Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 269 of 356
Found at i:88287006 original size:18 final size:18
Alignment explanation
Indices: 88286951--88286998 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
88286941 GATAACTAAA
88286951 AGGAAGCTGAGAACAAAG
1 AGGAAGCTGAGAACAAAG
* *
88286969 AGGAAACTGAGAACGAAG
1 AGGAAGCTGAGAACAAAG
88286987 AGGAAGCTGAGA
1 AGGAAGCTGAGA
88286999 CTAAAGAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.48, C:0.10, G:0.35, T:0.06
Consensus pattern (18 bp):
AGGAAGCTGAGAACAAAG
Found at i:88289272 original size:24 final size:25
Alignment explanation
Indices: 88289239--88289300 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
88289229 AGGTAGGACC
* *
88289239 TGATTTTGTATTTGAAA-TTGCATT
1 TGATTCTGTATCTGAAATTTGCATT
*
88289263 TGATTCTGTATCTGAAATTTGCATA
1 TGATTCTGTATCTGAAATTTGCATT
88289288 TG-TATCTGTATCT
1 TGAT-TCTGTATCT
88289301 TTTTGTTGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 16 0.48
25 17 0.52
ACGTcount: A:0.24, C:0.10, G:0.16, T:0.50
Consensus pattern (25 bp):
TGATTCTGTATCTGAAATTTGCATT
Found at i:88289512 original size:19 final size:19
Alignment explanation
Indices: 88289475--88289513 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
88289465 GGACTGTAAA
*
88289475 TTGTTTTAAACTTTATTTT
1 TTGTTTTAAACTTGATTTT
* *
88289494 TTGTTTTTAACTTGCTTTT
1 TTGTTTTAAACTTGATTTT
88289513 T
1 T
88289514 AAGATGAAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.08, G:0.08, T:0.69
Consensus pattern (19 bp):
TTGTTTTAAACTTGATTTT
Found at i:88290057 original size:33 final size:33
Alignment explanation
Indices: 88290020--88290086 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
88290010 TCTACTTTTG
88290020 AAAATAAGACTAAGATAACTCTGATAAAACTCT
1 AAAATAAGACTAAGATAACTCTGATAAAACTCT
88290053 AAAATAAGACTAAGATAACTCTGATAAAACTCT
1 AAAATAAGACTAAGATAACTCTGATAAAACTCT
88290086 A
1 A
88290087 GACTTAGAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.52, C:0.15, G:0.09, T:0.24
Consensus pattern (33 bp):
AAAATAAGACTAAGATAACTCTGATAAAACTCT
Found at i:88290940 original size:138 final size:138
Alignment explanation
Indices: 88290561--88291119 Score: 832
Period size: 138 Copynumber: 4.1 Consensus size: 138
88290551 TAGAAAAATG
* * * *
88290561 AATTATATTCTTTCCAAAATAATATTAATTTTCGTATCTTTTATATTTTAACCGAAATTAATTAA
1 AATTATATTCTTTTCAAAAGAATATTAATTTTCATTTCTTTTATATTTTAACCGAAATTAATTAA
* * * * *
88290626 TATATCTATTTATATAAATAAATTCAGTAAAATATATACAAGTAATATTTTGTATGAATCAAAAT
66 TATAACTGTTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
88290691 CATATATT
131 CATATATT
* * * * *
88290699 AATTATATTATGTTCAAAAGAATATT-ATTTTCATGTCTTTTATATTTTGACTGAAATTAATTAA
1 AATTATATTCTTTTCAAAAGAATATTAATTTTCATTTCTTTTATATTTTAACCGAAATTAATTAA
* *
88290763 TATAACTGTTTATATTAATAAATTCGGTAAAATATATACAAATAATATTTTGTATGAATCAAATT
66 TATAACTGTTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
88290828 CATATATT
131 CATATATT
* * * *
88290836 GATTATATTCTTTTCAAAAGAATATTAATTTTCATTTATTTTATATTTTAACCGGAATTAATTAG
1 AATTATATTCTTTTCAAAAGAATATTAATTTTCATTTCTTTTATATTTTAACCGAAATTAATTAA
* * *
88290901 TATAACTGTCTACATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTGTGAATCAAATT
66 TATAACTGTTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
88290966 CATATATT
131 CATATATT
* * * *
88290974 AATTATATTCTTTTTAAAAAAATACTAATTTTCATTTCTTTTATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTTCAAAAGAATATTAATTTTCATTTCTTTTATATTTTAACCGAAATTAATTAA
* * **
88291039 TATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGGTTCAAATT
66 TATAACTGTTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
88291104 CATATATT
131 CATATATT
88291112 AATTATAT
1 AATTATAT
88291120 CTATGTTCTT
Statistics
Matches: 377, Mismatches: 43, Indels: 2
0.89 0.10 0.00
Matches are distributed among these distances:
137 124 0.33
138 253 0.67
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.46
Consensus pattern (138 bp):
AATTATATTCTTTTCAAAAGAATATTAATTTTCATTTCTTTTATATTTTAACCGAAATTAATTAA
TATAACTGTTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
CATATATT
Found at i:88299765 original size:40 final size:40
Alignment explanation
Indices: 88299711--88299933 Score: 150
Period size: 41 Copynumber: 5.5 Consensus size: 40
88299701 TGCATTAAGA
* * *
88299711 GGTACTGAAATACAAAGAGGGCATGTATATGCAAGTCAAG
1 GGTACCGAAGTACAAACAGGGCATGTATATGCAAGTCAAG
*
88299751 GGTACCGAAGTACAAACAAGGGTATGT-T-TGTCTAA-TACCAA-
1 GGTACCGAAGTACAAAC-AGGGCATGTATATG-C-AAGT--CAAG
* *
88299792 GGTACCGAAGTACAAACAAGGCACGTATATGCAAGTCAAG
1 GGTACCGAAGTACAAACAGGGCATGTATATGCAAGTCAAG
* * * * * *
88299832 GGTATCGAAGTACAAACAGGGGCACGTTTGTGCAATTCAGG
1 GGTACCGAAGTACAAACA-GGGCATGTATATGCAAGTCAAG
** * * ** * * * *
88299873 GGTACTAAAGTATAAACAATGGCACATTTGTGCAAATCAGG
1 GGTACCGAAGTACAAAC-AGGGCATGTATATGCAAGTCAAG
88299914 GGTACC-AAGTACAAACAGGG
1 GGTACCGAAGTACAAACAGGG
88299934 GTACGCATGT
Statistics
Matches: 149, Mismatches: 23, Indels: 23
0.76 0.12 0.12
Matches are distributed among these distances:
39 8 0.05
40 51 0.34
41 84 0.56
42 6 0.04
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.20
Consensus pattern (40 bp):
GGTACCGAAGTACAAACAGGGCATGTATATGCAAGTCAAG
Found at i:88299820 original size:81 final size:81
Alignment explanation
Indices: 88299708--88299938 Score: 252
Period size: 81 Copynumber: 2.9 Consensus size: 81
88299698 AAGTGCATTA
* * * * *
88299708 AGAGGTACTGAAATACAAAGAGGGCATGTATATGCAAGTCAAGGGTACCGAAGTACAAACAAGGG
1 AGAGGTACTGAAGTACAAACAAGGCACGTATATGCAAGTCAAGGGTACCGAAGTACAAACAGGGG
*
88299773 TATGTTTGT-CTAATACC
66 TACGTTTGTGC-AAT-CC
* *
88299790 A-AGGTACCGAAGTACAAACAAGGCACGTATATGCAAGTCAAGGGTATCGAAGTACAAACAGGGG
1 AGAGGTACTGAAGTACAAACAAGGCACGTATATGCAAGTCAAGGGTACCGAAGTACAAACAGGGG
* *
88299854 CACGTTTGTGCAATTC
66 TACGTTTGTGCAATCC
* * * * * * * *
88299870 AGGGGTACTAAAGTATAAACAATGGCACATTTGTGCAAATCAGGGGTACC-AAGTACAAACAGGG
1 AGAGGTACTGAAGTACAAACAA-GGCACGTATATGCAAGTCAAGGGTACCGAAGTACAAACAGGG
88299934 GTACG
65 GTACG
88299939 CATGTGTAAA
Statistics
Matches: 125, Mismatches: 21, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
80 2 0.02
81 100 0.80
82 23 0.18
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.20
Consensus pattern (81 bp):
AGAGGTACTGAAGTACAAACAAGGCACGTATATGCAAGTCAAGGGTACCGAAGTACAAACAGGGG
TACGTTTGTGCAATCC
Found at i:88299934 original size:19 final size:20
Alignment explanation
Indices: 88299905--88299970 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 20
88299895 CACATTTGTG
88299905 CAAATCAGGGGTACCAAGTA
1 CAAATCAGGGGTACCAAGTA
* *
88299925 CAAA-CAGGGGTACGCATGTG
1 CAAATCAGGGGTAC-CAAGTA
* *
88299945 TAAATCAGGGGTGCCGAAGTA
1 CAAATCAGGGGTACC-AAGTA
88299966 CAAAT
1 CAAAT
88299971 AGAGGCATAT
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
19 9 0.25
20 12 0.33
21 15 0.42
ACGTcount: A:0.36, C:0.18, G:0.29, T:0.17
Consensus pattern (20 bp):
CAAATCAGGGGTACCAAGTA
Found at i:88299965 original size:81 final size:81
Alignment explanation
Indices: 88299792--88299969 Score: 205
Period size: 81 Copynumber: 2.2 Consensus size: 81
88299782 CTAATACCAA
* * *
88299792 GGTACCGAAGTACAAACAAGGCACGTATATGCAAGTCAAGGGTATCGAAGTACAAACAGGGGCAC
1 GGTACCGAAGTACAAACAAGGCACATATATGCAAATCAAGGGTATCCAAGTACAAACAGGGGCAC
** *
88299857 GTTTGTGCAATTCAGG
66 GCATGTGCAAATCAGG
** * * * * *
88299873 GGTACTAAAGTATAAACAATGGCACATTTGTGCAAATCAGGGGTA-CCAAGTACAAACAGGGGTA
1 GGTACCGAAGTACAAACAA-GGCACATATATGCAAATCAAGGGTATCCAAGTACAAACAGGGGCA
*
88299937 CGCATGTGTAAATCAGG
65 CGCATGTGCAAATCAGG
*
88299954 GGTGCCGAAGTACAAA
1 GGTACCGAAGTACAAA
88299970 TAGAGGCATA
Statistics
Matches: 78, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
81 58 0.74
82 20 0.26
ACGTcount: A:0.36, C:0.17, G:0.28, T:0.19
Consensus pattern (81 bp):
GGTACCGAAGTACAAACAAGGCACATATATGCAAATCAAGGGTATCCAAGTACAAACAGGGGCAC
GCATGTGCAAATCAGG
Found at i:88300724 original size:31 final size:31
Alignment explanation
Indices: 88300678--88300751 Score: 130
Period size: 31 Copynumber: 2.4 Consensus size: 31
88300668 TTTCAAAATT
*
88300678 CATTTTTTCTCTCTGCTGGAAAAATAATCTAG
1 CATTTCTT-TCTCTGCTGGAAAAATAATCTAG
88300710 CATTTCTTTCTCTGCTGGAAAAATAATCTAG
1 CATTTCTTTCTCTGCTGGAAAAATAATCTAG
88300741 CATTTCTTTCT
1 CATTTCTTTCT
88300752 TCTCCTTCCA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
31 34 0.83
32 7 0.17
ACGTcount: A:0.26, C:0.20, G:0.11, T:0.43
Consensus pattern (31 bp):
CATTTCTTTCTCTGCTGGAAAAATAATCTAG
Found at i:88302771 original size:25 final size:25
Alignment explanation
Indices: 88302743--88302791 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
88302733 TTGTTTTTGA
*
88302743 TAGTATATACTGAA-ATTACTATAGG
1 TAGTATATACT-AAGACTACTATAGG
88302768 TAGTATATACTAAGACTACTATAG
1 TAGTATATACTAAGACTACTATAG
88302792 ATAGACTGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 2 0.09
25 20 0.91
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (25 bp):
TAGTATATACTAAGACTACTATAGG
Found at i:88314998 original size:46 final size:44
Alignment explanation
Indices: 88314864--88315035 Score: 132
Period size: 46 Copynumber: 3.7 Consensus size: 44
88314854 CATTATGAGA
* * * * * *
88314864 GCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCATTGAGATGA
1 GCCAGTGTGAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGACGT
** * *
88314910 GCACTAGTGAAAGACATGTCTGAGACATGCTTCGGCCTCGAGACGT
1 GC-C-AGTGTGAGACATGTCTGGGACATGCATCGGCCTCGAGACGT
* *
88314956 AAGCTAGTGT-AGTACATGTCTGGGACATGCATCGG-CTACGAGATGT
1 --GCCAGTGTGAG-ACATGTCTGGGACATGCATCGGCCT-CGAGACGT
88315002 GCCAGTGTGAGACCATGTCTGGGACATGGCATCG
1 GCCAGTGTGAGA-CATGTCTGGGACAT-GCATCG
88315036 ACATAGATAT
Statistics
Matches: 103, Mismatches: 14, Indels: 18
0.76 0.10 0.13
Matches are distributed among these distances:
44 8 0.08
45 20 0.19
46 51 0.50
47 14 0.14
48 10 0.10
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.23
Consensus pattern (44 bp):
GCCAGTGTGAGACATGTCTGGGACATGCATCGGCCTCGAGACGT
Found at i:88316864 original size:39 final size:40
Alignment explanation
Indices: 88316748--88316971 Score: 262
Period size: 40 Copynumber: 5.7 Consensus size: 40
88316738 TTGAATGATG
* * * *
88316748 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * *
88316788 TCCGGACTAAGAT-CCAAAGGCATTTGTGCCG-GATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTG-CGAGTTACTAAA
*
88316828 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
88316867 TCCGGGTTAAGT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
88316906 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
88316947 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
88316972 AACGAGGAGC
Statistics
Matches: 159, Mismatches: 17, Indels: 16
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 68 0.43
40 79 0.50
41 9 0.06
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:88316937 original size:79 final size:79
Alignment explanation
Indices: 88316748--88316971 Score: 267
Period size: 79 Copynumber: 2.8 Consensus size: 79
88316738 TTGAATGATG
* * * * * *
88316748 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCAAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGCTAAG-TCCGAAGGCATT
*
88316812 TGTGCCGGATACTAAT
64 TGTGCCGGATACTAAA
* *
88316828 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTTAAGTCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCGAAGGCATTTG
*
88316892 TG-CGAGTTACTAAA
66 TGCCG-GATACTAAA
* *
88316906 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGCTAAGT-CCGAAGGCATT
88316970 TG
64 TG
88316972 AACGAGGAGC
Statistics
Matches: 125, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
77 2 0.02
78 32 0.26
79 59 0.47
80 32 0.26
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (79 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCGAAGGCATTTG
TGCCGGATACTAAA
Found at i:88316985 original size:40 final size:40
Alignment explanation
Indices: 88316829--88316990 Score: 136
Period size: 40 Copynumber: 4.1 Consensus size: 40
88316819 GATACTAATT
* ** *
88316829 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGACTATAA
* ** *
88316867 TCCGGGTTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
1 -CCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGACTATAA
* ** *
88316906 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGACTATAA
* *
88316947 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGA-CTATAA
88316987 CCGG
1 CCGG
88316991 TTAAATTCCG
Statistics
Matches: 111, Mismatches: 8, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
39 48 0.43
40 61 0.55
41 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.30, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGACTATAA
Found at i:88316993 original size:79 final size:79
Alignment explanation
Indices: 88316748--88317004 Score: 213
Period size: 79 Copynumber: 3.3 Consensus size: 79
88316738 TTGAATGATG
* * * * * * * *
88316748 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCAAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGCTAAG-TCCGAAGGCATT
** *
88316812 TGTGCCG-GAT-ACTAAT
64 TG-AACGAG-TGACTAAA
* *
88316828 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTTAAGTCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGCTAAGTCCGAAGGCATTTG
** *
88316892 TGCGAGTTACTAAA
66 AACGAGTGACTAAA
* *
88316906 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTGGTGCGAGTTACTA-AATCCGGGCTAAGT-CCGAAGGCATT
*
88316970 TGAACGAG-GAGCTATA
64 TGAACGAGTGA-CTAAA
* *
88316986 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
88317005 TACGTGATTT
Statistics
Matches: 149, Mismatches: 21, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
77 3 0.02
78 29 0.19
79 74 0.50
80 43 0.29
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGCTAAGTCCGAAGGCATTTG
AACGAGTGACTAAA
Found at i:88332195 original size:19 final size:20
Alignment explanation
Indices: 88332171--88332208 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
88332161 GGTACCACCA
88332171 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
88332190 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
88332209 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:88332592 original size:93 final size:93
Alignment explanation
Indices: 88332433--88332603 Score: 261
Period size: 93 Copynumber: 1.8 Consensus size: 93
88332423 GCCCCTAAGT
* ***
88332433 GAACTCAGACTCAACTCAATGAGCTCGGGTGTTCGCATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
*
88332498 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCAGATGCCTAGTTACATCTCAC
* * * *
88332526 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
88332591 CGAGTTCAGATGC
66 CGAGTTCAGATGC
88332604 TCAACCATCC
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 69 1.00
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
CGAGTTCAGATGCCTAGTTACATCTCAC
Found at i:88332593 original size:46 final size:46
Alignment explanation
Indices: 88332428--88332597 Score: 175
Period size: 46 Copynumber: 3.7 Consensus size: 46
88332418 AACCCGCCCC
* * * *** *
88332428 TAAGTGAACTCAGACTCAACTCAATGAGCTCGGGTGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
* * *
88332474 TAAATGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATCCA
* *
88332522 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
88332567 TAAGTGAACTCGGACTCAACTCAACGAGTTC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC
88332598 AGATGCTCAA
Statistics
Matches: 101, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 55 0.54
47 29 0.29
48 2 0.02
49 1 0.01
50 4 0.04
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
Found at i:88332619 original size:46 final size:45
Alignment explanation
Indices: 88332478--88332619 Score: 114
Period size: 46 Copynumber: 3.1 Consensus size: 45
88332468 CATCCATAAA
*
88332478 TGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CATCTCA-
1 TGAACTCGGACTCAACTCAACGAGTTCAGATGCTC-A---ACCATCT-AG
* * * * *
88332525 CGAACTCGGACTCAACTCAACGAGTTCGGACAT-TTGCATCCAT-AAG
1 TGAACTCGGACTCAACTCAACGAGTTC--AGATGCT-CAACCATCTAG
88332571 TGAACTCGGACTCAACTCAACGAGTTCAGATGCTCAACCATCCTAG
1 TGAACTCGGACTCAACTCAACGAGTTCAGATGCTCAACCAT-CTAG
88332617 TGA
1 TGA
88332620 CATGTCACTT
Statistics
Matches: 75, Mismatches: 11, Indels: 19
0.71 0.10 0.18
Matches are distributed among these distances:
44 9 0.12
45 2 0.03
46 31 0.41
47 29 0.39
49 3 0.04
50 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (45 bp):
TGAACTCGGACTCAACTCAACGAGTTCAGATGCTCAACCATCTAG
Found at i:88336716 original size:40 final size:40
Alignment explanation
Indices: 88336632--88336856 Score: 296
Period size: 40 Copynumber: 5.7 Consensus size: 40
88336622 TTGAATGATG
* * * *
88336632 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
88336672 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
88336712 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
88336751 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
88336791 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
88336832 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
88336857 AACGAGGAGC
Statistics
Matches: 165, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
39 34 0.21
40 121 0.73
41 10 0.06
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:88336878 original size:119 final size:119
Alignment explanation
Indices: 88336632--88336889 Score: 283
Period size: 119 Copynumber: 2.2 Consensus size: 119
88336622 TTGAATGATG
* *
88336632 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
* ** *
88336697 GTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
66 GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTGACTAAA
* * * **
88336751 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * * *
88336814 TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATA
64 TTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTGA-CTAAA
* *
88336871 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
88336890 TACGTGATTT
Statistics
Matches: 117, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
118 3 0.03
119 83 0.71
120 31 0.26
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTGACTAAA
Found at i:88344618 original size:40 final size:40
Alignment explanation
Indices: 88344538--88344758 Score: 261
Period size: 40 Copynumber: 5.5 Consensus size: 40
88344528 AATGATGTCC
* * * *
88344538 GGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCG
* * * *
88344578 GACTAAGAT-CCGAAGGCATTTGTGCGGGATACTAATTCCG
1 GGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAATCCG
*
88344618 GGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCG
* *
88344657 GGTTAATTCCCGAAGGCATTTGTGCGAGTTACTAAATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCG
* *
88344697 GGTTAAGTCCCAAAGGCATTTGTGCGAGTTACTATAA-CCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCCG
*
88344737 GGCTATGTCCCGAAGGCATTTG
1 GGCTAAGTCCCGAAGGCATTTG
88344759 AACGAGGAGC
Statistics
Matches: 155, Mismatches: 21, Indels: 10
0.83 0.11 0.05
Matches are distributed among these distances:
39 32 0.21
40 113 0.73
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCG
Found at i:88344776 original size:80 final size:79
Alignment explanation
Indices: 88344608--88344781 Score: 203
Period size: 80 Copynumber: 2.2 Consensus size: 79
88344598 TGTGCGGGAT
* * * *
88344608 ACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTTAATTCCCGAAGG
1 ACTAAATCCGGGTTAAGCCCAAAGGCATTGGTGCGAGTTACTAAATCCGGGCTAATTCCCGAAGG
** *
88344673 CATTTGTGCGAGTT
66 CATTTGAACGAGTG
*
88344687 ACTAAATCCGGGTTAAGTCCCAAAGGCATTTGTGCGAGTTACTATAA-CCGGGCT-ATGTCCCGA
1 ACTAAATCCGGGTTAAG-CCCAAAGGCATTGGTGCGAGTTACTA-AATCCGGGCTAAT-TCCCGA
88344750 AGGCATTTGAACGAG-G
63 AGGCATTTGAACGAGTG
*
88344766 AGCTATATCC-GGTTAA
1 A-CTAAATCCGGGTTAA
88344782 ATTCCGAAGG
Statistics
Matches: 82, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
79 24 0.29
80 56 0.68
81 2 0.02
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (79 bp):
ACTAAATCCGGGTTAAGCCCAAAGGCATTGGTGCGAGTTACTAAATCCGGGCTAATTCCCGAAGG
CATTTGAACGAGTG
Found at i:88353475 original size:46 final size:45
Alignment explanation
Indices: 88353357--88353522 Score: 167
Period size: 46 Copynumber: 3.6 Consensus size: 45
88353347 CACTTGTGTG
* * **
88353357 AGCTAGTGTAAGACATGTCTGGGACATGGCATCAGCATTAAGACG-
1 AGCTAGTGTAAGACATGTCTGGGACAT-GCATCGGCCTCGAGACGT
* * * *
88353402 AGCACTAGTGTAAGATATGTGTAGGACATGCTTCGGCCTCGAGACGT
1 AG--CTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGT
* *
88353449 AAGCTAGTGTAAGACATGTCTCGGACATGCATCGG-CTACGAGATGT
1 -AGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGACGT
88353495 -GCTAGTGTAAGACCATGTCTGGGACATG
1 AGCTAGTGTAAGA-CATGTCTGGGACATG
88353523 GCATTAGCAT
Statistics
Matches: 101, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
44 12 0.12
45 18 0.18
46 47 0.47
47 22 0.22
48 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.24
Consensus pattern (45 bp):
AGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGT
Found at i:88356240 original size:41 final size:41
Alignment explanation
Indices: 88356186--88356388 Score: 237
Period size: 41 Copynumber: 5.0 Consensus size: 41
88356176 AAAAGTGCAT
* * *
88356186 TCAGCGGTACCGAAGTACAAACAGGGGCATGTTTGTGTAAG
1 TCAGGGGTACCGAAGTACAAACAGGGGCATGTTTGTGCAAA
* * *
88356227 TCAGGGGTACCGAAATACAAACAGGGGCATGGTTGTGCAAT
1 TCAGGGGTACCGAAGTACAAACAGGGGCATGTTTGTGCAAA
* * *
88356268 TTA-AGGTACCAAAGTACAAACAGGGGCATGTTTGTGCAAA
1 TCAGGGGTACCGAAGTACAAACAGGGGCATGTTTGTGCAAA
** * * *
88356308 TCAGGGGTACCGAAGTACAAACAAAGCCACGTATGTGCAAA
1 TCAGGGGTACCGAAGTACAAACAGGGGCATGTTTGTGCAAA
* * * *
88356349 TCAGGGGTACCAAAGTACAAATAGGGGCACGTATGTGCAA
1 TCAGGGGTACCGAAGTACAAACAGGGGCATGTTTGTGCAA
88356389 CTCAACAGTA
Statistics
Matches: 137, Mismatches: 24, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
40 34 0.25
41 103 0.75
ACGTcount: A:0.34, C:0.18, G:0.29, T:0.19
Consensus pattern (41 bp):
TCAGGGGTACCGAAGTACAAACAGGGGCATGTTTGTGCAAA
Found at i:88356315 original size:81 final size:82
Alignment explanation
Indices: 88356186--88356388 Score: 248
Period size: 81 Copynumber: 2.5 Consensus size: 82
88356176 AAAAGTGCAT
* * * * *
88356186 TCAGCGGTACCGAAGTACAAACAGGGGCATGTTTGTGTAAGTCAGGGGTACCGAAATACAAACAG
1 TCAGAGGTACCAAAGTACAAACAGGGGCATGTTTGTGCAAATCAGGGGTACCGAAATACAAACAA
* * * *
88356251 GGGCATGGT-TGTGCAAT
66 AGCCA-CGTATGTGCAAA
* *
88356268 TTA-AGGTACCAAAGTACAAACAGGGGCATGTTTGTGCAAATCAGGGGTACCGAAGTACAAACAA
1 TCAGAGGTACCAAAGTACAAACAGGGGCATGTTTGTGCAAATCAGGGGTACCGAAATACAAACAA
88356332 AGCCACGTATGTGCAAA
66 AGCCACGTATGTGCAAA
* * * *
88356349 TCAGGGGTACCAAAGTACAAATAGGGGCACGTATGTGCAA
1 TCAGAGGTACCAAAGTACAAACAGGGGCATGTTTGTGCAA
88356389 CTCAACAGTA
Statistics
Matches: 103, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
80 2 0.02
81 67 0.65
82 34 0.33
ACGTcount: A:0.34, C:0.18, G:0.29, T:0.19
Consensus pattern (82 bp):
TCAGAGGTACCAAAGTACAAACAGGGGCATGTTTGTGCAAATCAGGGGTACCGAAATACAAACAA
AGCCACGTATGTGCAAA
Found at i:88356328 original size:21 final size:21
Alignment explanation
Indices: 88356304--88356375 Score: 51
Period size: 20 Copynumber: 3.5 Consensus size: 21
88356294 CATGTTTGTG
88356304 CAAATCAGGGGTACCGAAGTA
1 CAAATCAGGGGTACCGAAGTA
** ** * *
88356325 CAAA-CAAAGCCA-CGTATGTG
1 CAAATCAGGGGTACCG-AAGTA
*
88356345 CAAATCAGGGGTACCAAAGTA
1 CAAATCAGGGGTACCGAAGTA
88356366 CAAAT-AGGGG
1 CAAATCAGGGG
88356376 CACGTATGTG
Statistics
Matches: 35, Mismatches: 13, Indels: 7
0.64 0.24 0.13
Matches are distributed among these distances:
19 2 0.06
20 16 0.46
21 16 0.46
22 1 0.03
ACGTcount: A:0.40, C:0.19, G:0.26, T:0.14
Consensus pattern (21 bp):
CAAATCAGGGGTACCGAAGTA
Found at i:88365630 original size:37 final size:36
Alignment explanation
Indices: 88365567--88365652 Score: 102
Period size: 37 Copynumber: 2.4 Consensus size: 36
88365557 AAGTTCTGGC
* *
88365567 TCTTCATCTTCATCTTCACTTCTATCTCTAACCTCTA
1 TCTTCATCTTCATATTCACTTCTATCTCTAA-CACTA
* * *
88365604 TCTTGATCTTCATATTTATCTT-TATCTCTAACACTG
1 TCTTCATCTTCATATTCA-CTTCTATCTCTAACACTA
88365640 TCTTCATCTTCAT
1 TCTTCATCTTCAT
88365653 CTTGTTCTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
36 15 0.36
37 24 0.57
38 3 0.07
ACGTcount: A:0.20, C:0.29, G:0.02, T:0.49
Consensus pattern (36 bp):
TCTTCATCTTCATATTCACTTCTATCTCTAACACTA
Found at i:88366520 original size:37 final size:36
Alignment explanation
Indices: 88366457--88366542 Score: 111
Period size: 37 Copynumber: 2.4 Consensus size: 36
88366447 AAGTTCTGGC
* *
88366457 TCTTCATCTTCATCTTCACTTCTATCTCTAACCTCTA
1 TCTTCATCTTCATATTCACTTCTATCTCTAA-CACTA
* *
88366494 TCTTGATCTTCATATTTATCTT-TATCTCTAACACTA
1 TCTTCATCTTCATATTCA-CTTCTATCTCTAACACTA
88366530 TCTTCATCTTCAT
1 TCTTCATCTTCAT
88366543 CTTGTTCTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
36 16 0.37
37 24 0.56
38 3 0.07
ACGTcount: A:0.21, C:0.29, G:0.01, T:0.49
Consensus pattern (36 bp):
TCTTCATCTTCATATTCACTTCTATCTCTAACACTA
Found at i:88368392 original size:21 final size:22
Alignment explanation
Indices: 88368366--88368407 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
88368356 AAAAAAGAAA
*
88368366 AAAATAGT-AATGAAGAAATTG
1 AAAATAGTAAAAGAAGAAATTG
88368387 AAAATAGTAAAAGAAGAAATT
1 AAAATAGTAAAAGAAGAAATT
88368408 TGATATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.21
Consensus pattern (22 bp):
AAAATAGTAAAAGAAGAAATTG
Found at i:88369183 original size:35 final size:35
Alignment explanation
Indices: 88369137--88369209 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
88369127 TAAAAAGCCC
88369137 TAAGGGCATTTTGGTCATTTGGTAATCAAATGAAA
1 TAAGGGCATTTTGGTCATTTGGTAATCAAATGAAA
88369172 TAAGGGCATTTTGGTCATTTGGTAATCAAATGAAA
1 TAAGGGCATTTTGGTCATTTGGTAATCAAATGAAA
88369207 TAA
1 TAA
88369210 AAAGGGAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.08, G:0.22, T:0.34
Consensus pattern (35 bp):
TAAGGGCATTTTGGTCATTTGGTAATCAAATGAAA
Found at i:88372262 original size:25 final size:25
Alignment explanation
Indices: 88372228--88372280 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
88372218 ATGAAGACAT
*
88372228 ATCAATCCAAAAATGCCTAGATCAC
1 ATCAACCCAAAAATGCCTAGATCAC
*
88372253 ATCAACCCAAAAATGCCTAGATCCC
1 ATCAACCCAAAAATGCCTAGATCAC
88372278 ATC
1 ATC
88372281 CAAAAAGTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.42, C:0.32, G:0.08, T:0.19
Consensus pattern (25 bp):
ATCAACCCAAAAATGCCTAGATCAC
Found at i:88374900 original size:25 final size:25
Alignment explanation
Indices: 88374871--88374921 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
88374861 GTGTTCTGGG
88374871 TGTAGGATTATTTGACTATATTCTA
1 TGTAGGATTATTTGACTATATTCTA
*
88374896 TGTAGGATTATTTGACTGTATTCTA
1 TGTAGGATTATTTGACTATATTCTA
88374921 T
1 T
88374922 CTGATTGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.25, C:0.08, G:0.18, T:0.49
Consensus pattern (25 bp):
TGTAGGATTATTTGACTATATTCTA
Found at i:88377048 original size:9 final size:9
Alignment explanation
Indices: 88377019--88377077 Score: 64
Period size: 9 Copynumber: 6.6 Consensus size: 9
88377009 ATAAGTATAA
*
88377019 AATTAATCG
1 AATTAACCG
* *
88377028 AGTTAACTG
1 AATTAACCG
*
88377037 AATTACCCG
1 AATTAACCG
*
88377046 AATTACCCG
1 AATTAACCG
*
88377055 AATTAATCG
1 AATTAACCG
88377064 AATTAACCG
1 AATTAACCG
88377073 AATTA
1 AATTA
88377078 TTTGTATAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 41 1.00
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.29
Consensus pattern (9 bp):
AATTAACCG
Found at i:88377430 original size:18 final size:18
Alignment explanation
Indices: 88377407--88377442 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
88377397 TTCGATTAAC
88377407 CGACCGATTAACCGAATT
1 CGACCGATTAACCGAATT
*
88377425 CGACCGGTTAACCGAATT
1 CGACCGATTAACCGAATT
88377443 TTTTCAGTTT
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:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (18 bp):
CGACCGATTAACCGAATT
Found at i:88384694 original size:148 final size:148
Alignment explanation
Indices: 88384426--88384722 Score: 400
Period size: 148 Copynumber: 2.0 Consensus size: 148
88384416 AATCCCCATG
* * * * ** *
88384426 AAAAGTTTCCAGAACCTAGGAATCCTAATCTTCATTTTCCAGATATCCCGGGATTTTTGGGTGTT
1 AAAAGTTTCCAGAACCCAAGAATCCTAATCATCATTTTCCAGATATCCCAGGATTCATGGGTATT
* *
88384491 ATTTTCAAACATCTCGGTCAAGTGATTTTGTTTTTATTTTGAAAACACTTTTAAGAACACA-TTT
66 ATTTTCAAACATCTCGATCAAGTGATTTTGTTTTTATTTTGAAAACACTTCTAAGAACACACTTT
88384555 TTTTTTAAAATCTCTCAA
131 TTTTTTAAAATCTCTCAA
* * * *
88384573 AAAAGTTTTCAGAACCCAAGAAT-CTCGATCATCATTTTTCAGATATCCTAGGATTCATGGGATA
1 AAAAGTTTCCAGAACCCAAGAATCCT-AATCATCATTTTCCAGATATCCCAGGATTCATGGG-TA
* *
88384637 TTATTTTTAGACATCTCGATCAAGTGATTTTGTTTTTATTTTGAAAACACTTCTAAGAACACACT
64 TTATTTTCAAACATCTCGATCAAGTGATTTTGTTTTTATTTTGAAAACACTTCTAAGAACACA--
*
88384702 CTTTTTTTTTTAAATCTCTCA
127 CTTTTTTTTTAAAATCTCTCA
88384723 GAATTGTAAT
Statistics
Matches: 129, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
146 2 0.02
147 48 0.37
148 60 0.47
151 19 0.15
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (148 bp):
AAAAGTTTCCAGAACCCAAGAATCCTAATCATCATTTTCCAGATATCCCAGGATTCATGGGTATT
ATTTTCAAACATCTCGATCAAGTGATTTTGTTTTTATTTTGAAAACACTTCTAAGAACACACTTT
TTTTTTAAAATCTCTCAA
Found at i:88390384 original size:39 final size:39
Alignment explanation
Indices: 88390330--88390455 Score: 207
Period size: 39 Copynumber: 3.2 Consensus size: 39
88390320 TTTAGTGATG
*
88390330 TATATCCGAACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
88390369 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
* * *
88390408 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAA
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
*
88390447 TATGTCCGG
1 TATATCCGG
88390456 GCTAAAGTCC
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 82 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.27
Consensus pattern (39 bp):
TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
Found at i:88390469 original size:39 final size:39
Alignment explanation
Indices: 88390330--88390493 Score: 197
Period size: 39 Copynumber: 4.2 Consensus size: 39
88390320 TTTAGTGATG
* * *
88390330 TATATCCGAACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAT
* *
88390369 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAT
*
88390408 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAA
1 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAT
* * * * * *
88390447 TATGTCCGGGC-TAAAGTCCCGCAGGCTTCGAGCTGGTAT
1 TATATCCGGACTTAAGGT-CCGCAGGCTACGTGCTGGAAT
88390486 TATA-CCGG
1 TATATCCGG
88390494 GTTTAAATTC
Statistics
Matches: 112, Mismatches: 12, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
38 9 0.08
39 103 0.92
ACGTcount: A:0.22, C:0.23, G:0.29, T:0.26
Consensus pattern (39 bp):
TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAT
Found at i:88390508 original size:78 final size:78
Alignment explanation
Indices: 88390330--88390520 Score: 192
Period size: 78 Copynumber: 2.5 Consensus size: 78
88390320 TTTAGTGATG
* ** * **
88390330 TATATCCGAACTTAGGGTCCGCAGGCTATGTGCTGGAATTATATCCGGACTTAGGGTCCGCAGGC
1 TATATCCGGACTTAAAGTCCGCAGGCTATGTGCTGGAAATATATCCGGACTTAAAGTCCGCAGGC
*
88390395 TATGTGCTGGAAT
66 TATGAGCTGGAAT
* * * *
88390408 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATGTCCGGGC-TAAAGTCCCGCAGG
1 TATATCCGGACTTAAAGTCCGCAGGCTATGTGCTGGAAATATATCCGGACTTAAAGT-CCGCAGG
*
88390472 CT-TCGAGCTGGTAT
65 CTAT-GAGCTGGAAT
** *
88390486 TATA-CCGGGTTTAAATTCCCGCAGGCT-TGTGCTGG
1 TATATCCGGACTTAAAGT-CCGCAGGCTATGTGCTGG
88390521 TAATTGGTTT
Statistics
Matches: 95, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
77 21 0.22
78 74 0.78
ACGTcount: A:0.21, C:0.23, G:0.29, T:0.27
Consensus pattern (78 bp):
TATATCCGGACTTAAAGTCCGCAGGCTATGTGCTGGAAATATATCCGGACTTAAAGTCCGCAGGC
TATGAGCTGGAAT
Found at i:88390520 original size:38 final size:38
Alignment explanation
Indices: 88390348--88390525 Score: 148
Period size: 39 Copynumber: 4.6 Consensus size: 38
88390338 AACTTAGGGT
* **
88390348 CCGCAGGCTATGTGCTGGAATTATATCCGGACTTAGGGT-
1 CCGCAGGCTATGTGCTGGAATTATA-CCGG-GTTAAAGTC
* *
88390387 CCGCAGGCTATGTGCTGGAATTATATCCGGACTTAAGGT-
1 CCGCAGGCTATGTGCTGGAATTATA-CCGG-GTTAAAGTC
* * * *
88390426 CCGCAGGCTACGTGCTGGAAATATGTCCGGGCTAAAGTC
1 CCGCAGGCTATGTGCTGGAATTAT-ACCGGGTTAAAGTC
* * *
88390465 CCGCAGGCT-TCGAGCTGGTATTATACCGGGTTTAAATTC
1 CCGCAGGCTAT-GTGCTGGAATTATACCGGG-TTAAAGTC
88390504 CCGCAGGCT-TGTGCTGGTAATT
1 CCGCAGGCTATGTGCTGG-AATT
88390526 GGTTTCAAGT
Statistics
Matches: 118, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
38 16 0.14
39 102 0.86
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (38 bp):
CCGCAGGCTATGTGCTGGAATTATACCGGGTTAAAGTC
Found at i:88392306 original size:132 final size:138
Alignment explanation
Indices: 88392142--88392410 Score: 408
Period size: 132 Copynumber: 2.0 Consensus size: 138
88392132 AATCTTCCTA
*
88392142 GCAAGAATAAGTAAATTTTTATTTTCTGTTTTTTTTCTTTTTTACTCATTCGCTTTTCTATTTTC
1 GCAAGAATAAGTAAATTTTTATTTTCTATTTTTTTTCTTTTTTACTCATTCGCTTTTCTATTTTC
88392207 TT-G-A-G-CG-T-ACTATTTTGACCTTTTCAAACTTTTTCTTCTGATTGATTCTCAAAATTTTC
66 TTAGAACGTCGCTCACTATTTTGACCTTTTCAAACTTTTTCTTCTGATTGATTCTCAAAATTTTC
88392266 TATAATGT
131 TATAATGT
**
88392274 GCAAGAA-AGAGTAAATTTTTATTTTCTATTTTTTTTCTTTTTTACTCATTTTCTTTTCTATTTT
1 GCAAGAATA-AGTAAATTTTTATTTTCTATTTTTTTTCTTTTTTACTCATTCGCTTTTCTATTTT
*
88392338 CTTGAGAACGTCTCGCTCGACTATTTTGGCCTTTTCAAACTTTTTCTTCTGATTGATTCTCAAAA
65 CTT-AGAACG--TCGCTC-ACTATTTTGACCTTTTCAAACTTTTTCTTCTGATTGATTCTCAAAA
88392403 TTTTCTAT
126 TTTTCTAT
88392411 TTAAGCACAA
Statistics
Matches: 122, Mismatches: 4, Indels: 12
0.88 0.03 0.09
Matches are distributed among these distances:
131 1 0.01
132 62 0.51
134 1 0.01
135 1 0.01
136 1 0.01
139 2 0.02
140 1 0.01
142 53 0.43
ACGTcount: A:0.22, C:0.16, G:0.09, T:0.53
Consensus pattern (138 bp):
GCAAGAATAAGTAAATTTTTATTTTCTATTTTTTTTCTTTTTTACTCATTCGCTTTTCTATTTTC
TTAGAACGTCGCTCACTATTTTGACCTTTTCAAACTTTTTCTTCTGATTGATTCTCAAAATTTTC
TATAATGT
Found at i:88392314 original size:16 final size:16
Alignment explanation
Indices: 88392289--88392337 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
88392279 AAAGAGTAAA
*
88392289 TTTTTATTTTCTATTT
1 TTTTTCTTTTCTATTT
* * *
88392305 TTTTTCTTTTTTACTC
1 TTTTTCTTTTCTATTT
*
88392321 ATTTTCTTTTCTATTT
1 TTTTTCTTTTCTATTT
88392337 T
1 T
88392338 CTTGAGAACG
Statistics
Matches: 24, Mismatches: 9, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTCTTTTCTATTT
Found at i:88393285 original size:16 final size:16
Alignment explanation
Indices: 88393266--88393300 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
88393256 CCAAAAAATA
*
88393266 AAAAATTACAAGTCCC
1 AAAAATTAAAAGTCCC
*
88393282 AAAAATTAAAAGTTCC
1 AAAAATTAAAAGTCCC
88393298 AAA
1 AAA
88393301 GTTTTTAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.57, C:0.17, G:0.06, T:0.20
Consensus pattern (16 bp):
AAAAATTAAAAGTCCC
Found at i:88396860 original size:16 final size:15
Alignment explanation
Indices: 88396839--88396869 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
88396829 TAAAGTGTTT
88396839 ATAATATGAAAATAAA
1 ATAATAT-AAAATAAA
88396855 ATAATATAAAATAAA
1 ATAATATAAAATAAA
88396870 TAACATTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (15 bp):
ATAATATAAAATAAA
Found at i:88399265 original size:22 final size:21
Alignment explanation
Indices: 88399212--88399265 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 21
88399202 GAAGATATGA
88399212 AATCTTAGAG--ATAACTTGT
1 AATCTTAGAGATATAACTTGT
*
88399231 AATCTTAGAAGATATAATTTTGT
1 AATCTTAG-AGATATAA-CTTGT
88399254 AATCTTAGAGAT
1 AATCTTAGAGAT
88399266 TTGATTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 8 0.27
20 2 0.07
22 8 0.27
23 12 0.40
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (21 bp):
AATCTTAGAGATATAACTTGT
Found at i:88410244 original size:12 final size:12
Alignment explanation
Indices: 88410227--88410253 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
88410217 GTTGTTAGTG
88410227 GTTAGTGGGGAT
1 GTTAGTGGGGAT
88410239 GTTAGTGGGGAT
1 GTTAGTGGGGAT
88410251 GTT
1 GTT
88410254 GAGATAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.48, T:0.37
Consensus pattern (12 bp):
GTTAGTGGGGAT
Found at i:88411773 original size:18 final size:18
Alignment explanation
Indices: 88411750--88411795 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
88411740 AGTTTTGTAA
88411750 TTTTTGGACTCTCCGGAC
1 TTTTTGGACTCTCCGGAC
88411768 TTTTTGGACTCTCCGGAC
1 TTTTTGGACTCTCCGGAC
88411786 TTTTTGGACT
1 TTTTTGGACT
88411796 GTTTTGTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.11, C:0.24, G:0.22, T:0.43
Consensus pattern (18 bp):
TTTTTGGACTCTCCGGAC
Found at i:88419522 original size:43 final size:43
Alignment explanation
Indices: 88419475--88419598 Score: 135
Period size: 43 Copynumber: 2.9 Consensus size: 43
88419465 ACCGAGATGA
*
88419475 GATTACATGTAAAACCATGTCTGGGACATTGGCATTGTAT-TGT
1 GATTACATGTAAGACCATGTCTGGGACA-TGGCATTGTATATGT
** * **
88419518 GATTATGTGTAAGACCATGTCTGGGACAGTCGCA-TCAATATGT
1 GATTACATGTAAGACCATGTCTGGGACA-TGGCATTGTATATGT
* * *
88419561 GATAACATGTAAGACCATATCTGGGATATGGCATTGTA
1 GATTACATGTAAGACCATGTCTGGGACATGGCATTGTA
88419599 CGAGCTATAT
Statistics
Matches: 64, Mismatches: 15, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
42 7 0.11
43 57 0.89
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (43 bp):
GATTACATGTAAGACCATGTCTGGGACATGGCATTGTATATGT
Found at i:88431475 original size:13 final size:13
Alignment explanation
Indices: 88431457--88431483 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
88431447 TAAATAAAGT
88431457 CGTTAGATTATCC
1 CGTTAGATTATCC
88431470 CGTTAGATTATCC
1 CGTTAGATTATCC
88431483 C
1 C
88431484 AAGGCCCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (13 bp):
CGTTAGATTATCC
Found at i:88435878 original size:40 final size:39
Alignment explanation
Indices: 88435780--88436002 Score: 241
Period size: 40 Copynumber: 5.6 Consensus size: 39
88435770 TCCTCGTTCA
* * * * *
88435780 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
* *
88435819 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
88435858 GAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
* *
88435898 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
* * * * * *
88435938 AAAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCAC
* *
88435979 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
88436003 CAGCATTCAA
Statistics
Matches: 160, Mismatches: 20, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
39 37 0.23
40 115 0.72
41 8 0.05
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
Found at i:88436002 original size:120 final size:119
Alignment explanation
Indices: 88435780--88436002 Score: 272
Period size: 120 Copynumber: 1.9 Consensus size: 119
88435770 TCCTCGTTCA
* * * *
88435780 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATT
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATA
* *
88435845 TAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
66 TAACAACTAGCACGAAAGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * *
88435899 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAATCCGGA
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGA-CATAACCCGGA
* *
88435963 TATATTC-ACTTAGCAC-AAAGCCTTCGGGACTTAGCCCGGA
64 TATA-ACAAC-TAGCACGAAAGCCTTCGGGACTTAACCCGGA
88436003 CAGCATTCAA
Statistics
Matches: 87, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
119 37 0.43
120 44 0.51
121 6 0.07
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATA
TAACAACTAGCACGAAAGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:88441902 original size:26 final size:26
Alignment explanation
Indices: 88441866--88441973 Score: 198
Period size: 26 Copynumber: 4.2 Consensus size: 26
88441856 ATGAATTCCA
88441866 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
88441892 ATCATGGAACATTTACCTAACTCATT
1 ATCATGGAACATTTACCTAACCCATT
*
88441918 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
88441944 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
88441970 ATCA
1 ATCA
88441974 ATTTGTATCA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.36, C:0.26, G:0.06, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:88441984 original size:10 final size:10
Alignment explanation
Indices: 88441969--88442000 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
88441959 CCTAACCCAT
88441969 TATCAATTTG
1 TATCAATTTG
88441979 TATCAATTTG
1 TATCAATTTG
88441989 TATCAATTTG
1 TATCAATTTG
88441999 TA
1 TA
88442001 CCATAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.31, C:0.09, G:0.09, T:0.50
Consensus pattern (10 bp):
TATCAATTTG
Found at i:88453050 original size:21 final size:21
Alignment explanation
Indices: 88452989--88453050 Score: 52
Period size: 21 Copynumber: 3.0 Consensus size: 21
88452979 TAGCTTTTTT
* *
88452989 GAGCTTCAGTTTAACCCTTAT
1 GAGCTTCAGTTCAACCCTTAC
* * * * *
88453010 GGGTTTCCGTTCAGCTCTTAC
1 GAGCTTCAGTTCAACCCTTAC
*
88453031 GAGCTTCTGTTCAACCCTTA
1 GAGCTTCAGTTCAACCCTTA
88453051 TAGGTTTCTT
Statistics
Matches: 29, Mismatches: 12, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.37
Consensus pattern (21 bp):
GAGCTTCAGTTCAACCCTTAC
Found at i:88453079 original size:42 final size:42
Alignment explanation
Indices: 88452989--88453082 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
88452979 TAGCTTTTTT
* * * *
88452989 GAGCTTCAGTTTAACCCTTATGGGTTTCCGTTCAGCTCTTAC
1 GAGCTTCTGTTCAACCCTTATAGGTTTCCGTTCAGCACTTAC
** * *
88453031 GAGCTTCTGTTCAACCCTTATAGGTTTCTTTTTAGCACTTAT
1 GAGCTTCTGTTCAACCCTTATAGGTTTCCGTTCAGCACTTAC
*
88453073 GTGCTTCTGT
1 GAGCTTCTGT
88453083 GCTGCCTTCA
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.16, C:0.23, G:0.18, T:0.43
Consensus pattern (42 bp):
GAGCTTCTGTTCAACCCTTATAGGTTTCCGTTCAGCACTTAC
Found at i:88456607 original size:44 final size:43
Alignment explanation
Indices: 88456532--88456632 Score: 120
Period size: 44 Copynumber: 2.4 Consensus size: 43
88456522 TTGATATATG
* *
88456532 ATTTCGTGT-ATGACCACATCTGGGACGTTGGCATCG-ATTTGAA
1 ATTTCGTGTAATGACCACATCTAGGACATTGGCATCGTATTT--A
*
88456575 ATTTACGTGTAAT-ACCATATCTAGGACATTGGCATCGTATTTA
1 ATTT-CGTGTAATGACCACATCTAGGACATTGGCATCGTATTTA
88456618 ATTTCGTGTAA-GACC
1 ATTTCGTGTAATGACC
88456633 CTGTTTGGGA
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
42 10 0.20
43 9 0.18
44 26 0.51
45 6 0.12
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.35
Consensus pattern (43 bp):
ATTTCGTGTAATGACCACATCTAGGACATTGGCATCGTATTTA
Found at i:88456644 original size:42 final size:42
Alignment explanation
Indices: 88456499--88456652 Score: 123
Period size: 43 Copynumber: 3.6 Consensus size: 42
88456489 ATATCATGTC
* * * * * *
88456499 AGACCCTGTCTGGGATAGTGGCATTGATATATGATTTCGTGTA
1 AGACCCTATCTGGGACATTGGCATCG-TATTTAATTTCGTGTA
* *
88456542 TGACCAC-ATCTGGGACGTTGGCATCG-ATTTGAAATTTACGTGTA
1 AGACC-CTATCTGGGACATTGGCATCGTATTT--AATTT-CGTGTA
* * *
88456586 ATACCATATCTAGGACATTGGCATCGTATTTAATTTCGTGTA
1 AGACCCTATCTGGGACATTGGCATCGTATTTAATTTCGTGTA
* * *
88456628 AGACCCTGTTTGGGACAATGGCATC
1 AGACCCTATCTGGGACATTGGCATC
88456653 AATATTTGAT
Statistics
Matches: 86, Mismatches: 19, Indels: 13
0.73 0.16 0.11
Matches are distributed among these distances:
41 3 0.03
42 25 0.29
43 27 0.31
44 27 0.31
45 4 0.05
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (42 bp):
AGACCCTATCTGGGACATTGGCATCGTATTTAATTTCGTGTA
Found at i:88456699 original size:5 final size:5
Alignment explanation
Indices: 88456689--88456719 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
88456679 TGAGCATTCG
*
88456689 ATCGA ATCGA ATCGA ATCGA ATCAA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA A
88456720 AATTTTTGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.45, C:0.19, G:0.16, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:88456999 original size:19 final size:19
Alignment explanation
Indices: 88456975--88457016 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
88456965 TACAAGCGAC
*
88456975 ACAACATCAATCCAAATAA
1 ACAACATCAATCCAAAAAA
* *
88456994 ACAACATTAGTCCAAAAAA
1 ACAACATCAATCCAAAAAA
88457013 ACAA
1 ACAA
88457017 AAAAAAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.60, C:0.24, G:0.02, T:0.14
Consensus pattern (19 bp):
ACAACATCAATCCAAAAAA
Found at i:88459914 original size:30 final size:30
Alignment explanation
Indices: 88459878--88459944 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 30
88459868 GTTAAATTAA
*
88459878 AAATTAATTAATATAATAGTATAAGAGCAT
1 AAATTAATTAATATAATAGTACAAGAGCAT
*
88459908 AAATTAATTAATATAATAGTACAATAGCAT
1 AAATTAATTAATATAATAGTACAAGAGCAT
88459938 AAATTAA
1 AAATTAA
88459945 AAATAGATAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.55, C:0.04, G:0.07, T:0.33
Consensus pattern (30 bp):
AAATTAATTAATATAATAGTACAAGAGCAT
Found at i:88470812 original size:25 final size:25
Alignment explanation
Indices: 88470799--88470876 Score: 156
Period size: 25 Copynumber: 3.1 Consensus size: 25
88470789 ATAATTGTTA
88470799 TATATTATAATATATTTTCATTTGT
1 TATATTATAATATATTTTCATTTGT
88470824 TATATTATAATATATTTTCATTTGT
1 TATATTATAATATATTTTCATTTGT
88470849 TATATTATAATATATTTTCATTTGT
1 TATATTATAATATATTTTCATTTGT
88470874 TAT
1 TAT
88470877 TTTTATATTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 53 1.00
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (25 bp):
TATATTATAATATATTTTCATTTGT
Found at i:88470923 original size:21 final size:22
Alignment explanation
Indices: 88470884--88470924 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
88470874 TATTTTTATA
* *
88470884 TTATAGAAATAATATACAAATT
1 TTATAAAAAAAATATACAAATT
88470906 TTATAAAAAAAAT-TACAAA
1 TTATAAAAAAAATATACAAA
88470925 AACAACAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (22 bp):
TTATAAAAAAAATATACAAATT
Found at i:88471330 original size:20 final size:20
Alignment explanation
Indices: 88471305--88471345 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
88471295 ATAATGAATA
88471305 TTTAAAATTTATATGTAAAC
1 TTTAAAATTTATATGTAAAC
*
88471325 TTTAAAATTTATATTTAAAC
1 TTTAAAATTTATATGTAAAC
88471345 T
1 T
88471346 CACTTGAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (20 bp):
TTTAAAATTTATATGTAAAC
Found at i:88471672 original size:30 final size:29
Alignment explanation
Indices: 88471609--88471664 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
88471599 AGGTTATATC
*
88471609 TTTA-TATTTTTAGAAGATTAAATCAAATT
1 TTTATTATTTTTAGAAGATCAAA-CAAATT
88471638 TTTATTATTTTTAGAAGATCAAA-AAAT
1 TTTATTATTTTTAGAAGATCAAACAAAT
88471665 AATTTTATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 4 0.16
29 4 0.16
30 17 0.68
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (29 bp):
TTTATTATTTTTAGAAGATCAAACAAATT
Found at i:88482393 original size:16 final size:17
Alignment explanation
Indices: 88482356--88482394 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
88482346 TGAAGTTCTT
*
88482356 AATAAACACAAGTTGAA
1 AATAAACACAACTTGAA
*
88482373 CATAAACA-AACTTGAA
1 AATAAACACAACTTGAA
88482389 AATAAA
1 AATAAA
88482395 TAAATGAGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.62, C:0.13, G:0.08, T:0.18
Consensus pattern (17 bp):
AATAAACACAACTTGAA
Found at i:88482735 original size:22 final size:21
Alignment explanation
Indices: 88482710--88482753 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
88482700 CGTATATTGA
*
88482710 TAATTTTATATTAAATTTATTT
1 TAATTTTATA-AAAATTTATTT
*
88482732 TAATTTTTTAAAAATTTATTT
1 TAATTTTATAAAAATTTATTT
88482753 T
1 T
88482754 TTCAAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TAATTTTATAAAAATTTATTT
Found at i:88483200 original size:22 final size:22
Alignment explanation
Indices: 88483174--88483227 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
88483164 AACTTTATCG
88483174 ATCATATTATTACTGGAATGTT
1 ATCATATTATTACTGGAATGTT
88483196 ATCATATTATTACTGGAATGTT
1 ATCATATTATTACTGGAATGTT
*
88483218 AT-ACATTATT
1 ATCATATTATT
88483228 TAATAAATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 7 0.23
22 24 0.77
ACGTcount: A:0.33, C:0.09, G:0.11, T:0.46
Consensus pattern (22 bp):
ATCATATTATTACTGGAATGTT
Found at i:88495586 original size:22 final size:22
Alignment explanation
Indices: 88495561--88495608 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
88495551 AGAAACAACA
88495561 AAGGACCTATCTATGAAGAACG
1 AAGGACCTATCTATGAAGAACG
*
88495583 AAGGACCTATCTATGAAGAATG
1 AAGGACCTATCTATGAAGAACG
88495605 AAGG
1 AAGG
88495609 CTACAAATCG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.42, C:0.15, G:0.25, T:0.19
Consensus pattern (22 bp):
AAGGACCTATCTATGAAGAACG
Found at i:88502475 original size:60 final size:60
Alignment explanation
Indices: 88502381--88502517 Score: 202
Period size: 60 Copynumber: 2.3 Consensus size: 60
88502371 ATTTCCACCC
* * *
88502381 CCAACCGCTACAGACCATCTCTGACCATCCCAACACCCCATATGAGGTTTGAAATACCCAT
1 CCAACC-CTACACACCATCTCTGACCATCCCAACACACCATATGAGGTTTGAAACACCCAT
* *
88502442 CCAACCCTACACACCATCTCTGACCATCCCAACACACTATATGGGGTTTGAAACACCCAT
1 CCAACCCTACACACCATCTCTGACCATCCCAACACACCATATGAGGTTTGAAACACCCAT
* *
88502502 CTAACCCTAAACACCA
1 CCAACCCTACACACCA
88502518 CTTAGTGTCA
Statistics
Matches: 69, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
60 63 0.91
61 6 0.09
ACGTcount: A:0.33, C:0.39, G:0.09, T:0.19
Consensus pattern (60 bp):
CCAACCCTACACACCATCTCTGACCATCCCAACACACCATATGAGGTTTGAAACACCCAT
Found at i:88510556 original size:18 final size:18
Alignment explanation
Indices: 88510533--88510567 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
88510523 GCATGAGTGA
88510533 GGCATGTGGGCCCATAAG
1 GGCATGTGGGCCCATAAG
88510551 GGCATGTGGGCCCATAA
1 GGCATGTGGGCCCATAA
88510568 TTTTAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.23, G:0.37, T:0.17
Consensus pattern (18 bp):
GGCATGTGGGCCCATAAG
Found at i:88510765 original size:14 final size:15
Alignment explanation
Indices: 88510740--88510768 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
88510730 TTATGCATGA
88510740 TATTTCTGTATCTGT
1 TATTTCTGTATCTGT
88510755 TATTT-TGTATCTGT
1 TATTTCTGTATCTGT
88510769 GACTGGAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.14, C:0.10, G:0.14, T:0.62
Consensus pattern (15 bp):
TATTTCTGTATCTGT
Found at i:88515642 original size:13 final size:13
Alignment explanation
Indices: 88515620--88515649 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
88515610 TTTGAATTAC
88515620 TTAGTAATAATAT
1 TTAGTAATAATAT
*
88515633 TTAGTGATAATAT
1 TTAGTAATAATAT
88515646 TTAG
1 TTAG
88515650 GAAAAATCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (13 bp):
TTAGTAATAATAT
Found at i:88516566 original size:17 final size:17
Alignment explanation
Indices: 88516523--88516571 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
88516513 TTTTCCTAAA
88516523 TTTATTTTTTATTTTTG
1 TTTATTTTTTATTTTTG
**
88516540 AATATATTTTTATTTTAT-
1 TTTAT-TTTTTATTTT-TG
88516558 TTTATTTTTTATTT
1 TTTATTTTTTATTT
88516572 CCATATTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 12 0.46
18 13 0.50
19 1 0.04
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (17 bp):
TTTATTTTTTATTTTTG
Found at i:88518101 original size:26 final size:26
Alignment explanation
Indices: 88518037--88518159 Score: 151
Period size: 26 Copynumber: 4.8 Consensus size: 26
88518027 CCTCTTTAAT
* **
88518037 AACTGGGGCA-AAGTCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCAATA
* *
88518062 AACTGGGGCA-AAGCTCTTTTTAATA
1 AACTGGGGCATAAGCCCTTTTCAATA
**
88518087 AACTGGGGCATAAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCAATA
* *
88518113 GACTAGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCAATA
88518139 AACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
88518160 GCACTTCCTC
Statistics
Matches: 82, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
25 30 0.37
26 52 0.63
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTCAATA
Found at i:88518145 original size:52 final size:51
Alignment explanation
Indices: 88518037--88518159 Score: 185
Period size: 52 Copynumber: 2.4 Consensus size: 51
88518027 CCTCTTTAAT
* * * *
88518037 AACTGGGGCA-AAGTCCTTTTCGGTAAACTGGGGCAAAGCTCTTTTTAATA
1 AACTGGGGCATAAGCCCTTTTCGGTAAACTAGGGCAAAGCCCTTTTCAATA
*
88518087 AACTGGGGCATAAGCCCTTTTCGGTAGACTAGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCGGTAAACTAGGGCA-AAGCCCTTTTCAATA
88518139 AACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
88518160 GCACTTCCTC
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
50 10 0.15
51 22 0.33
52 34 0.52
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (51 bp):
AACTGGGGCATAAGCCCTTTTCGGTAAACTAGGGCAAAGCCCTTTTCAATA
Found at i:88519060 original size:27 final size:27
Alignment explanation
Indices: 88518960--88519043 Score: 125
Period size: 27 Copynumber: 3.1 Consensus size: 27
88518950 GGGCATATTC
* * *
88518960 GTCATTTTACCATACAGTGG-TATTACG
1 GTCACTTTACCCTACAGGGGCT-TTACG
88518987 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCACTTTACCCTACAGGGGCTTTACG
88519014 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCACTTTACCCTACAGGGGCTTTACG
88519041 GTC
1 GTC
88519044 TTTTTACCTA
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
27 52 0.98
28 1 0.02
ACGTcount: A:0.20, C:0.26, G:0.21, T:0.32
Consensus pattern (27 bp):
GTCACTTTACCCTACAGGGGCTTTACG
Found at i:88519135 original size:27 final size:27
Alignment explanation
Indices: 88519105--88519239 Score: 80
Period size: 27 Copynumber: 4.9 Consensus size: 27
88519095 GTAAATCTAC
88519105 AAACTAAGGGTATTTCAGTAATTTTGT
1 AAACTAAGGGTATTTCAGTAATTTTGT
* *
88519132 AAACCAATGGTATTTCTA-TAATTTT-T
1 AAACTAAGGGTATTTC-AGTAATTTTGT
* **
88519158 AGAAAGTCAAGGGTATTTTTGTAATTTTGT
1 --AAACT-AAGGGTATTTCAGTAATTTTGT
* **
88519188 AAA-TCAGGGGTATTTTGGTAATTTTAG-
1 AAACT-AAGGGTATTTCAGTAATTTT-GT
* * * *
88519215 AAATTGAGGTTATTTCGGTAATTTT
1 AAACTAAGGGTATTTCAGTAATTTT
88519240 ACAAACCAGT
Statistics
Matches: 87, Mismatches: 13, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
26 1 0.01
27 60 0.69
28 9 0.10
29 16 0.18
30 1 0.01
ACGTcount: A:0.31, C:0.06, G:0.19, T:0.44
Consensus pattern (27 bp):
AAACTAAGGGTATTTCAGTAATTTTGT
Found at i:88519254 original size:54 final size:53
Alignment explanation
Indices: 88519111--88519321 Score: 181
Period size: 54 Copynumber: 3.9 Consensus size: 53
88519101 CTACAAACTA
* ** ** * *
88519111 AGGGTATTTCAGTAATTTTGTAAACCAATGGTATTTCT-ATAATTTTTAGAAAGTCA
1 AGGGTATTTCGGTAATTTTACAAACCAGGGGTATTT-TGGTAA-TTTTAGAAA-T-T
** ** *
88519167 AGGGTATTTTTGTAATTTTGTAAATCAGGGGTATTTTGGTAATTTTAGAAATT
1 AGGGTATTTCGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTAGAAATT
* * * * *
88519220 GAGGTTATTTCGGTAATTTTACAAACCAGTGGTATTTTGGTAACTTTACAAACT
1 -AGGGTATTTCGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTAGAAATT
* * *
88519274 AGGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTAGCAATTTTA
1 A-GGGTATTTCGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTA
88519322 CAGACCAGGT
Statistics
Matches: 129, Mismatches: 23, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
53 1 0.01
54 84 0.65
55 10 0.08
56 34 0.26
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (53 bp):
AGGGTATTTCGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTAGAAATT
Found at i:88519255 original size:27 final size:27
Alignment explanation
Indices: 88519168--88519330 Score: 175
Period size: 27 Copynumber: 6.0 Consensus size: 27
88519158 AGAAAGTCAA
* ** *
88519168 GGGTATTTTTGTAATTTTGTAAATCAG
1 GGGTATTTTGGTAATTTTACAAACCAG
* **
88519195 GGGTATTTTGGTAATTTTAGAAA-TTG
1 GGGTATTTTGGTAATTTTACAAACCAG
* *
88519221 AGGTTATTTCGGTAATTTTACAAACCAG
1 -GGGTATTTTGGTAATTTTACAAACCAG
* * *
88519249 TGGTATTTTGGTAACTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACCAG
88519276 GGGTATTTTGGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAG
* * *
88519303 GGGTATTTTAGCAATTTTACAGACCAG
1 GGGTATTTTGGTAATTTTACAAACCAG
88519330 G
1 G
88519331 TGTGACAGCC
Statistics
Matches: 113, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
26 1 0.01
27 111 0.98
28 1 0.01
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.40
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACCAG
Found at i:88519310 original size:81 final size:80
Alignment explanation
Indices: 88519084--88519330 Score: 194
Period size: 81 Copynumber: 3.0 Consensus size: 80
88519074 TCACCCTACA
* * * ** ** **
88519084 AGGGTGTTTTGGTAAATCTACAAACTAAGGGTATTTCAGTAATTTTGTAAACCAATGGTATTTCT
1 AGGGTATTTTGGTAAATTTACAAACTAGGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTC-
* *
88519149 A-TAATTTTTAGAAAGTCA
65 AGTAA-TTTTACAAA--CC
* * ** * ** *
88519167 AGGGTATTTTTGTAATTTTGTAAA-TCAGGGGTATTTTGGTAATTTTAGAAA-TTGAGGTTATTT
1 AGGGTATTTTGGTAAATTTACAAACT-AGGGGTATTTTGGTAATTTTACAAACCAG-GGGTATTT
*
88519230 CGGTAATTTTACAAACC
64 CAGTAATTTTACAAACC
* *
88519247 AGTGGTATTTTGGTAACTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTT
1 AG-GGTATTTTGGTAAATTTACAAACTAGGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTC
* *
88519312 AGCAATTTTACAGACC
65 AGTAATTTTACAAACC
88519328 AGG
1 AGG
88519331 TGTGACAGCC
Statistics
Matches: 127, Mismatches: 31, Indels: 15
0.73 0.18 0.09
Matches are distributed among these distances:
80 4 0.03
81 64 0.50
82 11 0.09
83 48 0.38
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.39
Consensus pattern (80 bp):
AGGGTATTTTGGTAAATTTACAAACTAGGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTCA
GTAATTTTACAAACC
Found at i:88520945 original size:40 final size:40
Alignment explanation
Indices: 88520914--88521123 Score: 271
Period size: 40 Copynumber: 5.3 Consensus size: 40
88520904 GGACTAAGAT
* * *
88520914 CCGAAGGCATTTGTGCGAGATA-CAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATATTAAA-TCCGGGTTAAGTC
* *
88520954 CCGAAGGCCTTTGTGCGAGATATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATATTAAATCCGGGTTAAGTC
*
88520994 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATATTAAATCCGGGTTAAGTC
* *
88521034 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGATATTAAATCCGGGTTAAGTC
* * * * * *
88521074 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATATTAAATCCGGGTTAAGTC
88521113 CCGAAGGCATT
1 CCGAAGGCATT
88521124 TGAACGAGGA
Statistics
Matches: 158, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 35 0.22
40 120 0.76
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGATATTAAATCCGGGTTAAGTC
Found at i:88521077 original size:120 final size:120
Alignment explanation
Indices: 88520861--88521123 Score: 300
Period size: 120 Copynumber: 2.2 Consensus size: 120
88520851 TTGAATGCTG
* *
88520861 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
* * *
88520925 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATATTAAA
66 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTAAA
* * * * **
88520981 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT
* * * * * *
88521044 TCGTGCGAGTTATTAAA-TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
* *
88521100 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
88521124 TGAACGAGGA
Statistics
Matches: 120, Mismatches: 20, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
119 37 0.31
120 74 0.62
121 9 0.08
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:88521143 original size:79 final size:80
Alignment explanation
Indices: 88520862--88521158 Score: 221
Period size: 80 Copynumber: 3.7 Consensus size: 80
88520852 TGAATGCTGT
* ** * * * **
88520862 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTCGAAC-GAGTGACTAAATCCGGGTTAAG-TCCCGAAGGCATT
* * *
88520925 TGTGCGAGATAC-AAATT
64 CGTGCGAGTTACTAAA-A
* * * * ** *
88520942 CCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGAT-ATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAG-TGACTAAATCCGGGTTAAGTCCCGAAGGCATTC
* *
88521006 GTGCGAGTTATTAAAT
65 GTGCGAGTTACTAAAA
* ** * * *
88521022 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATT-G
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
*
88521086 TGTGAGTTACTAAAA
66 TGCGAGTTACTAAAA
* * * *
88521101 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
88521159 TACGTGATTT
Statistics
Matches: 184, Mismatches: 27, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
78 15 0.08
79 47 0.26
80 111 0.60
81 11 0.06
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
TGCGAGTTACTAAAA
Found at i:88528513 original size:40 final size:40
Alignment explanation
Indices: 88528482--88528690 Score: 271
Period size: 40 Copynumber: 5.3 Consensus size: 40
88528472 GGACTAAGAT
* * *
88528482 CCGAAGGCATTTGTGCGAGATA-CAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATATTAAA-TCCGGGTTAAGTC
* *
88528522 CCGAAGGCCTTTGTGCGAGATATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATATTAAATCCGGGTTAAGTC
*
88528562 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATATTAAATCCGGGTTAAGTC
* *
88528602 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGATATTAAATCCGGGTTAAGTC
* * * * *
88528642 CCGAAGGCATT-GTGTGAGTTACTAAA-CCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATATTAAATCCGGGTTAAGTC
88528680 CCGAAGGCATT
1 CCGAAGGCATT
88528691 TGAACGAGGA
Statistics
Matches: 158, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
38 22 0.14
39 13 0.08
40 120 0.76
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGATATTAAATCCGGGTTAAGTC
Found at i:88530161 original size:54 final size:54
Alignment explanation
Indices: 88530079--88530325 Score: 212
Period size: 54 Copynumber: 4.6 Consensus size: 54
88530069 GTTACACCAG
* *** * *
88530079 GGTATTTT-GATAATTTTACT-GATCGAGGGTATTTTGGTAATTTTGTAAACCAAT
1 GGTATTTTAG-TAATTTTA-TAAATCGAGGGTAAAATGGTAATTCTGTAAATCAAT
** *
88530133 GGTATTTTAGTAATTTTATAAATCGAGGGTAAAACAGTAATTCTGTAAATCAAG
1 GGTATTTTAGTAATTTTATAAATCGAGGGTAAAATGGTAATTCTGTAAATCAAT
*** *
88530187 GGTAAAATAGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTGTAAATCAAT
1 GGTATTTTAGTAATTTTATAAATCGAGGGTAAAATGGTAATTCTGTAAATCAAT
*** * ** * ** *
88530241 GGTAAAATAGCAATTCCATAAATCAAGGGTAAAACAGTAATTCTGTAAATCGGA-
1 GGTATTTTAGTAATTTTATAAATCGAGGGTAAAATGGTAATTCTGTAAATC-AAT
* * *
88530295 GGTACTTTAGTAATTTTACAAGTCGAGGGTA
1 GGTATTTTAGTAATTTTATAAATCGAGGGTA
88530326 TTTCAATAAT
Statistics
Matches: 159, Mismatches: 31, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
53 1 0.01
54 156 0.98
55 2 0.01
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.34
Consensus pattern (54 bp):
GGTATTTTAGTAATTTTATAAATCGAGGGTAAAATGGTAATTCTGTAAATCAAT
Found at i:88530163 original size:27 final size:27
Alignment explanation
Indices: 88530077--88530217 Score: 97
Period size: 27 Copynumber: 5.2 Consensus size: 27
88530067 GTGTTACACC
*
88530077 AGGGTATTTT-GATAATTTTACT-GATCG
1 AGGGTATTTTAG-TAATTTTA-TAAATCG
* * * *
88530104 AGGGTATTTTGGTAATTTTGTAAACCA
1 AGGGTATTTTAGTAATTTTATAAATCG
*
88530131 ATGGTATTTTAGTAATTTTATAAATCG
1 AGGGTATTTTAGTAATTTTATAAATCG
**** * * *
88530158 AGGGTAAAACAGTAATTCTGTAAATCA
1 AGGGTATTTTAGTAATTTTATAAATCG
*** *
88530185 AGGGTAAAATAGTAATTCTATAAATCG
1 AGGGTATTTTAGTAATTTTATAAATCG
88530212 AGGGTA
1 AGGGTA
88530218 AAATGGTAAT
Statistics
Matches: 92, Mismatches: 20, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
26 1 0.01
27 90 0.98
28 1 0.01
ACGTcount: A:0.35, C:0.07, G:0.21, T:0.37
Consensus pattern (27 bp):
AGGGTATTTTAGTAATTTTATAAATCG
Found at i:88530298 original size:27 final size:27
Alignment explanation
Indices: 88530140--88530291 Score: 196
Period size: 27 Copynumber: 5.6 Consensus size: 27
88530130 AATGGTATTT
* *
88530140 TAGTAATTTTATAAATCGAGGGTAAAA
1 TAGTAATTCTATAAATCAAGGGTAAAA
* *
88530167 CAGTAATTCTGTAAATCAAGGGTAAAA
1 TAGTAATTCTATAAATCAAGGGTAAAA
*
88530194 TAGTAATTCTATAAATCGAGGGTAAAA
1 TAGTAATTCTATAAATCAAGGGTAAAA
* * *
88530221 TGGTAATTCTGTAAATCAATGGTAAAA
1 TAGTAATTCTATAAATCAAGGGTAAAA
* *
88530248 TAGCAATTCCATAAATCAAGGGTAAAA
1 TAGTAATTCTATAAATCAAGGGTAAAA
* *
88530275 CAGTAATTCTGTAAATC
1 TAGTAATTCTATAAATC
88530292 GGAGGTACTT
Statistics
Matches: 105, Mismatches: 20, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 105 1.00
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.30
Consensus pattern (27 bp):
TAGTAATTCTATAAATCAAGGGTAAAA
Found at i:88530308 original size:81 final size:81
Alignment explanation
Indices: 88530133--88530309 Score: 203
Period size: 81 Copynumber: 2.2 Consensus size: 81
88530123 GTAAACCAAT
* * * * ** *
88530133 GGTATTTTAGTAATTTTATAAATCGAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAATAGT
1 GGTAATTTAGTAATTCTATAAATCAAGGGTAAAACAGCAATTCCATAAATCAAGGGTAAAACAGT
88530198 AATTCTATAAATCGAG
66 AATTCTATAAATCGAG
** * * * *
88530214 GGTAAAATGGTAATTCTGTAAATCAATGGTAAAATAGCAATTCCATAAATCAAGGGTAAAACAGT
1 GGTAATTTAGTAATTCTATAAATCAAGGGTAAAACAGCAATTCCATAAATCAAGGGTAAAACAGT
*
88530279 AATTCTGTAAATCG-G
66 AATTCTATAAATCGAG
*
88530294 AGGTACTTTAGTAATT
1 -GGTAATTTAGTAATT
88530310 TTACAAGTCG
Statistics
Matches: 77, Mismatches: 18, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
80 1 0.01
81 76 0.99
ACGTcount: A:0.41, C:0.09, G:0.19, T:0.32
Consensus pattern (81 bp):
GGTAATTTAGTAATTCTATAAATCAAGGGTAAAACAGCAATTCCATAAATCAAGGGTAAAACAGT
AATTCTATAAATCGAG
Found at i:88532211 original size:27 final size:27
Alignment explanation
Indices: 88532181--88532234 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
88532171 TGTCATGTGA
* *
88532181 AATTGAATGGAAAATTATTGTTACATG
1 AATTGAATGGAAAATTACTATTACATG
**
88532208 AATTGAATGTTAAATTACTATTACATG
1 AATTGAATGGAAAATTACTATTACATG
88532235 GGTTGTAGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.41, C:0.06, G:0.15, T:0.39
Consensus pattern (27 bp):
AATTGAATGGAAAATTACTATTACATG
Found at i:88537065 original size:28 final size:29
Alignment explanation
Indices: 88537032--88537094 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 29
88537022 GTAGAAATTA
* *
88537032 TTAAATTTTAATAAAAAATA-AAAAATAT
1 TTAAATTTAAATAAAAAATAGAAAAAAAT
*
88537060 TTAAATTTAAATAAAAATTAGAAAAAAAT
1 TTAAATTTAAATAAAAAATAGAAAAAAAT
88537089 TATAAA
1 T-TAAA
88537095 AATTGAATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 18 0.60
29 8 0.27
30 4 0.13
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (29 bp):
TTAAATTTAAATAAAAAATAGAAAAAAAT
Found at i:88541366 original size:15 final size:16
Alignment explanation
Indices: 88541340--88541369 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
88541330 GGGGGAAATA
88541340 AAAAGTTTTGAGGGAT
1 AAAAGTTTTGAGGGAT
88541356 AAAAG-TTTGAGGGA
1 AAAAGTTTTGAGGGA
88541370 AAATAAATGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.00, G:0.33, T:0.27
Consensus pattern (16 bp):
AAAAGTTTTGAGGGAT
Found at i:88541827 original size:18 final size:18
Alignment explanation
Indices: 88541801--88541835 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
88541791 ATTCAAGTTG
*
88541801 ACTCGAATAACTCGATTA
1 ACTCAAATAACTCGATTA
88541819 ACTCAAATAACTCGATT
1 ACTCAAATAACTCGATT
88541836 CGTTTAACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.29
Consensus pattern (18 bp):
ACTCAAATAACTCGATTA
Found at i:88545574 original size:25 final size:25
Alignment explanation
Indices: 88545540--88545621 Score: 92
Period size: 25 Copynumber: 3.2 Consensus size: 25
88545530 AGTATGTCTA
*
88545540 TTATGTATGTTATTTATAATACTAT
1 TTATGTATGTTATTTATATTACTAT
* * *
88545565 TTATGTATGTTATGTAGTTTATTATTGT
1 TTATGTATGTTAT-T--TATATTACTAT
*
88545593 TTATGTATGTTATGTATATTACTAT
1 TTATGTATGTTATTTATATTACTAT
88545618 TTAT
1 TTAT
88545622 ATAATGTATG
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
25 25 0.54
26 1 0.02
28 20 0.43
ACGTcount: A:0.27, C:0.02, G:0.12, T:0.59
Consensus pattern (25 bp):
TTATGTATGTTATTTATATTACTAT
Found at i:88545579 original size:9 final size:10
Alignment explanation
Indices: 88545564--88545609 Score: 55
Period size: 9 Copynumber: 4.9 Consensus size: 10
88545554 TATAATACTA
88545564 TTTATGTATG
1 TTTATGTATG
88545574 -TTATGTA-G
1 TTTATGTATG
88545582 TTTAT-TATTG
1 TTTATGTA-TG
88545592 TTTATGTATG
1 TTTATGTATG
88545602 -TTATGTAT
1 TTTATGTAT
88545610 ATTACTATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
8 3 0.09
9 19 0.59
10 8 0.25
11 2 0.06
ACGTcount: A:0.22, C:0.00, G:0.17, T:0.61
Consensus pattern (10 bp):
TTTATGTATG
Found at i:88545628 original size:21 final size:21
Alignment explanation
Indices: 88545602--88545689 Score: 76
Period size: 21 Copynumber: 4.3 Consensus size: 21
88545592 TTTATGTATG
88545602 TTATGTATATTACTATTTATA
1 TTATGTATATTACTATTTATA
* * *
88545623 TAATGTAT-GT--TATGTATA
1 TTATGTATATTACTATTTATA
* * * *
88545641 TTGTTGTTTA-TATTATTTATG
1 TT-ATGTATATTACTATTTATA
88545662 TTATGTATATTACTATTTATA
1 TTATGTATATTACTATTTATA
88545683 TTATGTA
1 TTATGTA
88545690 CTTGACTTTA
Statistics
Matches: 50, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
18 8 0.16
19 5 0.10
20 6 0.12
21 31 0.62
ACGTcount: A:0.30, C:0.02, G:0.10, T:0.58
Consensus pattern (21 bp):
TTATGTATATTACTATTTATA
Found at i:88545631 original size:30 final size:30
Alignment explanation
Indices: 88545538--88545689 Score: 158
Period size: 30 Copynumber: 5.3 Consensus size: 30
88545528 TTAGTATGTC
* *
88545538 TATTATGTATGTTAT-T-TA-TAATA-CTA
1 TATTATGTATGTTATGTATATTACTATTTA
* *
88545564 T-TTATGTATGTTATGTAGT-TTATTA-TTG
1 TATTATGTATGTTATGTA-TATTACTATTTA
88545592 T-TTATGTATGTTATGTATATTACTATTTA
1 TATTATGTATGTTATGTATATTACTATTTA
* ** *
88545621 TATAATGTATGTTATGTATATTGTTGTTTA
1 TATTATGTATGTTATGTATATTACTATTTA
*
88545651 TATTATTTATGTTATGTATATTACTATTTA
1 TATTATGTATGTTATGTATATTACTATTTA
88545681 TATTATGTA
1 TATTATGTA
88545690 CTTGACTTTA
Statistics
Matches: 104, Mismatches: 15, Indels: 10
0.81 0.12 0.08
Matches are distributed among these distances:
25 13 0.12
26 2 0.02
27 1 0.01
28 28 0.27
29 3 0.03
30 57 0.55
ACGTcount: A:0.28, C:0.02, G:0.12, T:0.58
Consensus pattern (30 bp):
TATTATGTATGTTATGTATATTACTATTTA
Found at i:88546072 original size:17 final size:17
Alignment explanation
Indices: 88546050--88546083 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
88546040 GACACACTTG
*
88546050 ATGTTATTGATGATACC
1 ATGTTATTGATCATACC
88546067 ATGTTATTGATCATACC
1 ATGTTATTGATCATACC
88546084 TCCCGGTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (17 bp):
ATGTTATTGATCATACC
Found at i:88546151 original size:26 final size:26
Alignment explanation
Indices: 88546115--88546168 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
88546105 TAACATACAA
* *
88546115 TGGAAAATTTGATTGTTCTATTTTGT
1 TGGAAAATTTGATGGTTCTACTTTGT
*
88546141 TGGATAATTTGATGGTTCTACTTTGT
1 TGGAAAATTTGATGGTTCTACTTTGT
88546167 TG
1 TG
88546169 ATGTCAACCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.20, C:0.06, G:0.22, T:0.52
Consensus pattern (26 bp):
TGGAAAATTTGATGGTTCTACTTTGT
Found at i:88550230 original size:22 final size:21
Alignment explanation
Indices: 88550190--88550231 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
88550180 TTTTAAATTA
*
88550190 TTTTAAATATAAAATATTTAT
1 TTTTAAATATAAAAAATTTAT
*
88550211 TTTTATATCATAAAAAATTTA
1 TTTTAAAT-ATAAAAAATTTA
88550232 AATCAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
TTTTAAATATAAAAAATTTAT
Found at i:88551830 original size:11 final size:11
Alignment explanation
Indices: 88551814--88551846 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
88551804 TAATGCATAT
88551814 ATGAAATTAAA
1 ATGAAATTAAA
88551825 ATGAAATTAAA
1 ATGAAATTAAA
88551836 AT--AATTAAA
1 ATGAAATTAAA
88551845 AT
1 AT
88551847 ACAAATGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.41
11 13 0.59
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (11 bp):
ATGAAATTAAA
Found at i:88551873 original size:16 final size:16
Alignment explanation
Indices: 88551849--88551880 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
88551839 ATTAAAATAC
*
88551849 AAATGATAAATTAGTT
1 AAATCATAAATTAGTT
88551865 AAATCATAAATTAGTT
1 AAATCATAAATTAGTT
88551881 GGTTGTTACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.03, G:0.09, T:0.38
Consensus pattern (16 bp):
AAATCATAAATTAGTT
Found at i:88555260 original size:26 final size:24
Alignment explanation
Indices: 88555214--88555269 Score: 78
Period size: 26 Copynumber: 2.3 Consensus size: 24
88555204 TTGTCAGGTG
88555214 AAAA-TTAAATTTATTTAAAATAA
1 AAAATTTAAATTTATTTAAAATAA
*
88555237 AAAATTTAAATTTAAATTTAAAATAG
1 AAAATTTAAATTT--ATTTAAAATAA
88555263 AAAATTT
1 AAAATTT
88555270 TGATATTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 4 0.14
24 8 0.28
26 17 0.59
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (24 bp):
AAAATTTAAATTTATTTAAAATAA
Found at i:88555779 original size:24 final size:23
Alignment explanation
Indices: 88555743--88555807 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 23
88555733 ATTTTATTTT
*
88555743 TATATATTCTTTTTTTAGATTATA
1 TATATTTTCTTTTTTTAGA-TATA
* * *
88555767 TATATTTTGTTTTCTTATATATA
1 TATATTTTCTTTTTTTAGATATA
*
88555790 TATTATTTTCATTTTTTA
1 TA-TATTTTCTTTTTTTA
88555808 TTTTTTTAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
23 6 0.18
24 27 0.82
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (23 bp):
TATATTTTCTTTTTTTAGATATA
Found at i:88555798 original size:19 final size:19
Alignment explanation
Indices: 88555762--88555799 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
88555752 TTTTTTTAGA
* *
88555762 TTATATATATTTTGTTTTC
1 TTATATATATATTATTTTC
88555781 TTATATATATATTATTTTC
1 TTATATATATATTATTTTC
88555800 ATTTTTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (19 bp):
TTATATATATATTATTTTC
Found at i:88556089 original size:20 final size:21
Alignment explanation
Indices: 88556050--88556089 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
88556040 ATGAATTAAG
* *
88556050 CCTAAAAAGAAATACACTATC
1 CCTAAAAACAAAAACACTATC
88556071 CCTAAAAACAAAAAC-CTAT
1 CCTAAAAACAAAAACACTAT
88556090 TTTTATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.55, C:0.25, G:0.03, T:0.17
Consensus pattern (21 bp):
CCTAAAAACAAAAACACTATC
Found at i:88570648 original size:13 final size:13
Alignment explanation
Indices: 88570632--88570657 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
88570622 CTTTGCATAT
88570632 TGTCTTCAACAGG
1 TGTCTTCAACAGG
88570645 TGTCTTCAACAGG
1 TGTCTTCAACAGG
88570658 CTCGCACTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (13 bp):
TGTCTTCAACAGG
Found at i:88572498 original size:16 final size:16
Alignment explanation
Indices: 88572477--88572522 Score: 60
Period size: 15 Copynumber: 3.0 Consensus size: 16
88572467 AAAAATAATT
88572477 TTAAAAAATATATAAA
1 TTAAAAAATATATAAA
* *
88572493 TTAAAATATTTA-AAA
1 TTAAAAAATATATAAA
88572508 TTAAAAAA-ATATAAA
1 TTAAAAAATATATAAA
88572523 AAGTTCATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
14 2 0.08
15 13 0.52
16 10 0.40
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TTAAAAAATATATAAA
Found at i:88572523 original size:16 final size:15
Alignment explanation
Indices: 88572477--88572523 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
88572467 AAAAATAATT
88572477 TTAAAAAATATATAAA
1 TTAAAAAATATA-AAA
* *
88572493 TTAAAATATTTAAAA
1 TTAAAAAATATAAAA
88572508 TTAAAAAAATATAAAA
1 TT-AAAAAATATAAAA
88572524 AGTTCATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
15 5 0.19
16 21 0.81
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
TTAAAAAATATAAAA
Found at i:88573249 original size:23 final size:25
Alignment explanation
Indices: 88573219--88573265 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
88573209 GACTAAAGTG
88573219 AACAAAAAT-AAATA-AAAAATTTC
1 AACAAAAATCAAATATAAAAATTTC
*
88573242 AACAAAAATCAAATATTAAAATTT
1 AACAAAAATCAAATATAAAAATTT
88573266 AAAAATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.43
24 5 0.24
25 7 0.33
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.26
Consensus pattern (25 bp):
AACAAAAATCAAATATAAAAATTTC
Found at i:88573384 original size:16 final size:15
Alignment explanation
Indices: 88573363--88573392 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
88573353 TTATGCATTA
88573363 TTTTAATATTAAATAT
1 TTTTAA-ATTAAATAT
88573379 TTTTAAATTAAATA
1 TTTTAAATTAAATA
88573393 ACATTAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTTAAATTAAATAT
Found at i:88578358 original size:21 final size:20
Alignment explanation
Indices: 88578302--88578375 Score: 73
Period size: 19 Copynumber: 3.8 Consensus size: 20
88578292 CTAAACCCAT
* *
88578302 AATCTTAAACTTTAAA-CCTG
1 AATCTTAAAC-TCAAACCCTA
88578322 AA-CTTAAACTCAAACCCTA
1 AATCTTAAACTCAAACCCTA
* *
88578341 AATTTTAAACTCCAAACCTTA
1 AATCTTAAACT-CAAACCCTA
88578362 AATCTTAAA-TCAAA
1 AATCTTAAACTCAAA
88578376 AGGCCAAATT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
18 4 0.09
19 16 0.35
20 10 0.22
21 16 0.35
ACGTcount: A:0.46, C:0.23, G:0.01, T:0.30
Consensus pattern (20 bp):
AATCTTAAACTCAAACCCTA
Found at i:88581479 original size:46 final size:46
Alignment explanation
Indices: 88581375--88581484 Score: 116
Period size: 46 Copynumber: 2.4 Consensus size: 46
88581365 TGCAGTTAAA
* * * *
88581375 CTGCCAGATCAAATATATGTGGTCACACCACTATATTGCAGCCAAG
1 CTGCCAGAACAGATATGTGTGGTCACACCACTATATTGCAGACAAG
*
88581421 CTGCCAGAACAGATATGTGTGGTCA-AGCCACTATAATTGTAGACAAG
1 CTGCCAGAACAGATATGTGTGGTCACA-CCACTAT-ATTGCAGACAAG
* * *
88581468 TTGCTAG-ACAGAAATGT
1 CTGCCAGAACAGATATGT
88581485 AGATAAACCA
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
45 1 0.02
46 38 0.70
47 15 0.28
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.25
Consensus pattern (46 bp):
CTGCCAGAACAGATATGTGTGGTCACACCACTATATTGCAGACAAG
Found at i:88583466 original size:20 final size:22
Alignment explanation
Indices: 88583441--88583490 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 22
88583431 TGTACCAATT
*
88583441 TTCAAACAAAGTAAAGT-A-CA
1 TTCAAACAAAATAAAGTCATCA
* *
88583461 TTCAAATAAAATAAATTCATCA
1 TTCAAACAAAATAAAGTCATCA
88583483 TTCAAACA
1 TTCAAACA
88583491 TATATATTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 14 0.58
21 1 0.04
22 9 0.38
ACGTcount: A:0.54, C:0.16, G:0.04, T:0.26
Consensus pattern (22 bp):
TTCAAACAAAATAAAGTCATCA
Found at i:88588279 original size:23 final size:23
Alignment explanation
Indices: 88588252--88588306 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
88588242 AATGGGATCA
88588252 AATTAATTTGAGTACAAAGATTT
1 AATTAATTTGAGTACAAAGATTT
** * *
88588275 AATT-ATAAAGATTATAAAGATTT
1 AATTAAT-TTGAGTACAAAGATTT
88588298 AATTAATTT
1 AATTAATTT
88588307 TTTCGAAAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
22 2 0.08
23 20 0.83
24 2 0.08
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (23 bp):
AATTAATTTGAGTACAAAGATTT
Found at i:88596410 original size:16 final size:16
Alignment explanation
Indices: 88596391--88596437 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 16
88596381 AATATATACC
88596391 ATATTTAATATAAATA
1 ATATTTAATATAAATA
*
88596407 ATATTTAAGATAAATA
1 ATATTTAATATAAATA
88596423 ATATTT--TATAAATA
1 ATATTTAATATAAATA
88596437 A
1 A
88596438 AAGAGATTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 8 0.28
16 21 0.72
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (16 bp):
ATATTTAATATAAATA
Found at i:88596809 original size:13 final size:14
Alignment explanation
Indices: 88596790--88596822 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
88596780 TAATTAAACT
88596790 ATAATTAAG-TTAA
1 ATAATTAAGATTAA
*
88596803 TTAATTAAGATTAA
1 ATAATTAAGATTAA
88596817 ATAATT
1 ATAATT
88596823 TCTAATCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (14 bp):
ATAATTAAGATTAA
Found at i:88598315 original size:18 final size:20
Alignment explanation
Indices: 88598274--88598313 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
88598264 AACTAGTAGT
88598274 TTGATGATAGTATATGAAATA
1 TTGATGATAGTATATG-AATA
*
88598295 TTGATGATATTATATGAAT
1 TTGATGATAGTATATGAAT
88598314 TGGTATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.42
Consensus pattern (20 bp):
TTGATGATAGTATATGAATA
Found at i:88600541 original size:21 final size:21
Alignment explanation
Indices: 88600512--88600551 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
88600502 ATTCATGCAT
*
88600512 TTTATTATATATGTATATATC
1 TTTAATATATATGTATATATC
*
88600533 TTTAATATATATTTATATA
1 TTTAATATATATGTATATA
88600552 AGTATATCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (21 bp):
TTTAATATATATGTATATATC
Found at i:88600577 original size:29 final size:27
Alignment explanation
Indices: 88600513--88600577 Score: 67
Period size: 29 Copynumber: 2.3 Consensus size: 27
88600503 TTCATGCATT
* *
88600513 TTATTATATATGTATATATCTTTAATA
1 TTATTATATAAGTATATATCTGTAATA
*
88600540 TATATTTATATAAGTATATCTTCATGTAATA
1 T-TA-TTATATAAGTATAT-ATC-TGTAATA
88600571 TTATTAT
1 TTATTAT
88600578 TATTATTAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
27 1 0.03
28 2 0.06
29 17 0.55
30 4 0.13
31 7 0.23
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.54
Consensus pattern (27 bp):
TTATTATATAAGTATATATCTGTAATA
Done.