Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015237.1 Kokia drynarioides strain JFW-HI SEQ_130282, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 810367
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 195 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:7833 original size:14 final size:14
Alignment explanation
Indices: 7809--7876 Score: 68
Period size: 14 Copynumber: 5.0 Consensus size: 14
7799 GGGGTTCGAG
*
7809 GTTTG-GGTTTAGG
1 GTTTGAGGTTTAGA
*
7822 GTTTGAGGTTTAAA
1 GTTTGAGGTTTAGA
*
7836 GTTTAAGGTTT-GA
1 GTTTGAGGTTTAGA
* * *
7849 GTTTAATGTTTAAA
1 GTTTGAGGTTTAGA
7863 GTTTGAGGTTTAGA
1 GTTTGAGGTTTAGA
7877 TATAATTGTT
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
13 16 0.36
14 28 0.64
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.46
Consensus pattern (14 bp):
GTTTGAGGTTTAGA
Found at i:7839 original size:27 final size:27
Alignment explanation
Indices: 7809--7876 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
7799 GGGGTTCGAG
* *
7809 GTTTGGGTTTAGGGTTTGAGGTTTAAA
1 GTTTGGGTTTAGAGTTTAAGGTTTAAA
* *
7836 GTTTAAGGTTT-GAGTTTAATGTTTAAA
1 GTTT-GGGTTTAGAGTTTAAGGTTTAAA
7863 GTTTGAGGTTTAGA
1 GTTTG-GGTTTAGA
7877 TATAATTGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
27 26 0.79
28 7 0.21
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.46
Consensus pattern (27 bp):
GTTTGGGTTTAGAGTTTAAGGTTTAAA
Found at i:7845 original size:21 final size:21
Alignment explanation
Indices: 7815--7874 Score: 86
Period size: 20 Copynumber: 2.9 Consensus size: 21
7805 CGAGGTTTGG
*
7815 GTTTAGGGTTTGAGGTTTAAA
1 GTTTAAGGTTTGAGGTTTAAA
*
7836 GTTTAAGGTTTGA-GTTTAAT
1 GTTTAAGGTTTGAGGTTTAAA
*
7856 GTTTAAAGTTTGAGGTTTA
1 GTTTAAGGTTTGAGGTTTA
7875 GATATAATTG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
20 18 0.51
21 17 0.49
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (21 bp):
GTTTAAGGTTTGAGGTTTAAA
Found at i:7882 original size:27 final size:27
Alignment explanation
Indices: 7829--7882 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
7819 AGGGTTTGAG
*
7829 GTTTAAAGTTTAAGGTTTGAGTTTAAT
1 GTTTAAAGTTTAAGGTTTGAGTATAAT
*
7856 GTTTAAAGTTTGAGGTTT-AGATATAAT
1 GTTTAAAGTTTAAGGTTTGAG-TATAAT
7883 TGTTATCACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 2 0.08
27 22 0.92
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.46
Consensus pattern (27 bp):
GTTTAAAGTTTAAGGTTTGAGTATAAT
Found at i:18929 original size:4 final size:4
Alignment explanation
Indices: 18913--18958 Score: 65
Period size: 4 Copynumber: 11.2 Consensus size: 4
18903 ACGAAAATTG
* *
18913 AAGA AAAA AAGA AAGA AAAA AGAGA AAGA AAGA AAGA AAGA AAGA A
1 AAGA AAGA AAGA AAGA AAGA A-AGA AAGA AAGA AAGA AAGA AAGA A
18959 GAAGGAAGGA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
4 34 0.92
5 3 0.08
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:18942 original size:25 final size:25
Alignment explanation
Indices: 18913--18960 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
18903 ACGAAAATTG
18913 AAGAAAAAAAGAAAGAAAAAAGAGA
1 AAGAAAAAAAGAAAGAAAAAAGAGA
* *
18938 AAGAAAGAAAGAAAGAAAGAAGA
1 AAGAAAAAAAGAAAGAAAAAAGA
18961 AGGAAGGAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (25 bp):
AAGAAAAAAAGAAAGAAAAAAGAGA
Found at i:19390 original size:20 final size:21
Alignment explanation
Indices: 19351--19391 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
19341 ATTTACTTTT
19351 ATTTAATTTTGCTAGTTAGTA
1 ATTTAATTTTGCTAGTTAGTA
* *
19372 ATTTTATTTTG-TTGTTAGTA
1 ATTTAATTTTGCTAGTTAGTA
19392 GTAGTAAGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.24, C:0.02, G:0.15, T:0.59
Consensus pattern (21 bp):
ATTTAATTTTGCTAGTTAGTA
Found at i:20114 original size:17 final size:17
Alignment explanation
Indices: 20091--20152 Score: 79
Period size: 17 Copynumber: 3.6 Consensus size: 17
20081 ACCCAACAAG
20091 ATTTAAATTTATTTTAA
1 ATTTAAATTTATTTTAA
* * *
20108 GTTTAAATTTACTTAAA
1 ATTTAAATTTATTTTAA
*
20125 ATTTAAATTTATTATAA
1 ATTTAAATTTATTTTAA
*
20142 ATTTAATTTTA
1 ATTTAAATTTA
20153 AATCTATTTA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (17 bp):
ATTTAAATTTATTTTAA
Found at i:20142 original size:11 final size:10
Alignment explanation
Indices: 20109--20166 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
20099 TTATTTTAAG
20109 TTTAAATTTA
1 TTTAAATTTA
*
20119 CTTAAA---A
1 TTTAAATTTA
20126 TTTAAATTTA
1 TTTAAATTTA
20136 TTATAAATTTAA
1 TT-TAAATTT-A
*
20148 TTTTAAATCTA
1 -TTTAAATTTA
20159 TTTAAATT
1 TTTAAATT
20167 AAAGTCCAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
7 6 0.16
10 15 0.39
11 8 0.21
12 7 0.18
13 2 0.05
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (10 bp):
TTTAAATTTA
Found at i:20206 original size:23 final size:24
Alignment explanation
Indices: 20160--20206 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
20150 TTAAATCTAT
*
20160 TTAAATTAAAGTCCAAAATTACAAA
1 TTAAATCAAAGTCC-AAATTACAAA
20185 TTAAATCAAAGTCC-AATTACAA
1 TTAAATCAAAGTCCAAATTACAA
20207 GTAAAATGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.38
25 13 0.62
ACGTcount: A:0.53, C:0.15, G:0.04, T:0.28
Consensus pattern (24 bp):
TTAAATCAAAGTCCAAATTACAAA
Found at i:20213 original size:23 final size:24
Alignment explanation
Indices: 20162--20213 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
20152 AAATCTATTT
* *
20162 AAATTAAAGTCCAAAATTACAAATT
1 AAATCAAAGTCC-AAATTACAAATA
*
20187 AAATCAAAGTCC-AATTACAAGTA
1 AAATCAAAGTCCAAATTACAAATA
20210 AAAT
1 AAAT
20214 GTCCAAAGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 13 0.54
25 11 0.46
ACGTcount: A:0.56, C:0.13, G:0.06, T:0.25
Consensus pattern (24 bp):
AAATCAAAGTCCAAATTACAAATA
Found at i:22098 original size:30 final size:29
Alignment explanation
Indices: 22003--22119 Score: 139
Period size: 29 Copynumber: 4.0 Consensus size: 29
21993 GGATGTCCCT
**
22003 AAACTATCCAAAAATTACATTTTTAACCCCG
1 AAACT-TCCAAAAATCCCATTTTT-ACCCCG
*
22034 -AACTTCCAAAAATCCCATTTTTACCCCT
1 AAACTTCCAAAAATCCCATTTTTACCCCG
*
22062 AAACTTCCAAAAATCCCATTTTTGACCTCG
1 AAACTTCCAAAAATCCCATTTTT-ACCCCG
*
22092 AAACTTCCAAAAATTACCA-TTTTACCCC
1 AAACTTCCAAAAA-TCCCATTTTTACCCC
22120 CAGATGTCCA
Statistics
Matches: 76, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
28 5 0.07
29 42 0.55
30 25 0.33
31 4 0.05
ACGTcount: A:0.37, C:0.31, G:0.03, T:0.30
Consensus pattern (29 bp):
AAACTTCCAAAAATCCCATTTTTACCCCG
Found at i:22191 original size:58 final size:57
Alignment explanation
Indices: 21999--22236 Score: 198
Period size: 59 Copynumber: 4.1 Consensus size: 57
21989 CCCTGGATGT
* * * *
21999 CCCTAAACTATCCAAAAATTACATTTTTAACCCCG-AACTTCCAAAAA-TCCCATTTTTAC
1 CCCTAAA-T-TCCAAAAA-TCCATTTTTGACCTCGAAACTTCCAAAAATTACCA-TTTTAC
22058 CCCTAAACTTCCAAAAATCCCATTTTTGACCTCGAAACTTCCAAAAATTACCATTTTAC
1 CCCTAAA-TTCCAAAAAT-CCATTTTTGACCTCGAAACTTCCAAAAATTACCATTTTAC
* * * * *
22117 CCCCAGATGTCCAAAAACTCTATTTTCGACCTCGAAGC-TCTC-AAAATTACTC-TTTTAC
1 CCCTAAAT-TCCAAAAA-TCCATTTTTGACCTCGAAACTTC-CAAAAATTAC-CATTTTAC
* * ** * *
22175 CCCTAAATATCTAAAAATTCCATTTTTGACCCCGAATTTTCCTAAAATTACCATTTCAC
1 CCCTAAAT-TCCAAAAA-TCCATTTTTGACCTCGAAACTTCCAAAAATTACCATTTTAC
22234 CCC
1 CCC
22237 CGAGAATCCA
Statistics
Matches: 149, Mismatches: 20, Indels: 20
0.79 0.11 0.11
Matches are distributed among these distances:
57 1 0.01
58 67 0.45
59 76 0.51
60 5 0.03
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.32
Consensus pattern (57 bp):
CCCTAAATTCCAAAAATCCATTTTTGACCTCGAAACTTCCAAAAATTACCATTTTAC
Found at i:22201 original size:29 final size:28
Alignment explanation
Indices: 21999--22230 Score: 119
Period size: 29 Copynumber: 7.9 Consensus size: 28
21989 CCCTGGATGT
*
21999 CCCTAAACTATCCAAAAATTACATTTTTAAC
1 CCCTAAA-T-TCCAAAAATTCCATTTTT-AC
* * *
22030 CCCGAACTTCCAAAAATCCCATTTTTAC
1 CCCTAAATTCCAAAAATTCCATTTTTAC
*
22058 CCCTAAACTTCCAAAAATCCCATTTTTGAC
1 CCCTAAA-TTCCAAAAATTCCATTTTT-AC
* *
22088 CTCGAAACTTCCAAAAATTACCA-TTTTAC
1 CCCTAAA-TTCCAAAAATT-CCATTTTTAC
* * * * *
22117 CCCCAGATGTCCAAAAACTCTATTTTCGAC
1 CCCTAAAT-TCCAAAAATTCCATTTT-TAC
* * ** *
22147 CTCGAAGCTCTC-AAAATTAC-TCTTTTAC
1 CCCTAAATTC-CAAAAATTCCAT-TTTTAC
*
22175 CCCTAAATATCTAAAAATTCCATTTTTGAC
1 CCCTAAAT-TCCAAAAATTCCATTTTT-AC
* * *
22205 CCCGAATTTTCCTAAAATTACCATTT
1 CCCTAA-ATTCCAAAAATT-CCATTT
22231 CACCCCCGAG
Statistics
Matches: 153, Mismatches: 34, Indels: 28
0.71 0.16 0.13
Matches are distributed among these distances:
28 17 0.11
29 76 0.50
30 45 0.29
31 15 0.10
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.32
Consensus pattern (28 bp):
CCCTAAATTCCAAAAATTCCATTTTTAC
Found at i:22236 original size:59 final size:59
Alignment explanation
Indices: 21999--22236 Score: 220
Period size: 58 Copynumber: 4.1 Consensus size: 59
21989 CCCTGGATGT
* * * *
21999 CCCTAAACTATCCAAAAATTACATTTTTAACCCCGAACTTCC-AAAAATCCCATTTTTAC
1 CCCTAAACTATCCAAAAATTCCATTTTTGACCCCGAACTTCCTAAAATTACCA-TTTTAC
* * *
22058 CCCTAAACT-TCCAAAAATCCCATTTTTGACCTCGAAACTTCCAAAAATTACCATTTTAC
1 CCCTAAACTATCCAAAAATTCCATTTTTGACCCCG-AACTTCCTAAAATTACCATTTTAC
* * * * * * *
22117 CCCCAGA-TGTCCAAAAACTCTATTTTCGACCTCGAAGC-T-CTCAAAATTACTC-TTTTAC
1 CCCTAAACTATCCAAAAATTCCATTTTTGACCCCGAA-CTTCCT-AAAATTAC-CATTTTAC
* * *
22175 CCCTAAA-TATCTAAAAATTCCATTTTTGACCCCGAATTTTCCTAAAATTACCATTTCAC
1 CCCTAAACTATCCAAAAATTCCATTTTTGACCCCGAA-CTTCCTAAAATTACCATTTTAC
22234 CCC
1 CCC
22237 CGAGAATCCA
Statistics
Matches: 146, Mismatches: 24, Indels: 18
0.78 0.13 0.10
Matches are distributed among these distances:
57 1 0.01
58 68 0.47
59 67 0.46
60 10 0.07
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.32
Consensus pattern (59 bp):
CCCTAAACTATCCAAAAATTCCATTTTTGACCCCGAACTTCCTAAAATTACCATTTTAC
Found at i:24956 original size:30 final size:29
Alignment explanation
Indices: 24861--24977 Score: 139
Period size: 29 Copynumber: 4.0 Consensus size: 29
24851 GGATGTCCCT
**
24861 AAACTATCCAAAAATTACATTTTTAACCCCG
1 AAACT-TCCAAAAATCCCATTTTT-ACCCCG
*
24892 -AACTTCCAAAAATCCCATTTTTACCCCT
1 AAACTTCCAAAAATCCCATTTTTACCCCG
*
24920 AAACTTCCAAAAATCCCATTTTTGACCTCG
1 AAACTTCCAAAAATCCCATTTTT-ACCCCG
*
24950 AAACTTCCAAAAATTACCA-TTTTACCCC
1 AAACTTCCAAAAA-TCCCATTTTTACCCC
24978 CAGATGTCCA
Statistics
Matches: 76, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
28 5 0.07
29 42 0.55
30 25 0.33
31 4 0.05
ACGTcount: A:0.37, C:0.31, G:0.03, T:0.30
Consensus pattern (29 bp):
AAACTTCCAAAAATCCCATTTTTACCCCG
Found at i:25049 original size:58 final size:57
Alignment explanation
Indices: 24857--25094 Score: 198
Period size: 59 Copynumber: 4.1 Consensus size: 57
24847 CCCTGGATGT
* * * *
24857 CCCTAAACTATCCAAAAATTACATTTTTAACCCCG-AACTTCCAAAAA-TCCCATTTTTAC
1 CCCTAAA-T-TCCAAAAA-TCCATTTTTGACCTCGAAACTTCCAAAAATTACCA-TTTTAC
24916 CCCTAAACTTCCAAAAATCCCATTTTTGACCTCGAAACTTCCAAAAATTACCATTTTAC
1 CCCTAAA-TTCCAAAAAT-CCATTTTTGACCTCGAAACTTCCAAAAATTACCATTTTAC
* * * * *
24975 CCCCAGATGTCCAAAAACTCTATTTTCGACCTCGAAGC-TCTC-AAAATTACTC-TTTTAC
1 CCCTAAAT-TCCAAAAA-TCCATTTTTGACCTCGAAACTTC-CAAAAATTAC-CATTTTAC
* * ** * *
25033 CCCTAAATATCTAAAAATTCCATTTTTGACCCCGAATTTTCCTAAAATTACCATTTCAC
1 CCCTAAAT-TCCAAAAA-TCCATTTTTGACCTCGAAACTTCCAAAAATTACCATTTTAC
25092 CCC
1 CCC
25095 CGAGAATCCA
Statistics
Matches: 149, Mismatches: 20, Indels: 20
0.79 0.11 0.11
Matches are distributed among these distances:
57 1 0.01
58 67 0.45
59 76 0.51
60 5 0.03
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.32
Consensus pattern (57 bp):
CCCTAAATTCCAAAAATCCATTTTTGACCTCGAAACTTCCAAAAATTACCATTTTAC
Found at i:25059 original size:29 final size:28
Alignment explanation
Indices: 24857--25088 Score: 119
Period size: 29 Copynumber: 7.9 Consensus size: 28
24847 CCCTGGATGT
*
24857 CCCTAAACTATCCAAAAATTACATTTTTAAC
1 CCCTAAA-T-TCCAAAAATTCCATTTTT-AC
* * *
24888 CCCGAACTTCCAAAAATCCCATTTTTAC
1 CCCTAAATTCCAAAAATTCCATTTTTAC
*
24916 CCCTAAACTTCCAAAAATCCCATTTTTGAC
1 CCCTAAA-TTCCAAAAATTCCATTTTT-AC
* *
24946 CTCGAAACTTCCAAAAATTACCA-TTTTAC
1 CCCTAAA-TTCCAAAAATT-CCATTTTTAC
* * * * *
24975 CCCCAGATGTCCAAAAACTCTATTTTCGAC
1 CCCTAAAT-TCCAAAAATTCCATTTT-TAC
* * ** *
25005 CTCGAAGCTCTC-AAAATTAC-TCTTTTAC
1 CCCTAAATTC-CAAAAATTCCAT-TTTTAC
*
25033 CCCTAAATATCTAAAAATTCCATTTTTGAC
1 CCCTAAAT-TCCAAAAATTCCATTTTT-AC
* * *
25063 CCCGAATTTTCCTAAAATTACCATTT
1 CCCTAA-ATTCCAAAAATT-CCATTT
25089 CACCCCCGAG
Statistics
Matches: 153, Mismatches: 34, Indels: 28
0.71 0.16 0.13
Matches are distributed among these distances:
28 17 0.11
29 76 0.50
30 45 0.29
31 15 0.10
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.32
Consensus pattern (28 bp):
CCCTAAATTCCAAAAATTCCATTTTTAC
Found at i:25094 original size:59 final size:59
Alignment explanation
Indices: 24857--25094 Score: 220
Period size: 58 Copynumber: 4.1 Consensus size: 59
24847 CCCTGGATGT
* * * *
24857 CCCTAAACTATCCAAAAATTACATTTTTAACCCCGAACTTCC-AAAAATCCCATTTTTAC
1 CCCTAAACTATCCAAAAATTCCATTTTTGACCCCGAACTTCCTAAAATTACCA-TTTTAC
* * *
24916 CCCTAAACT-TCCAAAAATCCCATTTTTGACCTCGAAACTTCCAAAAATTACCATTTTAC
1 CCCTAAACTATCCAAAAATTCCATTTTTGACCCCG-AACTTCCTAAAATTACCATTTTAC
* * * * * * *
24975 CCCCAGA-TGTCCAAAAACTCTATTTTCGACCTCGAAGC-T-CTCAAAATTACTC-TTTTAC
1 CCCTAAACTATCCAAAAATTCCATTTTTGACCCCGAA-CTTCCT-AAAATTAC-CATTTTAC
* * *
25033 CCCTAAA-TATCTAAAAATTCCATTTTTGACCCCGAATTTTCCTAAAATTACCATTTCAC
1 CCCTAAACTATCCAAAAATTCCATTTTTGACCCCGAA-CTTCCTAAAATTACCATTTTAC
25092 CCC
1 CCC
25095 CGAGAATCCA
Statistics
Matches: 146, Mismatches: 24, Indels: 18
0.78 0.13 0.10
Matches are distributed among these distances:
57 1 0.01
58 68 0.47
59 67 0.46
60 10 0.07
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.32
Consensus pattern (59 bp):
CCCTAAACTATCCAAAAATTCCATTTTTGACCCCGAACTTCCTAAAATTACCATTTTAC
Found at i:37023 original size:21 final size:21
Alignment explanation
Indices: 36990--37039 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
36980 ATAATAGCAT
*
36990 AATCCAAATATAAAGTTTAGA
1 AATCCAAACATAAAGTTTAGA
* *
37011 AATTCAAACATAAAGTTTATA
1 AATCCAAACATAAAGTTTAGA
37032 AATCCAAA
1 AATCCAAA
37040 TTTCATAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.54, C:0.12, G:0.06, T:0.28
Consensus pattern (21 bp):
AATCCAAACATAAAGTTTAGA
Found at i:39970 original size:17 final size:17
Alignment explanation
Indices: 39948--39983 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
39938 ATTTTACTAT
39948 TTAAAAATAATTAAATA
1 TTAAAAATAATTAAATA
* *
39965 TTAAAAATATTTTAATA
1 TTAAAAATAATTAAATA
39982 TT
1 TT
39984 TATTTAACTT
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAAAATAATTAAATA
Found at i:53764 original size:3 final size:3
Alignment explanation
Indices: 53758--53793 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
53748 CATGCAAGAA
*
53758 CTG CTG CTG CTG CTG CTG CTG CTG TTG CTG CTG CTG
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG
53794 TAGTGGTTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.31, G:0.33, T:0.36
Consensus pattern (3 bp):
CTG
Found at i:54182 original size:83 final size:82
Alignment explanation
Indices: 54009--54217 Score: 203
Period size: 83 Copynumber: 2.6 Consensus size: 82
53999 GGATTTGTAA
* * * *
54009 AACTACCGTCACTGAACAAATGATAAACAACAACCTCAGCACCTTTTTAAAGGCAAAGCCAAGCA
1 AACTACTGTCACTGAACAAATTA-AAACAACAATCTCAGCAACTTTTTAAAGGCAAAGCCAAGCA
** * *
54074 CAAATGAATTATAGAAGC
65 CAAATGAAGAACACAAGC
* *
54092 AATTACTGTCACTGAACAAATTAAAAACAACAATCTCAGCAACTTTTTAGAA-GC-ACGACCAAG
1 AACTACTGTCACTGAACAAATT-AAAACAACAATCTCAGCAACTTTTTA-AAGGCAAAG-CCAAG
* * *
54155 CATAATTGAAGAACACAATC
63 CACAAATGAAGAACACAAGC
* * *
54175 TACTACTGTTACTGAACAAA-T-AAA-AACGATCTCAGCAACTTTT
1 AACTACTGTCACTGAACAAATTAAAACAACAATCTCAGCAACTTTT
54218 ATAAGTAAAT
Statistics
Matches: 106, Mismatches: 17, Indels: 10
0.80 0.13 0.08
Matches are distributed among these distances:
79 18 0.17
80 3 0.03
82 3 0.03
83 79 0.75
84 3 0.03
ACGTcount: A:0.44, C:0.22, G:0.11, T:0.22
Consensus pattern (82 bp):
AACTACTGTCACTGAACAAATTAAAACAACAATCTCAGCAACTTTTTAAAGGCAAAGCCAAGCAC
AAATGAAGAACACAAGC
Found at i:54245 original size:78 final size:82
Alignment explanation
Indices: 54010--54245 Score: 189
Period size: 83 Copynumber: 2.9 Consensus size: 82
54000 GATTTGTAAA
* * * *
54010 ACTACCGTCACTGAACAAATGATAAACAACAACCTCAGCACCTTTTTA-AAGGCA-AAGCCAAGC
1 ACTACTGTCACTGAACAAATTA-AAACAACAATCTCAGCAACTTTTTAGAA-GCACAA-CCAAGC
* * * ** * * * *
54073 ACAAATGAATTATAGAAGCA
63 ATAATTAAAGAACACAATCT
* *
54093 ATTACTGTCACTGAACAAATTAAAAACAACAATCTCAGCAACTTTTTAGAAGCACGACCAAGCAT
1 ACTACTGTCACTGAACAAATT-AAAACAACAATCTCAGCAACTTTTTAGAAGCACAACCAAGCAT
*
54158 AATTGAAGAACACAATCT
65 AATTAAAGAACACAATCT
* * * * *
54176 ACTACTGTTACTGAACAAA-T-AAA-AACGATCTCAGCAAC-TTTTATAAGTA-AATCCAAGGAT
1 ACTACTGTCACTGAACAAATTAAAACAACAATCTCAGCAACTTTTTAGAAGCACAA-CCAAGCAT
54236 AATTAAAGAA
65 AATTAAAGAA
54246 GAGAAGTGGG
Statistics
Matches: 127, Mismatches: 22, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
77 1 0.01
78 25 0.20
79 14 0.11
80 3 0.02
82 1 0.01
83 79 0.62
84 4 0.03
ACGTcount: A:0.45, C:0.21, G:0.12, T:0.22
Consensus pattern (82 bp):
ACTACTGTCACTGAACAAATTAAAACAACAATCTCAGCAACTTTTTAGAAGCACAACCAAGCATA
ATTAAAGAACACAATCT
Found at i:55637 original size:14 final size:14
Alignment explanation
Indices: 55618--55644 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
55608 AGCGGAAAGC
55618 TTTTGCTTAGCTGG
1 TTTTGCTTAGCTGG
55632 TTTTGCTTAGCTG
1 TTTTGCTTAGCTG
55645 TTTCTTCATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.15, G:0.26, T:0.52
Consensus pattern (14 bp):
TTTTGCTTAGCTGG
Found at i:56146 original size:15 final size:16
Alignment explanation
Indices: 56128--56165 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
56118 GGTATTTATT
56128 TAATTTTT-TTATTAA
1 TAATTTTTATTATTAA
*
56143 TAATTTTTCATTTTTAA
1 TAATTTTT-ATTATTAA
56160 TAATTT
1 TAATTT
56166 GTTGTTCTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 8 0.40
17 12 0.60
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (16 bp):
TAATTTTTATTATTAA
Found at i:57661 original size:23 final size:25
Alignment explanation
Indices: 57612--57672 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 25
57602 AATATGCAAA
*
57612 TTTACTA-TAATATTTTAAGTGTAG
1 TTTACTATTATTATTTTAAGTGTAG
*
57636 TTTA-TATT-TTATTTTAATTG-ATG
1 TTTACTATTATTATTTTAAGTGTA-G
57659 TTTACTATTATTAT
1 TTTACTATTATTAT
57673 CATGAACTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
22 1 0.03
23 17 0.55
24 9 0.29
25 4 0.13
ACGTcount: A:0.30, C:0.03, G:0.08, T:0.59
Consensus pattern (25 bp):
TTTACTATTATTATTTTAAGTGTAG
Found at i:61167 original size:27 final size:27
Alignment explanation
Indices: 61133--61254 Score: 95
Period size: 27 Copynumber: 4.5 Consensus size: 27
61123 ATGAGAAGCC
*
61133 CGTCAGGACTATTTAATGCGAGAAGTT
1 CGTCAGGACTATCTAATGCGAGAAGTT
* * * *
61160 CGTTAGGATTATCTACTGTGAGAAGTT
1 CGTCAGGACTATCTAATGCGAGAAGTT
* **
61187 TGTCAAAACTATCTAATGCGAGAAG-T
1 CGTCAGGACTATCTAATGCGAGAAGTT
* * *
61213 CTATCAGGACTATCTACTGCTG-GAAGTC
1 C-GTCAGGACTATCTAATGC-GAGAAGTT
* *
61241 CATCAAGACTATCT
1 CGTCAGGACTATCT
61255 GATGGGTGGA
Statistics
Matches: 73, Mismatches: 19, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
26 1 0.01
27 70 0.96
28 2 0.03
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (27 bp):
CGTCAGGACTATCTAATGCGAGAAGTT
Found at i:61252 original size:54 final size:54
Alignment explanation
Indices: 61124--61254 Score: 133
Period size: 54 Copynumber: 2.4 Consensus size: 54
61114 ATCATTTATA
* * * * *
61124 TGAGAAGCCCGTCAGGACTATTTAATGCGAGAAGTTCGTTAGGATTATCTACTG
1 TGAGAAGTCCATCAAGACTATCTAATGCGAGAAGTTCGTTAGGACTATCTACTG
*** *
61178 TGAGAAGTTTGTCAAAACTATCTAATGCGAGAAG-TC-TATCAGGACTATCTACTG
1 TGAGAAGTCCATCAAGACTATCTAATGCGAGAAGTTCGT-T-AGGACTATCTACTG
61232 CTG-GAAGTCCATCAAGACTATCT
1 -TGAGAAGTCCATCAAGACTATCT
61255 GATGGGTGGA
Statistics
Matches: 63, Mismatches: 11, Indels: 6
0.79 0.14 0.08
Matches are distributed among these distances:
52 1 0.02
53 3 0.05
54 57 0.90
55 2 0.03
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (54 bp):
TGAGAAGTCCATCAAGACTATCTAATGCGAGAAGTTCGTTAGGACTATCTACTG
Found at i:67939 original size:58 final size:58
Alignment explanation
Indices: 67885--68068 Score: 189
Period size: 57 Copynumber: 3.2 Consensus size: 58
67875 GTAAAAACAT
** * *
67885 AATTTTTGGAAGTTTAGGGGT-AAGCGGTAATTTTTAGAAAAATCGAGGTCAAAAATGG
1 AATTTTTGGAAG-TTAGGGGTAAAAAGGTAATTTTTGGAAAAATCGAGGTCAAAAATAG
* ** *
67943 AA-TTTTGGAAGTTAGGGGTAAAAATGT-ATTCTTTGGTGAAATCGAGGTTAAAAATAG
1 AATTTTTGGAAGTTAGGGGTAAAAAGGTAATT-TTTGGAAAAATCGAGGTCAAAAATAG
* * * *
68000 AATTTTTGGAAGATTGGGGGTAAAATGGTAATTTTTGGAAAAATC-AGGGTAAAAAATGG
1 AATTTTTGGAAG-TTAGGGGTAAAAAGGTAATTTTTGGAAAAATCGA-GGTCAAAAATAG
68059 AA-TTTTGGAA
1 AATTTTTGGAA
68069 AGTTCGAGAG
Statistics
Matches: 105, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
56 11 0.10
57 36 0.34
58 20 0.19
59 35 0.33
60 3 0.03
ACGTcount: A:0.38, C:0.03, G:0.27, T:0.32
Consensus pattern (58 bp):
AATTTTTGGAAGTTAGGGGTAAAAAGGTAATTTTTGGAAAAATCGAGGTCAAAAATAG
Found at i:67947 original size:116 final size:117
Alignment explanation
Indices: 67818--68069 Score: 273
Period size: 116 Copynumber: 2.2 Consensus size: 117
67808 GTCCGGGGGT
*
67818 AAAATGGTAAATTTTGGAAAAATCGGCGTAAAAAATGGAATC-TTGG-GAAATTC-AGGGGTAAA
1 AAAATGG--AATTTTGGAAAAATAGGCGT-AAAAATGGAATCTTTGGTGAAA-TCGA-GGGTAAA
* * * *
67880 AACATAATTTTTGGAAGTTTAGGGGT-AAGCGGTAATTTTTAGAAAAATC-GAGGTCA
61 AACAGAATTTTTGGAAGATTAGGGGTAAAACGGTAATTTTTAGAAAAATCAG-GGTAA
** * * * * *
67936 AAAATGGAATTTTGG-AAGTTAGGGGTAAAAATGTATTCTTTGGTGAAATCGAGGTTAAAAATAG
1 AAAATGGAATTTTGGAAAAATAGGCGTAAAAATGGAATCTTTGGTGAAATCGAGGGTAAAAACAG
* * *
68000 AATTTTTGGAAGATTGGGGGTAAAATGGTAATTTTTGGAAAAATCAGGGTAA
66 AATTTTTGGAAGATTAGGGGTAAAACGGTAATTTTTAGAAAAATCAGGGTAA
68052 AAAATGGAATTTTGGAAA
1 AAAATGGAATTTTGGAAA
68070 GTTCGAGAGT
Statistics
Matches: 113, Mismatches: 15, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
114 10 0.09
115 41 0.36
116 52 0.46
117 3 0.03
118 7 0.06
ACGTcount: A:0.40, C:0.04, G:0.26, T:0.30
Consensus pattern (117 bp):
AAAATGGAATTTTGGAAAAATAGGCGTAAAAATGGAATCTTTGGTGAAATCGAGGGTAAAAACAG
AATTTTTGGAAGATTAGGGGTAAAACGGTAATTTTTAGAAAAATCAGGGTAA
Found at i:68090 original size:59 final size:55
Alignment explanation
Indices: 67888--68093 Score: 182
Period size: 59 Copynumber: 3.5 Consensus size: 55
67878 AAAACATAAT
*** * *
67888 TTTTGGAAGTTTAGGGGTAAGCGGTAATTTTTAGAAAAATCGAGGTCAAAAATGGAA
1 TTTTGGAAG-TT-GGGGTAAAATGTAATTTTTGGAAAAATCGAGGTAAAAAATGGAA
** * *
67945 TTTTGGAAGTTAGGGGTAAAAATGT-ATTCTTTGGTGAAATCGAGGTTAAAAATAGAA
1 TTTTGGAAGTT-GGGGT-AAAATGTAATT-TTTGGAAAAATCGAGGTAAAAAATGGAA
68002 TTTTTGGAAGATTGGGGGTAAAATGGTAATTTTTGGAAAAATC-AGGGTAAAAAATGGAA
1 -TTTTGGAAG-TT-GGGGTAAAAT-GTAATTTTTGGAAAAATCGA-GGTAAAAAATGGAA
*
68061 TTTTGGAAAGTTCGAGAGTGAAAATGTAATTTT
1 TTTTGG-AAGTT-G-GGGT-AAAATGTAATTTT
68094 AGAAAAGTTT
Statistics
Matches: 124, Mismatches: 15, Indels: 18
0.79 0.10 0.11
Matches are distributed among these distances:
56 11 0.09
57 36 0.29
58 24 0.19
59 45 0.36
60 8 0.06
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.33
Consensus pattern (55 bp):
TTTTGGAAGTTGGGGTAAAATGTAATTTTTGGAAAAATCGAGGTAAAAAATGGAA
Found at i:69273 original size:3 final size:3
Alignment explanation
Indices: 69261--69309 Score: 53
Period size: 3 Copynumber: 15.3 Consensus size: 3
69251 TTTTTGTTAC
* *
69261 TAT TATT TAT TAT TAT TAAT TAA TGT TAT TAT TAT TATT TAT TAT TAT
1 TAT TA-T TAT TAT TAT T-AT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
69309 T
1 T
69310 TAAAATATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
3 30 0.77
4 9 0.23
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:69276 original size:10 final size:10
Alignment explanation
Indices: 69261--69311 Score: 59
Period size: 10 Copynumber: 4.9 Consensus size: 10
69251 TTTTTGTTAC
69261 TATTATTTAT
1 TATTATTTAT
*
69271 TATTATTAAT
1 TATTATTTAT
69281 TAATGT-TATTAT
1 T-AT-TAT-TTAT
69293 TATTATTTAT
1 TATTATTTAT
69303 TATTATTTA
1 TATTATTTA
69312 AAATATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
10 24 0.69
11 6 0.17
12 5 0.14
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (10 bp):
TATTATTTAT
Found at i:69302 original size:13 final size:14
Alignment explanation
Indices: 69261--69309 Score: 57
Period size: 13 Copynumber: 3.5 Consensus size: 14
69251 TTTTTGTTAC
69261 TATTATT-TATTAT
1 TATTATTATATTAT
*
69274 TATTAATTAATGTTAT
1 TATT-ATT-ATATTAT
69290 TATTATTAT-TTAT
1 TATTATTATATTAT
69303 TATTATT
1 TATTATT
69310 TAAAATATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 15 0.47
14 5 0.16
15 3 0.09
16 9 0.28
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (14 bp):
TATTATTATATTAT
Found at i:69302 original size:29 final size:29
Alignment explanation
Indices: 69255--69312 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
69245 TTCCCTTTTT
69255 TGTTACTATTATTTATTATTATTAATTAA
1 TGTTACTATTATTTATTATTATTAATTAA
* *
69284 TGTTATTATTA-TTATTTATTATTATTTAA
1 TGTTACTATTATTTA-TTATTATTAATTAA
69313 AATATTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 23 0.88
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (29 bp):
TGTTACTATTATTTATTATTATTAATTAA
Found at i:70017 original size:11 final size:11
Alignment explanation
Indices: 69995--70104 Score: 55
Period size: 11 Copynumber: 9.7 Consensus size: 11
69985 TTTGGACTTT
69995 TTAAAGTTTAAA
1 TTAAA-TTTAAA
*
70007 TTTAATTTAAA
1 TTAAATTTAAA
*
70018 ATAAATTTAAA
1 TTAAATTTAAA
70029 TTCAAA-TTAAA
1 TT-AAATTTAAA
* * *
70040 TCCAAACTCAAA
1 T-TAAATTTAAA
* * *
70052 ATAAGTTCAAA
1 TTAAATTTAAA
*
70063 TTTAAA-GTAAA
1 -TTAAATTTAAA
70074 TTCAAATTTAAA
1 TT-AAATTTAAA
*
70086 -TAAATTTAGAT
1 TTAAATTTA-AA
70097 TTAAATTT
1 TTAAATTT
70105 TAAAAAGAGG
Statistics
Matches: 74, Mismatches: 16, Indels: 16
0.70 0.15 0.15
Matches are distributed among these distances:
10 9 0.12
11 40 0.54
12 25 0.34
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:70028 original size:6 final size:6
Alignment explanation
Indices: 69994--70104 Score: 56
Period size: 6 Copynumber: 19.5 Consensus size: 6
69984 ATTTGGACTT
* *
69994 TTTAAA GTTTAAA TTT-AA TTTAAA -ATAAA TTTAAA TTCAAA -TTAAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
** * * * * * * *
70040 TCCAAA CTCAAA -ATAAG TTCAAA TTTAAA -GTAAA TTCAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
70086 --TAAA TTTAGA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTT
70105 TAAAAAGAGG
Statistics
Matches: 76, Mismatches: 21, Indels: 15
0.68 0.19 0.13
Matches are distributed among these distances:
4 4 0.05
5 19 0.25
6 47 0.62
7 6 0.08
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (6 bp):
TTTAAA
Found at i:70039 original size:17 final size:17
Alignment explanation
Indices: 70010--70103 Score: 82
Period size: 17 Copynumber: 5.6 Consensus size: 17
70000 GTTTAAATTT
* *
70010 AATTTAAAATAAATTTA
1 AATTTAAATTAAATTCA
* *
70027 AATTCAAATTAAATCCA
1 AATTTAAATTAAATTCA
* * * *
70044 AACTCAAAATAAGTTCA
1 AATTTAAATTAAATTCA
*
70061 AATTTAAAGTAAATTCA
1 AATTTAAATTAAATTCA
*
70078 AATTTAAA-TAAATTTA
1 AATTTAAATTAAATTCA
*
70094 GATTTAAATT
1 AATTTAAATT
70104 TTAAAAAGAG
Statistics
Matches: 62, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
16 14 0.23
17 48 0.77
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.36
Consensus pattern (17 bp):
AATTTAAATTAAATTCA
Found at i:70054 original size:34 final size:33
Alignment explanation
Indices: 70015--70103 Score: 97
Period size: 34 Copynumber: 2.7 Consensus size: 33
70005 AATTTAATTT
*
70015 AAAATAAATTTAAATTCAAATTAAATCCAAACTC
1 AAAATAAATTTAAATTTAAATTAAATCCAAA-TC
* * * * *
70049 AAAATAAGTTCAAATTTAAAGTAAATTCAAATT
1 AAAATAAATTTAAATTTAAATTAAATCCAAATC
* *
70082 TAAATAAATTTAGATTTAAATT
1 AAAATAAATTTAAATTTAAATT
70104 TTAAAAAGAG
Statistics
Matches: 44, Mismatches: 11, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
33 18 0.41
34 26 0.59
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.35
Consensus pattern (33 bp):
AAAATAAATTTAAATTTAAATTAAATCCAAATC
Found at i:72625 original size:18 final size:18
Alignment explanation
Indices: 72602--72639 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
72592 TTGTTCCATC
72602 ACCCTTTTCGACTTTATT
1 ACCCTTTTCGACTTTATT
72620 ACCCTTTTCGACTTTATT
1 ACCCTTTTCGACTTTATT
72638 AC
1 AC
72640 ATAGACCAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.18, C:0.29, G:0.05, T:0.47
Consensus pattern (18 bp):
ACCCTTTTCGACTTTATT
Found at i:77356 original size:14 final size:14
Alignment explanation
Indices: 77316--77358 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
77306 TTTAATATCA
*
77316 TTATTTTATTTTTC
1 TTATTTAATTTTTC
*
77330 TTTTTTCAA-TTTTC
1 TTATTT-AATTTTTC
77344 TTATTTAATTTTTC
1 TTATTTAATTTTTC
77358 T
1 T
77359 AACTATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 2 0.08
14 21 0.88
15 1 0.04
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.74
Consensus pattern (14 bp):
TTATTTAATTTTTC
Found at i:85623 original size:17 final size:18
Alignment explanation
Indices: 85597--85638 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
85587 AAATGTAAGT
85597 AAAT-AAATAAAATA-TA
1 AAATAAAATAAAATACTA
85613 AAATAAAATAAAATATCTA
1 AAATAAAATAAAATA-CTA
85632 AAATAAA
1 AAATAAA
85639 GTTTAAACCC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.17
17 10 0.43
19 9 0.39
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (18 bp):
AAATAAAATAAAATACTA
Found at i:86824 original size:30 final size:29
Alignment explanation
Indices: 86790--86970 Score: 204
Period size: 30 Copynumber: 6.1 Consensus size: 29
86780 AAAATTATAT
*
86790 TTTGACTCCTAAACTTTTAAAAAATTCAAA
1 TTTGAC-CCTAAACTTTTCAAAAATTCAAA
* * * *
86820 TTTGACCCCCAAAC-TTTCTAAAATCCAAG
1 TTTGA-CCCTAAACTTTTCAAAAATTCAAA
*
86849 TTTTACCCTTAAA-TTTTCCAAAAATTCAAA
1 TTTGACCC-TAAACTTTT-CAAAAATTCAAA
86879 TTTGACCCTAAACTTTTCAAAAATTCAAA
1 TTTGACCCTAAACTTTTCAAAAATTCAAA
* **
86908 TTTGACCCTTAAACTTTCCAAAAATTTGAA
1 TTTGACCC-TAAACTTTTCAAAAATTCAAA
*
86938 TTTGACCCCTAAACTTTCCAAAAATTCAAA
1 TTTGA-CCCTAAACTTTTCAAAAATTCAAA
86968 TTT
1 TTT
86971 AACCTGGTTT
Statistics
Matches: 128, Mismatches: 16, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
28 3 0.02
29 45 0.35
30 76 0.59
31 4 0.03
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.35
Consensus pattern (29 bp):
TTTGACCCTAAACTTTTCAAAAATTCAAA
Found at i:86875 original size:59 final size:59
Alignment explanation
Indices: 86790--86970 Score: 222
Period size: 59 Copynumber: 3.1 Consensus size: 59
86780 AAAATTATAT
** * * *
86790 TTTGACTCC-TAAACTTTTAAAAAATTCAAATTTGACCCCCAAACTTTCTAAAATCCAAG
1 TTTGAC-CCTTAAACTTTCCAAAAATTCAAATTTGACCCCTAAACTTTCAAAAATCCAAA
* * *
86849 TTTTACCCTTAAATTTTCCAAAAATTCAAATTTGA-CCCTAAACTTTTCAAAAATTCAAA
1 TTTGACCCTTAAACTTTCCAAAAATTCAAATTTGACCCCTAAAC-TTTCAAAAATCCAAA
** *
86908 TTTGACCCTTAAACTTTCCAAAAATTTGAATTTGACCCCTAAACTTTCCAAAAATTCAAA
1 TTTGACCCTTAAACTTTCCAAAAATTCAAATTTGACCCCTAAACTTT-CAAAAATCCAAA
86968 TTT
1 TTT
86971 AACCTGGTTT
Statistics
Matches: 106, Mismatches: 12, Indels: 7
0.85 0.10 0.06
Matches are distributed among these distances:
58 9 0.08
59 74 0.70
60 23 0.22
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.35
Consensus pattern (59 bp):
TTTGACCCTTAAACTTTCCAAAAATTCAAATTTGACCCCTAAACTTTCAAAAATCCAAA
Found at i:93740 original size:20 final size:21
Alignment explanation
Indices: 93704--93753 Score: 52
Period size: 20 Copynumber: 2.4 Consensus size: 21
93694 TCATTAAGCT
*
93704 TTAATT-AATCATTTTTA-ATC
1 TTAATTAAATCATATTTACA-C
93724 TTAATTAAATC-TATTTACAC
1 TTAATTAAATCATATTTACAC
93744 TTAATATAAA
1 TTAAT-TAAA
93754 CCATGCCAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (21 bp):
TTAATTAAATCATATTTACAC
Found at i:96354 original size:43 final size:43
Alignment explanation
Indices: 96293--96386 Score: 181
Period size: 43 Copynumber: 2.2 Consensus size: 43
96283 CACACCTCAG
96293 GTAGTTTTCTAGAGGACAAGCCATCTCATTCAAAACTCTTAAT
1 GTAGTTTTCTAGAGGACAAGCCATCTCATTCAAAACTCTTAAT
96336 GTAGTTTTCTAGAGGACAAGCCATCTCATTCAAAACTCTTAAT
1 GTAGTTTTCTAGAGGACAAGCCATCTCATTCAAAACTCTTAAT
96379 GT-GTTTTC
1 GTAGTTTTC
96387 CAACTAGTAT
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 6 0.12
43 45 0.88
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (43 bp):
GTAGTTTTCTAGAGGACAAGCCATCTCATTCAAAACTCTTAAT
Found at i:99056 original size:20 final size:21
Alignment explanation
Indices: 99020--99069 Score: 52
Period size: 20 Copynumber: 2.4 Consensus size: 21
99010 TAATTAAGCT
*
99020 TTAATT-AATCATTTTTA-ATC
1 TTAATTAAATCATATTTACA-C
99040 TTAATTAAATC-TATTTACAC
1 TTAATTAAATCATATTTACAC
99060 TTAATATAAA
1 TTAAT-TAAA
99070 CCATGTCGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (21 bp):
TTAATTAAATCATATTTACAC
Found at i:100284 original size:43 final size:42
Alignment explanation
Indices: 100203--100375 Score: 147
Period size: 43 Copynumber: 4.0 Consensus size: 42
100193 GTTGAGAATG
* * * * *
100203 ATTTGTATAAATGGAAGACTTATTTCTCAGGTTAAGCATGAGA
1 ATTTATATAAATGGAAGACTTATGTCTC-GGGTGAGAATGAGA
* *
100246 ATTTATATAAATGGAAGACTTATGACTCGGAGTGAGCATGAGA
1 ATTTATATAAATGGAAGACTTATGTCTCGG-GTGAGAATGAGA
* * *
100289 ATATGAT-TAAAT-GAAGACTCATGTCTTGGGATGAGAATGAG-
1 AT-TTATATAAATGGAAGACTTATGTCTCGGG-TGAGAATGAGA
* *
100330 ATTTATGATTAAAT-GAAGACTGATGTCTCGGAATGAGAATGAGA
1 ATTTAT-A-TAAATGGAAGACTTATGTCTCGG-GTGAGAATGAGA
100374 AT
1 AT
100376 ATGATTGAAG
Statistics
Matches: 108, Mismatches: 14, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
40 3 0.03
41 3 0.03
42 25 0.23
43 72 0.67
44 5 0.05
ACGTcount: A:0.37, C:0.08, G:0.24, T:0.31
Consensus pattern (42 bp):
ATTTATATAAATGGAAGACTTATGTCTCGGGTGAGAATGAGA
Found at i:100329 original size:42 final size:42
Alignment explanation
Indices: 100240--100392 Score: 173
Period size: 43 Copynumber: 3.6 Consensus size: 42
100230 CAGGTTAAGC
* * * * *
100240 ATGAGAAT-TTATATAAATGGAAGACTTATGACTCGGAGTGAGC
1 ATGAGAATATGAT-TAAAT-GAAGACTCATGTCTCGGAATGAGA
* *
100283 ATGAGAATATGATTAAATGAAGACTCATGTCTTGGGATGAGA
1 ATGAGAATATGATTAAATGAAGACTCATGTCTCGGAATGAGA
* *
100325 ATGAGATTTATGATTAAATGAAGACTGATGTCTCGGAATGAGA
1 ATGAGA-ATATGATTAAATGAAGACTCATGTCTCGGAATGAGA
* *
100368 ATGAGAATATGATTGAAGGAAGACT
1 ATGAGAATATGATTAAATGAAGACT
100393 TAAGACTCGA
Statistics
Matches: 94, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
42 40 0.43
43 51 0.54
44 3 0.03
ACGTcount: A:0.39, C:0.07, G:0.26, T:0.28
Consensus pattern (42 bp):
ATGAGAATATGATTAAATGAAGACTCATGTCTCGGAATGAGA
Found at i:101124 original size:21 final size:20
Alignment explanation
Indices: 101100--101139 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
101090 TGTTACACTT
*
101100 GTATCGGTAGAAGTATTACAA
1 GTATCGGTAAAAGT-TTACAA
101121 GTATCGGTAAAAGTTTACA
1 GTATCGGTAAAAGTTTACA
101140 TCGTTTCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.30
Consensus pattern (20 bp):
GTATCGGTAAAAGTTTACAA
Found at i:103571 original size:53 final size:53
Alignment explanation
Indices: 103492--103598 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
103482 CAAGAATTGC
103492 TAGATAGAGGGTTTATACGACCTAGCATATCACCTTCGGGTGTGCCCGTGTTA
1 TAGATAGAGGGTTTATACGACCTAGCATATCACCTTCGGGTGTGCCCGTGTTA
*
103545 TAGATAGAGGGTTTATACGACCTAGCATATCACCTTGGGGTGTGCCCGTGTTA
1 TAGATAGAGGGTTTATACGACCTAGCATATCACCTTCGGGTGTGCCCGTGTTA
103598 T
1 T
103599 TCTTGAAAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (53 bp):
TAGATAGAGGGTTTATACGACCTAGCATATCACCTTCGGGTGTGCCCGTGTTA
Found at i:106326 original size:37 final size:37
Alignment explanation
Indices: 106246--106329 Score: 93
Period size: 37 Copynumber: 2.3 Consensus size: 37
106236 GCACTTCCAG
* *
106246 ATTGCACCCAAAGTTGTCGCTGCATTATTATTTTCGAA
1 ATTGCACCCAAAGTTGTCGCTGCATGAGTATTTTC-AA
*
106284 A-TGCACCC-AAGATTGTCGTTGCATGAGTATTCTT-AA
1 ATTGCACCCAAAG-TTGTCGCTGCATGAGTATT-TTCAA
106320 ATTGCACCCA
1 ATTGCACCCA
106330 GGAATTTGCT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
36 6 0.15
37 30 0.77
38 3 0.08
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (37 bp):
ATTGCACCCAAAGTTGTCGCTGCATGAGTATTTTCAA
Found at i:107076 original size:80 final size:80
Alignment explanation
Indices: 106985--107147 Score: 317
Period size: 80 Copynumber: 2.0 Consensus size: 80
106975 ACTTTTGTAT
*
106985 TTACATTGACAATTTTAACTATCTTAATGTGCAGATCAGATTTAATTGTGTTGACATCTTTACTC
1 TTACATTGACAATTTTAACTATCTTAATGTGCAGATCAGATTTAATTGTGCTGACATCTTTACTC
107050 ACATTGTCTCTAATC
66 ACATTGTCTCTAATC
107065 TTACATTGACAATTTTAACTATCTTAATGTGCAGATCAGATTTAATTGTGCTGACATCTTTACTC
1 TTACATTGACAATTTTAACTATCTTAATGTGCAGATCAGATTTAATTGTGCTGACATCTTTACTC
107130 ACATTGTCTCTAATC
66 ACATTGTCTCTAATC
107145 TTA
1 TTA
107148 GTTTTAATTG
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 82 1.00
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.42
Consensus pattern (80 bp):
TTACATTGACAATTTTAACTATCTTAATGTGCAGATCAGATTTAATTGTGCTGACATCTTTACTC
ACATTGTCTCTAATC
Found at i:109242 original size:17 final size:17
Alignment explanation
Indices: 109211--109268 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
109201 TAATTGTTCC
* *
109211 TGCATTATTAATGTCAT
1 TGCATTTTTATTGTCAT
**
109228 TGCATTTTTATTGTCGC
1 TGCATTTTTATTGTCAT
* **
109245 TGCATCTACATTGTCAT
1 TGCATTTTTATTGTCAT
109262 TGCATTT
1 TGCATTT
109269 CCATATATAT
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.21, C:0.17, G:0.14, T:0.48
Consensus pattern (17 bp):
TGCATTTTTATTGTCAT
Found at i:109831 original size:15 final size:15
Alignment explanation
Indices: 109811--109845 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
109801 CCAGTCACAT
109811 AAAAAGAAAGAA-AAA
1 AAAAAGAAA-AAGAAA
109826 AAAAAGAAAAAGAAA
1 AAAAAGAAAAAGAAA
109841 AAAAA
1 AAAAA
109846 ATATTTATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 2 0.11
15 17 0.89
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAGAAA
Found at i:110488 original size:37 final size:36
Alignment explanation
Indices: 110406--110488 Score: 87
Period size: 37 Copynumber: 2.2 Consensus size: 36
110396 TTTGCGCCCA
* *
110406 AAACTGTTGCCGCATGAGTACTTTCGGATTGCACCC
1 AAACTGTCGCCGCATGAGTACTTTCGGAATGCACCC
* * *
110442 AAAGTTGTCGCCGCATTATTA-TTTCTGGAATGCACCC
1 AAA-CTGTCGCCGCATGAGTACTTTC-GGAATGCACCC
110479 AAGACTGTCG
1 AA-ACTGTCG
110489 TTGCATAAGT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
36 7 0.18
37 30 0.79
38 1 0.03
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (36 bp):
AAACTGTCGCCGCATGAGTACTTTCGGAATGCACCC
Found at i:112704 original size:42 final size:42
Alignment explanation
Indices: 112630--112777 Score: 181
Period size: 42 Copynumber: 3.5 Consensus size: 42
112620 TGATGTATAA
* *
112630 AAAGGAAGACTCATGACTCG-GAGTGAGCATGAGAATATGATT
1 AAAGGAAGACTCATGTCTCGAGA-TGAGAATGAGAATATGATT
* *
112672 AAAGGAAGACTCTTGTCTCGAGATGAGAATGAGATTTATGATT
1 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGA-ATATGATT
* *
112715 AAAAGAAGACTCATGTCTCGAGATGAGAATTAGAATATGATT
1 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATT
* * * *
112757 TAAGAAAGACTTATGACTCGA
1 AAAGGAAGACTCATGTCTCGA
112778 TAAAGCATAA
Statistics
Matches: 91, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
42 51 0.56
43 40 0.44
ACGTcount: A:0.39, C:0.11, G:0.24, T:0.26
Consensus pattern (42 bp):
AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATT
Found at i:112725 original size:43 final size:42
Alignment explanation
Indices: 112629--112756 Score: 168
Period size: 43 Copynumber: 3.0 Consensus size: 42
112619 TTGATGTATA
* *
112629 AAAAGGAAGACTCATGACTCG-GAGTGAGCATGAGAATATGATT
1 AAAA-GAAGACTCATGTCTCGAGA-TGAGAATGAGAATATGATT
* * *
112672 AAAGGAAGACTCTTGTCTCGAGATGAGAATGAGATTTATGATT
1 AAAAGAAGACTCATGTCTCGAGATGAGAATGAGA-ATATGATT
*
112715 AAAAGAAGACTCATGTCTCGAGATGAGAATTAGAATATGATT
1 AAAAGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATT
112757 TAAGAAAGAC
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
42 31 0.42
43 43 0.58
ACGTcount: A:0.39, C:0.10, G:0.25, T:0.26
Consensus pattern (42 bp):
AAAAGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATT
Found at i:113461 original size:21 final size:21
Alignment explanation
Indices: 113432--113510 Score: 88
Period size: 21 Copynumber: 3.8 Consensus size: 21
113422 CTGAAGTTTT
113432 TAGTATCGGTAGAAGTATAAC
1 TAGTATCGGTAGAAGTATAAC
* *
113453 TAGTTTCGGTAGATGT-TACAC
1 TAGTATCGGTAGAAGTATA-AC
* *
113474 TTGTATCGGTAGAAGTATTAC
1 TAGTATCGGTAGAAGTATAAC
* *
113495 AAGTATCGGTAAAAGT
1 TAGTATCGGTAGAAGT
113511 CTACATCGTT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
20 2 0.04
21 44 0.94
22 1 0.02
ACGTcount: A:0.33, C:0.10, G:0.24, T:0.33
Consensus pattern (21 bp):
TAGTATCGGTAGAAGTATAAC
Found at i:119352 original size:43 final size:43
Alignment explanation
Indices: 119299--119380 Score: 137
Period size: 43 Copynumber: 1.9 Consensus size: 43
119289 GAGCATTAGA
119299 TATGATTAAAAGAAGACTCATGTCTCAGGATGAGAATGACATT
1 TATGATTAAAAGAAGACTCATGTCTCAGGATGAGAATGACATT
* * *
119342 TATGATTAAAAGAAGATTGATGTCTCGGGATGAGAATGA
1 TATGATTAAAAGAAGACTCATGTCTCAGGATGAGAATGA
119381 GAATATGATT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.39, C:0.09, G:0.24, T:0.28
Consensus pattern (43 bp):
TATGATTAAAAGAAGACTCATGTCTCAGGATGAGAATGACATT
Found at i:123843 original size:50 final size:50
Alignment explanation
Indices: 123729--123844 Score: 128
Period size: 50 Copynumber: 2.3 Consensus size: 50
123719 AAATAATGAG
* *
123729 TCTTATACTCCCTAAAGCTGTAGAGGAGCAGATTGAAGCCAGAATGGTGAG
1 TCTTATACT-CCTAAAGCTGTAGAGGAGCAGATTGAAGCCAGAATGGCGAA
* * * * *
123780 TCTCATACACCTAAAGCTGTAGAGGGGTAGATTGAAG-CTGCAA-GAGCGAA
1 TCTTATACTCCTAAAGCTGTAGAGGAGCAGATTGAAGCCAG-AATG-GCGAA
123830 TCTTATACTCCTAAA
1 TCTTATACTCCTAAA
123845 CCTAAAAAAG
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
49 3 0.06
50 44 0.81
51 7 0.13
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (50 bp):
TCTTATACTCCTAAAGCTGTAGAGGAGCAGATTGAAGCCAGAATGGCGAA
Found at i:124066 original size:40 final size:40
Alignment explanation
Indices: 124017--124471 Score: 411
Period size: 40 Copynumber: 11.4 Consensus size: 40
124007 GAAGTCACCA
* * *
124017 CATCTAATCTCTTACCCCGACCATGGGGCAGATCGAAGAC
1 CATCCAATCTTTTACCCCGACCATGGGGCAGATTGAAGAC
** * ** * *
124057 CATCCAATCTTTTACCCTAATCAAAGGCCAGATTGATGAC
1 CATCCAATCTTTTACCCCGACCATGGGGCAGATTGAAGAC
*
124097 CATCCAATCTTTTACCCCGACCATGGGGTAGATTGAA-AC
1 CATCCAATCTTTTACCCCGACCATGGGGCAGATTGAAGAC
* * ** *
124136 AATTCAATCTTTTACCCTAACCA-GAGGGTAGATTGAAGACC
1 CATCCAATCTTTTACCCCGACCATG-GGGCAGATTGAAGA-C
* * *
124177 ACATCCAATCTCTTACCCCGATCATGGGGCAGATCGAAGAC
1 -CATCCAATCTTTTACCCCGACCATGGGGCAGATTGAAGAC
* ** * *
124218 CATCCAATCTTTTA-CCCTAATAAGAGGGTAGATTGAAGAC
1 CATCCAATCTTTTACCCCGACCATG-GGGCAGATTGAAGAC
*
124258 CATCCAATCTTTTACCTCGACCATGGGGCAGATTGAAG-C
1 CATCCAATCTTTTACCCCGACCATGGGGCAGATTGAAGAC
* * *** **
124297 AATCTAATCTTTTACCTTAACCATATGGCAGATTGAAGAC
1 CATCCAATCTTTTACCCCGACCATGGGGCAGATTGAAGAC
*
124337 CATCCAATCTTTTACCCCTACCATGGGGCAGATTGAAG-C
1 CATCCAATCTTTTACCCCGACCATGGGGCAGATTGAAGAC
* ** * **
124376 AATCCAATCTTTTACCCTAACTAAAGGGCAGATTGAAGAC
1 CATCCAATCTTTTACCCCGACCATGGGGCAGATTGAAGAC
* * * * * *
124416 AATTCGATCTCTTACCTCGACCATAGGGCAGATTGAAGTA-
1 CATCCAATCTTTTACCCCGACCATGGGGCAGATTGAAG-AC
124456 -ATCCAATCTTTTACCC
1 CATCCAATCTTTTACCC
124472 TTAAAGCTAT
Statistics
Matches: 331, Mismatches: 74, Indels: 21
0.78 0.17 0.05
Matches are distributed among these distances:
38 1 0.00
39 117 0.35
40 175 0.53
41 8 0.02
42 29 0.09
43 1 0.00
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (40 bp):
CATCCAATCTTTTACCCCGACCATGGGGCAGATTGAAGAC
Found at i:124170 original size:79 final size:79
Alignment explanation
Indices: 124017--124472 Score: 554
Period size: 79 Copynumber: 5.7 Consensus size: 79
124007 GAAGTCACCA
* * * *
124017 CATCTAATCTCTTACCCCGACCATGGGGCAGATCGAAGACCATCCAATCTTTTACCCTAATCAAA
1 CATCCAATCTCTTACCCCGACCATGGGGCAGATTGAA-ACAATCCAATCTTTTACCCTAACCAAA
* *
124082 GGCCAGATTGATGAC
65 GGGCAGATTGAAGAC
* * * *
124097 CATCCAATCTTTTACCCCGACCATGGGGTAGATTGAAACAATTCAATCTTTTACCCTAACCAGAG
1 CATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAACAATCCAATCTTTTACCCTAACCAAAG
*
124162 GGTAGATTGAAGACC
66 GGCAGATTGAAGA-C
* * * *
124177 ACATCCAATCTCTTACCCCGATCATGGGGCAGATCGAAGACCATCCAATCTTTTACCCTAA-TAA
1 -CATCCAATCTCTTACCCCGACCATGGGGCAGATTGAA-ACAATCCAATCTTTTACCCTAACCAA
*
124241 GAGGGTAGATTGAAGAC
64 -AGGGCAGATTGAAGAC
* * * * * * *
124258 CATCCAATCTTTTACCTCGACCATGGGGCAGATTGAAGCAATCTAATCTTTTACCTTAACCATAT
1 CATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAACAATCCAATCTTTTACCCTAACCAAAG
124323 GGCAGATTGAAGAC
66 GGCAGATTGAAGAC
* * * *
124337 CATCCAATCTTTTACCCCTACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCCTAACTAAAG
1 CATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAACAATCCAATCTTTTACCCTAACCAAAG
124402 GGCAGATTGAAGAC
66 GGCAGATTGAAGAC
* * * * * **
124416 AATTCGATCTCTTACCTCGACCATAGGGCAGATTGAAGTAATCCAATCTTTTACCCT
1 CATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAACAATCCAATCTTTTACCCT
124473 TAAAGCTATA
Statistics
Matches: 325, Mismatches: 46, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
79 187 0.58
80 68 0.21
81 35 0.11
82 35 0.11
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (79 bp):
CATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAACAATCCAATCTTTTACCCTAACCAAAG
GGCAGATTGAAGAC
Found at i:124281 original size:161 final size:160
Alignment explanation
Indices: 124013--124472 Score: 649
Period size: 161 Copynumber: 2.9 Consensus size: 160
124003 GAGCGAAGTC
*
124013 ACCACATCTAATCTCTTACCCCGACCATGGGGCAGATCGAAGACCATCCAATCTTTTACCCTAAT
1 ACCACATCCAATCTCTTACCCCGACCATGGGGCAGATCGAAGACCATCCAATCTTTTACCCTAAT
* * * * *
124078 CAAAGGCCAGATTGATGACCATCCAATCTTTTACCCCGACCATGGGGTAGATTGAAACAATTCAA
66 -AAAGGGCAGATTGAAGACCATCCAATCTTTTACCTCGACCATGGGGCAGATTGAAGCAATTCAA
*
124143 TCTTTTACCCTAACCAGAGGGTAGATTGAAG
130 TCTTTTACCCTAACCAGAGGGCAGATTGAAG
*
124174 ACCACATCCAATCTCTTACCCCGATCATGGGGCAGATCGAAGACCATCCAATCTTTTACCCTAAT
1 ACCACATCCAATCTCTTACCCCGACCATGGGGCAGATCGAAGACCATCCAATCTTTTACCCTAAT
*
124239 AAGAGGGTAGATTGAAGACCATCCAATCTTTTACCTCGACCATGGGGCAGATTGAAGCAA-TCTA
66 AA-AGGGCAGATTGAAGACCATCCAATCTTTTACCTCGACCATGGGGCAGATTGAAGCAATTC-A
* * *
124303 ATCTTTTACCTTAACCATATGGCAGATTGAAG
129 ATCTTTTACCCTAACCAGAGGGCAGATTGAAG
* * * *
124335 A-C-CATCCAATCTTTTACCCCTACCATGGGGCAGATTGAAG-CAATCCAATCTTTTACCCTAAC
1 ACCACATCCAATCTCTTACCCCGACCATGGGGCAGATCGAAGACCATCCAATCTTTTACCCTAA-
* * * * * * *
124397 TAAAGGGCAGATTGAAGACAATTCGATCTCTTACCTCGACCATAGGGCAGATTGAAGTAATCCAA
65 TAAAGGGCAGATTGAAGACCATCCAATCTTTTACCTCGACCATGGGGCAGATTGAAGCAATTCAA
124462 TCTTTTACCCT
130 TCTTTTACCCT
124473 TAAAGCTATA
Statistics
Matches: 269, Mismatches: 26, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
158 82 0.30
159 38 0.14
160 5 0.02
161 144 0.54
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.26
Consensus pattern (160 bp):
ACCACATCCAATCTCTTACCCCGACCATGGGGCAGATCGAAGACCATCCAATCTTTTACCCTAAT
AAAGGGCAGATTGAAGACCATCCAATCTTTTACCTCGACCATGGGGCAGATTGAAGCAATTCAAT
CTTTTACCCTAACCAGAGGGCAGATTGAAG
Found at i:125228 original size:22 final size:22
Alignment explanation
Indices: 125187--125229 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
125177 ACAAAACCCA
*
125187 ATTTTATTTATTTTGTATTTTT
1 ATTTTATTTATTTTGCATTTTT
125209 ATTTTATTTATTTAT-CATTTT
1 ATTTTATTTATTT-TGCATTTT
125230 ATAAATGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (22 bp):
ATTTTATTTATTTTGCATTTTT
Found at i:125324 original size:10 final size:10
Alignment explanation
Indices: 125309--125347 Score: 62
Period size: 10 Copynumber: 3.9 Consensus size: 10
125299 CCGTTTTAAC
125309 TTTATTTAT-
1 TTTATTTATA
125318 TTATATTTATA
1 TT-TATTTATA
125329 TTTATTTATA
1 TTTATTTATA
125339 TTTATTTAT
1 TTTATTTAT
125348 CTATTTATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 2 0.07
10 24 0.86
11 2 0.07
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTATTTATA
Found at i:125332 original size:16 final size:16
Alignment explanation
Indices: 125311--125343 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
125301 GTTTTAACTT
125311 TATTTATTTATATTTA
1 TATTTATTTATATTTA
125327 TATTTATTTATATTTA
1 TATTTATTTATATTTA
125343 T
1 T
125344 TTATCTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTTATTTATATTTA
Found at i:126305 original size:30 final size:30
Alignment explanation
Indices: 126266--126467 Score: 212
Period size: 30 Copynumber: 6.7 Consensus size: 30
126256 TTAATCCTCA
* * ** *
126266 AACTGTCCAAAAATTTAAATTTGATTCTTG
1 AACTTTCCAAAAATTCAAATTTGACCCCTG
*
126296 AACTTTCCAAAAA-TCAAAGTTTTACCCCTG
1 AACTTTCCAAAAATTCAAA-TTTGACCCCTG
*
126326 AATTTTCCAAAAATTCAAATTTGACACCC-G
1 AACTTTCCAAAAATTCAAATTTGAC-CCCTG
* * *
126356 AACTTTCCAAAAATTTAAATTT-AACCCTCA
1 AACTTTCCAAAAATTCAAATTTGACCCCT-G
** *
126386 AACTTTCCAAAAATTTGAATTTGACCCCTA
1 AACTTTCCAAAAATTCAAATTTGACCCCTG
* *
126416 AACTTTCCAAAAATTCAAATTTGACACTTG
1 AACTTTCCAAAAATTCAAATTTGACCCCTG
*
126446 AACTTTCAAAAAATTCAAATTT
1 AACTTTCCAAAAATTCAAATTT
126468 AACCTGGTTT
Statistics
Matches: 146, Mismatches: 20, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
28 3 0.02
29 5 0.03
30 125 0.86
31 13 0.09
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.34
Consensus pattern (30 bp):
AACTTTCCAAAAATTCAAATTTGACCCCTG
Found at i:126398 original size:90 final size:90
Alignment explanation
Indices: 126266--126471 Score: 261
Period size: 90 Copynumber: 2.3 Consensus size: 90
126256 TTAATCCTCA
* * ** ** * * *
126266 AACTGTCCAAAAATTTAAATTTGATTCTTGAACTTTCCAAAAA-TCAAAGTTTTACCCCTGAATT
1 AACTTTCCAAAAATTTAAATTTAACCCTCAAACTTTCCAAAAATTCAAA-TTTGACCCCTAAACT
126330 TTCCAAAAATTCAAATTTGACACCCG
65 TTCCAAAAATTCAAATTTGACACCCG
**
126356 AACTTTCCAAAAATTTAAATTTAACCCTCAAACTTTCCAAAAATTTGAATTTGACCCCTAAACTT
1 AACTTTCCAAAAATTTAAATTTAACCCTCAAACTTTCCAAAAATTCAAATTTGACCCCTAAACTT
**
126421 TCCAAAAATTCAAATTTGACACTTG
66 TCCAAAAATTCAAATTTGACACCCG
* *
126446 AACTTTCAAAAAATTCAAATTTAACC
1 AACTTTCCAAAAATTTAAATTTAACC
126472 TGGTTTTAAT
Statistics
Matches: 100, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
90 97 0.97
91 3 0.03
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.33
Consensus pattern (90 bp):
AACTTTCCAAAAATTTAAATTTAACCCTCAAACTTTCCAAAAATTCAAATTTGACCCCTAAACTT
TCCAAAAATTCAAATTTGACACCCG
Found at i:127972 original size:14 final size:15
Alignment explanation
Indices: 127953--127982 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
127943 ATCAAACAAA
127953 ATGGAAAGAAC-TTG
1 ATGGAAAGAACGTTG
127967 ATGGAAAGAACGTTG
1 ATGGAAAGAACGTTG
127982 A
1 A
127983 GGTACATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.43, C:0.07, G:0.30, T:0.20
Consensus pattern (15 bp):
ATGGAAAGAACGTTG
Found at i:129295 original size:14 final size:15
Alignment explanation
Indices: 129278--129310 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
129268 TAGGGTTTAG
129278 TTTTTA-TCTTCATCT
1 TTTTTACTCTTCAT-T
129293 TTTTTACTCTTCATT
1 TTTTTACTCTTCATT
129308 TTT
1 TTT
129311 CTTCATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTTACTCTTCATT
Found at i:139495 original size:102 final size:102
Alignment explanation
Indices: 139299--139488 Score: 256
Period size: 102 Copynumber: 1.9 Consensus size: 102
139289 ACTCAATATT
* * * *
139299 CTCCGACTCATGATGCTGCTCACACAAGCTGTCGAGAATCCACGACGTATGTCAGATCTCAGCCA
1 CTCCCACTCACGATGCTGCTCACACAAGCTGTCGAGAATCCACAACATATGTCAGATCTCAGCCA
*
139364 TCGTGACGGTGTGTATCATCAGAGAACAATATCCATC
66 TCGTGACGGTGTATATCATCAGAGAACAATATCCATC
* * * ** *
139401 CTCCCACTCACGATGTTGCTCACACAAGTTGTTGAGAATCGGCAACATATGT-AGGATCTTAGCC
1 CTCCCACTCACGATGCTGCTCACACAAGCTGTCGAGAATCCACAACATATGTCA-GATCTCAGCC
*
139465 ATCGTGACGGTTTATATCATCAGA
65 ATCGTGACGGTGTATATCATCAGA
139489 ACACAATCCA
Statistics
Matches: 75, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
101 1 0.01
102 74 0.99
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (102 bp):
CTCCCACTCACGATGCTGCTCACACAAGCTGTCGAGAATCCACAACATATGTCAGATCTCAGCCA
TCGTGACGGTGTATATCATCAGAGAACAATATCCATC
Found at i:150770 original size:12 final size:12
Alignment explanation
Indices: 150755--150784 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
150745 GTGGAAACAG
150755 AGGAAGAAAAAA
1 AGGAAGAAAAAA
*
150767 AGGAAGAAAGAA
1 AGGAAGAAAAAA
150779 AGGAAG
1 AGGAAG
150785 GAAACGATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (12 bp):
AGGAAGAAAAAA
Found at i:151222 original size:51 final size:51
Alignment explanation
Indices: 151146--151247 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
151136 ACAAACTAAG
*
151146 TTAGTTTTTATTTCAGTTCTTAGTTTTAGTTTTCAGGCATAACATATAGCT
1 TTAGTTTTTATTTCAGATCTTAGTTTTAGTTTTCAGGCATAACATATAGCT
151197 TTAGTTTTTATTTCAGATCTTAGTTTTAGTTTTCAGGCATAACATATAGCT
1 TTAGTTTTTATTTCAGATCTTAGTTTTAGTTTTCAGGCATAACATATAGCT
151248 GTAATTTAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.50
Consensus pattern (51 bp):
TTAGTTTTTATTTCAGATCTTAGTTTTAGTTTTCAGGCATAACATATAGCT
Found at i:152435 original size:26 final size:26
Alignment explanation
Indices: 152374--152436 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
152364 CACCCAAAAT
* *
152374 TGTCGCTGCAGGAACCTGTTCAGAAA
1 TGTCGCTGCATGAACCTGTCCAGAAA
* * * *
152400 TATTGATGCATGAACCTGTCCAGAAG
1 TGTCGCTGCATGAACCTGTCCAGAAA
152426 TGTCGCTGCAT
1 TGTCGCTGCAT
152437 AAGATGATCC
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.27
Consensus pattern (26 bp):
TGTCGCTGCATGAACCTGTCCAGAAA
Found at i:157449 original size:37 final size:37
Alignment explanation
Indices: 157391--157488 Score: 151
Period size: 37 Copynumber: 2.6 Consensus size: 37
157381 CATTCTTGGG
157391 TGCAATTAAAGAATACTTATGCAGCGATAGTCCTGGA
1 TGCAATTAAAGAATACTTATGCAGCGATAGTCCTGGA
* * *
157428 TGTAATTGAAGAATATTTATGCAGCGATAGTCCTGGA
1 TGCAATTAAAGAATACTTATGCAGCGATAGTCCTGGA
* *
157465 TGCAATTAAAGGATACTCATGCAG
1 TGCAATTAAAGAATACTTATGCAG
157489 TGACAGCCTT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (37 bp):
TGCAATTAAAGAATACTTATGCAGCGATAGTCCTGGA
Found at i:161415 original size:39 final size:38
Alignment explanation
Indices: 161356--161500 Score: 96
Period size: 39 Copynumber: 3.7 Consensus size: 38
161346 GCTATCGAAC
* * * *
161356 TACTAAACTGGCAGTGACACTGTAACCACTGC-AATGAGA
1 TACTAAACTGACGGTAACACTGTAAACA-T-CAAATGAGA
* ** * *
161395 TACTAAACTGATGGTAACACTAAAAATATCATAATGTGA
1 TACTAAACTGACGGTAACACTGTAAACATCA-AATGAGA
* * * *
161434 TACTAAACTGACGGTAACACTGTAAATACCGTAACGCA-A
1 TACTAAACTGACGGTAACACTGTAAACATC-AAATG-AGA
* *
161473 TACTAAACTGACGATGACACTGTAAACA
1 TACTAAACTGACGGTAACACTGTAAACA
161501 CCATAATACT
Statistics
Matches: 83, Mismatches: 19, Indels: 8
0.75 0.17 0.07
Matches are distributed among these distances:
37 1 0.01
38 1 0.01
39 81 0.98
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23
Consensus pattern (38 bp):
TACTAAACTGACGGTAACACTGTAAACATCAAATGAGA
Found at i:162505 original size:20 final size:20
Alignment explanation
Indices: 162482--162521 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
162472 ATTTTATTGT
162482 AATA-AAATTAATTTAAAATA
1 AATAGAAATTAA-TTAAAATA
*
162502 AATAGAATTTAATTAAAATA
1 AATAGAAATTAATTAAAATA
162522 TACAATTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (20 bp):
AATAGAAATTAATTAAAATA
Found at i:162529 original size:54 final size:53
Alignment explanation
Indices: 162482--162777 Score: 270
Period size: 54 Copynumber: 5.6 Consensus size: 53
162472 ATTTTATTGT
162482 AATA-AAATTAATTTAAAATAAATAGAATTTAATTAAAATATACAATTTCAAGC
1 AATATAAATTAATTTAAAATAAATAGAATTTAATTAAAA-ATACAATTTCAAGC
** * * * * *
162535 AATATAAATTAATTTTTTTAA-AAATAAAATTTAATTCAAAAGTAAAATTTAAAGT
1 AATATAAATTAA--TTTAAAATAAATAGAATTTAATT-AAAAATACAATTTCAAGC
* *
162590 AATA-AAATTAAATTTAAAAGAAATAGAATTTAATTAAAAAATACAATTTCAACC
1 AATATAAATT-AATTTAAAATAAATAGAATTTAATT-AAAAATACAATTTCAAGC
* ** *
162644 AAAATAAATTAATTTAAAATAAATATTATTTAA-TAAAAAT-CAAAATT-AATTG-
1 AATATAAATTAATTTAAAATAAATAGAATTTAATTAAAAATAC-AATTTCAA--GC
* * * *
162696 AATATAAATAAATTTAAAATAAATAGAATTTAATTAAAAATAAAATTTAAAAC
1 AATATAAATTAATTTAAAATAAATAGAATTTAATTAAAAATACAATTTCAAGC
*
162749 AA-A-AAACTT-ATTTAAAATAAATACAATTT
1 AATATAAA-TTAATTTAAAATAAATAGAATTT
162778 CAACATGCTT
Statistics
Matches: 197, Mismatches: 31, Indels: 32
0.76 0.12 0.12
Matches are distributed among these distances:
51 25 0.13
52 41 0.21
53 23 0.12
54 64 0.32
55 35 0.18
56 9 0.05
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.34
Consensus pattern (53 bp):
AATATAAATTAATTTAAAATAAATAGAATTTAATTAAAAATACAATTTCAAGC
Found at i:162609 original size:21 final size:21
Alignment explanation
Indices: 162579--162629 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
162569 TTCAAAAGTA
*
162579 AAATTT-AAAGTAATAAAATT
1 AAATTTAAAAGAAATAAAATT
*
162599 AAATTTAAAAGAAATAGAATT
1 AAATTTAAAAGAAATAAAATT
* *
162620 TAATTAAAAA
1 AAATTTAAAA
162630 ATACAATTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 6 0.23
21 20 0.77
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (21 bp):
AAATTTAAAAGAAATAAAATT
Found at i:162620 original size:109 final size:104
Alignment explanation
Indices: 162480--162777 Score: 338
Period size: 109 Copynumber: 2.8 Consensus size: 104
162470 TAATTTTATT
* *
162480 GTAATAAAATT-AATTTAAAATAAATAGAATTTAATTAAAATATACAATTTCAAGCAATATAAAT
1 GTAATAAAATTAAATTTAAAATAAATAGAATTTAATTAAAA-ATACAATTTCAACCAAAATAAAT
** *
162544 TAATTTTTTTAA-AAATAAAATTTAATTCAAAAGT-AAAATTTAAA
65 TAA--TTTAAAATAAATAAAATTTAA-T-AAAAATCAAAA-TT-AA
*
162588 GTAATAAAATTAAATTTAAAAGAAATAGAATTTAATTAAAAAATACAATTTCAACCAAAATAAAT
1 GTAATAAAATTAAATTTAAAATAAATAGAATTTAATT-AAAAATACAATTTCAACCAAAATAAAT
**
162653 TAATTTAAAATAAATATTATTTAATAAAAATCAAAATTAA
65 TAATTTAAAATAAATAAAATTTAATAAAAATCAAAATTAA
* * * * *
162693 TTGAATATAAA-TAAATTTAAAATAAATAGAATTTAATTAAAAATAAAATTTAAAACAAAA-AAC
1 GT-AATA-AAATTAAATTTAAAATAAATAGAATTTAATTAAAAATACAATTTCAACCAAAATAAA
*
162756 TT-ATTTAAAATAAATACAATTT
64 TTAATTTAAAATAAATAAAATTT
162778 CAACATGCTT
Statistics
Matches: 168, Mismatches: 16, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
103 18 0.11
104 4 0.02
105 22 0.13
106 37 0.22
107 13 0.08
108 22 0.13
109 48 0.29
110 4 0.02
ACGTcount: A:0.58, C:0.04, G:0.03, T:0.35
Consensus pattern (104 bp):
GTAATAAAATTAAATTTAAAATAAATAGAATTTAATTAAAAATACAATTTCAACCAAAATAAATT
AATTTAAAATAAATAAAATTTAATAAAAATCAAAATTAA
Found at i:162664 original size:15 final size:15
Alignment explanation
Indices: 162644--162719 Score: 53
Period size: 15 Copynumber: 4.6 Consensus size: 15
162634 AATTTCAACC
162644 AAAATAAATTAATTT
1 AAAATAAATTAATTT
*
162659 AAAATAAATATTATTTAAT
1 AAAAT-AA-ATTAATT--T
*
162678 AAAAATCAAAATTAATTG
1 -AAAAT--AAATTAATTT
* *
162696 AATATAAATAAATTT
1 AAAATAAATTAATTT
162711 AAAATAAAT
1 AAAATAAAT
162720 AGAATTTAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
15 21 0.44
16 2 0.04
17 10 0.21
19 1 0.02
20 11 0.23
21 3 0.06
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (15 bp):
AAAATAAATTAATTT
Found at i:162714 original size:26 final size:26
Alignment explanation
Indices: 162675--162742 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 26
162665 AATATTATTT
*
162675 AATAAAAATCAAAATTAATTGAATATA
1 AATAAAAAT-AAAATTAATAGAATATA
** * *
162702 AATAAATTTAAAATAAATAGAATTTA
1 AATAAAAATAAAATTAATAGAATATA
*
162728 ATTAAAAATAAAATT
1 AATAAAAATAAAATT
162743 TAAAACAAAA
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
26 25 0.78
27 7 0.22
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.32
Consensus pattern (26 bp):
AATAAAAATAAAATTAATAGAATATA
Found at i:162720 original size:15 final size:15
Alignment explanation
Indices: 162644--162777 Score: 65
Period size: 16 Copynumber: 8.0 Consensus size: 15
162634 AATTTCAACC
*
162644 AAAATAAATTAATTT
1 AAAATAAATAAATTT
*
162659 AAAATAAATATTATTT
1 AAAATAAATA-AATTT
162675 AATAA-AAATCAAAATTAATT
1 AA-AATAAAT--AAA-T--TT
*
162695 GAATATAAATAAATTT
1 -AAAATAAATAAATTT
162711 AAAATAAATAGAATTT
1 AAAATAAATA-AATTT
162727 AATTAA-AAATAAAATTT
1 AA--AATAAAT-AAATTT
* *
162744 AAAACAAAAAACTTATTT
1 AAAATAAATAA---ATTT
162762 AAAATAAATACAATTT
1 AAAATAAATA-AATTT
162778 CAACATGCTT
Statistics
Matches: 93, Mismatches: 8, Indels: 35
0.68 0.06 0.26
Matches are distributed among these distances:
15 22 0.24
16 26 0.28
17 14 0.15
18 18 0.19
19 4 0.04
20 3 0.03
21 6 0.06
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.34
Consensus pattern (15 bp):
AAAATAAATAAATTT
Found at i:162720 original size:21 final size:21
Alignment explanation
Indices: 162696--162739 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
162686 AAATTAATTG
* *
162696 AATATAAATAAATTTAAAATA
1 AATAGAAATAAATTAAAAATA
* *
162717 AATAGAATTTAATTAAAAATA
1 AATAGAAATAAATTAAAAATA
162738 AA
1 AA
162740 ATTTAAAACA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
AATAGAAATAAATTAAAAATA
Found at i:164200 original size:13 final size:13
Alignment explanation
Indices: 164160--164211 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
164150 TTAAACCAAG
* *
164160 TTTTTCAAAAGTAT
1 TTTTT-AAAAGCAC
*
164174 TTTTTAAAACCAC
1 TTTTTAAAAGCAC
164187 TTTTTAAAAGCAC
1 TTTTTAAAAGCAC
* *
164200 TTCTCAAAAGCA
1 TTTTTAAAAGCA
164212 ATAATAAACT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
13 27 0.84
14 5 0.16
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.38
Consensus pattern (13 bp):
TTTTTAAAAGCAC
Found at i:169086 original size:19 final size:18
Alignment explanation
Indices: 169052--169336 Score: 69
Period size: 21 Copynumber: 14.4 Consensus size: 18
169042 TATTCTTAGC
169052 TAAAAATTTATTAAAATATTA
1 TAAAAATTTA--AAAA-ATTA
169073 TAACAAATTTAAAAAATTA
1 TAA-AAATTTAAAAAATTA
169092 TAAAAATTATAGAGAAAATTA
1 TAAAAATT-TA-A-AAAATTA
* **
169113 TAAACA-TTATTAAA--A
1 TAAAAATTTAAAAAATTA
*
169128 T--AAATTAAGAAAAATTA
1 TAAAAATTTA-AAAAATTA
**
169145 TTATGAAAATTTATCAAGTATTA
1 -TA--AAAATTTA--AAAAATTA
*
169168 TAAAACATTTTCAAAAGATTA
1 TAAAA-A-TTT-AAAAAATTA
*
169189 TGAAAAAATATAAAAATATTA
1 T--AAAAATTTAAAAA-ATTA
* *
169210 GAAAAATATAAAAAATTA
1 TAAAAATTTAAAAAATTA
* **
169228 TAAATATTTATTAACTATTA
1 TAAAAATTTA--AAAAATTA
* * *
169248 TGAAAAACATGAAATAATTA
1 T-AAAAA-TTTAAAAAATTA
*
169268 TAAAAGTATTATAGAAAATTTA
1 TAAAA--ATT-TA-AAAAATTA
*
169290 GAAAAATTGTTGAAAAAA-TA
1 TAAAAA-T-TT-AAAAAATTA
* *
169310 TAAAAACTGTAAAAAATCA
1 TAAAAA-TTTAAAAAATTA
169329 TAAAAATT
1 TAAAAATT
169337 ATATGAAATC
Statistics
Matches: 195, Mismatches: 37, Indels: 67
0.65 0.12 0.22
Matches are distributed among these distances:
13 2 0.01
14 2 0.01
15 5 0.03
17 4 0.02
18 24 0.12
19 36 0.18
20 37 0.19
21 41 0.21
22 33 0.17
23 11 0.06
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.33
Consensus pattern (18 bp):
TAAAAATTTAAAAAATTA
Found at i:169097 original size:10 final size:10
Alignment explanation
Indices: 169052--169339 Score: 96
Period size: 10 Copynumber: 28.2 Consensus size: 10
169042 TATTCTTAGC
*
169052 TAAAAATTTA
1 TAAAAAATTA
*
169062 TTAAAATATTA
1 -TAAAAAATTA
*
169073 TAACAAATT-
1 TAAAAAATTA
169082 TAAAAAATTA
1 TAAAAAATTA
169092 T-AAAAATTA
1 TAAAAAATTA
169101 TAGAGAAAATTA
1 TA-A-AAAATTA
*
169113 T-AAACATTA
1 TAAAAAATTA
169122 TTAAAATAAATTA
1 -T-AAA-AAATTA
169135 -AGAAAAATTA
1 TA-AAAAATTA
*
169145 TTATGAAAATTTA
1 -TA--AAAAATTA
* **
169158 TCAAGTATTA
1 TAAAAAATTA
* *
169168 TAAAACATTT
1 TAAAAAATTA
*
169178 TCAAAAGATTA
1 T-AAAAAATTA
169189 TGAAAAAA-TA
1 T-AAAAAATTA
169199 TAAAAATATTA
1 TAAAAA-ATTA
*
169210 -GAAAAA-TA
1 TAAAAAATTA
169218 TAAAAAATTA
1 TAAAAAATTA
* *
169228 TAAATATTTA
1 TAAAAAATTA
* **
169238 TTAACTATTA
1 TAAAAAATTA
* *
169248 TGAAAAA-CA
1 TAAAAAATTA
*
169257 TGAAATAATTA
1 T-AAAAAATTA
*
169268 TAAAAGTATTA
1 TAAAA-AATTA
*
169279 TAGAAAATT-
1 TAAAAAATTA
*
169288 TAGAAAAATTGT
1 TA-AAAAATT-A
169300 TGAAAAAA-TA
1 T-AAAAAATTA
* *
169310 T-AAAAACTG
1 TAAAAAATTA
*
169319 TAAAAAATCA
1 TAAAAAATTA
169329 T-AAAAATTA
1 TAAAAAATTA
169338 TA
1 TA
169340 TGAAATCATT
Statistics
Matches: 204, Mismatches: 46, Indels: 55
0.67 0.15 0.18
Matches are distributed among these distances:
8 7 0.03
9 48 0.24
10 80 0.39
11 37 0.18
12 18 0.09
13 14 0.07
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.33
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:169109 original size:21 final size:19
Alignment explanation
Indices: 169052--169362 Score: 104
Period size: 19 Copynumber: 15.8 Consensus size: 19
169042 TATTCTTAGC
*
169052 TAAAAATTTATTAAAATATTA
1 TAAAAA-TTA-TAAAAAATTA
169073 TAACAAATT-TAAAAAATTA
1 TAA-AAATTATAAAAAATTA
169092 TAAAAATTATAGAGAAAATTA
1 TAAAAATTATA-A-AAAATTA
* *
169113 TAAACATTAT--TAAA--A
1 TAAAAATTATAAAAAATTA
169128 T--AAATTA-AGAAAAATTA
1 TAAAAATTATA-AAAAATTA
* **
169145 TTATGAAAATTTATCAAGTATTA
1 -TA--AAAA-TTATAAAAAATTA
* *
169168 TAAAACATTTTCAAAAGATTA
1 TAAAA-ATTAT-AAAAAATTA
*
169189 TGAAAAAATATAAAAATATTA
1 T-AAAAATTATAAAAA-ATTA
*
169210 GAAAAA-TATAAAAAATTA
1 TAAAAATTATAAAAAATTA
* * **
169228 TAAATATTTATTAACTATTA
1 TAAA-AATTATAAAAAATTA
* *
169248 TGAAAAA-CATGAAATAATTA
1 T-AAAAATTAT-AAAAAATTA
*
169268 TAAAAGTATTATAGAAAATTTA
1 TAAAA--ATTATA-AAAAATTA
* *
169290 GAAAAATTGTTGAAAAAA-TA
1 TAAAAATT-AT-AAAAAATTA
* * *
169310 TAAAAACTGTAAAAAATCA
1 TAAAAATTATAAAAAATTA
** *
169329 TAAAAATTATATGAAATCA
1 TAAAAATTATAAAAAATTA
* *
169348 TTAAAATGATAAAAA
1 TAAAAATTATAAAAA
169363 TAAAATTATT
Statistics
Matches: 215, Mismatches: 44, Indels: 64
0.67 0.14 0.20
Matches are distributed among these distances:
13 5 0.02
15 5 0.02
17 4 0.02
18 19 0.09
19 57 0.27
20 45 0.21
21 46 0.21
22 25 0.12
23 9 0.04
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (19 bp):
TAAAAATTATAAAAAATTA
Found at i:169398 original size:8 final size:8
Alignment explanation
Indices: 169349--169406 Score: 52
Period size: 8 Copynumber: 7.4 Consensus size: 8
169339 ATGAAATCAT
*
169349 TAAAATGA
1 TAAAATTA
169357 TAAAA--A
1 TAAAATTA
169363 TAAAATTA
1 TAAAATTA
169371 TTAAAA--A
1 -TAAAATTA
169378 TAATAAGTTA
1 TAA-AA-TTA
169388 TAAAATTA
1 TAAAATTA
169396 TAAAATTA
1 TAAAATTA
169404 TAA
1 TAA
169407 TTTTCTATTA
Statistics
Matches: 43, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
6 9 0.21
7 3 0.07
8 20 0.47
9 7 0.16
10 4 0.09
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (8 bp):
TAAAATTA
Found at i:169672 original size:19 final size:20
Alignment explanation
Indices: 169650--169697 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 20
169640 AAGTATTAGT
169650 AATTATTAAAATATCAT-TA
1 AATTATTAAAATATCATATA
*
169669 AATT-TTAAAA-ATTATATA
1 AATTATTAAAATATCATATA
169687 AATTA-TAAAAT
1 AATTATTAAAAT
169698 TATAAAAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 4 0.16
18 17 0.68
19 4 0.16
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
AATTATTAAAATATCATATA
Found at i:169698 original size:17 final size:17
Alignment explanation
Indices: 169673--169716 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
169663 TCATTAAATT
*
169673 TTAAAAATTATATAAA-
1 TTAAAAATTATAAAAAC
169689 TTATAAAATTATAAAAAC
1 TTA-AAAATTATAAAAAC
169707 TTAAAAATTA
1 TTAAAAATTA
169717 CTCCTCTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 3 0.12
17 19 0.76
18 3 0.12
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (17 bp):
TTAAAAATTATAAAAAC
Found at i:169705 original size:9 final size:9
Alignment explanation
Indices: 169668--169716 Score: 57
Period size: 9 Copynumber: 5.7 Consensus size: 9
169658 AAATATCATT
*
169668 AAATTTTAA
1 AAATTATAA
*
169677 AAATTATAT
1 AAATTATAA
169686 AAATTAT-A
1 AAATTATAA
169694 AAATTATAA
1 AAATTATAA
*
169703 AAACT-TAA
1 AAATTATAA
169711 AAATTA
1 AAATTA
169717 CTCCTCTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
8 14 0.42
9 19 0.58
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (9 bp):
AAATTATAA
Found at i:170189 original size:22 final size:22
Alignment explanation
Indices: 170164--170208 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
170154 TAGTAGGAAT
170164 AATTAGGCATAAGATTATAGGC
1 AATTAGGCATAAGATTATAGGC
170186 AATTAGGCATAAGATTATAGGC
1 AATTAGGCATAAGATTATAGGC
170208 A
1 A
170209 TTAACACTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.42, C:0.09, G:0.22, T:0.27
Consensus pattern (22 bp):
AATTAGGCATAAGATTATAGGC
Found at i:180761 original size:2 final size:2
Alignment explanation
Indices: 180754--180806 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
180744 CATAAATTAA
180754 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT -T
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
180795 CT CT CT CT CT CT
1 CT CT CT CT CT CT
180807 GTTAATGCTG
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:180932 original size:6 final size:6
Alignment explanation
Indices: 180923--180964 Score: 75
Period size: 6 Copynumber: 6.8 Consensus size: 6
180913 GTTTACGTTG
180923 GCTTTT GCTTTT GCTTTTT GCTTTT GCTTTT GCTTTT GCTTT
1 GCTTTT GCTTTT GC-TTTT GCTTTT GCTTTT GCTTTT GCTTT
180965 GATTTCACCT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 29 0.83
7 6 0.17
ACGTcount: A:0.00, C:0.17, G:0.17, T:0.67
Consensus pattern (6 bp):
GCTTTT
Found at i:180943 original size:13 final size:13
Alignment explanation
Indices: 180925--180964 Score: 73
Period size: 13 Copynumber: 3.2 Consensus size: 13
180915 TTACGTTGGC
180925 TTTTGCTTTTGCT
1 TTTTGCTTTTGCT
180938 TTTTGCTTTTGC-
1 TTTTGCTTTTGCT
180950 TTTTGCTTTTGCT
1 TTTTGCTTTTGCT
180963 TT
1 TT
180965 GATTTCACCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 12 0.46
13 14 0.54
ACGTcount: A:0.00, C:0.15, G:0.15, T:0.70
Consensus pattern (13 bp):
TTTTGCTTTTGCT
Found at i:180947 original size:19 final size:18
Alignment explanation
Indices: 180923--180964 Score: 75
Period size: 19 Copynumber: 2.3 Consensus size: 18
180913 GTTTACGTTG
180923 GCTTTTGCTTTTGCTTTTT
1 GCTTTTGCTTTTGC-TTTT
180942 GCTTTTGCTTTTGCTTTT
1 GCTTTTGCTTTTGCTTTT
180960 GCTTT
1 GCTTT
180965 GATTTCACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.00, C:0.17, G:0.17, T:0.67
Consensus pattern (18 bp):
GCTTTTGCTTTTGCTTTT
Found at i:182894 original size:17 final size:18
Alignment explanation
Indices: 182872--182920 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
182862 ATTCATACAA
182872 AAATTTAAAAAATC-A-AT
1 AAATTTAAAAAA-CAATAT
182889 AAATTTAAGAAAACAATTAT
1 AAATTTAA-AAAACAA-TAT
182909 AAATTTAAAAAA
1 AAATTTAAAAAA
182921 AAAAAAACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
17 9 0.32
18 5 0.18
19 4 0.14
20 10 0.36
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (18 bp):
AAATTTAAAAAACAATAT
Found at i:186034 original size:31 final size:30
Alignment explanation
Indices: 185984--186055 Score: 126
Period size: 30 Copynumber: 2.4 Consensus size: 30
185974 AAGGTTTGTG
*
185984 CAAAAATATAAATCCAAAAAATGGACTTAAA
1 CAAAAA-AAAAATCCAAAAAATGGACTTAAA
186015 CAAAAAAAAAATCCAAAAAATGGACTTAAA
1 CAAAAAAAAAATCCAAAAAATGGACTTAAA
186045 CAAAAAAAAAA
1 CAAAAAAAAAA
186056 AAAAGTCTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
30 34 0.85
31 6 0.15
ACGTcount: A:0.68, C:0.12, G:0.06, T:0.14
Consensus pattern (30 bp):
CAAAAAAAAAATCCAAAAAATGGACTTAAA
Found at i:190415 original size:14 final size:14
Alignment explanation
Indices: 190396--190428 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
190386 TGTTTGACTA
*
190396 AAAATGATTTCTGG
1 AAAATGATTTCTAG
190410 AAAATGATTTCTAG
1 AAAATGATTTCTAG
190424 AAAAT
1 AAAAT
190429 AAATTACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.33
Consensus pattern (14 bp):
AAAATGATTTCTAG
Found at i:190844 original size:45 final size:46
Alignment explanation
Indices: 190793--190896 Score: 140
Period size: 45 Copynumber: 2.3 Consensus size: 46
190783 TAATATTACA
* * *
190793 AATTAGTAGTT-CACCACATGATAACTACAATAT-TTTCAAGTGCAT
1 AATTAGTA-TTACACCACATGATAACTACAACATCGTCCAAGTGCAT
190838 AATTAGTATTACACCACATGATAACTACAACATCGTCCAAGTGCAT
1 AATTAGTATTACACCACATGATAACTACAACATCGTCCAAGTGCAT
* *
190884 AACTAATATTACA
1 AATTAGTATTACA
190897 AATTAGTAGT
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
44 2 0.04
45 29 0.56
46 21 0.40
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (46 bp):
AATTAGTATTACACCACATGATAACTACAACATCGTCCAAGTGCAT
Found at i:191083 original size:67 final size:68
Alignment explanation
Indices: 190976--191161 Score: 241
Period size: 67 Copynumber: 2.7 Consensus size: 68
190966 TTTCTTATTC
* * * *
190976 TATTTATTTATTTATTATTTTATAAATATAAATAAATAAAT-ATAAAATAATATTAATTTTGTTT
1 TATTTATTTATTTATTATTATATGAATATAAATAAATAAATAATAAAATAATATCAATTTTATTT
191040 TAT
66 TAT
*
191043 TATTTATTTATTTATTATTGTATGAATATAAATAAATAAATAAATGTAAAATAATATCAATTTTA
1 TATTTATTTATTTATTATTATATGAATATAAATAAATAAAT-AA--TAAAATAATATCAATTTTA
191108 TTTTAT
63 TTTTAT
* * *
191114 TATTTATTTATTTTATGAATATA-GATAAATAAATAAATAAATAATAAA
1 TATTTATTTA-TTTATTATTATATGA-ATATAAATAAATAAATAATAAA
191162 CCCAAATTAC
Statistics
Matches: 105, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
67 39 0.37
69 5 0.05
71 37 0.35
72 24 0.23
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (68 bp):
TATTTATTTATTTATTATTATATGAATATAAATAAATAAATAATAAAATAATATCAATTTTATTT
TAT
Found at i:191093 original size:71 final size:69
Alignment explanation
Indices: 190976--191161 Score: 247
Period size: 71 Copynumber: 2.7 Consensus size: 69
190966 TTTCTTATTC
* * *
190976 TATTTATTTATTTATTATTTTATAAAT--ATAAATAAATAAATATAAAATAATATTAATTTTGTT
1 TATTTATTTATTTATTATTGTATAAATAAATAAATAAATAAATATAAAATAATATCAATTTTATT
191039 TTAT
66 TTAT
*
191043 TATTTATTTATTTATTATTGTATGAATATAAATAAATAAATAAATGTAAAATAATATCAATTTTA
1 TATTTATTTATTTATTATTGTAT-AA-ATAAATAAATAAATAAATATAAAATAATATCAATTTTA
191108 TTTTAT
64 TTTTAT
*
191114 TATTTATTTA-TT-TTA-TGAATATAGATAAATAAATAAATAAATAATAAA
1 TATTTATTTATTTATTATTG--TATAAATAAATAAATAAATAAAT-ATAAA
191162 CCCAAATTAC
Statistics
Matches: 106, Mismatches: 6, Indels: 12
0.85 0.05 0.10
Matches are distributed among these distances:
67 22 0.21
68 22 0.21
69 10 0.09
70 5 0.05
71 47 0.44
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (69 bp):
TATTTATTTATTTATTATTGTATAAATAAATAAATAAATAAATATAAAATAATATCAATTTTATT
TTAT
Found at i:192272 original size:30 final size:30
Alignment explanation
Indices: 192221--192305 Score: 118
Period size: 30 Copynumber: 2.9 Consensus size: 30
192211 TTATGTTTTG
* *
192221 ACCCTTAAAC-TTTCTAAAATTCCAATTTA
1 ACCCTTAAACTTTTCAAAAATTCAAATTTA
* *
192250 ACCCCTAAACTTTTCAAAAATTCAAATTTG
1 ACCCTTAAACTTTTCAAAAATTCAAATTTA
*
192280 ACCCTTTAACTTTTCAAAAATTCAAA
1 ACCCTTAAACTTTTCAAAAATTCAAA
192306 ATTTGACTCG
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
29 9 0.18
30 40 0.82
ACGTcount: A:0.40, C:0.24, G:0.01, T:0.35
Consensus pattern (30 bp):
ACCCTTAAACTTTTCAAAAATTCAAATTTA
Found at i:197634 original size:19 final size:16
Alignment explanation
Indices: 197593--197635 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
197583 GAAAGGACAT
197593 AATTACAACAATTGAA
1 AATTACAACAATTGAA
197609 AATTACAACAATTGAA
1 AATTACAACAATTGAA
*
197625 AATTACTACAA
1 AATTACAACAA
197636 GTTTCATGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.56, C:0.14, G:0.05, T:0.26
Consensus pattern (16 bp):
AATTACAACAATTGAA
Found at i:204085 original size:40 final size:40
Alignment explanation
Indices: 204023--204416 Score: 359
Period size: 40 Copynumber: 9.9 Consensus size: 40
204013 GAAGTCACCA
* * * * *
204023 CATCCGATCTCTTAACCGGACCATGGGGCAGATTAAAGAC
1 CATCCAATCTTTTACCCTGACCATGGGGCAGATTGAAGAC
* * ** *
204063 CATCCAATCTTTTATCCTGACCATGTGTAAAATTGAAG-C
1 CATCCAATCTTTTACCCTGACCATGGGGCAGATTGAAGAC
* *
204102 AATTCAATCTTTTACCCT-ACTCA-GAGGGCAGATTGAAGAC
1 CATCCAATCTTTTACCCTGAC-CATG-GGGCAGATTGAAGAC
* * * *
204142 CATCCAATCTTTTACCCCGACTATGGGGTAGATTGAAGAT
1 CATCCAATCTTTTACCCTGACCATGGGGCAGATTGAAGAC
* * * *
204182 CATTCAATCTTTTACCCTAATCA-GTGGGTAGATTGAAGAC
1 CATCCAATCTTTTACCCTGACCATG-GGGCAGATTGAAGAC
*
204222 CATCCAATCTTTTACCTTGACCATGGGGCAGATTGAAGAC
1 CATCCAATCTTTTACCCTGACCATGGGGCAGATTGAAGAC
* * ** * *
204262 CATCCAATCTTTTACCCTAATCAAAGGGCAAATTGAAGAT
1 CATCCAATCTTTTACCCTGACCATGGGGCAGATTGAAGAC
* * * * *
204302 CATCTAATTTTTTA-CCTCGACCATGGGGAAGATTTAAGAT
1 CATCCAATCTTTTACCCT-GACCATGGGGCAGATTGAAGAC
* * **
204342 CATCCAATCTTTTACCCTAATCA-GAGGATAGATTGAAGAC
1 CATCCAATCTTTTACCCTGACCATG-GGGCAGATTGAAGAC
* *
204382 CATCCAATCTTTTACCCCGACCATGGGGTAGATTG
1 CATCCAATCTTTTACCCTGACCATGGGGCAGATTG
204417 GATTGAAGCA
Statistics
Matches: 282, Mismatches: 61, Indels: 22
0.77 0.17 0.06
Matches are distributed among these distances:
38 3 0.01
39 32 0.11
40 239 0.85
41 8 0.03
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (40 bp):
CATCCAATCTTTTACCCTGACCATGGGGCAGATTGAAGAC
Found at i:204218 original size:80 final size:80
Alignment explanation
Indices: 204048--204416 Score: 474
Period size: 80 Copynumber: 4.6 Consensus size: 80
204038 CCGGACCATG
* * * * * *
204048 GGGCAGATTAAAGACCATCCAATCTTTTATCCTGACCAT-GTGTAAAATTGAAG--CAATTCAAT
1 GGGCAGATTGAAGACCATCCAATCTTTTACCCCGACCATGGGGT-AGATTGAAGATC-ATCCAAT
*
204110 CTTTTACCCTACTCAGA
64 CTTTTACCCTAATCAGA
* *
204127 GGGCAGATTGAAGACCATCCAATCTTTTACCCCGACTATGGGGTAGATTGAAGATCATTCAATCT
1 GGGCAGATTGAAGACCATCCAATCTTTTACCCCGACCATGGGGTAGATTGAAGATCATCCAATCT
*
204192 TTTACCCTAATCAGT
66 TTTACCCTAATCAGA
* ** * *
204207 GGGTAGATTGAAGACCATCCAATCTTTTACCTTGACCATGGGGCAGATTGAAGACCATCCAATCT
1 GGGCAGATTGAAGACCATCCAATCTTTTACCCCGACCATGGGGTAGATTGAAGATCATCCAATCT
*
204272 TTTACCCTAATCAAA
66 TTTACCCTAATCAGA
* * * * * * *
204287 GGGCAAATTGAAGATCATCTAATTTTTTACCTCGACCATGGGGAAGATTTAAGATCATCCAATCT
1 GGGCAGATTGAAGACCATCCAATCTTTTACCCCGACCATGGGGTAGATTGAAGATCATCCAATCT
204352 TTTACCCTAATCAGA
66 TTTACCCTAATCAGA
**
204367 GGATAGATTGAAGACCATCCAATCTTTTACCCCGACCATGGGGTAGATTG
1 GGGCAGATTGAAGACCATCCAATCTTTTACCCCGACCATGGGGTAGATTG
204417 GATTGAAGCA
Statistics
Matches: 251, Mismatches: 36, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
79 43 0.17
80 207 0.82
81 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (80 bp):
GGGCAGATTGAAGACCATCCAATCTTTTACCCCGACCATGGGGTAGATTGAAGATCATCCAATCT
TTTACCCTAATCAGA
Found at i:205169 original size:67 final size:67
Alignment explanation
Indices: 205059--205198 Score: 221
Period size: 67 Copynumber: 2.1 Consensus size: 67
205049 TACTTTTCTT
* * * *
205059 TTTA-TTATTATTTTATGAATATAAATAAATAAATAGAATATAATATTAATTTTGTTTTATTATT
1 TTTATTTATTATTGTATAAATATAAATAAACAAATAGAAAATAATATTAATTTTGTTTTATTATT
205123 TA
66 TA
205125 TTTATTTATTATTGTATAAATATAAATAAACAAAT-GTAAAATAATATTAATTTTGTTTTATTAT
1 TTTATTTATTATTGTATAAATATAAATAAACAAATAG-AAAATAATATTAATTTTGTTTTATTAT
205189 TTA
65 TTA
205192 TTTATTT
1 TTTATTT
205199 TATGAATATA
Statistics
Matches: 68, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
66 5 0.07
67 63 0.93
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (67 bp):
TTTATTTATTATTGTATAAATATAAATAAACAAATAGAAAATAATATTAATTTTGTTTTATTATT
TA
Found at i:205238 original size:13 final size:13
Alignment explanation
Indices: 205220--205263 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
205210 ATAAATAAAT
*
205220 AAATAATAAACCC
1 AAATAATAAACCA
205233 AAATAATAAACCA
1 AAATAATAAACCA
* * *
205246 AAATTACAAGCCA
1 AAATAATAAACCA
205259 AAATA
1 AAATA
205264 TACCAAAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.64, C:0.18, G:0.02, T:0.16
Consensus pattern (13 bp):
AAATAATAAACCA
Found at i:206386 original size:30 final size:29
Alignment explanation
Indices: 206350--206469 Score: 107
Period size: 29 Copynumber: 4.1 Consensus size: 29
206340 AAAAGTATAT
* *
206350 TTTGACCACTAAGCTTTTT-AAAATTTCAAA
1 TTTGACC-CTAA-ATTTTTCAAAAATTCAAA
* *
206380 TTTGACCCCAAATTTTTCAAAAATTCTAA
1 TTTGACCCTAAATTTTTCAAAAATTCAAA
** * *
206409 TTTGACCCTAAACCTTCCAAAAATTTAAA
1 TTTGACCCTAAATTTTTCAAAAATTCAAA
* * * *
206438 TTTAACCCAAAACTTTCCAAAAATTCAAA
1 TTTGACCCTAAATTTTTCAAAAATTCAAA
206467 TTT
1 TTT
206470 TGACTGAGTT
Statistics
Matches: 75, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
28 5 0.07
29 63 0.84
30 7 0.09
ACGTcount: A:0.40, C:0.21, G:0.03, T:0.36
Consensus pattern (29 bp):
TTTGACCCTAAATTTTTCAAAAATTCAAA
Found at i:206429 original size:29 final size:29
Alignment explanation
Indices: 206369--206469 Score: 121
Period size: 29 Copynumber: 3.5 Consensus size: 29
206359 TAAGCTTTTT
* * * *
206369 AAAATTTCAAATTTGACCCCAAATTTTTC
1 AAAAATTCAAATTTGACCCAAAACTTTCC
* * *
206398 AAAAATTCTAATTTGACCCTAAACCTTCC
1 AAAAATTCAAATTTGACCCAAAACTTTCC
* *
206427 AAAAATTTAAATTTAACCCAAAACTTTCC
1 AAAAATTCAAATTTGACCCAAAACTTTCC
206456 AAAAATTCAAATTT
1 AAAAATTCAAATTT
206470 TGACTGAGTT
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.44, C:0.21, G:0.02, T:0.34
Consensus pattern (29 bp):
AAAAATTCAAATTTGACCCAAAACTTTCC
Found at i:206689 original size:18 final size:19
Alignment explanation
Indices: 206642--206689 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
206632 ATCTACTTAA
206642 TTTATTATTT-TATTGTAT
1 TTTATTATTTATATTGTAT
206660 TTTATGTA--TATATTGT-T
1 TTTAT-TATTTATATTGTAT
206677 TTTATTATTTATA
1 TTTATTATTTATA
206690 CCTATAAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
16 2 0.08
17 7 0.27
18 15 0.58
19 2 0.08
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (19 bp):
TTTATTATTTATATTGTAT
Found at i:214087 original size:24 final size:25
Alignment explanation
Indices: 214055--214116 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
214045 ATAATATATG
*
214055 AAAT-ATTAATTTTAAA-TATTTTT
1 AAATAATTAATTTTAAATTATTTGT
*
214078 AAATAATTAA-TATAAATTATTTGT
1 AAATAATTAATTTTAAATTATTTGT
*
214102 AAA-ATTTAATTTTAA
1 AAATAATTAATTTTAA
214117 TACATATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
23 14 0.44
24 18 0.56
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (25 bp):
AAATAATTAATTTTAAATTATTTGT
Found at i:215038 original size:23 final size:23
Alignment explanation
Indices: 215003--215072 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
214993 TATTATAAAA
215003 TATAAAATTTTAATTTTAAATATT
1 TATAAAA-TTTAATTTTAAATATT
* *
215027 TATAAAAATTAA-TATAAACTATT
1 TATAAAATTTAATTTTAAA-TATT
*
215050 TGTAAAATTTAATTTTAATATAT
1 TATAAAATTTAATTTTAA-ATAT
215073 ATATCATATT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
22 5 0.13
23 18 0.47
24 14 0.37
25 1 0.03
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (23 bp):
TATAAAATTTAATTTTAAATATT
Found at i:218185 original size:10 final size:10
Alignment explanation
Indices: 218164--218248 Score: 54
Period size: 10 Copynumber: 8.4 Consensus size: 10
218154 AAATTTAAAA
218164 TTTA-AAATT
1 TTTATAAATT
*
218173 TTTATATATT
1 TTTATAAATT
218183 TTT-TAGAATT
1 TTTATA-AATT
218193 TTT-TAGAATT
1 TTTATA-AATT
218203 TTTAT-AATT
1 TTTATAAATT
*
218212 TTTAAATATAAAT
1 TTT--ATA-AATT
*
218225 TTT-GAAATT
1 TTTATAAATT
218234 TTTATAAATAT
1 TTTATAAAT-T
218245 TTTA
1 TTTA
218249 ATTTTAATTT
Statistics
Matches: 61, Mismatches: 6, Indels: 16
0.73 0.07 0.19
Matches are distributed among these distances:
9 19 0.31
10 28 0.46
11 8 0.13
13 6 0.10
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.59
Consensus pattern (10 bp):
TTTATAAATT
Found at i:218194 original size:9 final size:9
Alignment explanation
Indices: 218182--218215 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
218172 TTTTATATAT
218182 TTTTTAGAA
1 TTTTTAGAA
218191 TTTTTTAGAA
1 -TTTTTAGAA
*
218201 TTTTTATAA
1 TTTTTAGAA
218210 TTTTTA
1 TTTTTA
218216 AATATAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (9 bp):
TTTTTAGAA
Found at i:219246 original size:293 final size:292
Alignment explanation
Indices: 218655--219538 Score: 1419
Period size: 293 Copynumber: 3.0 Consensus size: 292
218645 AATAGGCTAA
** * *
218655 TCTTGGACTCCTGGACTCTACTTGTGCTTTTATGAGTGACTTAAAGCTTGTCTTACATCTCCTTG
1 TCTT-GACTCCTGGACTCTACTTGTATTTTTATGAGTGACTTCAAGCTTGTCTTATATCTCCTTG
* *
218720 GCATTGTCACACAAAGAGACTCTATTGTATTCATTAGGACCAAGGACACAAAATAAAATGTGCAT
65 GCATTGTCACACAAAGAGACTCTATTGTATTCATTGGGACCAAGGACACAAAATAAAGTGTGCAT
* * *
218785 AGCTTTGTCGTTTAGTTGAACCATCTTGATATCAACTTTATCCCACTCATTTTCCTTTTTTATGA
130 AGCTTTGTCATTTAGTTGCACCATCTTGATATCAACTTCATCCCACTCATTTTCCTTTTTTATGA
* *
218850 CAATGACACGGTCAACTCTTTTCTTTGGAATGGATGATCCATTTGTAACCACCCTCCATTCTTCA
195 CAATGACACGGTCAACTCTTTTCTTTGGAATGGATGACCCATTTGTAACCACCCTCCATACTTCA
* *
218915 TAGTCATTTGTTTGGATGAGATAAAACCATTTC
260 TAGTCATTTGCTTGGATGAGATAAAACCACTTC
* *
218948 TCTTGACTCCTGGACTTTACTTGTATTTTTATGAGTGACTTCAAGCTTGTCTTATATGTCCTTGG
1 TCTTGACTCCTGGACTCTACTTGTATTTTTATGAGTGACTTCAAGCTTGTCTTATATCTCCTTGG
*
219013 CATTGTCACACAAAGAGACTCTATTGTATTCATTGGGACCAAGGACACGAAATAAAGTGTGCATA
66 CATTGTCACACAAAGAGACTCTATTGTATTCATTGGGACCAAGGACACAAAATAAAGTGTGCATA
* * * *
219078 ACTTTGTTATTTAAATTGCACCATATTGATATCAACTTCATCCCACTCATTTTCCTTTTTTATGA
131 GCTTTGTCATTT-AGTTGCACCATCTTGATATCAACTTCATCCCACTCATTTTCCTTTTTTATGA
* * *
219143 CAATAACACAGTCAACTCTTTTCTTTGGAATGGATGACCCATTTGTAACCACTCTCCATACTTCA
195 CAATGACACGGTCAACTCTTTTCTTTGGAATGGATGACCCATTTGTAACCACCCTCCATACTTCA
* * *
219208 TAATCATTTACTTGGATGAGATAAAATCACTTC
260 TAGTCATTTGCTTGGATGAGATAAAACCACTTC
*
219241 TCTTGACTCCTGGACTCTACTTGTATTTTTATGAGTGACTTCAAGCTTGTCTTATATTTCCTTGG
1 TCTTGACTCCTGGACTCTACTTGTATTTTTATGAGTGACTTCAAGCTTGTCTTATATCTCCTTGG
* * *
219306 CATTATCACACAAAGAGACTTTATTGTATTCGTTGGGACCAA-GAGCACAAAATAAAGTGTGCAT
66 CATTGTCACACAAAGAGACTCTATTGTATTCATTGGGACCAAGGA-CACAAAATAAAGTGTGCAT
*
219370 AGCTTTGTCATTTAGTTGCACCATCTTGATATCAACTTCATCCTACTCATTTTCCTTTTTTATGA
130 AGCTTTGTCATTTAGTTGCACCATCTTGATATCAACTTCATCCCACTCATTTTCCTTTTTTATGA
*
219435 AAATGACACGGTCAACTCTTTTCTTTGGAATGGATGACCTCTATTTGTAACCACCCTCCATACTT
195 CAATGACACGGTCAACTCTTTTCTTTGGAATGGATGACC-C-ATTTGTAACCACCCTCCATACTT
*
219500 CACAGTCATTTGCTTGGATGAGATAAAACCACTTC
258 CATAGTCATTTGCTTGGATGAGATAAAACCACTTC
219535 TCTT
1 TCTT
219539 AAAGTTTTCT
Statistics
Matches: 542, Mismatches: 45, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
292 213 0.39
293 272 0.50
294 57 0.11
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (292 bp):
TCTTGACTCCTGGACTCTACTTGTATTTTTATGAGTGACTTCAAGCTTGTCTTATATCTCCTTGG
CATTGTCACACAAAGAGACTCTATTGTATTCATTGGGACCAAGGACACAAAATAAAGTGTGCATA
GCTTTGTCATTTAGTTGCACCATCTTGATATCAACTTCATCCCACTCATTTTCCTTTTTTATGAC
AATGACACGGTCAACTCTTTTCTTTGGAATGGATGACCCATTTGTAACCACCCTCCATACTTCAT
AGTCATTTGCTTGGATGAGATAAAACCACTTC
Found at i:221455 original size:23 final size:24
Alignment explanation
Indices: 221429--221477 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
221419 AATTTGTACA
221429 AATATTTTA-TTTTAGTAT-TTTAT
1 AATA-TTTACTTTTAGTATATTTAT
*
221452 AATATTTACTTTTATTATATTTAT
1 AATATTTACTTTTAGTATATTTAT
221476 AA
1 AA
221478 ATGATTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 4 0.17
23 12 0.52
24 7 0.30
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (24 bp):
AATATTTACTTTTAGTATATTTAT
Done.