Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 131 of 205
Found at i:39737782 original size:26 final size:25
Alignment explanation
Indices: 39737729--39737793 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
39737719 GATAAACCGT
*
39737729 GGCAAAAGCCCTTTTAATAAACTGG
1 GGCAAAAGCCCTTTTAATAAACTAG
* **
39737754 GGCAGAAGCCCTTTTCGGTAAACTAG
1 GGCAAAAGCCCTTTT-AATAAACTAG
*
39737780 GGCATAA-CCCTTTT
1 GGCAAAAGCCCTTTT
39737794 TACACTTCCT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
25 21 0.62
26 13 0.38
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (25 bp):
GGCAAAAGCCCTTTTAATAAACTAG
Found at i:39737795 original size:51 final size:48
Alignment explanation
Indices: 39737692--39737793 Score: 118
Period size: 51 Copynumber: 2.1 Consensus size: 48
39737682 GCCTAGCCTA
* *
39737692 TTTTAATAACTGGGGCAAATCCCTTTCGATAAACCGTGGCAAAAGCCC
1 TTTTAATAACTGGGGCAAAGCCCTTTCGATAAACAGTGGCAAAAGCCC
* *
39737740 TTTTAATAAACTGGGGCAGAAGCCCTTTTCGGTAAACTAG-GGCATAA-CCC
1 TTTTAAT-AACTGGGGCA-AAGCCC-TTTCGATAAAC-AGTGGCAAAAGCCC
39737790 TTTT
1 TTTT
39737794 TACACTTCCT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
48 7 0.15
49 10 0.22
50 12 0.26
51 16 0.35
52 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (48 bp):
TTTTAATAACTGGGGCAAAGCCCTTTCGATAAACAGTGGCAAAAGCCC
Found at i:39737863 original size:9 final size:9
Alignment explanation
Indices: 39737849--39737905 Score: 69
Period size: 9 Copynumber: 5.9 Consensus size: 9
39737839 ACATCATGTG
39737849 CATATCATA
1 CATATCATA
39737858 CATATCATGTA
1 CATATCA--TA
39737869 CATATCATA
1 CATATCATA
39737878 CATATCATA
1 CATATCATA
*
39737887 TGCATATTATA
1 --CATATCATA
39737898 CATATCAT
1 CATATCAT
39737906 GTGCATATCA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
9 25 0.60
11 17 0.40
ACGTcount: A:0.40, C:0.19, G:0.04, T:0.37
Consensus pattern (9 bp):
CATATCATA
Found at i:39737864 original size:20 final size:20
Alignment explanation
Indices: 39737841--39737927 Score: 131
Period size: 20 Copynumber: 4.3 Consensus size: 20
39737831 TTATGAATAC
39737841 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
39737861 ATCATGTACATATCATACAT
1 ATCATGTGCATATCATACAT
* *
39737881 ATCATATGCATATTATACAT
1 ATCATGTGCATATCATACAT
39737901 ATCATGTGCATATCATATCA-
1 ATCATGTGCATATCATA-CAT
39737921 ATCATGT
1 ATCATGT
39737928 ATATCAAAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
20 58 0.97
21 2 0.03
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:39737870 original size:11 final size:11
Alignment explanation
Indices: 39737841--39737928 Score: 66
Period size: 9 Copynumber: 8.7 Consensus size: 11
39737831 TTATGAATAC
*
39737841 ATCATGTGCAT
1 ATCATGTACAT
39737852 ATCA--TACAT
1 ATCATGTACAT
39737861 ATCATGTACAT
1 ATCATGTACAT
39737872 ATCA--TACAT
1 ATCATGTACAT
* *
39737881 ATCATATGCAT
1 ATCATGTACAT
*
39737892 AT--TATACAT
1 ATCATGTACAT
*
39737901 ATCATGTGCAT
1 ATCATGTACAT
*
39737912 ATCATAT-CA-
1 ATCATGTACAT
39737921 ATCATGTA
1 ATCATGTA
39737929 TATCAAAACC
Statistics
Matches: 63, Mismatches: 7, Indels: 15
0.74 0.08 0.18
Matches are distributed among these distances:
9 31 0.49
10 2 0.03
11 30 0.48
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (11 bp):
ATCATGTACAT
Found at i:39741199 original size:50 final size:49
Alignment explanation
Indices: 39741128--39741312 Score: 228
Period size: 50 Copynumber: 3.7 Consensus size: 49
39741118 TGAATACACA
* *
39741128 TGTAGTACTAAGTGTAGGCTACTACGTGTATCATACTGTTAAGTCGCATG
1 TGTAGTACTAAGTGCAGGCTACTACGTGTATCAGA-TGTTAAGTCGCATG
* * * *
39741178 TGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGATGAGGTCACGTG
1 TGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATG-TTAAGTCGCATG
* * *
39741228 TGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATTGTTGA-TCGCATG
1 TGTAGTACTAAGTGCAGGCTACTACGTGTATCAGA-TGTTAAGTCGCATG
* * *
39741277 TGTAGTATTAAGTGCAGGCTACTATGCGTATCAGAT
1 TGTAGTACTAAGTGCAGGCTACTACGTGTATCAGAT
39741313 ATCTTCAGCT
Statistics
Matches: 115, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
48 1 0.01
49 37 0.32
50 75 0.65
51 2 0.02
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.31
Consensus pattern (49 bp):
TGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGTTAAGTCGCATG
Found at i:39741300 original size:99 final size:100
Alignment explanation
Indices: 39741128--39741312 Score: 282
Period size: 99 Copynumber: 1.9 Consensus size: 100
39741118 TGAATACACA
* * *
39741128 TGTAGTACTAAGTGTAGGCTACTACGTGTATCATACTGTTAAGTCGCATGTGTAGTACTAAGTGC
1 TGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTGTTAAGTCGCATGTGTAGTACTAAGTGC
*
39741193 AGGCTACTACGTGTATCAGATGATGAGGTCACGTG
66 AGGCTACTACGCGTATCAGATGATGAGGTCACGTG
* * * *
39741228 TGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATTGTTGA-TCGCATGTGTAGTATTAAGTGC
1 TGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTGTTAAGTCGCATGTGTAGTACTAAGTGC
*
39741292 AGGCTACTATGCGTATCAGAT
66 AGGCTACTACGCGTATCAGAT
39741313 ATCTTCAGCT
Statistics
Matches: 76, Mismatches: 9, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
99 40 0.53
100 36 0.47
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.31
Consensus pattern (100 bp):
TGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTGTTAAGTCGCATGTGTAGTACTAAGTGC
AGGCTACTACGCGTATCAGATGATGAGGTCACGTG
Found at i:39753666 original size:52 final size:52
Alignment explanation
Indices: 39753588--39753694 Score: 178
Period size: 52 Copynumber: 2.1 Consensus size: 52
39753578 TTGATAAAGT
* *
39753588 ATGCAAGAAATGTCCTTTGATAGTTAGAGGTCAGTGTTTTCCAATCGATTTG
1 ATGCAAGAAATGTCCTTTGATAGTTAGAGGTCAGTGTTTTCCAACCGATTGG
* *
39753640 ATGCAATAAATGTCCTTTGATAGTTAGAGGTCATTGTTTTCCAACCGATTGG
1 ATGCAAGAAATGTCCTTTGATAGTTAGAGGTCAGTGTTTTCCAACCGATTGG
39753692 ATG
1 ATG
39753695 TTGTTACCAT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.36
Consensus pattern (52 bp):
ATGCAAGAAATGTCCTTTGATAGTTAGAGGTCAGTGTTTTCCAACCGATTGG
Found at i:39760526 original size:12 final size:12
Alignment explanation
Indices: 39760456--39760519 Score: 94
Period size: 12 Copynumber: 5.3 Consensus size: 12
39760446 GGATATTCGT
*
39760456 AATTTTGAATTA
1 AATTGTGAATTA
*
39760468 AATATGT-TATTA
1 AAT-TGTGAATTA
39760480 AATTGTGAATTA
1 AATTGTGAATTA
39760492 AATTGTGAATTA
1 AATTGTGAATTA
39760504 AATTGTGAATTA
1 AATTGTGAATTA
39760516 AATT
1 AATT
39760520 TGTAATTTTG
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
11 3 0.06
12 42 0.89
13 2 0.04
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.45
Consensus pattern (12 bp):
AATTGTGAATTA
Found at i:39766241 original size:40 final size:40
Alignment explanation
Indices: 39766161--39766385 Score: 294
Period size: 40 Copynumber: 5.6 Consensus size: 40
39766151 AACCCAAGTA
* ** *
39766161 CCTTCGGGATTTAG-CCGGATATAG-CAACTCCCACACATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
*
39766200 CCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
39766240 CCTTCGGGACTTAGCCCGGGTATA-TCAACTACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTA---GCACAAATG
*
39766283 CCTTCGGGACTTCGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
* *
39766323 CCTTCGGGACTTAGCCCGAATATGGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
39766363 CCTTTGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
39766386 CATCCGAATA
Statistics
Matches: 165, Mismatches: 14, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
39 14 0.08
40 113 0.68
41 1 0.01
43 35 0.21
44 2 0.01
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:39766289 original size:83 final size:82
Alignment explanation
Indices: 39766161--39766385 Score: 309
Period size: 83 Copynumber: 2.8 Consensus size: 82
39766151 AACCCAAGTA
* * * *
39766161 CCTTCGGGATTTAG-CCGGATATAGCAACT-CC-CACACATGCCTTCGGGTCTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATATATCAACTACCGCACAAATGCCTTCGGGACTTAGCCCGGATAT
39766223 AGTCACTAGCACAAATG
66 AGTCACTAGCACAAATG
* *
39766240 CCTTCGGGACTTAGCCCGGGTATATCAACTACTCGCACAAATGCCTTCGGGACTTCGCCCGGATA
1 CCTTCGGGACTTAGCCCGGATATATCAACTAC-CGCACAAATGCCTTCGGGACTTAGCCCGGATA
39766305 TAGTCACTAGCACAAATG
65 TAGTCACTAGCACAAATG
* * *
39766323 CCTTCGGGACTTAGCCCGAATATGGTC-ACTA--GCACAAATGCCTTTGGGACTTAGCCCGGATA
1 CCTTCGGGACTTAGCCCGGATAT-ATCAACTACCGCACAAATGCCTTCGGGACTTAGCCCGGATA
39766385 T
65 T
39766386 CATCCGAATA
Statistics
Matches: 130, Mismatches: 11, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
79 13 0.10
80 43 0.33
81 1 0.01
82 1 0.01
83 70 0.54
84 2 0.02
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (82 bp):
CCTTCGGGACTTAGCCCGGATATATCAACTACCGCACAAATGCCTTCGGGACTTAGCCCGGATAT
AGTCACTAGCACAAATG
Found at i:39780148 original size:13 final size:13
Alignment explanation
Indices: 39780130--39780154 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39780120 TGGTCATCAT
39780130 GGTGTGAACACAA
1 GGTGTGAACACAA
39780143 GGTGTGAACACA
1 GGTGTGAACACA
39780155 TGATCAATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:39780674 original size:10 final size:10
Alignment explanation
Indices: 39780661--39780698 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
39780651 TTGTAGCTAA
39780661 ATTGAGCTCG
1 ATTGAGCTCG
39780671 ATTGAGCT-G
1 ATTGAGCTCG
39780680 ACTTGAGCTCG
1 A-TTGAGCTCG
*
39780691 AGTGAGCT
1 ATTGAGCT
39780699 GGAAACGAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (10 bp):
ATTGAGCTCG
Found at i:39780678 original size:20 final size:20
Alignment explanation
Indices: 39780638--39780698 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
39780628 ACCAATAAAA
39780638 TAAA-TGAGCT-GAATTGTAGC
1 TAAATTGAGCTCG-ATTG-AGC
39780658 TAAATTGAGCTCGATTGAGC
1 TAAATTGAGCTCGATTGAGC
* * *
39780678 TGACTTGAGCTCGAGTGAGC
1 TAAATTGAGCTCGATTGAGC
39780698 T
1 T
39780699 GGAAACGAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 25 0.69
21 10 0.28
22 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (20 bp):
TAAATTGAGCTCGATTGAGC
Found at i:39780699 original size:20 final size:20
Alignment explanation
Indices: 39780662--39780699 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
39780652 TGTAGCTAAA
*
39780662 TTGAGCTCGATTGAGCTGAC
1 TTGAGCTCGAGTGAGCTGAC
39780682 TTGAGCTCGAGTGAGCTG
1 TTGAGCTCGAGTGAGCTG
39780700 GAAACGAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.29
Consensus pattern (20 bp):
TTGAGCTCGAGTGAGCTGAC
Found at i:39795577 original size:13 final size:13
Alignment explanation
Indices: 39795559--39795622 Score: 58
Period size: 13 Copynumber: 4.8 Consensus size: 13
39795549 TTGTAGATTC
39795559 AAAAAAAAATCGAAA
1 AAAAAAAAATCG--A
39795574 AAAAAAACAATCG-
1 AAAAAAA-AATCGA
*
39795587 AAAAAAAAATTGA
1 AAAAAAAAATCGA
** *
39795600 AAAAAAATTTTGA
1 AAAAAAAAATCGA
39795613 AAAAAAAAAT
1 AAAAAAAAAT
39795623 TGCATACGGT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
12 4 0.10
13 26 0.62
15 7 0.17
16 5 0.12
ACGTcount: A:0.75, C:0.05, G:0.06, T:0.14
Consensus pattern (13 bp):
AAAAAAAAATCGA
Found at i:39795579 original size:15 final size:16
Alignment explanation
Indices: 39795559--39795595 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
39795549 TTGTAGATTC
39795559 AAAAAAA-AATCGAAA
1 AAAAAAACAATCGAAA
39795574 AAAAAAACAATCGAAA
1 AAAAAAACAATCGAAA
39795590 AAAAAA
1 AAAAAA
39795596 TTGAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.81, C:0.08, G:0.05, T:0.05
Consensus pattern (16 bp):
AAAAAAACAATCGAAA
Found at i:39796808 original size:67 final size:67
Alignment explanation
Indices: 39796705--39796838 Score: 268
Period size: 67 Copynumber: 2.0 Consensus size: 67
39796695 AAAGCGATTC
39796705 ATTCCTGCTTACTATCACCGGGAGTTGTATCAAAAGCTCCAAAGCTTAACTCAAGGCCAACGAAG
1 ATTCCTGCTTACTATCACCGGGAGTTGTATCAAAAGCTCCAAAGCTTAACTCAAGGCCAACGAAG
39796770 CG
66 CG
39796772 ATTCCTGCTTACTATCACCGGGAGTTGTATCAAAAGCTCCAAAGCTTAACTCAAGGCCAACGAAG
1 ATTCCTGCTTACTATCACCGGGAGTTGTATCAAAAGCTCCAAAGCTTAACTCAAGGCCAACGAAG
39796837 CG
66 CG
39796839 TGGAGGATTA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.22
Consensus pattern (67 bp):
ATTCCTGCTTACTATCACCGGGAGTTGTATCAAAAGCTCCAAAGCTTAACTCAAGGCCAACGAAG
CG
Found at i:39797153 original size:66 final size:66
Alignment explanation
Indices: 39797047--39797178 Score: 255
Period size: 66 Copynumber: 2.0 Consensus size: 66
39797037 CGTTCCGTTC
*
39797047 TTTCCCTAATACTTCTTCTATGACTAAGTGGGGGCAAGGGTCCAACAAACGAGACTTGCCGAGTC
1 TTTCCCTAATACTTCTTCTACGACTAAGTGGGGGCAAGGGTCCAACAAACGAGACTTGCCGAGTC
39797112 G
66 G
39797113 TTTCCCTAATACTTCTTCTACGACTAAGTGGGGGCAAGGGTCCAACAAACGAGACTTGCCGAGTC
1 TTTCCCTAATACTTCTTCTACGACTAAGTGGGGGCAAGGGTCCAACAAACGAGACTTGCCGAGTC
39797178 G
66 G
39797179 AAATAAAGAA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.26, C:0.25, G:0.24, T:0.25
Consensus pattern (66 bp):
TTTCCCTAATACTTCTTCTACGACTAAGTGGGGGCAAGGGTCCAACAAACGAGACTTGCCGAGTC
G
Found at i:39803882 original size:13 final size:12
Alignment explanation
Indices: 39803866--39803899 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
39803856 AAGAGTTCGA
39803866 AAAAAAAAATTTG
1 AAAAAAAAA-TTG
39803879 AAAAAAAAATTG
1 AAAAAAAAATTG
39803891 AAAAAAAAA
1 AAAAAAAAA
39803900 ATTGCATACG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.57
13 9 0.43
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (12 bp):
AAAAAAAAATTG
Found at i:39803900 original size:14 final size:14
Alignment explanation
Indices: 39803848--39803900 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 14
39803838 ATAGGTACAT
39803848 AAAAAAAAAAGAGTTCG
1 AAAAAAAAAA-A-TT-G
*
39803865 AAAAAAAAAATTTG
1 AAAAAAAAAAATTG
39803879 --AAAAAAAAATTG
1 AAAAAAAAAAATTG
39803891 AAAAAAAAAA
1 AAAAAAAAAA
39803901 TTGCATACGG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
12 11 0.34
14 9 0.28
15 2 0.06
17 10 0.31
ACGTcount: A:0.75, C:0.02, G:0.09, T:0.13
Consensus pattern (14 bp):
AAAAAAAAAAATTG
Found at i:39803903 original size:13 final size:14
Alignment explanation
Indices: 39803849--39803900 Score: 63
Period size: 13 Copynumber: 3.7 Consensus size: 14
39803839 TAGGTACATA
39803849 AAAAAAAAAGAGTTCG
1 AAAAAAAAA-AGTT-G
*
39803865 AAAAAAAAAATTTG
1 AAAAAAAAAAGTTG
39803879 -AAAAAAAAA-TTG
1 AAAAAAAAAAGTTG
39803891 AAAAAAAAAA
1 AAAAAAAAAA
39803901 TTGCATACGG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
12 3 0.09
13 18 0.53
14 1 0.03
15 3 0.09
16 9 0.26
ACGTcount: A:0.75, C:0.02, G:0.10, T:0.13
Consensus pattern (14 bp):
AAAAAAAAAAGTTG
Found at i:39808673 original size:20 final size:20
Alignment explanation
Indices: 39808650--39808695 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
39808640 CCAGCTCGAA
*
39808650 TTAGCTCACATGAGCTTAAT
1 TTAGCTCACATGAGCTCAAT
***
39808670 TTAGCTCGTTTGAGCTCAAT
1 TTAGCTCACATGAGCTCAAT
39808690 TTAGCT
1 TTAGCT
39808696 TACTTTAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (20 bp):
TTAGCTCACATGAGCTCAAT
Found at i:39808677 original size:30 final size:30
Alignment explanation
Indices: 39808642--39808715 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
39808632 AGTTTTTCCC
39808642 AGCTCGAATT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-ATTGAGCTCA-ATTGAGCTTAATTT
* * *
39808672 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGATTGAGCTCAATTGAGCTTAATTT
*
39808702 AGCTCGTTTGAGCT
1 AGCTCGATTGAGCT
39808716 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 3 0.08
30 36 0.92
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCGATTGAGCTCAATTGAGCTTAATTT
Found at i:39812034 original size:21 final size:21
Alignment explanation
Indices: 39811991--39812053 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
39811981 TTTGAACCAT
*
39811991 TACCAATTT-GTACCAAATACCA
1 TACC-ATTTCGTACC-AATTCCA
39812013 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
39812034 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
39812054 CAAATACCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 28 0.76
22 9 0.24
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.32
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:39813183 original size:167 final size:169
Alignment explanation
Indices: 39812866--39813201 Score: 640
Period size: 167 Copynumber: 2.0 Consensus size: 169
39812856 GGATTTGTTG
39812866 GAGGCCTATATAAGCATTGGCCAGCCACCCTTTGTAAACACATCTTATTATTATTTTTCTATCAA
1 GAGGCCTATATAAGCATTGGCCAGCCACCCTTTGTAAACACATCTTATTATTATTTTTCTATCAA
*
39812931 ATTTTAGATTTGTTGAGTGCAGAATTTTCTTTGGGGTTTTCTCCAAGAATTCTCTCTTGAGTTTT
66 ATTTCAGATTTGTTGAGTGCAGAATTTTCTTTGGGGTTTTCTCCAAGAATTCTCTCTTGAGTTTT
39812996 CTTTAGAAGTTGTTTTAACAATCTTTTGATTGTGGGAGC
131 CTTTAGAAGTTGTTTTAACAATCTTTTGATTGTGGGAGC
*
39813035 GAGGCCTATATAAGCATTGGCCAGCCACCCTTTGTAAACATATCTTATTATTATTTTT-TATCAA
1 GAGGCCTATATAAGCATTGGCCAGCCACCCTTTGTAAACACATCTTATTATTATTTTTCTATCAA
39813099 ATTTCAGATTTGTTGAGTGCAGAATTTT-TTTGGGGTTTTCTCCAAGAATTCTCTCTTGAGTTTT
66 ATTTCAGATTTGTTGAGTGCAGAATTTTCTTTGGGGTTTTCTCCAAGAATTCTCTCTTGAGTTTT
39813163 CTTTAGAAGTTGTTTTAACAATCTTTTGATTGTGGGAGC
131 CTTTAGAAGTTGTTTTAACAATCTTTTGATTGTGGGAGC
39813202 CATCTTCAAC
Statistics
Matches: 165, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
167 75 0.45
168 33 0.20
169 57 0.35
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.43
Consensus pattern (169 bp):
GAGGCCTATATAAGCATTGGCCAGCCACCCTTTGTAAACACATCTTATTATTATTTTTCTATCAA
ATTTCAGATTTGTTGAGTGCAGAATTTTCTTTGGGGTTTTCTCCAAGAATTCTCTCTTGAGTTTT
CTTTAGAAGTTGTTTTAACAATCTTTTGATTGTGGGAGC
Found at i:39817264 original size:16 final size:16
Alignment explanation
Indices: 39817229--39817267 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
39817219 GAAAATTTCG
* **
39817229 AAAAAAAAAATTGATT
1 AAAAAAAAAATTCAAA
39817245 AAAAAAAAAATTCAAA
1 AAAAAAAAAATTCAAA
39817261 AAAAAAA
1 AAAAAAA
39817268 GTGAAAAGTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (16 bp):
AAAAAAAAAATTCAAA
Found at i:39818205 original size:15 final size:16
Alignment explanation
Indices: 39818185--39818216 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
39818175 AGAAAATGAA
39818185 AAAGAAAAAGAA-ATG
1 AAAGAAAAAGAAGATG
39818200 AAAGAAAAAGAAGATG
1 AAAGAAAAAGAAGATG
39818216 A
1 A
39818217 GTGTGAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAGAAGATG
Found at i:39818331 original size:17 final size:18
Alignment explanation
Indices: 39818299--39818332 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39818289 AAAAGAGAGT
*
39818299 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
39818317 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
39818333 GGAGTGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:39819612 original size:20 final size:20
Alignment explanation
Indices: 39819583--39819636 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
39819573 GTTTTTTCCC
*
39819583 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
39819603 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
39819623 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
39819637 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:39819618 original size:30 final size:30
Alignment explanation
Indices: 39819583--39819656 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
39819573 GTTTTTTCCC
39819583 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
39819613 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
39819643 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
39819657 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:39819646 original size:20 final size:20
Alignment explanation
Indices: 39819583--39819647 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
39819573 GTTTTTTCCC
* * * *
39819583 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
39819603 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
39819622 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
39819643 AGCTC
1 AGCTC
39819648 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:39822063 original size:27 final size:26
Alignment explanation
Indices: 39822033--39822085 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
39822023 TCAATCTCAA
39822033 TCTCAATCTCAAATTCTTTTTCCTTTT
1 TCTCAATCTCAAATTCTTTTT-CTTTT
* **
39822060 TCTCACTCTCATTTTCTTTTTCTTTT
1 TCTCAATCTCAAATTCTTTTTCTTTT
39822086 ATTTCTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.13, C:0.26, G:0.00, T:0.60
Consensus pattern (26 bp):
TCTCAATCTCAAATTCTTTTTCTTTT
Found at i:39822090 original size:15 final size:15
Alignment explanation
Indices: 39822072--39822100 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
39822062 TCACTCTCAT
39822072 TTTCTTTTTCTTTTA
1 TTTCTTTTTCTTTTA
39822087 TTTCTTTTTCTTTT
1 TTTCTTTTTCTTTT
39822101 TCTCTCATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTCTTTTTCTTTTA
Found at i:39822115 original size:20 final size:21
Alignment explanation
Indices: 39822071--39822127 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
39822061 CTCACTCTCA
* * *
39822071 TTTTCTTTTTCTTTTATTTCT
1 TTTTCTTTTTCTCTCATTGCT
39822092 TTTTCTTTTTCTCTCATTGCT
1 TTTTCTTTTTCTCTCATTGCT
*
39822113 TTTT-TTCTTCTCTCA
1 TTTTCTTTTTCTCTCA
39822128 ATTTCATTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 10 0.31
21 22 0.69
ACGTcount: A:0.05, C:0.21, G:0.02, T:0.72
Consensus pattern (21 bp):
TTTTCTTTTTCTCTCATTGCT
Found at i:39823025 original size:11 final size:11
Alignment explanation
Indices: 39823011--39823044 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
39823001 TTTTTAAATT
39823011 ATTTTTTTTCA
1 ATTTTTTTTCA
39823022 A-TTTTTTTCA
1 ATTTTTTTTCA
*
39823032 ATTTTTTTACA
1 ATTTTTTTTCA
39823043 AT
1 AT
39823045 ACCGTAATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.68
Consensus pattern (11 bp):
ATTTTTTTTCA
Found at i:39823028 original size:9 final size:10
Alignment explanation
Indices: 39823013--39823044 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
39823003 TTTAAATTAT
39823013 TTTTTTTCAA
1 TTTTTTTCAA
39823023 TTTTTTTCAA
1 TTTTTTTCAA
39823033 TTTTTTTACAA
1 TTTTTTT-CAA
39823044 T
1 T
39823045 ACCGTAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 17 0.81
11 4 0.19
ACGTcount: A:0.22, C:0.09, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTTTTTCAA
Found at i:39824141 original size:188 final size:190
Alignment explanation
Indices: 39823811--39824183 Score: 714
Period size: 188 Copynumber: 2.0 Consensus size: 190
39823801 AAATAAAGAG
*
39823811 GAAACAATAACAAATTAATTGGCTAAGACCGAAAATGAACCAACAATAACGAATTGTTGACCCGA
1 GAAACAATAACAAATTAATTGGCTAAGACCGAAAATGAACCAACAATAACAAATTGTTGACCCGA
39823876 ATCTCAAAATGGTCTTTAGGTGTTTTTCGGTTAAAGGAAACAGGAAAGGAACCTTGACCCACTAT
66 ATCTCAAAATGGTCTTTAGGTGTTTTTCGGTTAAAGGAAACAGGAAAGGAACCTTGACCCACTAT
39823941 CAACTATGATAGGAACCAAAGGTATATTGAACGCCACACCAAAGGTGATAAGTTCGAGAA
131 CAACTATGATAGGAACCAAAGGTATATTGAACGCCACACCAAAGGTGATAAGTTCGAGAA
*
39824001 GAAACTATAACAAATTAATTGGCTAAGACCGAAAATGAACCAACAATAACAAATTGTTGA-CCGA
1 GAAACAATAACAAATTAATTGGCTAAGACCGAAAATGAACCAACAATAACAAATTGTTGACCCGA
39824065 ATCTCAAAATGGTCTTTAGGTG-TTTTCGGTTAAAGGAAACAGGAAAGGAACCTTGACCCACTAT
66 ATCTCAAAATGGTCTTTAGGTGTTTTTCGGTTAAAGGAAACAGGAAAGGAACCTTGACCCACTAT
39824129 CAACTATGATAGGAACCAAAGGTATATTGAACGCCACACCAAAGGTGATAAGTTC
131 CAACTATGATAGGAACCAAAGGTATATTGAACGCCACACCAAAGGTGATAAGTTC
39824184 AGCAACAAAG
Statistics
Matches: 181, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
188 97 0.54
189 26 0.14
190 58 0.32
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (190 bp):
GAAACAATAACAAATTAATTGGCTAAGACCGAAAATGAACCAACAATAACAAATTGTTGACCCGA
ATCTCAAAATGGTCTTTAGGTGTTTTTCGGTTAAAGGAAACAGGAAAGGAACCTTGACCCACTAT
CAACTATGATAGGAACCAAAGGTATATTGAACGCCACACCAAAGGTGATAAGTTCGAGAA
Found at i:39824825 original size:21 final size:23
Alignment explanation
Indices: 39824780--39824826 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
39824770 TCACCTGCAA
* *
39824780 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
39824803 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
39824824 TAA
1 TAA
39824827 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:39827542 original size:20 final size:20
Alignment explanation
Indices: 39827517--39827571 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
39827507 TGTGGTTCAA
*
39827517 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
39827537 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
39827557 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
39827572 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:39828227 original size:84 final size:84
Alignment explanation
Indices: 39828125--39828293 Score: 311
Period size: 84 Copynumber: 2.0 Consensus size: 84
39828115 AAGGAACGGC
39828125 ATTAAAGGAGTTGTTTGTGCTTTTTCATGTGGCCATTTAATGGACAAAATTAAAGAAGCTGCTTG
1 ATTAAAGGAGTTGTTTGTGCTTTTTCATGTGGCCATTTAATGGACAAAATTAAAGAAGCTGCTTG
*
39828190 CTGATTTAATGTGCAGCAA
66 CTGATTTAATATGCAGCAA
* *
39828209 ATTAAATGAGTTGTTTGTGCTTTTTCATGTGGCCATTTAATGGACGAAATTAAAGAAGCTGCTTG
1 ATTAAAGGAGTTGTTTGTGCTTTTTCATGTGGCCATTTAATGGACAAAATTAAAGAAGCTGCTTG
39828274 CTGATTTAATATGCAGCAA
66 CTGATTTAATATGCAGCAA
39828293 A
1 A
39828294 GACATGAATT
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 82 1.00
ACGTcount: A:0.30, C:0.12, G:0.22, T:0.36
Consensus pattern (84 bp):
ATTAAAGGAGTTGTTTGTGCTTTTTCATGTGGCCATTTAATGGACAAAATTAAAGAAGCTGCTTG
CTGATTTAATATGCAGCAA
Found at i:39828322 original size:84 final size:84
Alignment explanation
Indices: 39828150--39828322 Score: 222
Period size: 84 Copynumber: 2.1 Consensus size: 84
39828140 TGTGCTTTTT
* *
39828150 CATGTGGCCATTTAATGGACAAAATTAAAGAAGCTGCTTGCTGATTTAATGTGCAGCAAATTAAA
1 CATGTGGCCATTTAATGGACAAAATTAAAGAAGCTGCTTGCTGATTTAATATGCAGCAAATGAAA
* *** * * **
39828215 TGAGTTGTTTGTGCTTTTT
66 TGAATTAAATGAGATTTCC
* *
39828234 CATGTGGCCATTTAATGGACGAAATTAAAGAAGCTGCTTGCTGATTTAATATGCAGCAAA-GACA
1 CATGTGGCCATTTAATGGACAAAATTAAAGAAGCTGCTTGCTGATTTAATATGCAGCAAATGAAA
39828298 TGAATTAAATGAGATGTTCC
66 TGAATTAAATGAGAT-TTCC
39828318 CATGT
1 CATGT
39828323 ATGGAACGGC
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
83 11 0.14
84 65 0.86
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.33
Consensus pattern (84 bp):
CATGTGGCCATTTAATGGACAAAATTAAAGAAGCTGCTTGCTGATTTAATATGCAGCAAATGAAA
TGAATTAAATGAGATTTCC
Found at i:39829200 original size:20 final size:20
Alignment explanation
Indices: 39829177--39829222 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
39829167 CCAGCTCGAA
*
39829177 TTAGCTCACATGAGCTTAAT
1 TTAGCTCACATGAGCTCAAT
***
39829197 TTAGCTCGTTTGAGCTCAAT
1 TTAGCTCACATGAGCTCAAT
39829217 TTAGCT
1 TTAGCT
39829223 TACTTTAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (20 bp):
TTAGCTCACATGAGCTCAAT
Found at i:39829204 original size:30 final size:30
Alignment explanation
Indices: 39829169--39829242 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
39829159 AGTTTTTCCC
39829169 AGCTCGAATT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-ATTGAGCTCA-ATTGAGCTTAATTT
* * *
39829199 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGATTGAGCTCAATTGAGCTTAATTT
*
39829229 AGCTCGTTTGAGCT
1 AGCTCGATTGAGCT
39829243 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 3 0.08
30 36 0.92
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCGATTGAGCTCAATTGAGCTTAATTT
Found at i:39833693 original size:21 final size:21
Alignment explanation
Indices: 39833642--39833706 Score: 55
Period size: 21 Copynumber: 3.0 Consensus size: 21
39833632 TCTATCTTGT
39833642 AATGAAAGAAAGACAGAAAAAGA-
1 AATGAAA-AAA-AC-GAAAAAGAG
*
39833665 AAT-CAAAAAACGAAAAAGAG
1 AATGAAAAAAACGAAAAAGAG
*
39833685 AATGAAAAAGA-GCAAAAAGAG
1 AATGAAAAAAACG-AAAAAGAG
39833706 A
1 A
39833707 TTGAGAGTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
19 8 0.22
20 6 0.17
21 17 0.47
22 2 0.06
23 3 0.08
ACGTcount: A:0.69, C:0.06, G:0.20, T:0.05
Consensus pattern (21 bp):
AATGAAAAAAACGAAAAAGAG
Found at i:39836771 original size:27 final size:27
Alignment explanation
Indices: 39836741--39836918 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
39836731 ATATTGAGTC
* * * *
39836741 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
39836768 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
39836795 CGCACACTTAATGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
39836823 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
39836850 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
39836877 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
39836904 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
39836919 GTACAATTTA
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 105 0.82
28 23 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:39836880 original size:82 final size:81
Alignment explanation
Indices: 39836762--39836917 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
39836752 TGCTATATAA
* *
39836762 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAATGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAATGCAACATAGTCAAA-TCGCA
39836827 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
39836844 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAATGCAACATAGTCAAATCGCA
39836908 CACTTAGTGC
65 CACTTAGTGC
39836918 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 16 0.24
82 50 0.76
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAATGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:39840364 original size:10 final size:10
Alignment explanation
Indices: 39840349--39840397 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
39840339 TTGGGTTAAG
39840349 ATTGAGCTGA
1 ATTGAGCTGA
39840359 ATTGAGCTCGA
1 ATTGAGCT-GA
39840370 A-TGAGCTGA
1 ATTGAGCTGA
* *
39840379 CTTGAGCTCA
1 ATTGAGCTGA
*
39840389 AGTGAGCTG
1 ATTGAGCTG
39840398 GAAACGAGCT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 2 0.06
10 27 0.84
11 3 0.09
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.27
Consensus pattern (10 bp):
ATTGAGCTGA
Found at i:39840374 original size:20 final size:20
Alignment explanation
Indices: 39840351--39840397 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
39840341 GGGTTAAGAT
39840351 TGAGCTGAATTGAGCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
*
39840371 TGAGCTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
39840391 TGAGCTG
1 TGAGCTG
39840398 GAAACGAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:39845493 original size:20 final size:20
Alignment explanation
Indices: 39845447--39845493 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
39845437 AGCTCGTTTC
*
39845447 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
39845467 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
39845487 CAGCTCA
1 CAGCTCA
39845494 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:39846666 original size:9 final size:9
Alignment explanation
Indices: 39846652--39846686 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
39846642 AGAAGTGAAC
39846652 AAAAAAAG-
1 AAAAAAAGA
39846660 AAAAAAAGTA
1 AAAAAAAG-A
39846670 AAAAAAAGA
1 AAAAAAAGA
39846679 AAAAAAAG
1 AAAAAAAG
39846687 TGAAAAGTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 8 0.32
9 9 0.36
10 8 0.32
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:39846685 original size:19 final size:19
Alignment explanation
Indices: 39846638--39846692 Score: 67
Period size: 19 Copynumber: 2.7 Consensus size: 19
39846628 AAATTCGAAA
39846638 AAAAAGAAGTGAACAAAAAAAG
1 AAAAA-AAGTG-A-AAAAAAAG
39846660 AAAAAAAGT-AAAAAAAAG
1 AAAAAAAGTGAAAAAAAAG
39846678 AAAAAAAAGTGAAAA
1 -AAAAAAAGTGAAAA
39846693 GTCTTGTGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
18 8 0.26
19 10 0.32
20 4 0.13
21 4 0.13
22 5 0.16
ACGTcount: A:0.78, C:0.02, G:0.15, T:0.05
Consensus pattern (19 bp):
AAAAAAAGTGAAAAAAAAG
Found at i:39849562 original size:20 final size:20
Alignment explanation
Indices: 39849516--39849562 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
39849506 AGCTCGTTTC
*
39849516 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
39849536 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
39849556 CAGCTCA
1 CAGCTCA
39849563 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:39854684 original size:20 final size:20
Alignment explanation
Indices: 39854659--39854713 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
39854649 AACTAAAGTA
39854659 AGCTAAAAATGAGCTCATTG
1 AGCTAAAAATGAGCTCATTG
* **
39854679 AGCTAAGAACAAGCTCATTG
1 AGCTAAAAATGAGCTCATTG
*
39854699 AGCTAAAATTGAGCT
1 AGCTAAAAATGAGCT
39854714 GAATTAAACT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (20 bp):
AGCTAAAAATGAGCTCATTG
Found at i:39856352 original size:21 final size:21
Alignment explanation
Indices: 39856307--39856369 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
39856297 TTTGAACCAT
* * *
39856307 TACCAATTCGTACCAAATACCA
1 TACCATTTCGAACC-AATTCCA
*
39856329 TACCATTTCGCACCAATTCCA
1 TACCATTTCGAACCAATTCCA
*
39856350 TACTATTTCGAACCAATTCC
1 TACCATTTCGAACCAATTCC
39856370 CAAATACCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 24 0.67
22 12 0.33
ACGTcount: A:0.33, C:0.33, G:0.05, T:0.29
Consensus pattern (21 bp):
TACCATTTCGAACCAATTCCA
Found at i:39863917 original size:14 final size:14
Alignment explanation
Indices: 39863898--39863928 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
39863888 CTATTTGAAC
39863898 CTTTCTTAACCTTT
1 CTTTCTTAACCTTT
39863912 CTTTCTTAACCTTT
1 CTTTCTTAACCTTT
39863926 CTT
1 CTT
39863929 CAACTATCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.13, C:0.29, G:0.00, T:0.58
Consensus pattern (14 bp):
CTTTCTTAACCTTT
Found at i:39885349 original size:24 final size:24
Alignment explanation
Indices: 39885322--39885377 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
39885312 TCTTCTCACA
*
39885322 TTCTTTTTCGC-TCTCGATCTCTTT
1 TTCTTTTTC-CTTCTCGATCTCTAT
**
39885346 TTCTTTTTCCTTCTCTTTCTCTAT
1 TTCTTTTTCCTTCTCGATCTCTAT
39885370 TTCTTTTT
1 TTCTTTTT
39885378 TTCTTTCACA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 1 0.04
24 27 0.96
ACGTcount: A:0.04, C:0.27, G:0.04, T:0.66
Consensus pattern (24 bp):
TTCTTTTTCCTTCTCGATCTCTAT
Found at i:39888816 original size:112 final size:112
Alignment explanation
Indices: 39888618--39888842 Score: 432
Period size: 112 Copynumber: 2.0 Consensus size: 112
39888608 TGAAAATTCA
39888618 AAAATCTAATCTTTTAATTTTCTGTTTCATTTCAGATCTAATTGTTTAGGGTTTTCGTAGGAGTT
1 AAAATCTAATCTTTTAATTTTCTGTTTCATTTCAGATCTAATTGTTTAGGGTTTTCGTAGGAGTT
39888683 TCTCGTGACTTGGCAACTCGATCTTGGTCCGCGCGCAACCCCGTATC
66 TCTCGTGACTTGGCAACTCGATCTTGGTCCGCGCGCAACCCCGTATC
*
39888730 AAAATCTAATCTTTTAATTTTCTGTTTCGTTTCAGATCTAATTGTTTAGGGTTTTCGTAGGAGTT
1 AAAATCTAATCTTTTAATTTTCTGTTTCATTTCAGATCTAATTGTTTAGGGTTTTCGTAGGAGTT
*
39888795 TCTCGTGACTTGGCAAGTCGATCTTGGTCCGCGCGCAACCCCGTATC
66 TCTCGTGACTTGGCAACTCGATCTTGGTCCGCGCGCAACCCCGTATC
39888842 A
1 A
39888843 TTTGGTATCA
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
112 111 1.00
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.39
Consensus pattern (112 bp):
AAAATCTAATCTTTTAATTTTCTGTTTCATTTCAGATCTAATTGTTTAGGGTTTTCGTAGGAGTT
TCTCGTGACTTGGCAACTCGATCTTGGTCCGCGCGCAACCCCGTATC
Found at i:39892982 original size:9 final size:9
Alignment explanation
Indices: 39892968--39892999 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
39892958 ATTTTTTTTA
39892968 CAAAACGCC
1 CAAAACGCC
*
39892977 CAAAACGTC
1 CAAAACGCC
39892986 CAAAACGCC
1 CAAAACGCC
39892995 CAAAA
1 CAAAA
39893000 TCTGATACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.50, C:0.38, G:0.09, T:0.03
Consensus pattern (9 bp):
CAAAACGCC
Found at i:39897935 original size:19 final size:17
Alignment explanation
Indices: 39897911--39897949 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
39897901 AATTTTATTA
39897911 AATTAATTAATCTTAAGCT
1 AATTAATTAAT-TTAA-CT
*
39897930 AATTAATTTATTTAACT
1 AATTAATTAATTTAACT
39897947 AAT
1 AAT
39897950 CAGCAACTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 4 0.21
19 10 0.53
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.46
Consensus pattern (17 bp):
AATTAATTAATTTAACT
Found at i:39898462 original size:12 final size:12
Alignment explanation
Indices: 39898445--39898469 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39898435 TTATACTTGT
39898445 GCCGTTTGAAGA
1 GCCGTTTGAAGA
39898457 GCCGTTTGAAGA
1 GCCGTTTGAAGA
39898469 G
1 G
39898470 ATTTGTGAAA
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:0.24, C:0.16, G:0.36, T:0.24
Consensus pattern (12 bp):
GCCGTTTGAAGA
Found at i:39901848 original size:16 final size:18
Alignment explanation
Indices: 39901827--39901865 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
39901817 ATTGAGATTG
39901827 AGAAAAA-A-ATTGAAAA
1 AGAAAAATATATTGAAAA
*
39901843 AGAAAAATATGTTGAAAA
1 AGAAAAATATATTGAAAA
39901861 AGAAA
1 AGAAA
39901866 CGAGAGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 1 0.05
18 12 0.60
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (18 bp):
AGAAAAATATATTGAAAA
Found at i:39903587 original size:21 final size:21
Alignment explanation
Indices: 39903542--39903604 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
39903532 TTTGAACCAC
* * *
39903542 TACCAATTCGTACCAAATACCA
1 TACCATTTCATACC-AATTCCA
*
39903564 TACCGTTTCATACCAATTCCA
1 TACCATTTCATACCAATTCCA
*
39903585 TACCATTTCGTACCAATTCC
1 TACCATTTCATACCAATTCC
39903605 CACATACCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
21 24 0.69
22 11 0.31
ACGTcount: A:0.32, C:0.33, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCATACCAATTCCA
Found at i:39904942 original size:72 final size:72
Alignment explanation
Indices: 39904825--39904968 Score: 270
Period size: 72 Copynumber: 2.0 Consensus size: 72
39904815 TACCTATGTA
*
39904825 GAGGTAAGAACCAAAGGTATAAAAATATGGTTGAACGCCACACCGGTTTAGTGATAAGTTTAATT
1 GAGGTAAGAACCAAAGGTATAAAAATATGGTTGAACGCCACACCGGTTTAGTGATAAGTTCAATT
39904890 GAGTTTG
66 GAGTTTG
*
39904897 GAGGTAAGAACCAAAGGTATAAAAATATGGTTGAACGCCACACCGGTTTGGTGATAAGTTCAATT
1 GAGGTAAGAACCAAAGGTATAAAAATATGGTTGAACGCCACACCGGTTTAGTGATAAGTTCAATT
39904962 GAGTTTG
66 GAGTTTG
39904969 TATGGACGCC
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.27
Consensus pattern (72 bp):
GAGGTAAGAACCAAAGGTATAAAAATATGGTTGAACGCCACACCGGTTTAGTGATAAGTTCAATT
GAGTTTG
Found at i:39905357 original size:84 final size:84
Alignment explanation
Indices: 39905216--39905382 Score: 289
Period size: 84 Copynumber: 2.0 Consensus size: 84
39905206 AGCTTATTTT
* * *
39905216 TAGCTTTCTTTAGTTTACATTTATTTTGCTGAAATAAACCATTTAATTTGTCTTTAGTTGAATTA
1 TAGCTTTCTTTAGCTTACATTTATTTTGCTGAAATAAACCATTTAATTTGTCATTAGTTAAATTA
*
39905281 GTTGTTTATTTTAAGTTAA
66 GTTGTTTATCTTAAGTTAA
*
39905300 TAGCTTTCTTTAGCTTGCATTTATTTTGCTGAAATAAACCATTTAATTTGTCATTAGTTAAATTA
1 TAGCTTTCTTTAGCTTACATTTATTTTGCTGAAATAAACCATTTAATTTGTCATTAGTTAAATTA
39905365 GTTGTTTATCTTAAGTTA
66 GTTGTTTATCTTAAGTTA
39905383 GTTAATTTGT
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
84 78 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.51
Consensus pattern (84 bp):
TAGCTTTCTTTAGCTTACATTTATTTTGCTGAAATAAACCATTTAATTTGTCATTAGTTAAATTA
GTTGTTTATCTTAAGTTAA
Found at i:39906328 original size:42 final size:42
Alignment explanation
Indices: 39906279--39906362 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
39906269 ACTTATCTAG
*
39906279 CTTGCTAGTGGCGTCCATACAAACTCAATTGAACTTATCACC
1 CTTGCTAGTGGCGTCAATACAAACTCAATTGAACTTATCACC
* * * *
39906321 CTTGCTAGTGGTGTCAATCCGAACTCCATTGAACTTATCACC
1 CTTGCTAGTGGCGTCAATACAAACTCAATTGAACTTATCACC
39906363 GAATCGGTGT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.30
Consensus pattern (42 bp):
CTTGCTAGTGGCGTCAATACAAACTCAATTGAACTTATCACC
Found at i:39908252 original size:20 final size:19
Alignment explanation
Indices: 39908229--39908293 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
39908219 AAGCTCAAAC
39908229 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
39908249 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
39908269 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
39908289 GAGCT
1 GAGCT
39908294 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:39909581 original size:17 final size:18
Alignment explanation
Indices: 39909559--39909592 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39909549 ACAACACTCC
*
39909559 TTTCTT-CTTCACTCTCG
1 TTTCTTCCTTCAATCTCG
39909576 TTTCTTCCTTCAATCTC
1 TTTCTTCCTTCAATCTC
39909593 ACTCTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.09, C:0.35, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTCTTCCTTCAATCTCG
Found at i:39909700 original size:15 final size:16
Alignment explanation
Indices: 39909675--39909706 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
39909665 TATCTCACAC
39909675 TCATCTTCTTTTTCTT
1 TCATCTTCTTTTTCTT
39909691 TCAT-TTCTTTTTCTT
1 TCATCTTCTTTTTCTT
39909706 T
1 T
39909707 TTCATTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (16 bp):
TCATCTTCTTTTTCTT
Found at i:39910655 original size:18 final size:17
Alignment explanation
Indices: 39910634--39910675 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
39910624 TTTAACTTGA
39910634 TTTTTTTTGCTC-ACCTTT
1 TTTTTTTTGCTCGA--TTT
39910652 TTTTTTTTGCTCGATTT
1 TTTTTTTTGCTCGATTT
39910669 TTTTTTT
1 TTTTTTT
39910676 CACTTTTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.43
18 12 0.52
19 1 0.04
ACGTcount: A:0.05, C:0.14, G:0.07, T:0.74
Consensus pattern (17 bp):
TTTTTTTTGCTCGATTT
Found at i:39912315 original size:26 final size:26
Alignment explanation
Indices: 39912285--39912336 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
39912275 CCAACCTTTA
39912285 AAACCATTTGAAAGCTTCCGCATCTT
1 AAACCATTTGAAAGCTTCCGCATCTT
*
39912311 AAACCATTTGAAAGCTTCTGCATCTT
1 AAACCATTTGAAAGCTTCCGCATCTT
39912337 TAGCCTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.33
Consensus pattern (26 bp):
AAACCATTTGAAAGCTTCCGCATCTT
Found at i:39913672 original size:34 final size:34
Alignment explanation
Indices: 39913628--39913703 Score: 134
Period size: 34 Copynumber: 2.2 Consensus size: 34
39913618 GAGTTAGTTT
*
39913628 ATTAACTTTAGTTCAGCTCAAATAAGTGTTAGTA
1 ATTAATTTTAGTTCAGCTCAAATAAGTGTTAGTA
*
39913662 ATTAATTTTAGTTCAGCTTAAATAAGTGTTAGTA
1 ATTAATTTTAGTTCAGCTCAAATAAGTGTTAGTA
39913696 ATTAATTT
1 ATTAATTT
39913704 GTTTAAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.43
Consensus pattern (34 bp):
ATTAATTTTAGTTCAGCTCAAATAAGTGTTAGTA
Found at i:39915991 original size:22 final size:22
Alignment explanation
Indices: 39915939--39915991 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
39915929 ACAGACTTAG
*
39915939 AAAAATTAAAACATGCATTAAAA
1 AAAAAATAAAACA-GCATTAAAA
39915962 AAACAAATAAAACA-CATTTAAAA
1 AAA-AAATAAAACAGCA-TTAAAA
*
39915985 TAAAAAT
1 AAAAAAT
39915992 TAATATGTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 6 0.23
23 11 0.42
24 9 0.35
ACGTcount: A:0.68, C:0.09, G:0.02, T:0.21
Consensus pattern (22 bp):
AAAAAATAAAACAGCATTAAAA
Found at i:39917788 original size:58 final size:58
Alignment explanation
Indices: 39917698--39917962 Score: 521
Period size: 58 Copynumber: 4.6 Consensus size: 58
39917688 AAAGTCATGC
39917698 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
1 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
39917756 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
1 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
39917814 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
1 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
39917872 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
1 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
*
39917930 ATTATGTAACTTTCATGTTAGTTAAATTTGCAT
1 ATTATGTAACTTTCATGTTAGTTAAGTTTGCAT
39917963 TTCAAAACCA
Statistics
Matches: 206, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 206 1.00
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (58 bp):
ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
Found at i:39918474 original size:60 final size:60
Alignment explanation
Indices: 39918381--39918495 Score: 230
Period size: 60 Copynumber: 1.9 Consensus size: 60
39918371 TGTTATAAAG
39918381 GGAGCTTAAAGATCATTAAAATGAGATTTTAAAGAGCATTTTATGCCCTTTAAAAAAAAA
1 GGAGCTTAAAGATCATTAAAATGAGATTTTAAAGAGCATTTTATGCCCTTTAAAAAAAAA
39918441 GGAGCTTAAAGATCATTAAAATGAGATTTTAAAGAGCATTTTATGCCCTTTAAAA
1 GGAGCTTAAAGATCATTAAAATGAGATTTTAAAGAGCATTTTATGCCCTTTAAAA
39918496 TTCAGCAGCA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.43, C:0.10, G:0.16, T:0.31
Consensus pattern (60 bp):
GGAGCTTAAAGATCATTAAAATGAGATTTTAAAGAGCATTTTATGCCCTTTAAAAAAAAA
Found at i:39919340 original size:12 final size:12
Alignment explanation
Indices: 39919323--39919367 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
39919313 GTAGTTTCTC
*
39919323 AAAAAAAACTCG
1 AAAAAAAATTCG
*
39919335 AAAAAAAAATTCA
1 -AAAAAAAATTCG
*
39919348 AAAAAAAATTTG
1 AAAAAAAATTCG
39919360 AAAAAAAA
1 AAAAAAAA
39919368 AACTAGTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 18 0.64
13 10 0.36
ACGTcount: A:0.76, C:0.07, G:0.04, T:0.13
Consensus pattern (12 bp):
AAAAAAAATTCG
Found at i:39919341 original size:13 final size:13
Alignment explanation
Indices: 39919323--39919368 Score: 67
Period size: 13 Copynumber: 3.6 Consensus size: 13
39919313 GTAGTTTCTC
*
39919323 AAAAAAAACTCGA
1 AAAAAAAATTCGA
39919336 AAAAAAAATTC-A
1 AAAAAAAATTCGA
*
39919348 AAAAAAAATTTGA
1 AAAAAAAATTCGA
39919361 AAAAAAAA
1 AAAAAAAA
39919369 ACTAGTTTCC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.76, C:0.07, G:0.04, T:0.13
Consensus pattern (13 bp):
AAAAAAAATTCGA
Found at i:39923534 original size:324 final size:324
Alignment explanation
Indices: 39922945--39923593 Score: 1226
Period size: 324 Copynumber: 2.0 Consensus size: 324
39922935 AGCAAGACTA
39922945 TTGATTTGAGGTGCGCGAATAACGAAGTAATCCGAGTTGAGTCTACGGACTTAAAGGGGTTGCCA
1 TTGATTTGAGGTGCGCGAATAACGAAGTAATCCGAGTTGAGTCTACGGACTTAAAGGGGTTGCCA
39923010 GCTGTAATATCCTCAATGTTGGCCCAGAAATATGTAAGAAAAGGGTGCGAAGCATACCTTGCGTA
66 GCTGTAATATCCTCAATGTTGGCCCAGAAATATGTAAGAAAAGGGTGCGAAGCATACCTTGCGTA
* * * *
39923075 TGTACTGGATGACCAAGAATTAGAAAGGAAACCCGAATCTGTGCCGGTGGTTTGTAAATACCCGG
131 TGTAATGGATGACAAAGAATTAGAAAAGAAACCCGAATCTATGCCGGTGGTTTGTAAATACCCGG
39923140 ATGTTTTTCCTGAAGAATTACCGGGTTTACCACCTGTTCGGGAGATAGAGTTTGGTATTGAGCTT
196 ATGTTTTTCCTGAAGAATTACCGGGTTTACCACCTGTTCGGGAGATAGAGTTTGGTATTGAGCTT
39923205 GTACCTGGGACTACGCCGATTTCGATAGCTCCGTATCGTATGGCACCAACCGAGTTAAAAGAGT
261 GTACCTGGGACTACGCCGATTTCGATAGCTCCGTATCGTATGGCACCAACCGAGTTAAAAGAGT
**
39923269 TTGATTTGAGGTGCGCGAATAACGAAGTAATCCGAGTTGAGTCTACGGACTTGGAGGGGTTGCCA
1 TTGATTTGAGGTGCGCGAATAACGAAGTAATCCGAGTTGAGTCTACGGACTTAAAGGGGTTGCCA
39923334 GCTGTAATATCCTCAATGTTGGCCCAGAAATATGTAAGAAAAGGGTGCGAAGCATACCTTGCGTA
66 GCTGTAATATCCTCAATGTTGGCCCAGAAATATGTAAGAAAAGGGTGCGAAGCATACCTTGCGTA
* *
39923399 TGTAATTGATGACAAAGAATTAGAAAAGAAACCCGAATCTATGCCGGTGGTTTGTGAATACCCGG
131 TGTAATGGATGACAAAGAATTAGAAAAGAAACCCGAATCTATGCCGGTGGTTTGTAAATACCCGG
39923464 ATGTTTTTCCTGAAGAATTACCGGGTTTACCACCTGTTCGGGAGATAGAGTTTGGTATTGAGCTT
196 ATGTTTTTCCTGAAGAATTACCGGGTTTACCACCTGTTCGGGAGATAGAGTTTGGTATTGAGCTT
39923529 GTACCTGGGACTACGCCGATTTCGATAGCTCCGTATCGTATGGCACCAACCGAGTTAAAAGAGT
261 GTACCTGGGACTACGCCGATTTCGATAGCTCCGTATCGTATGGCACCAACCGAGTTAAAAGAGT
39923593 T
1 T
39923594 GAAAGCTCAG
Statistics
Matches: 317, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
324 317 1.00
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (324 bp):
TTGATTTGAGGTGCGCGAATAACGAAGTAATCCGAGTTGAGTCTACGGACTTAAAGGGGTTGCCA
GCTGTAATATCCTCAATGTTGGCCCAGAAATATGTAAGAAAAGGGTGCGAAGCATACCTTGCGTA
TGTAATGGATGACAAAGAATTAGAAAAGAAACCCGAATCTATGCCGGTGGTTTGTAAATACCCGG
ATGTTTTTCCTGAAGAATTACCGGGTTTACCACCTGTTCGGGAGATAGAGTTTGGTATTGAGCTT
GTACCTGGGACTACGCCGATTTCGATAGCTCCGTATCGTATGGCACCAACCGAGTTAAAAGAGT
Found at i:39928135 original size:40 final size:40
Alignment explanation
Indices: 39928076--39928223 Score: 251
Period size: 40 Copynumber: 3.7 Consensus size: 40
39928066 GAACATTGGA
*
39928076 ATATATCCGGGCTAAGACCCGAAGGCAATTACGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
39928116 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
39928156 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
39928196 ATATGTCCGGGTTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
39928224 ATGTGTTTGC
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 102 1.00
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
Found at i:39929314 original size:66 final size:66
Alignment explanation
Indices: 39929211--39929341 Score: 237
Period size: 66 Copynumber: 2.0 Consensus size: 66
39929201 TTATCCAGAG
39929211 ATAATTAGAAGTCATTCCTTATATGTATAGATTCCCCTTTGAGTCTAGTTTCATTAGAAACAAAC
1 ATAATTAGAAGTCATTCCTTATATGTATAGATTCCCCTTTGAGTCTAGTTTCATTAG-AACAAAC
39929276 GC
65 GC
*
39929278 ATAATTAGAAGTCATTCCTTA-ATGTATGGATTCCCCTTTGAGTCTAGTTTCATTAGAACAAACG
1 ATAATTAGAAGTCATTCCTTATATGTATAGATTCCCCTTTGAGTCTAGTTTCATTAGAACAAACG
39929342 GCATGAGTAT
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
65 8 0.13
66 34 0.54
67 21 0.33
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.36
Consensus pattern (66 bp):
ATAATTAGAAGTCATTCCTTATATGTATAGATTCCCCTTTGAGTCTAGTTTCATTAGAACAAACG
C
Found at i:39934489 original size:39 final size:39
Alignment explanation
Indices: 39934435--39934513 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
39934425 ACGTTTAACG
39934435 AACATGTTCATTGGTACTTGATGATGAAAGTTTTGGAAT
1 AACATGTTCATTGGTACTTGATGATGAAAGTTTTGGAAT
39934474 AACATGTTCATTGGTACTTGATGATGAAAGTTTTGGAAT
1 AACATGTTCATTGGTACTTGATGATGAAAGTTTTGGAAT
39934513 A
1 A
39934514 TGTATGCGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.32, C:0.08, G:0.23, T:0.38
Consensus pattern (39 bp):
AACATGTTCATTGGTACTTGATGATGAAAGTTTTGGAAT
Found at i:39939170 original size:27 final size:27
Alignment explanation
Indices: 39939140--39939196 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
39939130 TCTGCTCACT
39939140 TTGTTCCAGTTCGTACAAATTACTCGC
1 TTGTTCCAGTTCGTACAAATTACTCGC
*
39939167 TTGTTCCAGTTCGTACAGATTACTCGC
1 TTGTTCCAGTTCGTACAAATTACTCGC
39939194 TTG
1 TTG
39939197 ATAAACTGGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.39
Consensus pattern (27 bp):
TTGTTCCAGTTCGTACAAATTACTCGC
Found at i:39944350 original size:129 final size:129
Alignment explanation
Indices: 39944117--39944371 Score: 447
Period size: 129 Copynumber: 2.0 Consensus size: 129
39944107 CTCGTTTGGG
* *
39944117 TTGGGCGTCGGCTAAGAGTGCTCGAAGCTTGGATTAACTCCAGTCGCCAATCAGGTGTGTATTTC
1 TTGGGCATCGGCTAAGAGTGCTCGAAGCTTAGATTAACTCCAGTCGCCAATCAGGTGTGTATTTC
* * *
39944182 TCGCTACTCTAGCTGTAGGATGGGTACTTCGGGCTGCGATAGGCCGAAAGGGGTCATGTGGGCA
66 TCACTACTCTAGCTGTAGGATGGCTACTTCGGGCCGCGATAGGCCGAAAGGGGTCATGTGGGCA
* *
39944246 TTGGGCATTGGCTAAGAGTGCTCGGAGCTTAGATTAACTCCAGTCGCCAATCAGGTGTGTATTTC
1 TTGGGCATCGGCTAAGAGTGCTCGAAGCTTAGATTAACTCCAGTCGCCAATCAGGTGTGTATTTC
39944311 TCACTACTCTAGCTGTAGGATGGCTACTTCGGGCCGCGATAGGCCGAAAGGGGTCATGTGG
66 TCACTACTCTAGCTGTAGGATGGCTACTTCGGGCCGCGATAGGCCGAAAGGGGTCATGTGG
39944372 ACTAGGCTAG
Statistics
Matches: 119, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
129 119 1.00
ACGTcount: A:0.20, C:0.21, G:0.32, T:0.27
Consensus pattern (129 bp):
TTGGGCATCGGCTAAGAGTGCTCGAAGCTTAGATTAACTCCAGTCGCCAATCAGGTGTGTATTTC
TCACTACTCTAGCTGTAGGATGGCTACTTCGGGCCGCGATAGGCCGAAAGGGGTCATGTGGGCA
Found at i:39944579 original size:27 final size:27
Alignment explanation
Indices: 39944522--39944665 Score: 146
Period size: 27 Copynumber: 5.3 Consensus size: 27
39944512 TATTGAAATG
* * **
39944522 CCCTCGACTTGTAAAATTACCAAAGTT-
1 CCCTCGATTTATAAAATTACC-ATTTTA
*
39944549 CCCTCGATTTACAAAATTACCATTTTA
1 CCCTCGATTTATAAAATTACCATTTTA
* * *
39944576 CCCTCGATTTATAGAATTATCGTTTTA
1 CCCTCGATTTATAAAATTACCATTTTA
** *
39944603 CCCTTAATTTATAGAATTACCATTTTA
1 CCCTCGATTTATAAAATTACCATTTTA
* *
39944630 CCCTTGATTTATAAAATTACCGTTTTA
1 CCCTCGATTTATAAAATTACCATTTTA
*
39944657 CCATCGATT
1 CCCTCGATT
39944666 GTGAAATTAC
Statistics
Matches: 98, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
26 3 0.03
27 95 0.97
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.40
Consensus pattern (27 bp):
CCCTCGATTTATAAAATTACCATTTTA
Found at i:39944727 original size:27 final size:27
Alignment explanation
Indices: 39944664--39944837 Score: 138
Period size: 27 Copynumber: 6.4 Consensus size: 27
39944654 TTACCATCGA
* *
39944664 TTGTGAAATTACTAAAATACCCCT-GT
1 TTGTAAAATTACCAAAATACCCCTAGT
** *
39944690 AAGATAGAATTACCAAAATACCCCTAGT
1 TTG-TAAAATTACCAAAATACCCCTAGT
* * *
39944718 TCGTAAAATTACCAAAATACCACTGGT
1 TTGTAAAATTACCAAAATACCCCTAGT
* * *
39944745 TTGTGAAATTACCGAAATA-CCCTCAAT
1 TTGTAAAATTACCAAAATACCCCT-AGT
*
39944772 TTGTAAAATTACCAAAATACCCCTAAT
1 TTGTAAAATTACCAAAATACCCCTAGT
** * *
39944799 TTACAAAGTTA-CAGAAATACCCTTGAGT
1 TTGTAAAATTACCA-AAATACCCCT-AGT
*
39944827 TTCTAAAATTA
1 TTGTAAAATTA
39944838 TGGAAATACC
Statistics
Matches: 116, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
26 6 0.05
27 93 0.80
28 17 0.15
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (27 bp):
TTGTAAAATTACCAAAATACCCCTAGT
Found at i:39944852 original size:28 final size:27
Alignment explanation
Indices: 39944797--39944864 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 27
39944787 AATACCCCTA
* ** *
39944797 ATTTACAAAGTTACAGAAATACCCTTG
1 ATTTACAAAATTATGGAAATACCATTG
39944824 AGTTT-CTAAAATTATGGAAATACCATTG
1 A-TTTAC-AAAATTATGGAAATACCATTG
39944852 ATTTACAAAATTA
1 ATTTACAAAATTA
39944865 CTAAAATACC
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
27 12 0.35
28 22 0.65
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34
Consensus pattern (27 bp):
ATTTACAAAATTATGGAAATACCATTG
Found at i:39944871 original size:27 final size:27
Alignment explanation
Indices: 39944776--39944878 Score: 95
Period size: 27 Copynumber: 3.8 Consensus size: 27
39944766 CTCAATTTGT
* * *
39944776 AAAATTACCAAAATACCCCTAATTTAC
1 AAAATTACTAAAATACCCTTGATTTAC
*
39944803 AAAGTTAC-AGAAATACCCTTGAGTTT-C
1 AAAATTACTA-AAATACCCTTGA-TTTAC
* *
39944830 TAAAATTA-TGGAAATACCATTGATTTAC
1 -AAAATTACT-AAAATACCCTTGATTTAC
39944858 AAAATTACTAAAATACCCTTG
1 AAAATTACTAAAATACCCTTG
39944879 GTTTGTAGAT
Statistics
Matches: 61, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
26 1 0.02
27 38 0.62
28 22 0.36
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.30
Consensus pattern (27 bp):
AAAATTACTAAAATACCCTTGATTTAC
Found at i:39945000 original size:27 final size:26
Alignment explanation
Indices: 39944934--39945000 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 26
39944924 ATACCCCTAA
*
39944934 TAGGTAAAAAGACCGTAAAGCCCTTG
1 TAGGTAAAATGACCGTAAAGCCCTTG
*
39944960 TAGAGTAAAGTGACCGTAATA-CCCTTG
1 TAG-GTAAAATGACCGTAA-AGCCCTTG
39944987 TATGGTAAAATGAC
1 TA-GGTAAAATGAC
39945001 GAATATGCCC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 3 0.09
27 30 0.86
28 2 0.06
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.24
Consensus pattern (26 bp):
TAGGTAAAATGACCGTAAAGCCCTTG
Found at i:39945829 original size:26 final size:26
Alignment explanation
Indices: 39945800--39945949 Score: 239
Period size: 26 Copynumber: 5.8 Consensus size: 26
39945790 GAGGAAGTGC
* *
39945800 AAAAGGGCTTATGCCCTAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACTG
*
39945826 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACTG
*
39945852 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACTG
*
39945878 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACTG
*
39945904 AAAAGGGCTTATACCCCAGTTTACTG
1 AAAAGGGCTTATGCCCCAGTTTACTG
39945930 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
39945950 CTTAAAGAGG
Statistics
Matches: 114, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
25 9 0.08
26 105 0.92
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACTG
Found at i:39945878 original size:52 final size:52
Alignment explanation
Indices: 39945800--39945949 Score: 266
Period size: 52 Copynumber: 2.9 Consensus size: 52
39945790 GAGGAAGTGC
*
39945800 AAAAGGGCTTATGCCCTAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
39945852 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
* *
39945904 AAAAGGGCTTATACCCCAGTTTACTGAAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTT
39945950 CTTAAAGAGG
Statistics
Matches: 95, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
51 10 0.11
52 85 0.89
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (52 bp):
AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
Found at i:39946153 original size:42 final size:42
Alignment explanation
Indices: 39946094--39946173 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 42
39946084 TAGTCTCCCC
* ** *
39946094 AAATGGGCTTGCATACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
39946136 AAATGGGCTTGCATACATCCATTGACATTACATGTGAT
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGAT
39946174 GTATTTCATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
Found at i:39946190 original size:56 final size:56
Alignment explanation
Indices: 39946118--39946226 Score: 209
Period size: 56 Copynumber: 1.9 Consensus size: 56
39946108 ACATTCATTG
39946118 GTATTTCATGTGATATTGAAATGGGCTTGCATACATCCATTGACATTACATGTGAT
1 GTATTTCATGTGATATTGAAATGGGCTTGCATACATCCATTGACATTACATGTGAT
*
39946174 GTATTTCATGTGATATTGAAATGGGCTTGCATACATCTATTGACATTACATGT
1 GTATTTCATGTGATATTGAAATGGGCTTGCATACATCCATTGACATTACATGT
39946227 AATATTGAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (56 bp):
GTATTTCATGTGATATTGAAATGGGCTTGCATACATCCATTGACATTACATGTGAT
Found at i:39948600 original size:27 final size:27
Alignment explanation
Indices: 39948581--39948969 Score: 517
Period size: 27 Copynumber: 14.4 Consensus size: 27
39948571 ATTACCAAAG
* **
39948581 TACCCTCGATTTATAGAATTACTATTT
1 TACCCTTGATTTATAGAATTACCGTTT
*
39948608 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTTGATTTATAGAATTACCGTTT
* *
39948635 TACCCTTAATTTATAGAATTACTGTTT
1 TACCCTTGATTTATAGAATTACCGTTT
*
39948662 TACCCTTGATTTATAGAATTACCATTT
1 TACCCTTGATTTATAGAATTACCGTTT
* * *
39948689 TACCCTCGATTTACAAAATTACCGTTT
1 TACCCTTGATTTATAGAATTACCGTTT
* *
39948716 TACCCTTAATTTATAGAATTACTGTTT
1 TACCCTTGATTTATAGAATTACCGTTT
*
39948743 TACCCTTGATTTATAGAATTACCATTT
1 TACCCTTGATTTATAGAATTACCGTTT
* * *
39948770 TACCCTCGATTTACAAAATTACCGTTT
1 TACCCTTGATTTATAGAATTACCGTTT
* *
39948797 TACCCTTAATTTATAGAATTACTGTTT
1 TACCCTTGATTTATAGAATTACCGTTT
*
39948824 TACCCTTGATTTATAGAATTACCATTT
1 TACCCTTGATTTATAGAATTACCGTTT
* * *
39948851 TACCCTCGATTTACAAAATTACCGTTT
1 TACCCTTGATTTATAGAATTACCGTTT
* *
39948878 TACCCTTAATTTATAGAATTACTGTTT
1 TACCCTTGATTTATAGAATTACCGTTT
*
39948905 TACCCTTGATTTATAGAATTACCATTT
1 TACCCTTGATTTATAGAATTACCGTTT
* * *
39948932 TACCCTCGATTTACAAAATTACCGTTT
1 TACCCTTGATTTATAGAATTACCGTTT
*
39948959 TACCCTCGATT
1 TACCCTTGATT
39948970 GTGAAATTAC
Statistics
Matches: 314, Mismatches: 48, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 314 1.00
ACGTcount: A:0.29, C:0.20, G:0.08, T:0.43
Consensus pattern (27 bp):
TACCCTTGATTTATAGAATTACCGTTT
Found at i:39948680 original size:81 final size:81
Alignment explanation
Indices: 39948581--39948964 Score: 732
Period size: 81 Copynumber: 4.7 Consensus size: 81
39948571 ATTACCAAAG
* * * *
39948581 TACCCTCGATTTATAGAATTACTATTTTACCCTCGATTTATAGAATTACCGTTTTACCCTTAATT
1 TACCCTTGATTTATAGAATTACCATTTTACCCTCGATTTACAAAATTACCGTTTTACCCTTAATT
39948646 TATAGAATTACTGTTT
66 TATAGAATTACTGTTT
39948662 TACCCTTGATTTATAGAATTACCATTTTACCCTCGATTTACAAAATTACCGTTTTACCCTTAATT
1 TACCCTTGATTTATAGAATTACCATTTTACCCTCGATTTACAAAATTACCGTTTTACCCTTAATT
39948727 TATAGAATTACTGTTT
66 TATAGAATTACTGTTT
39948743 TACCCTTGATTTATAGAATTACCATTTTACCCTCGATTTACAAAATTACCGTTTTACCCTTAATT
1 TACCCTTGATTTATAGAATTACCATTTTACCCTCGATTTACAAAATTACCGTTTTACCCTTAATT
39948808 TATAGAATTACTGTTT
66 TATAGAATTACTGTTT
39948824 TACCCTTGATTTATAGAATTACCATTTTACCCTCGATTTACAAAATTACCGTTTTACCCTTAATT
1 TACCCTTGATTTATAGAATTACCATTTTACCCTCGATTTACAAAATTACCGTTTTACCCTTAATT
39948889 TATAGAATTACTGTTT
66 TATAGAATTACTGTTT
39948905 TACCCTTGATTTATAGAATTACCATTTTACCCTCGATTTACAAAATTACCGTTTTACCCT
1 TACCCTTGATTTATAGAATTACCATTTTACCCTCGATTTACAAAATTACCGTTTTACCCT
39948965 CGATTGTGAA
Statistics
Matches: 299, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 299 1.00
ACGTcount: A:0.29, C:0.20, G:0.08, T:0.43
Consensus pattern (81 bp):
TACCCTTGATTTATAGAATTACCATTTTACCCTCGATTTACAAAATTACCGTTTTACCCTTAATT
TATAGAATTACTGTTT
Found at i:39949033 original size:27 final size:27
Alignment explanation
Indices: 39949003--39949124 Score: 106
Period size: 27 Copynumber: 4.5 Consensus size: 27
39948993 TAGGATAGAC
39949003 TTACCAAAATACCCCTAGTTTATAAAA
1 TTACCAAAATACCCCTAGTTTATAAAA
* * * * *
39949030 TTACCAAAGTACCACTGGTTTGTGAAA
1 TTACCAAAATACCCCTAGTTTATAAAA
* * *
39949057 TTACCGAAATA-CCCTCAATTTGTAAAA
1 TTACCAAAATACCCCT-AGTTTATAAAA
* *
39949084 TTACCAAAATACCCCT-GATTTACAAAG
1 TTACCAAAATACCCCTAG-TTTATAAAA
39949111 TTA-CAGAAATACCC
1 TTACCA-AAATACCC
39949125 TTGACTTTCT
Statistics
Matches: 75, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
26 5 0.07
27 66 0.88
28 4 0.05
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.28
Consensus pattern (27 bp):
TTACCAAAATACCCCTAGTTTATAAAA
Found at i:39949175 original size:27 final size:27
Alignment explanation
Indices: 39949136--39949187 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
39949126 TGACTTTCTA
39949136 AAAATTATGGAAATACCATTGGTTTAC
1 AAAATTATGGAAATACCATTGGTTTAC
*
39949163 AAAATTACT-GAAATACCCTTGGTTT
1 AAAATTA-TGGAAATACCATTGGTTT
39949188 GTAGATTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.35
Consensus pattern (27 bp):
AAAATTATGGAAATACCATTGGTTTAC
Found at i:39951362 original size:39 final size:39
Alignment explanation
Indices: 39951308--39951618 Score: 487
Period size: 39 Copynumber: 8.0 Consensus size: 39
39951298 AAGACACTGA
*
39951308 AAATGTATCCGGGCTAAAATCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
*
39951347 AAATGTATCCGGGCTAAAGTCCCGCAAGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* * *
39951386 AAATATATCCGGGCTAAAGTCTCGCAGGCTTCGTGCTAG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* *
39951425 AAATATATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
*
39951464 AAATGTATCCGGACTAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* *
39951503 AAATGTATCCGGGCCAAAGTCCGGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* * *
39951542 AAATGTATCCGGGCCAAAGTCCGGCAGGCTTCATGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* *
39951581 AAATGTATCCGGGTTAAAGTCCCGCAGGCTTTGTGCTG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
39951619 ATAATATAAT
Statistics
Matches: 251, Mismatches: 21, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 251 1.00
ACGTcount: A:0.23, C:0.25, G:0.29, T:0.23
Consensus pattern (39 bp):
AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
Found at i:39953969 original size:16 final size:16
Alignment explanation
Indices: 39953948--39953978 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39953938 CAAATATGGG
39953948 CATGACATTCTGCATA
1 CATGACATTCTGCATA
*
39953964 CATGACATTTTGCAT
1 CATGACATTCTGCAT
39953979 TGGGTTGGGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (16 bp):
CATGACATTCTGCATA
Found at i:39954267 original size:42 final size:42
Alignment explanation
Indices: 39954202--39954293 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
39954192 TAGTCTCCCC
* ** *
39954202 AAATGGGCTTGCATACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
*
39954244 AACTGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
39954286 AAATGGGC
1 AAATGGGC
39954294 CTAAGGGCAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
Found at i:39954394 original size:31 final size:31
Alignment explanation
Indices: 39954317--39954395 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
39954307 CGTTTGCAGT
* * *
39954317 AAAGGCTTCGGCCTAATGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATAATTTATGA
39954348 AAAGGCTTCGGCCCAGTGATATAATTTATGA
1 AAAGGCTTCGGCCCAGTGATATAATTTATGA
39954379 AAAGGCTTCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
39954396 AACCGTTAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATAATTTATGA
Found at i:39956682 original size:27 final size:27
Alignment explanation
Indices: 39956663--39956808 Score: 211
Period size: 27 Copynumber: 5.4 Consensus size: 27
39956653 ATTACCAAAG
*
39956663 TACCCTCGATTTATAGAATTACTATTT
1 TACCCTCGATTTATAGAATTACCATTT
**
39956690 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTATAGAATTACCATTT
* **
39956717 TACCCTCGATTTACAGAATTACTGTTT
1 TACCCTCGATTTATAGAATTACCATTT
*
39956744 TACCCTTGATTTATAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACCATTT
* *
39956771 TACCCTCGATTTATAAAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCATTT
39956798 TACCCTCGATT
1 TACCCTCGATT
39956809 GTGAAATTTC
Statistics
Matches: 110, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 110 1.00
ACGTcount: A:0.27, C:0.21, G:0.09, T:0.42
Consensus pattern (27 bp):
TACCCTCGATTTATAGAATTACCATTT
Found at i:39956870 original size:27 final size:27
Alignment explanation
Indices: 39956840--39956938 Score: 128
Period size: 27 Copynumber: 3.7 Consensus size: 27
39956830 TGTAGGATAG
39956840 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
* * * *
39956867 AATTACTAAAATACCACTGGTTTGTGA
1 AATTACCAAAATACCCCTAGTTTGTAA
* *
39956894 AATTACCGAAATA-CCCTCAATTTGTAA
1 AATTACCAAAATACCCCT-AGTTTGTAA
39956921 AATTACCAAAATACCCCT
1 AATTACCAAAATACCCCT
39956939 GATTTACAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
26 3 0.05
27 52 0.88
28 4 0.07
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.29
Consensus pattern (27 bp):
AATTACCAAAATACCCCTAGTTTGTAA
Found at i:39956881 original size:54 final size:53
Alignment explanation
Indices: 39956798--39956939 Score: 137
Period size: 54 Copynumber: 2.7 Consensus size: 53
39956788 ATTACCGTTT
* * * *
39956798 TACCCTCGA-TTGTGAAATTTCTGAAATACCCCTGTAGGAT-AGAATTACCAAAA
1 TACCCTCAATTTGTAAAATTACTAAAATACCCCTGTAGG-TGA-AATTACCAAAA
* * ** *
39956851 TACCC-CTAGTTTGTAAAATTACTAAAATACCACTGGTTTGTGAAATTACCGAAA
1 TACCCTC-AATTTGTAAAATTACTAAAATACCCCT-GTAGGTGAAATTACCAAAA
*
39956905 TACCCTCAATTTGTAAAATTACCAAAATACCCCTG
1 TACCCTCAATTTGTAAAATTACTAAAATACCCCTG
39956940 ATTTACAAAG
Statistics
Matches: 72, Mismatches: 12, Indels: 10
0.77 0.13 0.11
Matches are distributed among these distances:
52 1 0.01
53 6 0.08
54 60 0.83
55 5 0.07
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.30
Consensus pattern (53 bp):
TACCCTCAATTTGTAAAATTACTAAAATACCCCTGTAGGTGAAATTACCAAAA
Found at i:39956959 original size:54 final size:54
Alignment explanation
Indices: 39956860--39956963 Score: 138
Period size: 54 Copynumber: 1.9 Consensus size: 54
39956850 ATACCCCTAG
* * ** *
39956860 TTTGTAAAATTACTAAAATACCACTGGTTTGTGAAATTACCGAAATACCCTCAA
1 TTTGTAAAATTACCAAAATACCACTGATTTGACAAATTACAGAAATACCCTCAA
*
39956914 TTTGTAAAATTACCAAAATACCCCTGATTT-ACAAAGTTACAGAAATACCC
1 TTTGTAAAATTACCAAAATACCACTGATTTGACAAA-TTACAGAAATACCC
39956964 GTGACTTTCT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
53 3 0.07
54 40 0.93
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (54 bp):
TTTGTAAAATTACCAAAATACCACTGATTTGACAAATTACAGAAATACCCTCAA
Found at i:39957018 original size:27 final size:27
Alignment explanation
Indices: 39956975--39957026 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
39956965 TGACTTTCTA
39956975 AAAATTATGGAAATACCATTGGTTTAC
1 AAAATTATGGAAATACCATTGGTTTAC
* *
39957002 AAAATTACT-GAAGTACCCTTGGTTT
1 AAAATTA-TGGAAATACCATTGGTTT
39957027 GTAGATTTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (27 bp):
AAAATTATGGAAATACCATTGGTTTAC
Found at i:39958023 original size:52 final size:51
Alignment explanation
Indices: 39957945--39958054 Score: 161
Period size: 52 Copynumber: 2.2 Consensus size: 51
39957935 GAGGAAGTGC
*
39957945 AAAAAGGCTCATGCCCTAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAAGGCTCATGCCCCAGTTTACCGAAAAGGGCTT-TGCCCCAGTTTATTG
* * *
39957997 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTTGCCCCAG-TTGTT-
1 AAAAAGGCTCATGCCCCAGTTTACCGAAAAGGGCTTTGCCCCAGTTTATTG
39958046 AAAAAGGCT
1 AAAAAGGCT
39958055 AGGCATCCAG
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
49 8 0.15
50 4 0.08
51 8 0.15
52 33 0.62
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (51 bp):
AAAAAGGCTCATGCCCCAGTTTACCGAAAAGGGCTTTGCCCCAGTTTATTG
Found at i:39958042 original size:25 final size:26
Alignment explanation
Indices: 39957945--39958042 Score: 144
Period size: 26 Copynumber: 3.8 Consensus size: 26
39957935 GAGGAAGTGC
* * *
39957945 AAAAAGGCTCATGCCCTAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
**
39957971 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
39957997 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
39958023 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
39958043 GTTAAAAAGG
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
25 10 0.15
26 55 0.85
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:39958246 original size:42 final size:42
Alignment explanation
Indices: 39958187--39958278 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
39958177 TAGTCTCCCC
* ** *
39958187 AAATGGGCTTGCATACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
*
39958229 AAATGGGCTTGCATACATCCATTGACATTACATGTGATGTTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
39958271 AAATGGGC
1 AAATGGGC
39958279 CTAAGGGCCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
Found at i:39958379 original size:31 final size:31
Alignment explanation
Indices: 39958302--39958380 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
39958292 CGTTTGCAGT
* * * *
39958302 AAAGGCTTCGGCCTAATGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATAATTTATAA
39958333 AAAGGCTTCGGCCCAGTGATATAATTTATAA
1 AAAGGCTTCGGCCCAGTGATATAATTTATAA
39958364 AAAGGCTTCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
39958381 AACCGTTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.28
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATAATTTATAA
Found at i:39960350 original size:27 final size:27
Alignment explanation
Indices: 39960306--39960450 Score: 184
Period size: 27 Copynumber: 5.4 Consensus size: 27
39960296 ATTTCCAAAG
* *
39960306 TACCCTC-ATTTACAGAATTACTATTT
1 TACCCTCGATTTATAGAATTACCATTT
* *
39960332 TACCCTCGATTTATTGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCATTT
* **
39960359 TATCCTCGATTTATAGAATTATTATTT
1 TACCCTCGATTTATAGAATTACCATTT
*
39960386 TACCCTTGATTTATAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACCATTT
* * *
39960413 TACCCTCGATTTACAAAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCATTT
39960440 TACCCTCGATT
1 TACCCTCGATT
39960451 GTGAAATTAC
Statistics
Matches: 101, Mismatches: 17, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
26 7 0.07
27 94 0.93
ACGTcount: A:0.28, C:0.21, G:0.08, T:0.43
Consensus pattern (27 bp):
TACCCTCGATTTATAGAATTACCATTT
Found at i:39960472 original size:27 final size:26
Alignment explanation
Indices: 39960442--39960584 Score: 85
Period size: 27 Copynumber: 5.3 Consensus size: 26
39960432 TACCGTTTTA
**
39960442 CCCTCGATTGTGAAATTACTGAAATAC
1 CCCT-GATTGTGAAATTACCAAAATAC
*
39960469 CCCT-ATAG-GATAGAATTACCAAAATAC
1 CCCTGATTGTG--A-AATTACCAAAATAC
* *
39960496 CCCTAGTTTGTAAAATTACCAAAATAC
1 CCCT-GATTGTGAAATTACCAAAATAC
* * **
39960523 CACTGGTTTGTGAAATTACTGAAATA-
1 CCCT-GATTGTGAAATTACCAAAATAC
* * *
39960549 CCCTCAATTTATAAAATTACCAAAATAC
1 CCCT-GA-TTGTGAAATTACCAAAATAC
39960577 CCCTGATT
1 CCCTGATT
39960585 TTCAAAGTTA
Statistics
Matches: 88, Mismatches: 20, Indels: 17
0.70 0.16 0.14
Matches are distributed among these distances:
24 1 0.01
25 3 0.03
26 6 0.07
27 71 0.81
28 5 0.06
29 2 0.02
ACGTcount: A:0.38, C:0.22, G:0.10, T:0.29
Consensus pattern (26 bp):
CCCTGATTGTGAAATTACCAAAATAC
Found at i:39960585 original size:27 final size:27
Alignment explanation
Indices: 39960482--39960619 Score: 113
Period size: 27 Copynumber: 5.1 Consensus size: 27
39960472 TATAGGATAG
39960482 AATTACCAAAATACCCCT-AGTTTGTAA
1 AATTACCAAAATACCCCTGA-TTTGTAA
* * *
39960509 AATTACCAAAATACCACTGGTTTGTGA
1 AATTACCAAAATACCCCTGATTTGTAA
** * *
39960536 AATTACTGAAATA-CCCTCAATTTATAA
1 AATTACCAAAATACCCCT-GATTTGTAA
39960563 AATTACCAAAATACCCCTGATTT-TCAA
1 AATTACCAAAATACCCCTGATTTGT-AA
* * *
39960590 AGTTA-CAGAAATACCCTTGACTTTCTAA
1 AATTACCA-AAATACCCCTGA-TTTGTAA
39960618 AA
1 AA
39960620 ATTATGGAAG
Statistics
Matches: 88, Mismatches: 16, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
26 6 0.07
27 71 0.81
28 10 0.11
29 1 0.01
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.30
Consensus pattern (27 bp):
AATTACCAAAATACCCCTGATTTGTAA
Found at i:39960647 original size:28 final size:27
Alignment explanation
Indices: 39960617--39960668 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
39960607 TGACTTTCTA
*
39960617 AAAATTATGGAAGTACCATTGGTTTAC
1 AAAATTATGGAAATACCATTGGTTTAC
* *
39960644 AAAATTATTGAAATACCCTTGGTTT
1 AAAATTATGGAAATACCATTGGTTT
39960669 GTAGATTTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (27 bp):
AAAATTATGGAAATACCATTGGTTTAC
Found at i:39961618 original size:26 final size:26
Alignment explanation
Indices: 39961588--39961735 Score: 221
Period size: 26 Copynumber: 5.8 Consensus size: 26
39961578 GAGGAAGTGC
*
39961588 AAAAGGGCTTATGCCCCAGTTTACCA
1 AAAAGGGCTTATGCCCCAGTTTACCG
**
39961614 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
39961640 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
**
39961666 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
39961692 AAAAGGGCTT-TGCCTCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
39961717 AAAA-GGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
39961736 ATTAAAGAGG
Statistics
Matches: 111, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
24 14 0.13
25 16 0.14
26 81 0.73
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:39961670 original size:52 final size:52
Alignment explanation
Indices: 39961588--39961735 Score: 257
Period size: 52 Copynumber: 2.9 Consensus size: 52
39961578 GAGGAAGTGC
*
39961588 AAAAGGGCTTATGCCCCAGTTTACCAAAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
39961640 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
*
39961692 AAAAGGGCTT-TGCCTCAGTTTACCGAAAA-GGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTT
39961736 ATTAAAGAGG
Statistics
Matches: 94, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
49 10 0.11
50 5 0.05
51 18 0.19
52 61 0.65
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (52 bp):
AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
Found at i:39961939 original size:42 final size:42
Alignment explanation
Indices: 39961880--39961971 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
39961870 TAGTCTCCCC
* ** * *
39961880 AAATGGGCTTGCATACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATACTG
39961922 AAATGGGCTTGCATACATCCATTGACATTACATGTGATACTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATACTG
39961964 AAATGGGC
1 AAATGGGC
39961972 CTAAGGGCCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGATACTG
Found at i:39962030 original size:31 final size:31
Alignment explanation
Indices: 39961995--39962071 Score: 136
Period size: 31 Copynumber: 2.5 Consensus size: 31
39961985 CATTTGCAGT
39961995 AAAGGCTTCGGCCCAATGATATGATTTATGA
1 AAAGGCTTCGGCCCAATGATATGATTTATGA
* *
39962026 AAAGGCTTCGGCCTAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAATGATATGATTTATGA
39962057 AAAGGCTTCGGCCCA
1 AAAGGCTTCGGCCCA
39962072 GTAACCGTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAATGATATGATTTATGA
Found at i:39965188 original size:43 final size:43
Alignment explanation
Indices: 39965117--39965278 Score: 209
Period size: 43 Copynumber: 3.8 Consensus size: 43
39965107 CTTAAATTCA
*
39965117 TTCACCGGCATT-TTGCCTGCTAGGCTCGAAGCCTGATATTAT
1 TTCACCGGCATTATAGCCTGCTAGGCTCGAAGCCTGATATTAT
* * * *
39965159 TTCACCGGCATTATAGCTTGCTAGGCTCGAGGCTTGACATTAT
1 TTCACCGGCATTATAGCCTGCTAGGCTCGAAGCCTGATATTAT
* * * * * *
39965202 TTTACTGGTATTATAACCTGCTAGGCTCGAGGCCCGATATTAT
1 TTCACCGGCATTATAGCCTGCTAGGCTCGAAGCCTGATATTAT
*
39965245 TTCACTGGCATTATAGCCTGCTAGGCTCGAAGCC
1 TTCACCGGCATTATAGCCTGCTAGGCTCGAAGCC
39965279 CGAATGGTAC
Statistics
Matches: 102, Mismatches: 17, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
42 12 0.12
43 90 0.88
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.32
Consensus pattern (43 bp):
TTCACCGGCATTATAGCCTGCTAGGCTCGAAGCCTGATATTAT
Found at i:39978250 original size:30 final size:30
Alignment explanation
Indices: 39978216--39978276 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
39978206 TCCTTAACTC
39978216 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
39978246 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
39978276 A
1 A
39978277 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:39980158 original size:117 final size:117
Alignment explanation
Indices: 39979952--39980188 Score: 456
Period size: 117 Copynumber: 2.0 Consensus size: 117
39979942 TTATAAAATT
*
39979952 TATTTTCCAGACACTGCCCAATCTGTGTACTAGTCGTTTTAGAAATCATATCTTGAGTTTCGTAA
1 TATTTTCCAGACACTGCCCAATCTGTGTACTAGTCGTTTTAAAAATCATATCTTGAGTTTCGTAA
39980017 CTCAAAAATCAGTTTCGTAATTTTTCCCAGAAACTAGACTCATGTACCCATC
66 CTCAAAAATCAGTTTCGTAATTTTTCCCAGAAACTAGACTCATGTACCCATC
39980069 TATTTTCCAGACACTGCCCAATCTGTGTACTAGTCGTTTTAAAAATCATATCTTGAGTTTCGTAA
1 TATTTTCCAGACACTGCCCAATCTGTGTACTAGTCGTTTTAAAAATCATATCTTGAGTTTCGTAA
*
39980134 CTCAAAAATCAGTTTCGTAATTTTTCCCAGAAACTAGACTCATGTGCCCATC
66 CTCAAAAATCAGTTTCGTAATTTTTCCCAGAAACTAGACTCATGTACCCATC
39980186 TAT
1 TAT
39980189 GTATTTTTTT
Statistics
Matches: 118, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
117 118 1.00
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (117 bp):
TATTTTCCAGACACTGCCCAATCTGTGTACTAGTCGTTTTAAAAATCATATCTTGAGTTTCGTAA
CTCAAAAATCAGTTTCGTAATTTTTCCCAGAAACTAGACTCATGTACCCATC
Done.