Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12
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: 24583705
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1509421 characters in sequence are not A, C, G, or T
File 19 of 75
Found at i:5323663 original size:21 final size:19
Alignment explanation
Indices: 5323623--5323697 Score: 105
Period size: 19 Copynumber: 3.8 Consensus size: 19
5323613 AATCATATCT
5323623 TCCAAGATTGCATATCATA
1 TCCAAGATTGCATATCATA
*
5323642 TCCAAGATTGCATATATAATA
1 TCCAAGATTGC--ATATCATA
*
5323663 TCTAAGATTGCATATCATA
1 TCCAAGATTGCATATCATA
*
5323682 TCTAAGATTGCATATC
1 TCCAAGATTGCATATC
5323698 CTTGAAGATT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 34 0.67
21 17 0.33
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (19 bp):
TCCAAGATTGCATATCATA
Found at i:5324851 original size:27 final size:27
Alignment explanation
Indices: 5324813--5324875 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
5324803 TTTTAGTCCT
* * *
5324813 GTGCCGTCAATGGGAATGGCACCATCG
1 GTGCCGCCAATGAGAATGGCACCACCG
5324840 GTGCCGCCAATGAGAATGGCACCACCG
1 GTGCCGCCAATGAGAATGGCACCACCG
5324867 GTGCCGCCA
1 GTGCCGCCA
5324876 TTCCATTACC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.22, C:0.32, G:0.32, T:0.14
Consensus pattern (27 bp):
GTGCCGCCAATGAGAATGGCACCACCG
Found at i:5324941 original size:11 final size:11
Alignment explanation
Indices: 5324925--5324950 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5324915 GTAAATAATT
5324925 TTTTTATATTA
1 TTTTTATATTA
5324936 TTTTTATATTA
1 TTTTTATATTA
5324947 TTTT
1 TTTT
5324951 ATTTCTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTTATATTA
Found at i:5325754 original size:22 final size:22
Alignment explanation
Indices: 5325724--5325766 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
5325714 ACAACAAAAC
*
5325724 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGGCGCTTTTTT
5325746 AGGCCTTTAGCGGCGCTTTTT
1 AGGCCTTTAGCGGCGCTTTTT
5325767 AGCGCCAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.09, C:0.21, G:0.28, T:0.42
Consensus pattern (22 bp):
AGGCCTTTAGCGGCGCTTTTTT
Found at i:5325925 original size:43 final size:43
Alignment explanation
Indices: 5325838--5326284 Score: 508
Period size: 43 Copynumber: 10.3 Consensus size: 43
5325828 TCGTCGCTAA
* * * *
5325838 CTTTAACGGCGCTTCCAGTA-AAAAACGCCGCTAAAGGCCGAGAC
1 CTTTAGCGGCGCTTCCA--ACACAAACGCCGCTAAAGACCAAGAC
*
5325882 CTTTAGCGGCGCTTCCAACACAAACGCCGCCAAAGACCAAGAC
1 CTTTAGCGGCGCTTCCAACACAAACGCCGCTAAAGACCAAGAC
* *
5325925 CTTTAGCGGAGCTTTCC-ACATAAACGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGC-TTCCAACACAAACGCCGCTAAAGACCAAGAC
* *
5325968 CTTTAGCGGCGCTTTTC-ATACAAACGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGC-TTCCAACACAAACGCCGCTAAAGACCAAGAC
* *
5326011 CTTTAGCGGCACTTCCAACACAAACGCCGCCAAAAGACCAAGAC
1 CTTTAGCGGCGCTTCCAACACAAACGCCG-CTAAAGACCAAGAC
** * *
5326055 CTTTAGCGGCGCTTTTAATACAAACGCTGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTCCAACACAAACGCCGCTAAAGACCAAGAC
* *
5326098 CTTTAGCGGCGCTTCCCACACAAACGCCGCTATAGACCAAGAC
1 CTTTAGCGGCGCTTCCAACACAAACGCCGCTAAAGACCAAGAC
*
5326141 CTTTAGCGGCGCTTCCCACACAAACGCCGCTAAAGA-CAACGAC
1 CTTTAGCGGCGCTTCCAACACAAACGCCGCTAAAGACCAA-GAC
* * * *
5326184 CATTTAGCGGCGCTTAC-ACGACAAATGCCGCTAAAGATCGAGAC
1 C-TTTAGCGGCGCTTCCAAC-ACAAACGCCGCTAAAGACCAAGAC
* * **** * *
5326228 CTTTAGCGACGTTTTTTTCACAAATGCCGCTAAAGATCAAGAC
1 CTTTAGCGGCGCTTCCAACACAAACGCCGCTAAAGACCAAGAC
*
5326271 CTTTAGCAGCGCTT
1 CTTTAGCGGCGCTT
5326285 TTCCCAAAAA
Statistics
Matches: 353, Mismatches: 41, Indels: 19
0.85 0.10 0.05
Matches are distributed among these distances:
42 7 0.02
43 252 0.71
44 92 0.26
45 2 0.01
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.19
Consensus pattern (43 bp):
CTTTAGCGGCGCTTCCAACACAAACGCCGCTAAAGACCAAGAC
Found at i:5326080 original size:173 final size:173
Alignment explanation
Indices: 5325860--5326303 Score: 574
Period size: 173 Copynumber: 2.6 Consensus size: 173
5325850 TTCCAGTAAA
* ** * *
5325860 AAACGCCGCTAAAGGCCGAGACCTTTAGCGGCGCTTCCAACACAAACGCCGCCAAAGACCAAGAC
1 AAACGCCGCTAAAGACCGAGACCTTTAGCGGCGCTTTTAATACAAACGCCGCTAAAGACCAAGAC
* * ** *
5325925 CTTTAGCGGAGCTTTCCACATAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCATACA
66 CTTTAGCGGCGCTTTCCACAAAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCCCACACA
*
5325990 AACGCCGCTAAAGACCAA-GACC-TTTAGCGGCACTTCCAAC-AC
131 AACGCCGCTAAAGA-CAACGACCATTTAGCGGCACTTAC-ACGAC
* * *
5326032 AAACGCCGCCAAAAGACCAAGACCTTTAGCGGCGCTTTTAATACAAACGCTGCTAAAGACCAAGA
1 AAACGCCG-CTAAAGACCGAGACCTTTAGCGGCGCTTTTAATACAAACGCCGCTAAAGACCAAGA
* * *
5326097 CCTTTAGCGGCGCTTCCCACACAAACGCCGCTATAGACCAAGACCTTTAGCGGCGCTTCCCACAC
65 CCTTTAGCGGCGCTTTCCACAAAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCCCACAC
*
5326162 AAACGCCGCTAAAGACAACGACCATTTAGCGGCGCTTACACGAC
130 AAACGCCGCTAAAGACAACGACCATTTAGCGGCACTTACACGAC
* * * ** * *
5326206 AAATGCCGCTAAAGATCGAGACCTTTAGCGACG-TTTTTTTCACAAATGCCGCTAAAGATCAAGA
1 AAACGCCGCTAAAGACCGAGACCTTTAGCGGCGCTTTTAAT-ACAAACGCCGCTAAAGACCAAGA
*
5326270 CCTTTAGCAGCGCTTTTCC-CAAAAACGCCGCTAA
65 CCTTTAGCGGCGC-TTTCCACAAAAACGCCGCTAA
5326304 TTTTGGCAGA
Statistics
Matches: 235, Mismatches: 31, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
172 16 0.07
173 193 0.82
174 26 0.11
ACGTcount: A:0.32, C:0.32, G:0.19, T:0.18
Consensus pattern (173 bp):
AAACGCCGCTAAAGACCGAGACCTTTAGCGGCGCTTTTAATACAAACGCCGCTAAAGACCAAGAC
CTTTAGCGGCGCTTTCCACAAAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCCCACACA
AACGCCGCTAAAGACAACGACCATTTAGCGGCACTTACACGAC
Found at i:5326088 original size:130 final size:129
Alignment explanation
Indices: 5325860--5326284 Score: 559
Period size: 130 Copynumber: 3.3 Consensus size: 129
5325850 TTCCAGTAAA
* *
5325860 AAACGCCGCTAAAGGCCGAGACCTTTAGCGGCGCTTCCAACACAAACGCCGCCAAAGACCAAGAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCCAACACAAACGCCGCCAAAGACCAAGAC
* * *
5325925 CTTTAGCGGAGCTTTCCACATAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCATAC
66 CTTTAGCGGCGCTTTCAACACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCATAC
*
5325989 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCACTTCCAACACAAACGCCGCCAAAAGACCAAGA
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCCAACACAAACGCCGCC-AAAGACCAAGA
* * * ** *
5326054 CCTTTAGCGGCGCTTTTAATACAAACGCTGCTAAAGACCAAGACCTTTAGCGGCGCTTCCCACAC
65 CCTTTAGCGGCGCTTTCAACACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCATAC
* * *
5326119 AAACGCCGCTATAGACCAAGACCTTTAGCGGCGCTTCCCACACAAACGCCGCTAAAGA-CAACGA
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCCAACACAAACGCCGCCAAAGACCAA-GA
* * * * * **
5326183 CCATTTAGCGGCGCTTAC-ACGACAAATGCCGCTAAAGATCGAGACCTTTAGCGACG-TTTTTTT
65 CC-TTTAGCGGCGCTTTCAAC-ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCAT
5326246 CAC
128 -AC
* * *
5326249 AAATGCCGCTAAAGATCAAGACCTTTAGCAGCGCTT
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTT
5326285 TTCCCAAAAA
Statistics
Matches: 258, Mismatches: 33, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
128 3 0.01
129 62 0.24
130 193 0.75
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (129 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCCAACACAAACGCCGCCAAAGACCAAGAC
CTTTAGCGGCGCTTTCAACACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCATAC
Found at i:5341455 original size:13 final size:13
Alignment explanation
Indices: 5341437--5341470 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
5341427 TACTATAAAC
5341437 AATAATTGTTTAT
1 AATAATTGTTTAT
5341450 AATAATTGTTTAT
1 AATAATTGTTTAT
5341463 AATAATTG
1 AATAATTG
5341471 AGACCGAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (13 bp):
AATAATTGTTTAT
Found at i:5342084 original size:24 final size:22
Alignment explanation
Indices: 5342046--5342091 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 22
5342036 CTAGGGTTCT
5342046 AAATTTGGGGGATTTTTGGGGA
1 AAATTTGGGGGATTTTTGGGGA
5342068 AAATTTGGGGGGAATTTTTGGGGA
1 AAATTT-GGGGG-ATTTTTGGGGA
5342092 GAAAAGTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 6 0.27
23 5 0.23
24 11 0.50
ACGTcount: A:0.24, C:0.00, G:0.41, T:0.35
Consensus pattern (22 bp):
AAATTTGGGGGATTTTTGGGGA
Found at i:5342293 original size:43 final size:43
Alignment explanation
Indices: 5342227--5342311 Score: 152
Period size: 43 Copynumber: 2.0 Consensus size: 43
5342217 GGTGTCATGT
* *
5342227 AAAATGACAGCGTTTCTCTAAAATGGGCGGAAAATTTGCGGCC
1 AAAACGACAGCGTTTCTCAAAAATGGGCGGAAAATTTGCGGCC
5342270 AAAACGACAGCGTTTCTCAAAAATGGGCGGAAAATTTGCGGC
1 AAAACGACAGCGTTTCTCAAAAATGGGCGGAAAATTTGCGGC
5342312 GTTTTATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (43 bp):
AAAACGACAGCGTTTCTCAAAAATGGGCGGAAAATTTGCGGCC
Found at i:5342917 original size:19 final size:20
Alignment explanation
Indices: 5342890--5342930 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
5342880 AAAATTTTAA
5342890 TTAAATAAT-TATTAAAA-TT
1 TTAAATAATAT-TTAAAAGTT
*
5342909 TTAAGTAATATTTAAAAGTT
1 TTAAATAATATTTAAAAGTT
5342929 TT
1 TT
5342931 TGATAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
TTAAATAATATTTAAAAGTT
Found at i:5343351 original size:15 final size:15
Alignment explanation
Indices: 5343333--5343387 Score: 69
Period size: 15 Copynumber: 3.6 Consensus size: 15
5343323 ACCCTTGACA
5343333 CCCTAACCCCTAAAT
1 CCCTAACCCCTAAAT
5343348 CCCTAACCCCT-AAT
1 CCCTAACCCCTAAAT
5343362 CCCTAAATCCCCTTAAA-
1 CCCT-AA-CCCC-TAAAT
5343379 CCCTAACCC
1 CCCTAACCC
5343388 TTAATTAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
14 7 0.19
15 16 0.44
16 6 0.17
17 5 0.14
18 2 0.06
ACGTcount: A:0.31, C:0.49, G:0.00, T:0.20
Consensus pattern (15 bp):
CCCTAACCCCTAAAT
Found at i:5343365 original size:22 final size:22
Alignment explanation
Indices: 5343333--5343439 Score: 99
Period size: 22 Copynumber: 4.6 Consensus size: 22
5343323 ACCCTTGACA
*
5343333 CCCTAACCCCTAAATCCCTAAC
1 CCCTAACCCCTAAATCACTAAC
* * *
5343355 CCCTAATCCCTAAATCCCCTTAAA
1 CCCTAACCCCTAAAT-CAC-TAAC
*
5343379 CCCTAACCCTTAATTAAATCACTAAC
1 CCCTAACCC----CTAAATCACTAAC
*
5343405 CCCTAACCCCTAAATTACTAA-
1 CCCTAACCCCTAAATCACTAAC
5343426 CCCTAACCCCTAAA
1 CCCTAACCCCTAAA
5343440 CATTAATCCC
Statistics
Matches: 71, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
21 14 0.20
22 24 0.34
23 3 0.04
24 11 0.15
26 12 0.17
27 2 0.03
28 5 0.07
ACGTcount: A:0.36, C:0.42, G:0.00, T:0.22
Consensus pattern (22 bp):
CCCTAACCCCTAAATCACTAAC
Found at i:5343445 original size:50 final size:50
Alignment explanation
Indices: 5343343--5343439 Score: 119
Period size: 50 Copynumber: 2.0 Consensus size: 50
5343333 CCCTAACCCC
* * * *
5343343 TAAATCCCTAACCCCTAATCCCTAAATCCCCTTAAACCCTAACCCTTAAT
1 TAAATCACTAACCCCTAACCCCTAAATCCACTTAAACCCTAACCCTAAAT
*
5343393 TAAATCACTAACCCCTAACCCCTAAAT-TAC-T-AACCCTAACCCCTAAA
1 TAAATCACTAACCCCTAACCCCTAAATCCACTTAAACCCTAA-CCCTAAA
5343440 CATTAATCCC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
47 8 0.20
48 7 0.17
49 1 0.02
50 25 0.61
ACGTcount: A:0.37, C:0.39, G:0.00, T:0.24
Consensus pattern (50 bp):
TAAATCACTAACCCCTAACCCCTAAATCCACTTAAACCCTAACCCTAAAT
Found at i:5343459 original size:13 final size:14
Alignment explanation
Indices: 5343333--5343461 Score: 54
Period size: 14 Copynumber: 9.1 Consensus size: 14
5343323 ACCCTTGACA
*
5343333 CCCTAACCCCTAAAT
1 CCCTAAACCCT-AAT
*
5343348 CCCTAACCCCTAAT
1 CCCTAAACCCTAAT
*
5343362 CCCTAAATCCCCTTAAA
1 CCCTAAA--CCC-TAAT
5343379 CCCT-AACCCTTAAT
1 CCCTAAACCC-TAAT
* *
5343393 ---TAAATCACTAAC
1 CCCTAAA-CCCTAAT
*
5343405 CCCTAACCCCTAAAT
1 CCCTAAACCCT-AAT
** *
5343420 TACT-AACCCTAAC
1 CCCTAAACCCTAAT
**
5343433 CCCTAAACATTAAT
1 CCCTAAACCCTAAT
5343447 CCC-AAACCCTAAT
1 CCCTAAACCCTAAT
5343460 CC
1 CC
5343462 ATACCCTGAC
Statistics
Matches: 85, Mismatches: 19, Indels: 22
0.67 0.15 0.17
Matches are distributed among these distances:
11 1 0.01
12 5 0.06
13 16 0.19
14 33 0.39
15 18 0.21
16 5 0.06
17 7 0.08
ACGTcount: A:0.36, C:0.42, G:0.00, T:0.22
Consensus pattern (14 bp):
CCCTAAACCCTAAT
Found at i:5343840 original size:41 final size:41
Alignment explanation
Indices: 5343794--5343948 Score: 126
Period size: 41 Copynumber: 3.8 Consensus size: 41
5343784 GTTTCCATCA
*
5343794 AAACGCCGCT-AAAACTC-CAACATTAGCGGCGCTTTACAAAC
1 AAACGCCACTAAAAAC-CACAACATTAGCGGCGC-TTACAAAC
**
5343835 AAACGCCACTAAAAACCTTAAC-TATAGCGGCGCATTATC-AA-
1 AAACGCCACTAAAAACCACAACAT-TAGCGGCGC-TTA-CAAAC
* * * *
5343876 AAACGCCGCTAAAAGCC-CTAA-AGTTAGCGGCGCTCAGAAAC
1 AAACGCCACTAAAAACCAC-AACA-TTAGCGGCGCTTACAAAC
*
5343917 AAACGCCACTAAAAACCATAACATTAGCGGCG
1 AAACGCCACTAAAAACCACAACATTAGCGGCG
5343949 TTTGTTTAAA
Statistics
Matches: 92, Mismatches: 11, Indels: 22
0.74 0.09 0.18
Matches are distributed among these distances:
40 4 0.04
41 63 0.68
42 24 0.26
43 1 0.01
ACGTcount: A:0.39, C:0.29, G:0.16, T:0.15
Consensus pattern (41 bp):
AAACGCCACTAAAAACCACAACATTAGCGGCGCTTACAAAC
Found at i:5343864 original size:42 final size:41
Alignment explanation
Indices: 5343817--5343948 Score: 128
Period size: 41 Copynumber: 3.2 Consensus size: 41
5343807 ACTCCAACAT
5343817 TAGCGGCGCTTTACAAACAAACGCCACTAAAAACCTTAACTA
1 TAGCGGCGC-TTACAAACAAACGCCACTAAAAACCTTAACTA
* * * *
5343859 TAGCGGCGCATTATC-AA-AAACGCCGCTAAAAGCCCTAAAGT-
1 TAGCGGCGC-TTA-CAAACAAACGCCACTAAAA-ACCTTAACTA
* * *
5343900 TAGCGGCGCTCAGAAACAAACGCCACTAAAAACCATAAC-A
1 TAGCGGCGCTTACAAACAAACGCCACTAAAAACCTTAACTA
5343940 TTAGCGGCG
1 -TAGCGGCG
5343949 TTTGTTTAAA
Statistics
Matches: 72, Mismatches: 12, Indels: 13
0.74 0.12 0.13
Matches are distributed among these distances:
40 8 0.11
41 43 0.60
42 20 0.28
43 1 0.01
ACGTcount: A:0.39, C:0.28, G:0.17, T:0.16
Consensus pattern (41 bp):
TAGCGGCGCTTACAAACAAACGCCACTAAAAACCTTAACTA
Found at i:5343964 original size:82 final size:82
Alignment explanation
Indices: 5343793--5343948 Score: 221
Period size: 82 Copynumber: 1.9 Consensus size: 82
5343783 CGTTTCCATC
* *
5343793 AAAACGCCGCTAAAACTCCAACATTAGCGGCGCTTTACAAACAAACGCCACTAAAAACCTTAACT
1 AAAACGCCGCTAAAACTCCAACATTAGCGGCGCTTCACAAACAAACGCCACTAAAAACCATAACT
5343858 ATAGCGGCGCATTATCA
66 ATAGCGGCGCATTATCA
*
5343875 AAAACGCCGCTAAAAGC-CCTAA-AGTTAGCGGCGC-TCAGAAACAAACGCCACTAAAAACCATA
1 AAAACGCCGCTAAAA-CTCC-AACA-TTAGCGGCGCTTCACAAACAAACGCCACTAAAAACCATA
5343937 AC-ATTAGCGGCG
63 ACTA-TAGCGGCG
5343949 TTTGTTTAAA
Statistics
Matches: 67, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
81 1 0.01
82 53 0.79
83 13 0.19
ACGTcount: A:0.40, C:0.29, G:0.16, T:0.15
Consensus pattern (82 bp):
AAAACGCCGCTAAAACTCCAACATTAGCGGCGCTTCACAAACAAACGCCACTAAAAACCATAACT
ATAGCGGCGCATTATCA
Found at i:5348153 original size:1 final size:1
Alignment explanation
Indices: 5348147--5348181 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
5348137 ATATTAAAGC
5348147 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5348182 CAATCAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:5348750 original size:24 final size:24
Alignment explanation
Indices: 5348705--5348750 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
5348695 ATTTAAATAT
*
5348705 AAAATTTAATCCACAACTTAACCG
1 AAAATTTAATCCACAACATAACCG
5348729 AAAATTTAATCC-CTAACATAAC
1 AAAATTTAATCCAC-AACATAAC
5348751 TTCCCCTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.48, C:0.24, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATTTAATCCACAACATAACCG
Found at i:5348791 original size:11 final size:11
Alignment explanation
Indices: 5348775--5348800 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5348765 ATTAGAAAAA
5348775 AAAAAAAAAGG
1 AAAAAAAAAGG
5348786 AAAAAAAAAGG
1 AAAAAAAAAGG
5348797 AAAA
1 AAAA
5348801 CAGTTTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGG
Found at i:5349420 original size:71 final size:71
Alignment explanation
Indices: 5349338--5349471 Score: 241
Period size: 71 Copynumber: 1.9 Consensus size: 71
5349328 AACCGCCACA
5349338 AGAGTAAGTAAGAATTTGATTTTATGATATTCTGTCATATATTAAGGAGAAGTTTGTGTTAAGTG
1 AGAGTAAGTAAGAATTTGATTTTATGATATTCTGTCATATATTAAGGAGAAGTTTGTGTTAAGTG
5349403 ATTAAG
66 ATTAAG
* * *
5349409 AGAGTAAGTAAGACTTTGATTTTCTGATATTCTGTCATGTATTAAGGAGAAGTTTGTGTTAAG
1 AGAGTAAGTAAGAATTTGATTTTATGATATTCTGTCATATATTAAGGAGAAGTTTGTGTTAAG
5349472 AAATTAACGT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
71 60 1.00
ACGTcount: A:0.33, C:0.04, G:0.23, T:0.40
Consensus pattern (71 bp):
AGAGTAAGTAAGAATTTGATTTTATGATATTCTGTCATATATTAAGGAGAAGTTTGTGTTAAGTG
ATTAAG
Found at i:5354336 original size:9 final size:10
Alignment explanation
Indices: 5354314--5354373 Score: 58
Period size: 9 Copynumber: 6.4 Consensus size: 10
5354304 TTTACATCTC
*
5354314 AAAAAATTAT
1 AAAAAACTAT
5354324 AAAAAACTA-
1 AAAAAACTAT
5354333 AAAAATA-TAT
1 AAAAA-ACTAT
*
5354343 AATAAACT-T
1 AAAAAACTAT
5354352 AAAAAA-TAT
1 AAAAAACTAT
5354361 AAAAAACTA-
1 AAAAAACTAT
5354370 AAAA
1 AAAA
5354374 CCTTAAACCC
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
8 1 0.02
9 25 0.60
10 16 0.38
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (10 bp):
AAAAAACTAT
Found at i:5354337 original size:18 final size:18
Alignment explanation
Indices: 5354314--5354373 Score: 86
Period size: 18 Copynumber: 3.3 Consensus size: 18
5354304 TTTACATCTC
5354314 AAAAAATTATAAAAAACT
1 AAAAAATTATAAAAAACT
*
5354332 AAAAAATATATAATAAACTT
1 AAAAAAT-TATAAAAAAC-T
5354352 AAAAAA-TATAAAAAACT
1 AAAAAATTATAAAAAACT
5354369 AAAAA
1 AAAAA
5354374 CCTTAAACCC
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
17 6 0.16
18 16 0.42
19 9 0.24
20 7 0.18
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (18 bp):
AAAAAATTATAAAAAACT
Found at i:5357517 original size:41 final size:41
Alignment explanation
Indices: 5357466--5357631 Score: 192
Period size: 42 Copynumber: 4.0 Consensus size: 41
5357456 GTGCTATCAT
*
5357466 ATATCGATGCCAATAG-CTAG-CTATGGTCTTACACGAATCTC
1 ATATCGATGCCAAT-GCCCAGAC-ATGGTCTTACACGAATCTC
*
5357507 ATATCGATGCCAATGTCCCAGACATGGTCTTACATGAATCTC
1 ATATCGATGCCAATG-CCCAGACATGGTCTTACACGAATCTC
* * * * *
5357549 GTATTGATGCCAATGTCCCAGACATGGTCTTAGATGAATCAC
1 ATATCGATGCCAATG-CCCAGACATGGTCTTACACGAATCTC
*
5357591 ATAACGATGCCAATGTCCCAGACATGGTCTTACACGTAATC
1 ATATCGATGCCAATG-CCCAGACATGGTCTTACACG-AATC
5357632 ACATCTCAGT
Statistics
Matches: 110, Mismatches: 11, Indels: 6
0.87 0.09 0.05
Matches are distributed among these distances:
40 1 0.01
41 14 0.13
42 90 0.82
43 5 0.05
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.28
Consensus pattern (41 bp):
ATATCGATGCCAATGCCCAGACATGGTCTTACACGAATCTC
Found at i:5357534 original size:42 final size:42
Alignment explanation
Indices: 5357488--5357631 Score: 216
Period size: 42 Copynumber: 3.4 Consensus size: 42
5357478 ATAGCTAGCT
5357488 ATGGTCTTACACGAATCTCATATCGATGCCAATGTCCCAGAC
1 ATGGTCTTACACGAATCTCATATCGATGCCAATGTCCCAGAC
* * *
5357530 ATGGTCTTACATGAATCTCGTATTGATGCCAATGTCCCAGAC
1 ATGGTCTTACACGAATCTCATATCGATGCCAATGTCCCAGAC
* * * *
5357572 ATGGTCTTAGATGAATCACATAACGATGCCAATGTCCCAGAC
1 ATGGTCTTACACGAATCTCATATCGATGCCAATGTCCCAGAC
5357614 ATGGTCTTACACGTAATC
1 ATGGTCTTACACG-AATC
5357632 ACATCTCAGT
Statistics
Matches: 91, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
42 87 0.96
43 4 0.04
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (42 bp):
ATGGTCTTACACGAATCTCATATCGATGCCAATGTCCCAGAC
Found at i:5357922 original size:20 final size:19
Alignment explanation
Indices: 5357891--5357942 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
5357881 ATCTATATAA
* *
5357891 TAACAAAATTTACT-TATT
1 TAACACAATTTACTCAATT
5357909 TAATCACTAATTTACTCAATT
1 TAA-CAC-AATTTACTCAATT
5357930 TAACACAATTTAC
1 TAACACAATTTAC
5357943 ACATTAGAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 3 0.10
19 9 0.31
20 11 0.38
21 6 0.21
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.40
Consensus pattern (19 bp):
TAACACAATTTACTCAATT
Found at i:5358886 original size:24 final size:24
Alignment explanation
Indices: 5358854--5358901 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
5358844 AACTTTACGA
5358854 TCCGCTTCCACGTTCATCCACATC
1 TCCGCTTCCACGTTCATCCACATC
5358878 TCCGCTTCCACGTTCATCCACATC
1 TCCGCTTCCACGTTCATCCACATC
5358902 ATTCTTTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.17, C:0.46, G:0.08, T:0.29
Consensus pattern (24 bp):
TCCGCTTCCACGTTCATCCACATC
Found at i:5383404 original size:42 final size:42
Alignment explanation
Indices: 5383333--5383474 Score: 187
Period size: 42 Copynumber: 3.4 Consensus size: 42
5383323 CTTTCCATTG
*
5383333 AGCTCTCATGAGCTTCAGTTTAACCCTTATGGGTTTCTGTTT
1 AGCTCTTATGAGCTTCAGTTTAACCCTTATGGGTTTCTGTTT
* * * *
5383375 AGCTTTTTTGAGCTTCAGTTTAACTCTTATGGGTTTCTGTTC
1 AGCTCTTATGAGCTTCAGTTTAACCCTTATGGGTTTCTGTTT
*
5383417 AGCTCTTATGAGCTTCCA-TTCAACCCTTATGGGTTTCTGTTT
1 AGCTCTTATGAGCTT-CAGTTTAACCCTTATGGGTTTCTGTTT
* * *
5383459 GGCACTTATGTGCTTC
1 AGCTCTTATGAGCTTC
5383475 TGTGCAGCCT
Statistics
Matches: 86, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
41 1 0.01
42 83 0.97
43 2 0.02
ACGTcount: A:0.15, C:0.21, G:0.19, T:0.44
Consensus pattern (42 bp):
AGCTCTTATGAGCTTCAGTTTAACCCTTATGGGTTTCTGTTT
Found at i:5383424 original size:21 final size:21
Alignment explanation
Indices: 5383358--5383457 Score: 74
Period size: 21 Copynumber: 4.8 Consensus size: 21
5383348 CAGTTTAACC
* *
5383358 CTTATGGGTTTCTGTTTAGCT
1 CTTATGGGTTTCTGTTCAACT
* * * * * *
5383379 TTTTTGAGCTTCAGTTTAACT
1 CTTATGGGTTTCTGTTCAACT
*
5383400 CTTATGGGTTTCTGTTCAGCT
1 CTTATGGGTTTCTGTTCAACT
* * ** *
5383421 CTTATGAGCTTCCATTCAACC
1 CTTATGGGTTTCTGTTCAACT
5383442 CTTATGGGTTTCTGTT
1 CTTATGGGTTTCTGTT
5383458 TGGCACTTAT
Statistics
Matches: 56, Mismatches: 23, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.14, C:0.19, G:0.19, T:0.48
Consensus pattern (21 bp):
CTTATGGGTTTCTGTTCAACT
Found at i:5402856 original size:2 final size:2
Alignment explanation
Indices: 5402849--5402875 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5402839 AATAATCATA
5402849 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
5402876 GGGAGAGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5409657 original size:20 final size:20
Alignment explanation
Indices: 5409629--5409677 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
5409619 GTGATTTCTT
*
5409629 AATTAAATTAGTTTTCTATA
1 AATTCAATTAGTTTTCTATA
* *
5409649 AATTCAATTCGTTTTCTGTA
1 AATTCAATTAGTTTTCTATA
5409669 AATTCAATT
1 AATTCAATT
5409678 GATCAGACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.49
Consensus pattern (20 bp):
AATTCAATTAGTTTTCTATA
Found at i:5411695 original size:99 final size:98
Alignment explanation
Indices: 5411476--5411820 Score: 279
Period size: 101 Copynumber: 3.4 Consensus size: 98
5411466 TTACTCATTC
* * * *
5411476 TGGTGACTCCATATTGAAGTGGCGGGACCGAAAAA--TTAAAAAAAATATTGGTGCCGCCATATC
1 TGGTGACTCCATA-TGAAGTGGCAGCACCGAAAAATTTTAAAAAAAATATTAGTGTCGCCATATC
* * * * * *
5411539 TGGAGAAAGGACTAGGGAAATTTTATTTTTTTATTGTTT
65 TAGAGTAGGGACCA--GAAA--AT-TTTTTTTATTATTT
*** * * * *
5411578 TGGTGACTTTGTGTGAAGTGGCAGCACTGAAAAATTTTAAAAAAAATACTAGTGTCACCATATCT
1 TGGTGACTCCATATGAAGTGGCAGCACCGAAAAATTTTAAAAAAAATATTAGTGTCGCCATATCT
5411643 AGAGTAGGGACCAGAAAATTTTTTTTATTCATTT
66 AGAGTAGGGACCAGAAAATTTTTTTTATT-ATTT
* * ** *
5411677 TGGTGACTCCATATGAAGTGGCGGGACCGAAAAATTAAAAAAAAAACTTATTAGTGTCGTCATAT
1 TGGTGACTCCATATGAAGTGGCAGCACCGAAAAATTTTAAAAAAAA--TATTAGTGTCGCCATAT
* * *
5411742 CTAGGGTAGGGACCA-AGAGTTTCTTTTTAACTT-TTT
64 CTAGAGTAGGGACCAGAAAATTT-TTTTT-A-TTATTT
* *
5411778 TAGTGACTCCATGTGAAGT-G-ATGACACCGAAAAATTTTAAAAA
1 TGGTGACTCCATATGAAGTGGCA-G-CACCGAAAAATTTTAAAAA
5411821 TGCGGCACCA
Statistics
Matches: 195, Mismatches: 38, Indels: 21
0.77 0.15 0.08
Matches are distributed among these distances:
98 10 0.05
99 41 0.21
100 7 0.04
101 91 0.47
102 10 0.05
103 36 0.18
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (98 bp):
TGGTGACTCCATATGAAGTGGCAGCACCGAAAAATTTTAAAAAAAATATTAGTGTCGCCATATCT
AGAGTAGGGACCAGAAAATTTTTTTTATTATTT
Found at i:5414335 original size:96 final size:97
Alignment explanation
Indices: 5414235--5414417 Score: 239
Period size: 96 Copynumber: 1.9 Consensus size: 97
5414225 AGGTTGAGGG
*
5414235 TTACTTGAGTAATTTAATTA-AAAGTTATTTA-AAAA-TCAAATAAGGGTTTAGAGTTAAGGGTT
1 TTACTTGAGTAAATTAATTATAAA-TT-TTTACAAAATTCAAATAAGGG-TTAGAGTTAAGGGTT
5414297 TTTAAG-AAAAAATCAAATAAATTAGGGTGCAAGA
63 TTTAAGTAAAAAATCAAATAAATTAGGGTGCAAGA
** * * * *
5414331 TTACTTGAGTAAATTAATTATAAATTTTTACAAAATTTGATTAAGGGTTAGTGTTTAGTGTTTTT
1 TTACTTGAGTAAATTAATTATAAATTTTTACAAAATTCAAATAAGGGTTAGAGTTAAGGGTTTTT
*
5414396 AAGTAAAAACTCAAATAAATTA
66 AAGTAAAAAATCAAATAAATTA
5414418 AGGTTTGGGA
Statistics
Matches: 75, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
95 4 0.05
96 43 0.57
97 28 0.37
ACGTcount: A:0.43, C:0.04, G:0.15, T:0.38
Consensus pattern (97 bp):
TTACTTGAGTAAATTAATTATAAATTTTTACAAAATTCAAATAAGGGTTAGAGTTAAGGGTTTTT
AAGTAAAAAATCAAATAAATTAGGGTGCAAGA
Found at i:5414687 original size:126 final size:126
Alignment explanation
Indices: 5414462--5415004 Score: 872
Period size: 126 Copynumber: 4.3 Consensus size: 126
5414452 TTTTTAATTT
* ** * **
5414462 AAAGAAGCTCCCACGTGGACGCACTTTTATTGCAGTAACTCCTGAAAAAATAATTTCGAGTAGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTGGCTCCTGAAAAAATAATTTCGAGTAGAC
*
5414527 GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGC-GAGATGCTTTGTCAGCAGAAGTAATG
66 GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAG-GATGCTTTGTCAGCAGAAGTACTG
*
5414588 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTAGAGTGGCTCCTGAAAAAATAATTTCGAGTAGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTGGCTCCTGAAAAAATAATTTCGAGTAGAC
* *
5414653 GTTTCTGAGCAAATAGTGTCAAAAACGTTTTAAGCAGGATACTTTGTCAGCAGAAGTACTG
66 GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTG
* * * * *
5414714 AAAGAAGCTCCCATGTGGACGCACTTTTGCTATAGTAGCTCCTCAAAAAATAATTTCGAGTAGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTGGCTCCTGAAAAAATAATTTCGAGTAGAC
* * *
5414779 GTTTCTGAGCAAATAGTGTCAAAAAAGCTTTAAGCAGGATGTTTTGTCAGTAGAAGTACTG
66 GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTG
* *
5414840 AAAGAAGCTCCTACGTAGACGCGCTTTTGCTACAGTGGCTCCTGAAAAAATAATTTCGAGTAGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTGGCTCCTGAAAAAATAATTTCGAGTAGAC
*
5414905 GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCATGATGCTTTGTCAGCAGAAGTACTG
66 GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTG
*
5414966 AAAGAAGCTCCCACATGGACGCGCTTTTGCTACAGTGGC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTGGC
5415005 GCATGTTTGG
Statistics
Matches: 382, Mismatches: 34, Indels: 2
0.91 0.08 0.00
Matches are distributed among these distances:
126 381 1.00
127 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (126 bp):
AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTGGCTCCTGAAAAAATAATTTCGAGTAGAC
GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTG
Found at i:5420439 original size:22 final size:21
Alignment explanation
Indices: 5420414--5420463 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
5420404 TCTTTTAAAT
* *
5420414 AGAAATTTGAGAGGAATTTGAG
1 AGAAATTAGAGA-GAAATTGAG
*
5420436 AGAATACTAGAGAGAAATTGAG
1 AGAA-ATTAGAGAGAAATTGAG
5420458 AGAAAT
1 AGAAAT
5420464 GATTTAGTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 1 0.04
22 16 0.70
23 6 0.26
ACGTcount: A:0.48, C:0.02, G:0.28, T:0.22
Consensus pattern (21 bp):
AGAAATTAGAGAGAAATTGAG
Found at i:5432901 original size:875 final size:875
Alignment explanation
Indices: 5431206--5432957 Score: 3452
Period size: 875 Copynumber: 2.0 Consensus size: 875
5431196 ATGTAATTTA
*
5431206 TAACACATTAAAAAAATAAACTTATGCTAAATATATAACACTACTCTAATGTAAACATTAAAATA
1 TAACACATTAAAAAAATAAACTTATACTAAATATATAACACTACTCTAATGTAAACATTAAAATA
5431271 ATGTTAAGATGACTATATAAAAATTTTCAATAAATAAAAAATATATAAAATAATATAAATATTTT
66 ATGTTAAGATGACTATATAAAAATTTTCAATAAATAAAAAATATATAAAATAATATAAATATTTT
5431336 TAAAAAAAATTAAAAATAATATGGGCGAGTTTAAAATGGGCTTGAGTTAATCTTTTGCAAATGTG
131 TAAAAAAAATTAAAAATAATATGGGCGAGTTTAAAATGGGCTTGAGTTAATCTTTTGCAAATGTG
5431401 GATGGGTTTGGGCAAAATTTTAGGCTCATATTTTGGGTCAGGTTGGATTTGGGCTTGTATAAACT
196 GATGGGTTTGGGCAAAATTTTAGGCTCATATTTTGGGTCAGGTTGGATTTGGGCTTGTATAAACT
5431466 ATATTAATATTATGCTTAGGCTTGACCAATGAGCACCTCTAATCTACAATTAATAACAAATTTTG
261 ATATTAATATTATGCTTAGGCTTGACCAATGAGCACCTCTAATCTACAATTAATAACAAATTTTG
5431531 CACTAGTATCTTCTGTACAGGTTAAACCCTCTCATCCTAATAATAAATTCAAACAATAAATTTTA
326 CACTAGTATCTTCTGTACAGGTTAAACCCTCTCATCCTAATAATAAATTCAAACAATAAATTTTA
5431596 GTTTTTAATTACATTTTAAAATAAAATATAATCATATAATTAAGTTATTGGATATAATTAATATT
391 GTTTTTAATTACATTTTAAAATAAAATATAATCATATAATTAAGTTATTGGATATAATTAATATT
5431661 TTCATATAAATATGTGTAATTCAAATACATTTACATGTATATATATTTAAAAGATACAGGTAAAT
456 TTCATATAAATATGTGTAATTCAAATACATTTACATGTATATATATTTAAAAGATACAGGTAAAT
5431726 TCGAAATGATATATCAAAATACTTTGTACTAGTATGTATCTATACATAACAAAAACGATATGATT
521 TCGAAATGATATATCAAAATACTTTGTACTAGTATGTATCTATACATAACAAAAACGATATGATT
5431791 CTCTAAGGCAGAAGCAGAATAAAGTTTTAAGGGACTATAATTGAATTATAAATTCTTGAAGTCCA
586 CTCTAAGGCAGAAGCAGAATAAAGTTTTAAGGGACTATAATTGAATTATAAATTCTTGAAGTCCA
5431856 GAGACAATTTTACTATTATATTAATTTTTAATTTTATATTTTTTAAGGGCTTTAAAGTAATTTTA
651 GAGACAATTTTACTATTATATTAATTTTTAATTTTATATTTTTTAAGGGCTTTAAAGTAATTTTA
5431921 CTATTTAGGGGCAAGGCTTCTACCCTTGGATTCACCACTAATGGTATTGACTATCGACTACCTTG
716 CTATTTAGGGGCAAGGCTTCTACCCTTGGATTCACCACTAATGGTATTGACTATCGACTACCTTG
5431986 CATTTTATTAAAAAATAGTAAATTAAGAAGATTTTGATTTGAGTTAAATTAATATTGGATTCTAA
781 CATTTTATTAAAAAATAGTAAATTAAGAAGATTTTGATTTGAGTTAAATTAATATTGGATTCTAA
5432051 TTGTAATTGTTACTAAAATTAATTTTAATT
846 TTGTAATTGTTACTAAAATTAATTTTAATT
* * *
5432081 TAACCCATTAAAAAAATAAA-TCTATACTAAATATATAATACTACTCTAATGTAACCATTAAAAT
1 TAACACATTAAAAAAATAAACT-TATACTAAATATATAACACTACTCTAATGTAAACATTAAAAT
5432145 AATGTTAAGATGACTATATAAAAATTTTCAATAAATAAAAAATATATAAAATAATATAAATATTT
65 AATGTTAAGATGACTATATAAAAATTTTCAATAAATAAAAAATATATAAAATAATATAAATATTT
5432210 TTAAAAAAAATTAAAAATAATATGGGCGAGTTTAAAATGGGCTTGAGTTAATCTTTTGCAAATGT
130 TTAAAAAAAATTAAAAATAATATGGGCGAGTTTAAAATGGGCTTGAGTTAATCTTTTGCAAATGT
5432275 GGATGGGTTTGGGCAAAATTTTAGGCTCATATTTTGGGTCAGGTTGGATTTGGGCTTGTATAAAC
195 GGATGGGTTTGGGCAAAATTTTAGGCTCATATTTTGGGTCAGGTTGGATTTGGGCTTGTATAAAC
5432340 TATATTAATATTATGCTTAGGCTTGACCAATGAGCACCTCTAATCTACAATTAATAACAAATTTT
260 TATATTAATATTATGCTTAGGCTTGACCAATGAGCACCTCTAATCTACAATTAATAACAAATTTT
5432405 GCACTAGTATCTTCTGTACAGGTTAAACCCTCTCATCCTAATAATAAATTCAAACAATAAATTTT
325 GCACTAGTATCTTCTGTACAGGTTAAACCCTCTCATCCTAATAATAAATTCAAACAATAAATTTT
5432470 AGTTTTTAATTACATTTTAAAATAAAATATAATCATATAATTAAGTTATTGGATATAATTAATAT
390 AGTTTTTAATTACATTTTAAAATAAAATATAATCATATAATTAAGTTATTGGATATAATTAATAT
5432535 TTTCATATAAATATGTGTAATTCAAATACATTTACATGTATATATATTTAAAAGATACAGGTAAA
455 TTTCATATAAATATGTGTAATTCAAATACATTTACATGTATATATATTTAAAAGATACAGGTAAA
5432600 TTCGAAATGATATATCAAAATACTTTGTACTAGTATGTATCTATACATAACAAAAACGATATGAT
520 TTCGAAATGATATATCAAAATACTTTGTACTAGTATGTATCTATACATAACAAAAACGATATGAT
5432665 TCTCTAAGGCAGAAGCAGAATAAAGTTTTAAGGGACTATAATTGAATTATAAATTCTTGAAGTCC
585 TCTCTAAGGCAGAAGCAGAATAAAGTTTTAAGGGACTATAATTGAATTATAAATTCTTGAAGTCC
5432730 AGAGACAATTTTACTATTATATTAATTTTTAATTTTATATTTTTTAAGGGCTTTAAAGTAATTTT
650 AGAGACAATTTTACTATTATATTAATTTTTAATTTTATATTTTTTAAGGGCTTTAAAGTAATTTT
5432795 ACTATTTAGGGGCAAGGCTTCTACCCTTGGATTCACCACTAATGGTATTGACTATCGACTACCTT
715 ACTATTTAGGGGCAAGGCTTCTACCCTTGGATTCACCACTAATGGTATTGACTATCGACTACCTT
5432860 GCATTTTATTAAAAAATAGTAAATTAAGAAGATTTTGATTTGAGTTAAATTAATATTGGATTCTA
780 GCATTTTATTAAAAAATAGTAAATTAAGAAGATTTTGATTTGAGTTAAATTAATATTGGATTCTA
5432925 ATTGTAATTGTTACTAAAATTAATTTTAATT
845 ATTGTAATTGTTACTAAAATTAATTTTAATT
5432956 TA
1 TA
5432958 GAAAAACAAC
Statistics
Matches: 872, Mismatches: 4, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
874 1 0.00
875 871 1.00
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (875 bp):
TAACACATTAAAAAAATAAACTTATACTAAATATATAACACTACTCTAATGTAAACATTAAAATA
ATGTTAAGATGACTATATAAAAATTTTCAATAAATAAAAAATATATAAAATAATATAAATATTTT
TAAAAAAAATTAAAAATAATATGGGCGAGTTTAAAATGGGCTTGAGTTAATCTTTTGCAAATGTG
GATGGGTTTGGGCAAAATTTTAGGCTCATATTTTGGGTCAGGTTGGATTTGGGCTTGTATAAACT
ATATTAATATTATGCTTAGGCTTGACCAATGAGCACCTCTAATCTACAATTAATAACAAATTTTG
CACTAGTATCTTCTGTACAGGTTAAACCCTCTCATCCTAATAATAAATTCAAACAATAAATTTTA
GTTTTTAATTACATTTTAAAATAAAATATAATCATATAATTAAGTTATTGGATATAATTAATATT
TTCATATAAATATGTGTAATTCAAATACATTTACATGTATATATATTTAAAAGATACAGGTAAAT
TCGAAATGATATATCAAAATACTTTGTACTAGTATGTATCTATACATAACAAAAACGATATGATT
CTCTAAGGCAGAAGCAGAATAAAGTTTTAAGGGACTATAATTGAATTATAAATTCTTGAAGTCCA
GAGACAATTTTACTATTATATTAATTTTTAATTTTATATTTTTTAAGGGCTTTAAAGTAATTTTA
CTATTTAGGGGCAAGGCTTCTACCCTTGGATTCACCACTAATGGTATTGACTATCGACTACCTTG
CATTTTATTAAAAAATAGTAAATTAAGAAGATTTTGATTTGAGTTAAATTAATATTGGATTCTAA
TTGTAATTGTTACTAAAATTAATTTTAATT
Found at i:5448362 original size:14 final size:14
Alignment explanation
Indices: 5448343--5448379 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
5448333 TTAGCAATGC
5448343 TAAAGAAAGAAATA
1 TAAAGAAAGAAATA
5448357 TAAAGAATA-AAATA
1 TAAAGAA-AGAAATA
5448371 -AAAGAAAGA
1 TAAAGAAAGA
5448380 GATGCTCATG
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 1 0.05
13 7 0.33
14 12 0.57
15 1 0.05
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
TAAAGAAAGAAATA
Found at i:5449208 original size:16 final size:15
Alignment explanation
Indices: 5449189--5449240 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 15
5449179 AAAATTAGCT
5449189 AAAAATAAAAATGAAA
1 AAAAATAAAAAT-AAA
5449205 AAAAATAAAAATAAACA
1 AAAAATAAAAAT-AA-A
*
5449222 AAAAAGGAAAAATAAA
1 AAAAA-TAAAAATAAA
5449238 AAA
1 AAA
5449241 TTTGACTTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 18 0.56
17 8 0.25
18 6 0.19
ACGTcount: A:0.83, C:0.02, G:0.06, T:0.10
Consensus pattern (15 bp):
AAAAATAAAAATAAA
Found at i:5449224 original size:26 final size:25
Alignment explanation
Indices: 5449152--5449239 Score: 63
Period size: 26 Copynumber: 3.4 Consensus size: 25
5449142 AAACAAATAG
*
5449152 AAAAATAAACATGAAGACAAAAAGAAA
1 AAAAATAAAAAT-AA-ACAAAAAGAAA
* ** *
5449179 AAAATTAGCTAA-AAATAAAAATGAAA
1 AAAAATA-AAAATAAACAAAAA-GAAA
**
5449205 AAAAATAAAAATAAACAAAAA-AGG
1 AAAAATAAAAATAAACAAAAAGAAA
5449229 AAAAATAAAAA
1 AAAAATAAAAA
5449240 ATTTGACTTG
Statistics
Matches: 47, Mismatches: 11, Indels: 9
0.70 0.16 0.13
Matches are distributed among these distances:
24 12 0.26
25 8 0.17
26 20 0.43
27 6 0.13
28 1 0.02
ACGTcount: A:0.76, C:0.05, G:0.08, T:0.11
Consensus pattern (25 bp):
AAAAATAAAAATAAACAAAAAGAAA
Found at i:5463125 original size:18 final size:18
Alignment explanation
Indices: 5463081--5463209 Score: 134
Period size: 18 Copynumber: 7.2 Consensus size: 18
5463071 TTATCTACCG
*
5463081 TACATATAAGGGTTCGCT
1 TACATATAAGGGTTCGCA
** *
5463099 TACGCATAAGAGTTCGCA
1 TACATATAAGGGTTCGCA
5463117 TACATATAAGGGCTT-GCA
1 TACATATAAGGG-TTCGCA
* * *
5463135 TGCATATAAAGGTTCACA
1 TACATATAAGGGTTCGCA
*
5463153 TACATATAAAGGTTCGCA
1 TACATATAAGGGTTCGCA
* * *
5463171 TGCATATAAGGGTCCACA
1 TACATATAAGGGTTCGCA
*
5463189 TACATATAAGGGTTCACA
1 TACATATAAGGGTTCGCA
5463207 TAC
1 TAC
5463210 CAACAATTTG
Statistics
Matches: 91, Mismatches: 18, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
17 2 0.02
18 87 0.96
19 2 0.02
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (18 bp):
TACATATAAGGGTTCGCA
Found at i:5464605 original size:24 final size:24
Alignment explanation
Indices: 5464575--5464622 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
5464565 TTAAGAATGA
5464575 AAATGAATCCACAAAGTTTGATTG
1 AAATGAATCCACAAAGTTTGATTG
*
5464599 AAATGAATCCACAAATTTTGATTG
1 AAATGAATCCACAAAGTTTGATTG
5464623 TCTCTACAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (24 bp):
AAATGAATCCACAAAGTTTGATTG
Found at i:5474134 original size:24 final size:23
Alignment explanation
Indices: 5474107--5474160 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
5474097 TGCGCATTAT
* *
5474107 ATATATGCTAATTAAATTTATTTA
1 ATATATGCTAAATAAATTTA-TCA
**
5474131 ATATATATTAAATAAATTTATCA
1 ATATATGCTAAATAAATTTATCA
5474154 ATATATG
1 ATATATG
5474161 TATATATATA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (23 bp):
ATATATGCTAAATAAATTTATCA
Found at i:5479611 original size:28 final size:27
Alignment explanation
Indices: 5479562--5479615 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
5479552 ATTAAATAAA
* *
5479562 TTCAATAAACACTAATTTTATACTTAAG
1 TTCAATAAACACTAAATATATA-TTAAG
5479590 TTCATATAAACA-TAAATATATATTAA
1 TTCA-ATAAACACTAAATATATATTAA
5479616 CAGTGACTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 4 0.17
28 12 0.52
29 7 0.30
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (27 bp):
TTCAATAAACACTAAATATATATTAAG
Found at i:5485025 original size:5 final size:5
Alignment explanation
Indices: 5484997--5485056 Score: 79
Period size: 5 Copynumber: 12.2 Consensus size: 5
5484987 TTTTTATGTT
* *
5484997 TTATA -TATA TTATT TTAT- TATATA TTATA TTATA TTATA TTATA TTGTA
1 TTATA TTATA TTATA TTATA T-TATA TTATA TTATA TTATA TTATA TTATA
5485046 TTATA TTATA T
1 TTATA TTATA T
5485057 AAGTAAAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
4 5 0.10
5 43 0.88
6 1 0.02
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:5499240 original size:22 final size:23
Alignment explanation
Indices: 5499215--5499265 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
5499205 TTCAAAACTA
*
5499215 AAAAAT-AACTCTTTCACCAATC
1 AAAAATCAACTATTTCACCAATC
* *
5499237 AAAAATCATCTATTTCATCAATC
1 AAAAATCAACTATTTCACCAATC
5499260 AAAAAT
1 AAAAAT
5499266 TATTTAAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 6 0.24
23 19 0.76
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.29
Consensus pattern (23 bp):
AAAAATCAACTATTTCACCAATC
Found at i:5511267 original size:14 final size:14
Alignment explanation
Indices: 5511241--5511267 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5511231 CTGACGTTAT
5511241 AATATGGTCGTTGC
1 AATATGGTCGTTGC
5511255 AATATGGTCGTTG
1 AATATGGTCGTTG
5511268 AATTTTTTTA
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:0.22, C:0.11, G:0.30, T:0.37
Consensus pattern (14 bp):
AATATGGTCGTTGC
Found at i:5516566 original size:28 final size:28
Alignment explanation
Indices: 5516521--5516613 Score: 98
Period size: 28 Copynumber: 3.4 Consensus size: 28
5516511 AATTTGACCA
* *
5516521 TTACAATATGGTTGTTGGAATCTGATTG
1 TTACAATATGGCTGTTGGAATCTGACTG
* * **
5516549 TTACAATATGGCTATTGGAATTTGACCA
1 TTACAATATGGCTGTTGGAATCTGACTG
* *
5516577 TTACAA-ATGGCCGTTGGAATCTAACTG
1 TTACAATATGGCTGTTGGAATCTGACTG
*
5516604 TTGCAATATG
1 TTACAATATG
5516614 ACCGTTGAAT
Statistics
Matches: 51, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
27 20 0.39
28 31 0.61
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.37
Consensus pattern (28 bp):
TTACAATATGGCTGTTGGAATCTGACTG
Found at i:5519309 original size:31 final size:31
Alignment explanation
Indices: 5519274--5519332 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
5519264 ATGTGTATAG
5519274 TTGAATCACAATAAAAATTTCATATATACAT
1 TTGAATCACAATAAAAATTTCATATATACAT
* * *
5519305 TTGAATTACAATCAAAGTTTCATATATA
1 TTGAATCACAATAAAAATTTCATATATA
5519333 TTGTTAGAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.46, C:0.12, G:0.05, T:0.37
Consensus pattern (31 bp):
TTGAATCACAATAAAAATTTCATATATACAT
Found at i:5525653 original size:10 final size:9
Alignment explanation
Indices: 5525639--5525685 Score: 62
Period size: 8 Copynumber: 5.3 Consensus size: 9
5525629 CAGACTCAAA
5525639 AAAAAAATC
1 AAAAAAATC
5525648 AAAAAAAT-
1 AAAAAAATC
*
5525656 TAAAAAATC
1 AAAAAAATC
5525665 -AAAAAATC
1 AAAAAAATC
5525673 AAAAAAAATC
1 -AAAAAAATC
5525683 AAA
1 AAA
5525686 GTAAAAAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
8 15 0.44
9 11 0.32
10 8 0.24
ACGTcount: A:0.79, C:0.09, G:0.00, T:0.13
Consensus pattern (9 bp):
AAAAAAATC
Found at i:5525693 original size:17 final size:15
Alignment explanation
Indices: 5525636--5525685 Score: 55
Period size: 18 Copynumber: 3.0 Consensus size: 15
5525626 GTCCAGACTC
5525636 AAAAAAAAAATCAAA
1 AAAAAAAAAATCAAA
5525651 AAAATTAAAAAATCAAAA
1 AAAA--AAAAAATC-AAA
5525669 AATCAAAAAAAATCAAA
1 AA--AAAAAAAATCAAA
5525686 GTAAAAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
15 4 0.13
17 11 0.37
18 13 0.43
20 2 0.07
ACGTcount: A:0.80, C:0.08, G:0.00, T:0.12
Consensus pattern (15 bp):
AAAAAAAAAATCAAA
Found at i:5525705 original size:14 final size:14
Alignment explanation
Indices: 5525688--5525721 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
5525678 AAATCAAAGT
*
5525688 AAAAAATAGGAGAA
1 AAAAAATAGAAGAA
5525702 AAAAAATAGAAGAA
1 AAAAAATAGAAGAA
5525716 AAAAAA
1 AAAAAA
5525722 GAAAAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (14 bp):
AAAAAATAGAAGAA
Found at i:5525718 original size:27 final size:25
Alignment explanation
Indices: 5525673--5525745 Score: 74
Period size: 27 Copynumber: 2.8 Consensus size: 25
5525663 TCAAAAAATC
* * *
5525673 AAAAAAAATCAAAGTAAAAAATAGGAG
1 AAAAAAAATAAAAG-AAAAAA-AAGAA
*
5525700 AAAAAAAATAGAAGAAAAAAAAGAA
1 AAAAAAAATAAAAGAAAAAAAAGAA
5525725 AAATAAAAATAAAAAGAAAAA
1 AAA-AAAAAT-AAAAGAAAAA
5525746 GAAAAAGGAG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
25 6 0.15
26 12 0.31
27 21 0.54
ACGTcount: A:0.79, C:0.01, G:0.11, T:0.08
Consensus pattern (25 bp):
AAAAAAAATAAAAGAAAAAAAAGAA
Found at i:5525732 original size:6 final size:6
Alignment explanation
Indices: 5525698--5525752 Score: 60
Period size: 6 Copynumber: 9.3 Consensus size: 6
5525688 AAAAAATAGG
* * *
5525698 AGAAAA A-AAAT AGAAGAA A-AAAA AGAAAA ATAAAA ATAAAA AGAAAA
1 AGAAAA AGAAAA AGAA-AA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA
5525745 AGAAAA AG
1 AGAAAA AG
5525753 GAGAGGTCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
5 7 0.17
6 33 0.79
7 2 0.05
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.05
Consensus pattern (6 bp):
AGAAAA
Found at i:5527685 original size:8 final size:8
Alignment explanation
Indices: 5527674--5527707 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
5527664 AATAAAAAAT
5527674 AAATGAAA
1 AAATGAAA
5527682 AAATGAAAA
1 AAATG-AAA
5527691 AAATGAAA
1 AAATGAAA
*
5527699 AAGTGAAA
1 AAATGAAA
5527707 A
1 A
5527708 TGGAGAGGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 16 0.67
9 8 0.33
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.12
Consensus pattern (8 bp):
AAATGAAA
Found at i:5527696 original size:17 final size:18
Alignment explanation
Indices: 5527669--5527708 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
5527659 AAAATAATAA
5527669 AAAATAAATGAAAAAATG
1 AAAATAAATGAAAAAATG
*
5527687 AAAA-AAATGAAAAAGTG
1 AAAATAAATGAAAAAATG
5527704 AAAAT
1 AAAAT
5527709 GGAGAGGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.15
Consensus pattern (18 bp):
AAAATAAATGAAAAAATG
Found at i:5529052 original size:44 final size:44
Alignment explanation
Indices: 5528917--5529054 Score: 111
Period size: 44 Copynumber: 3.1 Consensus size: 44
5528907 ACAACAGATT
* * *
5528917 TTGCCTTCCTGCATTGACAGCGACGCAGATCGAAGACACAAACC
1 TTGCCTTCCTGCATTGACAACGAAGCAGGTCGAAGACACAAACC
* ** * * * * * * *
5528961 TTGCC-TCTCT-CGGTT-ATGATGGAGCTGGTTGAAGATAAAAGATC
1 TTGCCTTC-CTGC-ATTGACAACGAAGCAGGTCGAAGACACAA-ACC
5529005 TTGCCTTCCTGCATTGACAACGAAGCAGGTCGAAGACACAAACC
1 TTGCCTTCCTGCATTGACAACGAAGCAGGTCGAAGACACAAACC
5529049 TTGCCT
1 TTGCCT
5529055 CTCTCNNNNN
Statistics
Matches: 65, Mismatches: 23, Indels: 12
0.65 0.23 0.12
Matches are distributed among these distances:
43 17 0.26
44 28 0.43
45 20 0.31
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (44 bp):
TTGCCTTCCTGCATTGACAACGAAGCAGGTCGAAGACACAAACC
Found at i:5530263 original size:44 final size:44
Alignment explanation
Indices: 5530146--5530759 Score: 212
Period size: 44 Copynumber: 13.8 Consensus size: 44
5530136 ATGCATTAGG
* * ** * **
5530146 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG--CTAGAAA
* * * *
5530192 TCTTATCTCCCTGAGATTATAGCGGAGCAGATTGAAGTTAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGAAA
* * * *
5530236 TCCTATCTCCCTGAGATTACAGTGGAGCGGATTGAA-ATAAAAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGAA-A
* * * *
5530280 TTTTATCTCTCTGA-AGTTACAGCAGAGTAGATCGCATCAGATTGAAGCCAGAAA
1 TCTTATCTCCCTGAGA-TT--A-C--AGT-G---G-AGCAGATTGAAGCTAGAAA
* *
5530334 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGAAA
* * * * *
5530378 TCCTATCTCCCTGAGA-TACAGTGGAGC-GAATTAAAACCA-AGGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAG-ATTGAAGCTAGA-AA
* ** * * * *
5530421 TCTTATCTCTCTGA-AGTTACAGTAAAGTAGATTGCA-CCAG--G
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGCTAGAAA
* * * ** * ** *
5530462 TCTTATTTCCCTAAGATTACAGTGGAACAGACCGAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG--CTAGAAA
* * *
5530508 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTGGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGAAA
* * * * * * * *
5530552 TCCTATCTCCCTAAGATTACACTGGAGCGGATTAAAACCA-AGGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGA-AA
* * * * * * *
5530596 TCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGCA-CCAG--G
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGCTAGAAA
* * * * ** ** ** *
5530637 TCTTGTTTCCCTGAGATTATAGTGGAACAGACCGAAAATTTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTG--AAGCTAGAAA
* * * * * *
5530683 TCTTATCTCCCTGAGACTGCAGCGGAGCATATTGAAGCTGGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGAAA
* *
5530727 TCTTATCTCCCTAAGATTACAGTGGAGCGGATT
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATT
5530760 AAAATAAAGG
Statistics
Matches: 404, Mismatches: 129, Indels: 72
0.67 0.21 0.12
Matches are distributed among these distances:
41 48 0.12
42 4 0.01
43 42 0.10
44 182 0.45
45 2 0.00
46 87 0.22
47 1 0.00
48 1 0.00
49 5 0.01
50 1 0.00
51 1 0.00
52 1 0.00
53 1 0.00
54 24 0.06
55 4 0.01
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.28
Consensus pattern (44 bp):
TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGAAA
Found at i:5530351 original size:308 final size:311
Alignment explanation
Indices: 5530009--5530631 Score: 871
Period size: 316 Copynumber: 2.0 Consensus size: 311
5529999 TACAGTGGAG
* * *
5530009 CAGATTGAAGCCAGAGATCTTATTTCCTTGAGATTACAGCGGAGCAGATCGAAGAC-ACT-ATCC
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAG-CTACTAATCC
* * * * *
5530072 TATCTCCCTGAGATTACAGTGGAGCGGATTGAAATAAAAGATTTTATCTCTCTGAAGTTACAG-C
65 TATCTCCCTGAGA-TACAGTGGAGCGAATTAAAACAAAAGATCTTATCTCTCTGAAGTTACAGAA
* * **
5530136 A-T-GCATT-AGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAAATCTTAT
129 AGTAG-ATTCAGGTCTTATCTCCCTAAGATTACAGTGGAACAGACCGAAGAATTTCAAATCTTAT
* * * *
5530198 CTCCCTGAGATTATAGCGGAGCAGATTGAAGTTAGTAATCCTATCTCCCTGAGATTACAGTGGAG
193 CTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTAAGATTACACTGGAG
* * *
5530263 CGGATTGAAATAAAAGATTTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCAT
258 CGGATTAAAACAAAAGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCAT
* *
5530317 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGCTACTAATCCT
* *
5530382 ATCTCCCTGAGATACAGTGGAGCGAATTAAAACCAAGGATCTTATCTCTCTGAAGTTACAGTAAA
66 ATCTCCCTGAGATACAGTGGAGCGAATTAAAACAAAAGATCTTATCTCTCTGAAGTTACAG-AAA
* *
5530447 GTAGATTGCACCAGGTCTTATTTCCCTAAGATTACAGTGGAACAGACCGAAGAATTTCAGATCTT
130 GTAGATT----CAGGTCTTATCTCCCTAAGATTACAGTGGAACAGACCGAAGAATTTCAAATCTT
*
5530512 ATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTGGTAATCCTATCTCCCTAAGATTACACTGG
191 ATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTAAGATTACACTGG
* * *
5530577 AGCGGATTAAAACCAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCA
256 AGCGGATTAAAACAAAAGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCA
5530632 CCAGGTCTTG
Statistics
Matches: 275, Mismatches: 29, Indels: 14
0.86 0.09 0.04
Matches are distributed among these distances:
307 1 0.00
308 95 0.35
309 17 0.06
310 1 0.00
311 4 0.01
312 1 0.00
316 156 0.57
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (311 bp):
CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGCTACTAATCCT
ATCTCCCTGAGATACAGTGGAGCGAATTAAAACAAAAGATCTTATCTCTCTGAAGTTACAGAAAG
TAGATTCAGGTCTTATCTCCCTAAGATTACAGTGGAACAGACCGAAGAATTTCAAATCTTATCTC
CCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTAAGATTACACTGGAGCGG
ATTAAAACAAAAGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCAT
Found at i:5530510 original size:87 final size:86
Alignment explanation
Indices: 5530419--5530696 Score: 267
Period size: 87 Copynumber: 3.2 Consensus size: 86
5530409 TAAAACCAAG
* *
5530419 GATCTTATCTCTCTGAAGTTACAGTAAAGTAGATTGCACCAGGTCTTATTTCCCTAAGATTACAG
1 GATCTTATCTCCCTGAAGTTACAGTAGAGTAGATTGCACCAGGTCTTATTTCCCTAAGATTACAG
5530484 TGGAACAGACCGAAGAATTTCA
66 TGGAACAGACCGAA-AATTTCA
** * * * * * *
5530506 GATCTTATCTCCCTG-AGATTACAGCGGAGCAGATTGAAGCTGGTAATCCTATCTCCCTAAGATT
1 GATCTTATCTCCCTGAAG-TTACAGTAGAGTAGATTGCACCAGG---TCTTATTTCCCTAAGATT
* * * ** *
5530570 ACACTGGAGCGGA-TTAAAA--CCAA
62 ACAGTGGAACAGACCGAAAATTTC-A
* * * * *
5530593 GGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCACCAGGTCTTGTTTCCCTGAGATTATA
1 -GATCTTATCTCCCTGAAGTTACAGTAGAGTAGATTGCACCAGGTCTTATTTCCCTAAGATTACA
5530658 GTGGAACAGACCGAAAATTTTCA
65 GTGGAACAGACCGAAAA-TTTCA
5530681 GATCTTATCTCCCTGA
1 GATCTTATCTCCCTGA
5530697 GACTGCAGCG
Statistics
Matches: 144, Mismatches: 36, Indels: 22
0.71 0.18 0.11
Matches are distributed among these distances:
85 23 0.16
86 7 0.05
87 48 0.33
88 35 0.24
89 5 0.03
90 26 0.18
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (86 bp):
GATCTTATCTCCCTGAAGTTACAGTAGAGTAGATTGCACCAGGTCTTATTTCCCTAAGATTACAG
TGGAACAGACCGAAAATTTCA
Found at i:5530635 original size:175 final size:175
Alignment explanation
Indices: 5530333--5530804 Score: 786
Period size: 175 Copynumber: 2.7 Consensus size: 175
5530323 GAAGCCAGAA
* *
5530333 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA-TAC
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTGGTAATCCTATCTCCCTAAGATTAC
* *
5530397 AGTGGAGCGAATTAAAACCAAGGATCTTATCTCTCTGAAGTTACAGTAAAGTAGATTGCACCAGG
66 AGTGGAGCGGATTAAAACCAAGGATCTTATCTCTCTGAAGTTACAGTAAAGTAGATCGCACCAGG
5530462 TCTTATTTCCCTAAGATTACAGTGGAACAGACCGAAGAA-TTTCAG
131 TCTTATTTCCCTAAGATTACAGTGGAACAGACCGAA-AATTTTCAG
5530507 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTGGTAATCCTATCTCCCTAAGATTAC
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTGGTAATCCTATCTCCCTAAGATTAC
* *
5530572 ACTGGAGCGGATTAAAACCAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCACCAGG
66 AGTGGAGCGGATTAAAACCAAGGATCTTATCTCTCTGAAGTTACAGTAAAGTAGATCGCACCAGG
* * *
5530637 TCTTGTTTCCCTGAGATTATAGTGGAACAGACCGAAAATTTTCAG
131 TCTTATTTCCCTAAGATTACAGTGGAACAGACCGAAAATTTTCAG
* * * *
5530682 ATCTTATCTCCCTGAGACTGCAGCGGAGCATATTGAAGCTGGTAATCTTATCTCCCTAAGATTAC
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTGGTAATCCTATCTCCCTAAGATTAC
**
5530747 AGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAAAGTAGATCG
66 AGTGGAGCGGATTAAAACCAAGGATCTTATCTCTCTGAAGTTACAGTAAAGTAGATCG
5530805 TATTAAATCT
Statistics
Matches: 279, Mismatches: 17, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
174 61 0.22
175 218 0.78
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (175 bp):
ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTGGTAATCCTATCTCCCTAAGATTAC
AGTGGAGCGGATTAAAACCAAGGATCTTATCTCTCTGAAGTTACAGTAAAGTAGATCGCACCAGG
TCTTATTTCCCTAAGATTACAGTGGAACAGACCGAAAATTTTCAG
Found at i:5530975 original size:95 final size:95
Alignment explanation
Indices: 5530855--5531033 Score: 306
Period size: 95 Copynumber: 1.9 Consensus size: 95
5530845 AAGATGGCGA
*
5530855 ATTTTACCTCCTTGTGACTACAGTGGAGTACATTGAAGCC-GATAATTCTATCTCCCTGGTTGGC
1 ATTTTACCTCCCTGTGACTACAGTGGAGTACATTGAAGCCAG-TAATTCTATCTCCCTGGTTGGC
*
5530919 AGTGGAATAGATTGCAGATTGAAAATGTCAG
65 AGTGGAATAGATTGAAGATTGAAAATGTCAG
* *
5530950 ATTTTACCTCCCTGTGATTATAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGTTGGCA
1 ATTTTACCTCCCTGTGACTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGTTGGCA
5531015 GTGGAATAGATTGAAGATT
66 GTGGAATAGATTGAAGATT
5531034 CTAGATTCTG
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
95 78 0.99
96 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (95 bp):
ATTTTACCTCCCTGTGACTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGTTGGCA
GTGGAATAGATTGAAGATTGAAAATGTCAG
Found at i:5532957 original size:2 final size:2
Alignment explanation
Indices: 5532950--5532974 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5532940 GAAAATGTAC
5532950 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5532975 AAACTAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5534804 original size:43 final size:42
Alignment explanation
Indices: 5534755--5534892 Score: 118
Period size: 44 Copynumber: 3.2 Consensus size: 42
5534745 CAAGATCTGT
5534755 TGTCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTG
1 TGTCTTCAACCAGCTCCACTACAA-CGAGAGAGGCAAGGTTTG
* * * * * * ** *
5534798 TGTCTTCGA-TATGCTTCGCTGTCAAGGCAG-GAAGGCAAAATCTG
1 TGTCTTCAACCA-GCTCCACT-ACAACG-AGAG-AGGCAAGGTTTG
5534842 TTGTCTTCAACCAGCTCCACTACAATCGAGAGAGGCAAGGTTTG
1 -TGTCTTCAACCAGCTCCACTACAA-CGAGAGAGGCAAGGTTTG
5534886 TGTCTTC
1 TGTCTTC
5534893 GATCTGCTTC
Statistics
Matches: 69, Mismatches: 18, Indels: 16
0.67 0.17 0.16
Matches are distributed among these distances:
42 1 0.01
43 23 0.33
44 28 0.41
45 16 0.23
46 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.26
Consensus pattern (42 bp):
TGTCTTCAACCAGCTCCACTACAACGAGAGAGGCAAGGTTTG
Found at i:5534834 original size:44 final size:44
Alignment explanation
Indices: 5534786--5534924 Score: 115
Period size: 44 Copynumber: 3.2 Consensus size: 44
5534776 CAACCGAGAG
5534786 AGGCAAGGTTTGTGTCTTCGATATGCTTCGCTGTCAAGGCAGGA
1 AGGCAAGGTTTGTGTCTTCGATATGCTTCGCTGTCAAGGCAGGA
** * * * * * * *
5534830 AGGCAAAATCTGTTGTCTTCAACCA-GCTCCACT-ACAA-TC-GAGA
1 AGGCAAGGTTTG-TGTCTTCGA-TATGCTTCGCTGTCAAGGCAG-GA
* *
5534873 GAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTTAAGGCAGGA
1 -AGGCAAGGTTTGTGTCTTCGATATGCTTCGCTGTCAAGGCAGGA
5534918 AGGCAAG
1 AGGCAAG
5534925 ATCTACTATC
Statistics
Matches: 67, Mismatches: 20, Indels: 16
0.65 0.19 0.16
Matches are distributed among these distances:
42 1 0.01
43 17 0.25
44 30 0.45
45 17 0.25
46 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (44 bp):
AGGCAAGGTTTGTGTCTTCGATATGCTTCGCTGTCAAGGCAGGA
Found at i:5535011 original size:43 final size:43
Alignment explanation
Indices: 5534962--5535098 Score: 100
Period size: 43 Copynumber: 3.2 Consensus size: 43
5534952 CAACCGATGG
5534962 AGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGCATGA
1 AGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGCATGA
* * * * * * * * * *
5535005 AGGCAAGATCTGCTATCTTTAG-CCAGCTCCACTG-CAACTG-ATGG
1 AGGCAAG-GCT-TTGT-TTTCGATCTGCTTCGCTGTTAA-TGCATGA
* *
5535049 AGGCAAGGCTTTGTTTTCTATCTGCTTCGCTGTTAATGCGTGA
1 AGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGCATGA
*
5535092 ATGCAAG
1 AGGCAAG
5535099 ATCTGCTATC
Statistics
Matches: 64, Mismatches: 23, Indels: 14
0.63 0.23 0.14
Matches are distributed among these distances:
41 3 0.05
42 12 0.19
43 19 0.30
44 14 0.22
45 12 0.19
46 4 0.06
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (43 bp):
AGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGCATGA
Found at i:5535011 original size:87 final size:87
Alignment explanation
Indices: 5534633--5535427 Score: 1030
Period size: 87 Copynumber: 9.0 Consensus size: 87
5534623 CTATCTTCAG
* * * *
5534633 TCTGCTCCGCTGTTAACGCAGGAAGACAAGATCTAC-ATCTTTAACCAGCTCCACTACAATCGAT
1 TCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGAT
*
5534697 GGAGGCAATGCTTTGTTTTCGA
66 GGAGGCAAGGCTTTGTTTTCGA
* * *
5534719 TCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCACTACAACCGA-
1 TCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGAT
5534783 GAGAGGCAAGG-TTTGTGTCTTCGA
66 G-GAGGCAAGGCTTTGT-T-TTCGA
* * * * * * * *
5534807 TATGCTTCGCTGTCAAGGCAGGAAGGCAAAATCTGTTGTCTTCAACCAGCTCCACTACAATCGA-
1 TCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGAT
5534871 GAGAGGCAAGG-TTTGTGTCTTCGA
66 G-GAGGCAAGGCTTTGT-T-TTCGA
* * *
5534895 TCTGCTTCGCTGTTAAGGCAGGAAGGCAAGATCTACTATCTTTAACCAGCTCCACTGCAACCGAT
1 TCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGAT
5534960 GGAGGCAAGGCTTTGTTTTCGA
66 GGAGGCAAGGCTTTGTTTTCGA
* * * * *
5534982 TCTGCTTCGCTGTTAATGCATGAAGGCAAGATCTGCTATCTTTAGCCAGCTCCACTGCAACTGAT
1 TCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGAT
*
5535047 GGAGGCAAGGCTTTGTTTTCTA
66 GGAGGCAAGGCTTTGTTTTCGA
* *
5535069 TCTGCTTCGCTGTTAATGC-GTGAATGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGA
1 TCTGCTTCGCTGTTAACGCAG-GAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGA
* **
5535133 TGGAGGGAAAACTTTGTTTTCGA
65 TGGAGGCAAGGCTTTGTTTTCGA
* *
5535156 TCTGCTTCACTGTTAACGCAGGAAGGCAAGATTTGCTATCTTTAACCAGCTCCACTACAACCGAT
1 TCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGAT
*
5535221 GGAGGCAAGACTTTGTTTTCGA
66 GGAGGCAAGGCTTTGTTTTCGA
*
5535243 TCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCT-TCTTTAACCAGCTCCACTGCAACCGAT
1 TCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGAT
5535307 GGAGGCAAGGCTTTGTTTTCGA
66 GGAGGCAAGGCTTTGTTTTCGA
*
5535329 TCTGCTTCGCTGTTAACTTTGCTGTTAACGCAGCAAGGCGAGATCTGCT-TCTTTAACCAGCTCC
1 TCTGCTTCGCTGTTAAC---GC-----A-G--G-AAGGCAAGATCTGCTATCTTTAACCAGCTCC
* *
5535393 ACTGCAACCGATGCAGGCAAGGCTTTGTTTTCGA
54 ACTACAACCGATGGAGGCAAGGCTTTGTTTTCGA
5535427 T
1 T
5535428 GTTCACTGAT
Statistics
Matches: 640, Mismatches: 49, Indels: 28
0.89 0.07 0.04
Matches are distributed among these distances:
86 102 0.16
87 310 0.48
88 154 0.24
89 8 0.01
94 1 0.00
95 1 0.00
97 1 0.00
98 63 0.10
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (87 bp):
TCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGAT
GGAGGCAAGGCTTTGTTTTCGA
Found at i:5535420 original size:98 final size:98
Alignment explanation
Indices: 5535251--5535427 Score: 327
Period size: 98 Copynumber: 1.8 Consensus size: 98
5535241 GATCTGCTTC
* *
5535251 GCTGTTAACGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAG
1 GCTGTTAACGCAGCAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGCAGGCAAG
5535316 GCTTTGTTTTCGATCTGCTTCGCTGTTAACTTT
66 GCTTTGTTTTCGATCTGCTTCGCTGTTAACTTT
*
5535349 GCTGTTAACGCAGCAAGGCGAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGCAGGCAAG
1 GCTGTTAACGCAGCAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGCAGGCAAG
5535414 GCTTTGTTTTCGAT
66 GCTTTGTTTTCGAT
5535428 GTTCACTGAT
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 76 1.00
ACGTcount: A:0.22, C:0.25, G:0.24, T:0.29
Consensus pattern (98 bp):
GCTGTTAACGCAGCAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGCAGGCAAG
GCTTTGTTTTCGATCTGCTTCGCTGTTAACTTT
Found at i:5536663 original size:6 final size:6
Alignment explanation
Indices: 5536662--5536697 Score: 54
Period size: 6 Copynumber: 5.7 Consensus size: 6
5536652 ACTTTTCATT
5536662 TTTTCA TTTTCA TTTTCA TTTTTCA TCTTTCA TTTT
1 TTTTCA TTTTCA TTTTCA -TTTTCA T-TTTCA TTTT
5536698 TTTGAACTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 16 0.57
7 12 0.43
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTTCA
Found at i:5536669 original size:20 final size:20
Alignment explanation
Indices: 5536654--5536697 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
5536644 TCCATTTTAC
5536654 TTTTCATTTTTTCATTTTCA
1 TTTTCATTTTTTCATTTTCA
5536674 TTTTCA-TTTTTCATCTTTCA
1 TTTTCATTTTTTCAT-TTTCA
5536694 TTTT
1 TTTT
5536698 TTTGAACTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTCATTTTTTCATTTTCA
Found at i:5536671 original size:7 final size:7
Alignment explanation
Indices: 5536654--5536698 Score: 58
Period size: 7 Copynumber: 6.6 Consensus size: 7
5536644 TCCATTTTAC
5536654 TTTTCATT
1 TTTTCA-T
5536662 TTTTCA-
1 TTTTCAT
5536668 TTTTCA-
1 TTTTCAT
5536674 TTTTCAT
1 TTTTCAT
5536681 TTTTCAT
1 TTTTCAT
*
5536688 CTTTCAT
1 TTTTCAT
5536695 TTTT
1 TTTT
5536699 TTGAACTTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
6 12 0.35
7 16 0.47
8 6 0.18
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTTCAT
Found at i:5537103 original size:49 final size:49
Alignment explanation
Indices: 5537043--5537141 Score: 135
Period size: 49 Copynumber: 2.0 Consensus size: 49
5537033 TTGCGTTTCA
* * **
5537043 TATTTTTATTTTGACTTTGATTGATTTCTCTTTTTCTTTTTGTTTTTTT
1 TATTTTGATTTTGACTTTGATTGATTTCTCTTTTTATTTTCCTTTTTTT
* **
5537092 TATTTTGATTTTGATTTTGATTTTTTTCTCTTTTTATTTTCCTTTTTTT
1 TATTTTGATTTTGACTTTGATTGATTTCTCTTTTTATTTTCCTTTTTTT
5537141 T
1 T
5537142 CGAATCGGAT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.10, C:0.08, G:0.07, T:0.75
Consensus pattern (49 bp):
TATTTTGATTTTGACTTTGATTGATTTCTCTTTTTATTTTCCTTTTTTT
Found at i:5537124 original size:43 final size:43
Alignment explanation
Indices: 5537045--5537131 Score: 115
Period size: 43 Copynumber: 2.0 Consensus size: 43
5537035 GCGTTTCATA
* *
5537045 TTTTTATTTTGACTTTGATTGATTTCTCTTTTTCTTTTTGTTT
1 TTTTTATTTTGACTTTGATTGATTTCTCTTTCTCTTTTTATTT
*
5537088 TTTTTATTTTGATTTTGATTTTGATTT-T-TTTCTCTTTTTATTT
1 TTTTTATTTTGACTTTGA--TTGATTTCTCTTTCTCTTTTTATTT
5537131 T
1 T
5537132 CCTTTTTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
43 31 0.79
44 1 0.03
45 7 0.18
ACGTcount: A:0.10, C:0.07, G:0.08, T:0.75
Consensus pattern (43 bp):
TTTTTATTTTGACTTTGATTGATTTCTCTTTCTCTTTTTATTT
Found at i:5543011 original size:2 final size:2
Alignment explanation
Indices: 5543004--5543040 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
5542994 AATGTACATT
*
5543004 TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5543041 TAGCAAAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5545982 original size:2 final size:2
Alignment explanation
Indices: 5545975--5546005 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5545965 TTCCACATCC
5545975 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5546006 GAGAATCTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5549733 original size:124 final size:124
Alignment explanation
Indices: 5549514--5549769 Score: 352
Period size: 124 Copynumber: 2.1 Consensus size: 124
5549504 AAATAGTGGG
** * * * * *
5549514 AAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTGAAATCGTGGCCTCGGGGACGCGATT
1 AAATCGCTGATACCAAGATGCCATATGAGAAGAAATTGTGAAATCGCGCCCTCGGGGACGCGATT
*
5549579 TCGCTATAGTGGTCATGTAAGAAATAAA-TTTTTTTGACGTTTTCTGAGCAAATAGTATA
66 TCGCTAAAGTGGTCATGTAAGAAATAAATTTTTTTTGACG-TTTCTGAGCAAATAGTATA
*
5549638 AAATCGCTGATACCAAGATGCCATATGAGAAGAAATTGTGAAATCGCGCCCTCGTGGACGCGATT
1 AAATCGCTGATACCAAGATGCCATATGAGAAGAAATTGTGAAATCGCGCCCTCGGGGACGCGATT
* * * * * *
5549703 TCGCTACAATTGGTCATGTAGGAAATAATTTTTTTTTGATGTTTCTGAGCAAATAGTGTC
66 TCGCTA-AAGTGGTCATGTAAGAAATAAATTTTTTTTGACGTTTCTGAGCAAATAGTATA
5549763 AAATCGC
1 AAATCGC
5549770 ACCCTCGTGG
Statistics
Matches: 115, Mismatches: 15, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
124 63 0.55
125 42 0.37
126 10 0.09
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (124 bp):
AAATCGCTGATACCAAGATGCCATATGAGAAGAAATTGTGAAATCGCGCCCTCGGGGACGCGATT
TCGCTAAAGTGGTCATGTAAGAAATAAATTTTTTTTGACGTTTCTGAGCAAATAGTATA
Found at i:5551342 original size:40 final size:39
Alignment explanation
Indices: 5551298--5551384 Score: 95
Period size: 40 Copynumber: 2.2 Consensus size: 39
5551288 AATATGGTAC
5551298 AAATTAGTAAGATTATCAAATTA-GGTTAGGGTTTTTAATT
1 AAATTAGTAAGATTAT--AATTAGGGTTAGGGTTTTTAATT
* * * **
5551338 AAATTAAATTAGGTTATGGTTAGGGTTAGGGTTTTTAATT
1 AAATT-AGTAAGATTATAATTAGGGTTAGGGTTTTTAATT
5551378 AAATTAG
1 AAATTAG
5551385 GTTAGGGTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
39 4 0.10
40 27 0.69
41 8 0.21
ACGTcount: A:0.36, C:0.01, G:0.21, T:0.43
Consensus pattern (39 bp):
AAATTAGTAAGATTATAATTAGGGTTAGGGTTTTTAATT
Found at i:5551388 original size:29 final size:29
Alignment explanation
Indices: 5551355--5551410 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
5551345 ATTAGGTTAT
*
5551355 GGTTAGGGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTAGGGTTTTTAATCAAATTA
5551384 GGTTAGGGTTAGGGTTTTTAATCAAAT
1 GGTTAGGGTTAGGGTTTTTAATCAAAT
5551411 AATGTCAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.27, C:0.02, G:0.29, T:0.43
Consensus pattern (29 bp):
GGTTAGGGTTAGGGTTTTTAATCAAATTA
Found at i:5551390 original size:40 final size:41
Alignment explanation
Indices: 5551321--5551399 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 41
5551311 TATCAAATTA
*
5551321 GGTTAGGGTTTTTAATTAAATTAAATTA-GGTTATGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAAATTAGGGTTAGGGTTAG
**
5551361 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTT
1 GGTTAGGGTTTTTAATTAAATTAAATTAGGGTTAGGGTT
5551400 TTTAATCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
40 26 0.74
41 9 0.26
ACGTcount: A:0.27, C:0.00, G:0.29, T:0.44
Consensus pattern (41 bp):
GGTTAGGGTTTTTAATTAAATTAAATTAGGGTTAGGGTTAG
Found at i:5552808 original size:22 final size:21
Alignment explanation
Indices: 5552783--5552829 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
5552773 TTTTAAAACA
*
5552783 AAAAATAAATTAATAAATATCT
1 AAAAATAAATAAATAAA-ATCT
* *
5552805 AAAAATATATAAATAAAATTT
1 AAAAATAAATAAATAAAATCT
5552826 AAAA
1 AAAA
5552830 TTTAAATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (21 bp):
AAAAATAAATAAATAAAATCT
Found at i:5553059 original size:22 final size:23
Alignment explanation
Indices: 5553007--5553059 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
5552997 TTAAATATGG
*
5553007 ATTTGAGA-GATTTTTTGAAGGA
1 ATTTGAGAGGATTTTTGGAAGGA
* *
5553029 AATTAAGAGGA-TTTTGGAAGGA
1 ATTTGAGAGGATTTTTGGAAGGA
5553051 ATTTGAGAG
1 ATTTGAGAG
5553060 TTTAAGAGGA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
22 23 0.92
23 2 0.08
ACGTcount: A:0.36, C:0.00, G:0.30, T:0.34
Consensus pattern (23 bp):
ATTTGAGAGGATTTTTGGAAGGA
Found at i:5553203 original size:20 final size:20
Alignment explanation
Indices: 5553178--5553217 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5553168 AATATTTTCC
*
5553178 AGTAAATCATTTTATAGAAA
1 AGTAAAACATTTTATAGAAA
*
5553198 AGTAAAACATTTTCTAGAAA
1 AGTAAAACATTTTATAGAAA
5553218 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (20 bp):
AGTAAAACATTTTATAGAAA
Found at i:5553232 original size:34 final size:35
Alignment explanation
Indices: 5553166--5553232 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
5553156 CAAACACCAG
* *
5553166 AAAATATTTTCCAGTAAATCATTTTATAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
5553201 AAAACATTTTCTAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
5553233 CATTTTACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.46, C:0.10, G:0.09, T:0.34
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:5553699 original size:29 final size:29
Alignment explanation
Indices: 5553666--5553722 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
5553656 AAAAGCTCTT
*
5553666 TTTTTTCAA-AATTTACTGAAATGGGCCAC
1 TTTTTT-AATAATTTACCGAAATGGGCCAC
* *
5553695 TTTTTTAATTATTTACCGGAATGGGCCA
1 TTTTTTAATAATTTACCGAAATGGGCCA
5553723 TTTCTGCGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (29 bp):
TTTTTTAATAATTTACCGAAATGGGCCAC
Found at i:5553999 original size:143 final size:144
Alignment explanation
Indices: 5553776--5554067 Score: 543
Period size: 143 Copynumber: 2.0 Consensus size: 144
5553766 TGACAGATCA
*
5553776 TCGCGTCCACGTCAGCGCAACCTGCTGACGTGGAAGGAAATCGCTTCCCCAAGGACGTGATTTCC
1 TCGCGTCCACGTCAGCGCAACCGGCTGACGTGGAAGGAAATCGCTTCCCCAAGGACGTGATTTCC
5553841 TTCCACGTCAACAGGTCGCGCTGACGTGGACGCAATGTCCTGTCACGTA-CCTGACATCGGCGCT
66 TTCCACGTCAACAGGTCGCGCTGACGTGGACGCAATGTCCTGTCACGTACCCTGACATC-GCGCT
5553905 GACGTGGCCGCGATT
130 GACGTGGCCGCGATT
*
5553920 TCGCG-CCGCGTCAGCGCAACCGGCTGACGTGGAAGGAAATCGCTTCCCCAAGGACGTGATTTCC
1 TCGCGTCCACGTCAGCGCAACCGGCTGACGTGGAAGGAAATCGCTTCCCCAAGGACGTGATTTCC
5553984 TTCCACGTCAACAGGTCGCGCTGACGTGGACGCAATGTCCTGTCACGTACCCTGACATCGCGCTG
66 TTCCACGTCAACAGGTCGCGCTGACGTGGACGCAATGTCCTGTCACGTACCCTGACATCGCGCTG
5554049 ACGTGGCCGCGATT
131 ACGTGGCCGCGATT
5554063 TCGCG
1 TCGCG
5554068 AAAAATGGCC
Statistics
Matches: 145, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
143 131 0.90
144 14 0.10
ACGTcount: A:0.19, C:0.33, G:0.28, T:0.20
Consensus pattern (144 bp):
TCGCGTCCACGTCAGCGCAACCGGCTGACGTGGAAGGAAATCGCTTCCCCAAGGACGTGATTTCC
TTCCACGTCAACAGGTCGCGCTGACGTGGACGCAATGTCCTGTCACGTACCCTGACATCGCGCTG
ACGTGGCCGCGATT
Found at i:5554876 original size:21 final size:21
Alignment explanation
Indices: 5554846--5554886 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
5554836 TCTGTTGCCC
5554846 TTTCTTTCTTTTTT-CTTTTA
1 TTTCTTTCTTTTTTCCTTTTA
5554866 TTTCTATTCTTTTTTCCTTTT
1 TTTCT-TTCTTTTTTCCTTTT
5554887 TCAATCTCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTCTTTCTTTTTTCCTTTTA
Found at i:5566665 original size:16 final size:17
Alignment explanation
Indices: 5566634--5566666 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
5566624 TGTTATTCTT
*
5566634 TTAAAGAAAATTTATAA
1 TTAAAGAAAATATATAA
5566651 TTAAA-AAAATATATAA
1 TTAAAGAAAATATATAA
5566667 AAAAATAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
TTAAAGAAAATATATAA
Found at i:5566978 original size:19 final size:20
Alignment explanation
Indices: 5566937--5566978 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
5566927 TTAAAAATAA
**
5566937 TTTAATTCAATTCACTTGGT
1 TTTAATTCAATTCACTTAAT
*
5566957 TTTAATTC-ATTCATTTAAT
1 TTTAATTCAATTCACTTAAT
5566976 TTT
1 TTT
5566979 CAGTTTTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.26, C:0.12, G:0.05, T:0.57
Consensus pattern (20 bp):
TTTAATTCAATTCACTTAAT
Found at i:5574097 original size:40 final size:40
Alignment explanation
Indices: 5574053--5574128 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
5574043 CTGCCAGGGG
*
5574053 CACCGGAGTGCATT-CAGGGGCACA-TATGTGCAAACATGGA
1 CACCGAAGTG-ATTACAGGGGCACAGT-TGTGCAAACATGGA
*
5574093 CACCGAAGTGTTTACAGGGGCACAGTTGTGCAAACA
1 CACCGAAGTGATTACAGGGGCACAGTTGTGCAAACA
5574129 AGAACATAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
39 2 0.06
40 29 0.91
41 1 0.03
ACGTcount: A:0.30, C:0.22, G:0.29, T:0.18
Consensus pattern (40 bp):
CACCGAAGTGATTACAGGGGCACAGTTGTGCAAACATGGA
Found at i:5574141 original size:40 final size:40
Alignment explanation
Indices: 5574067--5574144 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
5574057 GGAGTGCATT
* * *
5574067 CAGGGGCACATATGTGCAAACATGGACACCGAAGTGTTTA
1 CAGGGGCACATATGTGCAAACAAGAACACAGAAGTGTTTA
*
5574107 CAGGGGCACAGT-TGTGCAAACAAGAACATAGAAGTGTT
1 CAGGGGCACA-TATGTGCAAACAAGAACACAGAAGTGTT
5574145 ATGAAGGAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 32 0.97
41 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (40 bp):
CAGGGGCACATATGTGCAAACAAGAACACAGAAGTGTTTA
Found at i:5579576 original size:16 final size:16
Alignment explanation
Indices: 5579530--5579578 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
5579520 AAAAATTCTA
***
5579530 AAAAAATAAAACTTTG
1 AAAAAATAAAACTAAC
5579546 AAAAAAT--AA-TAAC
1 AAAAAATAAAACTAAC
5579559 AAAAAATAAAACTAAC
1 AAAAAATAAAACTAAC
5579575 AAAA
1 AAAA
5579579 CAAAATCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
13 8 0.30
14 2 0.07
15 2 0.07
16 15 0.56
ACGTcount: A:0.73, C:0.08, G:0.02, T:0.16
Consensus pattern (16 bp):
AAAAAATAAAACTAAC
Found at i:5589635 original size:30 final size:29
Alignment explanation
Indices: 5589601--5589669 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 29
5589591 ATGGGTTCAG
* *
5589601 GTGACTGATTTGTCAC-TTTCGTGAAGTTTA
1 GTGACTGATTTGTAACTTTTC--AAAGTTTA
*
5589631 GTGACTGAGTTGTAACTTTTCAAAGTTTA
1 GTGACTGATTTGTAACTTTTCAAAGTTTA
5589660 GTGACT-ATTT
1 GTGACTGATTT
5589670 TATTATTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
28 3 0.09
29 13 0.38
30 14 0.41
31 4 0.12
ACGTcount: A:0.23, C:0.12, G:0.22, T:0.43
Consensus pattern (29 bp):
GTGACTGATTTGTAACTTTTCAAAGTTTA
Found at i:5591484 original size:136 final size:136
Alignment explanation
Indices: 5591251--5591515 Score: 530
Period size: 136 Copynumber: 1.9 Consensus size: 136
5591241 TCCGACTTGG
5591251 TGGTAGTATATTTATTTGTGTTTTTTAATATAATAAAACATTTATTATATTAATGACAGTATTTT
1 TGGTAGTATATTTATTTGTGTTTTTTAATATAATAAAACATTTATTATATTAATGACAGTATTTT
5591316 TTAATATGTTTTTATTGTGTTAGAAAACTTTTATTTTAGTCTTTTTTAGTGCATTTAGTATATTG
66 TTAATATGTTTTTATTGTGTTAGAAAACTTTTATTTTAGTCTTTTTTAGTGCATTTAGTATATTG
5591381 TTTTTA
131 TTTTTA
5591387 TGGTAGTATATTTATTTGTGTTTTTTAATATAATAAAACATTTATTATATTAATGACAGTATTTT
1 TGGTAGTATATTTATTTGTGTTTTTTAATATAATAAAACATTTATTATATTAATGACAGTATTTT
5591452 TTAATATGTTTTTATTGTGTTAGAAAACTTTTATTTTAGTCTTTTTTAGTGCATTTAGTATATT
66 TTAATATGTTTTTATTGTGTTAGAAAACTTTTATTTTAGTCTTTTTTAGTGCATTTAGTATATT
5591516 ATATTTTTTA
Statistics
Matches: 129, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
136 129 1.00
ACGTcount: A:0.29, C:0.04, G:0.12, T:0.55
Consensus pattern (136 bp):
TGGTAGTATATTTATTTGTGTTTTTTAATATAATAAAACATTTATTATATTAATGACAGTATTTT
TTAATATGTTTTTATTGTGTTAGAAAACTTTTATTTTAGTCTTTTTTAGTGCATTTAGTATATTG
TTTTTA
Found at i:5591537 original size:136 final size:136
Alignment explanation
Indices: 5591254--5591546 Score: 511
Period size: 136 Copynumber: 2.2 Consensus size: 136
5591244 GACTTGGTGG
5591254 TAGTATATTTATTTGTGTTTTTTAATATAATAAAACATTTATTATATTAATGACAGTATTTTTTA
1 TAGTATATTTATTTGTGTTTTTTAATATAATAAAACATTTATTATATTAATGACAGTATTTTTTA
*
5591319 ATATGTTTTTATTGTGTTAGAAAACTTTTATTTTAGTCTTTTTTAGTGCATTTAGTATATTGTTT
66 ATATGTTTTTATTGTGTTAGAAAACTTTTATTTTAGTCTTTTTTAGTGCATTTAGTATATTATTT
**
5591384 TTATGG
131 TTATAA
5591390 TAGTATATTTATTTGTGTTTTTTAATATAATAAAACATTTATTATATTAATGACAGTATTTTTTA
1 TAGTATATTTATTTGTGTTTTTTAATATAATAAAACATTTATTATATTAATGACAGTATTTTTTA
5591455 ATATGTTTTTATTGTGTTAGAAAACTTTTATTTTAGTCTTTTTTAGTGCATTTAGTATATTATAT
66 ATATGTTTTTATTGTGTTAGAAAACTTTTATTTTAGTCTTTTTTAGTGCATTTAGTATATTAT-T
*
5591520 TTTTTAA
130 TTTATAA
5591527 TATGT-T-TTTA-TTGTGTTTTT
1 TA-GTATATTTATTTGTGTTTTT
5591547 AGTGCATTTA
Statistics
Matches: 151, Mismatches: 4, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
135 10 0.07
136 131 0.87
137 8 0.05
138 2 0.01
ACGTcount: A:0.28, C:0.03, G:0.11, T:0.57
Consensus pattern (136 bp):
TAGTATATTTATTTGTGTTTTTTAATATAATAAAACATTTATTATATTAATGACAGTATTTTTTA
ATATGTTTTTATTGTGTTAGAAAACTTTTATTTTAGTCTTTTTTAGTGCATTTAGTATATTATTT
TTATAA
Found at i:5594046 original size:39 final size:39
Alignment explanation
Indices: 5593950--5594048 Score: 119
Period size: 39 Copynumber: 2.5 Consensus size: 39
5593940 ATTCACTTTT
* * * **
5593950 AAGCATATATCACATTACACATATAATTAGATAATGTTC
1 AAGCATATATCGCAATACTCATATAATTAGATAACATTC
* *
5593989 AAGCACATATCGCAATACTCATATAA-TCGCATAACATTC
1 AAGCATATATCGCAATACTCATATAATTAG-ATAACATTC
5594028 AAGCATATATCGCAATACTCA
1 AAGCATATATCGCAATACTCA
5594049 AAAACATGTT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
38 2 0.04
39 49 0.96
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.28
Consensus pattern (39 bp):
AAGCATATATCGCAATACTCATATAATTAGATAACATTC
Found at i:5603082 original size:2 final size:2
Alignment explanation
Indices: 5603075--5603108 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5603065 TGAGTTGTGC
5603075 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5603109 GTGTGTGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5603124 original size:12 final size:12
Alignment explanation
Indices: 5603109--5603152 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
5603099 ATATATATAT
5603109 GTGTGTGTGTG-
1 GTGTGTGTGTGC
5603120 G-GTGTGTGTGC
1 GTGTGTGTGTGC
*
5603131 GTGCGTGTGTGC
1 GTGTGTGTGTGC
*
5603143 GTGCGTGTGT
1 GTGTGTGTGT
5603153 NNNNNNNNNN
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 9 0.30
11 2 0.07
12 19 0.63
ACGTcount: A:0.00, C:0.09, G:0.52, T:0.39
Consensus pattern (12 bp):
GTGTGTGTGTGC
Found at i:5603125 original size:14 final size:14
Alignment explanation
Indices: 5603108--5603152 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
5603098 TATATATATA
* *
5603108 TGTGTGTGTGTGGG
1 TGTGTGTGCGTGCG
5603122 TGTGTGTGCGTGC-
1 TGTGTGTGCGTGCG
5603135 -GTGTGTGCGTGCG
1 TGTGTGTGCGTGCG
5603148 TGTGT
1 TGTGT
5603153 NNNNNNNNNN
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 12 0.44
14 15 0.56
ACGTcount: A:0.00, C:0.09, G:0.51, T:0.40
Consensus pattern (14 bp):
TGTGTGTGCGTGCG
Found at i:5603329 original size:2 final size:2
Alignment explanation
Indices: 5603322--5603359 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5603312 NNNNNNNNNN
5603322 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
5603360 AACCCTCTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:5604014 original size:27 final size:27
Alignment explanation
Indices: 5603969--5604034 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
5603959 TTGATTTTCG
* *
5603969 TATTTCATAATTTAATTATA-AATTATT
1 TATTT-ATATTTTAATTATATAAATATT
*
5603996 CTATTTATATTTTATTTATATAAATATT
1 -TATTTATATTTTAATTATATAAATATT
5604024 TATTTATATTT
1 TATTTATATTT
5604035 ATCTATTTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 23 0.68
28 11 0.32
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (27 bp):
TATTTATATTTTAATTATATAAATATT
Found at i:5610907 original size:12 final size:11
Alignment explanation
Indices: 5610890--5610925 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
5610880 AACAAATCAT
5610890 CTCTCATATTTC
1 CTCTCA-ATTTC
*
5610902 CTCTCAATTTT
1 CTCTCAATTTC
5610913 CTCTCAATTTC
1 CTCTCAATTTC
5610924 CT
1 CT
5610926 TCCAAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 16 0.73
12 6 0.27
ACGTcount: A:0.17, C:0.33, G:0.00, T:0.50
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:5611020 original size:51 final size:51
Alignment explanation
Indices: 5610905--5611022 Score: 166
Period size: 51 Copynumber: 2.3 Consensus size: 51
5610895 ATATTTCCTC
* * * *
5610905 TCAATTTTCTCTCAATTTCCTTCCAAAAATTCTCATAAATCCATATTTAATT
1 TCAATTTCCTCTCAAATTCATTCCAAAAATTCTCA-AAACCCATATTTAATT
5610957 TCAATTTCCTCTCAAATTCATTCCAAAAATCTCTC-AAACCCATATTTAATT
1 TCAATTTCCTCTCAAATTCATTCCAAAAAT-TCTCAAAACCCATATTTAATT
*
5611008 TCAATTTGCTCTCAA
1 TCAATTTCCTCTCAA
5611023 TTTCCTTTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
51 29 0.48
52 27 0.45
53 4 0.07
ACGTcount: A:0.33, C:0.25, G:0.01, T:0.41
Consensus pattern (51 bp):
TCAATTTCCTCTCAAATTCATTCCAAAAATTCTCAAAACCCATATTTAATT
Found at i:5611064 original size:16 final size:17
Alignment explanation
Indices: 5611028--5611065 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
5611018 CTCAATTTCC
* *
5611028 TTTTTTAAATAGTTCTT
1 TTTTTAAAATAGTTCTA
5611045 TTTTTAAAATAGTT-TA
1 TTTTTAAAATAGTTCTA
5611061 TTTTT
1 TTTTT
5611066 TTTTATATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (17 bp):
TTTTTAAAATAGTTCTA
Found at i:5612767 original size:18 final size:18
Alignment explanation
Indices: 5612741--5612775 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5612731 AGGTGCGTTT
* *
5612741 CCTAGCCCTTATATGTAC
1 CCTAACCCTTACATGTAC
5612759 CCTAACCCTTACATGTA
1 CCTAACCCTTACATGTA
5612776 TCCTTTTCCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.34, G:0.09, T:0.31
Consensus pattern (18 bp):
CCTAACCCTTACATGTAC
Found at i:5618101 original size:125 final size:125
Alignment explanation
Indices: 5617879--5618105 Score: 391
Period size: 125 Copynumber: 1.8 Consensus size: 125
5617869 CCCAAACTTG
* * *
5617879 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCATAATTTCTTCTCAAATAGCATCCTGG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCAATTTCACAATTTCTTCTCAAATAGCATCCTCG
* * * *
5617944 TAGAAGTGATTTTATATTTTTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTACTTGAC
66 TAGAAGCGATTTTATACTATTTGATCAGAAACGTCAAAAAAAAATTATTTCTTACTTGAC
5618004 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCAATTTCACAATTTCTTCTCAAATAGCATCCTCG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCAATTTCACAATTTCTTCTCAAATAGCATCCTCG
5618069 TAGAAGCGATTTTATACTATTTGATCAGAAACGTCAA
66 TAGAAGCGATTTTATACTATTTGATCAGAAACGTCAA
5618106 CTCGAAATAA
Statistics
Matches: 95, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
125 95 1.00
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.31
Consensus pattern (125 bp):
CTACTGTAGCAAAATCGCGTCCACGAGGGCGCAATTTCACAATTTCTTCTCAAATAGCATCCTCG
TAGAAGCGATTTTATACTATTTGATCAGAAACGTCAAAAAAAAATTATTTCTTACTTGAC
Found at i:5618823 original size:48 final size:48
Alignment explanation
Indices: 5618752--5618846 Score: 163
Period size: 48 Copynumber: 2.0 Consensus size: 48
5618742 TTCTTTGCTT
*
5618752 AAAAACGCCTAAGTCAGCCTAACTCGCAATGATAAAGGATTCGACAGC
1 AAAAACGCCTAAGTCAGCCTAACTCGCAATGATAAAGGATTCAACAGC
* *
5618800 AAAAACGCCTAAGTCGGCCTAACTTGCAATGATAAAGGATTCAACAG
1 AAAAACGCCTAAGTCAGCCTAACTCGCAATGATAAAGGATTCAACAG
5618847 AATTCCCTCA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.18
Consensus pattern (48 bp):
AAAAACGCCTAAGTCAGCCTAACTCGCAATGATAAAGGATTCAACAGC
Found at i:5619093 original size:19 final size:19
Alignment explanation
Indices: 5619069--5619122 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 19
5619059 AAAGTTGTAT
5619069 ACAATTAGAACTCTAAGAC
1 ACAATTAGAACTCTAAGAC
* *
5619088 ACAATTAGAA-GCT--GTAT
1 ACAATTAGAACTCTAAG-AC
5619105 ACAATTAGAACTCTAAGA
1 ACAATTAGAACTCTAAGA
5619123 TTACATAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
16 1 0.04
17 11 0.39
18 4 0.14
19 11 0.39
20 1 0.04
ACGTcount: A:0.46, C:0.17, G:0.13, T:0.24
Consensus pattern (19 bp):
ACAATTAGAACTCTAAGAC
Found at i:5624229 original size:36 final size:37
Alignment explanation
Indices: 5624174--5624245 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 37
5624164 ATCAAAGGCT
*
5624174 ACAATTTAAAAGCTGTATACAATTAGAACTCTAAGAC
1 ACAATTTAAAAGCCGTATACAATTAGAACTCTAAGAC
*
5624211 ACAA-TTAGAAGCCGTATACAATTAGAACTCTAAGA
1 ACAATTTAAAAGCCGTATACAATTAGAACTCTAAGA
5624246 TTACATAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
36 29 0.88
37 4 0.12
ACGTcount: A:0.46, C:0.17, G:0.12, T:0.25
Consensus pattern (37 bp):
ACAATTTAAAAGCCGTATACAATTAGAACTCTAAGAC
Found at i:5630557 original size:22 final size:21
Alignment explanation
Indices: 5630514--5630557 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
5630504 ACACACAAAC
*
5630514 ATTTATAAAAGTCCTTATACA
1 ATTTATAAAAGTCCATATACA
5630535 ATTTATAGAAAGTCTCATA-ACA
1 ATTTATA-AAAGTC-CATATACA
5630557 A
1 A
5630558 CACAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 7 0.35
22 10 0.50
23 3 0.15
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.34
Consensus pattern (21 bp):
ATTTATAAAAGTCCATATACA
Found at i:5633661 original size:17 final size:18
Alignment explanation
Indices: 5633641--5633678 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
5633631 AGTTAAATTT
*
5633641 TTTTGTTTCTAGTT-TAG
1 TTTTATTTCTAGTTGTAG
*
5633658 TTTTATTTCTATTTGTAG
1 TTTTATTTCTAGTTGTAG
5633676 TTT
1 TTT
5633679 AGGTTTCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.13, C:0.05, G:0.13, T:0.68
Consensus pattern (18 bp):
TTTTATTTCTAGTTGTAG
Found at i:5633696 original size:23 final size:23
Alignment explanation
Indices: 5633650--5633697 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
5633640 TTTTTGTTTC
* *
5633650 TAGTTTAGTTTTATTTCTATTTG
1 TAGTTTAGGTTTATTTCTAGTTG
* *
5633673 TAGTTTAGGTTTCTTTTTAGTTG
1 TAGTTTAGGTTTATTTCTAGTTG
5633696 TA
1 TA
5633698 ATCGTAGTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.17, C:0.04, G:0.17, T:0.62
Consensus pattern (23 bp):
TAGTTTAGGTTTATTTCTAGTTG
Found at i:5640796 original size:68 final size:69
Alignment explanation
Indices: 5640716--5640851 Score: 256
Period size: 68 Copynumber: 2.0 Consensus size: 69
5640706 ACATTTGAGT
*
5640716 TTGGAAGTAGATTTAAGAGAAAATTAAGAATGATGTTAAATAAAATAA-TTTATTTGAATGAATT
1 TTGGAAGTAGATTTAAAAGAAAATTAAGAATGATGTTAAATAAAATAACTTTATTTGAATGAATT
5640780 TGGG
66 TGGG
5640784 TTGGAAGTAGATTTAAAAGAAAATTAAGAATGATGTTAAATAAAATAACTTTATTTGAATGAATT
1 TTGGAAGTAGATTTAAAAGAAAATTAAGAATGATGTTAAATAAAATAACTTTATTTGAATGAATT
5640849 TGG
66 TGG
5640852 AAGTGAATAT
Statistics
Matches: 66, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
68 47 0.71
69 19 0.29
ACGTcount: A:0.45, C:0.01, G:0.19, T:0.35
Consensus pattern (69 bp):
TTGGAAGTAGATTTAAAAGAAAATTAAGAATGATGTTAAATAAAATAACTTTATTTGAATGAATT
TGGG
Found at i:5647540 original size:51 final size:51
Alignment explanation
Indices: 5647479--5647669 Score: 176
Period size: 51 Copynumber: 3.8 Consensus size: 51
5647469 CCGGTTCACA
* * *
5647479 TAGTAGCCTGCACATAGTACTAGACATGTGACCATCACTATCTTATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCTCATACACG
* * * *
5647530 TAGTATCCTGCACATAGTACTACACACGTGATCGA--AGCTATC-CAGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTATCTCA-TACACG
* * * * * **
5647581 TACTAGCCTACACATAGCACTACACATGCGACCTATCA-T-TCTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTATCTCATACACG
*
5647631 TAGTAGCCTGCACATAGTACTACATACGTGACCATCACT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
5647670 TTCACTTTCA
Statistics
Matches: 108, Mismatches: 24, Indels: 17
0.72 0.16 0.11
Matches are distributed among these distances:
49 4 0.04
50 37 0.34
51 64 0.59
52 2 0.02
53 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCTCATACACG
Found at i:5647634 original size:101 final size:102
Alignment explanation
Indices: 5647477--5647661 Score: 266
Period size: 101 Copynumber: 1.8 Consensus size: 102
5647467 TACCGGTTCA
* * * * * * *
5647477 CATAGTAGCCTGCACATAGTACTAGACATGTGACCATCACTATCTTATACACGTAGTATCCTGCA
1 CATACTAGCCTACACATAGCACTACACATGCGACCATCACTATCTGATACACGTAGTAGCCTGCA
5647542 CATAGTACTACACACGTGATCGAAGCTATCCAGTACG
66 CATAGTACTACACACGTGATCGAAGCTATCCAGTACG
*
5647579 CATACTAGCCTACACATAGCACTACACATGCGACCTATCA-T-TCTGGTACACGTAGTAGCCTGC
1 CATACTAGCCTACACATAGCACTACACATGCGACC-ATCACTATCTGATACACGTAGTAGCCTGC
*
5647642 ACATAGTACTACATACGTGA
65 ACATAGTACTACACACGTGA
5647662 CCATCACTTT
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
101 38 0.52
102 31 0.42
103 4 0.05
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (102 bp):
CATACTAGCCTACACATAGCACTACACATGCGACCATCACTATCTGATACACGTAGTAGCCTGCA
CATAGTACTACACACGTGATCGAAGCTATCCAGTACG
Found at i:5649126 original size:122 final size:122
Alignment explanation
Indices: 5648904--5649167 Score: 352
Period size: 122 Copynumber: 2.2 Consensus size: 122
5648894 GAAGTCTTTT
** * * * *
5648904 TGTACCGGTAGAACTCTAATGGTTTCATTTGGTATTGGTAGAACCCATCAAAATATCGATAGAAA
1 TGTACCGGTAGAACTCTGGTGCTTTCAATTGGTATTGGTAGAACCCAACAAAACATCGATAGAAA
* *
5648969 TGTAGGGGAGGCTGAACCTTGACTACTATTTTGACTTGTTTCAG-TAAAAGTCCTCAA
66 TGCAGGGGAGGCTGAAACTTGACTACTATTTTGACTTGTTTC-GCTAAAAGTCCTCAA
* *
5649026 TGTAGCGGTAGAACTCTGGTGCTTTCAATTGGTATTGGTAGAACCCAACAAAGCATCGATAGAAA
1 TGTACCGGTAGAACTCTGGTGCTTTCAATTGGTATTGGTAGAACCCAACAAAACATCGATAGAAA
* * *
5649091 TGCAGGAGG-GGCTGAAATTTGGCTACTATTTTGACTTGTTTCGCTAGAAGTCCTCAA
66 TGCAGG-GGAGGCTGAAACTTGACTACTATTTTGACTTGTTTCGCTAAAAGTCCTCAA
* * *
5649148 GGTATCGGTATAACTCTGGT
1 TGTACCGGTAGAACTCTGGT
5649168 TGTATCGATA
Statistics
Matches: 124, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
121 1 0.01
122 121 0.98
123 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (122 bp):
TGTACCGGTAGAACTCTGGTGCTTTCAATTGGTATTGGTAGAACCCAACAAAACATCGATAGAAA
TGCAGGGGAGGCTGAAACTTGACTACTATTTTGACTTGTTTCGCTAAAAGTCCTCAA
Found at i:5652410 original size:22 final size:22
Alignment explanation
Indices: 5652385--5652440 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
5652375 TGATATAATC
* *
5652385 CAACCAAAAAGTATATAAAAGG
1 CAACCAAGAAGTATATAAAAAG
5652407 CAACCAAGAAGTATATAAAAAG
1 CAACCAAGAAGTATATAAAAAG
5652429 CAACCAAGAAGT
1 CAACCAAGAAGT
5652441 GAGGTCATAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.57, C:0.16, G:0.14, T:0.12
Consensus pattern (22 bp):
CAACCAAGAAGTATATAAAAAG
Found at i:5675211 original size:19 final size:20
Alignment explanation
Indices: 5675168--5675213 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
5675158 CTATTTCAAT
* **
5675168 CCAAATGAGCTAAATGAAGC
1 CCAAATGAACTAAAACAAGC
5675188 CCAAATGAACTAAAACAA-C
1 CCAAATGAACTAAAACAAGC
5675207 CCAAATG
1 CCAAATG
5675214 GCCATATTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.50, C:0.24, G:0.13, T:0.13
Consensus pattern (20 bp):
CCAAATGAACTAAAACAAGC
Found at i:5678181 original size:12 final size:12
Alignment explanation
Indices: 5678164--5678188 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5678154 GTTCAAAGTG
5678164 AAAATTAAATTA
1 AAAATTAAATTA
5678176 AAAATTAAATTA
1 AAAATTAAATTA
5678188 A
1 A
5678189 TTGGTTATCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATTAAATTA
Found at i:5683748 original size:24 final size:21
Alignment explanation
Indices: 5683720--5683767 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 21
5683710 AATAAATTAG
5683720 AAAGAAAGATACAGAAAAAAATGT
1 AAAGAAAGA-A-AGAAAAAAAT-T
5683744 AAAGAAAGAAAGAAAAAAATT
1 AAAGAAAGAAAGAAAAAAATT
5683765 AAA
1 AAA
5683768 AGATTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 4 0.17
22 10 0.42
23 1 0.04
24 9 0.38
ACGTcount: A:0.73, C:0.02, G:0.15, T:0.10
Consensus pattern (21 bp):
AAAGAAAGAAAGAAAAAAATT
Found at i:5683945 original size:16 final size:16
Alignment explanation
Indices: 5683926--5683959 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5683916 GTTTTTCTAT
*
5683926 TTTTCTATTTTTACAA
1 TTTTCTATTTTTAAAA
*
5683942 TTTTTTATTTTTAAAA
1 TTTTCTATTTTTAAAA
5683958 TT
1 TT
5683960 ATTTGATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTCTATTTTTAAAA
Done.