709 ATTAAAAACCCTAGCCTAACTTAATTTA
1 ATTAAAAACCCTAACCTAACCTAATTGA
* *
56143737 ATTAAAAACCCTAAAACCCTAACTTAATTTA
1 ATTAAAAACCCT--AA-CCTAACCTAATTGA
* *
56143768 ATTAAAAACCCTAACCTAACTTAATTTA
1 ATTAAAAACCCTAACCTAACCTAATTGA
56143796 ATTAAAAACCCTAACCTAACCTAATTGA
1 ATTAAAAACCCTAACCTAACCTAATTGA
56143824 ATTAAAAA--C---CCTAACCTAATTGA
1 ATTAAAAACCCTAACCTAACCTAATTGA
* *
56143847 ATTAAAAACCCTAACCTAACTTAATTTA
1 ATTAAAAACCCTAACCTAACCTAATTGA
* *
56143875 ATTATAAACCCTAACCTAACCTAATTTA
1 ATTAAAAACCCTAACCTAACCTAATTGA
56143903 ATTAAAAACCCTAACCTAACCTAATTGA
1 ATTAAAAACCCTAACCTAACCTAATTGA
56143931 ATTAAAAA--C---CCTAACCTAATTGA
1 ATTAAAAACCCTAACCTAACCTAATTGA
56143954 ATTAAAAACCCTAACC-AACCTAATTGA
1 ATTAAAAACCCTAACCTAACCTAATTGA
56143981 ATTAAAAA--C---CCTAACCTAATTGA
1 ATTAAAAACCCTAACCTAACCTAATTGA
56144004 ATTAAAAACCCTAA
1 ATTAAAAACCCTAA
56144018 AGGTCCAAAA
Statistics
Matches: 297, Mismatches: 11, Indels: 48
0.83 0.03 0.13
Matches are distributed among these distances:
22 2 0.01
23 85 0.29
25 5 0.02
26 3 0.01
27 19 0.06
28 154 0.52
29 2 0.01
30 1 0.00
31 26 0.09
ACGTcount: A:0.47, C:0.23, G:0.03, T:0.28
Consensus pattern (28 bp):
ATTAAAAACCCTAACCTAACCTAATTGA
Found at i:56143699 original size:23 final size:23
Alignment explanation
Indices: 56143672--56144017 Score: 253
Period size: 23 Copynumber: 13.2 Consensus size: 23
56143662 AAAACCCTAA
56143672 CCTAACCTAATTGAATTAAAAAC
1 CCTAACCTAATTGAATTAAAAAC
56143695 CCTAACCTAATTGAATTAAAAACCC
1 CCTAACCTAATTGAATTAAAAA--C
* *
56143720 TAGCCTAACTTAATTTAATTAAAAAC
1 ---CCTAACCTAATTGAATTAAAAAC
*
56143746 CCTAAAACCCTAACTTAATTTAATTAAAAAC
1 CCT--AA--C---C-TAATTGAATTAAAAAC
*
56143777 CCTAACCTAACTTAATTTAATTAAAAACCC
1 CCTAA-C---C-TAATTGAATTAAAAA--C
56143807 TAACCTAACCTAATTGAATTAAAAAC
1 ---CCTAACCTAATTGAATTAAAAAC
56143833 CCTAACCTAATTGAATTAAAAAC
1 CCTAACCTAATTGAATTAAAAAC
56143856 CCTAACCTAACTT-AATTTAATTATAAACCC
1 CCTAACCTAA-TTGAA-TT-A--A-AAA--C
*
56143886 TAACCTAACCTAATTTAATTAAAAACCC
1 ---CCTAACCTAATTGAATTAAAAA--C
56143914 TAACCTAACCTAATTGAATTAAAAAC
1 ---CCTAACCTAATTGAATTAAAAAC
56143940 CCTAACCTAATTGAATTAAAAAC
1 CCTAACCTAATTGAATTAAAAAC
56143963 CCTAACCAACCTAATTGAATTAAAAAC
1 CCT----AACCTAATTGAATTAAAAAC
56143990 CCTAACCTAATTGAATTAAAAAC
1 CCTAACCTAATTGAATTAAAAAC
56144013 CCTAA
1 CCTAA
56144018 AGGTCCAAAA
Statistics
Matches: 284, Mismatches: 5, Indels: 68
0.80 0.01 0.19
Matches are distributed among these distances:
23 111 0.39
24 4 0.01
25 4 0.01
26 3 0.01
27 25 0.09
28 89 0.31
29 4 0.01
30 2 0.01
31 20 0.07
32 5 0.02
33 17 0.06
ACGTcount: A:0.47, C:0.23, G:0.03, T:0.28
Consensus pattern (23 bp):
CCTAACCTAATTGAATTAAAAAC
Found at i:56143734 original size:51 final size:50
Alignment explanation
Indices: 56143658--56144017 Score: 287
Period size: 51 Copynumber: 6.8 Consensus size: 50
56143648 ACATTATTTG
56143658 ATTAAAAACCCTAACCTAACCTAATTGAATTAAAAACCCTAACCTAATTGA
1 ATTAAAAACCCT-ACCTAACCTAATTGAATTAAAAACCCTAACCTAATTGA
* * *
56143709 ATTAAAAACCCTAGCCTAACTTAATTTAATTAAAAACCCTAAAACCCTAACTTAATTTA
1 ATTAAAAACCCTA-CCTAACCTAATTGAATTAAAAACCCT--AA--C---C-TAATTGA
* *
56143768 ATTAAAAACCCTAACCTAACTTAATTTAATTAAAAACCCTAACCTAACCTAATTGA
1 ATTAAAAACCCT-ACCTAACCTAATTGAATTAAAAA--C---CCTAACCTAATTGA
56143824 ATTAAAAA--C--CCTAACCTAATTGAATTAAAAACCCTAACCTAACTT-A
1 ATTAAAAACCCTACCTAACCTAATTGAATTAAAAACCCTAACCTAA-TTGA
*
56143870 ATTTAATTATAAACCCTAACCTAACCTAATTTAATTAAAAACCCTAACCTAACCTAATTGA
1 A-TT-A--A-AAACCCT-ACCTAACCTAATTGAATTAAAAA--C---CCTAACCTAATTGA
56143931 ATTAAAAA--C--CCTAACCTAATTGAATTAAAAACCCTAACCAACCTAATTGA
1 ATTAAAAACCCTACCTAACCTAATTGAATTAAAAACCCT----AACCTAATTGA
56143981 ATTAAAAA--C--CCTAACCTAATTGAATTAAAAACCCTAA
1 ATTAAAAACCCTACCTAACCTAATTGAATTAAAAACCCTAA
56144018 AGGTCCAAAA
Statistics
Matches: 265, Mismatches: 8, Indels: 77
0.76 0.02 0.22
Matches are distributed among these distances:
46 17 0.06
47 4 0.02
48 1 0.00
49 2 0.01
50 48 0.18
51 80 0.30
53 3 0.01
54 2 0.01
55 1 0.00
56 38 0.14
57 2 0.01
58 2 0.01
59 41 0.15
60 6 0.02
61 13 0.05
62 2 0.01
64 3 0.01
ACGTcount: A:0.47, C:0.23, G:0.03, T:0.28
Consensus pattern (50 bp):
ATTAAAAACCCTACCTAACCTAATTGAATTAAAAACCCTAACCTAATTGA
Found at i:56143860 original size:79 final size:79
Alignment explanation
Indices: 56143749--56144017 Score: 406
Period size: 79 Copynumber: 3.4 Consensus size: 79
56143739 TAAAAACCCT
* *
56143749 AAAACCCTAACTTAATTTAATTAAAAACCCTAACCTAACTTAATTTAATTAAAAACCCTAACCTA
1 AAAACCCTAACCTAATTGAATTAAAAACCCTAACCTAACTTAATTTAATTAAAAACCCTAACCTA
56143814 ACCTAATTGAATTA
66 ACCTAATTGAATTA
*
56143828 AAAACCCTAACCTAATTGAATTAAAAACCCTAACCTAACTTAATTTAATTATAAACCCTAACCTA
1 AAAACCCTAACCTAATTGAATTAAAAACCCTAACCTAACTTAATTTAATTAAAAACCCTAACCTA
*
56143893 ACCTAATTTAATTA
66 ACCTAATTGAATTA
*
56143907 AAAACCCTAACCTAACCTAATTGAATTAAAAACCCTAA-C---C-TAATTGAATTAAAAACCCTA
1 AAAA--C---CCTAACCTAATTGAATTAAAAACCCTAACCTAACTTAATTTAATTAAAAACCCTA
56143967 ACC-AACCTAATTGAATTA
61 ACCTAACCTAATTGAATTA
56143985 AAAACCCTAACCTAATTGAATTAAAAACCCTAA
1 AAAACCCTAACCTAATTGAATTAAAAACCCTAA
56144018 AGGTCCAAAA
Statistics
Matches: 178, Mismatches: 7, Indels: 16
0.89 0.03 0.08
Matches are distributed among these distances:
73 28 0.16
76 1 0.01
78 18 0.10
79 100 0.56
80 1 0.01
81 1 0.01
83 1 0.01
84 28 0.16
ACGTcount: A:0.47, C:0.23, G:0.02, T:0.28
Consensus pattern (79 bp):
AAAACCCTAACCTAATTGAATTAAAAACCCTAACCTAACTTAATTTAATTAAAAACCCTAACCTA
ACCTAATTGAATTA
Found at i:56145945 original size:124 final size:124
Alignment explanation
Indices: 56145724--56145989 Score: 376
Period size: 124 Copynumber: 2.1 Consensus size: 124
56145714 CCACGAGGGC
56145724 GCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCCAACATGACCAACTGTAGCG
1 GCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCCAACATGACCAACTGTAGCG
* * **
56145789 AAATCGCGTCCACGAGGGCACGATTTAACAATTT-TTGCCCAATATAGCATCCTTGTATCA
66 AAATCGCGTCCACGAGGCCACGATTTAACAATTTCTT-CCCAA-ATAGCATCCTAGTAGAA
* * **
56145849 GCGATTTTATACTATTTGCTCAGAAAACGTCAAAAAAAA-TATTTCTTACATGACC-ACTGTAGC
1 GCGATTTGACACTATTTGCTCAG-AAACGTCAAAAAAAATTATTTCCAACATGACCAACTGTAGC
* *
56145912 GAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTAGTAGAA
65 GAAATCGCGTCCACGAGGCCACGATTTAACAATTTCTTCCCAAATAGCATCCTAGTAGAA
**
56145972 GCGATTTCCCACTATTTG
1 GCGATTTGACACTATTTG
56145990 ACCGGATACG
Statistics
Matches: 126, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
123 29 0.23
124 45 0.36
125 37 0.29
126 15 0.12
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (124 bp):
GCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCCAACATGACCAACTGTAGCG
AAATCGCGTCCACGAGGCCACGATTTAACAATTTCTTCCCAAATAGCATCCTAGTAGAA
Found at i:56150020 original size:30 final size:30
Alignment explanation
Indices: 56149986--56150047 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
56149976 TCAAGTCCCA
* *
56149986 TAAAATTTATG-AAATTTTTATTAAATCTCT
1 TAAAATTTATGAAAATATTAATTAAAT-TCT
*
56150016 TAAAATTTTTGAAAATATTAATTAAATTCT
1 TAAAATTTATGAAAATATTAATTAAATTCT
56150046 TA
1 TA
56150048 TTTTTACTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 15 0.54
31 13 0.46
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (30 bp):
TAAAATTTATGAAAATATTAATTAAATTCT
Found at i:56151315 original size:21 final size:21
Alignment explanation
Indices: 56151289--56151347 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
56151279 TCTCTAACCC
56151289 TGGTCAAAATTATTTTGAAAA
1 TGGTCAAAATTATTTTGAAAA
** * *
56151310 TGGTCAAAATTATAATGGAAG
1 TGGTCAAAATTATTTTGAAAA
56151331 TGGTCAAAATTATTTTG
1 TGGTCAAAATTATTTTG
56151348 CTGGTCAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.39, C:0.05, G:0.19, T:0.37
Consensus pattern (21 bp):
TGGTCAAAATTATTTTGAAAA
Found at i:56151354 original size:18 final size:18
Alignment explanation
Indices: 56151330--56151375 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
56151320 TATAATGGAA
*
56151330 GTGGTCAAAATTAT-TTT
1 GTGGTCAAAATTATGATT
56151347 GCTGGTCAAAATTATGATT
1 G-TGGTCAAAATTATGATT
56151366 GTGGTCAAAA
1 GTGGTCAAAA
56151376 GTGGTATGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 1 0.04
18 22 0.85
19 3 0.12
ACGTcount: A:0.33, C:0.09, G:0.22, T:0.37
Consensus pattern (18 bp):
GTGGTCAAAATTATGATT
Found at i:56151609 original size:69 final size:69
Alignment explanation
Indices: 56151496--56151631 Score: 191
Period size: 69 Copynumber: 2.0 Consensus size: 69
56151486 GCCGAACATC
* * * * *
56151496 TAGGCCTCAAGAGCATGGGCCGCATGATGGGATTGATGGTGCTATTAGGCCGTATGGTGGTGTTG
1 TAGGCCTCAAAAGCATGGGCCACATGATGGGATTGATGGAGCTATTAGGCCGAATAGTGGTGTTG
56151561 GGTA
66 GGTA
** * *
56151565 TAGGCCTCAAAATTATGGGCCACATGCTGGGATTGATGGAGCTATTGGGCCGAATAGTGGTGTTG
1 TAGGCCTCAAAAGCATGGGCCACATGATGGGATTGATGGAGCTATTAGGCCGAATAGTGGTGTTG
56151630 GG
66 GG
56151632 CCGAAGGATG
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
69 58 1.00
ACGTcount: A:0.21, C:0.15, G:0.38, T:0.27
Consensus pattern (69 bp):
TAGGCCTCAAAAGCATGGGCCACATGATGGGATTGATGGAGCTATTAGGCCGAATAGTGGTGTTG
GGTA
Found at i:56151643 original size:18 final size:18
Alignment explanation
Indices: 56151607--56151651 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
56151597 TTGATGGAGC
*
56151607 TATTGGGCCGAATAGTGG
1 TATTGGGCCGAAGAGTGG
*
56151625 TGTTGGGCCGAAG-GATGG
1 TATTGGGCCGAAGAG-TGG
56151643 TATTGGGCC
1 TATTGGGCC
56151652 ACATATTGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 1 0.04
18 22 0.96
ACGTcount: A:0.18, C:0.13, G:0.42, T:0.27
Consensus pattern (18 bp):
TATTGGGCCGAAGAGTGG
Found at i:56177552 original size:40 final size:40
Alignment explanation
Indices: 56177497--56177577 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
56177487 TCTGGTATGA
56177497 TTTCTGTATGTGGGCCAAGGCACACACTAGGCTTTTTAGC
1 TTTCTGTATGTGGGCCAAGGCACACACTAGGCTTTTTAGC
56177537 TTTCTGTATGTGGGCCAAGGCACACACTAGGCTTTTTAGC
1 TTTCTGTATGTGGGCCAAGGCACACACTAGGCTTTTTAGC
56177577 T
1 T
56177578 CACTTTGTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.33
Consensus pattern (40 bp):
TTTCTGTATGTGGGCCAAGGCACACACTAGGCTTTTTAGC
Found at i:56180913 original size:102 final size:101
Alignment explanation
Indices: 56180734--56181077 Score: 433
Period size: 102 Copynumber: 3.4 Consensus size: 101
56180724 TATCGATGAA
* * *
56180734 CACGTGTGTAGTATTGTGTGAAGGCTACTATGTGTATCGATAAATAATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAAT-ATGATCACATGTGTAGTAC
* * *
56180799 TAAGTGAAGGCTACTATGTGTACTGAGAAGTTTTGGT
65 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
* * *
56180836 CACGTGTGTAGTACTGTATGAAGGCTACTACGTGTACCGATAAATGATGAACACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAAT-ATGATCACATGTGTAGTAC
*
56180901 TAAGTGATGGCTACTATGTGTACCGAAAAGCTTTGGT
65 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
* * * *
56180938 CACGTGTGTAGTACTATGTAAAGGCTACTACGTGAATCG-TAAAATTTGATCACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGAT-AAATATGATCACATGTGTAGTAC
* ** * *
56181002 TATGTGAAGGCTACTACATGAACCGTAAAA-C-TTGAT
65 TAAGTGAAGGCTACTATGTGTACCG-AAAAGCTTTGGT
* * *
56181038 CACGAGTGTAGTACTATGTGAAGGCTACTAAGTGTATCGA
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGA
56181078 ATGATAAAAG
Statistics
Matches: 211, Mismatches: 28, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
100 39 0.18
101 39 0.18
102 133 0.63
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (101 bp):
CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATATGATCACATGTGTAGTACT
AAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
Found at i:56181004 original size:50 final size:50
Alignment explanation
Indices: 56180738--56181073 Score: 311
Period size: 51 Copynumber: 6.6 Consensus size: 50
56180728 GATGAACACG
* * * * * *
56180738 TGTGTAGTATTGTGTGAAGGCTACTATGTGTATCGATAAATAATGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAT-TTGATCACA
* * * * * * *
56180789 TGTGTAGTACTAAGTGAAGGCTACTATGTGTACTGAGAAGTTTTGGTCACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAA-ATTTGATCACA
* * * *
56180840 TGTGTAGTACTGTATGAAGGCTACTACGTGTACCGATAAATGATGAACACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAT-TTGATCACA
* * * * *
56180891 TGTGTAGTACTAAGTGATGGCTACTATGTGTACCGA-AAAGCTTTGGTCACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAA--TTTGATCACA
* * *
56180942 TGTGTAGTACTATGTAAAGGCTACTACGTGAATCG-TAAAATTTGATCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGAT-AAATTTGATCACA
* * *
56180992 TGTGTAGTACTATGTGAAGGCTACTACATGAACCG-TAAAACTTGATCACGA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGAT-AAATTTGATCAC-A
*
56181043 -GTGTAGTACTATGTGAAGGCTACTAAGTGTA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTA
56181074 TCGAATGATA
Statistics
Matches: 234, Mismatches: 44, Indels: 15
0.80 0.15 0.05
Matches are distributed among these distances:
50 85 0.36
51 144 0.62
52 5 0.02
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (50 bp):
TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATTTGATCACA
Found at i:56183476 original size:25 final size:25
Alignment explanation
Indices: 56183436--56183526 Score: 94
Period size: 25 Copynumber: 3.6 Consensus size: 25
56183426 CGCAATAATG
* * * *
56183436 TCCCGTTATTTAGCTCTTTTGAGCA
1 TCCCGTTATATGGCTCTCTTGAGCT
**
56183461 TCCCGTTATATGGCTCTCACGAGCT
1 TCCCGTTATATGGCTCTCTTGAGCT
**
56183486 TCCCAATA-ATTGGCTCTCTTGAGCT
1 TCCCGTTATA-TGGCTCTCTTGAGCT
56183511 TCCCGTTATATGGCTC
1 TCCCGTTATATGGCTC
56183527 ACATGAGCAT
Statistics
Matches: 52, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
24 1 0.02
25 50 0.96
26 1 0.02
ACGTcount: A:0.16, C:0.29, G:0.18, T:0.37
Consensus pattern (25 bp):
TCCCGTTATATGGCTCTCTTGAGCT
Found at i:56183584 original size:25 final size:25
Alignment explanation
Indices: 56183505--56183584 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
56183495 TTGGCTCTCT
*
56183505 TGAGCTTCCCG-TTATATGGCTCACA
1 TGAGCTTCCCGTTTATAT-GCTCGCA
* * ** *
56183530 TGAGCATCCTGTTCCGTA-GCTCGGA
1 TGAGCTTCCCGTT-TATATGCTCGCA
*
56183555 AGAGCTTCCCGTTTATATGCTCGCA
1 TGAGCTTCCCGTTTATATGCTCGCA
56183580 TGAGC
1 TGAGC
56183585 ATACCTGTAT
Statistics
Matches: 39, Mismatches: 13, Indels: 6
0.67 0.22 0.10
Matches are distributed among these distances:
24 2 0.05
25 34 0.87
26 1 0.03
27 2 0.05
ACGTcount: A:0.19, C:0.28, G:0.24, T:0.30
Consensus pattern (25 bp):
TGAGCTTCCCGTTTATATGCTCGCA
Found at i:56185187 original size:41 final size:41
Alignment explanation
Indices: 56185123--56185260 Score: 188
Period size: 41 Copynumber: 3.4 Consensus size: 41
56185113 TGTGATTTGG
** * *
56185123 AATAGCTTTGGCTATATATGGCACTTAGTGTGC-GAAATTAT
1 AATAGCTTCAGCTATGTAAGGCACTTAGTGTGCAG-AATTAT
*
56185164 AATAGCTTCAGCTATGTAAGGCACTTAGTGTACAGAATTAT
1 AATAGCTTCAGCTATGTAAGGCACTTAGTGTGCAGAATTAT
* *
56185205 AATAGCTTCGGCTAGGTAAGGCACTTAGTGTGCAGAATTAT
1 AATAGCTTCAGCTATGTAAGGCACTTAGTGTGCAGAATTAT
*
56185246 AATAGCTTTAGCTAT
1 AATAGCTTCAGCTAT
56185261 ATGATTGGCA
Statistics
Matches: 85, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
41 84 0.99
42 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (41 bp):
AATAGCTTCAGCTATGTAAGGCACTTAGTGTGCAGAATTAT
Found at i:56187489 original size:100 final size:100
Alignment explanation
Indices: 56187316--56187515 Score: 391
Period size: 100 Copynumber: 2.0 Consensus size: 100
56187306 CATTTATTGG
*
56187316 TATCAAAGCCACGATTTAGTCGATTCTCAGACTAACATAGTGTATATGAGTCTAGCTATACATGT
1 TATCAAAGCCACGATTTAGTCGATTCTCAGACTAACATAGCGTATATGAGTCTAGCTATACATGT
56187381 CATTATATAACTTGTGATAGTGTGATATCTCCTGA
66 CATTATATAACTTGTGATAGTGTGATATCTCCTGA
56187416 TATCAAAGCCACGATTTAGTCGATTCTCAGACTAACATAGCGTATATGAGTCTAGCTATACATGT
1 TATCAAAGCCACGATTTAGTCGATTCTCAGACTAACATAGCGTATATGAGTCTAGCTATACATGT
56187481 CATTATATAACTTGTGATAGTGTGATATCTCCTGA
66 CATTATATAACTTGTGATAGTGTGATATCTCCTGA
56187516 CCATTTTAAA
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
100 99 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (100 bp):
TATCAAAGCCACGATTTAGTCGATTCTCAGACTAACATAGCGTATATGAGTCTAGCTATACATGT
CATTATATAACTTGTGATAGTGTGATATCTCCTGA
Found at i:56193318 original size:25 final size:25
Alignment explanation
Indices: 56193240--56193331 Score: 105
Period size: 25 Copynumber: 3.7 Consensus size: 25
56193230 TTCCATTGTA
*
56193240 TGGCTCTCACGAGCTTTCCGATAAT
1 TGGCTCTCACGAGCTTCCCGATAAT
*
56193265 TGGCTCTCACGAGCTTCCCAATAAT
1 TGGCTCTCACGAGCTTCCCGATAAT
** *
56193290 TGGCTCTCTTGAGCTTCCCG-TTAT
1 TGGCTCTCACGAGCTTCCCGATAAT
* *
56193314 ATGGCTCACATGAGCTTC
1 -TGGCTCTCACGAGCTTC
56193332 ATGTTCCATG
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
24 3 0.05
25 55 0.95
ACGTcount: A:0.18, C:0.29, G:0.20, T:0.33
Consensus pattern (25 bp):
TGGCTCTCACGAGCTTCCCGATAAT
Found at i:56203124 original size:19 final size:19
Alignment explanation
Indices: 56203100--56203137 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
56203090 AGAAGAATGG
56203100 AGGTAATATGCTATTTGTT
1 AGGTAATATGCTATTTGTT
*
56203119 AGGTAATATGTTATTTGTT
1 AGGTAATATGCTATTTGTT
56203138 GCTCTTTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.03, G:0.21, T:0.50
Consensus pattern (19 bp):
AGGTAATATGCTATTTGTT
Found at i:56204174 original size:15 final size:15
Alignment explanation
Indices: 56204154--56204184 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
56204144 GTTATGTAAG
56204154 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
56204169 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
56204184 T
1 T
56204185 ATGTTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.32, T:0.23
Consensus pattern (15 bp):
TGAAAGGTCAAGAGT
Found at i:56206579 original size:95 final size:95
Alignment explanation
Indices: 56206465--56206644 Score: 315
Period size: 95 Copynumber: 1.9 Consensus size: 95
56206455 AAAAATATTT
* * *
56206465 ATATTATCAGCCGGCATCCCATGGGTAAAAGAAACTAGAATATTTTATTACAAGGTTGTTTAAAA
1 ATATGATCAGCCGACATCCCATGGGTAAAAGAAACTAGAATATTTTATTACAAGGCTGTTTAAAA
56206530 ATGAAAATAAAAAATCATGTGGCATTTCGC
66 ATGAAAATAAAAAATCATGTGGCATTTCGC
* *
56206560 ATATGATCAGCCGATATCCCATGGGTAAAATAAACTAGAATATTTTATTACAAGGCTGTTTAAAA
1 ATATGATCAGCCGACATCCCATGGGTAAAAGAAACTAGAATATTTTATTACAAGGCTGTTTAAAA
56206625 ATGAAAATAAAAAATCATGT
66 ATGAAAATAAAAAATCATGT
56206645 TCACACTCTT
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
95 80 1.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (95 bp):
ATATGATCAGCCGACATCCCATGGGTAAAAGAAACTAGAATATTTTATTACAAGGCTGTTTAAAA
ATGAAAATAAAAAATCATGTGGCATTTCGC
Found at i:56211438 original size:21 final size:21
Alignment explanation
Indices: 56211414--56211474 Score: 50
Period size: 21 Copynumber: 2.9 Consensus size: 21
56211404 AAATCATGCT
56211414 TATCACATTACAGATCATACA
1 TATCACATTACAGATCATACA
** * ** *
56211435 TATCGTATTACAAATTGTACT
1 TATCACATTACAGATCATACA
**
56211456 TATCACATTTTAGATCATA
1 TATCACATTACAGATCATA
56211475 TTGAACAAAT
Statistics
Matches: 27, Mismatches: 13, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.38
Consensus pattern (21 bp):
TATCACATTACAGATCATACA
Found at i:56211753 original size:40 final size:40
Alignment explanation
Indices: 56211709--56211798 Score: 171
Period size: 40 Copynumber: 2.2 Consensus size: 40
56211699 GCCCACATGG
56211709 CCTGGCACACTGTCTCACACATGCCCTGCCTACCACACGA
1 CCTGGCACACTGTCTCACACATGCCCTGCCTACCACACGA
56211749 CCTGGCACACTGTCTCACACATGCCCTGCCTACCACACGA
1 CCTGGCACACTGTCTCACACATGCCCTGCCTACCACACGA
*
56211789 CCTAGCACAC
1 CCTGGCACAC
56211799 GAGCCATGTG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.23, C:0.46, G:0.14, T:0.17
Consensus pattern (40 bp):
CCTGGCACACTGTCTCACACATGCCCTGCCTACCACACGA
Found at i:56214940 original size:8 final size:8
Alignment explanation
Indices: 56214927--56214978 Score: 104
Period size: 8 Copynumber: 6.5 Consensus size: 8
56214917 TTAATAAAAC
56214927 TTTTATAA
1 TTTTATAA
56214935 TTTTATAA
1 TTTTATAA
56214943 TTTTATAA
1 TTTTATAA
56214951 TTTTATAA
1 TTTTATAA
56214959 TTTTATAA
1 TTTTATAA
56214967 TTTTATAA
1 TTTTATAA
56214975 TTTT
1 TTTT
56214979 TCAAATTTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 44 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (8 bp):
TTTTATAA
Found at i:56222228 original size:17 final size:18
Alignment explanation
Indices: 56222198--56222231 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
56222188 GTGATGTATC
56222198 TTATGAAATCAACTTATG
1 TTATGAAATCAACTTATG
*
56222216 TTAT-AAATGAACTTAT
1 TTATGAAATCAACTTAT
56222232 ATGAGATGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (18 bp):
TTATGAAATCAACTTATG
Found at i:56222443 original size:16 final size:16
Alignment explanation
Indices: 56222422--56222462 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
56222412 ATATATTATC
56222422 GGAAGCTCGACCGGCT
1 GGAAGCTCGACCGGCT
*
56222438 GGAAGCTCGATCGGCT
1 GGAAGCTCGACCGGCT
56222454 GGAAGCTCG
1 GGAAGCTCG
56222463 TCGGAGACCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.20, C:0.27, G:0.39, T:0.15
Consensus pattern (16 bp):
GGAAGCTCGACCGGCT
Found at i:56222916 original size:18 final size:18
Alignment explanation
Indices: 56222893--56222933 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
56222883 TTAAATCCCT
56222893 TTGATCACTTTTAGGTAA
1 TTGATCACTTTTAGGTAA
56222911 TTGATCACTTTTAGGTAA
1 TTGATCACTTTTAGGTAA
56222929 TTGAT
1 TTGAT
56222934 GTGCATGGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.46
Consensus pattern (18 bp):
TTGATCACTTTTAGGTAA
Found at i:56223737 original size:2 final size:2
Alignment explanation
Indices: 56223732--56223797 Score: 123
Period size: 2 Copynumber: 33.0 Consensus size: 2
56223722 TCATTATTAT
56223732 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
*
56223774 CA CA CA CA CA CA CA CT CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA
56223798 TATATATGTC
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.48, C:0.50, G:0.00, T:0.02
Consensus pattern (2 bp):
CA
Found at i:56224701 original size:38 final size:37
Alignment explanation
Indices: 56224632--56224704 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 37
56224622 TTTTCATAAT
* *
56224632 TTCACTTTTTCACTTTTAATCACTATTCAATTCAAAA
1 TTCACTTTTCCACTTTTAATCAATATTCAATTCAAAA
56224669 TTCACTTTTCCA-TTTTCAAGTCAATATTCAATTCAA
1 TTCACTTTTCCACTTTT-AA-TCAATATTCAATTCAA
56224705 TTCCACACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
36 4 0.12
37 13 0.41
38 15 0.47
ACGTcount: A:0.32, C:0.22, G:0.01, T:0.45
Consensus pattern (37 bp):
TTCACTTTTCCACTTTTAATCAATATTCAATTCAAAA
Found at i:56224735 original size:23 final size:22
Alignment explanation
Indices: 56224692--56224735 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
56224682 TTTCAAGTCA
56224692 ATATTCAATTCAATTCCACACAT
1 ATATTCAATTCAATT-CACACAT
56224715 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
56224736 TTAATCGTTA
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:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACAT
Found at i:56224859 original size:23 final size:23
Alignment explanation
Indices: 56224833--56224886 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
56224823 CATAAGTGCC
56224833 ACACTGATATGTAGCCGAAGCTA
1 ACACTGATATGTAGCCGAAGCTA
*
56224856 ACACTGAAATGTAGCCGAAGCTA
1 ACACTGATATGTAGCCGAAGCTA
*
56224879 CCACTGAT
1 ACACTGAT
56224887 CAATAACACT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (23 bp):
ACACTGATATGTAGCCGAAGCTA
Found at i:56225369 original size:30 final size:30
Alignment explanation
Indices: 56225335--56225393 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
56225325 TCCTTGACTC
56225335 AAACTTTGGCAAAATTACAATTTTGCCCCT
1 AAACTTTGGCAAAATTACAATTTTGCCCCT
* * * *
56225365 AAACTTTTGCATATTTACACTTTTGCCCC
1 AAACTTTGGCAAAATTACAATTTTGCCCC
56225394 AAAGCTCGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AAACTTTGGCAAAATTACAATTTTGCCCCT
Found at i:56235450 original size:19 final size:18
Alignment explanation
Indices: 56235418--56235455 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
56235408 AAATAATTTA
56235418 ATATAAATTATATATGTAT
1 ATATAAATTATATAT-TAT
56235437 ATATAAA-TAGTATATTAT
1 ATATAAATTA-TATATTAT
56235455 A
1 A
56235456 AAACATTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (18 bp):
ATATAAATTATATATTAT
Found at i:56240451 original size:16 final size:16
Alignment explanation
Indices: 56240422--56240491 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
56240412 TTTGGTTCGC
* *
56240422 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
*
56240438 CGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
*
56240454 TGTAATGGATTAGAGG
1 TGTAATGGAATAGAGG
56240470 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
56240486 TGTAAT
1 TGTAAT
56240492 AACAAATCAA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.33, C:0.01, G:0.36, T:0.30
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:56240468 original size:32 final size:32
Alignment explanation
Indices: 56240422--56240491 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
56240412 TTTGGTTCGC
*
56240422 TGTATTGGATTAGAGGCGTAATGGAATAGAGG
1 TGTAATGGATTAGAGGCGTAATGGAATAGAGG
*
56240454 TGTAATGGATTAGAGGTGTAATGGAATAGAGG
1 TGTAATGGATTAGAGGCGTAATGGAATAGAGG
56240486 TGTAAT
1 TGTAAT
56240492 AACAAATCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.33, C:0.01, G:0.36, T:0.30
Consensus pattern (32 bp):
TGTAATGGATTAGAGGCGTAATGGAATAGAGG
Found at i:56240724 original size:16 final size:16
Alignment explanation
Indices: 56240705--56240745 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
56240695 TTAATCATAT
*
56240705 TTAAATATAATTATTA
1 TTAAATATAATTATAA
56240721 TTAAATAT-ATTATAA
1 TTAAATATAATTATAA
56240736 TTAAAATATA
1 TT-AAATATA
56240746 TAATTTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TTAAATATAATTATAA
Found at i:56240753 original size:14 final size:15
Alignment explanation
Indices: 56240705--56240755 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
56240695 TTAATCATAT
*
56240705 TTAAATATAATTATTA
1 TTAAATAT-ATTATAA
56240721 TTAAATATATTATAA
1 TTAAATATATTATAA
56240736 TTAAA-ATA-TATAA
1 TTAAATATATTATAA
*
56240749 TTTAATA
1 TTAAATA
56240756 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 9 0.28
14 4 0.12
15 11 0.34
16 8 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTAAATATATTATAA
Found at i:56240846 original size:120 final size:120
Alignment explanation
Indices: 56240711--56240926 Score: 414
Period size: 120 Copynumber: 1.8 Consensus size: 120
56240701 ATATTTAAAT
56240711 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
1 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
56240776 TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATTTAAATTAAC
66 TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATTTAAATTAAC
*
56240831 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
1 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
*
56240896 TCTTATATGAATTTACTCAAATCATCATATA
66 TCTTATATGAATTTACTCAAATCATAATATA
56240927 AAATCGTGTT
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 94 1.00
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.44
Consensus pattern (120 bp):
ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATTTAAATTAAC
Found at i:56240873 original size:14 final size:15
Alignment explanation
Indices: 56240824--56240875 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
56240814 ATAAAATTTA
56240824 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
56240839 TATTAAATATATTAT
1 AATTAAATATATTAT
56240854 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
56240867 AATTTAATA
1 AATTAAATA
56240876 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:56240926 original size:59 final size:58
Alignment explanation
Indices: 56240741--56240927 Score: 177
Period size: 59 Copynumber: 3.1 Consensus size: 58
56240731 TATAATTAAA
*
56240741 ATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATC
1 ATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATC
* * * * * * *
56240799 ATA-ATATATGATACTATAAAATT-TAAATTAACATAATTATTATTAAAT-ATATTATAATTAAA
1 ATATATA-AT-TTA--ATAAAATTCTTAA-TAA-TTAA-TATTCTTATATGA-ATT-TACTCAAA
56240861 --
57 TC
56240861 ATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATC
1 ATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATC
56240919 ATCATATAA
1 AT-ATATAA
56240928 AATCGTGTTG
Statistics
Matches: 99, Mismatches: 15, Indels: 29
0.69 0.10 0.20
Matches are distributed among these distances:
56 6 0.06
57 15 0.15
58 11 0.11
59 19 0.19
60 6 0.06
61 13 0.13
62 8 0.08
63 15 0.15
64 6 0.06
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (58 bp):
ATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATC
Found at i:56242249 original size:11 final size:11
Alignment explanation
Indices: 56242242--56242269 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
56242232 TAAGCACGCG
56242242 CAAAGCACACA
1 CAAAGCACACA
56242253 CAAAGCACACA
1 CAAAGCACACA
56242264 CAAAGC
1 CAAAGC
56242270 CATAACATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.54, C:0.36, G:0.11, T:0.00
Consensus pattern (11 bp):
CAAAGCACACA
Found at i:56252752 original size:17 final size:17
Alignment explanation
Indices: 56252723--56252768 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
56252713 AATAAATCTA
*
56252723 AATAAAAA-ATAAACAT
1 AATAAAAACTTAAACAT
*
56252739 AATAAAAACTTAAACCT
1 AATAAAAACTTAAACAT
*
56252756 AA-AATAACTTAAA
1 AATAAAAACTTAAA
56252769 AAGAAGTCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 18 0.69
17 8 0.31
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (17 bp):
AATAAAAACTTAAACAT
Found at i:56253314 original size:17 final size:18
Alignment explanation
Indices: 56253300--56253336 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
56253290 ATAATCTTTG
56253300 AGGATATGCAATCTTAGA
1 AGGATATGCAATCTTAGA
*
56253318 TATGATATGCAATCTTAGA
1 -AGGATATGCAATCTTAGA
56253337 GATTTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (18 bp):
AGGATATGCAATCTTAGA
Found at i:56253505 original size:28 final size:27
Alignment explanation
Indices: 56253466--56253553 Score: 83
Period size: 28 Copynumber: 3.3 Consensus size: 27
56253456 GGGGATCAAT
*
56253466 AAAAAAAGAGAGAACGATTGACAGTTTA
1 AAAAAAAAAGAGAACGATTGACAG-TTA
* **
56253494 AAAAAAAAAGAGAAAGAAGGAC-G--A
1 AAAAAAAAAGAGAACGATTGACAGTTA
* *
56253518 ATAAAAAAAGAGAACGATTGGCAGTCTA
1 AAAAAAAAAGAGAACGATTGACAGT-TA
56253546 AAAAAAAA
1 AAAAAAAA
56253554 GGTGGCTTAC
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
24 18 0.39
25 1 0.02
27 1 0.02
28 26 0.57
ACGTcount: A:0.61, C:0.07, G:0.20, T:0.11
Consensus pattern (27 bp):
AAAAAAAAAGAGAACGATTGACAGTTA
Found at i:56254044 original size:22 final size:23
Alignment explanation
Indices: 56254016--56254058 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
56254006 ATAATTTTTT
56254016 TATATGTA-ATTATTT-TTTTATC
1 TATATGTATA-TATTTATTTTATC
56254038 TATATGTATATATTTATTTTA
1 TATATGTATATATTTATTTTA
56254059 GTATACATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (23 bp):
TATATGTATATATTTATTTTATC
Found at i:56254434 original size:12 final size:13
Alignment explanation
Indices: 56254403--56254444 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
56254393 TATTTTTTTA
*
56254403 TTATGTATATTGATT
1 TTATTTATATT-A-T
56254418 TTATTTAT-TTAT
1 TTATTTATATTAT
56254430 TTATTTATATTAT
1 TTATTTATATTAT
56254443 TT
1 TT
56254445 CTACGACACT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 9 0.36
13 7 0.28
14 2 0.08
15 7 0.28
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (13 bp):
TTATTTATATTAT
Found at i:56259760 original size:41 final size:41
Alignment explanation
Indices: 56259700--56259790 Score: 146
Period size: 41 Copynumber: 2.2 Consensus size: 41
56259690 GCATAGCGCT
*
56259700 TAGCAGGCTTATTGCCGGTGAAACACTTCAGACTATATGTC
1 TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTATATGTC
* * *
56259741 TAGCAGGCTTAATGTCGGTGAAATATTTCAGACTATATGTC
1 TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTATATGTC
56259782 TAGCAGGCT
1 TAGCAGGCT
56259791 AAGTGCTGGT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (41 bp):
TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTATATGTC
Found at i:56261748 original size:6 final size:6
Alignment explanation
Indices: 56261739--56261772 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
56261729 TAAAAGTGAT
56261739 AAAAAG AAAAAG AAAAAG AAAAAG -AAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
56261773 TGGAGAGGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:56261762 original size:18 final size:17
Alignment explanation
Indices: 56261739--56261772 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
56261729 TAAAAGTGAT
56261739 AAAAAGAAAAAGAAAAAG
1 AAAAAG-AAAAGAAAAAG
56261757 AAAAAGAAAAGAAAAA
1 AAAAAGAAAAGAAAAA
56261773 TGGAGAGGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAGAAAAAG
Found at i:56263071 original size:44 final size:44
Alignment explanation
Indices: 56262980--56263619 Score: 544
Period size: 44 Copynumber: 14.5 Consensus size: 44
56262970 GTAGATCAGT
* * * *
56262980 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATC
1 GAAGAT-GCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* *
56263024 GAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGGAGTATG-TC
1 GAAGATGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTA-GATC
* * * * * * *
56263068 GAAGAAAGTAGATATTGTCTTCATTTATTGG-CGTGAAGTAGATC
1 GAAG-ATGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* * * * *
56263112 GAAGATAGCAGGTCCTGTCTTCTTATATTGGTAG-GAAGTGGATC
1 GAAGAT-GCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* * * *
56263156 GAAGATGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATC
1 GAAGATGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* * *
56263199 GAAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATC
1 GAAGAT-GCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
*
56263244 GAAGATGCAGATCTTGTCTTCCTATACTGGTGGCGAAGTAGATC
1 GAAGATGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* * * * *
56263288 GAAGAAAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATC
1 GAAG-ATGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* * * * * * * *
56263332 AAAGATAGTAGGTCATGACTTCCTATATTAGTAG-GAAGTGGATC
1 GAAGAT-GCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* * *
56263376 GAAGATGCAGATCTTATCTTCCCATACTGGTGGCGAAGTAGATC
1 GAAGATGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* * * * * *
56263420 GAAGAAAGTAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATC
1 GAAG-ATGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* * * * *
56263464 GAAAATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATC
1 GAAGAT-GCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* * * *
56263508 GAAGATACAGATCTTGCCTTCCCATACTGGTGGCGAAGTAGATC
1 GAAGATGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* * * * *
56263552 GAAGAAAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATC
1 GAAG-ATGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
*
56263596 GAAGATAGCAGATCTTGCCTTCCT
1 GAAGAT-GCAGATCTTGTCTTCCT
56263620 GTACCGACAG
Statistics
Matches: 470, Mismatches: 107, Indels: 38
0.76 0.17 0.06
Matches are distributed among these distances:
42 1 0.00
43 101 0.21
44 268 0.57
45 100 0.21
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (44 bp):
GAAGATGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
Found at i:56263238 original size:132 final size:133
Alignment explanation
Indices: 56262980--56263619 Score: 803
Period size: 132 Copynumber: 4.8 Consensus size: 133
56262970 GTAGATCAGT
* * * * * *
56262980 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATCGAAG-ATGCAGATCTTGTCT
1 GAAGATAGCAGATCTTGTCTTCCTATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCT
*** * * * * * ** * * *
56263043 TCCCATATTGGTGGCGGAGTATG-TCGAAGAAAGTAGATATTGTCTTCATTTATTGG-CGTGAAG
66 TCATGTATTGG-CGTGAAGTA-GATCGAAGATAGCAGATCCTGTCTTCCTATATTGGTAG-GAAG
*
56263106 TAGATC
128 TGGATC
* * * * * * *
56263112 GAAGATAGCAGGTCCTGTCTTCTTATATTGGTAG-GAAGTGGATCGAAG-ATGCAGATCTTGTCT
1 GAAGATAGCAGATCTTGTCTTCCTATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCT
56263175 TCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTG
66 TCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATATTGGTAG-GAAGTG
56263240 GATC
130 GATC
56263244 GAAGAT-GCAGATCTTGTCTTCCTATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCT
1 GAAGATAGCAGATCTTGTCTTCCTATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCT
* * * * * *
56263308 TCATGTATTGGCGTGAAGTAGATCAAAGATAGTAGGTCATGACTTCCTATATTAGTAGGAAGTGG
66 TCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATATTGGTAGGAAGTGG
56263373 ATC
131 ATC
* * *
56263376 GAAGAT-GCAGATCTTATCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGTAGATCTTGTCT
1 GAAGATAGCAGATCTTGTCTTCCTATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCT
* *
56263440 TCATGTATTGGCGTGAAGTAGATCGAAAATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGG
66 TCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATATTGGTAGGAAGTGG
56263505 ATC
131 ATC
* *
56263508 GAAGATA-CAGATCTTGCCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCT
1 GAAGATAGCAGATCTTGTCTTCCTATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCT
* *
56263572 TCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGCCTTCCT
66 TCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCT
56263620 GTACCGACAG
Statistics
Matches: 458, Mismatches: 45, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
130 1 0.00
131 55 0.12
132 336 0.73
133 66 0.14
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (133 bp):
GAAGATAGCAGATCTTGTCTTCCTATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCT
TCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATATTGGTAGGAAGTGG
ATC
Found at i:56263964 original size:132 final size:132
Alignment explanation
Indices: 56263721--56264087 Score: 504
Period size: 132 Copynumber: 2.8 Consensus size: 132
56263711 CCGATATTGA
* * * * *
56263721 AGCAGATCGAAGATGACGAATTTTACCTCCCTATGGCTACAGTGGAGTACATTGAAGCCAGCAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* ** * * *
56263786 TCTACTTCCTTAAACAACAGTGGAATAGATTGAAGATTTTAGATCTTATCTCCCTAAGTAGTAGT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAAATCTTATCTCCCTAAGCAGTAGT
56263851 GG
131 GG
* * * *
56263853 AGCATATCGAAGATGGCGGATTTTACCTCCCTGTAGTTATAGTAGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
56263918 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAAATCTTATCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAAATCTTATCTCCCTAAGCAGTAGT
56263983 GG
131 GG
* * *
56263985 AGCAGAACGAAGATGGCGGATTTTACATCCCTGTGGTTACAGTGGAATACATTGAAGCCAGTAA-
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * * *
56264049 TCATA-TCTCCCTGGTCAGCAGTGGAATAGGTTCAAGATT
66 TC-TACT-TCCCTGGACAACAGTGGAATAGATTGAAGATT
56264088 GTAAGTCCTA
Statistics
Matches: 207, Mismatches: 26, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
131 3 0.01
132 204 0.99
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (132 bp):
AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAAATCTTATCTCCCTAAGCAGTAGT
GG
Found at i:56264358 original size:19 final size:19
Alignment explanation
Indices: 56264334--56264408 Score: 105
Period size: 19 Copynumber: 3.8 Consensus size: 19
56264324 AATCTTCGAG
56264334 GATATGCAATCTTAGATAA
1 GATATGCAATCTTAGATAA
56264353 GATATGCAATCTTAGATATGA
1 GATATGCAATCTTAGATA--A
* *
56264374 TATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAA
*
56264393 GATATGTAATCTTAGA
1 GATATGCAATCTTAGA
56264409 AGATATGATT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
19 32 0.64
21 18 0.36
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAA
Found at i:56264380 original size:21 final size:21
Alignment explanation
Indices: 56264335--56264397 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
56264325 ATCTTCGAGG
*
56264335 ATATGCAATCTTAGATA--AG
1 ATATGCAATCTTAGATATGAT
56264354 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
56264375 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
56264396 AT
1 AT
56264398 GTAATCTTAG
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
19 17 0.41
21 24 0.59
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.37
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:56264427 original size:23 final size:22
Alignment explanation
Indices: 56264347--56264431 Score: 72
Period size: 21 Copynumber: 4.0 Consensus size: 22
56264337 ATGCAATCTT
* *
56264347 AGATAAGATATGCAATCTTAG-
1 AGATATGATATGTAATCTTAGA
* *
56264368 ATATGAT-ATATGCAATCTT---
1 AGAT-ATGATATGTAATCTTAGA
56264387 AGATATGATATGTAATCTTAGA
1 AGATATGATATGTAATCTTAGA
*
56264409 AGATATGATTTTGTAATCTTAGA
1 AGATATGA-TATGTAATCTTAGA
56264432 GATTTAATTT
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
18 2 0.04
19 14 0.26
21 15 0.28
22 9 0.17
23 13 0.25
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.38
Consensus pattern (22 bp):
AGATATGATATGTAATCTTAGA
Found at i:56264444 original size:21 final size:23
Alignment explanation
Indices: 56264387--56264445 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
56264377 ATGCAATCTT
*
56264387 AGATATG-ATATGTAATCTTAGA
1 AGATATGAATTTGTAATCTTAGA
*
56264409 AGATATGATTTTGTAATCTTAG-
1 AGATATGAATTTGTAATCTTAGA
*
56264431 AGAT-TTAATTTGTAA
1 AGATATGAATTTGTAA
56264446 ATACCCTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 9 0.28
22 11 0.34
23 12 0.38
ACGTcount: A:0.37, C:0.03, G:0.17, T:0.42
Consensus pattern (23 bp):
AGATATGAATTTGTAATCTTAGA
Found at i:56265038 original size:22 final size:23
Alignment explanation
Indices: 56265013--56265055 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
56265003 TAATTATTTT
56265013 TATATGTA-ATTATTT-TTTTATC
1 TATATGTATA-TATTTATTTTATC
56265035 TATATGTATATATTTATTTTA
1 TATATGTATATATTTATTTTA
56265056 GTATACATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (23 bp):
TATATGTATATATTTATTTTATC
Found at i:56265060 original size:22 final size:21
Alignment explanation
Indices: 56264949--56265060 Score: 58
Period size: 22 Copynumber: 5.3 Consensus size: 21
56264939 TTAAAAAATA
56264949 TATATATGTATATATATT-TTT
1 TATATATGTATATAT-TTATTT
* * *
56264970 CATATACG--CATATTTATTT
1 TATATATGTATATATTTATTT
* *
56264989 TTTGTA-GTATAATATAATTATTT
1 TATATATGTAT-ATAT--TTATTT
56265012 T-TATATGTA-ATTATTT-TTT
1 TATATATGTATA-TATTTATTT
56265031 TATCTATATGTATATATTTATTT
1 TA--TATATGTATATATTTATTT
56265054 TAGTATA
1 TA-TATA
56265061 CATATGTATG
Statistics
Matches: 69, Mismatches: 9, Indels: 25
0.67 0.09 0.24
Matches are distributed among these distances:
18 3 0.04
19 14 0.20
20 2 0.03
21 11 0.16
22 23 0.33
23 16 0.23
ACGTcount: A:0.32, C:0.04, G:0.06, T:0.58
Consensus pattern (21 bp):
TATATATGTATATATTTATTT
Found at i:56267008 original size:20 final size:20
Alignment explanation
Indices: 56266960--56267018 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 20
56266950 ATAAGAAAAT
* *
56266960 AAAATAAAAATAGATTCAA-
1 AAAATAAAAATAAATTTAAG
*
56266979 AAACACAAAAATAAATTTAAG
1 AAA-ATAAAAATAAATTTAAG
*
56267000 AAAAT-AAAATAATTTTAAG
1 AAAATAAAAATAAATTTAAG
56267019 CTTAGCCTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
19 16 0.48
20 14 0.42
21 3 0.09
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (20 bp):
AAAATAAAAATAAATTTAAG
Found at i:56267860 original size:13 final size:13
Alignment explanation
Indices: 56267842--56267897 Score: 82
Period size: 13 Copynumber: 4.5 Consensus size: 13
56267832 AAGATTTTTC
56267842 CTAAATATTATCA
1 CTAAATATTATCA
*
56267855 CTAAATA--AT-T
1 CTAAATATTATCA
56267865 CTAAATATTATCA
1 CTAAATATTATCA
56267878 CTAAATATTATCA
1 CTAAATATTATCA
56267891 CTAAATA
1 CTAAATA
56267898 ATTTTAAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
10 7 0.18
11 2 0.05
12 2 0.05
13 27 0.71
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:56268254 original size:18 final size:16
Alignment explanation
Indices: 56268208--56268255 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
56268198 TTGCTATCAC
** *
56268208 ATATTTAATGTAAGTA
1 ATATTTAAAATAAATA
56268224 ATATTTAAAATAAATA
1 ATATTTAAAATAAATA
56268240 ATATTTTATAAATAAA
1 ATA-TTTA-AAATAAA
56268256 AAGTTAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 16 0.59
17 4 0.15
18 7 0.26
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (16 bp):
ATATTTAAAATAAATA
Found at i:56270082 original size:19 final size:18
Alignment explanation
Indices: 56270060--56270109 Score: 82
Period size: 19 Copynumber: 2.7 Consensus size: 18
56270050 TATAAATGAT
56270060 AATAATAATAATAATAATA
1 AATAATAATAATAAT-ATA
56270079 AATAATAATAATAATATA
1 AATAATAATAATAATATA
56270097 ATATAATAATAAT
1 A-ATAATAATAAT
56270110 GTAAAAACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.13
19 26 0.87
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AATAATAATAATAATATA
Found at i:56270124 original size:3 final size:3
Alignment explanation
Indices: 56270058--56270109 Score: 81
Period size: 3 Copynumber: 17.7 Consensus size: 3
56270048 AATATAAATG
56270058 ATA ATA ATA ATA ATA ATA ATAA ATA ATA ATA ATA AT- ATA AT- ATA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA
56270102 ATA ATA AT
1 ATA ATA AT
56270110 GTAAAAACTA
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.09
3 39 0.85
4 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:56270712 original size:21 final size:21
Alignment explanation
Indices: 56270688--56270735 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
56270678 TATTTCACAA
56270688 AATAAATAAAAA-GAAAAAAAG
1 AATAAATAAAAATG-AAAAAAG
* *
56270709 AATAAGTAAAAATGAAAATAG
1 AATAAATAAAAATGAAAAAAG
56270730 AATAAA
1 AATAAA
56270736 CGCGATTAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.75, C:0.00, G:0.10, T:0.15
Consensus pattern (21 bp):
AATAAATAAAAATGAAAAAAG
Found at i:56271838 original size:44 final size:44
Alignment explanation
Indices: 56271772--56272659 Score: 226
Period size: 44 Copynumber: 20.2 Consensus size: 44
56271762 TTGTAACCTC
* * ** *
56271772 AGGGAGGTAAAATCTGCCATCTTCGATCTACTCCACTACTGCCTT
1 AGGGAGATAAGATCTGTAATCTTCAATCTACTCCACTACTGCC-T
* *
56271817 A-GGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCT
1 AGGGAGATAAGATCTGTAATCTTCAATCTACTCCACTACTGCCT
* * * * *
56271860 AGGGAGAT-AGA-AT-TACTGGCTTCAATGTACTCCACT-GTAACCT
1 AGGGAGATAAGATCTGTAAT--CTTCAATCTACTCCACTACT-GCCT
* * * * *
56271903 CAGGGAGGTGAA-ATCCGTCATCATT-GATCTGCTCCACTACTGCCT
1 -AGGGAGAT-AAGATCTGTAATC-TTCAATCTACTCCACTACTGCCT
* * *
56271948 AGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCC
1 AGGGAGATAAGATCTGTAATCTTCAATCTACTCCACTACTGCCT
* * * * * *
56271992 AGGGAGAT-AGA-AT-TACTGGGTTCAATGTACTCCACT-GTAACCT
1 AGGGAGATAAGATCTGTAAT--CTTCAATCTACTCCACTACT-GCCT
* * * ** * * * *
56272035 CAGGGAGGTAAAATCCGCCATCCTT-GATCTGCTCCACTACTTCTT
1 -AGGGAGATAAGATCTGTAAT-CTTCAATCTACTCCACTACTGCCT
* * * *
56272080 AGGGAGATAAGATTTGTAATCTTCAATCTATTCCACTGCTGCCC
1 AGGGAGATAAGATCTGTAATCTTCAATCTACTCCACTACTGCCT
* * * * * * *
56272124 AGGGAGAT-AGA-AT-TACTGGCTTCAATGTCCTCCACT-GTAACATT
1 AGGGAGATAAGATCTGTAAT--CTTCAATCTACTCCACTACT-GC-CT
** * * * * * * *
56272168 ATAGAGGTAAAATCTGTCATCCTT-GATATGCTCCACTACT-CTT
1 AGGGAGATAAGATCTGTAAT-CTTCAATCTACTCCACTACTGCCT
* * * ** *
56272211 AGGGAGATAAGATCTGTAATCTTAAATATATTCCACTGTTGCCC
1 AGGGAGATAAGATCTGTAATCTTCAATCTACTCCACTACTGCCT
* * * *
56272255 AGGAAGAT-AGAATTACTG--GT-TTCAATGTACTCCACTA-TAACCT
1 AGGGAGATAAG-A-T-CTGTAATCTTCAATCTACTCCACTACT-GCCT
* * * * * *
56272298 CAGGGAGGTAAAATCTGCT-ATCCTT-GATCTGCTCCACTATTGCTT
1 -AGGGAGATAAGATCTG-TAAT-CTTCAATCTACTCCACTACTGCCT
* * * *
56272343 AGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTACCC
1 AGGGAGATAAGATCTGTAATCTTCAATCTACTCCACTACTGCCT
* * * * * * *
56272387 AGGGAGAT-AGA-AT-TACTGGCTTCAATGTATTCTACT-GTAACCT
1 AGGGAGATAAGATCTGTAAT--CTTCAATCTACTCCACTACT-GCCT
* * * * * * * *
56272430 CAGGGAGGTAAAATATGTCATCCTT-GATATGCTCCACTACTGCTT
1 -AGGGAGATAAGATCTGTAAT-CTTCAATCTACTCCACTACTGCCT
* *
56272475 AGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCT
1 AGGGAGATAAGATCTGTAATCTTCAATCTACTCCACTACTGCCT
* * * * *
56272519 AGGGAGAT-AGA-AT-TACTGGCTTCAATGTACTCCACT-GTAACCT
1 AGGGAGATAAGATCTGTAAT--CTTCAATCTACTCCACTACT-GCCT
* * * * * * * * * *
56272562 CAAGGAGGTAAAATCCGTCATCCTT-GATCTGCTCTACTATTGCTT
1 -AGGGAGATAAGATCTGTAAT-CTTCAATCTACTCCACTACTGCCT
* * *
56272607 AGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCA
1 AGGGAGATAAGATCTGTAATCTTCAATCTACTCCACTACTGCCT
*
56272651 AAGGAGATA
1 AGGGAGATA
56272660 GAATTACTGG
Statistics
Matches: 589, Mismatches: 191, Indels: 127
0.65 0.21 0.14
Matches are distributed among these distances:
41 15 0.03
42 17 0.03
43 165 0.28
44 273 0.46
45 82 0.14
46 28 0.05
47 9 0.02
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (44 bp):
AGGGAGATAAGATCTGTAATCTTCAATCTACTCCACTACTGCCT
Found at i:56271891 original size:132 final size:132
Alignment explanation
Indices: 56271703--56272747 Score: 1603
Period size: 132 Copynumber: 7.9 Consensus size: 132
56271693 AGATCTTCTT
* * * * * *
56271703 TCTTCGATCGATTCCACTGCCGACC-GGAGAGATAGAATTACTGGCTTCAATATACTCCATTGTA
1 TCTTCAATCTATTCCACTGCTGCCCAGG-GAGATAGAATTACTGGCTTCAATGTACTCCACTGTA
* *
56271767 ACCTCAGGGAGGTAAAATCTGCCAT-CTTCGATCTACTCCACTACTGCCTTA-GGAGATAAGATC
65 ACCTCAGGGAGGTAAAATCCGCCATCCTT-GATCTGCTCCACTACTG-CTTAGGGAGATAAGATC
56271830 TGTAA
128 TGTAA
*
56271835 TCTTCAATCTATTCCACTGCTGCCTAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
* * * *
56271900 CCTCAGGGAGGTGAAATCCGTCATCATTGATCTGCTCCACTACTGCCTAGGGAGATAAGATCTGT
66 CCTCAGGGAGGTAAAATCCGCCATCCTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
56271965 AA
131 AA
*
56271967 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGGTTCAATGTACTCCACTGTAA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
* *
56272032 CCTCAGGGAGGTAAAATCCGCCATCCTTGATCTGCTCCACTACTTCTTAGGGAGATAAGATTTGT
66 CCTCAGGGAGGTAAAATCCGCCATCCTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
56272097 AA
131 AA
*
56272099 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTCCTCCACTGTAA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
* * ** * * *
56272164 CATTATAGAGGTAAAATCTGTCATCCTTGATATGCTCCACTACT-CTTAGGGAGATAAGATCTGT
66 CCTCAGGGAGGTAAAATCCGCCATCCTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
56272228 AA
131 AA
* * * * * *
56272230 TCTTAAATATATTCCACTGTTGCCCAGGAAGATAGAATTACTGGTTTCAATGTACTCCACTATAA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
* * *
56272295 CCTCAGGGAGGTAAAATCTGCTATCCTTGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGT
66 CCTCAGGGAGGTAAAATCCGCCATCCTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
56272360 AA
131 AA
* * *
56272362 TCTTCAATCTATTCCACTGCTACCCAGGGAGATAGAATTACTGGCTTCAATGTATTCTACTGTAA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
** * *
56272427 CCTCAGGGAGGTAAAATATGTCATCCTTGATATGCTCCACTACTGCTTAGGGAGATAAGATCTGT
66 CCTCAGGGAGGTAAAATCCGCCATCCTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
56272492 AA
131 AA
*
56272494 TCTTCAATCTATTCCACTGCTGCCTAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
* * * *
56272559 CCTCAAGGAGGTAAAATCCGTCATCCTTGATCTGCTCTACTATTGCTTAGGGAGATAAGATCTGT
66 CCTCAGGGAGGTAAAATCCGCCATCCTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
56272624 AA
131 AA
* *
56272626 TCTTCAATCTATTCCACTGCTGCCAAAGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
*
56272691 CCTCAGGGAGGTAAAATCCGCCATCCTTGATCTGCTCCACTACTGCTTATGGAGATA
66 CCTCAGGGAGGTAAAATCCGCCATCCTTGATCTGCTCCACTACTGCTTAGGGAGATA
56272748 GAATTACTGG
Statistics
Matches: 832, Mismatches: 77, Indels: 8
0.91 0.08 0.01
Matches are distributed among these distances:
131 118 0.14
132 710 0.85
133 4 0.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (132 bp):
TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
CCTCAGGGAGGTAAAATCCGCCATCCTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
AA
Found at i:56272435 original size:88 final size:89
Alignment explanation
Indices: 56272343--56272819 Score: 232
Period size: 88 Copynumber: 5.4 Consensus size: 89
56272333 ACTATTGCTT
* * *
56272343 AGGGAGATAAGATCTGTAAT-CTTCAATCTATTCCACTGCTACCCAGGGAGATAGAATTACTGGC
1 AGGGAGATAAGATCTGTAATCCTTCAATCTACTCCACTGCTGCCCAAGGAGATAGAATTACTGGC
*
56272407 TTCAATGTATTCTACTGTAACCTC
66 TTCAATGTATTCCACTGTAACCTC
* * * * * * * * ** * * *
56272431 AGGGAGGTAAAATATGTCATCCTT-GATATGCTCCACTACTGCTTAGGGAGATAAGATCTGTAAT
1 AGGGAGATAAGATCTGTAATCCTTCAATCTACTCCACTGCTGCCCAAGGAGAT-AGA-AT-TACT
* *
56272495 --CTTCAATCTATTCCACTGCT-GCCT-
63 GGCTTCAATGTATTCCACTG-TAACCTC
* * * * * * * *
56272519 AGGGAGAT-AGA-AT-TACTGGCTTCAATGTACTCCACTG-TAACCTCAAGGAGGTA-AAAT-CC
1 AGGGAGATAAGATCTGTAAT-CCTTCAATCTACTCCACTGCT-GCC-CAAGGAGATAGAATTACT
* * ** * ** *
56272578 GTCATCCTTG-ATCTGCTCTACTAT-TGCTT
63 GGCTTCAATGTAT-T-C-C-ACTGTAACCTC
* *
56272607 AGGGAGATAAGATCTGTAAT-CTTCAATCTATTCCACTGCTGCCAAAGGAGATAGAATTACTGGC
1 AGGGAGATAAGATCTGTAATCCTTCAATCTACTCCACTGCTGCCCAAGGAGATAGAATTACTGGC
*
56272671 TTCAATGTACTCCACTGTAACCTC
66 TTCAATGTATTCCACTGTAACCTC
* * * ** * * * ** *
56272695 AGGGAGGTAAAATCCGCCATCCTT-GATCTGCTCCACTACTGCTTATGGAGATAGAATTACTGGC
1 AGGGAGATAAGATCTGTAATCCTTCAATCTACTCCACTGCTGCCCAAGGAGATAGAATTACTGGC
*
56272759 TTCAATGTACTCCACTGTAACCTC
66 TTCAATGTATTCCACTGTAACCTC
* * * * * *
56272783 AGGGAGGTAAAATCCGTCATCCTT-GATCTGCTCCACT
1 AGGGAGATAAGATCTGTAATCCTTCAATCTACTCCACT
56272820 ACTGTCTAGG
Statistics
Matches: 291, Mismatches: 73, Indels: 50
0.70 0.18 0.12
Matches are distributed among these distances:
84 3 0.01
85 7 0.02
86 8 0.03
87 22 0.08
88 179 0.62
89 53 0.18
90 12 0.04
91 7 0.02
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (89 bp):
AGGGAGATAAGATCTGTAATCCTTCAATCTACTCCACTGCTGCCCAAGGAGATAGAATTACTGGC
TTCAATGTATTCCACTGTAACCTC
Found at i:56272543 original size:43 final size:43
Alignment explanation
Indices: 56272363--56272555 Score: 117
Period size: 43 Copynumber: 4.4 Consensus size: 43
56272353 GATCTGTAAT
*
56272363 CTTCAATCTATTCCACTGCTACCCAGGGAGATAGAATTACTGG
1 CTTCAATCTATTCCACTGCTACCTAGGGAGATAGAATTACTGG
* * * * *
56272406 CTTCAATGTATTCTACTG-TAACCTCAGGGAGGTA-AAATA-TGT
1 CTTCAATCTATTCCACTGCT-ACCT-AGGGAGATAGAATTACTGG
* ** * * * * * *
56272448 CATCCTTGATATGCTCCACTACTGCTTAGGGAGATAAGATCTGTAAT--
1 CTTCAAT-CTAT--TCCACTGCTACCTAGGGAGAT-AGA-AT-TACTGG
*
56272495 CTTCAATCTATTCCACTGCTGCCTAGGGAGATAGAATTACTGG
1 CTTCAATCTATTCCACTGCTACCTAGGGAGATAGAATTACTGG
* *
56272538 CTTCAATGTACTCCACTG
1 CTTCAATCTATTCCACTG
56272556 TAACCTCAAG
Statistics
Matches: 110, Mismatches: 27, Indels: 26
0.67 0.17 0.16
Matches are distributed among these distances:
41 3 0.03
42 8 0.07
43 45 0.41
44 34 0.31
45 8 0.07
46 5 0.05
47 4 0.04
48 2 0.02
49 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (43 bp):
CTTCAATCTATTCCACTGCTACCTAGGGAGATAGAATTACTGG
Found at i:56272686 original size:527 final size:528
Alignment explanation
Indices: 56271732--56272747 Score: 1671
Period size: 527 Copynumber: 1.9 Consensus size: 528
56271722 CCGACCGGAG
* *
56271732 AGATAGAATTACTGGCTTCAATATACTCCATTGTAACCTCAGGGAGGTAAAATCTGCCATCTTCG
1 AGATAGAATTACTGGCTTCAATATACTCCACTATAACCTCAGGGAGGTAAAATCTGCCATCTTCG
* *
56271797 ATCTACTCCACTACTGCCTTAGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCTAG
66 ATCTACTCCACTACTGCCTTAGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTACCCAG
* *
56271862 GGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTGAAATCCGTCATCAT
131 GGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATACGTCATCAT
*
56271927 TGATCTGCTCCACTACTGCCTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCC
196 TGATATGCTCCACTACTGCCTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCC
* *
56271992 AGGGAGATAGAATTACTGGGTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATC
261 AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAAGGAGGTAAAATCCGCCATC
*
56272057 CTTGATCTGCTCCACTACTTCTTAGGGAGATAAGATTTGTAATCTTCAATCTATTCCACTGCTGC
326 CTTGATCTGCTCCACTACTTCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGC
* * * * * * *
56272122 CCAGGGAGATAGAATTACTGGCTTCAATGTCCTCCACTGTAACATTATAGAGGTAAAATCTGTCA
391 CAAAGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACATCAGAGAGGTAAAATCCGCCA
56272187 TCCTTGATATGCTCCACTACT-CTTAGGGAGATAAGATCTGTAATCTTAAATATATTCCACTGTT
456 TCCTTGATATGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTAAATATATTCCACTGTT
56272251 GCCCAGGA
521 GCCCAGGA
* * *
56272259 AGATAGAATTACTGGTTTCAATGTACTCCACTATAACCTCAGGGAGGTAAAATCTGCTATCCTT-
1 AGATAGAATTACTGGCTTCAATATACTCCACTATAACCTCAGGGAGGTAAAATCTGCCAT-CTTC
* *
56272323 GATCTGCTCCACTATTG-CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTACCC
65 GATCTACTCCACTACTGCCTTA-GGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTACCC
* * *
56272387 AGGGAGATAGAATTACTGGCTTCAATGTATTCTACTGTAACCTCAGGGAGGTAAAATATGTCATC
129 AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATACGTCATC
* *
56272452 CTTGATATGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGC
194 ATTGATATGCTCCACTACTGCCTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGC
* *
56272517 CTAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAAGGAGGTAAAATCCGTCA
259 CCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAAGGAGGTAAAATCCGCCA
*
56272582 TCCTTGATCTGCTCTACTA-TTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGC
324 TCCTTGATCTGCTCCACTACTT-CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGC
* *
56272646 TGCCAAAGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCG
388 TGCCAAAGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACATCAGAGAGGTAAAATCCG
* *
56272711 CCATCCTTGATCTGCTCCACTACTGCTTATGGAGATA
453 CCATCCTTGATATGCTCCACTACTGCTTAGGGAGATA
56272748 GAATTACTGG
Statistics
Matches: 451, Mismatches: 34, Indels: 7
0.92 0.07 0.01
Matches are distributed among these distances:
526 6 0.01
527 431 0.96
528 14 0.03
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (528 bp):
AGATAGAATTACTGGCTTCAATATACTCCACTATAACCTCAGGGAGGTAAAATCTGCCATCTTCG
ATCTACTCCACTACTGCCTTAGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTACCCAG
GGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATACGTCATCAT
TGATATGCTCCACTACTGCCTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCC
AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAAGGAGGTAAAATCCGCCATC
CTTGATCTGCTCCACTACTTCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGC
CAAAGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACATCAGAGAGGTAAAATCCGCCA
TCCTTGATATGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTAAATATATTCCACTGTT
GCCCAGGA
Found at i:56272820 original size:88 final size:88
Alignment explanation
Indices: 56272653--56272823 Score: 333
Period size: 88 Copynumber: 1.9 Consensus size: 88
56272643 TGCTGCCAAA
56272653 GGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCCT
1 GGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCCT
56272718 TGATCTGCTCCACTACTGCTTAT
66 TGATCTGCTCCACTACTGCTTAT
*
56272741 GGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGTCATCCT
1 GGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCCT
56272806 TGATCTGCTCCACTACTG
66 TGATCTGCTCCACTACTG
56272824 TCTAGGGAGA
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 82 1.00
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (88 bp):
GGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCCT
TGATCTGCTCCACTACTGCTTAT
Found at i:56272884 original size:44 final size:44
Alignment explanation
Indices: 56272835--56272975 Score: 149
Period size: 44 Copynumber: 3.2 Consensus size: 44
56272825 CTAGGGAGAT
* *
56272835 AAGATCTGTTGTCCCTGATCTACTTCACGCCAATACATGAAGAC
1 AAGATCTGTTATCCTTGATCTACTTCACGCCAATACATGAAGAC
* * * * * ***
56272879 AAGATCTGTTTTCTTTGATCTACTTCGCCACCAGTATGGGAAGAC
1 AAGATCTGTTATCCTTGATCTACTTC-ACGCCAATACATGAAGAC
* *
56272924 AAGATCTGCTAT-CTTCGATCTACTTCATGCCAATACATGAAGAC
1 AAGATCTGTTATCCTT-GATCTACTTCACGCCAATACATGAAGAC
56272968 AAGATCTG
1 AAGATCTG
56272976 CTTTCTTCCT
Statistics
Matches: 76, Mismatches: 19, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
44 44 0.58
45 32 0.42
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (44 bp):
AAGATCTGTTATCCTTGATCTACTTCACGCCAATACATGAAGAC
Found at i:56272976 original size:44 final size:43
Alignment explanation
Indices: 56272851--56272983 Score: 160
Period size: 44 Copynumber: 3.0 Consensus size: 43
56272841 TGTTGTCCCT
* *
56272851 GATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTT
1 GATCTACTTCA-GCCAATACATGAAGACAAGATCTGCTTTCTTC
*** *
56272895 GATCTACTTC-GCCACCAGTATGGGAAGACAAGATCTGCTATCTTC
1 GATCTACTTCAGCCA--A-TACATGAAGACAAGATCTGCTTTCTTC
56272940 GATCTACTTCATGCCAATACATGAAGACAAGATCTGCTTTCTTC
1 GATCTACTTCA-GCCAATACATGAAGACAAGATCTGCTTTCTTC
56272984 CTAGCTTACT
Statistics
Matches: 74, Mismatches: 10, Indels: 10
0.79 0.11 0.11
Matches are distributed among these distances:
42 4 0.05
44 34 0.46
45 32 0.43
47 4 0.05
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.31
Consensus pattern (43 bp):
GATCTACTTCAGCCAATACATGAAGACAAGATCTGCTTTCTTC
Found at i:56273882 original size:13 final size:13
Alignment explanation
Indices: 56273864--56273888 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56273854 AAATTGTCGA
56273864 GGATAATAAAGAT
1 GGATAATAAAGAT
56273877 GGATAATAAAGA
1 GGATAATAAAGA
56273889 AATTGATTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.24, T:0.20
Consensus pattern (13 bp):
GGATAATAAAGAT
Found at i:56275252 original size:18 final size:18
Alignment explanation
Indices: 56275226--56275267 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
56275216 TAGTTTGGCA
*
56275226 GAAAAAATC-TAAGAGAAT
1 GAAAGAATCGTAA-AGAAT
56275244 GAAAGAATCGTAAAGAAT
1 GAAAGAATCGTAAAGAAT
56275262 GAAAGA
1 GAAAGA
56275268 GCATTTGCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.60, C:0.05, G:0.21, T:0.14
Consensus pattern (18 bp):
GAAAGAATCGTAAAGAAT
Found at i:56277217 original size:13 final size:13
Alignment explanation
Indices: 56277199--56277223 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56277189 GTTCAATTTT
56277199 TTTACTAGAAAAC
1 TTTACTAGAAAAC
56277212 TTTACTAGAAAA
1 TTTACTAGAAAA
56277224 TAAATCTCTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.12, G:0.08, T:0.32
Consensus pattern (13 bp):
TTTACTAGAAAAC
Found at i:56279843 original size:19 final size:20
Alignment explanation
Indices: 56279819--56279857 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
56279809 ATTATTTCAC
56279819 AAAATAAATAAAAA-GAAAA
1 AAAATAAATAAAAATGAAAA
*
56279838 AAAATAAGTAAAAATGAAAA
1 AAAATAAATAAAAATGAAAA
56279858 TAGAATAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.79, C:0.00, G:0.08, T:0.13
Consensus pattern (20 bp):
AAAATAAATAAAAATGAAAA
Found at i:56293785 original size:48 final size:48
Alignment explanation
Indices: 56293729--56293822 Score: 152
Period size: 48 Copynumber: 2.0 Consensus size: 48
56293719 CTTGTATATG
*
56293729 AGTTATGTCTATACTTGATCATAACTTTTTATAAATAAATACATTATA
1 AGTTATGTCCATACTTGATCATAACTTTTTATAAATAAATACATTATA
* * *
56293777 AGTTATGTCCATACTTGGTCGTAACTTTTTATAAATAAATATATTA
1 AGTTATGTCCATACTTGATCATAACTTTTTATAAATAAATACATTA
56293823 AAACACTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.44
Consensus pattern (48 bp):
AGTTATGTCCATACTTGATCATAACTTTTTATAAATAAATACATTATA
Found at i:56294693 original size:25 final size:25
Alignment explanation
Indices: 56294663--56294712 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
56294653 TATTATGTTG
56294663 ATATTATTTTCTTTTCTTTTTCTTT
1 ATATTATTTTCTTTTCTTTTTCTTT
56294688 ATATTATTTTCTTTTCTTTTTCTTT
1 ATATTATTTTCTTTTCTTTTTCTTT
56294713 TACTTTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (25 bp):
ATATTATTTTCTTTTCTTTTTCTTT
Found at i:56296188 original size:25 final size:24
Alignment explanation
Indices: 56296160--56296227 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
56296150 ACCAATTCTC
56296160 AGCTCGAGAGAGCTTACCGATATTT
1 AGCTC-AGAGAGCTTACCGATATTT
** * *
56296185 AGCTCACCTGA-CTTACGGTTATTT
1 AGCTCA-GAGAGCTTACCGATATTT
56296209 AGCTCAGAGGAGCTTACCG
1 AGCTCAGA-GAGCTTACCG
56296228 TTTACAGCTC
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
24 20 0.61
25 13 0.39
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.28
Consensus pattern (24 bp):
AGCTCAGAGAGCTTACCGATATTT
Done.