Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A06
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: 115140250
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2234201 characters in sequence are not A, C, G, or T
File 327 of 345
Found at i:109830897 original size:96 final size:97
Alignment explanation
Indices: 109830794--109830968 Score: 248
Period size: 96 Copynumber: 1.8 Consensus size: 97
109830784 CTTAAAATCC
* * ** *
109830794 TAATCTAATTTTTTTAAATTTA-TAATTAATTTACTCAAGTAAC-CTTAAACCCTAATTTATTTG
1 TAATCTAA-TTTTTTAAAATTAGTAATTAATTTAATCAACAAACAC-TAAACCCTAATTTATTTA
109830857 A-TTTTTTCCTTAAAAATCATAAACACTAAACCA
64 ATTTTTTTCCTTAAAAATCATAAACACTAAACCA
* *
109830890 TAATCTAATTTTTTAAAATTAGTAATTAATTTAATTAACAAACACTAAACTCTAATTTATTTAAT
1 TAATCTAATTTTTTAAAATTAGTAATTAATTTAATCAACAAACACTAAACCCTAATTTATTTAAT
109830955 TTTTTTCCTTAAAA
66 TTTTTTCCTTAAAA
109830969 CCCTAAAATT
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
95 12 0.17
96 42 0.61
97 15 0.22
ACGTcount: A:0.41, C:0.13, G:0.02, T:0.45
Consensus pattern (97 bp):
TAATCTAATTTTTTAAAATTAGTAATTAATTTAATCAACAAACACTAAACCCTAATTTATTTAAT
TTTTTTCCTTAAAAATCATAAACACTAAACCA
Found at i:109834896 original size:26 final size:27
Alignment explanation
Indices: 109834867--109834918 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
109834857 CAATTTAAAA
* *
109834867 AAAAGATAAAGCAAA-TTAAAATGAAT
1 AAAACATAAAACAAATTTAAAATGAAT
109834893 AAAACATAAAACAAATTTTAAAATGA
1 AAAACATAAAACAAA-TTTAAAATGA
109834919 TAAGAAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 13 0.59
28 9 0.41
ACGTcount: A:0.65, C:0.06, G:0.08, T:0.21
Consensus pattern (27 bp):
AAAACATAAAACAAATTTAAAATGAAT
Found at i:109835047 original size:26 final size:26
Alignment explanation
Indices: 109835009--109835084 Score: 73
Period size: 26 Copynumber: 2.8 Consensus size: 26
109834999 ATATGTGTAA
* **
109835009 GAAATTTTAAAATAGGTAATATA-GG
1 GAAAGTTTAAAATAAATAATATACGG
*
109835034 CGAAAGTTTGAAATAAATAATATACGG
1 -GAAAGTTTAAAATAAATAATATACGG
*
109835061 GAAAGAGTTTAAAATGAATAATAT
1 G-AA-AGTTTAAAATAAATAATAT
109835085 GTAAAATAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
26 20 0.49
27 4 0.10
28 17 0.41
ACGTcount: A:0.50, C:0.03, G:0.18, T:0.29
Consensus pattern (26 bp):
GAAAGTTTAAAATAAATAATATACGG
Found at i:109835106 original size:26 final size:28
Alignment explanation
Indices: 109835068--109835134 Score: 84
Period size: 26 Copynumber: 2.5 Consensus size: 28
109835058 CGGGAAAGAG
* *
109835068 TTTAAAATGAATAATATGTA-AAAT-AA
1 TTTAAAATAAATAATATATATAAATGAA
* *
109835094 TTTAAGATAAATAATATATATAAATGAG
1 TTTAAAATAAATAATATATATAAATGAA
109835122 TTTAAAATAAATA
1 TTTAAAATAAATA
109835135 TTAAGATTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
26 17 0.50
27 4 0.12
28 13 0.38
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (28 bp):
TTTAAAATAAATAATATATATAAATGAA
Found at i:109835125 original size:28 final size:27
Alignment explanation
Indices: 109835038--109835134 Score: 90
Period size: 28 Copynumber: 3.6 Consensus size: 27
109835028 TATAGGCGAA
* **
109835038 AGTTTGAAATAAATAATATACGGGAAA-G
1 AGTTTAAAATAAATAATATA--TAAAATG
* *
109835066 AGTTTAAAATGAATAATATGTAAAAT-
1 AGTTTAAAATAAATAATATATAAAATG
* *
109835092 AATTTAAGATAAATAATATATATAAATG
1 AGTTTAAAATAAATAATATATA-AAATG
109835120 AGTTTAAAATAAATA
1 AGTTTAAAATAAATA
109835135 TTAAGATTAA
Statistics
Matches: 55, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
26 21 0.38
27 4 0.07
28 30 0.55
ACGTcount: A:0.55, C:0.01, G:0.12, T:0.32
Consensus pattern (27 bp):
AGTTTAAAATAAATAATATATAAAATG
Found at i:109837912 original size:40 final size:41
Alignment explanation
Indices: 109837879--109838046 Score: 234
Period size: 41 Copynumber: 4.1 Consensus size: 41
109837869 GCGTTTGAAA
*
109837879 CAAAACGCCACTAAAAACTGAGCAATAGTGGCGTTTTTATC
1 CAAAACGCCGCTAAAAACTGAGCAATAGTGGCGTTTTTATC
109837920 CAAAACGCCGCTAAAAACTGAGCAATAGTGGCGTTTTTATC
1 CAAAACGCCGCTAAAAACTGAGCAATAGTGGCGTTTTTATC
** * *
109837961 CAAAACATCGCTAAAAACTGAGAAATAGTGGCGTTTTT-TT
1 CAAAACGCCGCTAAAAACTGAGCAATAGTGGCGTTTTTATC
*
109838001 CAAAACGCCGCAAAAAACTGAG-ATATAGTGGCGCTTTTGT-TC
1 CAAAACGCCGCTAAAAACTGAGCA-ATAGTGGCG-TTTT-TATC
109838043 CAAA
1 CAAA
109838047 TGCCACAAAA
Statistics
Matches: 115, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
39 1 0.01
40 29 0.25
41 79 0.69
42 6 0.05
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.25
Consensus pattern (41 bp):
CAAAACGCCGCTAAAAACTGAGCAATAGTGGCGTTTTTATC
Found at i:109838074 original size:81 final size:80
Alignment explanation
Indices: 109837891--109838046 Score: 217
Period size: 81 Copynumber: 1.9 Consensus size: 80
109837881 AAACGCCACT
* *
109837891 AAAAACTGAGCAATAGTGGCGTTTTTATCCAAAACGCCGCTAAAAACTGAGCAATAGTGGCGTTT
1 AAAAACTGAGCAATAGTGGCGTTTTT-TTCAAAACGCCGCAAAAAACTGAGCAATAGTGGCGTTT
*
109837956 TTATCCAAAACATCGCT
65 TTATCC-AAACATCGCC
*
109837973 AAAAACTGAGAAATAGTGGCGTTTTTTTCAAAACGCCGCAAAAAACTGAG-ATATAGTGGCGCTT
1 AAAAACTGAGCAATAGTGGCGTTTTTTTCAAAACGCCGCAAAAAACTGAGCA-ATAGTGGCG-TT
109838037 TTGT-TCCAAA
64 TT-TATCCAAA
109838047 TGCCACAAAA
Statistics
Matches: 68, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
80 1 0.01
81 34 0.50
82 32 0.47
83 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (80 bp):
AAAAACTGAGCAATAGTGGCGTTTTTTTCAAAACGCCGCAAAAAACTGAGCAATAGTGGCGTTTT
TATCCAAACATCGCC
Found at i:109840003 original size:20 final size:20
Alignment explanation
Indices: 109839958--109840009 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
109839948 CCCTACCCAA
*
109839958 ATTTCCCCAAATCCCTAACT
1 ATTTCCCCAAATCCCTAAAT
*
109839978 -TTTCCCCTAATCCCTAAAT
1 ATTTCCCCAAATCCCTAAAT
109839997 ATTTCCCCAAATC
1 ATTTCCCCAAATC
109840010 AAAATCGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.29, C:0.38, G:0.00, T:0.33
Consensus pattern (20 bp):
ATTTCCCCAAATCCCTAAAT
Found at i:109840052 original size:19 final size:19
Alignment explanation
Indices: 109840028--109840064 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
109840018 AATATCCTTC
109840028 TGCCGTTGAAGACTCCGAT
1 TGCCGTTGAAGACTCCGAT
109840047 TGCCGTTGAAGACTCCGA
1 TGCCGTTGAAGACTCCGA
109840065 GTGGACGACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (19 bp):
TGCCGTTGAAGACTCCGAT
Found at i:109841577 original size:14 final size:13
Alignment explanation
Indices: 109841554--109841583 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
109841544 ATTACTATAA
109841554 TAATTATATGAAG
1 TAATTATATGAAG
109841567 TAATATATATGAAG
1 TAAT-TATATGAAG
109841581 TAA
1 TAA
109841584 AATTATATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (13 bp):
TAATTATATGAAG
Found at i:109842657 original size:23 final size:23
Alignment explanation
Indices: 109842627--109842676 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
109842617 AACATTAATC
109842627 AAATGTATGAATTGCAGCCCTTT
1 AAATGTATGAATTGCAGCCCTTT
*
109842650 AAATGTATGAATTGCAGCCTTTT
1 AAATGTATGAATTGCAGCCCTTT
109842673 AAAT
1 AAAT
109842677 AAACTTGAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (23 bp):
AAATGTATGAATTGCAGCCCTTT
Found at i:109843057 original size:9 final size:9
Alignment explanation
Indices: 109843043--109843132 Score: 81
Period size: 9 Copynumber: 9.3 Consensus size: 9
109843033 TAGTTTAAAG
*
109843043 TTACATAAT
1 TTACATAAC
109843052 TTACATAACAAC
1 TTACAT-A--AC
109843064 TTACATAAC
1 TTACATAAC
*
109843073 TCACATAAC
1 TTACATAAC
*
109843082 TTACATAAT
1 TTACATAAC
109843091 TTACATAAC
1 TTACATAAC
*
109843100 TCACATAAC
1 TTACATAAC
*
109843109 GTACATAACAAC
1 TTACAT---AAC
109843121 TTACATAAC
1 TTACATAAC
109843130 TTA
1 TTA
109843133 ACTAATACAT
Statistics
Matches: 66, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
9 49 0.74
10 1 0.02
11 1 0.02
12 15 0.23
ACGTcount: A:0.46, C:0.22, G:0.01, T:0.31
Consensus pattern (9 bp):
TTACATAAC
Found at i:109843102 original size:27 final size:27
Alignment explanation
Indices: 109843064--109843116 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
109843054 ACATAACAAC
*
109843064 TTACATAACTCACATAACTTACATAAT
1 TTACATAACTCACATAACGTACATAAT
109843091 TTACATAACTCACATAACGTACATAA
1 TTACATAACTCACATAACGTACATAA
109843117 CAACTTACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.45, C:0.23, G:0.02, T:0.30
Consensus pattern (27 bp):
TTACATAACTCACATAACGTACATAAT
Found at i:109847856 original size:21 final size:22
Alignment explanation
Indices: 109847832--109847875 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
109847822 TTATGGATTC
109847832 TTTTTAT-TACATTATTT-ATGA
1 TTTTTATCTA-ATTATTTAATGA
*
109847853 TTTTTTTCTAATTATTTAATGA
1 TTTTTATCTAATTATTTAATGA
109847875 T
1 T
109847876 ATTTCAGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.64
Consensus pattern (22 bp):
TTTTTATCTAATTATTTAATGA
Found at i:109848047 original size:14 final size:14
Alignment explanation
Indices: 109848011--109848048 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 14
109848001 AGATTTGAGT
109848011 TTTAGGATTCAAGG
1 TTTAGGATTCAAGG
*
109848025 TTT-GGATTCAATG
1 TTTAGGATTCAAGG
109848038 TTTAGGATTCA
1 TTTAGGATTCA
109848049 GGATTCAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.26, C:0.08, G:0.24, T:0.42
Consensus pattern (14 bp):
TTTAGGATTCAAGG
Found at i:109849838 original size:28 final size:26
Alignment explanation
Indices: 109849797--109849848 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 26
109849787 TCTCGTCTTC
109849797 TTTTTTATTTTA-TTTCTTGTTTTCTG
1 TTTTTTATTTTATTTTC-TGTTTTCTG
109849823 TTTTCTTATTTTTATTTTCTGTTTTC
1 TTTT-TTA-TTTTATTTTCTGTTTTC
109849849 AAATTTGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 4 0.17
27 3 0.13
28 12 0.52
29 4 0.17
ACGTcount: A:0.08, C:0.10, G:0.06, T:0.77
Consensus pattern (26 bp):
TTTTTTATTTTATTTTCTGTTTTCTG
Found at i:109849842 original size:21 final size:22
Alignment explanation
Indices: 109849806--109849848 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
109849796 CTTTTTTATT
*
109849806 TTATTTCTTGTTTTCTGTTTTC
1 TTATTTCTTATTTTCTGTTTTC
109849828 TTATTT-TTATTTTCTGTTTTC
1 TTATTTCTTATTTTCTGTTTTC
109849849 AAATTTGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.07, C:0.12, G:0.07, T:0.74
Consensus pattern (22 bp):
TTATTTCTTATTTTCTGTTTTC
Found at i:109853004 original size:21 final size:21
Alignment explanation
Indices: 109852979--109853080 Score: 100
Period size: 21 Copynumber: 4.8 Consensus size: 21
109852969 ACACATATAT
*
109852979 ATATAAATAATAGTATTAGAA
1 ATATAAATAATAATATTAGAA
109853000 ATATACAAT-ATAATATTAGAA
1 ATATA-AATAATAATATTAGAA
* * *
109853021 ATATATATAATAGTATAAAGAAAA
1 ATATAAATAATAATAT-TAG--AA
*
109853045 ATATAACTAATAATATTA-AA
1 ATATAAATAATAATATTAGAA
*
109853065 ATATATATAATAATAT
1 ATATAAATAATAATAT
109853081 ATGTGAAATA
Statistics
Matches: 66, Mismatches: 10, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
20 18 0.27
21 27 0.41
22 5 0.08
23 1 0.02
24 15 0.23
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (21 bp):
ATATAAATAATAATATTAGAA
Found at i:109853025 original size:42 final size:44
Alignment explanation
Indices: 109852979--109853081 Score: 131
Period size: 44 Copynumber: 2.4 Consensus size: 44
109852969 ACACATATAT
* * *
109852979 ATATAAATAATAGTAT-TAGAAATATACAA-T-ATAATATTAGAA
1 ATATATATAATAGTATAAAGAAAAATACAACTAATAATATTA-AA
*
109853021 ATATATATAATAGTATAAAGAAAAATATAACTAATAATATTAAA
1 ATATATATAATAGTATAAAGAAAAATACAACTAATAATATTAAA
*
109853065 ATATATATAATAATATA
1 ATATATATAATAGTATA
109853082 TGTGAAATAT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
42 15 0.28
43 10 0.19
44 19 0.36
45 9 0.17
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (44 bp):
ATATATATAATAGTATAAAGAAAAATACAACTAATAATATTAAA
Found at i:109853025 original size:44 final size:46
Alignment explanation
Indices: 109852977--109853092 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 46
109852967 ACACACATAT
109852977 ATATATAAATAATAGTAT-TAGAAATATACAA-T-ATAATATTAGAA
1 ATATATAAATAATAGTATATAGAAATATACAACTAATAATATTA-AA
* * *
109853021 ATATAT--ATAATAGTATAAAGAAAAATATAACTAATAATATTAAA
1 ATATATAAATAATAGTATATAGAAATATACAACTAATAATATTAAA
*
109853065 ATATATATAATAATA-TATGT-GAAATATA
1 ATATATA-AATAATAGTATATAGAAATATA
109853093 ATATTAAAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
42 10 0.17
43 10 0.17
44 15 0.25
45 16 0.27
46 3 0.05
47 6 0.10
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34
Consensus pattern (46 bp):
ATATATAAATAATAGTATATAGAAATATACAACTAATAATATTAAA
Found at i:109853030 original size:18 final size:19
Alignment explanation
Indices: 109852992--109853096 Score: 61
Period size: 20 Copynumber: 4.9 Consensus size: 19
109852982 TAAATAATAG
109852992 TATTAGAAATATACAATATAA
1 TATTAGAAATAT--AATATAA
109853013 TATTAGAAATAT-ATATAA
1 TATTAGAAATATAATATAA
109853031 TAGTATAAAGAAAAATATAACTAATAA
1 TA-T-T--AG--AAATATAA-T-ATAA
109853058 TATTA-AAATATATATAATAA
1 TATTAGAAATATA-AT-ATAA
*
109853078 TATATGTGAAATATAATAT
1 TAT-T-AGAAATATAATAT
109853097 TAAAAACTTA
Statistics
Matches: 70, Mismatches: 1, Indels: 26
0.72 0.01 0.27
Matches are distributed among these distances:
18 8 0.11
19 1 0.01
20 17 0.24
21 16 0.23
22 4 0.06
23 8 0.11
24 6 0.09
25 2 0.03
26 2 0.03
27 6 0.09
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.35
Consensus pattern (19 bp):
TATTAGAAATATAATATAA
Found at i:109855377 original size:53 final size:55
Alignment explanation
Indices: 109855287--109855438 Score: 213
Period size: 55 Copynumber: 2.8 Consensus size: 55
109855277 CATATGACCT
* * *
109855287 AAGGCTCAACTCACTTCTCGTAATATGGGTT-ATTTTTTGAAAAAA-A-AAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAAACAGAAATTAA
* *
109855340 AATG-TACAACTCACCTCTCGCAATATGAGTTGCTTTTTGAAAAAACAGAAATTAA
1 AAGGCT-CAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAACAGAAATTAA
109855395 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
109855439 TAAGAATTGG
Statistics
Matches: 87, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
52 1 0.01
53 37 0.43
54 1 0.01
55 47 0.54
56 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (55 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAACAGAAATTAA
Found at i:109855713 original size:72 final size:72
Alignment explanation
Indices: 109855630--109855766 Score: 175
Period size: 72 Copynumber: 1.9 Consensus size: 72
109855620 ACAAGAGAAT
** * * * * *
109855630 TTGAAAATACCTCGGCGTGCCCCGATGCTCAACTTACTTTTCGCAATATGAGTTGATTTTTTGAA
1 TTGAAAATACCTCAACGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCTGAA
109855695 GCATAAA
66 GCATAAA
* * **
109855702 TTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCTGAA
1 TTGAAAATACCTCAACGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCTGAA
109855767 AATATGAATT
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
72 54 1.00
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.34
Consensus pattern (72 bp):
TTGAAAATACCTCAACGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCTGAA
GCATAAA
Found at i:109868344 original size:45 final size:46
Alignment explanation
Indices: 109868295--109868398 Score: 124
Period size: 45 Copynumber: 2.3 Consensus size: 46
109868285 ACATACACAC
** *
109868295 ATATATATAAATAATAGTATTAGAAATATACAA-T-ATAATATTAAA
1 ATATATATAAATAATA-TAAAAGAAAAATACAACTAATAATATTAAA
* *
109868340 ATATATAT-AATAGTATAAAAGAAAAATATAACTAATAATATTAAA
1 ATATATATAAATAATATAAAAGAAAAATACAACTAATAATATTAAA
109868385 ATATATATATAATA
1 ATATATATA-AATA
109868399 TATGTGAAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
43 12 0.24
44 7 0.14
45 27 0.54
47 4 0.08
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (46 bp):
ATATATATAAATAATATAAAAGAAAAATACAACTAATAATATTAAA
Found at i:109868392 original size:47 final size:42
Alignment explanation
Indices: 109868297--109868398 Score: 116
Period size: 41 Copynumber: 2.3 Consensus size: 42
109868287 ATACACACAT
* * *
109868297 ATATATAAATAATAGTATTAGAAATATACAATATAATATTAA
1 ATATATATATAATAGTATAAGAAAAATACAATATAATATTAA
*
109868339 A-ATATATATAATAGTATAAAAGAAAAATATAACTAATAATATTAAA
1 ATATATATATAATAGTAT--AAGAAAAATACAA-T-ATAATATT-AA
109868385 ATATATATATAATA
1 ATATATATATAATA
109868399 TATGTGAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
41 15 0.30
42 1 0.02
43 10 0.20
44 1 0.02
45 8 0.16
46 3 0.06
47 12 0.24
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (42 bp):
ATATATATATAATAGTATAAGAAAAATACAATATAATATTAA
Found at i:109871696 original size:26 final size:26
Alignment explanation
Indices: 109871658--109871715 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
109871648 CATGAAATTC
109871658 TTATCATGAAACATTTAACTAACCCA
1 TTATCATGAAACATTTAACTAACCCA
* * *
109871684 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTAACTAACCCA
109871710 TTATCA
1 TTATCA
109871716 ATTTGTACCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTAACTAACCCA
Found at i:109873839 original size:21 final size:23
Alignment explanation
Indices: 109873788--109873839 Score: 54
Period size: 26 Copynumber: 2.2 Consensus size: 23
109873778 TTCATGTGTA
109873788 ATATTTAATTTAAACTGTTTTAT
1 ATATTTAATTTAAACTGTTTTAT
*
109873811 ATGTTATTTACTTTAAA-T-TTTTAT
1 A---TATTTAATTTAAACTGTTTTAT
109873835 ATATT
1 ATATT
109873840 ATTTATTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
21 4 0.16
23 1 0.04
24 7 0.28
25 1 0.04
26 12 0.48
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.60
Consensus pattern (23 bp):
ATATTTAATTTAAACTGTTTTAT
Found at i:109873861 original size:28 final size:24
Alignment explanation
Indices: 109873789--109873854 Score: 87
Period size: 24 Copynumber: 2.7 Consensus size: 24
109873779 TCATGTGTAA
* *
109873789 TATTTAATTTAAACTGTTTTATATGT
1 TATTTACTTTAAA-T-TTTTATATAT
109873815 TATTTACTTTAAATTTTTATATAT
1 TATTTACTTTAAATTTTTATATAT
*
109873839 TATTTATTTTAAATTT
1 TATTTACTTTAAATTT
109873855 CTTTTTACAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
24 24 0.65
25 1 0.03
26 12 0.32
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (24 bp):
TATTTACTTTAAATTTTTATATAT
Found at i:109873921 original size:22 final size:23
Alignment explanation
Indices: 109873881--109873931 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
109873871 ACTTTGAGCC
* *
109873881 TCTTAATATTTATTTTAAA-TT-
1 TCTTTATATTTATTCTAAACTTG
109873902 TCTTTATATATTATTCTAAACTTG
1 TCTTTATAT-TTATTCTAAACTTG
109873926 TCTTTA
1 TCTTTA
109873932 CGTATATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 8 0.32
22 9 0.36
23 2 0.08
24 6 0.24
ACGTcount: A:0.29, C:0.10, G:0.02, T:0.59
Consensus pattern (23 bp):
TCTTTATATTTATTCTAAACTTG
Found at i:109876738 original size:15 final size:16
Alignment explanation
Indices: 109876718--109876817 Score: 72
Period size: 15 Copynumber: 6.3 Consensus size: 16
109876708 GATAAATAAA
109876718 ATAAAAATAT-ATATG
1 ATAAAAATATAATATG
109876733 ATAAAATGTATATAATAT-
1 ATAAAA---ATATAATATG
*
109876751 ATAAAAATATCATATGG
1 ATAAAAATATAATAT-G
109876768 AGT-AAAATATAATATG
1 A-TAAAAATATAATATG
109876784 -TAATAAA-ATAATATG
1 ATAA-AAATATAATATG
109876799 A-AAACAA-ATAATAT-
1 ATAAA-AATATAATATG
109876813 ATAAA
1 ATAAA
109876818 TATAGTGAAA
Statistics
Matches: 71, Mismatches: 2, Indels: 24
0.73 0.02 0.25
Matches are distributed among these distances:
14 3 0.04
15 37 0.52
16 4 0.06
17 12 0.17
18 11 0.15
19 4 0.06
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.31
Consensus pattern (16 bp):
ATAAAAATATAATATG
Found at i:109876776 original size:17 final size:17
Alignment explanation
Indices: 109876754--109876793 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
109876744 ATAATATATA
* *
109876754 AAAATATCATATGGAGT
1 AAAATATAATATGGAAT
*
109876771 AAAATATAATATGTAAT
1 AAAATATAATATGGAAT
109876788 AAAATA
1 AAAATA
109876794 ATATGAAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.57, C:0.03, G:0.10, T:0.30
Consensus pattern (17 bp):
AAAATATAATATGGAAT
Found at i:109878086 original size:24 final size:22
Alignment explanation
Indices: 109878024--109878086 Score: 56
Period size: 24 Copynumber: 2.7 Consensus size: 22
109878014 GAGGCCACCA
109878024 GCGTTGATTCGGCCGTCGATCACG
1 GCGTTGATTCGG--GTCGATCACG
* *
109878048 GCG-TGATACTAGGTCGGAGTCACG
1 GCGTTGATTC-GGGTC-GA-TCACG
109878072 GCGTTGATTCGGGTC
1 GCGTTGATTCGGGTC
109878087 ACTGCGAGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
22 3 0.10
23 7 0.23
24 16 0.52
25 5 0.16
ACGTcount: A:0.14, C:0.24, G:0.37, T:0.25
Consensus pattern (22 bp):
GCGTTGATTCGGGTCGATCACG
Found at i:109878250 original size:17 final size:17
Alignment explanation
Indices: 109878228--109878260 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
109878218 GTATTCGGGC
109878228 TTGGGT-GTAACCGGGTT
1 TTGGGTAGTAA-CGGGTT
109878245 TTGGGTAGTAACGGGT
1 TTGGGTAGTAACGGGT
109878261 CTGCTGGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.15, C:0.09, G:0.42, T:0.33
Consensus pattern (17 bp):
TTGGGTAGTAACGGGTT
Found at i:109883317 original size:17 final size:18
Alignment explanation
Indices: 109883269--109883316 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
109883259 AAATTTAAAG
109883269 AAATATATAAAAATACAT
1 AAATATATAAAAATACAT
*
109883287 AAATATTTAAAAATACAT
1 AAATATATAAAAATACAT
109883305 ATAATA-ATAAAA
1 A-AATATATAAAA
109883317 TTTAAAATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 23 0.85
19 4 0.15
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATATATAAAAATACAT
Found at i:109888035 original size:33 final size:33
Alignment explanation
Indices: 109887993--109888057 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
109887983 AGAGGATCTT
109887993 AGAATATGAT-ATTTAAAAT-GGAATTTGATTCTG
1 AGAATATGATCA-TTAAAATAGG-ATTTGATTCTG
*
109888026 AGAATATGATCATTAGAATAGGATTTGATTCT
1 AGAATATGATCATTAAAATAGGATTTGATTCT
109888058 TTAATGTTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 26 0.90
34 3 0.10
ACGTcount: A:0.38, C:0.05, G:0.18, T:0.38
Consensus pattern (33 bp):
AGAATATGATCATTAAAATAGGATTTGATTCTG
Found at i:109888095 original size:54 final size:55
Alignment explanation
Indices: 109888004--109888135 Score: 180
Period size: 54 Copynumber: 2.5 Consensus size: 55
109887994 GAATATGATA
* * *
109888004 TTTAA-AA-TGGAATTTGATTCTGAGAATATGATCATTAGAATAGGATTTGATTC
1 TTTAATAATTGGAATTTGATTCTCAGAATATGATAATTAGAATAGAATTTGATTC
** *
109888057 TTTAATGTTTGGAATTTAATTCTCA-AATATGATAATTAGAATAGAATTTGATTC
1 TTTAATAATTGGAATTTGATTCTCAGAATATGATAATTAGAATAGAATTTGATTC
*
109888111 TTTGATAATTGGAATTTGATTCTCA
1 TTTAATAATTGGAATTTGATTCTCA
109888136 TTTAGAATGG
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
53 5 0.07
54 48 0.72
55 14 0.21
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.43
Consensus pattern (55 bp):
TTTAATAATTGGAATTTGATTCTCAGAATATGATAATTAGAATAGAATTTGATTC
Found at i:109888349 original size:3 final size:3
Alignment explanation
Indices: 109888341--109888376 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
109888331 ATTTTAAATA
109888341 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
109888377 CAACCCGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:109888723 original size:26 final size:28
Alignment explanation
Indices: 109888687--109888746 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 28
109888677 TTATTTTAGA
* *
109888687 AAAAATTATATATATATTTTAAATTTTT-T
1 AAAAA-TATATA-AAATTTGAAATTTTTAT
109888716 AAAAATATATAAAATTTGAAATTTTTAT
1 AAAAATATATAAAATTTGAAATTTTTAT
109888744 AAA
1 AAA
109888747 TATTTTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 13 0.46
28 10 0.36
29 5 0.18
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (28 bp):
AAAAATATATAAAATTTGAAATTTTTAT
Found at i:109888741 original size:28 final size:29
Alignment explanation
Indices: 109888687--109888746 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
109888677 TTATTTTAGA
* * *
109888687 AAAAATTATATATATATTTTAAATTTTTT
1 AAAAATTATATATAAATTTGAAATTTTAT
109888716 AAAAA-TATATA-AAATTTGAAATTTTTAT
1 AAAAATTATATATAAATTTGAAA-TTTTAT
109888744 AAA
1 AAA
109888747 TATTTTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 8 0.30
28 14 0.52
29 5 0.19
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (29 bp):
AAAAATTATATATAAATTTGAAATTTTAT
Found at i:109888746 original size:18 final size:19
Alignment explanation
Indices: 109888723--109888760 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
109888713 TTTAAAAATA
109888723 TATAAA-ATTTGAAATTTT
1 TATAAATATTTGAAATTTT
*
109888741 TATAAATATTTTAAATTTT
1 TATAAATATTTGAAATTTT
109888760 T
1 T
109888761 TTGTAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (19 bp):
TATAAATATTTGAAATTTT
Found at i:109896749 original size:21 final size:20
Alignment explanation
Indices: 109896710--109896749 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
109896700 AACTCATTGT
*
109896710 AAATACATTAATTATATTAC
1 AAATACATTAATAATATTAC
*
109896730 AAATGCATTAAATAATATTA
1 AAATACATT-AATAATATTA
109896750 TTGTTTTGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.38
Consensus pattern (20 bp):
AAATACATTAATAATATTAC
Found at i:109897681 original size:68 final size:68
Alignment explanation
Indices: 109897568--109897708 Score: 201
Period size: 68 Copynumber: 2.1 Consensus size: 68
109897558 ACCAAGGTTT
** * * * * *
109897568 ATGTATAGCATTGTGTCACGGGCCACGGATTTCTAACCTCGTGACAATTGCACGTTCAATTAAAG
1 ATGTATAGCATTGTGTCACGGGCCACAAATTTCTAACCCCATGACAATCGCACATTCAATCAAAG
109897633 TTC
66 TTC
*
109897636 ATGTATAGCATTGTGTCATGGGCCACAAATTTCTAACCCCATGACAATCGCACATTCAATCAAAG
1 ATGTATAGCATTGTGTCACGGGCCACAAATTTCTAACCCCATGACAATCGCACATTCAATCAAAG
*
109897701 TTT
66 TTC
109897704 ATGTA
1 ATGTA
109897709 CAGTTTTGAT
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
68 64 1.00
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (68 bp):
ATGTATAGCATTGTGTCACGGGCCACAAATTTCTAACCCCATGACAATCGCACATTCAATCAAAG
TTC
Found at i:109898295 original size:23 final size:23
Alignment explanation
Indices: 109898268--109898312 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
109898258 GTTGATGACG
109898268 TTTTGGAGATAAAAAGTTGAAGA
1 TTTTGGAGATAAAAAGTTGAAGA
109898291 TTTTGGAGATAAAAAGTTGAAG
1 TTTTGGAGATAAAAAGTTGAAG
109898313 TTTACTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.31
Consensus pattern (23 bp):
TTTTGGAGATAAAAAGTTGAAGA
Found at i:109898613 original size:75 final size:75
Alignment explanation
Indices: 109898490--109898640 Score: 284
Period size: 75 Copynumber: 2.0 Consensus size: 75
109898480 TGGCACATGA
109898490 TTACCTATCAAAGGAAATGGTGACCATTTGCCTATGGTAGAATTTGAACTAATAGATCCTTCAAT
1 TTACCTATCAAAGGAAATGGTGACCATTTGCCTATGGTAGAATTTGAACTAATAGATCCTTCAAT
109898555 AAGTTGGCAT
66 AAGTTGGCAT
* *
109898565 TTACCTATCAAAGGAAATGGTGACCATTTGCCTATGGTAGAATTTGAACTAATCGATCCTTTAAT
1 TTACCTATCAAAGGAAATGGTGACCATTTGCCTATGGTAGAATTTGAACTAATAGATCCTTCAAT
109898630 AAGTTGGCAT
66 AAGTTGGCAT
109898640 T
1 T
109898641 GTCCCCATGT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (75 bp):
TTACCTATCAAAGGAAATGGTGACCATTTGCCTATGGTAGAATTTGAACTAATAGATCCTTCAAT
AAGTTGGCAT
Found at i:109899926 original size:75 final size:74
Alignment explanation
Indices: 109899805--109899945 Score: 230
Period size: 75 Copynumber: 1.9 Consensus size: 74
109899795 TAAGCGTGTT
*
109899805 TGTTAAAGAGTTCTATCTTTATTTGAATAATCACTCATTTTAACAAAATTGCAACAAGGAAAAAG
1 TGTTAAAGAGTTCTATCTTTACTTGAATAATCACTCATTTTAACAAAATTGCAACAAGGAAAAAG
109899870 GCGGGCGTG
66 GCGGGCGTG
* *
109899879 TGTTAAA-AGATTCTATTTTTTACTTGAATAATCACTCATTTTTACAAAATTGCAACAAGGAAAA
1 TGTTAAAGAG-TTCTA-TCTTTACTTGAATAATCACTCATTTTAACAAAATTGCAACAAGGAAAA
109899943 AGG
64 AGG
109899946 TTTTAGCTTG
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
73 2 0.03
74 12 0.19
75 48 0.77
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (74 bp):
TGTTAAAGAGTTCTATCTTTACTTGAATAATCACTCATTTTAACAAAATTGCAACAAGGAAAAAG
GCGGGCGTG
Found at i:109900472 original size:107 final size:108
Alignment explanation
Indices: 109900284--109900500 Score: 348
Period size: 107 Copynumber: 2.0 Consensus size: 108
109900274 AATGATCGCA
* **
109900284 AAACAATAAGAAAAGTAAAATAAAACACATAGATTTTATTTGGAAACCCTTTCAGAAAAAAACCA
1 AAACAATAAGAAAAGAAAAATAAAACACA-AGATTTTACGTGGAAACCCTTTCAGAAAAAAACCA
*
109900349 CAAGCAGAGAAGAAGAAATTCACTAATGTTGAAAACTGAATGAT
65 CAAGCAAAGAAGAAGAAATTCACTAATGTTGAAAACTGAATGAT
* *
109900393 AAACAATAAGAAAAGAAAAATAAAACAC-AGATTTTACGTGGAAACCCTTTCGGGAAAAAACCAC
1 AAACAATAAGAAAAGAAAAATAAAACACAAGATTTTACGTGGAAACCCTTTCAGAAAAAAACCAC
109900457 AAGCAAA-AGAGAAGAAATTCACTAATGTTGAAAACTGAATGAT
66 AAGCAAAGA-AGAAGAAATTCACTAATGTTGAAAACTGAATGAT
109900500 A
1 A
109900501 CAAGAGGTGT
Statistics
Matches: 101, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
106 1 0.01
107 73 0.72
109 27 0.27
ACGTcount: A:0.53, C:0.13, G:0.15, T:0.19
Consensus pattern (108 bp):
AAACAATAAGAAAAGAAAAATAAAACACAAGATTTTACGTGGAAACCCTTTCAGAAAAAAACCAC
AAGCAAAGAAGAAGAAATTCACTAATGTTGAAAACTGAATGAT
Found at i:109905059 original size:35 final size:35
Alignment explanation
Indices: 109905012--109905082 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
109905002 TTGTAAATCA
*
109905012 AAAGATGGTTTCTTCTTTTAAATGCAAAGTTATAT
1 AAAGATGATTTCTTCTTTTAAATGCAAAGTTATAT
* * *
109905047 AAAGATGATTTCTTGTTTTAAATTCAAGGTTATAT
1 AAAGATGATTTCTTCTTTTAAATGCAAAGTTATAT
109905082 A
1 A
109905083 TATATATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.44
Consensus pattern (35 bp):
AAAGATGATTTCTTCTTTTAAATGCAAAGTTATAT
Found at i:109906437 original size:2 final size:2
Alignment explanation
Indices: 109906430--109906459 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
109906420 CCCTGAATGA
109906430 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
109906460 TAGTCGTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:109907070 original size:111 final size:110
Alignment explanation
Indices: 109906922--109907142 Score: 370
Period size: 111 Copynumber: 2.0 Consensus size: 110
109906912 GACTATACCA
* *
109906922 ACTATTCCATATTCAACGATCTCTTTGGCAATGTGATCGATGTGTTTAGTCCTCTTAAAATGCCT
1 ACTATTCCATATTCAACAATCTCTTTGACAATGTGATCGATGTGTTTAGTCCTCTTAAAATGCCT
* *
109906987 ACTCTATTGTTTTATATTTTGTCACAATACAATGTAATAACTTTTC
66 ACTCTATTGTTTTAT-TGTTATCACAATACAATGTAATAACTTTTC
* * *
109907033 ACTATTCCATCTTTAACAATCTCTTTGACAATGTGATCGATGTGTTTAGTCCTCTTAAAATGTCT
1 ACTATTCCATATTCAACAATCTCTTTGACAATGTGATCGATGTGTTTAGTCCTCTTAAAATGCCT
109907098 ACTCTATTGTTTTATTGTTATCACAATACAATGTAATAACTTTTC
66 ACTCTATTGTTTTATTGTTATCACAATACAATGTAATAACTTTTC
109907143 TCGTATTAGG
Statistics
Matches: 103, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
110 28 0.27
111 75 0.73
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.43
Consensus pattern (110 bp):
ACTATTCCATATTCAACAATCTCTTTGACAATGTGATCGATGTGTTTAGTCCTCTTAAAATGCCT
ACTCTATTGTTTTATTGTTATCACAATACAATGTAATAACTTTTC
Found at i:109909488 original size:8 final size:8
Alignment explanation
Indices: 109909471--109909528 Score: 109
Period size: 8 Copynumber: 7.4 Consensus size: 8
109909461 TTCTTTTCGC
109909471 AAAAAT-A
1 AAAAATCA
109909478 AAAAATCA
1 AAAAATCA
109909486 AAAAATCA
1 AAAAATCA
109909494 AAAAATCA
1 AAAAATCA
109909502 AAAAATCA
1 AAAAATCA
109909510 AAAAATCA
1 AAAAATCA
109909518 AAAAATCA
1 AAAAATCA
109909526 AAA
1 AAA
109909529 GAGAAAACTT
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
7 6 0.12
8 44 0.88
ACGTcount: A:0.78, C:0.10, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAATCA
Found at i:109913797 original size:26 final size:26
Alignment explanation
Indices: 109913761--109913812 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
109913751 TCGCGAAGCT
109913761 CATATGTACATGAAGAAGGAATGGGA
1 CATATGTACATGAAGAAGGAATGGGA
109913787 CATATGTACATGAAGAAGGAATGGGA
1 CATATGTACATGAAGAAGGAATGGGA
109913813 GGTGATGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.08, G:0.31, T:0.19
Consensus pattern (26 bp):
CATATGTACATGAAGAAGGAATGGGA
Found at i:109917388 original size:27 final size:27
Alignment explanation
Indices: 109917358--109917464 Score: 81
Period size: 27 Copynumber: 3.9 Consensus size: 27
109917348 GTTATAAAAA
*
109917358 TAAAAAAAATACAAATAATAAAATTAT
1 TAAAAAAAATAAAAATAATAAAATTAT
* ** **
109917385 TAAAAAAATTAAAAATTGTAAAACAAT
1 TAAAAAAAATAAAAATAATAAAATTAT
* * *
109917412 TAGAAAAAATATATAATAAAAAAATTATT
1 TAAAAAAAATA-AAAATAATAAAATTA-T
** *
109917441 TAAAAATTATAAATATAA-AAAATT
1 TAAAAAAAATAAAAATAATAAAATT
109917465 GATTCATTCA
Statistics
Matches: 59, Mismatches: 19, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
27 36 0.61
28 14 0.24
29 9 0.15
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (27 bp):
TAAAAAAAATAAAAATAATAAAATTAT
Found at i:109917753 original size:19 final size:19
Alignment explanation
Indices: 109917726--109917764 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
109917716 ATTATATTTT
109917726 TTATATTAATTATTGTATC
1 TTATATTAATTATTGTATC
* *
109917745 TTATTTTAATTATTTTATC
1 TTATATTAATTATTGTATC
109917764 T
1 T
109917765 ATTAATAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (19 bp):
TTATATTAATTATTGTATC
Found at i:109917773 original size:19 final size:19
Alignment explanation
Indices: 109917732--109917774 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
109917722 TTTTTTATAT
*
109917732 TAATTATTGTATCTTATTT
1 TAATTATTGTATCTTATTA
*
109917751 TAATTATTTTATC-TATTAA
1 TAATTATTGTATCTTATT-A
109917770 TAATT
1 TAATT
109917775 TAACCTCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (19 bp):
TAATTATTGTATCTTATTA
Found at i:109920599 original size:13 final size:14
Alignment explanation
Indices: 109920578--109920610 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
109920568 GTTAAGCCAT
*
109920578 ATATTTATTTTA-A
1 ATATATATTTTATA
109920591 ATATATATTTTATA
1 ATATATATTTTATA
109920605 ATATAT
1 ATATAT
109920611 TTATTTTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
ATATATATTTTATA
Found at i:109922461 original size:18 final size:18
Alignment explanation
Indices: 109922434--109922469 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
109922424 GGTAGTTAAT
109922434 ATTAGCTGTTAGCAGTTA
1 ATTAGCTGTTAGCAGTTA
*
109922452 ATTAGTTGTTAGCAGTTA
1 ATTAGCTGTTAGCAGTTA
109922470 GCTTGTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.08, G:0.22, T:0.42
Consensus pattern (18 bp):
ATTAGCTGTTAGCAGTTA
Found at i:109924842 original size:31 final size:31
Alignment explanation
Indices: 109924805--109924876 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 31
109924795 TTTAGGTCAG
109924805 GACTAAAATTGACCAA-TTCAAAAAGTAT-AA
1 GACTAAAATTGACCAATTTCAAAAA-TATAAA
* *
109924835 GAGCTAAAATTGACTAATTTGAAAAATATAAA
1 GA-CTAAAATTGACCAATTTCAAAAATATAAA
109924867 GACTAAAATT
1 GACTAAAATT
109924877 TATCAAATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
30 2 0.05
31 24 0.65
32 11 0.30
ACGTcount: A:0.53, C:0.10, G:0.11, T:0.26
Consensus pattern (31 bp):
GACTAAAATTGACCAATTTCAAAAATATAAA
Found at i:109926259 original size:24 final size:24
Alignment explanation
Indices: 109926232--109926287 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
109926222 TTTTGAGCAA
*
109926232 TTTAATTTTTTTATTTTATATTTT
1 TTTAACTTTTTTATTTTATATTTT
109926256 TTTAACTTTTTTATTTTATA-TTT
1 TTTAACTTTTTTATTTTATATTTT
109926279 TTTAACTTT
1 TTTAACTTT
109926288 CCCTTTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 12 0.39
24 19 0.61
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (24 bp):
TTTAACTTTTTTATTTTATATTTT
Found at i:109926295 original size:23 final size:24
Alignment explanation
Indices: 109926243--109926289 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
109926233 TTAATTTTTT
**
109926243 TATTTTATATTTTTTTAACTTTTT
1 TATTTTATATTTTTTTAACTTTCC
109926267 TATTTTATA-TTTTTTAACTTTCC
1 TATTTTATATTTTTTTAACTTTCC
109926290 CTTTTTTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.70
Consensus pattern (24 bp):
TATTTTATATTTTTTTAACTTTCC
Found at i:109929747 original size:25 final size:24
Alignment explanation
Indices: 109929719--109929786 Score: 75
Period size: 25 Copynumber: 2.8 Consensus size: 24
109929709 CTCCAAAGAT
* *
109929719 CCATTAATCAGGAAGCTCGTGCGAG
1 CCATTAATCGGGAAGCTCG-GAGAG
109929744 CCA-TATATCGGGAAGCTCCGGAGAG
1 CCATTA-ATCGGGAAGCT-CGGAGAG
*
109929769 CCATTAGTCGGGAAGCTC
1 CCATTAATCGGGAAGCTC
109929787 ATAAAAAAGC
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
24 3 0.08
25 30 0.81
26 4 0.11
ACGTcount: A:0.26, C:0.25, G:0.29, T:0.19
Consensus pattern (24 bp):
CCATTAATCGGGAAGCTCGGAGAG
Found at i:109938917 original size:16 final size:16
Alignment explanation
Indices: 109938896--109938928 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
109938886 AACTCTTTGA
109938896 TGGCTTCGGCGGTTCT
1 TGGCTTCGGCGGTTCT
*
109938912 TGGCTTTGGCGGTTCT
1 TGGCTTCGGCGGTTCT
109938928 T
1 T
109938929 CGACGACCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.21, G:0.36, T:0.42
Consensus pattern (16 bp):
TGGCTTCGGCGGTTCT
Found at i:109939423 original size:23 final size:23
Alignment explanation
Indices: 109939393--109939443 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
109939383 TACTATTTCA
109939393 TATTTAAGCTTTATTCACCAAAG
1 TATTTAAGCTTTATTCACCAAAG
109939416 TATTTAAGCTTTATTCACCAAAG
1 TATTTAAGCTTTATTCACCAAAG
109939439 TATTT
1 TATTT
109939444 GAAATATCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (23 bp):
TATTTAAGCTTTATTCACCAAAG
Found at i:109940150 original size:42 final size:42
Alignment explanation
Indices: 109940087--109940213 Score: 154
Period size: 42 Copynumber: 3.0 Consensus size: 42
109940077 CTTCGTTTTC
** *
109940087 TCGATGCCATAGTTCAACTATGGTTTTACACAT-CTTCACATAA
1 TCGATGCCATAGCCCAGCTATGGTTTTACACATAC-TCACAT-A
*
109940130 T-GATGCCATAGCCCAGCTATGGTTTTACACATACTCATATA
1 TCGATGCCATAGCCCAGCTATGGTTTTACACATACTCACATA
*
109940171 TCGATGCCATAGCCCAGCTATGGTCTTACACGA-A-TCACATA
1 TCGATGCCATAGCCCAGCTATGGTTTTACAC-ATACTCACATA
109940212 TC
1 TC
109940214 TCACTGATGC
Statistics
Matches: 75, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
41 10 0.13
42 62 0.83
43 3 0.04
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTTTTACACATACTCACATA
Found at i:109940275 original size:47 final size:46
Alignment explanation
Indices: 109940172--109940295 Score: 151
Period size: 47 Copynumber: 2.7 Consensus size: 46
109940162 ACTCATATAT
* * * *
109940172 CGATGCCATAGCCCAGCTATGGTCTTACACGAATCACATATCTCAC
1 CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCTCAC
* * *
109940218 TGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCAT-AC
1 CGATGCCATATCCCAGATATGGTCTTATAC-GAAGCACATATC-TCAC
*
109940265 CGATGCCATATCCCATATATGGTCTTATACG
1 CGATGCCATATCCCAGATATGGTCTTATACG
109940296 GAAATCACTT
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
46 27 0.40
47 39 0.58
48 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (46 bp):
CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCTCAC
Found at i:109940356 original size:31 final size:32
Alignment explanation
Indices: 109940319--109940461 Score: 222
Period size: 31 Copynumber: 4.6 Consensus size: 32
109940309 ACTTGTAGTC
*
109940319 GAAGCTACCACTATTCACTGATCAGGTAGCCA
1 GAAGCTACCACTTTTCACTGATCAGGTAGCCA
* * *
109940351 G-AGCTACCATTTTTCACTGATCAGGCAGCTA
1 GAAGCTACCACTTTTCACTGATCAGGTAGCCA
109940382 G-AGCTACCACTTTTCACTGATCAGGTAG-CA
1 GAAGCTACCACTTTTCACTGATCAGGTAGCCA
109940412 GAAGCTACCACTTTTCACTGATCAGGTAGCC-
1 GAAGCTACCACTTTTCACTGATCAGGTAGCCA
109940443 GAAGCTACCACTTTTCACT
1 GAAGCTACCACTTTTCACT
109940462 TGTTATTTGT
Statistics
Matches: 102, Mismatches: 7, Indels: 5
0.89 0.06 0.04
Matches are distributed among these distances:
30 2 0.02
31 98 0.96
32 2 0.02
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.27
Consensus pattern (32 bp):
GAAGCTACCACTTTTCACTGATCAGGTAGCCA
Found at i:109946942 original size:43 final size:43
Alignment explanation
Indices: 109946877--109947022 Score: 247
Period size: 43 Copynumber: 3.4 Consensus size: 43
109946867 ACGGTACTAT
* * *
109946877 TCGGGCCTTCGAGCCTAGCAGGCTATAATGTCGGTGAGATAATA
1 TCGGG-CTTCGGGCCTAACAGGCTATAATGCCGGTGAGATAATA
109946921 TCGGGCTTCGGGCCTAACAGGCTATAATGCCGGTGAGATAATA
1 TCGGGCTTCGGGCCTAACAGGCTATAATGCCGGTGAGATAATA
*
109946964 TCGGGCTTCGGGCCTAACAGGTTATAATGCCGGTGAGATAATA
1 TCGGGCTTCGGGCCTAACAGGCTATAATGCCGGTGAGATAATA
109947007 TCGGGCTTCGGGCCTA
1 TCGGGCTTCGGGCCTA
109947023 GCAGACGAAA
Statistics
Matches: 98, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
43 93 0.95
44 5 0.05
ACGTcount: A:0.23, C:0.21, G:0.31, T:0.25
Consensus pattern (43 bp):
TCGGGCTTCGGGCCTAACAGGCTATAATGCCGGTGAGATAATA
Found at i:109949484 original size:21 final size:21
Alignment explanation
Indices: 109949460--109949527 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
109949450 ACTTATTTTT
109949460 TTTTATATAACAAGCACTTTA
1 TTTTATATAACAAGCACTTTA
* ** *
109949481 TTTTCTAT-AC--TTA-TTTT
1 TTTTATATAACAAGCACTTTA
109949498 TTTTATATAACAAGCACTTTA
1 TTTTATATAACAAGCACTTTA
*
109949519 TTTTTTATA
1 TTTTATATA
109949528 TAATTTATTA
Statistics
Matches: 34, Mismatches: 9, Indels: 8
0.67 0.18 0.16
Matches are distributed among these distances:
17 10 0.29
18 3 0.09
20 3 0.09
21 18 0.53
ACGTcount: A:0.31, C:0.12, G:0.03, T:0.54
Consensus pattern (21 bp):
TTTTATATAACAAGCACTTTA
Found at i:109949507 original size:38 final size:39
Alignment explanation
Indices: 109949447--109949527 Score: 146
Period size: 38 Copynumber: 2.1 Consensus size: 39
109949437 ATTTAATCTT
109949447 TATACTTATTTTTTTTTATATAACAAGCACTTTATTTTC
1 TATACTTATTTTTTTTTATATAACAAGCACTTTATTTTC
*
109949486 TATACTTA-TTTTTTTTATATAACAAGCACTTTATTTTT
1 TATACTTATTTTTTTTTATATAACAAGCACTTTATTTTC
109949524 TATA
1 TATA
109949528 TAATTTATTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
38 33 0.80
39 8 0.20
ACGTcount: A:0.30, C:0.11, G:0.02, T:0.57
Consensus pattern (39 bp):
TATACTTATTTTTTTTTATATAACAAGCACTTTATTTTC
Found at i:109956309 original size:17 final size:17
Alignment explanation
Indices: 109956287--109956327 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
109956277 TTATGATACG
109956287 TGCATATGATTATCCAT
1 TGCATATGATTATCCAT
109956304 TGCATATGATTATCCAT
1 TGCATATGATTATCCAT
*
109956321 TACATAT
1 TGCATAT
109956328 TTAACGGGGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.41
Consensus pattern (17 bp):
TGCATATGATTATCCAT
Found at i:109963466 original size:63 final size:61
Alignment explanation
Indices: 109963391--109963507 Score: 180
Period size: 63 Copynumber: 1.9 Consensus size: 61
109963381 CGGCCTAGAT
* * *
109963391 ACACACCCGTGTCTCTGACCCTTGTGGTCCCTAATAGTAAATAGTGAGTCACACAACCTGG
1 ACACACCCGTGTCTCTGACCCGTGTGGTCCCTAATAGCAAACAGTGAGTCACACAACCTGG
*
109963452 ACACACGCCAGTGTCTCTGGCCCGTGTGGTCCCTAATAGCAAACAGTGAGTCACAC
1 ACACAC-CC-GTGTCTCTGACCCGTGTGGTCCCTAATAGCAAACAGTGAGTCACAC
109963508 GGCCTATCAC
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
61 6 0.12
62 2 0.04
63 42 0.84
ACGTcount: A:0.26, C:0.31, G:0.21, T:0.22
Consensus pattern (61 bp):
ACACACCCGTGTCTCTGACCCGTGTGGTCCCTAATAGCAAACAGTGAGTCACACAACCTGG
Found at i:109966223 original size:13 final size:14
Alignment explanation
Indices: 109966207--109966242 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
109966197 CAATCTCATA
109966207 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
109966220 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
109966233 TCTC-ATTTCA
1 TCTCAATTTCA
109966243 TTCCAATAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:109966232 original size:18 final size:19
Alignment explanation
Indices: 109966194--109966234 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
109966184 TGGTTCATGT
109966194 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
109966213 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
109966231 TTTC
1 TTTC
109966235 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:109966365 original size:23 final size:23
Alignment explanation
Indices: 109966339--109966405 Score: 107
Period size: 23 Copynumber: 2.9 Consensus size: 23
109966329 GTGGATTCCT
109966339 CCCAAACACACCAGAATATTCAA
1 CCCAAACACACCAGAATATTCAA
*
109966362 CCCAAACACACCAGAATATCCAA
1 CCCAAACACACCAGAATATTCAA
*
109966385 CCCAAACACACCCGGAATATT
1 CCCAAACACA-CCAGAATATT
109966406 ATAAATACTC
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
23 32 0.80
24 8 0.20
ACGTcount: A:0.45, C:0.37, G:0.06, T:0.12
Consensus pattern (23 bp):
CCCAAACACACCAGAATATTCAA
Found at i:109966921 original size:15 final size:16
Alignment explanation
Indices: 109966896--109966945 Score: 68
Period size: 15 Copynumber: 3.2 Consensus size: 16
109966886 TATATAATAT
109966896 ATTTCAATCAATATAA
1 ATTTCAATCAATATAA
* *
109966912 ATTT-AATCAAAAT-G
1 ATTTCAATCAATATAA
109966926 ATTTCAATCAATATAA
1 ATTTCAATCAATATAA
109966942 ATTT
1 ATTT
109966946 GATAAATTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 4 0.14
15 16 0.57
16 8 0.29
ACGTcount: A:0.48, C:0.10, G:0.02, T:0.40
Consensus pattern (16 bp):
ATTTCAATCAATATAA
Found at i:109968243 original size:19 final size:20
Alignment explanation
Indices: 109968208--109968248 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
109968198 TTGCTTTGTT
*
109968208 TTTCTTTTTCATTTATTTTA
1 TTTCATTTTCATTTATTTTA
109968228 TTTCATTTTC-TTTATTTTA
1 TTTCATTTTCATTTATTTTA
109968247 TT
1 TT
109968249 ATTAAACTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTCATTTTCATTTATTTTA
Found at i:109969624 original size:3 final size:3
Alignment explanation
Indices: 109969616--109969640 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
109969606 CAAATATTAA
109969616 GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT G
109969641 GTGCAATACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:109973546 original size:18 final size:19
Alignment explanation
Indices: 109973509--109973569 Score: 65
Period size: 18 Copynumber: 3.3 Consensus size: 19
109973499 ATATGAGAAA
*
109973509 ATATTTAAATATATAATTTT
1 ATATATAAA-ATATAATTTT
109973529 ATATATAAAATA-AATTTT
1 ATATATAAAATATAATTTT
* *
109973547 A-ATA-AAAAAATAATTAT
1 ATATATAAAATATAATTTT
109973564 ATATAT
1 ATATAT
109973570 TATATAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
16 5 0.14
17 9 0.26
18 10 0.29
19 3 0.09
20 8 0.23
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATATATAAAATATAATTTT
Found at i:109973877 original size:10 final size:10
Alignment explanation
Indices: 109973862--109973913 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
109973852 ATTGGCTTTT
109973862 GTTTATGGTG
1 GTTTATGGTG
*
109973872 GTTTATTGTG
1 GTTTATGGTG
*
109973882 GTTTATGGCTTTT
1 GTTTATGG---TG
*
109973895 GTTTTTGGTG
1 GTTTATGGTG
109973905 GTTTATGGT
1 GTTTATGGT
109973914 TGTTGGTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
10 25 0.76
13 8 0.24
ACGTcount: A:0.08, C:0.02, G:0.33, T:0.58
Consensus pattern (10 bp):
GTTTATGGTG
Found at i:109973916 original size:20 final size:20
Alignment explanation
Indices: 109973862--109973917 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 20
109973852 ATTGGCTTTT
*
109973862 GTTTATGGTGGTTTATTGTG
1 GTTTATGGTTGTTTATTGTG
109973882 GTTTATGGCTTTTGTTT-TTGGTG
1 GTTTATGG---TTGTTTATT-GTG
109973905 GTTTATGGTTGTT
1 GTTTATGGTTGTT
109973918 GGTATTTGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
20 13 0.42
22 2 0.06
23 16 0.52
ACGTcount: A:0.07, C:0.02, G:0.32, T:0.59
Consensus pattern (20 bp):
GTTTATGGTTGTTTATTGTG
Found at i:109973930 original size:23 final size:23
Alignment explanation
Indices: 109973879--109973930 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
109973869 GTGGTTTATT
*
109973879 GTGGTTTATGGCTTTTGTTTTTG
1 GTGGTTTATGGCTTTTGTATTTG
109973902 GTGGTTTATGG-TTGTTGGTATTTG
1 GTGGTTTATGGCTT-TT-GTATTTG
109973926 G-GGTT
1 GTGGTT
109973931 AGGTCGGGGC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 2 0.08
23 17 0.65
24 7 0.27
ACGTcount: A:0.06, C:0.02, G:0.37, T:0.56
Consensus pattern (23 bp):
GTGGTTTATGGCTTTTGTATTTG
Found at i:109976291 original size:2 final size:2
Alignment explanation
Indices: 109976286--109976311 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
109976276 AAAAAAAAAG
109976286 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
109976312 AATCAGATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:109976853 original size:15 final size:16
Alignment explanation
Indices: 109976833--109976862 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
109976823 TAAAATTTTA
109976833 TTTAATT-GATTAAAT
1 TTTAATTCGATTAAAT
109976848 TTTAATTCGATTAAA
1 TTTAATTCGATTAAA
109976863 ATTAAAATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (16 bp):
TTTAATTCGATTAAAT
Found at i:109977234 original size:28 final size:29
Alignment explanation
Indices: 109977189--109977273 Score: 68
Period size: 28 Copynumber: 2.9 Consensus size: 29
109977179 TAAGATGGCT
* * * *
109977189 ATATAAAAATCTTCAATAAATAAAAAA-G
1 ATATAAAATTATTAAATAAATAAAAAACA
109977217 ATATAAAATTATTAAATATTAA-AATAAAACA
1 ATATAAAATTATTAAATA--AATAA-AAAACA
*
109977248 ATATAAATATTTTTAAA-AAATAAAAA
1 ATATAAA-ATTATTAAATAAATAAAAA
109977274 TAATATGGGT
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
28 15 0.33
29 7 0.15
30 8 0.17
31 8 0.17
32 8 0.17
ACGTcount: A:0.65, C:0.04, G:0.01, T:0.31
Consensus pattern (29 bp):
ATATAAAATTATTAAATAAATAAAAAACA
Found at i:109977272 original size:32 final size:32
Alignment explanation
Indices: 109977206--109977272 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
109977196 AATCTTCAAT
* *
109977206 AAATAAAAAAGATATAAAATTATTAAATATTA
1 AAATAAAAAAGATATAAAATTATTAAAAAATA
* *
109977238 AAATAAAACA-ATATAAATATTTTTAAAAAATA
1 AAATAAAAAAGATATAAA-ATTATTAAAAAATA
109977270 AAA
1 AAA
109977273 ATAATATGGG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 7 0.23
32 23 0.77
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (32 bp):
AAATAAAAAAGATATAAAATTATTAAAAAATA
Found at i:109982010 original size:147 final size:147
Alignment explanation
Indices: 109981726--109982137 Score: 529
Period size: 147 Copynumber: 2.8 Consensus size: 147
109981716 AGTTTTGAAC
* * * * *
109981726 CCAAGTCGACTATAGTTCAGTCTGGCATTTCATCGAACAATT-TAGATGCGGAAAACGTAATTAA
1 CCAAGTCGACAATAGTTCAGTCTGGCATTTCATCGAAC-ATTGGAGATGCTGAAAATGCAATTAA
* * * * *
109981790 GGAAGATAACTTGACATCTCAACTTAAGGAGGAGGTTACTGAAATGGATGATTCTGAGGTTGTGG
65 GGAAGATAACCTGACATCTGAACTTAAGGAGGAGGTTACCGAAATGGATGATTCTGAGGTCGTAG
*
109981855 AAGTTAAAGATAATGTAG
130 AAGATAAAGATAATGTAG
* * * **
109981873 CGAAGTCTACAATAGTTCAGTCTGACATTTCATCGAACATTGGAGATGCTGAAGGTGCAATTAAG
1 CCAAGTCGACAATAGTTCAGTCTGGCATTTCATCGAACATTGGAGATGCTGAAAATGCAATTAAG
* * *
109981938 GAAGATAACCTAACATCTGAACTTAAGGAGGAGGTTACCGAAATGGATGATTCTGGGGTCGTAGC
66 GAAGATAACCTGACATCTGAACTTAAGGAGGAGGTTACCGAAATGGATGATTCTGAGGTCGTAGA
*
109982003 AGATAAAGTTAATGTAG
131 AGATAAAGATAATGTAG
* ** * * * *
109982020 CCAAGTGGAGGATAGCTCAGTGTGGCATTTCATCAAACATTGGAGATGCTGAAAATGCAATCAAG
1 CCAAGTCGACAATAGTTCAGTCTGGCATTTCATCGAACATTGGAGATGCTGAAAATGCAATTAAG
* * * *
109982085 GAAGATAACCTGACGTCTGAACTTAAGGAGGAGGTCACCGAAAGGGTTGATTC
66 GAAGATAACCTGACATCTGAACTTAAGGAGGAGGTTACCGAAATGGATGATTC
109982138 CTTGATTGTG
Statistics
Matches: 227, Mismatches: 37, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
146 3 0.01
147 224 0.99
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.25
Consensus pattern (147 bp):
CCAAGTCGACAATAGTTCAGTCTGGCATTTCATCGAACATTGGAGATGCTGAAAATGCAATTAAG
GAAGATAACCTGACATCTGAACTTAAGGAGGAGGTTACCGAAATGGATGATTCTGAGGTCGTAGA
AGATAAAGATAATGTAG
Found at i:109988424 original size:7 final size:7
Alignment explanation
Indices: 109988412--109988443 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
109988402 TGCAGGATAT
109988412 AATTTAA
1 AATTTAA
109988419 AATTTAA
1 AATTTAA
109988426 AATTTAA
1 AATTTAA
*
109988433 AATTCAA
1 AATTTAA
109988440 AATT
1 AATT
109988444 ACTATTAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (7 bp):
AATTTAA
Found at i:109997194 original size:46 final size:46
Alignment explanation
Indices: 109997142--109997238 Score: 185
Period size: 46 Copynumber: 2.1 Consensus size: 46
109997132 ATTGTTAATT
109997142 TGAATTGTTGCTAAGAATCAAGCCAAGTGTGTGAAGAAGTGATAAA
1 TGAATTGTTGCTAAGAATCAAGCCAAGTGTGTGAAGAAGTGATAAA
109997188 TGAATTGTTGCTAAGAATCAAGCCAAGTGTGTGAAGAAGTGATAAA
1 TGAATTGTTGCTAAGAATCAAGCCAAGTGTGTGAAGAAGTGATAAA
*
109997234 GGAAT
1 TGAAT
109997239 AGTCACTCTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.39, C:0.08, G:0.27, T:0.26
Consensus pattern (46 bp):
TGAATTGTTGCTAAGAATCAAGCCAAGTGTGTGAAGAAGTGATAAA
Found at i:109999151 original size:16 final size:14
Alignment explanation
Indices: 109999123--109999163 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
109999113 AGCTAAATTT
109999123 AAAAGAAAAAAAAAG
1 AAAAG-AAAAAAAAG
*
109999138 AAAGAGAGAAAAAAG
1 AAA-AGAAAAAAAAG
109999153 AAAAGAAAAAA
1 AAAAGAAAAAA
109999164 TAAATTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 7 0.30
15 14 0.61
16 2 0.09
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAAAAG
Found at i:110000042 original size:31 final size:32
Alignment explanation
Indices: 110000001--110000063 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
109999991 CAATTTGATC
*
110000001 ATTGAACTATTTAAAAGT-TTTCATTTAAGTT
1 ATTGAACTATTCAAAAGTCTTTCATTTAAGTT
* *
110000032 ATTGAGCTATTCAAAAGTGCTTTTATTTAAGT
1 ATTGAACTATTCAAAAGT-CTTTCATTTAAGT
110000064 CACTGAATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 16 0.59
33 11 0.41
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (32 bp):
ATTGAACTATTCAAAAGTCTTTCATTTAAGTT
Found at i:110001837 original size:29 final size:29
Alignment explanation
Indices: 110001803--110001860 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
110001793 TTATAGGGAC
*
110001803 TGGATCAAATTAATCATTCTATTATTAAA
1 TGGATCAAATTAATCATTATATTATTAAA
* *
110001832 TGGATCAATTTAATCCTTATATTATTAAA
1 TGGATCAAATTAATCATTATATTATTAAA
110001861 AAGAATCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (29 bp):
TGGATCAAATTAATCATTATATTATTAAA
Found at i:110003942 original size:17 final size:17
Alignment explanation
Indices: 110003920--110003955 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
110003910 GGCATCACCC
* *
110003920 AAAGCCTCGTGCAGTCA
1 AAAGCCTCCTGCACTCA
110003937 AAAGCCTCCTGCACTCA
1 AAAGCCTCCTGCACTCA
110003954 AA
1 AA
110003956 GCCCACTACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.33, C:0.33, G:0.17, T:0.17
Consensus pattern (17 bp):
AAAGCCTCCTGCACTCA
Found at i:110007939 original size:301 final size:300
Alignment explanation
Indices: 110007397--110008047 Score: 1115
Period size: 301 Copynumber: 2.2 Consensus size: 300
110007387 GAAGATGTAA
110007397 TTGAGGTAGATGATACAAAATCTTTTGATTCTACCTGTGATGATAAGGTCCATGGGAGTGGCCCT
1 TTGAGGTAGATGATACAAAATCTTTTGATTCTACCTGTGATGATAAGGTCCATGGGAGTGGCCCT
*
110007462 TCTGATATCAAACCAGTCCAAGCCAAGGAAGGGATTGACAACAAAAGGTTTTTGTACATTTCTTA
66 TCTGATATCAAACCAGTCCAAACCAAGGAAGGGATTGACAACAAAAGGTTTTTGTACATTTCTTA
* *
110007527 TTGCTTAGTGCAAATTATTTTCAATAACAGTGTAGTCTTTAACTTTTTTGTTTGAAAATTCAGTG
131 TTGCTTAGTGCAAATTATTTTCAATAACAGTGCAGTCTTAAACTTTTTTGTTTGAAAATTCAGTG
* * *
110007592 ACAGAGGAAAATTCATTGTTTTTTTTATGTTTTGGTTGCAGGGTTTGTTTAAGAAGGCAACCTGC
196 ACA-AGGAAAATTCATGGTTTCTTTTATGTTTTGGTTGCAGGGTTTGTTTAAAAAGGCAACCTGC
*
110007657 TAGGTTTAAATCCCAAGAACCTGAAACTACTGAATATATGT
260 TAGGTTTAAAGCCCAAGAACCTGAAACTACTGAATATATGT
110007698 TTGAGGTAGATGATACAAAATCTTTTGATTCTACCTGTGATGATAAGGTCCATGGGAGTGGCCCT
1 TTGAGGTAGATGATACAAAATCTTTTGATTCTACCTGTGATGATAAGGTCCATGGGAGTGGCCCT
* *
110007763 TCTGATATCAAACCAGTCCAAACCAAGGAGGGGATTGACAACAAAGGGTTTTTGTACATTTCTTA
66 TCTGATATCAAACCAGTCCAAACCAAGGAAGGGATTGACAACAAAAGGTTTTTGTACATTTCTTA
110007828 TTGCTTAGTGCAAATTATTTTCAATAACAGTGCAGTCTTCAAACTTTTTTGTTTGAAAACTTCAG
131 TTGCTTAGTGCAAATTATTTTCAATAACAGTGCAGTCTT-AAACTTTTTTGTTTGAAAA-TTCAG
* *
110007893 TGAC-AGGAAAATTCATGGTTTCTTTTATGTTTTGGTTGCAGGGTTTGTTTAAAAAGGCTATCTG
194 TGACAAGGAAAATTCATGGTTTCTTTTATGTTTTGGTTGCAGGGTTTGTTTAAAAAGGCAACCTG
*
110007957 CTAGGTTTAAAGCCCAAGAACCTGAATCTACTGAATATATGT
259 CTAGGTTTAAAGCCCAAGAACCTGAAACTACTGAATATATGT
** * * *
110007999 GCGAGGTAGATGATACAAAATCTTTTGCTCCTATCTGTGATGATAAGGT
1 TTGAGGTAGATGATACAAAATCTTTTGATTCTACCTGTGATGATAAGGT
110008048 GTGTAAAAGT
Statistics
Matches: 331, Mismatches: 17, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
301 304 0.92
302 18 0.05
303 9 0.03
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (300 bp):
TTGAGGTAGATGATACAAAATCTTTTGATTCTACCTGTGATGATAAGGTCCATGGGAGTGGCCCT
TCTGATATCAAACCAGTCCAAACCAAGGAAGGGATTGACAACAAAAGGTTTTTGTACATTTCTTA
TTGCTTAGTGCAAATTATTTTCAATAACAGTGCAGTCTTAAACTTTTTTGTTTGAAAATTCAGTG
ACAAGGAAAATTCATGGTTTCTTTTATGTTTTGGTTGCAGGGTTTGTTTAAAAAGGCAACCTGCT
AGGTTTAAAGCCCAAGAACCTGAAACTACTGAATATATGT
Found at i:110009562 original size:19 final size:20
Alignment explanation
Indices: 110009538--110009579 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
110009528 TCTTACTATT
110009538 TTTTATT-AAAATAATATAA
1 TTTTATTCAAAATAATATAA
110009557 TTTTATTCCAAAAATAATATAA
1 TTTTATT-C-AAAATAATATAA
110009579 T
1 T
110009580 ATAATTTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.35
22 13 0.65
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTTATTCAAAATAATATAA
Found at i:110010131 original size:54 final size:54
Alignment explanation
Indices: 110010021--110010144 Score: 144
Period size: 54 Copynumber: 2.3 Consensus size: 54
110010011 AAAGTACCAA
* * * * * *
110010021 TGAAATCAAATCTTACAAACTCAAATAGATATTAGACAAACTCCCAAGTAATAT
1 TGAAATCAAATCATACAAACTCAAATAGACATTAAACAAACTCCAAAATAACAT
*
110010075 TGAAAGCAAATCATACAAACTCAAATTA-ACATTAAACAAA-TCCTAAAATAACAT
1 TGAAATCAAATCATACAAACTCAAA-TAGACATTAAACAAACTCC-AAAATAACAT
*
110010129 TGAAATTAAATCATAC
1 TGAAATCAAATCATAC
110010145 GAATACATTA
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
53 3 0.05
54 54 0.92
55 2 0.03
ACGTcount: A:0.52, C:0.18, G:0.06, T:0.25
Consensus pattern (54 bp):
TGAAATCAAATCATACAAACTCAAATAGACATTAAACAAACTCCAAAATAACAT
Found at i:110012474 original size:24 final size:24
Alignment explanation
Indices: 110012446--110012519 Score: 72
Period size: 24 Copynumber: 3.3 Consensus size: 24
110012436 TTCTCAGCCT
110012446 CACTCTCATTCTTGCTCAGACTTC
1 CACTCTCATTCTTGCTCAGACTTC
110012470 CACTCTCA--C-T-CTC--AC-TC
1 CACTCTCATTCTTGCTCAGACTTC
* *
110012487 AAATTCTCATTCTTGCTCAGACTTC
1 -CACTCTCATTCTTGCTCAGACTTC
110012512 CACTCTCA
1 CACTCTCA
110012520 CTCTCACTCA
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
17 2 0.05
18 8 0.21
20 4 0.11
21 2 0.05
22 4 0.11
24 16 0.42
25 2 0.05
ACGTcount: A:0.20, C:0.39, G:0.05, T:0.35
Consensus pattern (24 bp):
CACTCTCATTCTTGCTCAGACTTC
Found at i:110012474 original size:42 final size:41
Alignment explanation
Indices: 110012428--110012541 Score: 167
Period size: 42 Copynumber: 2.7 Consensus size: 41
110012418 TTCTTGCTTA
*
110012428 CACTCTCATTCTCAGCCTC-ACTCTCATTCTTGCTCAGACTTC
1 CACTCTCACTCTCA--CTCAACTCTCATTCTTGCTCAGACTTC
*
110012470 CACTCTCACTCTCACTCAAATTCTCATTCTTGCTCAGACTTC
1 CACTCTCACTCTCACTC-AACTCTCATTCTTGCTCAGACTTC
110012512 CACTCTCACTCTCACTCAAACTCTCATTCT
1 CACTCTCACTCTCACTC-AACTCTCATTCT
110012542 CGTTTTTCAT
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
40 3 0.04
42 64 0.96
ACGTcount: A:0.20, C:0.40, G:0.04, T:0.35
Consensus pattern (41 bp):
CACTCTCACTCTCACTCAACTCTCATTCTTGCTCAGACTTC
Found at i:110012529 original size:24 final size:24
Alignment explanation
Indices: 110012446--110012529 Score: 65
Period size: 24 Copynumber: 3.8 Consensus size: 24
110012436 TTCTCAGCCT
* **
110012446 CACTCTCATTCTTGCTCAGACTTC
1 CACTCTCACTCTCACTCAGACTTC
*
110012470 CACTCTCACTCTCACTCA-AATTC
1 CACTCTCACTCTCACTCAGACTTC
*
110012493 TCA-T-T--CT-T-GCTCAGACTTC
1 -CACTCTCACTCTCACTCAGACTTC
110012512 CACTCTCACTCTCACTCA
1 CACTCTCACTCTCACTCA
110012530 AACTCTCATT
Statistics
Matches: 45, Mismatches: 7, Indels: 16
0.66 0.10 0.24
Matches are distributed among these distances:
18 6 0.13
19 6 0.13
20 3 0.07
22 3 0.07
23 6 0.13
24 21 0.47
ACGTcount: A:0.20, C:0.40, G:0.05, T:0.35
Consensus pattern (24 bp):
CACTCTCACTCTCACTCAGACTTC
Found at i:110013243 original size:57 final size:53
Alignment explanation
Indices: 110013182--110013313 Score: 155
Period size: 55 Copynumber: 2.5 Consensus size: 53
110013172 TTATATTTTA
*
110013182 AAAATATTTGTTTATTTTTATATATTTTTAAATTTTGTATATTAT-TATTTTTGGTCC
1 AAAATA-TT-TTTATTTTTATATA-TTTTAAA-TTTAT-TATTATGTATTTTTGGTCC
**
110013239 AAAATATTTTTATTTTTATATATTTTAAATTTATTATTATGTATTTTT--TTG
1 AAAATATTTTTATTTTTATATATTTTAAATTTATTATTATGTATTTTTGGTCC
*
110013290 AAAATATTTAT-TTTTTATATATTT
1 AAAATATTTTTATTTTTATATATTT
110013314 CTTTGAATTT
Statistics
Matches: 70, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
50 13 0.19
51 11 0.16
52 6 0.09
53 11 0.16
54 7 0.10
55 14 0.20
56 2 0.03
57 6 0.09
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.63
Consensus pattern (53 bp):
AAAATATTTTTATTTTTATATATTTTAAATTTATTATTATGTATTTTTGGTCC
Found at i:110013981 original size:16 final size:15
Alignment explanation
Indices: 110013937--110013972 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
110013927 CCAAATTAAG
110013937 ATTTTTA-AAACATTC
1 ATTTTTACAAA-ATTC
110013952 ATTTTTACAAAATTC
1 ATTTTTACAAAATTC
110013967 ATTTTT
1 ATTTTT
110013973 TCTTAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 17 0.85
16 3 0.15
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTTTTACAAAATTC
Found at i:110025196 original size:12 final size:14
Alignment explanation
Indices: 110025165--110025193 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
110025155 ACAAACATAT
110025165 TATCATATGTAATA
1 TATCATATGTAATA
110025179 TATCATATGTAATA
1 TATCATATGTAATA
110025193 T
1 T
110025194 CATGTCAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (14 bp):
TATCATATGTAATA
Found at i:110025522 original size:18 final size:19
Alignment explanation
Indices: 110025501--110025542 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
110025491 AATTTAACAA
110025501 TATTTATTTACAG-ATTGT
1 TATTTATTTACAGTATTGT
* **
110025519 TATTTTTTTATTGTATTGT
1 TATTTATTTACAGTATTGT
110025538 TATTT
1 TATTT
110025543 TATGTTTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.21, C:0.02, G:0.10, T:0.67
Consensus pattern (19 bp):
TATTTATTTACAGTATTGT
Found at i:110025975 original size:29 final size:30
Alignment explanation
Indices: 110025943--110026011 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 30
110025933 TTTAATATGT
*
110025943 AATTATATATAT-AGAT-TTTGATTTTGTGC
1 AATTATATATATGA-ATCTTTGATTTGGTGC
* * *
110025972 AATTTTATACATGAATCTTTGATTTGGTTC
1 AATTATATATATGAATCTTTGATTTGGTGC
110026002 AATTAT-TATA
1 AATTATATATA
110026012 AATTATTAAC
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
29 15 0.47
30 17 0.53
ACGTcount: A:0.32, C:0.06, G:0.12, T:0.51
Consensus pattern (30 bp):
AATTATATATATGAATCTTTGATTTGGTGC
Found at i:110027645 original size:18 final size:17
Alignment explanation
Indices: 110027618--110027651 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
110027608 CTAATATCAC
*
110027618 AATTATATTTTATAATAA
1 AATTACATTTTA-AATAA
110027636 AATTACATTTTAAATA
1 AATTACATTTTAAATA
110027652 TTTTAACATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTACATTTTAAATAA
Found at i:110027709 original size:24 final size:23
Alignment explanation
Indices: 110027657--110027715 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
110027647 AAATATTTTA
* *
110027657 ACATTTTATTAAAAATTATATTG
1 ACATTTTAATAAAAATTATAGTG
*
110027680 ATATTTTAATAACAAATATATAGT-
1 ACATTTTAATAA-AAAT-TATAGTG
110027704 ACATTTT-ATAAA
1 ACATTTTAATAAA
110027716 TATTTAACAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
22 1 0.03
23 14 0.47
24 10 0.33
25 5 0.17
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.44
Consensus pattern (23 bp):
ACATTTTAATAAAAATTATAGTG
Found at i:110027756 original size:22 final size:23
Alignment explanation
Indices: 110027728--110027779 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
110027718 TTTAACAATA
110027728 AATATTTTAA-ATATAAAA-TATG
1 AATATTTTAATA-ATAAAACTATG
110027750 AATATTTTAATAATAAAACTATG
1 AATATTTTAATAATAAAACTATG
*
110027773 AACATTT
1 AATATTT
110027780 GTTTAAGTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 16 0.59
23 11 0.41
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (23 bp):
AATATTTTAATAATAAAACTATG
Found at i:110028298 original size:23 final size:23
Alignment explanation
Indices: 110028272--110028319 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
110028262 CATCTTCCCT
110028272 TACAATAACCTTGTTTCAAATCA
1 TACAATAACCTTGTTTCAAATCA
110028295 TACAATAACCTTGTTTCAAATCA
1 TACAATAACCTTGTTTCAAATCA
110028318 TA
1 TA
110028320 GTTGTACTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.35
Consensus pattern (23 bp):
TACAATAACCTTGTTTCAAATCA
Found at i:110031471 original size:12 final size:12
Alignment explanation
Indices: 110031438--110031472 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
110031428 TGAGACAAGA
110031438 TATTCTTTAAAT
1 TATTCTTTAAAT
*
110031450 TACTCTTTTAAAT
1 TATTC-TTTAAAT
110031463 TATTCTTTAA
1 TATTCTTTAA
110031473 GTAACATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.31, C:0.11, G:0.00, T:0.57
Consensus pattern (12 bp):
TATTCTTTAAAT
Found at i:110031506 original size:11 final size:11
Alignment explanation
Indices: 110031490--110031519 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
110031480 ATAGATTATG
110031490 CTATTCCAACT
1 CTATTCCAACT
110031501 CTATTCCAACT
1 CTATTCCAACT
*
110031512 TTATTCCA
1 CTATTCCA
110031520 TTCAACCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.27, C:0.33, G:0.00, T:0.40
Consensus pattern (11 bp):
CTATTCCAACT
Found at i:110031600 original size:45 final size:43
Alignment explanation
Indices: 110031513--110031604 Score: 132
Period size: 45 Copynumber: 2.1 Consensus size: 43
110031503 ATTCCAACTT
110031513 TATTCCATTCAACCAACACAAGAATACTATTACAATTCTATTC
1 TATTCCATTCAACCAACACAAGAATACTATTACAATTCTATTC
* *
110031556 TATTCCATTCAACCAA-ACAATTGAATTGCTATTACAGTTCTATTC
1 TATTCCATTCAACCAACACAA--GAA-TACTATTACAATTCTATTC
110031601 TATT
1 TATT
110031605 ATAACTCTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
42 4 0.09
43 16 0.36
44 3 0.07
45 21 0.48
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.37
Consensus pattern (43 bp):
TATTCCATTCAACCAACACAAGAATACTATTACAATTCTATTC
Found at i:110031605 original size:16 final size:16
Alignment explanation
Indices: 110031584--110031626 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
110031574 AATTGAATTG
110031584 CTATTACAGTTCTATT
1 CTATTACAGTTCTATT
* **
110031600 CTATTATAACTCTATT
1 CTATTACAGTTCTATT
*
110031616 CCATTACAGTT
1 CTATTACAGTT
110031627 TTAGTCCGTT
Statistics
Matches: 20, Mismatches: 7, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.21, G:0.05, T:0.47
Consensus pattern (16 bp):
CTATTACAGTTCTATT
Found at i:110036521 original size:31 final size:32
Alignment explanation
Indices: 110036470--110036538 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 32
110036460 ATTGATTTGC
110036470 TTAAA-AATTAAGTTAAAAGATATTTAT-TAA
1 TTAAATAATTAAGTTAAAAGATATTTATATAA
* * *
110036500 TTAAATAATTATA-TTATAAGATTTTTGTATAA
1 TTAAATAATTA-AGTTAAAAGATATTTATATAA
110036532 -TAAATAA
1 TTAAATAA
110036539 ATAAAAGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
30 5 0.15
31 24 0.73
32 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (32 bp):
TTAAATAATTAAGTTAAAAGATATTTATATAA
Found at i:110037069 original size:25 final size:25
Alignment explanation
Indices: 110037035--110037084 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
110037025 TGAAAGAAGT
110037035 TTTAAATTAGGGTTTTATTATGAAC
1 TTTAAATTAGGGTTTTATTATGAAC
110037060 TTTAAATTAGGGTTTTATTATGAAC
1 TTTAAATTAGGGTTTTATTATGAAC
110037085 ATTAGATAGT
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:0.32, C:0.04, G:0.16, T:0.48
Consensus pattern (25 bp):
TTTAAATTAGGGTTTTATTATGAAC
Found at i:110037184 original size:17 final size:18
Alignment explanation
Indices: 110037162--110037197 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
110037152 TAAATAAGTT
110037162 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
110037179 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
110037197 A
1 A
110037198 TAGAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:110049442 original size:24 final size:24
Alignment explanation
Indices: 110049407--110049480 Score: 139
Period size: 24 Copynumber: 3.1 Consensus size: 24
110049397 AGTGTTTGAG
110049407 TAAATGCTCTCAAAGTGTTTTTAT
1 TAAATGCTCTCAAAGTGTTTTTAT
*
110049431 TAAATGCCCTCAAAGTGTTTTTAT
1 TAAATGCTCTCAAAGTGTTTTTAT
110049455 TAAATGCTCTCAAAGTGTTTTTAT
1 TAAATGCTCTCAAAGTGTTTTTAT
110049479 TA
1 TA
110049481 CTTTGAAAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.45
Consensus pattern (24 bp):
TAAATGCTCTCAAAGTGTTTTTAT
Found at i:110050422 original size:21 final size:21
Alignment explanation
Indices: 110050398--110050441 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
110050388 TGACATGACA
110050398 TAAGAGATGTCGATTCTAGTC
1 TAAGAGATGTCGATTCTAGTC
110050419 TAAGAGATGTCGATTCTAGTC
1 TAAGAGATGTCGATTCTAGTC
110050440 TA
1 TA
110050442 TCTTTTTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.34
Consensus pattern (21 bp):
TAAGAGATGTCGATTCTAGTC
Found at i:110050816 original size:21 final size:21
Alignment explanation
Indices: 110050792--110050833 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
110050782 AGTAAATTAC
110050792 TAAA-AAAATTAATACATAAAA
1 TAAATAAAA-TAATACATAAAA
* *
110050813 TAAATACAATAATAGATAAAA
1 TAAATAAAATAATACATAAAA
110050834 CGAGATGCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (21 bp):
TAAATAAAATAATACATAAAA
Found at i:110054648 original size:18 final size:18
Alignment explanation
Indices: 110054625--110054666 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
110054615 TAATTAAATT
110054625 AAAGAAATAAAAGAAAAG
1 AAAGAAATAAAAGAAAAG
*
110054643 AAAGAAATAAAAGAGAAG
1 AAAGAAATAAAAGAAAAG
110054661 AGAAGA
1 A-AAGA
110054667 CAAGAAATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (18 bp):
AAAGAAATAAAAGAAAAG
Found at i:110054696 original size:25 final size:24
Alignment explanation
Indices: 110054634--110054698 Score: 69
Period size: 25 Copynumber: 2.7 Consensus size: 24
110054624 TAAAGAAATA
110054634 AAAGAAAAGAAAGAAATAAAAGAG
1 AAAGAAAAGAAAGAAATAAAAGAG
* ** *
110054658 -AAGAGAAGACAAGAAATAGCAGGG
1 AAAGAAAAGA-AAGAAATAAAAGAG
110054682 AAAGAAAAGGAAAGAAA
1 AAAGAAAA-GAAAGAAA
110054699 AAGAAAAGGA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
23 8 0.24
24 11 0.33
25 12 0.36
26 2 0.06
ACGTcount: A:0.68, C:0.03, G:0.26, T:0.03
Consensus pattern (24 bp):
AAAGAAAAGAAAGAAATAAAAGAG
Found at i:110075072 original size:47 final size:47
Alignment explanation
Indices: 110075003--110075097 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
110074993 GTATATGTAA
110075003 TGGCTTTATGCCTCAATTCATTGTATGAATGAAATTTTCAGAATTCT
1 TGGCTTTATGCCTCAATTCATTGTATGAATGAAATTTTCAGAATTCT
110075050 TGGCTTTATGCCTCAATTCATTGTATGAATGAAATTTTCAGAATTCT
1 TGGCTTTATGCCTCAATTCATTGTATGAATGAAATTTTCAGAATTCT
110075097 T
1 T
110075098 CTTCATTTTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (47 bp):
TGGCTTTATGCCTCAATTCATTGTATGAATGAAATTTTCAGAATTCT
Found at i:110078785 original size:22 final size:22
Alignment explanation
Indices: 110078757--110078812 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
110078747 GAACAGTGTC
*
110078757 ACACGCCTGTGTGACCTAGGGG
1 ACACGCCCGTGTGACCTAGGGG
110078779 ACACGCCCGTGTGACCTAGGGG
1 ACACGCCCGTGTGACCTAGGGG
110078801 ACACGCCCGTGT
1 ACACGCCCGTGT
110078813 TCCCTTCTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.18, C:0.32, G:0.34, T:0.16
Consensus pattern (22 bp):
ACACGCCCGTGTGACCTAGGGG
Done.