Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold591
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1432801
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.29
Warning! 160147 characters in sequence are not A, C, G, or T
File 2 of 4
Found at i:8546 original size:15 final size:16
Alignment explanation
Indices: 8526--8556 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
8516 ATTTGCCATG
8526 TTTCTT-TTTTTTTTT
1 TTTCTTCTTTTTTTTT
8541 TTTCTTCTTTTTTTTT
1 TTTCTTCTTTTTTTTT
8557 AAAGTCTACC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (16 bp):
TTTCTTCTTTTTTTTT
Found at i:11683 original size:18 final size:16
Alignment explanation
Indices: 11662--11708 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 16
11652 ATTTAATAAT
11662 ATAAAATGTTATATTAAA
1 ATAAAAT-TT-TATTAAA
*
11680 ATAAAATTTTATTATA
1 ATAAAATTTTATTAAA
11696 AT--AATTTTATTAA
1 ATAAAATTTTATTAA
11709 TTATTATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 10 0.37
16 8 0.30
17 2 0.07
18 7 0.26
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
ATAAAATTTTATTAAA
Found at i:25440 original size:21 final size:21
Alignment explanation
Indices: 25416--25458 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
25406 GCATAGCATT
*
25416 GCATTTAAATCTCATACCATA
1 GCATTGAAATCTCATACCATA
*
25437 GCATTGGAATCTCATACCATA
1 GCATTGAAATCTCATACCATA
25458 G
1 G
25459 TATACAATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.30
Consensus pattern (21 bp):
GCATTGAAATCTCATACCATA
Found at i:28601 original size:12 final size:12
Alignment explanation
Indices: 28584--28610 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
28574 CAAACACGTA
28584 ATTAGATCATAC
1 ATTAGATCATAC
28596 ATTAGATCATAC
1 ATTAGATCATAC
28608 ATT
1 ATT
28611 GGAGGCTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (12 bp):
ATTAGATCATAC
Found at i:33096 original size:21 final size:21
Alignment explanation
Indices: 33050--33090 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
33040 TTTGATAGGC
*
33050 CAAT-GTAATCTTATATAATA
1 CAATAGTAATCTGATATAATA
33070 CAATAGTAATCTGA-ATAATA
1 CAATAGTAATCTGATATAATA
33090 C
1 C
33091 TGATAGACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.34
Consensus pattern (21 bp):
CAATAGTAATCTGATATAATA
Found at i:45057 original size:2 final size:2
Alignment explanation
Indices: 45050--45078 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
45040 TTACTTGTAA
45050 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
45079 NNNNNNNNNN
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:45613 original size:2 final size:2
Alignment explanation
Indices: 45606--45651 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
45596 NNNNNNNNNN
45606 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
45648 TA TA
1 TA TA
45652 AATCGTTTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:52892 original size:18 final size:18
Alignment explanation
Indices: 52869--52903 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
52859 CATACCTTGC
52869 CAAAACAAAAAACAAAAG
1 CAAAACAAAAAACAAAAG
* *
52887 CAAAACCAAAAAGAAAA
1 CAAAACAAAAAACAAAA
52904 TGTAGACCTA
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:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (18 bp):
CAAAACAAAAAACAAAAG
Found at i:54594 original size:3 final size:3
Alignment explanation
Indices: 54588--54646 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
54578 TGTTAATGTA
54588 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
54636 TCT TCT TCT TC
1 TCT TCT TCT TC
54647 AGAATACTGA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:71731 original size:81 final size:80
Alignment explanation
Indices: 71597--71757 Score: 304
Period size: 81 Copynumber: 2.0 Consensus size: 80
71587 TTTTCCGAAA
*
71597 GGTGTCAGGTATAAAAGATTTTTTGTTAAGTTCTAATCTGCTGATTGGAACACTATAATTTTCGC
1 GGTGTCAGGTACAAAAGATTTTTTGTTAAGTTCTAATCTGCTGATTGGAACACTATAATTTTCGC
71662 TATTTCTTGCGTGAT
66 TATTTCTTGCGTGAT
71677 GGTGTCAGGTACAAAAGATTTTTTTGTTAAGTTCTAATCTGCTGATTGGAACACTATAATTTTCG
1 GGTGTCAGGTACAAAAGA-TTTTTTGTTAAGTTCTAATCTGCTGATTGGAACACTATAATTTTCG
71742 CTATTTCTTGCGTGAT
65 CTATTTCTTGCGTGAT
71758 ATATTGAGTT
Statistics
Matches: 79, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
80 17 0.22
81 62 0.78
ACGTcount: A:0.25, C:0.13, G:0.20, T:0.42
Consensus pattern (80 bp):
GGTGTCAGGTACAAAAGATTTTTTGTTAAGTTCTAATCTGCTGATTGGAACACTATAATTTTCGC
TATTTCTTGCGTGAT
Found at i:72385 original size:23 final size:23
Alignment explanation
Indices: 72352--72403 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
72342 GTATGTAGGC
*
72352 CCCGTACATTAAATTCACAATAG
1 CCCGTACATTAAATCCACAATAG
* *
72375 CCCGTATATTAGATCCACAATAG
1 CCCGTACATTAAATCCACAATAG
*
72398 CACGTA
1 CCCGTA
72404 AACCCCTGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.25
Consensus pattern (23 bp):
CCCGTACATTAAATCCACAATAG
Found at i:72841 original size:178 final size:177
Alignment explanation
Indices: 72540--72993 Score: 698
Period size: 178 Copynumber: 2.6 Consensus size: 177
72530 AAAAATACAT
* *
72540 CTTGAGATATATTGACAAAACCTCC-AAAAATAGAGATATTTGTAACAAAAGGCACAAGTAGCTG
1 CTTGAGATATATTGACAAAACCGCCAAAAAATAGAGATATTTGTAACAAAATGCACAAGTAGCTG
* *
72604 ACTACAAAAAGAGAGATATCTGAGTAATTGTGTCGTAATATTATGTGGATGAGTTGAAGGAATGT
66 ACTACATAAAGAGAGATATCTGAGTAATTGTGTCGTAATATTATGTGGATGACTTGAAGGAATGT
* * *
72669 TGATAATAACATGTCTGGCATATATCTTCTATTTAA-A-ATTACAGCTA
131 TGATAATAACAAGACTGGCATATATCTTC-AATTAATACA-TACAGCTA
* *
72716 TTTGAGATATATTGACAAAACCGCCAAAAAATAAAGATATTTGTACACAAAATGCACAAGTAGCT
1 CTTGAGATATATTGACAAAACCGCCAAAAAATAGAGATATTTGTA-ACAAAATGCACAAGTAGCT
* *
72781 GACTACATAAAGAGAGATATGTGAGTAATTGTGTCGTAATATTATGTGGATGACTTGAAGGAGTG
65 GACTACATAAAGAGAGATATCTGAGTAATTGTGTCGTAATATTATGTGGATGACTTGAAGGAATG
** *
72846 TTGATTTTACCAAGACTGGCATATATCTTCAATTAATACATACAGCTA
130 TTGATAATAACAAGACTGGCATATATCTTCAATTAATACATACAGCTA
* *
72894 CTTGAGATATATTGACAAAACCGCCAAAAAATAGAGATATTTGTAACAAAATACACATGTAGCTG
1 CTTGAGATATATTGACAAAACCGCCAAAAAATAGAGATATTTGTAACAAAATGCACAAGTAGCTG
* *
72959 ACTACATAAAGAGAGATATTTGAGTATTTGTGTCG
66 ACTACATAAAGAGAGATATCTGAGTAATTGTGTCG
72994 CAAATAGAAC
Statistics
Matches: 254, Mismatches: 20, Indels: 7
0.90 0.07 0.02
Matches are distributed among these distances:
176 23 0.09
177 74 0.29
178 156 0.61
179 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.30
Consensus pattern (177 bp):
CTTGAGATATATTGACAAAACCGCCAAAAAATAGAGATATTTGTAACAAAATGCACAAGTAGCTG
ACTACATAAAGAGAGATATCTGAGTAATTGTGTCGTAATATTATGTGGATGACTTGAAGGAATGT
TGATAATAACAAGACTGGCATATATCTTCAATTAATACATACAGCTA
Found at i:73136 original size:14 final size:14
Alignment explanation
Indices: 73117--73149 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
73107 TACTTCTCGA
*
73117 AGCCAGTTACTAGT
1 AGCCAGTTACGAGT
73131 AGCCAGTTACGAGT
1 AGCCAGTTACGAGT
73145 AGCCA
1 AGCCA
73150 ACTTTGATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.21
Consensus pattern (14 bp):
AGCCAGTTACGAGT
Found at i:73222 original size:14 final size:14
Alignment explanation
Indices: 73203--73235 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
73193 CTTACTTCTC
73203 GTAGCCAGTTACTA
1 GTAGCCAGTTACTA
73217 GTAGCCAGTTACTA
1 GTAGCCAGTTACTA
73231 GTAGC
1 GTAGC
73236 TAACTTTGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.27
Consensus pattern (14 bp):
GTAGCCAGTTACTA
Found at i:73226 original size:88 final size:88
Alignment explanation
Indices: 73077--73243 Score: 289
Period size: 88 Copynumber: 1.9 Consensus size: 88
73067 CCTTTCATCT
73077 CGTAGCCAGTTACTAGTAGCTAGCTTTTCTTACTTCTCGAAGCCAGTTACTAGTAGCCAGTTACG
1 CGTAGCCAGTTACTAGTAGCTAGCTTTTCTTACTTCTCGAAGCCAGTTACTAGTAGCCAGTTACG
73142 AGTAGCCAACTTTGATTTTATCC
66 AGTAGCCAACTTTGATTTTATCC
* * * *
73165 CGTAGTCAGTTACTAGTAGCTAGGTTTTCTTACTTCTCGTAGCCAGTTACTAGTAGCCAGTTACT
1 CGTAGCCAGTTACTAGTAGCTAGCTTTTCTTACTTCTCGAAGCCAGTTACTAGTAGCCAGTTACG
*
73230 AGTAGCTAACTTTG
66 AGTAGCCAACTTTG
73244 CCTATCTATA
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
88 74 1.00
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.35
Consensus pattern (88 bp):
CGTAGCCAGTTACTAGTAGCTAGCTTTTCTTACTTCTCGAAGCCAGTTACTAGTAGCCAGTTACG
AGTAGCCAACTTTGATTTTATCC
Found at i:74147 original size:2 final size:2
Alignment explanation
Indices: 74142--74182 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
74132 TTTATATACA
74142 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
74183 AATTATTTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:83819 original size:181 final size:180
Alignment explanation
Indices: 83515--84060 Score: 918
Period size: 181 Copynumber: 3.0 Consensus size: 180
83505 GGCTGCCAAA
*
83515 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCA
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCA
*
83580 GATCAATTGTACATAAATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTATCGA
66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTATCGA
* *
83645 AAAAATACCAGCATTTGAACTTAGTCATTTTTTTGGCAAAATATTGCATAT
131 AAAAATACTAGCTTTTGAACTTAGTCA-TTTTTTGGCAAAATATTGCATAT
* *
83696 AGGGTACCCTCATTGTATGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTCCTTTTGCA
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCA
* *
83761 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGGTTTTGATTTCCGATAATTTAT-GA
66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTATCG-
*
83825 AAAAAATACTAGCTTTTGAACTTAGTCATTTTTTGGCAAAATACTGCATAT
130 AAAAAATACTAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
*
83876 AGGGTAACCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCA
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCA
* * *
83941 GATTAATTGTACATATATAAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATTATTTA-CG-
66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTATCGA
* *
84004 AAAAATACTAGCTTTTGAACTTAGTCATTTTTTGGCAAAATGTTGCAAAT
131 AAAAATACTAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
84054 AGGGTAC
1 AGGGTAC
84061 TCCATTTCAC
Statistics
Matches: 342, Mismatches: 21, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
178 53 0.15
180 142 0.42
181 147 0.43
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.36
Consensus pattern (180 bp):
AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCA
GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTATCGA
AAAAATACTAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
Found at i:85623 original size:4 final size:4
Alignment explanation
Indices: 85614--85672 Score: 66
Period size: 4 Copynumber: 14.8 Consensus size: 4
85604 TCTCCATATG
** * *
85614 TTAT TTAT TTAT TTAT TTAT CGAT TTAT TAACT TT-T TCAT TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA-T TTAT TTAT TTAT TTAT
85662 TTAT TTAT TTA
1 TTAT TTAT TTA
85673 CATTCTGTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
3 2 0.04
4 41 0.91
5 2 0.04
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (4 bp):
TTAT
Found at i:87607 original size:2 final size:2
Alignment explanation
Indices: 87600--87673 Score: 121
Period size: 2 Copynumber: 37.0 Consensus size: 2
87590 CACATACAAA
* * *
87600 CT CT CT CT CT CT CT CT TT TT CT CT CT CT TT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
87642 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
87674 TATACATGTA
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
CT
Found at i:95852 original size:21 final size:21
Alignment explanation
Indices: 95824--95893 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 21
95814 CCAAATATTG
95824 ACTG-ACATTGTCTGACATCC
1 ACTGTACATTGTCTGACATCC
* *
95844 ACTGTACATTGACTGTACCT-C
1 ACTGTACATTGTCTG-ACATCC
*
95865 ACTGTACATT-TCACTGACTTCC
1 ACTGTACATTGT--CTGACATCC
95887 ACTGTAC
1 ACTGTAC
95894 CCCACTGTAC
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
20 4 0.10
21 23 0.56
22 14 0.34
ACGTcount: A:0.24, C:0.30, G:0.13, T:0.33
Consensus pattern (21 bp):
ACTGTACATTGTCTGACATCC
Found at i:95870 original size:10 final size:10
Alignment explanation
Indices: 95855--96084 Score: 53
Period size: 10 Copynumber: 21.8 Consensus size: 10
95845 CTGTACATTG
95855 ACTGTACCTC
1 ACTGTACCTC
*
95865 ACTGTACATTTC
1 ACTGTAC--CTC
*
95877 ACTG-ACTTCC
1 ACTGTACCT-C
*
95887 ACTGTACCCC
1 ACTGTACCTC
*
95897 ACTGTACCCC
1 ACTGTACCTC
*
95907 ACTGTACATTTC
1 ACTGTAC--CTC
* **
95919 TACTGAACAGC
1 -ACTGTACCTC
95930 ACTGTATCC-C
1 ACTGTA-CCTC
95940 ACTGTACAC-C
1 ACTGTAC-CTC
*
95950 ACTGTACAGTCC
1 ACTGTAC-CT-C
*
95962 TACTG-ACTTCC
1 -ACTGTACCT-C
*
95973 ACTGTACCCC
1 ACTGTACCTC
95983 ACTGTACAC-C
1 ACTGTAC-CTC
**
95993 ACTGTACAGGGC
1 ACTGTAC--CTC
*
96005 ACTG-ACCAAC
1 ACTGTACC-TC
*
96015 ACTGTACCCC
1 ACTGTACCTC
96025 ACTGTACGC-C
1 ACTGTAC-CTC
*
96035 ACTGTACCGGGC
1 ACTGTACC--TC
96047 ACTG-ACCATC
1 ACTGTACC-TC
*
96057 ACTGTACCCC
1 ACTGTACCTC
**
96067 ACTGTACGGC
1 ACTGTACCTC
96077 ACTGTACC
1 ACTGTACC
96085 ATTAATTTGA
Statistics
Matches: 172, Mismatches: 25, Indels: 46
0.71 0.10 0.19
Matches are distributed among these distances:
9 4 0.02
10 114 0.66
11 24 0.14
12 20 0.12
13 10 0.06
ACGTcount: A:0.24, C:0.38, G:0.14, T:0.24
Consensus pattern (10 bp):
ACTGTACCTC
Found at i:95889 original size:22 final size:21
Alignment explanation
Indices: 95835--95893 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
95825 CTGACATTGT
*
95835 CTGACATCCACTGTACATTGA
1 CTGACATCCACTGTACATTCA
*
95856 CTGTACCT-CACTGTACATTTCA
1 CTG-ACATCCACTGTACA-TTCA
*
95878 CTGACTTCCACTGTAC
1 CTGACATCCACTGTAC
95894 CCCACTGTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
21 15 0.47
22 17 0.53
ACGTcount: A:0.24, C:0.32, G:0.12, T:0.32
Consensus pattern (21 bp):
CTGACATCCACTGTACATTCA
Found at i:95902 original size:42 final size:42
Alignment explanation
Indices: 95855--96083 Score: 221
Period size: 42 Copynumber: 5.4 Consensus size: 42
95845 CTGTACATTG
* *
95855 ACTGTAC-CTCACTGTACATTTCACTGACTTCCACTGTACCCC
1 ACTGTACAC-CACTGTACAGTGCACTGACTTCCACTGTACCCC
* * * ** *
95897 ACTGTACCCCACTGTACATTTCTACTGAAC-AGCACTGTATCCC
1 ACTGTACACCACTGTACAGTGC-ACTG-ACTTCCACTGTACCCC
*
95940 ACTGTACACCACTGTACAGTCCTACTGACTTCCACTGTACCCC
1 ACTGTACACCACTGTACAGTGC-ACTGACTTCCACTGTACCCC
* ***
95983 ACTGTACACCACTGTACAGGGCACTGACCAACACTGTACCCC
1 ACTGTACACCACTGTACAGTGCACTGACTTCCACTGTACCCC
* * * *
96025 ACTGTACGCCACTGTACCGGGCACTGACCAT-CACTGTACCCC
1 ACTGTACACCACTGTACAGTGCACTGA-CTTCCACTGTACCCC
**
96067 ACTGTACGGCACTGTAC
1 ACTGTACACCACTGTAC
96084 CATTAATTTG
Statistics
Matches: 163, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
42 91 0.56
43 70 0.43
44 2 0.01
ACGTcount: A:0.24, C:0.38, G:0.14, T:0.24
Consensus pattern (42 bp):
ACTGTACACCACTGTACAGTGCACTGACTTCCACTGTACCCC
Found at i:96064 original size:22 final size:21
Alignment explanation
Indices: 95992--96064 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 21
95982 CACTGTACAC
*
95992 CACTGTACAGGGCACTGACCAA
1 CACTGTACCGGGCACTGACC-A
*
96014 CACTGTACC--CCACTGTACGC-
1 CACTGTACCGGGCACTG-AC-CA
96034 CACTGTACCGGGCACTGACCA
1 CACTGTACCGGGCACTGACCA
96055 TCACTGTACC
1 -CACTGTACC
96065 CCACTGTACG
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
20 15 0.36
21 4 0.10
22 23 0.55
ACGTcount: A:0.25, C:0.38, G:0.19, T:0.18
Consensus pattern (21 bp):
CACTGTACCGGGCACTGACCA
Found at i:96084 original size:42 final size:43
Alignment explanation
Indices: 95886--96083 Score: 231
Period size: 42 Copynumber: 4.7 Consensus size: 43
95876 CACTGACTTC
* *** * *
95886 CACTGTACCCCACTGTACCCCACTGTACATTTCTACTGAACAG
1 CACTGTACCCCACTGTACACCACTGTACAGGGCTACTGACCAT
* ** *
95929 CACTGTATCCCACTGTACACCACTGTACAGTCCTACTGA-CTT
1 CACTGTACCCCACTGTACACCACTGTACAGGGCTACTGACCAT
*
95971 CCACTGTACCCCACTGTACACCACTGTACAGGGC-ACTGACCAA
1 -CACTGTACCCCACTGTACACCACTGTACAGGGCTACTGACCAT
* *
96014 CACTGTACCCCACTGTACGCCACTGTACCGGGC-ACTGACCAT
1 CACTGTACCCCACTGTACACCACTGTACAGGGCTACTGACCAT
**
96056 CACTGTACCCCACTGTACGGCACTGTAC
1 CACTGTACCCCACTGTACACCACTGTAC
96084 CATTAATTTG
Statistics
Matches: 138, Mismatches: 15, Indels: 5
0.87 0.09 0.03
Matches are distributed among these distances:
42 72 0.52
43 66 0.48
ACGTcount: A:0.24, C:0.38, G:0.15, T:0.22
Consensus pattern (43 bp):
CACTGTACCCCACTGTACACCACTGTACAGGGCTACTGACCAT
Found at i:100357 original size:202 final size:201
Alignment explanation
Indices: 100011--100412 Score: 795
Period size: 202 Copynumber: 2.0 Consensus size: 201
100001 TTGGGGGGGG
100011 GGTCAAAGGATAATTTAATTTTTTTTAAACTTACATAGTACAACTATCCAAAATATGTCTAAGCT
1 GGTCAAAGGATAATTTAATTTTTTTTAAACTTACATAGTACAACTATCCAAAATATGTCTAAGCT
100076 CCCCCAGAAAACAAGTATCCCTGCCCTTTCCCTGGAAAGAATTCTGACCGCCCATGTAATTATTA
66 CCCCCAGAAAACAAGTATCCCTGCCCTTTCCCTGGAAAGAATTCTGACCGCCCATGTAATTATTA
100141 TATGAACTTAAAGAAATAGAAGCCCATTTTATCTCTTGTAAGCAATAGGAAAGAATCAAAACAAA
131 TATGAACTTAAAGAAATAGAAGCCCATTTTATCTCTTGTAAGCAATAGGAAAGAATCAAAACAAA
100206 TCCAGNC
196 TCCAG-C
100213 GGTCAAAGGATAATTTAATTTTTTTTAAACTTACATAGTACAACTATCCAAAATATGTCTAAGCT
1 GGTCAAAGGATAATTTAATTTTTTTTAAACTTACATAGTACAACTATCCAAAATATGTCTAAGCT
100278 CCCCCAGAAAACAAGTATCCCTGCCCTTTCCCTGGAAAGAATTCTGACCGCCCATGTAATTATTA
66 CCCCCAGAAAACAAGTATCCCTGCCCTTTCCCTGGAAAGAATTCTGACCGCCCATGTAATTATTA
100343 TATGAACTTAAAGAAATAGAAGCCCATTTTATCTCTTGTAAGCAATAGGAAAGAATCAAAACAAA
131 TATGAACTTAAAGAAATAGAAGCCCATTTTATCTCTTGTAAGCAATAGGAAAGAATCAAAACAAA
100408 TCCAG
196 TCCAG
100413 ATTTTGGTCT
Statistics
Matches: 200, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
202 200 1.00
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (201 bp):
GGTCAAAGGATAATTTAATTTTTTTTAAACTTACATAGTACAACTATCCAAAATATGTCTAAGCT
CCCCCAGAAAACAAGTATCCCTGCCCTTTCCCTGGAAAGAATTCTGACCGCCCATGTAATTATTA
TATGAACTTAAAGAAATAGAAGCCCATTTTATCTCTTGTAAGCAATAGGAAAGAATCAAAACAAA
TCCAGC
Found at i:100536 original size:10 final size:10
Alignment explanation
Indices: 100523--100736 Score: 105
Period size: 10 Copynumber: 20.1 Consensus size: 10
100513 GTCAGTACCC
100523 TGTACAGTGG
1 TGTACAGTGG
100533 TGTACAGTGG
1 TGTACAGTGG
* *
100543 GGTACAGTGC
1 TGTACAGTGG
*
100553 TGGT-CAGTGCCC
1 T-GTACAGTG--G
*
100565 CGTACAGTGG
1 TGTACAGTGG
100575 TGTACAGTGG
1 TGTACAGTGG
* *
100585 GGTACAGTGC
1 TGTACAGTGG
100595 TGGT-CAGTGGG
1 T-GTACAGT-GG
* *
100606 TAGGTACTGTGC
1 T--GTACAGTGG
*
100618 TGTCCAGTGG
1 TGTACAGTGG
*
100628 AGTACAGTGG
1 TGTACAGTGG
*
100638 AGTACAGTGG
1 TGTACAGTGG
100648 TTATGTACAGTGG
1 ---TGTACAGTGG
*
100661 GGTACAGTGG
1 TGTACAGTGG
100671 -GATACAGT-G
1 TG-TACAGTGG
*
100680 TGGTACAGTAGCTC
1 T-GTACAGT-G--G
100694 TGTACAGTGGG
1 TGTACAGT-GG
100705 TGTACAGTGG
1 TGTACAGTGG
*
100715 ATTTACAGTAGG
1 -TGTACAGT-GG
100727 -GTACAGTGG
1 TGTACAGTGG
100736 T
1 T
100737 TATACAGTAG
Statistics
Matches: 159, Mismatches: 24, Indels: 42
0.71 0.11 0.19
Matches are distributed among these distances:
9 4 0.03
10 97 0.61
11 24 0.15
12 13 0.08
13 20 0.13
14 1 0.01
ACGTcount: A:0.21, C:0.14, G:0.38, T:0.27
Consensus pattern (10 bp):
TGTACAGTGG
Found at i:100603 original size:42 final size:42
Alignment explanation
Indices: 100482--100603 Score: 174
Period size: 42 Copynumber: 2.9 Consensus size: 42
100472 AACATACTAG
* ** * * *
100482 GTACAGTGG-GTTACAGTGGTGTACAGTATTTGTCAGTACCCT
1 GTACAGTGGTG-TACAGTGGGGTACAGTGCTGGTCAGTGCCCC
100524 GTACAGTGGTGTACAGTGGGGTACAGTGCTGGTCAGTGCCCC
1 GTACAGTGGTGTACAGTGGGGTACAGTGCTGGTCAGTGCCCC
100566 GTACAGTGGTGTACAGTGGGGTACAGTGCTGGTCAGTG
1 GTACAGTGGTGTACAGTGGGGTACAGTGCTGGTCAGTG
100604 GGTAGGTACT
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
42 72 0.99
43 1 0.01
ACGTcount: A:0.19, C:0.17, G:0.36, T:0.28
Consensus pattern (42 bp):
GTACAGTGGTGTACAGTGGGGTACAGTGCTGGTCAGTGCCCC
Found at i:100669 original size:43 final size:43
Alignment explanation
Indices: 100523--100739 Score: 167
Period size: 43 Copynumber: 5.0 Consensus size: 43
100513 GTCAGTACCC
* * ***
100523 TGTACAGTGGTGTACAGTGGGGTACAGTGCTGGT-CAGT-GCCC
1 TGTACAGTGGGGTACAGTGGAGTACAGTG-TGGTACAGTGGTTA
* * * *
100565 CGTACAGTGGTGTACAGTGGGGTACAGTGCTGGT-CAGTGGGTA
1 TGTACAGTGGGGTACAGTGGAGTACAGTG-TGGTACAGTGGTTA
* * ** *
100608 GGTACTGTGCTGTCCAGTGGAGTACAGTG-GAGTACAGTGGTTA
1 TGTACAGTGGGGTACAGTGGAGTACAGTGTG-GTACAGTGGTTA
* * *
100651 TGTACAGTGGGGTACAGTGG-GATACAGTGTGGTACAGTAGCTC
1 TGTACAGTGGGGTACAGTGGAG-TACAGTGTGGTACAGTGGTTA
*
100694 TGTACAGTGGGTGTACAGTGGATTTACAGTAG-GGTACAGTGGTTA
1 TGTACAGTGGG-GTACAGTGGA-GTACAGT-GTGGTACAGTGGTTA
100739 T
1 T
100740 ACAGTAGATG
Statistics
Matches: 144, Mismatches: 22, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
41 1 0.01
42 40 0.28
43 75 0.52
44 10 0.07
45 17 0.12
46 1 0.01
ACGTcount: A:0.21, C:0.14, G:0.38, T:0.28
Consensus pattern (43 bp):
TGTACAGTGGGGTACAGTGGAGTACAGTGTGGTACAGTGGTTA
Found at i:103664 original size:19 final size:20
Alignment explanation
Indices: 103630--103674 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
103620 CCGTGTCGCA
*
103630 CCGTGGCCGCCTGTGTAACT
1 CCGTGGCCGACTGTGTAACT
*
103650 CCGTGGCC-ACTGTGTTACT
1 CCGTGGCCGACTGTGTAACT
103669 CCGTGG
1 CCGTGG
103675 ATATCGTTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.09, C:0.33, G:0.31, T:0.27
Consensus pattern (20 bp):
CCGTGGCCGACTGTGTAACT
Found at i:105130 original size:2 final size:2
Alignment explanation
Indices: 105123--105187 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
105113 ACACATACAC
105123 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
105165 AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG A
105188 TTTTACAACT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:106146 original size:2 final size:2
Alignment explanation
Indices: 106139--106187 Score: 82
Period size: 2 Copynumber: 24.5 Consensus size: 2
106129 ATACTGGTAT
106139 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC GT- TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC -TC TC TC TC TC TC
106181 TC TC TC T
1 TC TC TC T
106188 TATATGACGA
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 43 0.96
3 1 0.02
ACGTcount: A:0.00, C:0.47, G:0.02, T:0.51
Consensus pattern (2 bp):
TC
Found at i:107247 original size:19 final size:19
Alignment explanation
Indices: 107223--107262 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
107213 AATTCGTTGA
107223 AATGCTGTATTTTGTACAT
1 AATGCTGTATTTTGTACAT
107242 AATGCTGTATTTTGTACAT
1 AATGCTGTATTTTGTACAT
107261 AA
1 AA
107263 ACATAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.30, C:0.10, G:0.15, T:0.45
Consensus pattern (19 bp):
AATGCTGTATTTTGTACAT
Found at i:111287 original size:21 final size:21
Alignment explanation
Indices: 111261--111357 Score: 117
Period size: 21 Copynumber: 4.7 Consensus size: 21
111251 CAACATACAC
111261 CATAGCATAGCATTGAAATCT
1 CATAGCATAGCATTGAAATCT
*
111282 CATAGCATAGCATTGGAATCT
1 CATAGCATAGCATTGAAATCT
* *
111303 CATACCATAGCATTGGAATCT
1 CATAGCATAGCATTGAAATCT
*
111324 CATACCATAGCA-T-ACAATCT
1 CATAGCATAGCATTGA-AATCT
* *
111344 CATAGAATCGCATT
1 CATAGCATAGCATT
111358 CGTCATATCA
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
20 15 0.22
21 53 0.78
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (21 bp):
CATAGCATAGCATTGAAATCT
Found at i:111540 original size:5 final size:5
Alignment explanation
Indices: 111530--111567 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
111520 GTTCCAGTCT
* *
111530 CATAG CATAG CATAC CATAC CATAC CATAC CATAC CAT
1 CATAC CATAC CATAC CATAC CATAC CATAC CATAC CAT
111568 TAAGCCCTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.39, C:0.34, G:0.05, T:0.21
Consensus pattern (5 bp):
CATAC
Found at i:111613 original size:21 final size:21
Alignment explanation
Indices: 111587--111665 Score: 97
Period size: 21 Copynumber: 3.8 Consensus size: 21
111577 CATTTCAATT
111587 TCTCATAGCATAGCA-TACAAA
1 TCTCATAGCATAGCATTA-AAA
**
111608 TCTCATAGCATATTATTAAAA
1 TCTCATAGCATAGCATTAAAA
*
111629 TCTCATAGCATACCATTAAAA
1 TCTCATAGCATAGCATTAAAA
* *
111650 TTTCATACCATAGCAT
1 TCTCATAGCATAGCAT
111666 AGCATTAAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
21 48 0.96
22 2 0.04
ACGTcount: A:0.41, C:0.22, G:0.06, T:0.32
Consensus pattern (21 bp):
TCTCATAGCATAGCATTAAAA
Found at i:118820 original size:27 final size:30
Alignment explanation
Indices: 118781--118836 Score: 96
Period size: 29 Copynumber: 1.9 Consensus size: 30
118771 GAAAGTTTTC
*
118781 TATATATTTTATAAGTTTT-TATATATAAA
1 TATATATTATATAAGTTTTCTATATATAAA
118810 TATATATTATATAAGTTTTCTATATAT
1 TATATATTATATAAGTTTTCTATATAT
118837 TTTATATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (30 bp):
TATATATTATATAAGTTTTCTATATATAAA
Found at i:118860 original size:47 final size:48
Alignment explanation
Indices: 118773--118869 Score: 135
Period size: 49 Copynumber: 2.0 Consensus size: 48
118763 TTTATAAAGA
* *
118773 AAGTTTTCTATATATTTTATAAGTTTTTATATATAAATATATATTATAT
1 AAGTTTTCTATATATTTTATAAGTTTGTATATAT-AATATACATTATAT
*
118822 AAGTTTTCTATATATTTTATATA-TTTGTATATAT-ATATACATTGTAT
1 AAGTTTTCTATATATTTTATA-AGTTTGTATATATAATATACATTATAT
118869 A
1 A
118870 TTTATATTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
47 12 0.27
49 31 0.70
50 1 0.02
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (48 bp):
AAGTTTTCTATATATTTTATAAGTTTGTATATATAATATACATTATAT
Found at i:122477 original size:7 final size:7
Alignment explanation
Indices: 122465--122538 Score: 85
Period size: 7 Copynumber: 10.6 Consensus size: 7
122455 GAGAAGGATC
122465 ATTCGAG
1 ATTCGAG
*
122472 ATTCGAA
1 ATTCGAG
*
122479 ATACGAG
1 ATTCGAG
*
122486 ATTCGAA
1 ATTCGAG
*
122493 ATACGAG
1 ATTCGAG
*
122500 ATTCGAA
1 ATTCGAG
*
122507 ATACGAG
1 ATTCGAG
122514 ATTCGAG
1 ATTCGAG
*
122521 ATTCGAA
1 ATTCGAG
122528 ATTCGAG
1 ATTCGAG
122535 ATTC
1 ATTC
122539 AATATCTAAA
Statistics
Matches: 53, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
7 53 1.00
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.26
Consensus pattern (7 bp):
ATTCGAG
Found at i:122491 original size:21 final size:21
Alignment explanation
Indices: 122465--122538 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
122455 GAGAAGGATC
* * *
122465 ATTCGAGATTCGAAATACGAG
1 ATTCGAGATTCGAGATTCGAA
* *
122486 ATTCGAAATACGAGATTCGAA
1 ATTCGAGATTCGAGATTCGAA
*
122507 ATACGAGATTCGAGATTCGAA
1 ATTCGAGATTCGAGATTCGAA
122528 ATTCGAGATTC
1 ATTCGAGATTC
122539 AATATCTAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.26
Consensus pattern (21 bp):
ATTCGAGATTCGAGATTCGAA
Found at i:122538 original size:14 final size:14
Alignment explanation
Indices: 122468--122533 Score: 105
Period size: 14 Copynumber: 4.7 Consensus size: 14
122458 AAGGATCATT
122468 CGAGATTCGAAATA
1 CGAGATTCGAAATA
122482 CGAGATTCGAAATA
1 CGAGATTCGAAATA
122496 CGAGATTCGAAATA
1 CGAGATTCGAAATA
* *
122510 CGAGATTCGAGATT
1 CGAGATTCGAAATA
*
122524 CGAAATTCGA
1 CGAGATTCGA
122534 GATTCAATAT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 49 1.00
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.23
Consensus pattern (14 bp):
CGAGATTCGAAATA
Found at i:123041 original size:2 final size:2
Alignment explanation
Indices: 123034--123074 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
123024 TTTACATCGA
123034 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
123075 NNNNNNNNNN
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:125493 original size:7 final size:7
Alignment explanation
Indices: 125478--125544 Score: 89
Period size: 7 Copynumber: 9.6 Consensus size: 7
125468 TTTAGATATT
125478 GAATCTC
1 GAATCTC
*
125485 GAATTTC
1 GAATCTC
125492 GAATCTC
1 GAATCTC
125499 GAATCTC
1 GAATCTC
* *
125506 GTATTTC
1 GAATCTC
125513 GAATCTC
1 GAATCTC
* *
125520 GTATTTC
1 GAATCTC
125527 GAATCTC
1 GAATCTC
125534 GAATCTC
1 GAATCTC
125541 GAAT
1 GAAT
125545 GATCCTTCTC
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 50 1.00
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (7 bp):
GAATCTC
Found at i:125503 original size:21 final size:21
Alignment explanation
Indices: 125478--125544 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
125468 TTTAGATATT
125478 GAATCTCGAATTTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
*
125499 GAATCTCGTATTTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
* * *
125520 GTATTTCGAATCTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
125541 GAAT
1 GAAT
125545 GATCCTTCTC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (21 bp):
GAATCTCGAATTTCGAATCTC
Found at i:126851 original size:25 final size:24
Alignment explanation
Indices: 126804--126852 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
126794 TCAACATCAA
* * *
126804 ACGGTAATACTAAAATCCTGATAC
1 ACGGTAATACAAAAAACCGGATAC
126828 ACGGTAATACAAAAAACTCGGATAC
1 ACGGTAATACAAAAAAC-CGGATAC
126853 TTAATTAGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.45, C:0.20, G:0.14, T:0.20
Consensus pattern (24 bp):
ACGGTAATACAAAAAACCGGATAC
Found at i:127549 original size:8 final size:8
Alignment explanation
Indices: 127536--127570 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
127526 GATCACATTT
127536 TGTCCGTC
1 TGTCCGTC
127544 TGTCCGTC
1 TGTCCGTC
* *
127552 CGTCTGTC
1 TGTCCGTC
127560 TGTCCGTC
1 TGTCCGTC
127568 TGT
1 TGT
127571 AAACTTTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.00, C:0.34, G:0.26, T:0.40
Consensus pattern (8 bp):
TGTCCGTC
Found at i:127554 original size:12 final size:12
Alignment explanation
Indices: 127537--127570 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
127527 ATCACATTTT
127537 GTCCGTCTGTCC
1 GTCCGTCTGTCC
*
127549 GTCCGTCTGTCT
1 GTCCGTCTGTCC
127561 GTCCGTCTGT
1 GTCCGTCTGT
127571 AAACTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.00, C:0.35, G:0.26, T:0.38
Consensus pattern (12 bp):
GTCCGTCTGTCC
Found at i:132282 original size:2 final size:2
Alignment explanation
Indices: 132275--132348 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
132265 ATTGTAAAAG
132275 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
132317 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
132349 TTTCTCTCTT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:133636 original size:1 final size:1
Alignment explanation
Indices: 133632--133672 Score: 73
Period size: 1 Copynumber: 41.0 Consensus size: 1
133622 GGGGGGGGGG
*
133632 CCCCCCCCCCCCCCGCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
133673 TCTAGATCCG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.00, C:0.98, G:0.02, T:0.00
Consensus pattern (1 bp):
C
Found at i:159887 original size:2 final size:2
Alignment explanation
Indices: 159880--159962 Score: 166
Period size: 2 Copynumber: 41.5 Consensus size: 2
159870 GTTGTACTTT
159880 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
159922 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
159963 TTTCATAGTG
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:164111 original size:63 final size:62
Alignment explanation
Indices: 164040--164229 Score: 259
Period size: 63 Copynumber: 3.1 Consensus size: 62
164030 AAAAAAATAA
164040 TAATAATAGGGGAAAAGAAACAAAGCAATAACAATAAGGTCTTCCGTTGGAAACGGAAGACCT
1 TAATAATA-GGGAAAAGAAACAAAGCAATAACAATAAGGTCTTCCGTTGGAAACGGAAGACCT
* *
164103 TAATAATAGTGAAAAAGAAACAAAGCAATAACAAGAAGGTCTTCCGTTGGAAACGGAAGACCT
1 TAATAATAG-GGAAAAGAAACAAAGCAATAACAATAAGGTCTTCCGTTGGAAACGGAAGACCT
* *
164166 TAATAATA-AGAAACAG-TAC---G-AA-AACAATAAGGTCTTCCGTTGGAAACGGAAGACCT
1 TAATAATAGGGAAA-AGAAACAAAGCAATAACAATAAGGTCTTCCGTTGGAAACGGAAGACCT
*
164222 TAAAAATA
1 TAATAATA
164230 AAAACAAAAT
Statistics
Matches: 118, Mismatches: 7, Indels: 11
0.87 0.05 0.08
Matches are distributed among these distances:
56 40 0.34
57 2 0.02
58 1 0.01
61 5 0.04
62 3 0.03
63 67 0.57
ACGTcount: A:0.47, C:0.14, G:0.20, T:0.18
Consensus pattern (62 bp):
TAATAATAGGGAAAAGAAACAAAGCAATAACAATAAGGTCTTCCGTTGGAAACGGAAGACCT
Found at i:164178 original size:56 final size:55
Alignment explanation
Indices: 164117--164237 Score: 174
Period size: 56 Copynumber: 2.2 Consensus size: 55
164107 AATAGTGAAA
*
164117 AAGAAACAAA-GCAATAACAAGAAGGTCTTCCGTTGGAAACGGAAGACCTTAATAAT
1 AAGAAACAAACG-AA-AACAAGAAGGTCTTCCGTTGGAAACGGAAGACCTTAAAAAT
* *
164173 AAGAAACAGTACGAAAACAATAAGGTCTTCCGTTGGAAACGGAAGACCTTAAAAAT
1 AAGAAACA-AACGAAAACAAGAAGGTCTTCCGTTGGAAACGGAAGACCTTAAAAAT
164229 AA-AAACAAA
1 AAGAAACAAA
164238 ATTGATGTTA
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
54 1 0.02
55 5 0.08
56 49 0.83
57 3 0.05
58 1 0.02
ACGTcount: A:0.50, C:0.16, G:0.18, T:0.17
Consensus pattern (55 bp):
AAGAAACAAACGAAAACAAGAAGGTCTTCCGTTGGAAACGGAAGACCTTAAAAAT
Found at i:166837 original size:30 final size:30
Alignment explanation
Indices: 166797--166860 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
166787 TAATAAAATG
* *
166797 TATATGCATCTTATATAAT-TATTAGATGTA
1 TATATACATCTTATA-AATATATAAGATGTA
*
166827 TATATACATCTTATAGATATATAAGATGTA
1 TATATACATCTTATAAATATATAAGATGTA
166857 TATA
1 TATA
166861 AGTCAATTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 2 0.07
30 28 0.93
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (30 bp):
TATATACATCTTATAAATATATAAGATGTA
Found at i:170545 original size:166 final size:165
Alignment explanation
Indices: 170317--170732 Score: 706
Period size: 166 Copynumber: 2.5 Consensus size: 165
170307 GGTCACGATT
* * ** * *
170317 TTTACAATCTTCACTATATATACAACCTTTTGTGTATGTATTGGCATTTTTGGTGAAGTGGTTCT
1 TTTAGAATCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCT
170382 TGAGAAGAAAATTTTTAAACATTTTTCATATGTAGTTCTATGTTAAACTTTGAACCCCGCCTGGG
66 TGAGAAGAAAATTTTTAAACA-TTTTCATATGTAGTTCTATGTTAAACTTTGAACCCCGCCTGGG
* *
170447 GCCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAA
130 GCCACAATTTTGGTCCGAGGGTCACGATTTTTACAA
170483 TTTAGAATCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCT
1 TTTAGAATCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCT
* * *
170548 TGAGAAGAAGATTTTTTAAACATTTTCCTATGTATTTCTATGTTAAACTTTGAACCCCGCCTGGG
66 TGAGAAGAA-AATTTTTAAACATTTTCATATGTAGTTCTATGTTAAACTTTGAACCCCGCCTGGG
170613 GCCACAATTTTGGTCCGAGGGTCACGATTTTTACAA
130 GCCACAATTTTGGTCCGAGGGTCACGATTTTTACAA
170649 TTTAGAATCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCT
1 TTTAGAATCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCT
*
170714 TGAGAAGAAGATTTTTAAA
66 TGAGAAGAAAATTTTTAAA
170733 GACATGCACC
Statistics
Matches: 236, Mismatches: 13, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
165 8 0.03
166 217 0.92
167 11 0.05
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (165 bp):
TTTAGAATCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCT
TGAGAAGAAAATTTTTAAACATTTTCATATGTAGTTCTATGTTAAACTTTGAACCCCGCCTGGGG
CCACAATTTTGGTCCGAGGGTCACGATTTTTACAA
Found at i:170911 original size:4 final size:4
Alignment explanation
Indices: 170902--170947 Score: 67
Period size: 4 Copynumber: 11.8 Consensus size: 4
170892 AAAGTTTACA
* *
170902 GACG GACG GACA GACA GACG GACG GACG GACG GACG GAC- GACG GAC
1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GAC
170948 AACGGGTGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
3 3 0.08
4 36 0.92
ACGTcount: A:0.30, C:0.26, G:0.43, T:0.00
Consensus pattern (4 bp):
GACG
Found at i:170916 original size:12 final size:12
Alignment explanation
Indices: 170899--170952 Score: 67
Period size: 12 Copynumber: 4.7 Consensus size: 12
170889 TGAAAAGTTT
170899 ACAGACGGACGG
1 ACAGACGGACGG
*
170911 ACAGACAGACGG
1 ACAGACGGACGG
*
170923 ACGGACGGACGG
1 ACAGACGGACGG
*
170935 ACGGAC-GACGG
1 ACAGACGGACGG
170946 ACA-ACGG
1 ACAGACGG
170953 GTGATCAGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
10 2 0.05
11 8 0.22
12 27 0.73
ACGTcount: A:0.33, C:0.26, G:0.41, T:0.00
Consensus pattern (12 bp):
ACAGACGGACGG
Found at i:177573 original size:170 final size:169
Alignment explanation
Indices: 177267--178177 Score: 656
Period size: 170 Copynumber: 5.4 Consensus size: 169
177257 ATTTTTACAA
* * *
177267 TTTAAAATCTTCACTATATATACAAGCCTTTGTATAAATTTTGGCATTTCTGAGGCAGTGGTTCT
1 TTTAAAATCTTCACTATATATACTAGCTTTTGTATAAATATTGGCATTTCTGAGGCAGTGGTTCT
* * *
177332 TGAGAAAAAAAA-TTAATTGAACATTTCTCCCACGTAATTC---TATATTAAACTCTGAACCCCG
66 TGAGAAAAAAAATTTAA---AACATTTCTCCCACGTAATTCTAGTATATTTAACTCTCAACCTCG
*
177393 CCTTGGGCCCCAGGATTGGTCCGGGGGGTCACGAGTTTTGAG
128 CCTGGGGCCCCAGGATTGGTCCGGGGGGTCACGAGTTTTGAG
* * * * **
177435 TTTAAAATCTTCGCTATATATATACTAGTTTTTGTATAAATATTGGCTTTTTTGCTGCAGTGGTT
1 TTTAAAATCTTCAC--TATATATACTAGCTTTTGTATAAATATTGGCATTTCTGAGGCAGTGGTT
** * * *
177500 CTTGAGAAAAAAAA-TTAAAACATTTCTCGTATGTATTTCTAGTATATTTAACTTTCAACCTCGC
64 CTTGAGAAAAAAAATTTAAAACATTTCTCCCACGTAATTCTAGTATATTTAACTCTCAACCTCGC
** * ** * * *
177564 CTGGGGCCCCAGTTTTGGTCC-AGGGG-CAATAATTATTACAA
129 CTGGGGCCCCAGGATTGGTCCGGGGGGTCACGAGTT-TT-GAG
*
177605 TTTAAAATCTTCACTATATATAC-AGGCTTTTGTATAAATTTTGGCATTTCTGAGGCAGTGGTTC
1 TTTAAAATCTTCACTATATATACTA-GCTTTTGTATAAATATTGGCATTTCTGAGGCAGTGGTTC
* *
177669 TTGAGAAAAAAAAATTTAATTAAACATTT-TCCCCACATAATTCTATGT-TA---AACTCTGAAT
65 TTGAG-AAAAAAAATTT-A--AAACATTTCT-CCCACGTAATTCTA-GTATATTTAACTCTCAA-
* *
177729 CC-CGCTTTGGGCCCCAGGATTGGTCCGGGGGGTCACGAGTTTTGAG
123 CCTCGCCTGGGGCCCCAGGATTGGTCCGGGGGGTCACGAGTTTTGAG
* ** * * * **
177775 TTCAAAATCTTTGCCATATATACTAG-TTTCTGTATAGATATTGGCTTTTCTGCTGCAGTGGTTC
1 TTTAAAATCTTCACTATATATACTAGCTTT-TGTATAAATATTGGCATTTCTGAGGCAGTGGTTC
* ** * * * * *
177839 TTAAGAAAAAAAATTTAAAACATTTCTCGAATGTATTTCTAGCATGTTTAACTTTCAACCTCGCC
65 TTGAGAAAAAAAATTTAAAACATTTCTCCCACGTAATTCTAGTATATTTAACTCTCAACCTCGCC
** *
177904 TGGGGCCCCAGTTTTGGTCC--GGGGTCACGA-TTTGTACAG
130 TGGGGCCCCAGGATTGGTCCGGGGGGTCACGAGTTT-T-GAG
** * * * **
177943 TTTGCAATCTTTAATATATATACAAGCTTTTTTGTAAATACAATGTACAGGCATTTCTG-GTGCA
1 TTTAAAATCTTCACTATATATACTAGC--TTTTGT--ATA-AA--TATTGGCATTTCTGAG-GCA
* * * ** * * *
178007 ATGGTTCTTGAGAAGAAAAGTTTTGAACATTT-TCCCCACATAATTCTATGT-TA---AACTTTG
58 GTGGTTCTTGAGAAAAAAAATTTAAAACATTTCT-CCCACGTAATTCTA-GTATATTTAACTCTC
* ** *
178067 AACAC-CGCTTGGGGCCCCAGTTTTGGTCC--GGGGTCACGA-TTTTCAGAA
121 AAC-CTCGCCTGGGGCCCCAGGATTGGTCCGGGGGGTCACGAGTTTT--GAG
* ** * * *
178115 TTTAGAATCTTCACCGTATATACAAGCTTTTGTGTAAATATTGGCTTTTCTG-GTGCAGTGGTT
1 TTTAAAATCTTCACTATATATACTAGCTTTTGTATAAATATTGGCATTTCTGAG-GCAGTGGTT
178178 TTTGGGAAGA
Statistics
Matches: 588, Mismatches: 114, Indels: 85
0.75 0.14 0.11
Matches are distributed among these distances:
165 22 0.04
166 21 0.04
167 32 0.05
168 91 0.15
169 55 0.09
170 201 0.34
171 14 0.02
172 77 0.13
173 21 0.04
174 3 0.01
175 50 0.09
176 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (169 bp):
TTTAAAATCTTCACTATATATACTAGCTTTTGTATAAATATTGGCATTTCTGAGGCAGTGGTTCT
TGAGAAAAAAAATTTAAAACATTTCTCCCACGTAATTCTAGTATATTTAACTCTCAACCTCGCCT
GGGGCCCCAGGATTGGTCCGGGGGGTCACGAGTTTTGAG
Found at i:177850 original size:338 final size:333
Alignment explanation
Indices: 177219--178177 Score: 1252
Period size: 338 Copynumber: 2.8 Consensus size: 333
177209 TAACATTTTG
* * *
177219 AACCACGCCTGGGGCCCCAGTTTTTGTCCAGGGCCATAATTTTTACAATTTAAAATCTTCACTAT
1 AACCTCGCCTGGGGCCCCAGTTTTGGTCCAGGGGCATAA-TTTTACAATTTAAAATCTTCACTAT
*
177284 ATATACAAGCCTTTGTATAAATTTTGGCATTTCTGAGGCAGTGGTTCTTGAGAAAAAAAATTAAT
65 ATATACAAGCTTTTGTATAAATTTTGGCATTTCTGAGGCAGTGGTTCTTGAGAAAAAAAATTAAT
* * *
177349 TGAACA-TTTCTCCCACGTAATTCTATATTAAACTCTGAACCCCGCCTTGGGCCCCAGGATTGGT
130 TGAACATTTTC-CCCACATAATTCTATGTTAAACTCTGAA-CCCGCTTTGGGCCCCAGGATTGGT
*
177413 CCGGGGGGTCACGAGTTTTGAGTTTAAAATCTTCGCTATATATATACTAGTTTTTGTATAAATAT
193 CCGGGGGGTCACGAGTTTTGAGTTTAAAATCTTCGC--CATATATACTAG-TTTTGTATAAATAT
* * *
177478 TGGCTTTTTTGCTGCAGTGGTTCTTGAGAAAAAAAA-TTAAAACATTTCTCGTATGTATTTCTAG
255 TGGCTTTTCTGCTGCAGTGGTTCTTAAGAAAAAAAATTTAAAACATTTCTCGAATGTATTTCTAG
*
177542 TATATTTAACTTTC
320 CATATTTAACTTTC
177556 AACCTCGCCTGGGGCCCCAGTTTTGGTCCAGGGGCAATAATTATTACAATTTAAAATCTTCACTA
1 AACCTCGCCTGGGGCCCCAGTTTTGGTCCAGGGGC-ATAATT-TTACAATTTAAAATCTTCACTA
*
177621 TATATACAGGCTTTTGTATAAATTTTGGCATTTCTGAGGCAGTGGTTCTTGAGAAAAAAAAATTT
64 TATATACAAGCTTTTGTATAAATTTTGGCATTTCTGAGGCAGTGGTTCTTGAG-AAAAAAAA-TT
*
177686 AATTAAACATTTTCCCCACATAATTCTATGTTAAACTCTGAATCCCGCTTTGGGCCCCAGGATTG
127 AATTGAACATTTTCCCCACATAATTCTATGTTAAACTCTGAA-CCCGCTTTGGGCCCCAGGATTG
* * *
177751 GTCCGGGGGGTCACGAGTTTTGAGTTCAAAATCTTTGCCATATATACTAGTTTCTGTATAGATAT
191 GTCCGGGGGGTCACGAGTTTTGAGTTTAAAATCTTCGCCATATATACTAGTTT-TGTATAAATAT
177816 TGGCTTTTCTGCTGCAGTGGTTCTTAAGAAAAAAAATTTAAAACATTTCTCGAATGTATTTCTAG
255 TGGCTTTTCTGCTGCAGTGGTTCTTAAGAAAAAAAATTTAAAACATTTCTCGAATGTATTTCTAG
*
177881 CATGTTTAACTTTC
320 CATATTTAACTTTC
** * ** * *
177895 AACCTCGCCTGGGGCCCCAGTTTTGGTCC-GGGGTCACGATTTGTACAGTTTGCAATCTTTAATA
1 AACCTCGCCTGGGGCCCCAGTTTTGGTCCAGGGG-CATAATTT-TACAATTTAAAATCTTCACTA
** * *
177959 TATATACAAGCTTTTTTGTAAATACAATGTACAGGCATTTCTG-GTGCAATGGTTCTTGAGAAGA
64 TATATACAAGC--TTTTGT--ATA-AAT-T-TTGGCATTTCTGAG-GCAGTGGTTCTTGAGAAAA
* * *
178023 AAAGTT--TTGAACATTTTCCCCACATAATTCTATGTTAAACTTTGAACACCGCTTGGGGCCCCA
121 AAAATTAATTGAACATTTTCCCCACATAATTCTATGTTAAACTCTGAAC-CCGCTTTGGGCCCCA
** * * * * *
178086 GTTTTGGTCC--GGGGTCACGA-TTTTCAGAATTTAGAATCTTCACCGTATATACAAGCTTTTGT
185 GGATTGGTCCGGGGGGTCACGAGTTTT--GAGTTTAAAATCTTCGCCATATATACTAG-TTTTGT
* *
178148 GTAAATATTGGCTTTTCTGGTGCAGTGGTT
247 ATAAATATTGGCTTTTCTGCTGCAGTGGTT
178178 TTTGGGAAGA
Statistics
Matches: 554, Mismatches: 47, Indels: 39
0.87 0.07 0.06
Matches are distributed among these distances:
337 38 0.07
338 170 0.31
339 87 0.16
340 152 0.27
341 67 0.12
342 3 0.01
343 5 0.01
344 8 0.01
345 24 0.04
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (333 bp):
AACCTCGCCTGGGGCCCCAGTTTTGGTCCAGGGGCATAATTTTACAATTTAAAATCTTCACTATA
TATACAAGCTTTTGTATAAATTTTGGCATTTCTGAGGCAGTGGTTCTTGAGAAAAAAAATTAATT
GAACATTTTCCCCACATAATTCTATGTTAAACTCTGAACCCGCTTTGGGCCCCAGGATTGGTCCG
GGGGGTCACGAGTTTTGAGTTTAAAATCTTCGCCATATATACTAGTTTTGTATAAATATTGGCTT
TTCTGCTGCAGTGGTTCTTAAGAAAAAAAATTTAAAACATTTCTCGAATGTATTTCTAGCATATT
TAACTTTC
Found at i:178605 original size:13 final size:13
Alignment explanation
Indices: 178587--178611 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
178577 ACTATTGAAG
178587 GTTTTACATACAT
1 GTTTTACATACAT
178600 GTTTTACATACA
1 GTTTTACATACA
178612 GTACATGATA
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:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (13 bp):
GTTTTACATACAT
Found at i:178843 original size:22 final size:22
Alignment explanation
Indices: 178818--178863 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
178808 TATAGGGATA
178818 TAAAATATATT-GATTAAAATAT
1 TAAAATATATTGGA-TAAAATAT
* *
178840 TAAAATGTCTTGGATAAAATAT
1 TAAAATATATTGGATAAAATAT
178862 TA
1 TA
178864 TATTGTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.50, C:0.02, G:0.09, T:0.39
Consensus pattern (22 bp):
TAAAATATATTGGATAAAATAT
Found at i:181113 original size:18 final size:17
Alignment explanation
Indices: 181090--181125 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
181080 CTTAGAACCA
181090 GTGTGTGTGGGAAAGAAC
1 GTGTGTGTGGG-AAGAAC
181108 GTGTGTGTGGGAAGAAC
1 GTGTGTGTGGGAAGAAC
181125 G
1 G
181126 AGCTAAACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.25, C:0.06, G:0.47, T:0.22
Consensus pattern (17 bp):
GTGTGTGTGGGAAGAAC
Found at i:183381 original size:2 final size:2
Alignment explanation
Indices: 183374--183416 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
183364 ATGCACCTAC
183374 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
183416 C
1 C
183417 ACACAACTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:188172 original size:17 final size:17
Alignment explanation
Indices: 188150--188201 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
188140 CCGGTAACGG
*
188150 GACGTTTCGCTCCTACA
1 GACGTTTCGCTCCTAAA
* *
188167 GACGTTTCGC-GCT-GA
1 GACGTTTCGCTCCTAAA
188182 GACGTTTCGCTCCTAAA
1 GACGTTTCGCTCCTAAA
188199 GAC
1 GAC
188202 CTTTTGCGCT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 11 0.38
16 4 0.14
17 14 0.48
ACGTcount: A:0.19, C:0.31, G:0.23, T:0.27
Consensus pattern (17 bp):
GACGTTTCGCTCCTAAA
Found at i:188186 original size:15 final size:15
Alignment explanation
Indices: 188166--188223 Score: 62
Period size: 15 Copynumber: 3.7 Consensus size: 15
188156 TCGCTCCTAC
188166 AGACGTTTCGCGCTG
1 AGACGTTTCGCGCTG
* *
188181 AGACGTTTCGCTCCTAA
1 AGACGTTTCGC-GCT-G
* *
188198 AGACCTTTTGCGCTG
1 AGACGTTTCGCGCTG
188213 AGACGTTTCGC
1 AGACGTTTCGC
188224 ACTTATATTA
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
15 20 0.61
16 4 0.12
17 9 0.27
ACGTcount: A:0.17, C:0.28, G:0.26, T:0.29
Consensus pattern (15 bp):
AGACGTTTCGCGCTG
Found at i:188191 original size:32 final size:32
Alignment explanation
Indices: 188150--188223 Score: 121
Period size: 32 Copynumber: 2.3 Consensus size: 32
188140 CCGGTAACGG
* *
188150 GACGTTTCGCTCCTACAGACGTTTCGCGCTGA
1 GACGTTTCGCTCCTAAAGACCTTTCGCGCTGA
*
188182 GACGTTTCGCTCCTAAAGACCTTTTGCGCTGA
1 GACGTTTCGCTCCTAAAGACCTTTCGCGCTGA
188214 GACGTTTCGC
1 GACGTTTCGC
188224 ACTTATATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.16, C:0.30, G:0.24, T:0.30
Consensus pattern (32 bp):
GACGTTTCGCTCCTAAAGACCTTTCGCGCTGA
Found at i:189609 original size:2 final size:2
Alignment explanation
Indices: 189602--189665 Score: 92
Period size: 2 Copynumber: 32.0 Consensus size: 2
189592 GTAATAATGT
*
189602 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA CA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* * *
189644 GA CA GA CA CA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA
189666 TTACATGTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.06, G:0.44, T:0.00
Consensus pattern (2 bp):
GA
Found at i:189840 original size:2 final size:2
Alignment explanation
Indices: 189776--189825 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
189766 AAGAATAGGT
189776 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
189818 GA GA GA GA
1 GA GA GA GA
189826 TTACATCTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:193029 original size:2 final size:2
Alignment explanation
Indices: 193022--193063 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
193012 TCAAAGCTGG
193022 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
193064 AATCTCTTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:197400 original size:20 final size:21
Alignment explanation
Indices: 197361--197400 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
197351 TTGATTTTAA
197361 TTTTTCTTTGTTAACTAATTT
1 TTTTTCTTTGTTAACTAATTT
* *
197382 TTTTTTTTTTTTAAC-AATT
1 TTTTTCTTTGTTAACTAATT
197401 CTAGAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.20, C:0.07, G:0.03, T:0.70
Consensus pattern (21 bp):
TTTTTCTTTGTTAACTAATTT
Found at i:201163 original size:32 final size:32
Alignment explanation
Indices: 201122--201191 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
201112 CTAGCCATCT
201122 TTCCCCCCGGAAAAATGGCTATATAGCAGTTC
1 TTCCCCCCGGAAAAATGGCTATATAGCAGTTC
*
201154 TTCCCCCCGGAAAAATGGCTATATAGCAGTTT
1 TTCCCCCCGGAAAAATGGCTATATAGCAGTTC
201186 TTCCCC
1 TTCCCC
201192 TAGGGAAAGC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.27
Consensus pattern (32 bp):
TTCCCCCCGGAAAAATGGCTATATAGCAGTTC
Found at i:201209 original size:33 final size:32
Alignment explanation
Indices: 201122--201212 Score: 101
Period size: 32 Copynumber: 2.8 Consensus size: 32
201112 CTAGCCATCT
* *
201122 TTCCCCCCGGAAAAATGGCTATATAGCAGTTC
1 TTCCCCACGGAAAAATGACTATATAGCAGTTC
* * *
201154 TTCCCCCCGGAAAAATGGCTATATAGCAGTTT
1 TTCCCCACGGAAAAATGACTATATAGCAGTTC
* **
201186 TTCCCCTAGGGAAAGCTGACTATATAG
1 TTCCCC-ACGGAAAAATGACTATATAG
201213 TGGGCTTTCC
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
32 37 0.71
33 15 0.29
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (32 bp):
TTCCCCACGGAAAAATGACTATATAGCAGTTC
Found at i:208974 original size:177 final size:177
Alignment explanation
Indices: 208663--208983 Score: 441
Period size: 177 Copynumber: 1.8 Consensus size: 177
208653 GCGTCCGGAC
* *
208663 CTGGTTAAAGTTTTTGTTGCAGGTGCCCTTTGATAGCAATATCTAAGTTACTGCAGGTCCGTACT
1 CTGGTTAAAGTTTTTGTTGCAGGTGCCCTCTGATAGCAATATCTAAGTTACTACAGGTCCGTACT
*** * * * * *
208728 TCACCAAACTTGCATTGATGGTGTGTCTTATGATACTGATGCACCAGGCAGGCTTGGATGCTGAA
66 TCACCAAACGCCCATGGATGGTGTGTCTTATGATACAGATGCACCAGACAGGCATGGATGCTCAA
*
208793 TCTGAGCTATAGGTTACAGATGCTGAAGGAGGTCAAGGTTTTTAGAG
131 TCTGAGCCATAGGTTACAGATGCTGAAGGAGGTCAAGGTTTTTAGAG
* **
208840 CTGGTTAAAGTTTTTGTTGCAGGTGCCCTCTGAT-G-ATTATATCTTAGTTACTACTTGTCC-TA
1 CTGGTTAAAGTTTTTGTTGCAGGTGCCCTCTGATAGCA--ATATCTAAGTTACTACAGGTCCGT-
* * *
208902 ACTTCACCAGACGCCCATGGATGGTGTGTCTTATGATACAGATGCACCTGACAGGCATGGATGTT
63 ACTTCACCAAACGCCCATGGATGGTGTGTCTTATGATACAGATGCACCAGACAGGCATGGATGCT
208967 CAATCTGAGCCATAGGT
128 CAATCTGAGCCATAGGT
208984 CGCGGATGCT
Statistics
Matches: 124, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
175 1 0.01
176 2 0.02
177 121 0.98
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.33
Consensus pattern (177 bp):
CTGGTTAAAGTTTTTGTTGCAGGTGCCCTCTGATAGCAATATCTAAGTTACTACAGGTCCGTACT
TCACCAAACGCCCATGGATGGTGTGTCTTATGATACAGATGCACCAGACAGGCATGGATGCTCAA
TCTGAGCCATAGGTTACAGATGCTGAAGGAGGTCAAGGTTTTTAGAG
Found at i:209845 original size:17 final size:18
Alignment explanation
Indices: 209798--209853 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 18
209788 GATATTGCAA
209798 AATATAATATTGTATCCCAT
1 AATATAATATTGTA--CCAT
*
209818 AATACAATATTGTA-CAT
1 AATATAATATTGTACCAT
* *
209835 TATATAATATTGTATCAT
1 AATATAATATTGTACCAT
209853 A
1 A
209854 CGATATTGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
17 15 0.48
18 3 0.10
20 13 0.42
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (18 bp):
AATATAATATTGTACCAT
Found at i:209861 original size:15 final size:15
Alignment explanation
Indices: 209841--209875 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
209831 ACATTATATA
*
209841 ATATTGTATCATACG
1 ATATTGTATAATACG
*
209856 ATATTGTATAATATG
1 ATATTGTATAATACG
209871 ATATT
1 ATATT
209876 AGTTTCTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.46
Consensus pattern (15 bp):
ATATTGTATAATACG
Found at i:210267 original size:15 final size:15
Alignment explanation
Indices: 210249--210371 Score: 62
Period size: 15 Copynumber: 8.3 Consensus size: 15
210239 ATATTGCAAA
210249 ATATAATATTGTATC
1 ATATAATATTGTATC
*
210264 ATATGATACAATATGTAT-
1 ATAT-A-A-TAT-TGTATC
210282 AGTATAATATTGTATC
1 A-TATAATATTGTATC
**
210298 ATATTTTACTT-TATC
1 ATATAATA-TTGTATC
*
210313 AAATAATATTGTATC
1 ATATAATATTGTATC
* *
210328 ATTTGATA-TG----
1 ATATAATATTGTATC
* *
210338 ATACAATGTTGTATC
1 ATATAATATTGTATC
*
210353 AAATAATATTGTATC
1 ATATAATATTGTATC
210368 ATAT
1 ATAT
210372 GATACAATAT
Statistics
Matches: 77, Mismatches: 18, Indels: 26
0.64 0.15 0.21
Matches are distributed among these distances:
10 4 0.05
11 2 0.03
14 4 0.05
15 47 0.61
16 6 0.08
17 2 0.03
18 4 0.05
19 8 0.10
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.45
Consensus pattern (15 bp):
ATATAATATTGTATC
Found at i:210809 original size:16 final size:15
Alignment explanation
Indices: 210779--210824 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
210769 ATTTTATATG
210779 ATAAAGGTG-GTCTC
1 ATAAAGGTGAGTCTC
210793 ATAAAGGTGAAGTCTC
1 ATAAAGGTG-AGTCTC
*
210809 ATAAGGGTGATGTCTC
1 ATAAAGGTGA-GTCTC
210825 GTCTCGGTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 9 0.32
15 1 0.04
16 18 0.64
ACGTcount: A:0.30, C:0.13, G:0.28, T:0.28
Consensus pattern (15 bp):
ATAAAGGTGAGTCTC
Found at i:213664 original size:2 final size:2
Alignment explanation
Indices: 213657--213701 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
213647 TCAAAGCTGG
213657 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
213699 TC T
1 TC T
213702 TCATATATAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:217437 original size:54 final size:54
Alignment explanation
Indices: 217370--217482 Score: 217
Period size: 54 Copynumber: 2.1 Consensus size: 54
217360 TTGAATCAAA
*
217370 ATTTTGAGTGGTAGGGTGGGGCCACATTGGGGATCTAGTTGTACAAAGGAAGTC
1 ATTTTGAGGGGTAGGGTGGGGCCACATTGGGGATCTAGTTGTACAAAGGAAGTC
217424 ATTTTGAGGGGTAGGGTGGGGCCACATTGGGGATCTAGTTGTACAAAGGAAGTC
1 ATTTTGAGGGGTAGGGTGGGGCCACATTGGGGATCTAGTTGTACAAAGGAAGTC
217478 ATTTT
1 ATTTT
217483 AATTATTCAC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.24, C:0.11, G:0.36, T:0.29
Consensus pattern (54 bp):
ATTTTGAGGGGTAGGGTGGGGCCACATTGGGGATCTAGTTGTACAAAGGAAGTC
Found at i:219344 original size:1 final size:1
Alignment explanation
Indices: 219340--219370 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
219330 GGGGGGTTTG
219340 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
219371 GGGGGGGGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:219415 original size:47 final size:45
Alignment explanation
Indices: 219290--219417 Score: 157
Period size: 47 Copynumber: 2.8 Consensus size: 45
219280 GATTTAGTTT
*
219290 TTTGTTTTTGTTTATGTTCTTTTTTTTTTTTTTTGGGGGGGGGGGG
1 TTTGTTTTTGTTTTTGTT-TTTTTTTTTTTTTTTGGGGGGGGGGGG
* * *
219336 TTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGGGGGGGGGTG
1 TTTG--TTTTTGTTTTTGTTTTTTTTTTTTTTTTTGGGGGGGGGGGG
* * *
219383 TTTGTTTTTGTTTTTCGTGTTTTGTTTCTTTTTTG
1 TTTGTTTTTGTTTTT-GTTTTTTTTTTTTTTTTTG
219418 TGCCGATTTA
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
45 10 0.14
46 19 0.27
47 30 0.43
48 11 0.16
ACGTcount: A:0.01, C:0.02, G:0.26, T:0.71
Consensus pattern (45 bp):
TTTGTTTTTGTTTTTGTTTTTTTTTTTTTTTTTGGGGGGGGGGGG
Found at i:219884 original size:16 final size:16
Alignment explanation
Indices: 219863--219925 Score: 90
Period size: 16 Copynumber: 3.9 Consensus size: 16
219853 AATGCCGGGC
*
219863 GTCCGTCCGTCCGTGT
1 GTCCGTGCGTCCGTGT
*
219879 GTCCGTGGGTCCGTGT
1 GTCCGTGCGTCCGTGT
*
219895 GTCCGTGGGTCCGTGT
1 GTCCGTGCGTCCGTGT
*
219911 GTCCGTGTGTCCGTG
1 GTCCGTGCGTCCGTG
219926 CGTCTGTCCG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.00, C:0.29, G:0.40, T:0.32
Consensus pattern (16 bp):
GTCCGTGCGTCCGTGT
Found at i:219937 original size:8 final size:8
Alignment explanation
Indices: 219871--219925 Score: 92
Period size: 8 Copynumber: 6.9 Consensus size: 8
219861 GCGTCCGTCC
219871 GTCCGTGT
1 GTCCGTGT
*
219879 GTCCGTGG
1 GTCCGTGT
219887 GTCCGTGT
1 GTCCGTGT
*
219895 GTCCGTGG
1 GTCCGTGT
219903 GTCCGTGT
1 GTCCGTGT
219911 GTCCGTGT
1 GTCCGTGT
219919 GTCCGTG
1 GTCCGTG
219926 CGTCTGTCCG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 43 1.00
ACGTcount: A:0.00, C:0.25, G:0.42, T:0.33
Consensus pattern (8 bp):
GTCCGTGT
Found at i:220236 original size:172 final size:172
Alignment explanation
Indices: 219950--220770 Score: 1365
Period size: 172 Copynumber: 4.8 Consensus size: 172
219940 ACTTTTTTGT
* * *
219950 AAGCGCTCTGATGCCTACAAATTTTGACGGATTTTCATTTAATTTATACCAAATGTTTATAACAC
1 AAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATACCAC
* * * *
220015 TATTACTTTGGTCAAGTTCGAAAATCAGCATTTGTCGATACTTTTTGTTGGAGTTATGGGGCTTT
66 TATTACCTTGGTCAAGTTCGAAAATCAGCATTAGTCGATACTTTTTGTTGGCGTTATGGGACTTT
***
220080 GAGTGCAATAATGACTCCGTTTTATCCAAAAATTGACCTTGG
131 GACCACAATAATGACTCCGTTTTATCCAAAAATTGACCTTGG
* *
220122 AAGCGCTCTCATGCCTACAAATTTTGACAGATTTTCATTAAATTTATACCAAATGTTTATACTAC
1 AAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATACCAC
* *
220187 TATTACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGCGTTATTGGACTTT
66 TATTACCTTGGTCAAGTTCGAAAATCAGCATTAGTCGATACTTTTTGTTGGCGTTATGGGACTTT
* *
220252 GACCACAATCATGACTCCGTTTTACCCAAAAATTGACCTTGTG
131 GACCACAATAATGACTCCGTTTTATCCAAAAATTGACCTTG-G
220295 -AGCGCTCTCATGCCTACAAATTTTGACGGATTTTTCATTAAATTTATACCAAATGTTTATACCA
1 AAGCGCTCTCATGCCTACAAATTTTGACGGA-TTTTCATTAAATTTATACCAAATGTTTATACCA
*
220359 TTATTACCTTGGTCAAGTTCGAAAATCAGCATTAGTCGATACTTTTTGTTGGCGTTATGGGACTT
65 CTATTACCTTGGTCAAGTTCGAAAATCAGCATTAGTCGATACTTTTTGTTGGCGTTATGGGACTT
* * *
220424 TGACTACAATCATGACTCCGTTTTATCCAAAAATTGACCTTGT
130 TGACCACAATAATGACTCCGTTTTATCCAAAAATTGACCTTGG
* *
220467 AAGCGTTCTTATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATACCAC
1 AAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATACCAC
*
220532 TATTACCTTGGTCAAGTTCGAAAATCAGCGTTAGTCGATACTTTTTGTTGGCGTTATGGGACTTT
66 TATTACCTTGGTCAAGTTCGAAAATCAGCATTAGTCGATACTTTTTGTTGGCGTTATGGGACTTT
220597 GACCACAATAATGACTCCGTTTTATCCAAAAATTGACCTTGG
131 GACCACAATAATGACTCCGTTTTATCCAAAAATTGACCTTGG
*
220639 AAGCGCTCTCATGCCTACAAATTTTGACAGATTTTCATTAAATTTATACCAAATGTTTATACCAC
1 AAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATACCAC
* * * *
220704 TAATACTTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGACTTT
66 TATTACCTTGGTCAAGTTCGAAAATCAGCATTAGTCGATACTTTTTGTTGGCGTTATGGGACTTT
220769 GA
131 GA
220771 NNNNNNNNNN
Statistics
Matches: 608, Mismatches: 38, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
172 445 0.73
173 163 0.27
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.37
Consensus pattern (172 bp):
AAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATACCAC
TATTACCTTGGTCAAGTTCGAAAATCAGCATTAGTCGATACTTTTTGTTGGCGTTATGGGACTTT
GACCACAATAATGACTCCGTTTTATCCAAAAATTGACCTTGG
Found at i:220613 original size:345 final size:344
Alignment explanation
Indices: 219946--220770 Score: 1400
Period size: 345 Copynumber: 2.4 Consensus size: 344
219936 TCACACTTTT
* * *
219946 TTGTAAGCGCTCTGATGCCTACAAATTTTGACGGATTTTCATTTAATTTATACCAAATGTTTATA
1 TTGTGAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA
* * *
220011 ACACTATTACTTTGGTCAAGTTCGAAAATCAGCATTTGTCGATACTTTTTGTTGGAGTTATGGGG
66 CCACTATTACTTTGGTCAAGTTCGAAAATCAGCATTAGTCGATACTTTTTGTTGGAGTTATGGGA
* *
220076 CTTTGAGTGCAATAATGACTCCGTTTTATCCAAAAATTGACCTTGGAAGCGCTCTCATGCCTACA
131 CTTTGACTACAATAATGACTCCGTTTTATCCAAAAATTGACCTTGGAAGCGCTCTCATGCCTACA
*
220141 AATTTTGACAGATTTTCATTAAATTTATACCAAATGTTTATACTACTATTACCTTGGTCAAGTTC
196 AATTTTGACAGATTTTCATTAAATTTATACCAAATGTTTATACCACTATTACCTTGGTCAAGTTC
* * *
220206 GAAAATCAGCATTGGTCGATACTTTTTGTTGGCGTTATTGGACTTTGACCACAATCATGACTCCG
261 GAAAATCAGCATTAGTCGATACTTTTTGTTGGCGTTATGGGACTTTGACCACAATAATGACTCCG
220271 TTTTACCCAAAAATTGACC
326 TTTTACCCAAAAATTGACC
220290 TTGTGAGCGCTCTCATGCCTACAAATTTTGACGGATTTTTCATTAAATTTATACCAAATGTTTAT
1 TTGTGAGCGCTCTCATGCCTACAAATTTTGACGGA-TTTTCATTAAATTTATACCAAATGTTTAT
* * *
220355 ACCATTATTACCTTGGTCAAGTTCGAAAATCAGCATTAGTCGATACTTTTTGTTGGCGTTATGGG
65 ACCACTATTACTTTGGTCAAGTTCGAAAATCAGCATTAGTCGATACTTTTTGTTGGAGTTATGGG
* * * *
220420 ACTTTGACTACAATCATGACTCCGTTTTATCCAAAAATTGACCTTGTAAGCGTTCTTATGCCTAC
130 ACTTTGACTACAATAATGACTCCGTTTTATCCAAAAATTGACCTTGGAAGCGCTCTCATGCCTAC
*
220485 AAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATACCACTATTACCTTGGTCAAGTT
195 AAATTTTGACAGATTTTCATTAAATTTATACCAAATGTTTATACCACTATTACCTTGGTCAAGTT
*
220550 CGAAAATCAGCGTTAGTCGATACTTTTTGTTGGCGTTATGGGACTTTGACCACAATAATGACTCC
260 CGAAAATCAGCATTAGTCGATACTTTTTGTTGGCGTTATGGGACTTTGACCACAATAATGACTCC
*
220615 GTTTTATCCAAAAATTGACC
325 GTTTTACCCAAAAATTGACC
*
220635 TTG-GAAGCGCTCTCATGCCTACAAATTTTGACAGATTTTCATTAAATTTATACCAAATGTTTAT
1 TTGTG-AGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTAT
* *
220699 ACCACTAATACTTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGG
65 ACCACTATTACTTTGGTCAAGTTCGAAAATCAGCATTAGTCGATACTTTTTGTTGGAGTTATGGG
220764 ACTTTGA
130 ACTTTGA
220771 NNNNNNNNNN
Statistics
Matches: 451, Mismatches: 28, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
344 130 0.29
345 321 0.71
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.37
Consensus pattern (344 bp):
TTGTGAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA
CCACTATTACTTTGGTCAAGTTCGAAAATCAGCATTAGTCGATACTTTTTGTTGGAGTTATGGGA
CTTTGACTACAATAATGACTCCGTTTTATCCAAAAATTGACCTTGGAAGCGCTCTCATGCCTACA
AATTTTGACAGATTTTCATTAAATTTATACCAAATGTTTATACCACTATTACCTTGGTCAAGTTC
GAAAATCAGCATTAGTCGATACTTTTTGTTGGCGTTATGGGACTTTGACCACAATAATGACTCCG
TTTTACCCAAAAATTGACC
Found at i:224281 original size:12 final size:12
Alignment explanation
Indices: 224260--224304 Score: 81
Period size: 12 Copynumber: 3.8 Consensus size: 12
224250 AGTGTCACCG
224260 CCTCTGTATCCT
1 CCTCTGTATCCT
*
224272 CCTCTATATCCT
1 CCTCTGTATCCT
224284 CCTCTGTATCCT
1 CCTCTGTATCCT
224296 CCTCTGTAT
1 CCTCTGTAT
224305 TGACCTTGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.11, C:0.40, G:0.07, T:0.42
Consensus pattern (12 bp):
CCTCTGTATCCT
Found at i:228375 original size:12 final size:12
Alignment explanation
Indices: 228354--228401 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
228344 AAAGAAAATC
*
228354 TCTGATTCATCA
1 TCTGAATCATCA
228366 TCTGAATCATCA
1 TCTGAATCATCA
* *
228378 TCTGCATCGTCA
1 TCTGAATCATCA
*
228390 TCTGTATCATCA
1 TCTGAATCATCA
228402 GTCCTTTCTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.25, C:0.27, G:0.10, T:0.38
Consensus pattern (12 bp):
TCTGAATCATCA
Found at i:229076 original size:34 final size:34
Alignment explanation
Indices: 229037--229367 Score: 287
Period size: 34 Copynumber: 9.7 Consensus size: 34
229027 AACAACAACC
* ** *
229037 GAACAGCTATATCATGATTGATACACTACTACTA
1 GAACAGCTATATCAGGGCTGATACACTACTACCA
* *
229071 GAACAGCTATAT-ATGGGCTGATACATTTCTACCA
1 GAACAGCTATATCA-GGGCTGATACACTACTACCA
* * * *
229105 -AATCAGCTATACCAGAGCTGATTCATTACTACCA
1 GAA-CAGCTATATCAGGGCTGATACACTACTACCA
*
229139 GAACAGCTATATCAGGGCTGATACACTACTGCCA
1 GAACAGCTATATCAGGGCTGATACACTACTACCA
* * * *
229173 TAACAGCAATAGCAGGGCTGATACACTACTACTA
1 GAACAGCTATATCAGGGCTGATACACTACTACCA
* * * * *
229207 -AACCAGTTA-AGTCAAGGCTTATATACTACTATCA
1 GAA-CAGCTATA-TCAGGGCTGATACACTACTACCA
* * *
229241 AAACAGCTTTATCAGGGCTGATACACTATTACCA
1 GAACAGCTATATCAGGGCTGATACACTACTACCA
* * *
229275 AAACAGCTATATCATGGCTGATACATTACTACCA
1 GAACAGCTATATCAGGGCTGATACACTACTACCA
* * * * *
229309 CG-TCATCTTTATCAGGACTGATACAATA-TCACCA
1 -GAACAGCTATATCAGGGCTGATACACTACT-ACCA
229343 GAACAGCTATATCAGGGCTGATACA
1 GAACAGCTATATCAGGGCTGATACA
229368 TCGCTACCAT
Statistics
Matches: 236, Mismatches: 50, Indels: 22
0.77 0.16 0.07
Matches are distributed among these distances:
33 8 0.03
34 222 0.94
35 6 0.03
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (34 bp):
GAACAGCTATATCAGGGCTGATACACTACTACCA
Found at i:233681 original size:2 final size:2
Alignment explanation
Indices: 233674--233710 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
233664 TAAAAATTAT
233674 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
233711 CGTTAATTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:234623 original size:135 final size:136
Alignment explanation
Indices: 234463--234743 Score: 349
Period size: 135 Copynumber: 2.1 Consensus size: 136
234453 TAGACTCCTG
* * *
234463 ACCCCTAAACCATATATATTCTTGTTC-CTTGTGTT-AAGTGGCATCAAATAGTATGTAGGCCAT
1 ACCCCTAAACCATATATATTATTGTTCTC-TGTGTTAAAG-GCCATCAAATAGTATGAAGGCCAT
** *
234526 GGG-CCTCGGGGGTGGTCCT-G-TCCCACCTCAAACAGAAAGTGC-CAGAATATCTTGAAAACGG
64 GGGCCCT-GGGACTGGT-CTGGACCCCACCTCAAACAGAAAGTGCACA-AATATCTTGAAAACGG
*
234587 TTAAAAACCCT
126 TTAAAAACCCC
* *
234598 ACCCCTAAACCATATATATTATTGTTCTCTGTGTTAAAGGCCATCAAATGGTATGAAGGTCATGG
1 ACCCCTAAACCATATATATTATTGTTCTCTGTGTTAAAGGCCATCAAATAGTATGAAGGCCATGG
* * * *
234663 GCCCTGGGACTGGTCTGGACCCCATCTCAAACAGGAAGTGCACATATATCTTGAAAACGGTTAAT
66 GCCCTGGGACTGGTCTGGACCCCACCTCAAACAGAAAGTGCACAAATATCTTGAAAACGGTTAAA
*
234728 ATCCCC
131 AACCCC
234734 ACCCCTAAAC
1 ACCCCTAAAC
234744 TTGAAACCCG
Statistics
Matches: 126, Mismatches: 14, Indels: 11
0.83 0.09 0.07
Matches are distributed among these distances:
134 2 0.02
135 63 0.50
136 59 0.47
137 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.26
Consensus pattern (136 bp):
ACCCCTAAACCATATATATTATTGTTCTCTGTGTTAAAGGCCATCAAATAGTATGAAGGCCATGG
GCCCTGGGACTGGTCTGGACCCCACCTCAAACAGAAAGTGCACAAATATCTTGAAAACGGTTAAA
AACCCC
Found at i:235141 original size:135 final size:133
Alignment explanation
Indices: 234946--235283 Score: 401
Period size: 135 Copynumber: 2.5 Consensus size: 133
234936 GCCTTAAGGG
* * * *
234946 TGGTCCGGACCCCCCTCAAACAAGAAGGGCCAATATATCTAGAAAACGGTTAAGAACCCCACCCC
1 TGGTCCTGACCCCCCTCAAACAAGAAGTGCCAA-ATATCTTGAAAACGGTTAAGATCCCCACCCC
* ** *
235011 TAAACCATATATATTGTTGTTCCTTGTGTCAAGGGGCATCA-TATGGTATATAGGTCATGGGTCC
65 TAAACCATATAT-TTCTTGTTCCTTGTGTCAAGACGCATCACT-TGGTATATAAGTCATGGGTCC
235075 CGGAGA
128 CGGAGA
* * * * *
235081 TGGTCCTGACCCCCCTCAAACAGGAAGTGCACAAATAACTTGAACACGGTTGAGATCCCCAACCC
1 TGGTCCTGACCCCCCTCAAACAAGAAGTGC-CAAATATCTTGAAAACGGTTAAGATCCCCACCCC
* *
235146 TAAACCATATATTTCTTGTTCCTTGTGTCAAGACGCATCACTTGGTATGTAAGTCATGGGTCCTG
65 TAAACCATATATTTCTTGTTCCTTGTGTCAAGACGCATCACTTGGTATATAAGTCATGGGTCCCG
* *
235211 GGGG
130 GAGA
* * * * * * *
235215 TGGTCTTGA-CCTCCTCAAACAAGTAGTACCCGAATATCTTTAAAACGGTTAATATCCCCACCCC
1 TGGTCCTGACCCCCCTCAAACAAGAAGT-GCCAAATATCTTGAAAACGGTTAAGATCCCCACCCC
235279 TAAAC
65 TAAAC
235284 TATAATTATA
Statistics
Matches: 171, Mismatches: 29, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
133 47 0.27
134 56 0.33
135 65 0.38
136 3 0.02
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (133 bp):
TGGTCCTGACCCCCCTCAAACAAGAAGTGCCAAATATCTTGAAAACGGTTAAGATCCCCACCCCT
AAACCATATATTTCTTGTTCCTTGTGTCAAGACGCATCACTTGGTATATAAGTCATGGGTCCCGG
AGA
Found at i:238130 original size:1 final size:1
Alignment explanation
Indices: 238124--238155 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
238114 ATCTGGTTCA
238124 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
238156 TTTCGCCGCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:244211 original size:2 final size:2
Alignment explanation
Indices: 244196--244241 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
244186 NNNNNNNNNA
* *
244196 AG AG AG AA AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
244238 AG AG
1 AG AG
244242 GGGGAATTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:244649 original size:11 final size:11
Alignment explanation
Indices: 244633--244673 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
244623 CTAAAAAAAT
*
244633 GCTTAAAGGCG
1 GCTTAAAGGTG
*
244644 GCTTAAAGATG
1 GCTTAAAGGTG
244655 GCTTAAAGGTG
1 GCTTAAAGGTG
*
244666 ACTTAAAG
1 GCTTAAAG
244674 AAGTTTGGAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.34, C:0.12, G:0.29, T:0.24
Consensus pattern (11 bp):
GCTTAAAGGTG
Found at i:244658 original size:22 final size:22
Alignment explanation
Indices: 244633--244674 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
244623 CTAAAAAAAT
*
244633 GCTTAAAGGCGGCTTAAAGATG
1 GCTTAAAGGCGACTTAAAGATG
*
244655 GCTTAAAGGTGACTTAAAGA
1 GCTTAAAGGCGACTTAAAGA
244675 AGTTTGGACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.12, G:0.29, T:0.24
Consensus pattern (22 bp):
GCTTAAAGGCGACTTAAAGATG
Found at i:244759 original size:11 final size:11
Alignment explanation
Indices: 244743--244783 Score: 73
Period size: 11 Copynumber: 3.7 Consensus size: 11
244733 GATGGTATAT
244743 CCTTTAAGCCA
1 CCTTTAAGCCA
*
244754 CCTTTACGCCA
1 CCTTTAAGCCA
244765 CCTTTAAGCCA
1 CCTTTAAGCCA
244776 CCTTTAAG
1 CCTTTAAG
244784 GACTTGCTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.24, C:0.37, G:0.10, T:0.29
Consensus pattern (11 bp):
CCTTTAAGCCA
Found at i:247038 original size:17 final size:16
Alignment explanation
Indices: 247013--247047 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
247003 CTGGCTTGCG
247013 ACCAGTTCTCGCCGAGT
1 ACCAGTTCTCGCC-AGT
*
247030 ACCATTTCTCGCCAGT
1 ACCAGTTCTCGCCAGT
247046 AC
1 AC
247048 ATTGTGACGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.20, C:0.37, G:0.17, T:0.26
Consensus pattern (16 bp):
ACCAGTTCTCGCCAGT
Found at i:247445 original size:21 final size:21
Alignment explanation
Indices: 247421--247530 Score: 84
Period size: 21 Copynumber: 5.2 Consensus size: 21
247411 TGTATCAATC
*
247421 CTATCTTATCGTGCGTTAATT
1 CTATCTTATCGTGCGTTAATA
247442 CTATCTTATCGTGCGTGT-ATA
1 CTATCTTATCGTGCGT-TAATA
* *
247463 CTGT-TCTATCGTACGTGT-ATA
1 CTATCT-TATCGTGCGT-TAATA
* *
247484 CTGT-TCTATCGTGCGTTAATC
1 CTATCT-TATCGTGCGTTAATA
* * *
247505 CTATCCTATTGTGCGTTAATC
1 CTATCTTATCGTGCGTTAATA
247526 CTATC
1 CTATC
247531 AGGTTTATCG
Statistics
Matches: 77, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.03
21 74 0.96
22 1 0.01
ACGTcount: A:0.18, C:0.22, G:0.16, T:0.44
Consensus pattern (21 bp):
CTATCTTATCGTGCGTTAATA
Found at i:249990 original size:21 final size:22
Alignment explanation
Indices: 249960--250076 Score: 118
Period size: 21 Copynumber: 5.5 Consensus size: 22
249950 TGTATCAATC
*
249960 CTATCATATCGTGCGTGT-ATA
1 CTATCCTATCGTGCGTGTAATA
* * *
249981 CTGTTCTATCGTGCGT-TAATC
1 CTATCCTATCGTGCGTGTAATA
*
250002 CTATCCTTTCGTGCGTGT-ATA
1 CTATCCTATCGTGCGTGTAATA
* * *
250023 CTGTTCTATCGTGCGT-TAATG
1 CTATCCTATCGTGCGTGTAATA
*
250044 CTATCCTATCGTGCGTG-AATC
1 CTATCCTATCGTGCGTGTAATA
250065 CTATCCTATCGT
1 CTATCCTATCGT
250077 TTATCTTGTA
Statistics
Matches: 77, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
20 2 0.03
21 74 0.96
22 1 0.01
ACGTcount: A:0.17, C:0.24, G:0.19, T:0.40
Consensus pattern (22 bp):
CTATCCTATCGTGCGTGTAATA
Found at i:250076 original size:42 final size:42
Alignment explanation
Indices: 249942--250060 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
249932 GTTTATCCTT
** * *
249942 TTCTATCGTGTATCAATCCTATCATATCGTGCGTGTATACTG
1 TTCTATCGTGCGTTAATCCTATCCTATCGTGCGTGTATACTG
*
249984 TTCTATCGTGCGTTAATCCTATCCTTTCGTGCGTGTATACTG
1 TTCTATCGTGCGTTAATCCTATCCTATCGTGCGTGTATACTG
*
250026 TTCTATCGTGCGTTAATGCTATCCTATCGTGCGTG
1 TTCTATCGTGCGTTAATCCTATCCTATCGTGCGTG
250061 AATCCTATCC
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.41
Consensus pattern (42 bp):
TTCTATCGTGCGTTAATCCTATCCTATCGTGCGTGTATACTG
Found at i:250202 original size:2 final size:2
Alignment explanation
Indices: 250195--250225 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
250185 AGAAAGAAAT
250195 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
250226 TTGAAAAAAC
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:252735 original size:119 final size:119
Alignment explanation
Indices: 252524--252764 Score: 455
Period size: 119 Copynumber: 2.0 Consensus size: 119
252514 TGCCATAAGA
252524 TGTCTAATTACAATAAATACGTAGGTACATTAGGTCACAGTGATACTGGAGTATAGCATGATCTA
1 TGTCTAATTACAATAAATACGTAGGTACATTAGGTCACAGTGATACTGGAGTATAGCATGATCTA
*
252589 TGATATAAGATTGAGTTGGAGATCTGATAGCGGCAGATCATTTTCTATCTTTTT
66 CGATATAAGATTGAGTTGGAGATCTGATAGCGGCAGATCATTTTCTATCTTTTT
*
252643 TGTCTAATTACAATAAATACGTGGGTACATTAGGTCACAGTGATACTGGAGTATAGCATGATCTA
1 TGTCTAATTACAATAAATACGTAGGTACATTAGGTCACAGTGATACTGGAGTATAGCATGATCTA
*
252708 CGATATAAGATTGAGTTGGAGATCTGATAGCGGCATATCATTTTCTATCTTTTT
66 CGATATAAGATTGAGTTGGAGATCTGATAGCGGCAGATCATTTTCTATCTTTTT
252762 TGT
1 TGT
252765 TTATTTTTTC
Statistics
Matches: 119, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
119 119 1.00
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (119 bp):
TGTCTAATTACAATAAATACGTAGGTACATTAGGTCACAGTGATACTGGAGTATAGCATGATCTA
CGATATAAGATTGAGTTGGAGATCTGATAGCGGCAGATCATTTTCTATCTTTTT
Found at i:266192 original size:109 final size:108
Alignment explanation
Indices: 266063--266268 Score: 306
Period size: 109 Copynumber: 1.9 Consensus size: 108
266053 TTACAGCAGA
* * ** *
266063 CAAATACATGGCTGTTGTGGCATGGATCAAGTCAAATACATGACTATTGGCTATATATTGTGTAT
1 CAAATACATGACTGTTGTGGCATGGATCAAGTCAAATACATGACTAGTAACTATATATTGTATAT
*
266128 AAAATGTCAATTCAGTCAAATACATGACTGAAAATCCAAGTAGT
66 -AAATGTCAATACAGTCAAATACATGACTGAAAATCCAAGTAGT
* *
266172 CAAATACATGACTAG-TGTGGCATGGATCGAGTCAAATACATGACTAGTAACTTTATATTGTATA
1 CAAATACATGACT-GTTGTGGCATGGATCAAGTCAAATACATGACTAGTAACTATATATTGTATA
*
266236 TAAATGTCAATACAGTCAAATATATGACTGAAA
65 TAAATGTCAATACAGTCAAATACATGACTGAAA
266269 TCAAAGCAAT
Statistics
Matches: 87, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
108 30 0.34
109 56 0.64
110 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.30
Consensus pattern (108 bp):
CAAATACATGACTGTTGTGGCATGGATCAAGTCAAATACATGACTAGTAACTATATATTGTATAT
AAATGTCAATACAGTCAAATACATGACTGAAAATCCAAGTAGT
Found at i:275882 original size:18 final size:18
Alignment explanation
Indices: 275859--275894 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
275849 ACAGAGAGAT
275859 TGTTGATTAGGATTAAAC
1 TGTTGATTAGGATTAAAC
275877 TGTTGATTAGGATTAAAC
1 TGTTGATTAGGATTAAAC
275895 CTACGCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.22, T:0.39
Consensus pattern (18 bp):
TGTTGATTAGGATTAAAC
Found at i:281469 original size:20 final size:22
Alignment explanation
Indices: 281422--281472 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
281412 ATTTTTAGGC
281422 AATTTTAATATCAAATAGAGAT
1 AATTTTAATATCAAATAGAGAT
281444 AATTTTAATCAT-AAATA-AGAT
1 AATTTTAAT-ATCAAATAGAGAT
*
281465 -GTTTTAAT
1 AATTTTAAT
281473 TTTACAACTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 7 0.26
21 4 0.15
22 14 0.52
23 2 0.07
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.41
Consensus pattern (22 bp):
AATTTTAATATCAAATAGAGAT
Found at i:285698 original size:4 final size:4
Alignment explanation
Indices: 285691--285720 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
285681 TATATATATA
285691 TATC TATC TATC TATC TATC TATC TATC TA
1 TATC TATC TATC TATC TATC TATC TATC TA
285721 ACTGTATAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (4 bp):
TATC
Found at i:301541 original size:172 final size:165
Alignment explanation
Indices: 301243--301953 Score: 1000
Period size: 172 Copynumber: 4.2 Consensus size: 165
301233 NNNNNNNNNN
*
301243 CTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGATCATGAGAAGAAGA
1 CTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCCGATTAGTTTC---T-A--AGAAGAAGA
* * *
301308 TTTTTAAAGATTTCCTCTATATATTCCTATGTTAAACTTTGACCCCCCATTGTGGCCCTACCCTA
60 TTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTTGACCCCCCATTGTGGCCCCACCCTA
301373 CCCCCGGGGGTCATG-ATATTCACAACTTTGAATCTACACTA
125 CCCCCGGGGGTCATGAAT-TTCACAACTTTGAATCTACACTA
301414 GCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCCGATTAGTTTCTAAGAAGAAGA-TTTT
1 -CTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCCGATTAGTTTCTAAGAAGAAGATTTTT
*
301478 AAATATTTACTCTATATATTCCTATGTAAAACTTTGACCCCCCCCCATTGTGGCCCC-CCCTACC
65 AAAGATTTACTCTATATATTCCTATGTAAAACTTTGA---CCCCCCATTGTGGCCCCACCCTACC
* *
301542 CCCGGGGGTCATGAATTTCACATCTCTGAATCTACACTA
127 CCCGGGGGTCATGAATTTCACAACTTTGAATCTACACTA
*
301581 CATGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCCGATTAGTTTCTGAGAAGAAGATTTTT
1 C-TGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCCGATTAGTTTCTAAGAAGAAGATTTTT
* * * * *
301646 ATAGATTTACTCTATATATTCCTATGAAAAACTTTAACACCAACACCCCCATTGTGGTCCCACCA
65 AAAGATTTACTCTATATATTCCTATGTAAAACTTT------GAC-CCCCCATTGTGGCCCCACCC
*
301711 TACCTCC-GGGGTCATGAATTTCACAACTTTGAATCTACACTA
123 TACCCCCGGGGGTCATGAATTTCACAACTTTGAATCTACACTA
** * * * *
301753 TCTGAATATGCTTTCACACAAGTTTCAGCTTTCCTGACTGATTAGTTTCTGAGAAGAAGATTTTT
1 -CTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCCGATTAGTTTCTAAGAAGAAGATTTTT
* *
301818 AAAGATTTACTCTATATATTCTTATGTAAAACTTCGACCCCCC-TTGTGGCCCCACCCTACCCCC
65 AAAGATTTACTCTATATATTCCTATGTAAAACTTTGACCCCCCATTGTGGCCCCACCCTACCCCC
301882 GGGGGTCATGAATTTCACAACTTTGAATCTACACTA
130 GGGGGTCATGAATTTCACAACTTTGAATCTACACTA
301918 CCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTG
1 -CTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTG
301954 ATCATAACCT
Statistics
Matches: 489, Mismatches: 34, Indels: 39
0.87 0.06 0.07
Matches are distributed among these distances:
164 18 0.04
165 110 0.22
166 12 0.02
167 98 0.20
168 55 0.11
169 1 0.00
171 1 0.00
172 184 0.38
173 9 0.02
174 1 0.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.32
Consensus pattern (165 bp):
CTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCCGATTAGTTTCTAAGAAGAAGATTTTTA
AAGATTTACTCTATATATTCCTATGTAAAACTTTGACCCCCCATTGTGGCCCCACCCTACCCCCG
GGGGTCATGAATTTCACAACTTTGAATCTACACTA
Found at i:309242 original size:12 final size:12
Alignment explanation
Indices: 309221--309263 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
309211 AAAAAAGTTT
*
309221 ACAGATGGACAG
1 ACAGACGGACAG
309233 ACAGACGGACAG
1 ACAGACGGACAG
* *
309245 GCGGACGGACAG
1 ACAGACGGACAG
*
309257 ACGGACG
1 ACAGACG
309264 ATGGACAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.35, C:0.23, G:0.40, T:0.02
Consensus pattern (12 bp):
ACAGACGGACAG
Found at i:312915 original size:22 final size:21
Alignment explanation
Indices: 312885--312941 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
312875 AATTAGAGCA
312885 TAATTACGAGATAATAAACTCG
1 TAATTACGAGATAAT-AACTCG
* * **
312907 TAATAACGAGATCATTTCTCG
1 TAATTACGAGATAATAACTCG
312928 TAATTACGAGATAA
1 TAATTACGAGATAA
312942 AAATATTTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
21 16 0.55
22 13 0.45
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (21 bp):
TAATTACGAGATAATAACTCG
Found at i:315813 original size:30 final size:30
Alignment explanation
Indices: 315778--315848 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
315768 TTTCGATCCA
315778 TCTTGGTTTTGCGAATT-TTTTCGCAACCCT
1 TCTTGGTTTTGCGAATTGTTTT-GCAACCCT
*
315808 TCTTGGTTTTGCGAGTTGTTTTGCAACCCT
1 TCTTGGTTTTGCGAATTGTTTTGCAACCCT
*
315838 TCTTGGCTTTG
1 TCTTGGTTTTG
315849 TAAATTAGCT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 34 0.89
31 4 0.11
ACGTcount: A:0.10, C:0.21, G:0.21, T:0.48
Consensus pattern (30 bp):
TCTTGGTTTTGCGAATTGTTTTGCAACCCT
Found at i:329114 original size:12 final size:12
Alignment explanation
Indices: 329090--329122 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
329080 ATCACATTTT
329090 GTCTGTC-GTCC
1 GTCTGTCTGTCC
329101 GTCTGTCTGTCC
1 GTCTGTCTGTCC
329113 GTCTGTCTGT
1 GTCTGTCTGT
329123 AAACGTTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.33
12 14 0.67
ACGTcount: A:0.00, C:0.30, G:0.27, T:0.42
Consensus pattern (12 bp):
GTCTGTCTGTCC
Found at i:329626 original size:166 final size:165
Alignment explanation
Indices: 329355--330556 Score: 1668
Period size: 166 Copynumber: 7.3 Consensus size: 165
329345 AAGGCATCCT
* * * * *
329355 TATATAGTAAATTTAAAAAATCATCTTCTTAGAAACTAATCAGCCAGGAAAGCTAAAACTTGTGT
1 TATAGAGTAAATTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGT
* * * *
329420 GGAAGCATTCTCAAGTAGTGTATATTCAAAGTTGTGAAAATCATGACCCCCAGAGGTAGGGTGGG
66 GGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCAGGGGTAGGGTGGG
* *
329485 ACCACAATGGGGGGTCAAAGTTTAACATAGGAATA
131 GCCACAATGGGGGGTCGAAGTTTAACATAGGAATA
329520 TATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTG
1 TATAGAGTAAAT-TTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTG
* * *
329585 TGGAAGCATCCTCAGGTAGTGTATATTCAAAGTTGTGAAAATCATGACCCCC-GTGGGTAGGTTT
65 TGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCAG-GGGTAGGGTG
329649 GGGCCACAATGGGGGGTCGAAGTTTAACATAGGAATA
129 GGGCCACAATGGGGGGTCGAAGTTTAACATAGGAATA
* * *
329686 TACAGAGTAAATTTAAAAAATCTTCTTCTCAGAAACAAATCAGCCAGGAAAGCTGAAACTTGTGT
1 TATAGAGTAAATTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGT
* * * * **
329751 GGAGGCATCCTCAGGAAGTGTAGATTCATAGTTGTGAAATTCATGACCATCAGGGGTAGGGTGGG
66 GGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCAGGGGTAGGGTGGG
* * * *
329816 GCCATAAT-GGGGGTTGAATTTTAACATAGAAATA
131 GCCACAATGGGGGGTCGAAGTTTAACATAGGAATA
* * *
329850 TATAGAGTAGA---TAAAAATCTTCTTCGCAGAAACCT-ATCAGCCAGCAAAGCTGAAACTTGTG
1 TATAGAGTAAATTTTAAAAATCTTCTTCTCAGAAA-CTAATCAGCCAGGAAAGCTGAAACTTGTG
* * * * *
329911 TGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAATTAATAACCCCCGGGGGTAGAGTGG
65 TGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCAGGGGTAGGGTGG
* * *
329976 GACAACAATGTGGGGTCGAAGTTTAACATAGGAATA
130 GGCCACAATGGGGGGTCGAAGTTTAACATAGGAATA
* *
330012 TACAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACAAATCAGCCAGGAAAGCTGAAACTTGTG
1 TATAGAGTAAAT-TTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTG
* ** *
330077 TGGAAGCATCCTCAGGAAGTGTAGATTCAAAGTTGTGAAGTTCATGACCCCCAGGGGTATGGTGG
65 TGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCAGGGGTAGGGTGG
* * *
330142 GGCCACAAT-GGGGGTTGAATTTTAACATAGAAATA
130 GGCCACAATGGGGGGTCGAAGTTTAACATAGGAATA
*
330177 TATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACCT-ATCAGCCAGCAAAGCT-AAATCTTG
1 TATAGAGTAAAT-TTTAAAAATCTTCTTCTCAGAAA-CTAATCAGCCAGGAAAGCTGAAA-CTTG
*
330240 TGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCCGGAGGTAGGG
63 TGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCAGG-GGTAGGG
* *
330305 TGGGGCCACAAAGGGGGGTTGAAGTTTAACATAGGAATA
127 TGGGGCCACAATGGGGGGTCGAAGTTTAACATAGGAATA
* * * *
330344 TACAGAGTAAATTTAAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTAAAACTTGTTT
1 TATAGAGTAAATTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGT
* * *
330409 GGAAGCATCCTCAGGTAGTGTAGATACAAAGTTGTGAAAATCATGACCCCC-GCGGGTAGGTTTG
66 GGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCAG-GGGTAGGGTGG
** *
330473 GGCCACAATGGGGAATCAAAGTTTAACATAGGAATA
130 GGCCACAATGGGGGGTCGAAGTTTAACATAGGAATA
** *
330509 TATAGAGTAAATCTTTAAAAATCTTCTTCTTGGAATCTAATCAGCCAG
1 TATAGAGTAAAT-TTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAG
330557 ATGATTCTTT
Statistics
Matches: 923, Mismatches: 96, Indels: 35
0.88 0.09 0.03
Matches are distributed among these distances:
161 106 0.11
162 32 0.03
164 35 0.04
165 307 0.33
166 405 0.44
167 38 0.04
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (165 bp):
TATAGAGTAAATTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGT
GGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCAGGGGTAGGGTGGG
GCCACAATGGGGGGTCGAAGTTTAACATAGGAATA
Found at i:335261 original size:24 final size:24
Alignment explanation
Indices: 335226--335303 Score: 111
Period size: 24 Copynumber: 3.2 Consensus size: 24
335216 AAATATACTT
*
335226 TCCTTTCGACATCTGTTACAGAGA
1 TCCTTTCCACATCTGTTACAGAGA
* *
335250 TCCTTTCCACATCTTTTACAGAAA
1 TCCTTTCCACATCTGTTACAGAGA
*
335274 TCCTTTCCACATCTGTTACGGAGA
1 TCCTTTCCACATCTGTTACAGAGA
*
335298 TACTTT
1 TCCTTT
335304 TTAAATCTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.24, C:0.27, G:0.12, T:0.37
Consensus pattern (24 bp):
TCCTTTCCACATCTGTTACAGAGA
Found at i:335298 original size:48 final size:48
Alignment explanation
Indices: 335226--335319 Score: 134
Period size: 48 Copynumber: 2.0 Consensus size: 48
335216 AAATATACTT
* * *
335226 TCCTTTCGACATCTGTTACAGAGATCCTTTCCACATCTTTTACAGAAA
1 TCCTTTCCACATCTGTTACAGAGATACTTTCCAAATCTTTTACAGAAA
* **
335274 TCCTTTCCACATCTGTTACGGAGATACTTTTTAAATCTTTTACAGA
1 TCCTTTCCACATCTGTTACAGAGATACTTTCCAAATCTTTTACAGA
335320 GTTCAAAGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.27, C:0.24, G:0.11, T:0.38
Consensus pattern (48 bp):
TCCTTTCCACATCTGTTACAGAGATACTTTCCAAATCTTTTACAGAAA
Found at i:345596 original size:18 final size:18
Alignment explanation
Indices: 345573--345610 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
345563 TTGGAAAATT
345573 TTTGTATCTACACAATGG
1 TTTGTATCTACACAATGG
345591 TTTGTATCTACACAATGG
1 TTTGTATCTACACAATGG
345609 TT
1 TT
345611 AAGACTTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (18 bp):
TTTGTATCTACACAATGG
Found at i:349964 original size:2 final size:2
Alignment explanation
Indices: 349909--349951 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
349899 NNNNNNNNNN
349909 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
349950 AG
1 AG
349952 CATTATGGAG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:350754 original size:4 final size:4
Alignment explanation
Indices: 350747--350787 Score: 55
Period size: 4 Copynumber: 10.2 Consensus size: 4
350737 TTGTCGTCCA
* * *
350747 TCTG TCTG TCTG TCAG TCTG TCCG TCTG TCCG TCTG TCTG T
1 TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG T
350788 AAACTTTTCA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.02, C:0.29, G:0.24, T:0.44
Consensus pattern (4 bp):
TCTG
Found at i:350760 original size:8 final size:8
Alignment explanation
Indices: 350742--350784 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
350732 TTTGTTTGTC
*
350742 GTCCATCT
1 GTCCGTCT
*
350750 GTCTGTCT
1 GTCCGTCT
*
350758 GTCAGTCT
1 GTCCGTCT
350766 GTCCGTCT
1 GTCCGTCT
350774 GTCCGTCT
1 GTCCGTCT
350782 GTC
1 GTC
350785 TGTAAACTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.05, C:0.33, G:0.23, T:0.40
Consensus pattern (8 bp):
GTCCGTCT
Found at i:351536 original size:166 final size:166
Alignment explanation
Indices: 350964--351962 Score: 1400
Period size: 166 Copynumber: 6.0 Consensus size: 166
350954 TTCCATTAGA
* *
350964 CCAGAAAAGCTGAAACTTGTGTGTAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCA
1 CCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCA
* * * * *
351029 TGACCCCCGGGGGTAGCGTAGAGCCACAATGGGGGGGGGGTCGAAGTTTAACATAGGAATATATA
66 TAACCCCCGGGGGTAGGGTGGGGCCACAAT----GGGGGGTCGAAGTTTAACATATGAATATATA
* * * *
351094 GAGTTAATCTTTAAAAATCTTCTTCTTAAAAACTAATAAG
127 GAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAG
* *
351134 CCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAATGTAGATTCAAAATTGTGAAAATCA
1 CCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCA
* * * * *
351199 TGACCCCCAGGGTTAGGGTGGGGCCACAATTGGGGGTTGAAGTTTAACATATGAATATATAGAGT
66 TAACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTTAACATATGAATATATAGAGT
*
351264 AAATCTTTAAGAA---TCTTCTCAGAAACTAATCAG
131 AAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAG
* * *
351297 CCAGGAAAGCTGAAACTTGTGTGTAAGCATCCTCAGGAAGTGAAGATTCAAAGTTGTGAAAATCA
1 CCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCA
351362 TAACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTTAACATATGAATAT-TAAGAG
66 TAACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTTAACATATGAATATAT-AGAG
*
351426 TAAATCTTTAAAAATCTTCTTCTCAGAAATTAATCAG
130 TAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAG
* * * * *
351463 CCAGCAAAGCTGAAACGTGTGTGAAAGCATTCTTAGGTAGTGTAGATTCAATGTTGTGAAAATCA
1 CCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCA
* * * * * * * *
351528 TGACCCCCGGGGGGAGAGTGGGGCTACAATGGGGGGTCGAGGTTTTACATAAGAATATACAGAGT
66 TAACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTTAACATATGAATATATAGAGT
* *
351593 AAATCTTTAAAAATCCTCTTCTCAAAAACTAATCAG
131 AAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAG
*** *
351629 CCAGGAAAGCTGACTTTTGTGTTG-AAGCATCCTCAGGTAGTGTAGATACAAAGTTGTG-AAATC
1 CCAGGAAAGCTGAAACTTGTG-TGAAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATC
* * **
351692 ATAACTCCCGGGGGTAGGGTGGGGCCACAGTGGGGGGTTTAAGTTTAACATATGAATATATAGAG
65 ATAACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTTAACATATGAATATATAGAG
351757 TAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAG
130 TAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAG
* * * *
351794 CCAGCAAAGCTGAAACTTGTGTGAGAGCATCCTCGGGTAGTGTAGATACAAAGTTGTG-AAATCA
1 CCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCA
* ** * *
351858 TAACCCCCGGGGGTAGGGTGGGGCCACAGTGGGGGGTTTAAGTTTAACAAACGAATATATAGAGT
66 TAACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTTAACATATGAATATATAGAGT
351923 AAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAG
131 AAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAG
351959 CCAG
1 CCAG
351963 ATGATTCTTT
Statistics
Matches: 742, Mismatches: 80, Indels: 19
0.88 0.10 0.02
Matches are distributed among these distances:
162 1 0.00
163 147 0.20
164 2 0.00
165 250 0.34
166 254 0.34
167 2 0.00
170 86 0.12
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (166 bp):
CCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCA
TAACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTTAACATATGAATATATAGAGT
AAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAG
Found at i:351586 original size:329 final size:330
Alignment explanation
Indices: 350964--351962 Score: 1436
Period size: 329 Copynumber: 3.0 Consensus size: 330
350954 TTCCATTAGA
*
350964 CCAGAAAAGCTGAAACTTGTGTGTAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCA
1 CCAGGAAAGCTGAAACTTGTGTGTAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCA
* * * * *
351029 TGACCCCCGGGGGTAGCGTAGAGCCACAATGGGGGGGGGGTCGAAGTTTAACATAGGAATATATA
66 TAACCCCCGGGGGTAGGGTGGGGCCACAAT----GGGGGGTCGAAGTTTAACATATGAATATATA
* * * * *
351094 GAGTTAATCTTTAAAAATCTTCTTCTTAAAAACTAATAAGCCAGGAAAGCTGAAACTTGTGTGAA
127 GAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGCAAAGCTGAAACTTGTGTGAA
* * * *
351159 AGCATCCTCAGGTAATGTAGATTCAAAATTGTGAAAATCATGACCCCCAGGGTTAGGGTGGGGCC
192 AGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCC
* * *
351224 ACAATTGGGGGTTGAAGTTTAACATATGAATATATAGAGTAAATCTTTAAGAA-TCTTCTCAGAA
257 ACAATGGGGGGTTGAAGTTTAACATAAGAATATATAGAGTAAATCTTTAAAAACTCTTCTCAGAA
351288 ACTAATCAG
322 ACTAATCAG
* *
351297 CCAGGAAAGCTGAAACTTGTGTGTAAGCATCCTCAGGAAGTGAAGATTCAAAGTTGTGAAAATCA
1 CCAGGAAAGCTGAAACTTGTGTGTAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCA
351362 TAACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTTAACATATGAATAT-TAAGAG
66 TAACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTTAACATATGAATATAT-AGAG
* *
351426 TAAATCTTTAAAAATCTTCTTCTCAGAAATTAATCAGCCAGCAAAGCTGAAACGTGTGTGAAAGC
130 TAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGCAAAGCTGAAACTTGTGTGAAAGC
* * * * * *
351491 ATTCTTAGGTAGTGTAGATTCAATGTTGTGAAAATCATGACCCCCGGGGGGAGAGTGGGGCTACA
195 ATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACA
* * * * *
351556 ATGGGGGGTCGAGGTTTTACATAAGAATATACAGAGTAAATCTTTAAAAATCCTCTTCTCAAAAA
260 ATGGGGGGTTGAAGTTTAACATAAGAATATATAGAGTAAATCTTTAAAAA--CTCTTCTCAGAAA
351621 CTAATCAG
323 CTAATCAG
* *
351629 CCAGGAAAGCTG--ACTTTTGTGTTGAAGCATCCTCAGGTAGTGTAGATACAAAGTTGTG-AAAT
1 CCAGGAAAGCTGAAACTTGTGTG-T-AAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAAT
* * **
351691 CATAACTCCCGGGGGTAGGGTGGGGCCACAGTGGGGGGTTTAAGTTTAACATATGAATATATAGA
64 CATAACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTTAACATATGAATATATAGA
*
351756 GTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGCAAAGCTGAAACTTGTGTGAGAG
129 GTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGCAAAGCTGAAACTTGTGTGAAAG
* * *
351821 CATCCTCGGGTAGTGTAGATACAAAGTTGTG-AAATCATAACCCCCGGGGGTAGGGTGGGGCCAC
194 CATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCAC
* *
351885 AGTGGGGGGTTTAAGTTTAACA-AACGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGA
259 AATGGGGGGTTGAAGTTTAACATAA-GAATATATAGAGTAAATCTTTAAAAA-C-TCTTCTCAGA
351949 AACTAATCAG
321 AACTAATCAG
351959 CCAG
1 CCAG
351963 ATGATTCTTT
Statistics
Matches: 596, Mismatches: 61, Indels: 21
0.88 0.09 0.03
Matches are distributed among these distances:
328 1 0.00
329 190 0.32
330 102 0.17
331 152 0.26
332 63 0.11
333 88 0.15
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (330 bp):
CCAGGAAAGCTGAAACTTGTGTGTAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCA
TAACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTTAACATATGAATATATAGAGT
AAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGCAAAGCTGAAACTTGTGTGAAAGCA
TCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAA
TGGGGGGTTGAAGTTTAACATAAGAATATATAGAGTAAATCTTTAAAAACTCTTCTCAGAAACTA
ATCAG
Found at i:352970 original size:20 final size:20
Alignment explanation
Indices: 352926--352970 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
352916 GATTCCTATG
352926 ATATTGTATGATATGAAACA
1 ATATTGTATGATATGAAACA
* * * *
352946 CTATTGTTTTATATGATACA
1 ATATTGTATGATATGAAACA
352966 ATATT
1 ATATT
352971 AAATCATATA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.44
Consensus pattern (20 bp):
ATATTGTATGATATGAAACA
Done.