Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold160
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5021213
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 92036 characters in sequence are not A, C, G, or T
File 14 of 30
Found at i:2186376 original size:130 final size:131
Alignment explanation
Indices: 2186127--2186430 Score: 330
Period size: 130 Copynumber: 2.3 Consensus size: 131
2186117 TAATCATCGA
* * **
2186127 GGATACCCCAACCCCGTTATTTTCGAGGGCATACTCCAACCCCCGGTTTTATTTCTAAAACATCA
1 GGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCCGACTTTATTTCTAAAACATCA
* * * * *
2186192 ATTTTTCATAATCGGGGATACTCCAACCCCGGCTTTATTTCCAAAATATTGATTTCTCATAATTA
66 ATTTTTCATAATCGGGGACACTCCAACCCCGGCTTTACTTCCAAAATATCGATTTCTCACAATCA
2186257 G
131 G
** * * *
2186258 GGATACTCCAACCCTATTATTTTC-ACGGGGATACTCCAA-TCCCGACTTTATTTTTGAAACATC
1 GGATACTCCAACCCCGTTATTTTCGA-GGGGATACTCCAACCCCCGACTTTATTTCTAAAACATC
* * ** * *
2186321 TA-TTTTCTATAATCGGGGACACTTCAACCCTTG-TCTTACTT-CTAAATCATCGATTTTTCACA
65 AATTTTTC-ATAATCGGGGACACTCCAACCCCGGCT-TTACTTCCAAAAT-ATCGATTTCTCACA
*
2186383 ATCGG
127 ATCAG
* *
2186388 GGATTCTCCAACCCCGTTATTTTCGAGGGGATATTCCAACCCC
1 GGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCC
2186431 ATTATTATCT
Statistics
Matches: 141, Mismatches: 26, Indels: 12
0.79 0.15 0.07
Matches are distributed among these distances:
129 11 0.08
130 94 0.67
131 36 0.26
ACGTcount: A:0.26, C:0.27, G:0.13, T:0.34
Consensus pattern (131 bp):
GGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCCGACTTTATTTCTAAAACATCA
ATTTTTCATAATCGGGGACACTCCAACCCCGGCTTTACTTCCAAAATATCGATTTCTCACAATCA
G
Found at i:2198865 original size:11 final size:10
Alignment explanation
Indices: 2198849--2198906 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 10
2198839 CTTCTCTTTT
2198849 CAAAAAAAAA
1 CAAAAAAAAA
2198859 GCAAAAAAAAA
1 -CAAAAAAAAA
2198870 -AACAAACAAAA
1 CAA-AAA-AAAA
2198881 -AACAAAAAAA
1 CAA-AAAAAAA
2198891 CAAAAAGAAAA
1 CAAAAA-AAAA
2198902 CAAAA
1 CAAAA
2198907 CAAAGGAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
9 2 0.05
10 10 0.23
11 31 0.72
ACGTcount: A:0.84, C:0.12, G:0.03, T:0.00
Consensus pattern (10 bp):
CAAAAAAAAA
Found at i:2198867 original size:12 final size:11
Alignment explanation
Indices: 2198849--2198910 Score: 63
Period size: 12 Copynumber: 5.4 Consensus size: 11
2198839 CTTCTCTTTT
*
2198849 CAAAAAAAAAG
1 CAAAAAAAAAA
2198860 CAAAAAAAAAAA
1 C-AAAAAAAAAA
*
2198872 CAAACAAAAAA
1 CAAAAAAAAAA
2198883 CAAAAAAACAAA
1 CAAAAAAA-AAA
2198895 -AAGAAAACAAAA
1 CAA-AAAA-AAAA
2198907 CAAA
1 CAAA
2198911 GGAAAAAGAG
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
11 19 0.44
12 21 0.49
13 3 0.07
ACGTcount: A:0.84, C:0.13, G:0.03, T:0.00
Consensus pattern (11 bp):
CAAAAAAAAAA
Found at i:2198871 original size:16 final size:15
Alignment explanation
Indices: 2198850--2198910 Score: 77
Period size: 16 Copynumber: 3.9 Consensus size: 15
2198840 TTCTCTTTTC
*
2198850 AAAAAAAAAGCAAAA
1 AAAAAAAAAACAAAA
2198865 AAAAAAACAAACAAAA
1 AAAAAAA-AAACAAAA
*
2198881 AACAAAAAAACAAAA
1 AAAAAAAAAACAAAA
*
2198896 AGAAAACAAAACAAA
1 A-AAAAAAAAACAAA
2198911 GGAAAAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
15 16 0.40
16 24 0.60
ACGTcount: A:0.85, C:0.11, G:0.03, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAACAAAA
Found at i:2198875 original size:23 final size:24
Alignment explanation
Indices: 2198849--2198895 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
2198839 CTTCTCTTTT
2198849 CAAA-AAAAAAGCAAAAAAA-AAAA
1 CAAACAAAAAA-CAAAAAAACAAAA
2198872 CAAACAAAAAACAAAAAAACAAAA
1 CAAACAAAAAACAAAAAAACAAAA
2198896 AGAAAACAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.85, C:0.13, G:0.02, T:0.00
Consensus pattern (24 bp):
CAAACAAAAAACAAAAAAACAAAA
Found at i:2198889 original size:19 final size:19
Alignment explanation
Indices: 2198850--2198906 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
2198840 TTCTCTTTTC
2198850 AAAA-AAAAAGCAAAA-AAA
1 AAAACAAAAAG-AAAACAAA
2198868 AAAACAAACAA-AAAACAAA
1 AAAACAAA-AAGAAAACAAA
2198887 AAAACAAAAAGAAAACAAA
1 AAAACAAAAAGAAAACAAA
2198906 A
1 A
2198907 CAAAGGAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 10 0.29
19 23 0.66
20 2 0.06
ACGTcount: A:0.86, C:0.11, G:0.04, T:0.00
Consensus pattern (19 bp):
AAAACAAAAAGAAAACAAA
Found at i:2200273 original size:27 final size:27
Alignment explanation
Indices: 2200192--2200273 Score: 74
Period size: 27 Copynumber: 3.0 Consensus size: 27
2200182 GACGCCTTTC
2200192 AAAGCCCACACAAGTTGGTGGCATTTT
1 AAAGCCCACACAAGTTGGTGGCATTTT
** * * * * ** *
2200219 CCAGTCCTCAAAGAGTAGGACGCCTTTT
1 AAAGCCCACACA-AGTTGGTGGCATTTT
2200247 AAAGCCCACACAAGTTGGTGGCATTTT
1 AAAGCCCACACAAGTTGGTGGCATTTT
2200274 CTAGTCCTCA
Statistics
Matches: 36, Mismatches: 18, Indels: 2
0.64 0.32 0.04
Matches are distributed among these distances:
27 18 0.50
28 18 0.50
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (27 bp):
AAAGCCCACACAAGTTGGTGGCATTTT
Found at i:2200342 original size:61 final size:56
Alignment explanation
Indices: 2200021--2200479 Score: 543
Period size: 55 Copynumber: 8.0 Consensus size: 56
2200011 GACACCTTTT
* * * *
2200021 CTTTTTAAAGCCCACACAGGTTGGTGGCATTTTCTAGTCCTCAAAGAGTAGGACGC
1 CTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGC
* * *
2200077 CTCTT-AAAGCCCACATAAGTTAGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGC
1 CTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGC
* *
2200132 C-TTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAAAGCAGGACGC
1 CTTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACGC
*
2200187 C-TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGTAGGACGC
1 CTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGC
* *
2200242 CTTTT-AAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGATGC
1 CTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGC
* * *
2200297 TTTTTCTTTTCAAAGCCCACACAAGTGGGTGGCATTTTCCAGTCCTCAAAAAGAAGGACGCC
1 -----CTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG-C
* *
2200359 CTTTTCTTTCAAAGCCCATACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGCAGGACGC
1 C---T-TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGC
* * *
2200419 TTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAAGACGC
1 ---CT--TTTCAAAGCCCACACAAGTTGGTGGCATTTTCC-AGTCCTCAAAGAGCAGGACGC
2200480 TCTCTCCTTT
Statistics
Matches: 351, Mismatches: 32, Indels: 35
0.84 0.08 0.08
Matches are distributed among these distances:
54 5 0.01
55 184 0.52
56 10 0.03
57 1 0.00
60 12 0.03
61 137 0.39
62 1 0.00
63 1 0.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (56 bp):
CTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGC
Found at i:2200611 original size:60 final size:59
Alignment explanation
Indices: 2200518--2200749 Score: 231
Period size: 61 Copynumber: 3.9 Consensus size: 59
2200508 GAGCAGGATA
* * ** *
2200518 CCTTTTAAAGCCTACATAAGCCGGTGGCACTTTTAGTCCTCAAAGAGTAGGACGCCTTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTAGTCCTCAAAGAGCAGGACGCCTT-T
* *
2200578 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCTTCAAAGAGCAGGATG-CTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTT-AGTCCTCAAAGAGCAGGACGCCTTT
* * * **
2200637 CTTTTTACAAGGCCCACACAAGTTGGCGGCAC---CAGTCCTCAAA-AGGCAGGATACCTTT
1 CCTTTTA-AA-GCCCACACAAGTTGGTGGCACTTTTAGTCCTCAAAGA-GCAGGACGCCTTT
* * *
2200695 TCTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGTAGGAC
1 CCTTTT-AAAGCCCACACAAGTTGGTGGCAC-TTTTAGTCCTCAAAGAGCAGGAC
2200750 ACACTTCCTT
Statistics
Matches: 142, Mismatches: 19, Indels: 21
0.78 0.10 0.12
Matches are distributed among these distances:
56 1 0.01
57 35 0.25
58 10 0.07
59 8 0.06
60 35 0.25
61 52 0.37
62 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (59 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTAGTCCTCAAAGAGCAGGACGCCTTT
Found at i:2200833 original size:42 final size:42
Alignment explanation
Indices: 2200732--2200866 Score: 139
Period size: 42 Copynumber: 3.1 Consensus size: 42
2200722 GCACTTTTTA
* * * *
2200732 GTCCTCAAAGAGTAGGACACACTTC-CTTCCCTTCTTTTCTCTTTT
1 GTCCTCAAAGAGCAGGACGCATTTCATTTCCC-T-TTTTC-C-TTT
*
2200777 GTCCTCAAAGAGCAGGACGCACTTT-ATTTTCCTTTTTCCTTT
1 GTCCTCAAAGAGCAGGACGCA-TTTCATTTCCCTTTTTCCTTT
* * *
2200819 GTCCTCAGAGAGCAGGACGTATTTCGTTTCCCTTTTTCCTTT
1 GTCCTCAAAGAGCAGGACGCATTTCATTTCCCTTTTTCCTTT
2200861 GTCCTC
1 GTCCTC
2200867 GAAAAACGGG
Statistics
Matches: 78, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
41 3 0.04
42 43 0.55
43 1 0.01
44 5 0.06
45 20 0.26
46 6 0.08
ACGTcount: A:0.16, C:0.29, G:0.15, T:0.40
Consensus pattern (42 bp):
GTCCTCAAAGAGCAGGACGCATTTCATTTCCCTTTTTCCTTT
Found at i:2201526 original size:19 final size:21
Alignment explanation
Indices: 2201483--2201534 Score: 90
Period size: 19 Copynumber: 2.6 Consensus size: 21
2201473 TTTAACAATT
2201483 TGTATCGATACATTAAGTAAA
1 TGTATCGATACATTAAGTAAA
2201504 TGTATCGATACA-TAAGT-AA
1 TGTATCGATACATTAAGTAAA
2201523 TGTATCGATACA
1 TGTATCGATACA
2201535 GTGTATCGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 14 0.45
20 5 0.16
21 12 0.39
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (21 bp):
TGTATCGATACATTAAGTAAA
Found at i:2203985 original size:51 final size:51
Alignment explanation
Indices: 2203919--2204105 Score: 232
Period size: 51 Copynumber: 3.6 Consensus size: 51
2203909 GTTAAGTTCT
* * *
2203919 CAATTTTTCATAATCGAGGATACTCCAACCCCGATTTTATTTCTAAAACAC
1 CAATTTTCCACAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACAC
* * *
2203970 TAATTTTCCACAATCGGGGATATTCCAACCCCAATTTTATTT-TCAAAACAC
1 CAATTTTCCACAATCGGGGATACTCCAACCCCGATTTTATTTCT-AAAACAC
** * * *
2204021 CAATTTTCCTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCATAAGCAC
1 CAATTTTCC-ACAATCGGGGATACTCCAACCCCGATTTTATTTCTA-AAACAC
*
2204074 CAATTTTTCACAATCGGGGATACTCCAACCCC
1 CAATTTTCCACAATCGGGGATACTCCAACCCC
2204106 ATTAATCATT
Statistics
Matches: 114, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
50 1 0.01
51 51 0.45
52 49 0.43
53 13 0.11
ACGTcount: A:0.30, C:0.27, G:0.10, T:0.33
Consensus pattern (51 bp):
CAATTTTCCACAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACAC
Found at i:2204059 original size:52 final size:51
Alignment explanation
Indices: 2203919--2204105 Score: 232
Period size: 52 Copynumber: 3.6 Consensus size: 51
2203909 GTTAAGTTCT
* * *
2203919 CAATTTTTCATAATCGAGGATACTCCAACCCCGATTTTA-TTTCTAAAACAC
1 CAATTTTCCACAATCGGGGATACTCCAACCCCGATTTTATTTTC-AAAACAC
* * *
2203970 TAATTTTCCACAATCGGGGATATTCCAACCCCAATTTTATTTTCAAAACAC
1 CAATTTTCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACAC
** * * *
2204021 CAATTTTCCTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCATAAGCAC
1 CAATTTTCC-ACAATCGGGGATACTCCAACCCCGATTTTATTTTCA-AAACAC
*
2204074 CAATTTTTCACAATCGGGGATACTCCAACCCC
1 CAATTTTCCACAATCGGGGATACTCCAACCCC
2204106 ATTAATCATT
Statistics
Matches: 115, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
51 48 0.42
52 54 0.47
53 13 0.11
ACGTcount: A:0.30, C:0.27, G:0.10, T:0.33
Consensus pattern (51 bp):
CAATTTTCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACAC
Found at i:2204211 original size:52 final size:51
Alignment explanation
Indices: 2203919--2204211 Score: 218
Period size: 52 Copynumber: 5.6 Consensus size: 51
2203909 GTTAAGTTCT
* *
2203919 CAATTTTTCATAATCGAGGATACTCCAACCCCGATTTTATTTCTAAAACAC
1 CAATTTTTCATAATCGGGGATACTCCAACCCCCATTTTATTTCTAAAACAC
* * * * *
2203970 TAATTTTCCACAATCGGGGATATTCCAACCCCAATTTTATTT-TCAAAACAC
1 CAATTTTTCATAATCGGGGATACTCCAACCCCCATTTTATTTCT-AAAACAC
* * * * * *
2204021 CAATTTTCCTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCATAAGCAC
1 CAATTTTTC-ATAATCGGGGATACTCCAACCCCCATTTTATTTCTA-AAACAC
* * * ** *
2204074 CAATTTTTCACAATCGGGGATACTCCAA-CCCCA-TTAATCATT-GAGGATAC
1 CAATTTTTCATAATCGGGGATACTCCAACCCCCATTTTAT--TTCTAAAACAC
* * ** * *
2204124 TCAACCCTGTT-ATTTTCGAAGTGATACTCCAACCCCCAGTTTTATTTCTAAAACAT
1 -CAA--TTTTTCATAATCG--GGGATACTCCAACCCCCA-TTTTATTTCTAAAACAC
*
2204180 TAATTTTTCATAATCGGGGATACTCCAACCCC
1 CAATTTTTCATAATCGGGGATACTCCAACCCC
2204212 GTTATTTTCG
Statistics
Matches: 183, Mismatches: 43, Indels: 31
0.71 0.17 0.12
Matches are distributed among these distances:
50 7 0.04
51 58 0.32
52 67 0.37
53 19 0.10
54 16 0.09
55 9 0.05
56 3 0.02
57 4 0.02
ACGTcount: A:0.30, C:0.26, G:0.10, T:0.33
Consensus pattern (51 bp):
CAATTTTTCATAATCGGGGATACTCCAACCCCCATTTTATTTCTAAAACAC
Found at i:2204278 original size:79 final size:80
Alignment explanation
Indices: 2204113--2204310 Score: 249
Period size: 79 Copynumber: 2.5 Consensus size: 80
2204103 CCCATTAATC
* * * * *
2204113 ATTGAGGATACT-CAACCCTGTTATTTTCGAAGTGATACTCCAACCCCCAGTTTTATTTCTAAAA
1 ATTGGGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCCAGCTTTATTTCCAAAA
*
2204177 CATTAATTTTTCATA
66 CATTAATTTCTCATA
* * * *
2204192 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTTCAA-CCCCGGCTTTATTTCCAAAA
1 ATTGGGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCCAGCTTTATTTCCAAAA
* *
2204256 TATTGATTTCTCATA
66 CATTAATTTCTCATA
*
2204271 ATTGGGGATACTCCAACCCTATTATTTTC-ACGGGGATACT
1 ATTGGGGATACTCCAACCCTGTTATTTTCGA-GGGGATACT
2204311 ACAATCTTGA
Statistics
Matches: 102, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
78 1 0.01
79 74 0.73
80 27 0.26
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (80 bp):
ATTGGGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCCAGCTTTATTTCCAAAA
CATTAATTTCTCATA
Found at i:2204325 original size:79 final size:79
Alignment explanation
Indices: 2204118--2204368 Score: 229
Period size: 79 Copynumber: 3.2 Consensus size: 79
2204108 TAATCATTGA
** * * * * * *
2204118 GGATACT-CAACCCTGTTATTTTCGAAGTGATACTCCAACCCCCAGTTTTATTTCTAAAACATTA
1 GGATACTCCAACCCCATTATTTTCGAGGGGATACTACAACCCCGA-CTTTATTTCCAAAACATTA
*
2204182 ATTTTTCATAATCGG
65 ATTTCTCATAATCGG
* * * * *
2204197 GGATACTCCAACCCCGTTATTTTCGAGGGGATACTTCAACCCCGGCTTTATTTCCAAAATATTGA
1 GGATACTCCAACCCCATTATTTTCGAGGGGATACTACAACCCCGACTTTATTTCCAAAACATTAA
*
2204262 TTTCTCATAATTGG
66 TTTCTCATAATCGG
* * ** ***
2204276 GGATACTCCAACCCTATTATTTTC-ACGGGGATACTACAATCTTGACTTTATTTTTGAAACATCT
1 GGATACTCCAACCCCATTATTTTCGA-GGGGATACTACAACCCCGACTTTATTTCCAAAACAT-T
*
2204340 ATTTTCT-ATAATCGG
64 AATTTCTCATAATCGG
* *
2204355 GGACACTTCAACCC
1 GGATACTCCAACCC
2204369 TTGTCTAATT
Statistics
Matches: 141, Mismatches: 28, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
78 1 0.01
79 103 0.73
80 37 0.26
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (79 bp):
GGATACTCCAACCCCATTATTTTCGAGGGGATACTACAACCCCGACTTTATTTCCAAAACATTAA
TTTCTCATAATCGG
Found at i:2205679 original size:129 final size:130
Alignment explanation
Indices: 2205504--2205758 Score: 336
Period size: 129 Copynumber: 2.0 Consensus size: 130
2205494 CGGGAATAAC
* * *
2205504 AGGGTTGGACTATCACTGATTATAGAAAATCAGTAATTTGAAAATAAAATCGGGGTTGGAGTATT
1 AGGGTTGGACTATCACCGATTATAGAAAATCAGTAATTTGAAAATAAAATCGAGGTTGGAGTATC
* * *
2205569 CCCTTGAAAATAATGAGGTTGGAGTATCC-CGATTGTGAAAAATT-GATGCTTTAGAAATAAGGC
66 CCCTCGAAAATAACGAGGTTGGAGTATCCTCAATTGTGAAAAATTAG-TGCTTTAGAAATAAGGC
2205632 T
130 T
* * * * * * *
2205633 AGGGTTGGAGTATCCCCGATTGT-GAGAAATCATTATTTTGGAAATAAAATCGAGGTTGGAGTGT
1 AGGGTTGGACTATCACCGATTATAGA-AAATCAGTAATTTGAAAATAAAATCGAGGTTGGAGTAT
* *
2205697 CCCCTCGAAAATAACGGGGTTGGAGTATCCTCAATTGTGAAAAATTAGTGTTTTAGAAATAA
65 CCCCTCGAAAATAACGAGGTTGGAGTATCCTCAATTGTGAAAAATTAGTGCTTTAGAAATAA
2205759 AATCGAAGCT
Statistics
Matches: 108, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
128 2 0.02
129 78 0.72
130 27 0.25
131 1 0.01
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.30
Consensus pattern (130 bp):
AGGGTTGGACTATCACCGATTATAGAAAATCAGTAATTTGAAAATAAAATCGAGGTTGGAGTATC
CCCTCGAAAATAACGAGGTTGGAGTATCCTCAATTGTGAAAAATTAGTGCTTTAGAAATAAGGCT
Found at i:2205779 original size:79 final size:79
Alignment explanation
Indices: 2205634--2205779 Score: 193
Period size: 79 Copynumber: 1.8 Consensus size: 79
2205624 AATAAGGCTA
* * * * * * * *
2205634 GGGTTGGAGTATCCCCGATTGTGAGAAATCATTATTTTGGAAATAAAATCGAGGTTGGAGTGTCC
1 GGGTTGGAGTATCCCCAATTGTGAAAAATCAGTATTTTAGAAATAAAATCGAAGCTAGAGTATCC
2205699 CCTCGAAAATAACG
66 CCTCGAAAATAACG
* * *
2205713 GGGTTGGAGTATCCTCAATTGTGAAAAATTAGTGTTTTAGAAATAAAATCGAAGCTAGAGTATCC
1 GGGTTGGAGTATCCCCAATTGTGAAAAATCAGTATTTTAGAAATAAAATCGAAGCTAGAGTATCC
2205778 CC
66 CC
2205780 GATTGTGGAA
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
79 56 1.00
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (79 bp):
GGGTTGGAGTATCCCCAATTGTGAAAAATCAGTATTTTAGAAATAAAATCGAAGCTAGAGTATCC
CCTCGAAAATAACG
Found at i:2205800 original size:130 final size:129
Alignment explanation
Indices: 2205530--2205830 Score: 340
Period size: 130 Copynumber: 2.3 Consensus size: 129
2205520 TGATTATAGA
* * * * * *
2205530 AAATCAGTAATTTGAAAATAAAATCGGGGTTGGAGTATTCCCTTGAAAATAATGAGGTTGGAGTA
1 AAATCAGTATTTTGGAAATAAAATCGAGGTTGGAGTATCCCCTCGAAAATAACGAGGTTGGAGTA
* * * * * *
2205595 TCCCGATTGTGAAAAATTGATGCTTTAGAAATAAGGCTAGGGTTGGAGTATCCCCGATTGTGAG
66 TCCCAATTGTGAAAAATTGATGCTTTAGAAATAAAGCGAGAGCTAGAGTATCCCCGATTGTGAG
* * *
2205659 AAATCATTATTTTGGAAATAAAATCGAGGTTGGAGTGTCCCCTCGAAAATAACGGGGTTGGAGTA
1 AAATCAGTATTTTGGAAATAAAATCGAGGTTGGAGTATCCCCTCGAAAATAACGAGGTTGGAGTA
* *
2205724 TCCTCAATTGTGAAAAATT-AGTGTTTTAGAAATAAAATCGA-AGCTAGAGTATCCCCGATTGTG
66 TCC-CAATTGTGAAAAATTGA-TGCTTTAGAAAT-AAAGCGAGAGCTAGAGTATCCCCGATTGTG
2205787 -G
128 AG
** * *
2205788 AAAATTGGTATTTTAGAAATAAAATC-ACAGTTGGAGTATCCCC
1 -AAATCAGTATTTTGGAAATAAAATCGA-GGTTGGAGTATCCCC
2205831 GATTGTGGAA
Statistics
Matches: 144, Mismatches: 23, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
129 62 0.43
130 78 0.54
131 4 0.03
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.30
Consensus pattern (129 bp):
AAATCAGTATTTTGGAAATAAAATCGAGGTTGGAGTATCCCCTCGAAAATAACGAGGTTGGAGTA
TCCCAATTGTGAAAAATTGATGCTTTAGAAATAAAGCGAGAGCTAGAGTATCCCCGATTGTGAG
Found at i:2205872 original size:51 final size:51
Alignment explanation
Indices: 2205715--2205880 Score: 217
Period size: 51 Copynumber: 3.3 Consensus size: 51
2205705 AAATAACGGG
* * * * *
2205715 GTTGGAGTATCCTCAATTGTGAAAAATTAGTGTTTTAGAAATAAAATCGAA
1 GTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTTAGAAATAAAATCGGA
* * * **
2205766 GCTAGAGTATCCCCGATTGTGGAAAATTGGTATTTTAGAAATAAAATCACA
1 GTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTTAGAAATAAAATCGGA
*
2205817 GTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTTAGAAATAAAA-CTGGG
1 GTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTTAGAAATAAAATC-GGA
2205868 GTTGGAGTATCCC
1 GTTGGAGTATCCC
2205881 TTCGGAAATG
Statistics
Matches: 99, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
50 1 0.01
51 98 0.99
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTTAGAAATAAAATCGGA
Found at i:2205957 original size:181 final size:181
Alignment explanation
Indices: 2205583--2205958 Score: 463
Period size: 181 Copynumber: 2.1 Consensus size: 181
2205573 TGAAAATAAT
* * **
2205583 GAGGTTGGAGTAT-CCCGATTGTGAAAAATTGATGCTTTAGAAATAAGGCTAGGGTTGGAGTATC
1 GAGGTTGGAGTATCCCCGATTGTGAAAAATTGATACTTTAGAAATAAAGCTACAGTTGGAGTATC
* * *
2205647 CCCGATTGTGAGAAATCATTATTTTGGAAATAAAATCGAGGTTGGAGTGTCCCCTCGAAAATAAC
66 CCCGATTGTGAGAAATCAGTATTTTAGAAATAAAATCGAGGTTGGAGTATCCCCTCGAAAATAAC
* *
2205712 GGGGTTGGAGTATCCTCAATTGTGAAAAATTAGTGTTTTAGAAATAAAATC
131 GGGGTTGGAATATCCCCAATTGTGAAAAATTAGTGTTTTAGAAATAAAATC
* * * * * * *
2205763 GAAGCTAGAGTATCCCCGATTGTGGAAAATTGGTATTTTAGAAATAAA-ATCACAGTTGGAGTAT
1 GAGGTTGGAGTATCCCCGATTGTGAAAAATTGATACTTTAGAAATAAAGCT-ACAGTTGGAGTAT
** * * * *
2205827 CCCCGATTGTG-GAAAATTGGTGTTTTAGAAATAAAA-CTGGGGTTGGAGTATCCCTTCGGAAAT
65 CCCCGATTGTGAG-AAATCAGTATTTTAGAAATAAAATC-GAGGTTGGAGTATCCCCTCGAAAAT
* * *
2205890 GACGGGGTTGGAATATCCCCAATTGTGAAAAATTAGTGTTTTGGGAATAAAATC
128 AACGGGGTTGGAATATCCCCAATTGTGAAAAATTAGTGTTTTAGAAATAAAATC
*
2205944 GGGGTTGGAGTATCC
1 GAGGTTGGAGTATCC
2205959 TCCAGATGAA
Statistics
Matches: 163, Mismatches: 29, Indels: 7
0.82 0.15 0.04
Matches are distributed among these distances:
180 13 0.08
181 150 0.92
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (181 bp):
GAGGTTGGAGTATCCCCGATTGTGAAAAATTGATACTTTAGAAATAAAGCTACAGTTGGAGTATC
CCCGATTGTGAGAAATCAGTATTTTAGAAATAAAATCGAGGTTGGAGTATCCCCTCGAAAATAAC
GGGGTTGGAATATCCCCAATTGTGAAAAATTAGTGTTTTAGAAATAAAATC
Found at i:2211431 original size:52 final size:52
Alignment explanation
Indices: 2211370--2211547 Score: 153
Period size: 52 Copynumber: 3.4 Consensus size: 52
2211360 TAATTCACTA
* * * *
2211370 CCAACGACATTGAACTTAAAGACGAGAAGAATGCCAATAG-GCTGATTCAAGG
1 CCAATGACATTGAACTTAAAAACGAGAAGAATGCCAAT-GTACTGATTCAAAG
* * *
2211422 CCAATGACATTGGACTTAAAAATGAGAAGAATGCCAATGTATTGATTCAAAG
1 CCAATGACATTGAACTTAAAAACGAGAAGAATGCCAATGTACTGATTCAAAG
* ** * * * * * *
2211474 CCAGTGACATTGGGCTTAAAAATGATAA-AGGTGCGAATGTGCTGATTCAAGG
1 CCAATGACATTGAACTTAAAAACGAGAAGA-ATGCCAATGTACTGATTCAAAG
* * *
2211526 CTAGTGACATTGAGCTTAAAAA
1 CCAATGACATTGAACTTAAAAA
2211548 TGATACAGGC
Statistics
Matches: 107, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
51 2 0.02
52 105 0.98
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.23
Consensus pattern (52 bp):
CCAATGACATTGAACTTAAAAACGAGAAGAATGCCAATGTACTGATTCAAAG
Found at i:2211548 original size:52 final size:52
Alignment explanation
Indices: 2211396--2211702 Score: 205
Period size: 52 Copynumber: 5.9 Consensus size: 52
2211386 TAAAGACGAG
* *
2211396 AAGAATGCCAATAG-GCTGATTCAAGGCCAATGACATTGGACTTAAAAATGA-G
1 AAGAATGCCAAT-GTGCTGATTCAAGGCCAGTGACATTGG-CTTAAAAATGATA
** *
2211448 AAGAATGCCAATGTATTGATTCAAAGCCAGTGACATTGGGCTTAAAAATGATA
1 AAGAATGCCAATGTGCTGATTCAAGGCCAGTGACATT-GGCTTAAAAATGATA
* * *
2211501 AAG-GTGCGAATGTGCTGATTCAAGGCTAGTGACATTGAGCTTAAAAATGATA
1 AAGAATGCCAATGTGCTGATTCAAGGCCAGTGACATTG-GCTTAAAAATGATA
* ** * * * * * * * * * *
2211553 CAG-GCGCTAATATGTTGACTT-ACGGACAATGATATCGGACTTAAAGATGAGA
1 AAGAATGCCAATGTGCTGA-TTCAAGGCCAGTGACATTGG-CTTAAAAATGATA
* ** ** *
2211605 AA-AATACCAATGTGCTGATTCAAGGTTAGCCACATTGGGCTTAAAGATGATA
1 AAGAATGCCAATGTGCTGATTCAAGGCCAGTGACATT-GGCTTAAAAATGATA
* * * *
2211657 AA-AAGTGCCAATCTGCTAATTCAAGGCCAGCGATATTGGACTTAAA
1 AAGAA-TGCCAATGTGCTGATTCAAGGCCAGTGACATTGG-CTTAAA
2211703 GTGCCAATGT
Statistics
Matches: 197, Mismatches: 47, Indels: 21
0.74 0.18 0.08
Matches are distributed among these distances:
51 5 0.03
52 152 0.77
53 40 0.20
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (52 bp):
AAGAATGCCAATGTGCTGATTCAAGGCCAGTGACATTGGCTTAAAAATGATA
Found at i:2211695 original size:53 final size:52
Alignment explanation
Indices: 2211583--2211703 Score: 143
Period size: 53 Copynumber: 2.3 Consensus size: 52
2211573 TACGGACAAT
* * * **
2211583 GATATCGGACTTAAAGATGAGAAAAATACCAATGTGCTGATTCAAGGTTAGC
1 GATATTGGACTTAAAGATGAGAAAAATACCAATCTGCTAATTCAAGGCCAGC
* * * * *
2211635 CACATTGGGCTTAAAGATGATAAAAAGTGCCAATCTGCTAATTCAAGGCCAGC
1 GATATTGGACTTAAAGATGAGAAAAA-TACCAATCTGCTAATTCAAGGCCAGC
2211688 GATATTGGACTTAAAG
1 GATATTGGACTTAAAG
2211704 TGCCAATGTG
Statistics
Matches: 55, Mismatches: 13, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
52 21 0.38
53 34 0.62
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (52 bp):
GATATTGGACTTAAAGATGAGAAAAATACCAATCTGCTAATTCAAGGCCAGC
Found at i:2211721 original size:42 final size:42
Alignment explanation
Indices: 2211658--2211784 Score: 155
Period size: 42 Copynumber: 3.0 Consensus size: 42
2211648 AAGATGATAA
* * * *
2211658 AAAGTGCCAATCTGCTAATTCAAGGCCAGCGATATTGGACTT
1 AAAGTGCCAATGTGTTGATTCAAGGCCAACGATATTGGACTT
* ***
2211700 AAAGTGCCAATGTGTTGATTCAAGGCCAATGATATCAAACTT
1 AAAGTGCCAATGTGTTGATTCAAGGCCAACGATATTGGACTT
* * *
2211742 AAAGTGCCAATGTGTTGATTTAAGGCCAACGACATTGGGCTT
1 AAAGTGCCAATGTGTTGATTCAAGGCCAACGATATTGGACTT
2211784 A
1 A
2211785 GAAGGGTTGC
Statistics
Matches: 70, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (42 bp):
AAAGTGCCAATGTGTTGATTCAAGGCCAACGATATTGGACTT
Found at i:2211822 original size:33 final size:33
Alignment explanation
Indices: 2211784--2212352 Score: 129
Period size: 33 Copynumber: 17.8 Consensus size: 33
2211774 CATTGGGCTT
* * * *
2211784 AGAAGGGTTGCCACCGACCTGTGTGGACTTTAG
1 AGAAAGGTTGCCACCAACTTATGTGGACTTTAG
* * * *
2211817 AGAAGGGTTGCTACCCACTTATGT-GAGCATTAG
1 AGAAAGGTTGCCACCAACTTATGTGGA-CTTTAG
* *
2211850 AGAAAGGTTGCCACTAACTTATGTGGGCTTTAG
1 AGAAAGGTTGCCACCAACTTATGTGGACTTTAG
* * * * *
2211883 AGAAAGGTTGCCAACAATTTGTATGGGCTTT--
1 AGAAAGGTTGCCACCAACTTATGTGGACTTTAG
* * * * *
2211914 AG-AAGGATTACCACCAAGTTGTATGGGCTTTAG
1 AGAAAGG-TTGCCACCAACTTATGTGGACTTTAG
* * ** * * *
2211947 AGAATGATTGTTATCGACTTATGTGGGCTTT--
1 AGAAAGGTTGCCACCAACTTATGTGGACTTTAG
* ** *
2211978 -GTAAGGATTGCCACTGACTCATGTGG-CTTTAG
1 AGAAAGG-TTGCCACCAACTTATGTGGACTTTAG
* * *** * *
2212010 AGAATA-GTTACTACTGGCTTGTGTGGGCTTT--
1 AGAA-AGGTTGCCACCAACTTATGTGGACTTTAG
* * * ** *
2212041 AGAAAGATTGCC-CTTAACTTGTAAGGGCTTT--
1 AGAAAGGTTGCCAC-CAACTTATGTGGACTTTAG
* ** *
2212072 AGAAAGATTGCCATTAACTTGTGT-GAGCTTT--
1 AGAAAGGTTGCCACCAACTTATGTGGA-CTTTAG
**
2212103 AG-AAGGATTGTTACCAACTTATGTAGG-CTTTAG
1 AGAAAGG-TTGCCACCAACTTATGT-GGACTTTAG
* * *
2212136 AGAAAGGTTGCCACTAACTTGTGTGGGCTTT--
1 AGAAAGGTTGCCACCAACTTATGTGGACTTTAG
* * *
2212167 AG-AAGGATTG-CACCGACTTGTGTGGGCTTTAG
1 AGAAAGG-TTGCCACCAACTTATGTGGACTTTAG
* ** * *
2212199 AGAAGGGTTGCCATTAACTTGTGTGGGCTTT--
1 AGAAAGGTTGCCACCAACTTATGTGGACTTTAG
** * *
2212230 AG-AAGGATTGCCACTGACTTGTGTGGCCTTT--
1 AGAAAGG-TTGCCACCAACTTATGTGGACTTTAG
* * *
2212261 AG-AAGGATTGCCACCGAA-TTGTGTGGGCTTTAA
1 AGAAAGG-TTGCCACC-AACTTATGTGGACTTTAG
* * * *
2212294 AGAAGGGTTGCCACCGACTTATATAGG-TTTTAG
1 AGAAAGGTTGCCACCAACTTATGT-GGACTTTAG
* * *
2212327 AGAAGGGTTACCACCAACTTGTGTGG
1 AGAAAGGTTGCCACCAACTTATGTGG
2212353 GGTTTCTAAA
Statistics
Matches: 414, Mismatches: 87, Indels: 71
0.72 0.15 0.12
Matches are distributed among these distances:
30 42 0.10
31 153 0.37
32 27 0.07
33 179 0.43
34 13 0.03
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.31
Consensus pattern (33 bp):
AGAAAGGTTGCCACCAACTTATGTGGACTTTAG
Found at i:2212050 original size:63 final size:64
Alignment explanation
Indices: 2211777--2212353 Score: 366
Period size: 64 Copynumber: 9.1 Consensus size: 64
2211767 CCAACGACAT
* * * * * * ** *
2211777 TGGGC-TTAGAAGGGTTGCCACCGACCTGTGT-GGACTTTAGAGAAGGGTTGCTACCCACTTATG
1 TGGGCTTTAGAAGGATTGCCACTGACTTATGTAGG-CTTTAGAGAAGAGTTGCCACTAACTTGTG
* * * * *
2211840 TGAGCATTAGAGAAAGG-TTGCCACTAACTTATGTGGGCTTTAGAGAA-AGGTTGCCAAC-AATT
1 TGGGC-TT-TAG-AAGGATTGCCACTGACTTATGTAGGCTTTAGAGAAGA-GTTGCC-ACTAACT
*
2211902 TGTA
61 TGTG
* ** * * * * ** * *
2211906 TGGGCTTTAGAAGGATTACCACCAAGTTGTATGGGCTTTAGAGAATGA-TTGTTA-TCGACTTAT
1 TGGGCTTTAGAAGGATTGCCACTGACTTATGTAGGCTTTAGAGAA-GAGTTGCCACT-AACTTGT
2211969 G
64 G
* * * * **
2211970 TGGGCTTT-GTAAGGATTGCCACTGACTCATGT-GGCTTTAGAGAATAGTTACTACTGGCTTGTG
1 TGGGCTTTAG-AAGGATTGCCACTGACTTATGTAGGCTTTAGAGAAGAGTTGCCACTAACTTGTG
* * *
2212033 TGGGCTTTAGAAAGATTGCC-CTTAAC-T-TGTAAGGGCTTTAGA-AAGA-TTGCCATTAACTTG
1 TGGGCTTTAGAAGGATTGCCAC-TGACTTATGT-A-GGCTTTAGAGAAGAGTTGCCACTAACTTG
2212093 TG
63 TG
* ** **
2212095 TGAGCTTTAGAAGGATTGTTACCAACTTATGTAGGCTTTAGAGAA-AGGTTGCCACTAACTTGTG
1 TGGGCTTTAGAAGGATTGCCACTGACTTATGTAGGCTTTAGAGAAGA-GTTGCCACTAACTTGTG
* * * * *
2212159 TGGGCTTTAGAAGGATTG-CACCGACTTGTGTGGGCTTTAGAGAAGGGTTGCCATTAACTTGTG
1 TGGGCTTTAGAAGGATTGCCACTGACTTATGTAGGCTTTAGAGAAGAGTTGCCACTAACTTGTG
* * *
2212222 TGGGCTTTAGAAGGATTGCCACTGACTTGTGT-GGCCTTTAGA-AGGA-TTGCCACCGAA-TTGT
1 TGGGCTTTAGAAGGATTGCCACTGACTTATGTAGG-CTTTAGAGAAGAGTTGCCA-CTAACTTGT
2212283 G
64 G
* * * * * * *
2212284 TGGGCTTTAAAGAAGGGTTGCCACCGACTTATATAGGTTTTAGAGAAGGGTTACCACCAACTTGT
1 TGGGCTTT--AGAAGGATTGCCACTGACTTATGTAGGCTTTAGAGAAGAGTTGCCACTAACTTGT
2212349 G
64 G
2212350 TGGG
1 TGGG
2212354 GTTTCTAAAG
Statistics
Matches: 405, Mismatches: 73, Indels: 69
0.74 0.13 0.13
Matches are distributed among these distances:
61 3 0.01
62 61 0.15
63 122 0.30
64 148 0.37
65 10 0.02
66 53 0.13
67 8 0.02
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.31
Consensus pattern (64 bp):
TGGGCTTTAGAAGGATTGCCACTGACTTATGTAGGCTTTAGAGAAGAGTTGCCACTAACTTGTG
Found at i:2212069 original size:31 final size:30
Alignment explanation
Indices: 2212027--2212292 Score: 223
Period size: 31 Copynumber: 8.5 Consensus size: 30
2212017 TTACTACTGG
2212027 CTTGTGTGGGCTTTAGAAAGATTGCCCTTAA
1 CTTGTGTGGGCTTTAGAAAGATTGCCC-TAA
** *
2212058 CTTGTAAGGGCTTTAGAAAGATTGCCATTAA
1 CTTGTGTGGGCTTTAGAAAGATTGCC-CTAA
* * *
2212089 CTTGTGTGAGCTTTAGAAGGATTGTTACC-AA
1 CTTGTGTGGGCTTTAGAAAGATTG--CCCTAA
* * *
2212120 CTTATGTAGGCTTTAGAGAAAGGTTGCCACTAA
1 CTTGTGTGGGCTTT--AGAAAGATTGCC-CTAA
* *
2212153 CTTGTGTGGGCTTTAGAAGGATTGCACC-GA
1 CTTGTGTGGGCTTTAGAAAGATTGC-CCTAA
* *
2212183 CTTGTGTGGGCTTTAGAGAAGGGTTGCCATTAA
1 CTTGTGTGGGCTTTAGA-AA-GATTGCC-CTAA
* *
2212216 CTTGTGTGGGCTTTAGAAGGATTGCCACTGA
1 CTTGTGTGGGCTTTAGAAAGATTGCC-CTAA
* * *
2212247 CTTGTGTGGCCTTTAGAAGGATTGCCACCGAA
1 CTTGTGTGGGCTTTAGAAAGATTG-C-CCTAA
2212279 -TTGTGTGGGCTTTA
1 CTTGTGTGGGCTTTA
2212293 AAGAAGGGTT
Statistics
Matches: 189, Mismatches: 32, Indels: 28
0.76 0.13 0.11
Matches are distributed among these distances:
30 18 0.10
31 118 0.62
32 11 0.06
33 42 0.22
ACGTcount: A:0.23, C:0.15, G:0.29, T:0.33
Consensus pattern (30 bp):
CTTGTGTGGGCTTTAGAAAGATTGCCCTAA
Found at i:2212102 original size:158 final size:157
Alignment explanation
Indices: 2211866--2212270 Score: 405
Period size: 158 Copynumber: 2.6 Consensus size: 157
2211856 GTTGCCACTA
* ** * * *
2211866 ACTTATGTGGGCTTTAGAGAAAGG-TTGCCAACAATTTGTATGGGCTTTAGAAGGATTACCACCA
1 ACTTGTGTGGGCTTTAGAG-AAGGATTGCCATTAACTTGTATGGGCTTTAGAAGGATTGCCACTA
* * * * * * * *
2211930 AGTTGTATGGGCTTTAGAGAATGATTGTTATCGACTTATGTGGGCTTT-GTAAGGATTGCCACTG
65 ACTTGTGT-GGCTTTAGAGAAGGATTGTTACCAACTTATGTAGGCTTTAGAAAGG-TTGCCACTA
* *
2211994 ACTCATGT-GGCTTTAGAGAATAGTTACTACTG
128 ACTCATGTGGGCTTTAGA-AAGA-TTAC-ACCG
* * * * *
2212026 GCTTGTGTGGGCTTTAGA-AA-GATTGCCCTTAACTTGTAAGGGCTTTAGAAAGATTGCCATTAA
1 ACTTGTGTGGGCTTTAGAGAAGGATTGCCATTAACTTGTATGGGCTTTAGAAGGATTGCCACTAA
2212089 CTTGTGTGAGCTTT--AGAAGGATTGTTACCAACTTATGTAGGCTTTAGAGAAAGGTTGCCACTA
66 CTTGTGTG-GCTTTAGAGAAGGATTGTTACCAACTTATGTAGGCTTT--AGAAAGGTTGCCACTA
** * *
2212152 ACTTGTGTGGGCTTTAGAAGGATTGCACCG
128 ACTCATGTGGGCTTTAGAAAGATTACACCG
* * *
2212182 ACTTGTGTGGGCTTTAGAGAAGGGTTGCCATTAACTTGTGTGGGCTTTAGAAGGATTGCCACTGA
1 ACTTGTGTGGGCTTTAGAGAAGGATTGCCATTAACTTGTATGGGCTTTAGAAGGATTGCCACTAA
2212247 CTTGTGTGGCCTTT--AGAAGGATTG
66 CTTGTGTGG-CTTTAGAGAAGGATTG
2212271 CCACCGAATT
Statistics
Matches: 203, Mismatches: 33, Indels: 20
0.79 0.13 0.08
Matches are distributed among these distances:
156 47 0.23
157 8 0.04
158 118 0.58
159 14 0.07
160 16 0.08
ACGTcount: A:0.25, C:0.14, G:0.28, T:0.33
Consensus pattern (157 bp):
ACTTGTGTGGGCTTTAGAGAAGGATTGCCATTAACTTGTATGGGCTTTAGAAGGATTGCCACTAA
CTTGTGTGGCTTTAGAGAAGGATTGTTACCAACTTATGTAGGCTTTAGAAAGGTTGCCACTAACT
CATGTGGGCTTTAGAAAGATTACACCG
Found at i:2212370 original size:158 final size:158
Alignment explanation
Indices: 2212027--2212353 Score: 383
Period size: 158 Copynumber: 2.1 Consensus size: 158
2212017 TTACTACTGG
* * *
2212027 CTTGTGTGGGCTTTAGA-AA-GATTGCCCTTAACTTGTAAGGGCTTTAGAAAGATTGCCATTAAC
1 CTTGTGTGGGCTTTAGAGAAGGGTTGCCATTAACTTGTAAGGGCTTTAGAAAGATTGCCACTAAC
** * *
2212090 TTGTGTGAGCTTTAGAAGGATTGTTACCAACTTATGTAGGCTTTAGAGAAAGGTTGCCACTAACT
66 TTGTGTGAGCTTTAGAAGGATTGCCACCAACTTATGTAGGCTTTAAAGAAAGGTTGCCACCAACT
* * * * *
2212155 TGTGTGGGCTTTAGAAGGATTGCACCGA
131 TATATAGGCTTTAGAAGGATTCCACCAA
** * *
2212183 CTTGTGTGGGCTTTAGAGAAGGGTTGCCATTAACTTGTGTGGGCTTTAGAAGGATTGCCACTGAC
1 CTTGTGTGGGCTTTAGAGAAGGGTTGCCATTAACTTGTAAGGGCTTTAGAAAGATTGCCACTAAC
* * * *
2212248 TTGTGTG-GCCTTTAGAAGGATTGCCACCGAA-TTGTGTGGGCTTTAAAGAAGGGTTGCCACCGA
66 TTGTGTGAG-CTTTAGAAGGATTGCCACC-AACTTATGTAGGCTTTAAAGAAAGGTTGCCACCAA
* *
2212311 CTTATATAGGTTTTAGAGAAGGGTTACCACCAA
129 CTTATATAGGCTTT--AGAAGGATT-CCACCAA
2212344 CTTGTGTGGG
1 CTTGTGTGGG
2212354 GTTTCTAAAG
Statistics
Matches: 142, Mismatches: 22, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
156 17 0.12
157 3 0.02
158 97 0.68
159 2 0.01
160 8 0.06
161 15 0.11
ACGTcount: A:0.24, C:0.15, G:0.29, T:0.32
Consensus pattern (158 bp):
CTTGTGTGGGCTTTAGAGAAGGGTTGCCATTAACTTGTAAGGGCTTTAGAAAGATTGCCACTAAC
TTGTGTGAGCTTTAGAAGGATTGCCACCAACTTATGTAGGCTTTAAAGAAAGGTTGCCACCAACT
TATATAGGCTTTAGAAGGATTCCACCAA
Found at i:2212404 original size:28 final size:28
Alignment explanation
Indices: 2212372--2212473 Score: 107
Period size: 28 Copynumber: 3.6 Consensus size: 28
2212362 AGGTGCCATA
*
2212372 GAGTTGTAGACTTAAAAGGGGTACCACG
1 GAGTTGTAGACTTAAAAGAGGTACCACG
* * *
2212400 GAGTTGTGGACTTAATAA-AGATACCACA
1 GAGTTGTAGACTTAA-AAGAGGTACCACG
* * *
2212428 GAGTTATAAACTTTAAAAGAGGTGCCACG
1 GAGTTGTAGAC-TTAAAAGAGGTACCACG
*
2212457 GAGTTGTGGACTTAAAA
1 GAGTTGTAGACTTAAAA
2212474 AAAGTGCCAC
Statistics
Matches: 58, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
28 37 0.64
29 21 0.36
ACGTcount: A:0.36, C:0.13, G:0.26, T:0.25
Consensus pattern (28 bp):
GAGTTGTAGACTTAAAAGAGGTACCACG
Found at i:2212460 original size:57 final size:57
Alignment explanation
Indices: 2212383--2212491 Score: 166
Period size: 57 Copynumber: 1.9 Consensus size: 57
2212373 AGTTGTAGAC
* *
2212383 TTAAAAGGGGTACCACGGAGTTGTGGACTT-AATAAAGATACCACAGAGTTATAAACT
1 TTAAAAGAGGTACCACGGAGTTGTGGACTTAAAAAAAG-TACCACAGAGTTATAAACT
* *
2212440 TTAAAAGAGGTGCCACGGAGTTGTGGACTTAAAAAAAGTGCCACAGAGTTAT
1 TTAAAAGAGGTACCACGGAGTTGTGGACTTAAAAAAAGTACCACAGAGTTAT
2212492 GGACTTCGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
57 41 0.87
58 6 0.13
ACGTcount: A:0.38, C:0.14, G:0.25, T:0.24
Consensus pattern (57 bp):
TTAAAAGAGGTACCACGGAGTTGTGGACTTAAAAAAAGTACCACAGAGTTATAAACT
Found at i:2212480 original size:28 final size:28
Alignment explanation
Indices: 2212371--2212497 Score: 94
Period size: 28 Copynumber: 4.5 Consensus size: 28
2212361 AAGGTGCCAT
* ***
2212371 AGAGTTGTAGACTTAAAAGGGGTACCAC
1 AGAGTTGTGGACTTAAAAAAAGTACCAC
* *
2212399 GGAGTTGTGGACTT-AATAAAGATACCAC
1 AGAGTTGTGGACTTAAAAAAAG-TACCAC
* ** * * *
2212427 AGAGTTATAAACTTTAAAAGAGGTGCCAC
1 AGAGTTGTGGAC-TTAAAAAAAGTACCAC
* *
2212456 GGAGTTGTGGACTTAAAAAAAGTGCCAC
1 AGAGTTGTGGACTTAAAAAAAGTACCAC
*
2212484 AGAGTTATGGACTT
1 AGAGTTGTGGACTT
2212498 CGAAGAAAAA
Statistics
Matches: 74, Mismatches: 22, Indels: 6
0.73 0.22 0.06
Matches are distributed among these distances:
27 3 0.04
28 52 0.70
29 15 0.20
30 4 0.05
ACGTcount: A:0.36, C:0.13, G:0.26, T:0.24
Consensus pattern (28 bp):
AGAGTTGTGGACTTAAAAAAAGTACCAC
Found at i:2212559 original size:30 final size:30
Alignment explanation
Indices: 2212523--2212655 Score: 151
Period size: 30 Copynumber: 4.4 Consensus size: 30
2212513 CACAAACTTA
* * *
2212523 TGGACTTTGAGAAGGGATGTC-ACTGAGTTG
1 TGGACTTTGAGAAAGGATG-CGACTAAGTCG
*
2212553 TGGACTTTGAGAAAGGATGCGACTGAGTCG
1 TGGACTTTGAGAAAGGATGCGACTAAGTCG
* * *
2212583 TGGACTTTTAGAAAGGTTGCCACTAAGTCG
1 TGGACTTTGAGAAAGGATGCGACTAAGTCG
* * * *
2212613 TGGACTTTGAAAAAAGATGCTACTAAGTTG
1 TGGACTTTGAGAAAGGATGCGACTAAGTCG
2212643 TGGACTTTGAGAA
1 TGGACTTTGAGAA
2212656 GGAGCTACGA
Statistics
Matches: 89, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
29 1 0.01
30 88 0.99
ACGTcount: A:0.29, C:0.12, G:0.31, T:0.29
Consensus pattern (30 bp):
TGGACTTTGAGAAAGGATGCGACTAAGTCG
Found at i:2212587 original size:60 final size:60
Alignment explanation
Indices: 2212523--2212657 Score: 171
Period size: 60 Copynumber: 2.2 Consensus size: 60
2212513 CACAAACTTA
* * * * * *
2212523 TGGACTTTGAGAAGGGATGTCACTGAGTTGTGGACTTTGAGAAAGGATGCGACTGAGTCG
1 TGGACTTTGAGAAGGGATGCCACTAAGTCGTGGACTTTGAAAAAAGATGCGACTAAGTCG
* * * * *
2212583 TGGACTTTTAGAAAGGTTGCCACTAAGTCGTGGACTTTGAAAAAAGATGCTACTAAGTTG
1 TGGACTTTGAGAAGGGATGCCACTAAGTCGTGGACTTTGAAAAAAGATGCGACTAAGTCG
2212643 TGGACTTTGAGAAGG
1 TGGACTTTGAGAAGG
2212658 AGCTACGAAA
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.28, C:0.12, G:0.32, T:0.28
Consensus pattern (60 bp):
TGGACTTTGAGAAGGGATGCCACTAAGTCGTGGACTTTGAAAAAAGATGCGACTAAGTCG
Found at i:2219086 original size:13 final size:13
Alignment explanation
Indices: 2219068--2219093 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2219058 TACAGCAAGT
2219068 ATGTATCGATACA
1 ATGTATCGATACA
2219081 ATGTATCGATACA
1 ATGTATCGATACA
2219094 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2223176 original size:15 final size:15
Alignment explanation
Indices: 2223156--2223194 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
2223146 TAAAAATGTC
*
2223156 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
2223171 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
*
2223186 CCAAATGAA
1 CAAAATGAA
2223195 ATTGATGTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.51, C:0.15, G:0.21, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:2225284 original size:20 final size:21
Alignment explanation
Indices: 2225206--2225283 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 21
2225196 ATGTCCAAAA
*
2225206 TGTATCGATACATGTTTTTG-
1 TGTATCGATACATCTTTTTGT
** *
2225226 TGTATCGATACATCTGGAAATTCT
1 TGTATCGATACATCT---TTTTGT
2225250 ATGTATCGATACAT-TTTTTGT
1 -TGTATCGATACATCTTTTTGT
2225271 TGTATCGATACAT
1 TGTATCGATACAT
2225284 TGTATCGATA
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
20 27 0.59
21 3 0.07
23 2 0.04
24 1 0.02
25 13 0.28
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.45
Consensus pattern (21 bp):
TGTATCGATACATCTTTTTGT
Found at i:2225288 original size:13 final size:13
Alignment explanation
Indices: 2225270--2225308 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
2225260 ACATTTTTTG
2225270 TTGTATCGATACA
1 TTGTATCGATACA
2225283 TTGTATCGATACA
1 TTGTATCGATACA
*
2225296 CTGTATCGATACA
1 TTGTATCGATACA
2225309 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2227138 original size:16 final size:17
Alignment explanation
Indices: 2227114--2227160 Score: 78
Period size: 16 Copynumber: 2.8 Consensus size: 17
2227104 AATTACTTGA
2227114 TTAAAGGGGGAGATTTT
1 TTAAAGGGGGAGATTTT
2227131 TT-AAGGGGGAGATTTT
1 TTAAAGGGGGAGATTTT
2227147 TTAAACGGGGGAGA
1 TTAAA-GGGGGAGA
2227161 CAAAGGAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.57
17 4 0.14
18 8 0.29
ACGTcount: A:0.30, C:0.02, G:0.38, T:0.30
Consensus pattern (17 bp):
TTAAAGGGGGAGATTTT
Found at i:2227877 original size:13 final size:13
Alignment explanation
Indices: 2227859--2227884 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2227849 TACAGCAAGT
2227859 ATGTATCGATACA
1 ATGTATCGATACA
2227872 ATGTATCGATACA
1 ATGTATCGATACA
2227885 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2232067 original size:13 final size:13
Alignment explanation
Indices: 2232049--2232073 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2232039 CATACTGCTT
2232049 TGTATCGATACAA
1 TGTATCGATACAA
2232062 TGTATCGATACA
1 TGTATCGATACA
2232074 TGCTCATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2232070 original size:33 final size:32
Alignment explanation
Indices: 2232028--2232092 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 32
2232018 ACACTCCCAG
*
2232028 ATGTATCGATACATACTGCTTTGTATCGATACA
1 ATGTATCGATACATACT-CATTGTATCGATACA
*
2232061 ATGTATCGATACATGCTCATTGTATCGATACA
1 ATGTATCGATACATACTCATTGTATCGATACA
2232093 TGGACAATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.47
33 16 0.53
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.35
Consensus pattern (32 bp):
ATGTATCGATACATACTCATTGTATCGATACA
Found at i:2232104 original size:20 final size:20
Alignment explanation
Indices: 2232058--2232112 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 20
2232048 TTGTATCGAT
2232058 ACAA-TGTATCGATACATGC
1 ACAATTGTATCGATACATGC
* *
2232077 TC-ATTGTATCGATACATGG
1 ACAATTGTATCGATACATGC
2232096 ACAATTGTATCGATACA
1 ACAATTGTATCGATACA
2232113 CGAAACTGAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 1 0.03
19 16 0.52
20 14 0.45
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (20 bp):
ACAATTGTATCGATACATGC
Found at i:2232182 original size:13 final size:13
Alignment explanation
Indices: 2232164--2232212 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
2232154 CATGGGACAA
2232164 TGTATCGATACAT
1 TGTATCGATACAT
2232177 TGTATCGATACA-
1 TGTATCGATACAT
2232189 TG-AT-GA-A-AT
1 TGTATCGATACAT
*
2232198 TGTATCAATACAT
1 TGTATCGATACAT
2232211 TG
1 TG
2232213 CTTGGAACGG
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
8 1 0.03
9 3 0.10
10 4 0.13
11 3 0.10
12 3 0.10
13 16 0.53
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2232209 original size:34 final size:33
Alignment explanation
Indices: 2232146--2232212 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 33
2232136 TCACTATTTA
*
2232146 TATCGATACATGGGACAATGTATCGATACATTG
1 TATCGATACATGGGACAATGTATCAATACATTG
*
2232179 TATCGATACATGATGA-AATTGTATCAATACATTG
1 TATCGATACATG-GGACAA-TGTATCAATACATTG
2232213 CTTGGAACGG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 14 0.47
34 16 0.53
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (33 bp):
TATCGATACATGGGACAATGTATCAATACATTG
Found at i:2233939 original size:12 final size:12
Alignment explanation
Indices: 2233922--2233953 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
2233912 ATAAAATTAA
2233922 ATTTTAATTATT
1 ATTTTAATTATT
2233934 ATTTTAATTATT
1 ATTTTAATTATT
*
2233946 TTTTTAAT
1 ATTTTAAT
2233954 CTTTTATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
ATTTTAATTATT
Found at i:2234179 original size:149 final size:150
Alignment explanation
Indices: 2233955--2234241 Score: 443
Period size: 149 Copynumber: 1.9 Consensus size: 150
2233945 TTTTTTAATC
* * * *
2233955 TTTTATATTTCTATGGGCATCCGTAGGGGTATAACAGATTTCAAAAATGTTTCATATCCTTTCGA
1 TTTTATATTCCTATGGGCATCCGCAGAGGTATAAAAGATTTCAAAAATGTTTCATATCCTTTCGA
* * *
2234020 ACTTCCATTAGGGTACGAAATGGTATTTTCGAAAATAAATAAAATTAAACTGAATTAATACTTTC
66 ACTTCCATTAGGATACGAAATGGTATTTTCAAAAATAAATAAAATTAAACTAAATTAATACTTTC
2234085 GGGATAAATTTTAATTATTT
131 GGGATAAATTTTAATTATTT
2234105 TTTTATATTCCTATGGGCATCCGCA-AGGTATAAAAGATTTCAAAAATGTTTCATATCCTTTC-A
1 TTTTATATTCCTATGGGCATCCGCAGAGGTATAAAAGATTTCAAAAATGTTTCATATCCTTTCGA
* * * *
2234168 GGCTTCTATTAGGATATGAAATGGTATTTTCAAAAATAAATAAAATTAAATTAAATTAATACTTT
66 -ACTTCCATTAGGATACGAAATGGTATTTTCAAAAATAAATAAAATTAAACTAAATTAATACTTT
*
2234233 TGGGATAAA
130 CGGGATAAA
2234242 AGTATAAAAG
Statistics
Matches: 124, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
148 1 0.01
149 100 0.81
150 23 0.19
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.38
Consensus pattern (150 bp):
TTTTATATTCCTATGGGCATCCGCAGAGGTATAAAAGATTTCAAAAATGTTTCATATCCTTTCGA
ACTTCCATTAGGATACGAAATGGTATTTTCAAAAATAAATAAAATTAAACTAAATTAATACTTTC
GGGATAAATTTTAATTATTT
Found at i:2236544 original size:2 final size:2
Alignment explanation
Indices: 2236537--2236561 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2236527 TTAAAGGCAT
2236537 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2236562 TCTAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2240919 original size:21 final size:22
Alignment explanation
Indices: 2240893--2240944 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
2240883 AAAGGTATAT
2240893 TTGGATGAAATG-ACGCATTAA
1 TTGGATGAAATGAACGCATTAA
* **
2240914 TTGGATG-AATGAATGCATTTG
1 TTGGATGAAATGAACGCATTAA
2240935 TTGGATGAAA
1 TTGGATGAAA
2240945 GGATACACTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 4 0.15
21 20 0.77
22 2 0.08
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.33
Consensus pattern (22 bp):
TTGGATGAAATGAACGCATTAA
Found at i:2240956 original size:21 final size:21
Alignment explanation
Indices: 2240914--2240962 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
2240904 GACGCATTAA
* * *
2240914 TTGGATGAATGAATGCATTTG
1 TTGGATGAAAGAATACACTTG
*
2240935 TTGGATGAAAGGATACACTTG
1 TTGGATGAAAGAATACACTTG
*
2240956 TAGGATG
1 TTGGATG
2240963 GAAAATGCAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.31, C:0.06, G:0.31, T:0.33
Consensus pattern (21 bp):
TTGGATGAAAGAATACACTTG
Found at i:2241455 original size:21 final size:21
Alignment explanation
Indices: 2241429--2241470 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2241419 CTCCTTATTA
2241429 ATACTCTATTAAGAAATAGTT
1 ATACTCTATTAAGAAATAGTT
*
2241450 ATACTCTGTTAAGAAATAGTT
1 ATACTCTATTAAGAAATAGTT
2241471 CTTCTTCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (21 bp):
ATACTCTATTAAGAAATAGTT
Found at i:2245901 original size:18 final size:18
Alignment explanation
Indices: 2245880--2245916 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
2245870 ACTTTACGAA
2245880 TTCTATAAATTTATTAGT
1 TTCTATAAATTTATTAGT
2245898 TTCTATAAATTTATTAGT
1 TTCTATAAATTTATTAGT
2245916 T
1 T
2245917 AACTTTTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.57
Consensus pattern (18 bp):
TTCTATAAATTTATTAGT
Found at i:2248656 original size:14 final size:15
Alignment explanation
Indices: 2248626--2248676 Score: 59
Period size: 14 Copynumber: 3.4 Consensus size: 15
2248616 TTTTTTTGTG
* *
2248626 AAGAAAAGATGAAGA
1 AAGAAAAAATAAAGA
2248641 AAGAAAAAA-AAAGA
1 AAGAAAAAATAAAGA
*
2248655 AAAAAAAAATAAGAGA
1 AAGAAAAAATAA-AGA
2248671 AAGAAA
1 AAGAAA
2248677 GGTAAATTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
14 12 0.40
15 10 0.33
16 8 0.27
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (15 bp):
AAGAAAAAATAAAGA
Found at i:2248764 original size:16 final size:17
Alignment explanation
Indices: 2248739--2248772 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2248729 ATAATATAAA
*
2248739 AAAGAGAAAGAA-AAAG
1 AAAGAAAAAGAAGAAAG
2248755 AAAGAAAAAGAAGAAAG
1 AAAGAAAAAGAAGAAAG
2248772 A
1 A
2248773 TAGATTTGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAGAAGAAAG
Found at i:2248768 original size:9 final size:10
Alignment explanation
Indices: 2248738--2248770 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
2248728 TATAATATAA
2248738 AAAAGAGAAAG
1 AAAA-AGAAAG
2248749 AAAAAGAAAG
1 AAAAAGAAAG
2248759 AAAAAG-AAG
1 AAAAAGAAAG
2248768 AAA
1 AAA
2248771 GATAGATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 6 0.27
10 12 0.55
11 4 0.18
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:2249555 original size:16 final size:17
Alignment explanation
Indices: 2249529--2249566 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
2249519 AATTTTGATT
2249529 TATTT-ATTTAAA-AAA
1 TATTTAATTTAAATAAA
*
2249544 TATTTAATTTAAATAAT
1 TATTTAATTTAAATAAA
2249561 TATTTA
1 TATTTA
2249567 GTTAAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 5 0.25
16 7 0.35
17 8 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATTTAATTTAAATAAA
Found at i:2249571 original size:16 final size:15
Alignment explanation
Indices: 2249528--2249596 Score: 66
Period size: 16 Copynumber: 4.3 Consensus size: 15
2249518 CAATTTTGAT
2249528 TTATTTATTTAAAAA
1 TTATTTATTTAAAAA
*
2249543 ATATTTAATTTAAATAA
1 TTATTT-ATTTAAA-AA
* *
2249560 TTATTTAGTTAAAATT
1 TTATTTATTTAAAA-A
*
2249576 TTATATATTTAACAAA
1 TTATTTATTTAA-AAA
2249592 TTATT
1 TTATT
2249597 AATCGATACT
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
15 6 0.14
16 27 0.64
17 9 0.21
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (15 bp):
TTATTTATTTAAAAA
Found at i:2250177 original size:13 final size:14
Alignment explanation
Indices: 2250159--2250188 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2250149 TATTAAAAGT
2250159 TAAAA-TTTAAAAA
1 TAAAATTTTAAAAA
2250172 TAAAATTTTAAAAA
1 TAAAATTTTAAAAA
2250186 TAA
1 TAA
2250189 TAAATAATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TAAAATTTTAAAAA
Found at i:2254116 original size:27 final size:27
Alignment explanation
Indices: 2254086--2254157 Score: 126
Period size: 27 Copynumber: 2.6 Consensus size: 27
2254076 ATGAAAATTA
2254086 AATTAAAATTTTTATATTGAAAGAGCC
1 AATTAAAATTTTTATATTGAAAGAGCC
2254113 AATTAAAATTTTTATATTGAAAGAGCC
1 AATTAAAATTTTTATATTGAAAGAGCC
*
2254140 AATCAAAATTTTATATAT
1 AATTAAAATTTT-TATAT
2254158 GATAAAATTC
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
27 38 0.88
28 5 0.12
ACGTcount: A:0.46, C:0.07, G:0.08, T:0.39
Consensus pattern (27 bp):
AATTAAAATTTTTATATTGAAAGAGCC
Found at i:2259507 original size:52 final size:52
Alignment explanation
Indices: 2259398--2259514 Score: 155
Period size: 52 Copynumber: 2.2 Consensus size: 52
2259388 ATTTATCTGC
* ***
2259398 ATGTATCGATACATATGGGCAAATTTGCTTGCATGTATCGATACATTTTATA
1 ATGTATCGATACATATGGGCAAATTTGCCTGCATGTATCGATACATAAGATA
* *
2259450 ATGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACA-AAGATCG
1 ATGTATCGATACATATGGGCAAATTTGCCTGCATGTATCGATACATAAGAT-A
*
2259502 GTGTATCGATACA
1 ATGTATCGATACA
2259515 ATGTATCGAT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
51 2 0.04
52 55 0.96
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (52 bp):
ATGTATCGATACATATGGGCAAATTTGCCTGCATGTATCGATACATAAGATA
Found at i:2259521 original size:13 final size:13
Alignment explanation
Indices: 2259503--2259527 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2259493 CAAAGATCGG
2259503 TGTATCGATACAA
1 TGTATCGATACAA
2259516 TGTATCGATACA
1 TGTATCGATACA
2259528 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2259614 original size:13 final size:13
Alignment explanation
Indices: 2259596--2259620 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2259586 AAAATATATA
2259596 TGTATCGATACAT
1 TGTATCGATACAT
2259609 TGTATCGATACA
1 TGTATCGATACA
2259621 ACATTTTATG
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:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2262582 original size:32 final size:30
Alignment explanation
Indices: 2262546--2262604 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
2262536 GAAATCAAAT
2262546 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
2262578 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
2262605 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:2262903 original size:13 final size:13
Alignment explanation
Indices: 2262885--2262910 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2262875 CAATTTTTTG
2262885 TGTATCGATACAT
1 TGTATCGATACAT
2262898 TGTATCGATACAT
1 TGTATCGATACAT
2262911 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2262925 original size:32 final size:33
Alignment explanation
Indices: 2262865--2262928 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
2262855 TACAAGCCAA
** *
2262865 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
2262898 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
2262929 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:2265497 original size:13 final size:13
Alignment explanation
Indices: 2265479--2265514 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
2265469 ATAATCCCCC
2265479 TGTATCGATACAG
1 TGTATCGATACAG
*
2265492 TGTATCGATACAT
1 TGTATCGATACAG
2265505 TGTATCGATA
1 TGTATCGATA
2265515 TAAAGAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:2267619 original size:15 final size:15
Alignment explanation
Indices: 2267599--2267629 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2267589 ATTTCGTTTG
*
2267599 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
2267614 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
2267629 G
1 G
2267630 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:2271377 original size:32 final size:30
Alignment explanation
Indices: 2271341--2271399 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
2271331 GAAATCAAAT
2271341 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
2271373 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
2271400 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:2271698 original size:13 final size:13
Alignment explanation
Indices: 2271680--2271705 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2271670 CAATTTTTTG
2271680 TGTATCGATACAT
1 TGTATCGATACAT
2271693 TGTATCGATACAT
1 TGTATCGATACAT
2271706 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2271720 original size:32 final size:33
Alignment explanation
Indices: 2271660--2271723 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
2271650 TACAAGCCAA
** *
2271660 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
2271693 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
2271724 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:2273820 original size:14 final size:13
Alignment explanation
Indices: 2273796--2273823 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2273786 CATACTCAAT
2273796 TTTAAATAAAAAA
1 TTTAAATAAAAAA
2273809 TTTAAATAAAAAA
1 TTTAAATAAAAAA
2273822 TT
1 TT
2273824 ATTATTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TTTAAATAAAAAA
Found at i:2275625 original size:14 final size:14
Alignment explanation
Indices: 2275606--2275647 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
2275596 TAGCAAATTG
2275606 AAAAATA-ATAAATA
1 AAAAATAGA-AAATA
2275620 AAAAATAGAAAATA
1 AAAAATAGAAAATA
*
2275634 AAATAAAAGAAAAT
1 AAA-AATAGAAAAT
2275648 TGGAAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 15 0.60
15 10 0.40
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.17
Consensus pattern (14 bp):
AAAAATAGAAAATA
Found at i:2276202 original size:10 final size:10
Alignment explanation
Indices: 2276174--2276205 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
2276164 AATAATTACC
*
2276174 ATATATATAT
1 ATATATATGT
2276184 ATATATATGT
1 ATATATATGT
2276194 ATATATATGT
1 ATATATATGT
2276204 AT
1 AT
2276206 GTACTGGCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (10 bp):
ATATATATGT
Found at i:2279418 original size:32 final size:33
Alignment explanation
Indices: 2279377--2279438 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
2279367 TAGCCAAACT
**
2279377 TGTATCGATACACAAAGTA-TGTATCGATATAA
1 TGTATCGATACACAAAAAATTGTATCGATATAA
2279409 TGTATCGATACACAAAAAATTGTATCGATA
1 TGTATCGATACACAAAAAATTGTATCGATA
2279439 CATTGGCTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 17 0.63
33 10 0.37
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.31
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATATAA
Found at i:2281276 original size:19 final size:19
Alignment explanation
Indices: 2281252--2281304 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
2281242 ATATTATGCT
2281252 TTGTATCGATACATGTTCA
1 TTGTATCGATACATGTTCA
2281271 TTGTATCGATACATGTTCA
1 TTGTATCGATACATGTTCA
* *
2281290 TTATACCGATACATG
1 TTGTATCGATACATG
2281305 GACAATTGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (19 bp):
TTGTATCGATACATGTTCA
Found at i:2289472 original size:22 final size:22
Alignment explanation
Indices: 2289447--2289499 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
2289437 ATTGACAAAA
2289447 GGGGAGAAATGCTTTGATTAAG
1 GGGGAGAAATGCTTTGATTAAG
**
2289469 GGGGAGAAATTTTTTGATTAAG
1 GGGGAGAAATGCTTTGATTAAG
2289491 GGGGAGAAA
1 GGGGAGAAA
2289500 AACGAAAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.34, C:0.02, G:0.38, T:0.26
Consensus pattern (22 bp):
GGGGAGAAATGCTTTGATTAAG
Found at i:2290038 original size:20 final size:19
Alignment explanation
Indices: 2290015--2290087 Score: 67
Period size: 20 Copynumber: 3.7 Consensus size: 19
2290005 CTCACCAAGA
*
2290015 TGTATCGATACAT-TATGCTT
1 TGTATCGATACATGT-T-CAT
*
2290035 TGTATCGATAGATGTTCAT
1 TGTATCGATACATGTTCAT
**
2290054 TGTATCGATACATGGACAAT
1 TGTATCGATACATGTTC-AT
*
2290074 TGTATCAATACATG
1 TGTATCGATACATG
2290088 AACTTGGCAG
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 16 0.36
20 28 0.62
21 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATGTTCAT
Found at i:2295404 original size:12 final size:12
Alignment explanation
Indices: 2295359--2295403 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
2295349 TAAATAAAAT
*
2295359 TATTTATTTAAA
1 TATTTATATAAA
2295371 TATTTAT-TAAA
1 TATTTATATAAA
*
2295382 TATTTATATATA
1 TATTTATATAAA
2295394 TATTTATATA
1 TATTTATATA
2295404 TTAAAATAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
11 11 0.35
12 20 0.65
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TATTTATATAAA
Found at i:2297086 original size:13 final size:13
Alignment explanation
Indices: 2297047--2297079 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
2297037 TTTCTACTCC
2297047 TTTATTAATAATTA
1 TTTA-TAATAATTA
2297061 TTTATAATAATTA
1 TTTATAATAATTA
2297074 -TTATAA
1 TTTATAA
2297080 ATTATTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.32
13 9 0.47
14 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TTTATAATAATTA
Found at i:2297724 original size:14 final size:14
Alignment explanation
Indices: 2297707--2297746 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
2297697 GAACAATTGC
2297707 TTTAATTCAATTAG
1 TTTAATTCAATTAG
**
2297721 TTTAATTCAATTTT
1 TTTAATTCAATTAG
2297735 TTTAA-TCAATTA
1 TTTAATTCAATTA
2297747 TTAATTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 6 0.26
14 17 0.74
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (14 bp):
TTTAATTCAATTAG
Found at i:2298662 original size:102 final size:102
Alignment explanation
Indices: 2298543--2298746 Score: 338
Period size: 102 Copynumber: 2.0 Consensus size: 102
2298533 AATTAAAATT
* * *
2298543 TATGAAAATAAAAGGTCAAATATAACTCTTTTTCAATTTTTAT-TATATAAATTCATTTATATTT
1 TATGAAAATAAAAGGTCAAATATAAATCTTTTTCAATTTTTATCCA-ATAAATTCATTTATAGTT
*
2298607 TAAGGTTAATAAAAAAATTAAAACTTTGAAAACAAAAA
65 TAAAGTTAATAAAAAAATTAAAACTTTGAAAACAAAAA
*
2298645 TATGAAAATAAAAGGTCAAATTTAAATCTTTTTCAATTTTTATCCAATAAATTCATTTATAGTTT
1 TATGAAAATAAAAGGTCAAATATAAATCTTTTTCAATTTTTATCCAATAAATTCATTTATAGTTT
*
2298710 AAAGTTAATACAAAAATTAAAACTTTGAAAACAAAAA
66 AAAGTTAATAAAAAAATTAAAACTTTGAAAACAAAAA
2298747 AAAATCTAAT
Statistics
Matches: 95, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
102 94 0.99
103 1 0.01
ACGTcount: A:0.49, C:0.08, G:0.06, T:0.37
Consensus pattern (102 bp):
TATGAAAATAAAAGGTCAAATATAAATCTTTTTCAATTTTTATCCAATAAATTCATTTATAGTTT
AAAGTTAATAAAAAAATTAAAACTTTGAAAACAAAAA
Found at i:2300644 original size:2 final size:2
Alignment explanation
Indices: 2300637--2300661 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2300627 CAATTTGTTT
2300637 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2300662 CATTGGATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2301021 original size:19 final size:19
Alignment explanation
Indices: 2300966--2301021 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
2300956 TCAATAAATT
* *
2300966 AAAATTATTATTTAATTATA
1 AAAATTAATATTTAA-TAAA
* **
2300986 AAAATTTATATAAAATAAA
1 AAAATTAATATTTAATAAA
2301005 AAAATTAATATTTAATA
1 AAAATTAATATTTAATA
2301022 TATTTAGTGA
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AAAATTAATATTTAATAAA
Found at i:2303322 original size:20 final size:20
Alignment explanation
Indices: 2303283--2303334 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
2303273 TTACGATTTG
** *
2303283 TATCGATACAATTTGTGAATT
1 TATCGATAC-ATGAGTGAATA
2303304 TATCGATACATGAGTGAATA
1 TATCGATACATGAGTGAATA
2303324 TATCGATACAT
1 TATCGATACAT
2303335 ATCTCAAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 19 0.68
21 9 0.32
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (20 bp):
TATCGATACATGAGTGAATA
Found at i:2303364 original size:20 final size:21
Alignment explanation
Indices: 2303324--2303374 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 21
2303314 TGAGTGAATA
*
2303324 TATCGATACATATCTCAAATG
1 TATCGATACATATCCCAAATG
2303345 TATCGATACAT-TCCCAAATG
1 TATCGATACATATCCCAAATG
*
2303365 TATTGATACA
1 TATCGATACA
2303375 ATTTGCTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.33
Consensus pattern (21 bp):
TATCGATACATATCCCAAATG
Found at i:2303666 original size:138 final size:138
Alignment explanation
Indices: 2303495--2303756 Score: 488
Period size: 138 Copynumber: 1.9 Consensus size: 138
2303485 TTGCTATAAT
*
2303495 ACTTCCAATGCCCGATTCAAACAGGTTTTTTGCATCATTAAGGGTCTGAATTCATGTCAATATCG
1 ACTTCCAATGCCCGATTCAAACAGGTTTTTTGCATCATTAAGGGTCAGAATTCATGTCAATATCG
*
2303560 AATGCCAGACTTTAGATTTAAATGTAAACAATTTTTGAAGTCCAATGCATTGCATTAAATGCCCG
66 AATGCCAGACTTTAGATTTAAATGTAAACAATTTTTGAAGTCCAATGCAGTGCATTAAATGCCCG
2303625 ATTCAAAC
131 ATTCAAAC
*
2303633 ACTTCCAATGTCCGATTCAAACAGGTTTTTTGCATCATTAAGGGTCAGAATTCATGTCAATATCG
1 ACTTCCAATGCCCGATTCAAACAGGTTTTTTGCATCATTAAGGGTCAGAATTCATGTCAATATCG
*
2303698 AATGCCAGACTTTAGATTTAAATGTAAATAATTTTTGAAGTCCAATGCAGTGCATTAAA
66 AATGCCAGACTTTAGATTTAAATGTAAACAATTTTTGAAGTCCAATGCAGTGCATTAAA
2303757 AGGAAATGGC
Statistics
Matches: 120, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
138 120 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (138 bp):
ACTTCCAATGCCCGATTCAAACAGGTTTTTTGCATCATTAAGGGTCAGAATTCATGTCAATATCG
AATGCCAGACTTTAGATTTAAATGTAAACAATTTTTGAAGTCCAATGCAGTGCATTAAATGCCCG
ATTCAAAC
Found at i:2308028 original size:19 final size:18
Alignment explanation
Indices: 2308004--2308061 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 18
2307994 GAGGAAAGAG
2308004 GAAATAAAAAGAAAAAAAA
1 GAAATAAAAA-AAAAAAAA
* *
2308023 GAAATAAGGAACAAAAAAA
1 GAAATAA-AAAAAAAAAAA
2308042 GAAA-AAAAATAAAAGAAAA
1 GAAATAAAAA-AAAA-AAAA
2308061 G
1 G
2308062 GATGAAAGGG
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
17 2 0.06
18 5 0.16
19 23 0.72
20 2 0.06
ACGTcount: A:0.79, C:0.02, G:0.14, T:0.05
Consensus pattern (18 bp):
GAAATAAAAAAAAAAAAA
Found at i:2308656 original size:18 final size:18
Alignment explanation
Indices: 2308620--2308653 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2308610 AAAAGTTATA
2308620 TTTTTTCCATTGCAAAAC
1 TTTTTTCCATTGCAAAAC
2308638 TTTTTT-CATTGCAAAA
1 TTTTTTCCATTGCAAAA
2308654 ACTAATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.47
Consensus pattern (18 bp):
TTTTTTCCATTGCAAAAC
Found at i:2309840 original size:14 final size:14
Alignment explanation
Indices: 2309821--2309850 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2309811 TTTGTTTTTC
2309821 TTTATTATAATTAT
1 TTTATTATAATTAT
*
2309835 TTTATTTTAATTAT
1 TTTATTATAATTAT
2309849 TT
1 TT
2309851 ACAGCCATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTATTATAATTAT
Found at i:2312252 original size:20 final size:20
Alignment explanation
Indices: 2312223--2312279 Score: 89
Period size: 19 Copynumber: 2.9 Consensus size: 20
2312213 TACTGCCAGT
2312223 TTCATGTATCGATACAATTG
1 TTCATGTATCGATACAATTG
*
2312243 TTCATATATCGATACAA-TG
1 TTCATGTATCGATACAATTG
*
2312262 ATCATGTATCGATACAAT
1 TTCATGTATCGATACAAT
2312280 GTATTGATAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (20 bp):
TTCATGTATCGATACAATTG
Found at i:2312283 original size:13 final size:13
Alignment explanation
Indices: 2312265--2312304 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
2312255 TACAATGATC
2312265 ATGTATCGATACA
1 ATGTATCGATACA
*
2312278 ATGTATTGATACA
1 ATGTATCGATACA
2312291 ATGTATCGATACA
1 ATGTATCGATACA
2312304 A
1 A
2312305 AGCATAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2319443 original size:3 final size:3
Alignment explanation
Indices: 2319435--2319470 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
2319425 TCCGAGTCAC
* *
2319435 CAT CAT CAT CAT CAT CAT TAT CAT CTT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
2319471 TGATGGTTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.39
Consensus pattern (3 bp):
CAT
Found at i:2321095 original size:13 final size:13
Alignment explanation
Indices: 2321077--2321107 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
2321067 ACAATTCATC
2321077 ATGTATTGATACA
1 ATGTATTGATACA
2321090 ATGTATTGATACA
1 ATGTATTGATACA
2321103 ATGTA
1 ATGTA
2321108 CCATGTATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.16, T:0.39
Consensus pattern (13 bp):
ATGTATTGATACA
Found at i:2321095 original size:33 final size:33
Alignment explanation
Indices: 2321055--2321123 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
2321045 CCGTTACAAG
* *
2321055 CAATGTATCGATACAAT-TCATCATGTATTGATA
1 CAATGTATCGATACAATGT-ACCATGTATCGATA
*
2321088 CAATGTATTGATACAATGTACCATGTATCGATA
1 CAATGTATCGATACAATGTACCATGTATCGATA
2321121 CAA
1 CAA
2321124 ATAGTGGTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (33 bp):
CAATGTATCGATACAATGTACCATGTATCGATA
Found at i:2323907 original size:24 final size:23
Alignment explanation
Indices: 2323860--2323907 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
2323850 ATTTTCTTTG
*
2323860 AAAAAAAGAAAATGAAAAGTAAAA
1 AAAAAAAGAAAATGAAAA-AAAAA
* *
2323884 AAAAAAGGAAATTGAAAAAAAAA
1 AAAAAAAGAAAATGAAAAAAAAA
2323907 A
1 A
2323908 TTGAAAAGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.08
Consensus pattern (23 bp):
AAAAAAAGAAAATGAAAAAAAAA
Found at i:2323918 original size:18 final size:17
Alignment explanation
Indices: 2323861--2323918 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 17
2323851 TTTTCTTTGA
2323861 AAAAAAGAAAATGAAAAG
1 AAAAAA-AAAATGAAAAG
* *
2323879 TAAAAAAAAAAGGAAATTG
1 -AAAAAAAAAATGAAA-AG
2323898 AAAAAAAAAATTGAAAAG
1 AAAAAAAAAA-TGAAAAG
2323916 AAA
1 AAA
2323919 GAAACAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
18 22 0.67
19 11 0.33
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (17 bp):
AAAAAAAAAATGAAAAG
Found at i:2332457 original size:37 final size:37
Alignment explanation
Indices: 2332402--2332487 Score: 136
Period size: 37 Copynumber: 2.3 Consensus size: 37
2332392 TTGAAACATC
*
2332402 TAATTAAATATCCTTTAGAGAAGCTCTTGACAACTTT
1 TAATGAAATATCCTTTAGAGAAGCTCTTGACAACTTT
* * *
2332439 TAATGAAATATCCTTTAGAGAATCTCTTGATATCTTT
1 TAATGAAATATCCTTTAGAGAAGCTCTTGACAACTTT
2332476 TAATGAAATATC
1 TAATGAAATATC
2332488 TATAAAAGTG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (37 bp):
TAATGAAATATCCTTTAGAGAAGCTCTTGACAACTTT
Found at i:2332543 original size:36 final size:36
Alignment explanation
Indices: 2332473--2332543 Score: 83
Period size: 36 Copynumber: 2.0 Consensus size: 36
2332463 TCTTGATATC
* *
2332473 TTTTAATGAAATATCTATAAAAGTGGTTTAGAAAGT
1 TTTTAATGAAATATCTAAAAAAGTGCTTTAGAAAGT
*
2332509 TTTTAATGAAATTTCCTCAAAAAAG-GCTTT-GAAAG
1 TTTTAATGAAATAT-CT-AAAAAAGTGCTTTAGAAAG
2332544 ATTCTAGTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
36 18 0.60
37 6 0.20
38 6 0.20
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (36 bp):
TTTTAATGAAATATCTAAAAAAGTGCTTTAGAAAGT
Found at i:2337948 original size:21 final size:21
Alignment explanation
Indices: 2337907--2337950 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2337897 CTCCCCTTTA
* *
2337907 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
2337928 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
2337949 TC
1 TC
2337951 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:2339775 original size:13 final size:13
Alignment explanation
Indices: 2339757--2339828 Score: 93
Period size: 13 Copynumber: 6.0 Consensus size: 13
2339747 ATAATCACCC
2339757 TGTATCGATACAA
1 TGTATCGATACAA
2339770 TGTATCGATACAA
1 TGTATCGATACAA
2339783 TGTATCGATACAA
1 TGTATCGATACAA
*
2339796 ---A--GA-AAAA
1 TGTATCGATACAA
2339803 TGTATCGATACAA
1 TGTATCGATACAA
2339816 TGTATCGATACAA
1 TGTATCGATACAA
2339829 AGAACATTGA
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
7 3 0.06
8 2 0.04
10 2 0.04
12 2 0.04
13 42 0.82
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2339810 original size:33 final size:33
Alignment explanation
Indices: 2339768--2339879 Score: 138
Period size: 33 Copynumber: 3.4 Consensus size: 33
2339758 GTATCGATAC
2339768 AATGTATCGATACAATGTATCGATACAAAGAAA
1 AATGTATCGATACAATGTATCGATACAAAGAAA
*
2339801 AATGTATCGATACAATGTATCGATACAAAGAAC
1 AATGTATCGATACAATGTATCGATACAAAGAAA
* * * * *
2339834 ATTGAAT--TTCCAGATGTATCGATACACAGAAA
1 AATGTATCGATACA-ATGTATCGATACAAAGAAA
*
2339866 CATGTATCGATACA
1 AATGTATCGATACA
2339880 TTTTGGACAT
Statistics
Matches: 64, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
31 3 0.05
32 21 0.33
33 37 0.58
34 3 0.05
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (33 bp):
AATGTATCGATACAATGTATCGATACAAAGAAA
Found at i:2341916 original size:15 final size:15
Alignment explanation
Indices: 2341896--2341926 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2341886 ATTTCGTTTG
*
2341896 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
2341911 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
2341926 G
1 G
2341927 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:2343759 original size:21 final size:21
Alignment explanation
Indices: 2343730--2343774 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2343720 AAGTTTTCAT
*
2343730 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
2343750 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
2343772 TTT
1 TTT
2343775 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:2346005 original size:13 final size:13
Alignment explanation
Indices: 2345987--2346012 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2345977 CAATTTTTTG
2345987 TGTATCGATACAT
1 TGTATCGATACAT
2346000 TGTATCGATACAT
1 TGTATCGATACAT
2346013 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2346471 original size:51 final size:51
Alignment explanation
Indices: 2346394--2346513 Score: 161
Period size: 51 Copynumber: 2.4 Consensus size: 51
2346384 AGATCCTAAC
* * *
2346394 AAATGTATCGATACATTTGGGTCAAAAACCCATAATGT-CCGATACAATGAA
1 AAATGTATCGATACATTTAGGTC-AAAACCCAGAATGTACAGATACAATGAA
* ** *
2346445 GAATGTATCGATACATTTAGGTCAAAACTTAGAATGTATAGATACAATGAA
1 AAATGTATCGATACATTTAGGTCAAAACCCAGAATGTACAGATACAATGAA
2346496 AAATGTATCGATACATTT
1 AAATGTATCGATACATTT
2346514 TCATTTTAGA
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
50 11 0.18
51 49 0.82
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (51 bp):
AAATGTATCGATACATTTAGGTCAAAACCCAGAATGTACAGATACAATGAA
Found at i:2346619 original size:21 final size:20
Alignment explanation
Indices: 2346568--2346621 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
2346558 CATTTCAGAC
2346568 ATGTATCGATACATTTACTT
1 ATGTATCGATACATTTACTT
2346588 ATGTATCGATACA-TTACCTT
1 ATGTATCGATACATTTA-CTT
*
2346608 ATGGTATTGATACA
1 AT-GTATCGATACA
2346622 AATTATTGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 3 0.10
20 18 0.58
21 10 0.32
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTACTT
Found at i:2347312 original size:3 final size:3
Alignment explanation
Indices: 2347306--2347361 Score: 66
Period size: 3 Copynumber: 20.0 Consensus size: 3
2347296 AAAAAGAAAA
* *
2347306 AAT AAT AA- AA- AAT -AT AAT CAT AAT TA- AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2347350 AAT AAT AAT AAT
1 AAT AAT AAT AAT
2347362 TAGTTAAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 7 0.15
3 39 0.85
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2348406 original size:27 final size:27
Alignment explanation
Indices: 2348370--2348430 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
2348360 AATAGCATGC
* * *
2348370 AAAGAAAGCAGCAAATAGCAATAAACA
1 AAAGACAGCAGCAAACAACAATAAACA
2348397 AAAGACAGCAGCAAACAACAATAAACA
1 AAAGACAGCAGCAAACAACAATAAACA
2348424 AAAGACA
1 AAAGACA
2348431 ATAGAAAACA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.64, C:0.18, G:0.13, T:0.05
Consensus pattern (27 bp):
AAAGACAGCAGCAAACAACAATAAACA
Found at i:2348439 original size:27 final size:27
Alignment explanation
Indices: 2348388--2348440 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
2348378 CAGCAAATAG
* *
2348388 CAATAAACAAAAGACAGCAGCAAACAA
1 CAATAAACAAAAGACAACAGAAAACAA
*
2348415 CAATAAACAAAAGACAATAGAAAACA
1 CAATAAACAAAAGACAACAGAAAACA
2348441 TCAAGCAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.66, C:0.19, G:0.09, T:0.06
Consensus pattern (27 bp):
CAATAAACAAAAGACAACAGAAAACAA
Found at i:2348462 original size:23 final size:22
Alignment explanation
Indices: 2348436--2348494 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 22
2348426 AGACAATAGA
*
2348436 AAACATCAAGCAAAGACAGCAGC
1 AAACATCAAGCAAAAACA-CAGC
*
2348459 AAACATCAAGCAAAAACATAGC
1 AAACATCAAGCAAAAACACAGC
*
2348481 AAACAACAAGCAAA
1 AAACATCAAGCAAA
2348495 TGAAATAGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
22 16 0.48
23 17 0.52
ACGTcount: A:0.59, C:0.24, G:0.12, T:0.05
Consensus pattern (22 bp):
AAACATCAAGCAAAAACACAGC
Found at i:2348472 original size:11 final size:11
Alignment explanation
Indices: 2348456--2348494 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
2348446 CAAAGACAGC
*
2348456 AGCAAACATCA
1 AGCAAACAACA
2348467 AGCAAA-AACA
1 AGCAAACAACA
2348477 TAGCAAACAACA
1 -AGCAAACAACA
2348489 AGCAAA
1 AGCAAA
2348495 TGAAATAGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
10 3 0.12
11 18 0.72
12 4 0.16
ACGTcount: A:0.62, C:0.23, G:0.10, T:0.05
Consensus pattern (11 bp):
AGCAAACAACA
Found at i:2348655 original size:22 final size:22
Alignment explanation
Indices: 2348605--2348646 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2348595 AAGCTAGCGA
*
2348605 AACAGCATCAGCAAAAGAAAAG
1 AACAGCAGCAGCAAAAGAAAAG
*
2348627 AACAGCAGCAGCAAATGAAA
1 AACAGCAGCAGCAAAAGAAA
2348647 CAGCAAGCAA
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:0.57, C:0.19, G:0.19, T:0.05
Consensus pattern (22 bp):
AACAGCAGCAGCAAAAGAAAAG
Found at i:2351092 original size:154 final size:154
Alignment explanation
Indices: 2350895--2351266 Score: 403
Period size: 154 Copynumber: 2.4 Consensus size: 154
2350885 CACTTTTACA
* * * *
2350895 TCGAAGGTGGGTATTTAGGATAGGTTCATCCTTTCTATGATCTTTTAAAGTCCTTTAGGGGTGT-
1 TCGAAGGTGGATATTTAGGATAGGTTCATCCTTT-TATAATCTTTTTAAGTCCTTTAGGGGTATC
* * * * ** *
2350959 TGAGTACTTTTATATCAAAGGTAACCCCTAAGGGTATTTTTGTAGTT-TTCTAGAAC-CAAGTCC
65 AG-GCACTTCTATATCAAAGGTAACCCCTAAGGGCATTTTCATAATTCTTCTAGAACTCAA-TCC
* *
2351022 TAGGTTGTTATCAGGTCTGCTTTAATG
128 TAGGTTATCATCAGGTCTGCTTTAATG
**
2351049 TCGAAGGTGGATATTTAGGATAGGTTCATTCCATTTT-TAATCTTTTTAAGTATTTTAGGGGTAT
1 TCGAAGGTGGATATTTAGGATAGGTTCA-TCC-TTTTATAATCTTTTTAAGTCCTTTAGGGGTAT
* * * *
2351113 CAGGCACTTCTATGTCAAAGGTATCCCCTAAGGGCATTTTCATAATTCTTTTAGAACTGAATCCT
64 CAGGCACTTCTATATCAAAGGTAACCCCTAAGGGCATTTTCATAATTCTTCTAGAACTCAATCCT
* *
2351178 AGGTTATCATCGGGTCTGCTTTTATG
129 AGGTTATCATCAGGTCTGCTTTAATG
* * * *
2351204 CCAAAGGTGAATA-TTAGGATAGGTTCATCCCTTTTAAAATCCTTTTTGTAAGTCCTTTAGGGG
1 TCGAAGGTGGATATTTAGGATAGGTTCAT-CCTTTTATAAT-C-TTTT-TAAGTCCTTTAGGGG
2351267 CATCGGTGCT
Statistics
Matches: 181, Mismatches: 27, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
153 5 0.03
154 104 0.57
155 50 0.28
156 9 0.05
157 13 0.07
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.39
Consensus pattern (154 bp):
TCGAAGGTGGATATTTAGGATAGGTTCATCCTTTTATAATCTTTTTAAGTCCTTTAGGGGTATCA
GGCACTTCTATATCAAAGGTAACCCCTAAGGGCATTTTCATAATTCTTCTAGAACTCAATCCTAG
GTTATCATCAGGTCTGCTTTAATG
Found at i:2352959 original size:104 final size:104
Alignment explanation
Indices: 2352720--2353011 Score: 284
Period size: 104 Copynumber: 2.8 Consensus size: 104
2352710 GATGAGAAGA
* * *
2352720 GTGTCAATGTGCTGATTCAAGGCTAGTGACATTAGACATGAAGATGAGAAGAATGCTAATGTGTT
1 GTGTCAATGTGCTGATTCAAGGCTAGTGACATTAGACATAAAAATGAGAAGAATGCTAATGTGCT
* *** *
2352785 GATTTAAGGCTAGCGACATTGGATTTAAAAATAACAAGG
66 GATTTAAGGCGAGCGACATCAAATTTAAAAATAACAAAG
* * * * * * * *
2352824 GTGCCAATGTGCTGATTCAAGGCCAATGACATTGGGCTTAAAAATGATAA-AAGTGCTAATTTGC
1 GTGTCAATGTGCTGATTCAAGGCTAGTGACATTAGACATAAAAATGAGAAGAA-TGCTAATGTGC
* * * * *
2352888 TGATTTTAGGCGAGTGATATCAAATTTAAAGATGACAAAG
65 TGATTTAAGGCGAGCGACATCAAATTTAAAAATAACAAAG
* * * *
2352928 GTGTCAATGTGCTGATTCTAGGCTAGCGACATTAGAC-TAAAAACGA-AAGAGAGTGCCAATGTG
1 GTGTCAATGTGCTGATTCAAGGCTAGTGACATTAGACATAAAAATGAGAAGA-A-TGCTAATGTG
* * *
2352991 CTGATTCAAGGCTAGTGACAT
64 CTGATTTAAGGCGAGCGACAT
2353012 TAGACTTAGA
Statistics
Matches: 150, Mismatches: 35, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
102 2 0.01
103 11 0.07
104 137 0.91
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.27
Consensus pattern (104 bp):
GTGTCAATGTGCTGATTCAAGGCTAGTGACATTAGACATAAAAATGAGAAGAATGCTAATGTGCT
GATTTAAGGCGAGCGACATCAAATTTAAAAATAACAAAG
Found at i:2353016 original size:52 final size:52
Alignment explanation
Indices: 2352716--2353017 Score: 236
Period size: 52 Copynumber: 5.8 Consensus size: 52
2352706 TAAGGATGAG
* * * *
2352716 AAGAGTGTCAATGTGCTGATTCAAGGCTAGTGACATTAGACATGAAGATGA-G
1 AAGAGTGCCAATGTGCTGATTCAAGGCTAGTGACATTAGAC-TAAAAATGACA
* * * * * * * *
2352768 AAGAATGCTAATGTGTTGATTTAAGGCTAGCGACATTGGATTTAAAAATAAC-
1 AAGAGTGCCAATGTGCTGATTCAAGGCTAGTGACATTAGA-CTAAAAATGACA
* * * * * *
2352820 AAGGGTGCCAATGTGCTGATTCAAGGCCAATGACATTGGGCTTAAAAATGATA
1 AAGAGTGCCAATGTGCTGATTCAAGGCTAGTGACATTAGAC-TAAAAATGACA
* * ** * * * * * *
2352873 AA-AGTGCTAATTTGCTGATTTTAGGCGAGTGATATCAAATTTAAAGATGACA
1 AAGAGTGCCAATGTGCTGATTCAAGGCTAGTGACATTAGA-CTAAAAATGACA
* * * *
2352925 AAG-GTGTCAATGTGCTGATTCTAGGCTAGCGACATTAGACTAAAAACGA-A
1 AAGAGTGCCAATGTGCTGATTCAAGGCTAGTGACATTAGACTAAAAATGACA
2352975 AGAGAGTGCCAATGTGCTGATTCAAGGCTAGTGACATTAGACT
1 A-AGAGTGCCAATGTGCTGATTCAAGGCTAGTGACATTAGACT
2353018 TAGAAAGAGA
Statistics
Matches: 189, Mismatches: 53, Indels: 16
0.73 0.21 0.06
Matches are distributed among these distances:
50 2 0.01
51 9 0.05
52 176 0.93
53 2 0.01
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.27
Consensus pattern (52 bp):
AAGAGTGCCAATGTGCTGATTCAAGGCTAGTGACATTAGACTAAAAATGACA
Found at i:2353193 original size:30 final size:32
Alignment explanation
Indices: 2353090--2353291 Score: 117
Period size: 33 Copynumber: 6.3 Consensus size: 32
2353080 ATGGATATGT
* * *
2353090 CACCGACTTGTGTGGGCTTTTGAGAGGGTTGC
1 CACCGACTTGTATAGGCTTTTAAGAGGGTTGC
* * * *
2353122 CACCGACTTGTGT-GGTTTTTCAAAGAAGGATGC
1 CACCGACTTGTATAGGCTTTT--AAGAGGGTTGC
*
2353155 CACTGACTTGTAT-GG-TTTTAAGAGGGTTGC
1 CACCGACTTGTATAGGCTTTTAAGAGGGTTGC
* ** *
2353185 CACCGACTTGTATAGGTTTTTGGAA-ATAGATGC
1 CACCGACTTGTATAGGCTTTT--AAGAGGGTTGC
* * * * *
2353218 CACCAACTTGTGTGGGCTTTTAAAAGGGTTGT
1 CACCGACTTGTATAGGCTTTTAAGAGGGTTGC
** * * * *
2353250 CATTGACTTATGT-GGCTTTAAAAAGGGTTGC
1 CACCGACTTGTATAGGCTTTTAAGAGGGTTGC
*
2353281 CATCGACTTGT
1 CACCGACTTGT
2353292 GGGCTTTAAA
Statistics
Matches: 135, Mismatches: 28, Indels: 15
0.76 0.16 0.08
Matches are distributed among these distances:
30 21 0.16
31 35 0.26
32 34 0.25
33 43 0.32
34 2 0.01
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.34
Consensus pattern (32 bp):
CACCGACTTGTATAGGCTTTTAAGAGGGTTGC
Found at i:2353258 original size:65 final size:65
Alignment explanation
Indices: 2353090--2353248 Score: 200
Period size: 63 Copynumber: 2.5 Consensus size: 65
2353080 ATGGATATGT
* *
2353090 CACCGACTTGTGTGGGCTTTTGAGAGGGTTGCCACCGACTTGTGTGGTTTTTCAAAGAAGGATGC
1 CACCGACTTGTGTGGGCTTTTAAGAGGGTTGCCACCGACTTGTATGGTTTTTCAAAGAAGGATGC
* * * *
2353155 CACTGACTTGTAT-GG-TTTTAAGAGGGTTGCCACCGACTTGTATAGGTTTTTGGAAA-TA-GAT
1 CACCGACTTGTGTGGGCTTTTAAGAGGGTTGCCACCGACTTGTAT-GGTTTTT-CAAAGAAGGAT
2353216 GC
64 GC
* *
2353218 CACCAACTTGTGTGGGCTTTTAAAAGGGTTG
1 CACCGACTTGTGTGGGCTTTTAAGAGGGTTG
2353249 TCATTGACTT
Statistics
Matches: 80, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
63 41 0.51
64 12 0.15
65 27 0.34
ACGTcount: A:0.21, C:0.16, G:0.30, T:0.33
Consensus pattern (65 bp):
CACCGACTTGTGTGGGCTTTTAAGAGGGTTGCCACCGACTTGTATGGTTTTTCAAAGAAGGATGC
Found at i:2353302 original size:29 final size:29
Alignment explanation
Indices: 2353228--2353507 Score: 204
Period size: 29 Copynumber: 9.6 Consensus size: 29
2353218 CACCAACTTG
* *
2353228 TGTGGGCTTTTAAAAGGGTTGTCATTGACT
1 TGTGGGC-TTTAAAAGGGTTGCCATCGACT
*
2353258 TATGTGGCTTTAAAAAGGGTTGCCATCGACT
1 TGTG-GGCTTT-AAAAGGGTTGCCATCGACT
* *
2353289 TGTGGGCTTTAAAAGGGGATGCCA-CTAACT
1 TGTGGGCTTTAAAA-GGGTTGCCATC-GACT
* **
2353319 TGTGGGCTTTGACAAGGG-TGCCATTAACT
1 TGTGGGCTTT-AAAAGGGTTGCCATCGACT
*
2353348 TATGGGCTTTAAAAGGGTTGCCA-CTGACT
1 TGTGGGCTTTAAAAGGGTTGCCATC-GACT
** *
2353377 TGTGGGCTTGGAAAGGG-TGCCAAT-TACT
1 TGTGGGCTTTAAAAGGGTTGCC-ATCGACT
* * *
2353405 TGTGGGCTTTGACAA--GATGCCATTGACT
1 TGTGGGCTTT-AAAAGGGTTGCCATCGACT
* * *
2353433 TGTGGGCTTT-AAGGAGGATGCCA-CTAACT
1 TGTGGGCTTTAAAAG-GGTTGCCATC-GACT
*
2353462 TGTGGGCTTTGAAAGGG-TGCCA-CTGACT
1 TGTGGGCTTTAAAAGGGTTGCCATC-GACT
2353490 TGTGGGCTTTAAAAGGGT
1 TGTGGGCTTTAAAAGGGT
2353508 GCTATAGAGT
Statistics
Matches: 204, Mismatches: 27, Indels: 39
0.76 0.10 0.14
Matches are distributed among these distances:
26 1 0.00
27 3 0.01
28 65 0.32
29 70 0.34
30 39 0.19
31 26 0.13
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (29 bp):
TGTGGGCTTTAAAAGGGTTGCCATCGACT
Found at i:2353463 original size:57 final size:55
Alignment explanation
Indices: 2353286--2353509 Score: 243
Period size: 57 Copynumber: 3.9 Consensus size: 55
2353276 GTTGCCATCG
* * *
2353286 ACTTGTGGGCTTTAAAAGGGGATGCCACTAACTTGTGGGCTTTGACAAGGGTGCCATTA
1 ACTTGTGGGCTTTGAAA--GGATGCCACTGACTTGTGGGCTTT-A-AAGGGTGCCAATA
* * * * *
2353345 ACTTATGGGCTTTAAAAGGGTTGCCACTGACTTGTGGGCTTGGAAAGGGTGCCAATT
1 ACTTGTGGGCTTTGAAA-GGATGCCACTGACTTGTGGGCTT-TAAAGGGTGCCAATA
* * *
2353402 ACTTGTGGGCTTTGACAA-GATGCCATTGACTTGTGGGCTTTAAGGAGGATGCCACTA
1 ACTTGTGGGCTTTGA-AAGGATGCCACTGACTTGTGGGCTTTAA--AGGGTGCCAATA
*
2353459 ACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTAAAAGGGTGC
1 ACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTT-AAAGGGTGC
2353510 TATAGAGTTG
Statistics
Matches: 142, Mismatches: 17, Indels: 15
0.82 0.10 0.09
Matches are distributed among these distances:
55 2 0.01
56 28 0.20
57 69 0.49
58 27 0.19
59 16 0.11
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (55 bp):
ACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTAAAGGGTGCCAATA
Done.