Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000389.1 Hibiscus syriacus cultivar Beakdansim tig00000715_pilon, whole genome shotgun sequence
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: 2672246
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 15
Found at i:213713 original size:19 final size:19
Alignment explanation
Indices: 213666--213758 Score: 90
Period size: 19 Copynumber: 5.2 Consensus size: 19
213656 GCGAATTTAG
* *
213666 TTTCGCGTTACAATTTT-A
1 TTTCGCGTTGCGATTTTCA
213684 GTTTCGCGTTGCGATTTTCA
1 -TTTCGCGTTGCGATTTTCA
213704 TTTCGCGTTGCGA--TTC-
1 TTTCGCGTTGCGATTTTCA
*
213720 --TCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
* *
213737 TTTCGCATTGCGATTGTCA
1 TTTCGCGTTGCGATTTTCA
213756 TTT
1 TTT
213759 TTGCCTTCAA
Statistics
Matches: 62, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
14 10 0.16
16 3 0.05
17 3 0.05
19 45 0.73
20 1 0.02
ACGTcount: A:0.13, C:0.20, G:0.19, T:0.47
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:213876 original size:14 final size:14
Alignment explanation
Indices: 213857--213893 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
213847 CATCAATTAA
213857 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
213871 ACAAATCATCTTTT
1 ACAAATCAACTTTT
213885 ACAAATCAA
1 ACAAATCAA
213894 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:215310 original size:21 final size:21
Alignment explanation
Indices: 215244--215310 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
215234 GTGAATCGGG
*
215244 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
215264 CATCTTCAACGATGACAGTGGC
1 C-TCTTGAACGGTGGGAGGGGA
215286 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
215307 CTCT
1 CTCT
215311 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 28 0.88
22 3 0.09
ACGTcount: A:0.21, C:0.19, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:215329 original size:42 final size:41
Alignment explanation
Indices: 215244--215366 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
215234 GTGAATCGGG
* * * *
215244 CTCTTGAATGGTGGGA-GGGACATCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGAC-TC-TCGAGGATGACAGGGGC
*
215286 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
215328 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
215367 AGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 56 0.84
43 7 0.10
ACGTcount: A:0.24, C:0.18, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:215803 original size:19 final size:19
Alignment explanation
Indices: 215763--215852 Score: 91
Period size: 19 Copynumber: 4.9 Consensus size: 19
215753 TCTGGAACTT
*
215763 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAACGCG--AAATG
**
215784 ACTATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
215803 AAAATCGCAA--CG--A-G
1 AAAATCGCAACGCGAAATG
*
215817 AGAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
215836 AAAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
215853 CCAAAAGACA
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 30 0.53
21 11 0.19
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:215858 original size:19 final size:19
Alignment explanation
Indices: 215819--215858 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
215809 GCAACGAGAG
**
215819 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAACCAA
215838 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
215857 AA
1 AA
215859 GACAAAACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.50, C:0.25, G:0.17, T:0.07
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:215871 original size:12 final size:12
Alignment explanation
Indices: 215854--215879 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
215844 AACGCGAAAC
215854 CAAAAGACAAAA
1 CAAAAGACAAAA
215866 CAAAAGACAAAA
1 CAAAAGACAAAA
215878 CA
1 CA
215880 GTGTTACTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.73, C:0.19, G:0.08, T:0.00
Consensus pattern (12 bp):
CAAAAGACAAAA
Found at i:216057 original size:94 final size:94
Alignment explanation
Indices: 215951--216326 Score: 620
Period size: 94 Copynumber: 4.1 Consensus size: 94
215941 ATGGATTGTA
* *
215951 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
216015 TTAGCAGAATTGGCAGCAAACGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
216044 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAAT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
216109 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
216138 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
216203 TTAGCATAATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
216232 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTT----AATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* *
216292 TTTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
216322 TTACT
1 TTACT
216327 AAGCAATCTA
Statistics
Matches: 270, Mismatches: 10, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
90 40 0.15
93 23 0.09
94 207 0.77
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:218081 original size:34 final size:34
Alignment explanation
Indices: 218038--218136 Score: 146
Period size: 34 Copynumber: 2.9 Consensus size: 34
218028 CGAGATAATG
218038 AAAATCGCAACGCGGAAATGACTATCGCAACGAC
1 AAAATCGCAACGCGGAAATGACTATCGCAACGAC
* *
218072 AAAATCGCAACGCGGAAATGACTATCGCAATGAG
1 AAAATCGCAACGCGGAAATGACTATCGCAACGAC
* **
218106 AGAATCGCAACGC-GAAATGAAAATCGCAACG
1 AAAATCGCAACGCGGAAATGACTATCGCAACG
218137 CGAAATGAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 15 0.25
34 44 0.75
ACGTcount: A:0.42, C:0.23, G:0.22, T:0.12
Consensus pattern (34 bp):
AAAATCGCAACGCGGAAATGACTATCGCAACGAC
Found at i:218132 original size:19 final size:19
Alignment explanation
Indices: 218012--218158 Score: 116
Period size: 19 Copynumber: 8.1 Consensus size: 19
218002 TCTTTTGGTT
*
218012 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
218031 GATAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
218051 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
218069 G--A-CAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
218085 GGAAATGACTATCGCAA--T
1 -GAAATGAAAATCGCAACGC
*
218103 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
218119 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
218138 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
218157 GA
1 GA
218159 TTTTGGTTTC
Statistics
Matches: 100, Mismatches: 15, Indels: 26
0.71 0.11 0.18
Matches are distributed among these distances:
14 17 0.17
15 2 0.02
16 2 0.02
17 3 0.03
18 2 0.02
19 36 0.36
20 36 0.36
21 2 0.02
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:218207 original size:33 final size:33
Alignment explanation
Indices: 218154--218242 Score: 106
Period size: 33 Copynumber: 2.7 Consensus size: 33
218144 AAAATCGCAA
** *
218154 TGCGATTTTGGTTTCACGTTGCAATTATCTCGT
1 TGCGATTTTCATTTCGCGTTGCAATTATCTCGT
* *
218187 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCAATTATCTCGT
**
218220 TGCGATAGTCATTTCCGCGTTGC
1 TGCGATTTTCATTT-CGCGTTGC
218243 GATTTTCATT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 40 0.83
34 8 0.17
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.43
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCAATTATCTCGT
Found at i:218251 original size:20 final size:19
Alignment explanation
Indices: 218184--218252 Score: 67
Period size: 20 Copynumber: 3.8 Consensus size: 19
218174 GCAATTATCT
218184 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
218203 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
**
218217 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTT-CG
218237 CGTTGCGATTTTCATT
1 CGTTGCGATTTTCATT
218253 CTCAAAACTA
Statistics
Matches: 39, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
14 10 0.26
16 2 0.05
17 3 0.08
19 9 0.23
20 15 0.38
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:218870 original size:20 final size:20
Alignment explanation
Indices: 218797--218864 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
218787 CGATAGTCAG
218797 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
218817 ATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
218837 AATTCGCATTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGT
218858 ATTCGCA
1 ATTCGCA
218865 ACGCGAATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
20 25 0.58
21 18 0.42
ACGTcount: A:0.21, C:0.22, G:0.18, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:218885 original size:41 final size:41
Alignment explanation
Indices: 218799--218892 Score: 116
Period size: 41 Copynumber: 2.3 Consensus size: 41
218789 ATAGTCAGAT
** * * *
218799 TCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGTATTCGCAACGCGAATTTCCGAAA
**
218840 TCGCATTGCGATTTACGTATTCGCAACGCGAATTTGGGAAA
1 TCGCATTGCGATTTACGTATTCGCAACGCGAATTTCCGAAA
*
218881 TCGCAATGCGAT
1 TCGCATTGCGAT
218893 AGTCAGAATC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.34
Consensus pattern (41 bp):
TCGCATTGCGATTTACGTATTCGCAACGCGAATTTCCGAAA
Found at i:220795 original size:26 final size:25
Alignment explanation
Indices: 220745--220834 Score: 119
Period size: 26 Copynumber: 3.5 Consensus size: 25
220735 TAAGAATATG
*
220745 TCGATCGT-AAAAAAGGGTTTCTAC
1 TCGATCGTAAAAAAAGGGTTTTTAC
220769 TCGATCGTAAAAGAAAGGGTTTTTAC
1 TCGATCGTAAAA-AAAGGGTTTTTAC
*
220795 TCGATCGTAAAAAAATGGGTTCTTAC
1 TCGATCGTAAAAAAA-GGGTTTTTAC
*
220821 TCAAATCGTAAAAA
1 TC-GATCGTAAAAA
220835 GAAGACCTCG
Statistics
Matches: 59, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
24 8 0.14
25 6 0.10
26 35 0.59
27 10 0.17
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (25 bp):
TCGATCGTAAAAAAAGGGTTTTTAC
Found at i:221288 original size:146 final size:147
Alignment explanation
Indices: 221046--221337 Score: 505
Period size: 146 Copynumber: 2.0 Consensus size: 147
221036 ACACCATTCA
* *
221046 TAATTTTAGCTGATAAAATTTATCGATTTTATCTTTTTTTTAAGGTAATTTTTTATTTCTTTCTT
1 TAATTTTAGCTGATAAAATTTATCGATTTTATC-TTTTTTTAAGGTAAATTTTTATCTCTTTCTT
*
221111 ACATATAAATAATGAGTAAATAATTATTTAAAAATTATTTTGAAATGAATAAATTTTATTAATTA
65 ACATATAAATAAGGAGTAAATAATTATTTAAAAATTATTTTGAAATGAATAAATTTTATTAATTA
*
221176 GGATCATGAATGATGTCG
130 GAATCATGAATGATGTCG
221194 TAATTTTAGCTGATAAAATTTATCGATTTTATC-TTTTTTAAGGTAAATTTTTATCTCTTTCTTA
1 TAATTTTAGCTGATAAAATTTATCGATTTTATCTTTTTTTAAGGTAAATTTTTATCTCTTTCTTA
* *
221258 CATATAAATAAGGAGTAAATAATTATTTAAAAGTTATTTTGAAATGAATAAATTTTATTAGTTAG
66 CATATAAATAAGGAGTAAATAATTATTTAAAAATTATTTTGAAATGAATAAATTTTATTAATTAG
*
221323 AATCATGAATTATGT
131 AATCATGAATGATGT
221338 GAAGAACCAA
Statistics
Matches: 137, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
146 104 0.76
148 33 0.24
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.47
Consensus pattern (147 bp):
TAATTTTAGCTGATAAAATTTATCGATTTTATCTTTTTTTAAGGTAAATTTTTATCTCTTTCTTA
CATATAAATAAGGAGTAAATAATTATTTAAAAATTATTTTGAAATGAATAAATTTTATTAATTAG
AATCATGAATGATGTCG
Found at i:221755 original size:154 final size:160
Alignment explanation
Indices: 221491--221778 Score: 399
Period size: 154 Copynumber: 1.8 Consensus size: 160
221481 ACATGGGAGT
* * *
221491 TTTATTATGCGACCGATTAAGATGCAGTTAAAAAAGATAAAAACAAATAAGTGAAATTTAAAATG
1 TTTATTATGCGACAGATTAAGATGCAGTTAAAAAAGACAAAAACAAATAAGTAAAATTTAAAATG
* * * ** * **
221556 TTAGATTTTTTTGTAATATTTTATGTTGAACTCAACTTAAAATATTTT-TTAAAAAA-TGATATT
66 TTACATTTCTTCGTAATATTTTAAATTGAACTCAACCTAAAATATTTTGAAAAAAAAGTGATATT
221619 TTAAATTACATTTATTTTCATAACTTCTTA
131 TTAAATTACATTTATTTTCATAACTTCTTA
* * *
221649 TTTATTATGTGATAGATTAAGATGCAGTT-AAAAA-ACAATAA-AAATAAGTAAAATTTAAAATG
1 TTTATTATGCGACAGATTAAGATGCAGTTAAAAAAGACAAAAACAAATAAGTAAAATTTAAAATG
*
221711 TTACA-TTCTTCGTAATATTTTAAATTGAATTCAACCTAAAATATTTTGAAAAAAAAGTGATATT
66 TTACATTTCTTCGTAATATTTTAAATTGAACTCAACCTAAAATATTTTGAAAAAAAAGTGATATT
221775 TTAA
131 TTAA
221779 GATAAACTTA
Statistics
Matches: 113, Mismatches: 15, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
154 36 0.32
155 30 0.27
156 16 0.14
157 5 0.04
158 26 0.23
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.40
Consensus pattern (160 bp):
TTTATTATGCGACAGATTAAGATGCAGTTAAAAAAGACAAAAACAAATAAGTAAAATTTAAAATG
TTACATTTCTTCGTAATATTTTAAATTGAACTCAACCTAAAATATTTTGAAAAAAAAGTGATATT
TTAAATTACATTTATTTTCATAACTTCTTA
Found at i:236228 original size:45 final size:47
Alignment explanation
Indices: 236155--236260 Score: 162
Period size: 45 Copynumber: 2.3 Consensus size: 47
236145 TTTATTTTCG
*
236155 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGG-TTTA
1 TTTTTTGAAT-AATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
*
236202 TTTTTTGAATAA-GCATGCGAATTAGATATCATGCGGTTAGGATTTA
1 TTTTTTGAATAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
236248 TTTTTGTGAATAA
1 TTTTT-TGAATAA
236261 CAAAGCATGG
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
45 28 0.51
46 11 0.20
47 16 0.29
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (47 bp):
TTTTTTGAATAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
Found at i:245911 original size:14 final size:15
Alignment explanation
Indices: 245889--246056 Score: 67
Period size: 16 Copynumber: 10.1 Consensus size: 15
245879 ATTTCGCTTG
245889 AAGAAGAAATGAAAAAA
1 AAGAA-AAA-GAAAAAA
245906 AAGAAAAAGAAAAAA
1 AAGAAAAAGAAAAAA
*
245921 AGGAGGAAAAATAAAAGAA
1 A--A-GAAAAAGAAAA-AA
*
245940 AATAAAAAATGAGAAAAA
1 AA-GAAAAA-GA-AAAAA
245958 AATGAAAAATGGTGAAAAAA
1 AA-GAAAAA----GAAAAAA
245978 AA-AAGAAA-AATGAAAA
1 AAGAA-AAAGAA--AAAA
*
245994 ATGAAAAATG--AAAA
1 AAGAAAAA-GAAAAAA
*
246008 ATGAAAAATGAAAAAA
1 AAGAAAAA-GAAAAAA
246024 GAA-AAAAAGAAAAAAA
1 -AAGAAAAAG-AAAAAA
246040 AAGAAAAAGAAATAAA
1 AAGAAAAAGAAA-AAA
246056 A
1 A
246057 TGAGGGTTCT
Statistics
Matches: 123, Mismatches: 7, Indels: 43
0.71 0.04 0.25
Matches are distributed among these distances:
14 16 0.13
15 14 0.11
16 36 0.29
17 15 0.12
18 23 0.19
19 9 0.07
20 7 0.06
21 3 0.02
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (15 bp):
AAGAAAAAGAAAAAA
Found at i:245957 original size:21 final size:20
Alignment explanation
Indices: 245933--246047 Score: 71
Period size: 21 Copynumber: 5.8 Consensus size: 20
245923 GAGGAAAAAT
*
245933 AAAAGAAAATAAAAAATGAG
1 AAAAAAAAATAAAAAATGAG
* *
245953 --AAAAAAATGAAAAATGGTG
1 AAAAAAAAATAAAAAAT-GAG
245972 AAAAAAAAA-AGAAAAATGA-
1 AAAAAAAAATA-AAAAATGAG
* *
245991 AAAATGAAAAATGAAAAATGAA
1 AAAA--AAAAATAAAAAATGAG
*
246013 AAATGAAAAAAGAAAAAA--AG
1 AAA--AAAAAATAAAAAATGAG
*
246033 AAAAAAAAAGAAAAA
1 AAAAAAAAATAAAAA
246048 GAAATAAAAT
Statistics
Matches: 76, Mismatches: 9, Indels: 22
0.71 0.08 0.21
Matches are distributed among these distances:
18 25 0.33
19 6 0.08
20 5 0.07
21 26 0.34
22 13 0.17
24 1 0.01
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (20 bp):
AAAAAAAAATAAAAAATGAG
Found at i:245959 original size:18 final size:19
Alignment explanation
Indices: 245938--245978 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
245928 AAAATAAAAG
245938 AAAATAAAAAAT-GAGAAA
1 AAAATAAAAAATGGAGAAA
* *
245956 AAAATGAAAAATGGTGAAA
1 AAAATAAAAAATGGAGAAA
245975 AAAA
1 AAAA
245979 AAAGAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (19 bp):
AAAATAAAAAATGGAGAAA
Found at i:245965 original size:7 final size:7
Alignment explanation
Indices: 245955--246029 Score: 93
Period size: 7 Copynumber: 10.7 Consensus size: 7
245945 AAAATGAGAA
245955 AAAAATG
1 AAAAATG
245962 AAAAATGGTG
1 AAAAA---TG
245972 AAAAA--
1 AAAAATG
245977 AAAAA-G
1 AAAAATG
245983 AAAAATG
1 AAAAATG
245990 AAAAATG
1 AAAAATG
245997 AAAAATG
1 AAAAATG
246004 AAAAATG
1 AAAAATG
246011 AAAAATG
1 AAAAATG
*
246018 AAAAAAG
1 AAAAATG
246025 AAAAA
1 AAAAA
246030 AAGAAAAAAA
Statistics
Matches: 62, Mismatches: 1, Indels: 10
0.85 0.01 0.14
Matches are distributed among these distances:
5 5 0.08
6 5 0.08
7 45 0.73
10 7 0.11
ACGTcount: A:0.75, C:0.00, G:0.15, T:0.11
Consensus pattern (7 bp):
AAAAATG
Found at i:246047 original size:7 final size:7
Alignment explanation
Indices: 245972--246038 Score: 73
Period size: 7 Copynumber: 9.6 Consensus size: 7
245962 AAAAATGGTG
245972 AAAA-AA
1 AAAAGAA
245978 AAAAGAA
1 AAAAGAA
*
245985 AAATGAA
1 AAAAGAA
*
245992 AAATGAA
1 AAAAGAA
*
245999 AAATGAA
1 AAAAGAA
*
246006 AAATGAA
1 AAAAGAA
*
246013 AAATGAA
1 AAAAGAA
246020 AAAAGAAA
1 AAAAG-AA
246028 AAAAGAA
1 AAAAGAA
246035 AAAA
1 AAAA
246039 AAAGAAAAAG
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
6 4 0.07
7 46 0.81
8 7 0.12
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.07
Consensus pattern (7 bp):
AAAAGAA
Found at i:247538 original size:55 final size:55
Alignment explanation
Indices: 247409--247780 Score: 498
Period size: 55 Copynumber: 6.7 Consensus size: 55
247399 AATTTTGATA
* * * *
247409 AAGATTGTTCAAGTTCTATACTCCCTGAATGAATAGGGAGCGGACCCATTTTTATG
1 AAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCC-GTTTTATG
* *
247465 AAGATTGTTCGAGTTCTATATTCTCTGATGGAATAGGGAGCGGACCCGTTTTATG
1 AAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTTATG
*
247520 AAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATG
1 AAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTTATG
* * *
247575 AAGATTGTTCGAGTTCTATACTCTTTGAAGGAATTGAGAGCGGACCCGTTTTATG
1 AAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTTATG
* *
247630 AAGATTGTTCGAGTTATATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGT-TG
1 AAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTT-TATG
* * * * ***
247685 AAGATTGTTCGAG-TCTGATACTCCCTGAACGAATAGGGAACAGACATATTTTATG
1 AAGATTGTTCGAGTTCT-ATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTTATG
* *
247740 AAGATTGTTCGAGTTTTATACT-TCCTGAACGAATAGGGAGC
1 AAGATTGTTCGAGTTCTATACTCT-CTGAAGGAATAGGGAGC
247781 AGGCTCGTCA
Statistics
Matches: 285, Mismatches: 26, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
54 3 0.01
55 237 0.83
56 45 0.16
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.32
Consensus pattern (55 bp):
AAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTTATG
Found at i:257959 original size:12 final size:13
Alignment explanation
Indices: 257939--257977 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
257929 TTATCAAAAT
257939 ATATATTTTTTAA
1 ATATATTTTTTAA
*
257952 AT-TATTTTTAAA
1 ATATATTTTTTAA
257964 ATAATATTTTTTAA
1 AT-ATATTTTTTAA
257978 TATGTATAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 11 0.50
13 2 0.09
14 9 0.41
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATATATTTTTTAA
Found at i:257977 original size:26 final size:28
Alignment explanation
Indices: 257925--257977 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 28
257915 AGATGGAGGT
257925 TTATTTATCAAAATATATATTTTTTAAA
1 TTATTTATCAAAATATATATTTTTTAAA
*
257953 TTATTT-TTAAAATA-ATATTTTTTAA
1 TTATTTATCAAAATATATATTTTTTAA
257978 TATGTATAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 11 0.46
27 7 0.29
28 6 0.25
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (28 bp):
TTATTTATCAAAATATATATTTTTTAAA
Found at i:261328 original size:30 final size:29
Alignment explanation
Indices: 261289--261347 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
261279 GAGAATTTAC
* *
261289 ATGAACTACGTGATTAAATGTATATGTGA
1 ATGAACTACGAGATTAAATGAATATGTGA
* *
261318 ATGAAGCTACGAGTTTATATGAATATGTGA
1 ATGAA-CTACGAGATTAAATGAATATGTGA
261348 TATGTTTACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (29 bp):
ATGAACTACGAGATTAAATGAATATGTGA
Found at i:261645 original size:23 final size:23
Alignment explanation
Indices: 261578--261645 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
261568 CATCTTATAT
*
261578 GACACTTCGGTGCATTTATACAC
1 GACACTTCGGTGCATTTATACGC
* * * *
261601 GACACTTAGGTGCAATTGTACGT
1 GACACTTCGGTGCATTTATACGC
* *
261624 GGCACTTCGGTTCATTTATACG
1 GACACTTCGGTGCATTTATACG
261646 AGCTGTGGTT
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (23 bp):
GACACTTCGGTGCATTTATACGC
Found at i:263631 original size:24 final size:25
Alignment explanation
Indices: 263617--263670 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
263607 ATAAATTGCA
*
263617 CCGAAGTACCGCGTAGAAATTTGTC
1 CCGAAGGACCGCGTAGAAATTTGTC
263642 CCGAAGGACCGCGTAG-AATTTGTC
1 CCGAAGGACCGCGTAGAAATTTGTC
263666 CCGAA
1 CCGAA
263671 TGACTACATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 13 0.46
25 15 0.54
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (25 bp):
CCGAAGGACCGCGTAGAAATTTGTC
Found at i:270443 original size:24 final size:24
Alignment explanation
Indices: 270414--270478 Score: 103
Period size: 24 Copynumber: 2.7 Consensus size: 24
270404 GTCGCATAGA
270414 AATTTGTCCCGAATGACCGCGTAG
1 AATTTGTCCCGAATGACCGCGTAG
* * *
270438 AATTTGTCACAAAGGACCGCGTAG
1 AATTTGTCCCGAATGACCGCGTAG
270462 AATTTGTCCCGAATGAC
1 AATTTGTCCCGAATGAC
270479 TACATATAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (24 bp):
AATTTGTCCCGAATGACCGCGTAG
Found at i:276446 original size:23 final size:23
Alignment explanation
Indices: 276419--276484 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 23
276409 TCTTATATGA
276419 CACTTCGGTGCATTTCTACGCGAG
1 CACTTCGGTGCATTTCTACGCG-G
* * * **
276443 -ACTTAGGTGTAATTCTACATGG
1 CACTTCGGTGCATTTCTACGCGG
*
276465 CACTTCGGTGCATTTATACG
1 CACTTCGGTGCATTTCTACG
276485 AGCTGTGGTG
Statistics
Matches: 31, Mismatches: 10, Indels: 3
0.70 0.23 0.07
Matches are distributed among these distances:
22 1 0.03
23 30 0.97
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (23 bp):
CACTTCGGTGCATTTCTACGCGG
Found at i:278148 original size:4 final size:4
Alignment explanation
Indices: 278139--278167 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
278129 GTTTAAATTA
278139 TTAG TTAG TTAG TTAG TTAG TTAG TTAG T
1 TTAG TTAG TTAG TTAG TTAG TTAG TTAG T
278168 GGGCATAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TTAG
Found at i:280762 original size:17 final size:17
Alignment explanation
Indices: 280742--280783 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
280732 ATTATTATCA
280742 AATAATTAAATATTAAT
1 AATAATTAAATATTAAT
* * *
280759 AATAAATCATTATTAAT
1 AATAATTAAATATTAAT
280776 AATAATTA
1 AATAATTA
280784 CTAAATCATT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
AATAATTAAATATTAAT
Found at i:280776 original size:14 final size:13
Alignment explanation
Indices: 280760--280871 Score: 105
Period size: 14 Copynumber: 8.8 Consensus size: 13
280750 AATATTAATA
280760 ATAAATCATTATT
1 ATAAATCATTATT
280773 A-ATAAT-A--ATT
1 ATA-AATCATTATT
280783 ACTAAATCATTA-T
1 A-TAAATCATTATT
280796 -TAAATCATTATT
1 ATAAATCATTATT
280808 ATCAAATCATTATT
1 AT-AAATCATTATT
*
280822 AT-AATGATTATT
1 ATAAATCATTATT
280834 ACTAAATCATTATT
1 A-TAAATCATTATT
*
280848 AT-AATGATTATT
1 ATAAATCATTATT
280860 ATCAAATCATTA
1 AT-AAATCATTA
280872 CAAAATCATC
Statistics
Matches: 82, Mismatches: 4, Indels: 25
0.74 0.04 0.23
Matches are distributed among these distances:
10 4 0.05
11 13 0.16
12 26 0.32
13 8 0.10
14 31 0.38
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.44
Consensus pattern (13 bp):
ATAAATCATTATT
Found at i:280779 original size:26 final size:26
Alignment explanation
Indices: 280746--280871 Score: 106
Period size: 26 Copynumber: 5.0 Consensus size: 26
280736 TTATCAAATA
280746 ATTA-AAT-ATTAATAATAAATCATT
1 ATTATAATGATTAATAATAAATCATT
* *
280770 ATTAATAAT-A--ATTACTAAATCATT
1 ATT-ATAATGATTAATAATAAATCATT
* *
280794 ATTA-AATCATT-ATTATCAAATCATT
1 ATTATAATGATTAATAAT-AAATCATT
* *
280819 ATTATAATGATTATTACTAAATCATT
1 ATTATAATGATTAATAATAAATCATT
*
280845 ATTATAATGATT-ATTATCAAATCATT
1 ATTATAATGATTAATAAT-AAATCATT
280871 A
1 A
280872 CAAAATCATC
Statistics
Matches: 81, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
22 3 0.04
23 2 0.02
24 20 0.25
25 15 0.19
26 39 0.48
27 2 0.02
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.44
Consensus pattern (26 bp):
ATTATAATGATTAATAATAAATCATT
Found at i:281293 original size:21 final size:20
Alignment explanation
Indices: 281266--281429 Score: 72
Period size: 21 Copynumber: 8.2 Consensus size: 20
281256 ATAATTTCAT
281266 TATTACTAATAATTATTAAA
1 TATTACTAATAATTATTAAA
* *
281286 TCATTACTATTAAATCATTAAA
1 T-ATTACTAAT-AATTATTAAA
* * * *
281308 TATGAATAATAA-T-TTCAT
1 TATTACTAATAATTATTAAA
* * *
281326 TATTACTAGTCATTACTAAA
1 TATTACTAATAATTATTAAA
*
281346 TCATTACT-ATCAAATCATTAAA
1 T-ATTACTAAT--AATTATTAAA
* * *
281368 TATTAATAATAA-T-TTCAT
1 TATTACTAATAATTATTAAA
** *
281386 TATTACTAATCGTTACTAAA
1 TATTACTAATAATTATTAAA
*
281406 TAATTA-TTATAATT-TTAAA
1 T-ATTACTAATAATTATTAAA
281425 TATTA
1 TATTA
281430 AATCGTTATT
Statistics
Matches: 100, Mismatches: 33, Indels: 24
0.64 0.21 0.15
Matches are distributed among these distances:
18 27 0.27
19 7 0.07
20 17 0.17
21 29 0.29
22 20 0.20
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.44
Consensus pattern (20 bp):
TATTACTAATAATTATTAAA
Found at i:281298 original size:14 final size:14
Alignment explanation
Indices: 281279--281305 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
281269 TACTAATAAT
281279 TATTAAATCATTAC
1 TATTAAATCATTAC
281293 TATTAAATCATTA
1 TATTAAATCATTA
281306 AATATGAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (14 bp):
TATTAAATCATTAC
Found at i:281430 original size:57 final size:59
Alignment explanation
Indices: 281256--281430 Score: 246
Period size: 60 Copynumber: 3.0 Consensus size: 59
281246 AATCATTATT
* * *
281256 ATAATTTCATTATTACTAATAATTATTAAATCATTACTATTAAATCATTAAATATGAATA
1 ATAATTTCATTATTACTAATCATTACTAAATCATTACTA-TAAATCATTAAATATTAATA
*
281316 ATAATTTCATTATTACTAGTCATTACTAAATCATTACTATCAAATCATTAAATATTAATA
1 ATAATTTCATTATTACTAATCATTACTAAATCATTACTAT-AAATCATTAAATATTAATA
* * * *
281376 ATAATTTCATTATTACTAATCGTTACTAAATAATTATTAT-AAT-TTTAAATATTAA
1 ATAATTTCATTATTACTAATCATTACTAAATCATTACTATAAATCATTAAATATTAA
281431 ATCGTTATTA
Statistics
Matches: 105, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
57 11 0.10
58 3 0.03
59 1 0.01
60 90 0.86
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.44
Consensus pattern (59 bp):
ATAATTTCATTATTACTAATCATTACTAAATCATTACTATAAATCATTAAATATTAATA
Found at i:284368 original size:27 final size:26
Alignment explanation
Indices: 284338--284392 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
284328 ACTTGATTGA
*
284338 TTAATTACTAATATTAATAATAATGAT
1 TTAATAACTAATATTAAT-ATAATGAT
* * *
284365 TTAATAATTATTATTAATCTAATGAT
1 TTAATAACTAATATTAATATAATGAT
284391 TT
1 TT
284393 GATATTTAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.49
Consensus pattern (26 bp):
TTAATAACTAATATTAATATAATGAT
Found at i:284786 original size:14 final size:14
Alignment explanation
Indices: 284767--284795 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
284757 ACACATACAC
284767 AACAACAAAAAATA
1 AACAACAAAAAATA
284781 AACAACAAAAAATA
1 AACAACAAAAAATA
284795 A
1 A
284796 TAAATTACCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.79, C:0.14, G:0.00, T:0.07
Consensus pattern (14 bp):
AACAACAAAAAATA
Found at i:284787 original size:17 final size:17
Alignment explanation
Indices: 284765--284799 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
284755 TTACACATAC
284765 ACAACAACAAAA-AATAA
1 ACAACAA-AAAATAATAA
284782 ACAACAAAAAATAATAA
1 ACAACAAAAAATAATAA
284799 A
1 A
284800 TTACCCCGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.77, C:0.14, G:0.00, T:0.09
Consensus pattern (17 bp):
ACAACAAAAAATAATAA
Found at i:284952 original size:5 final size:5
Alignment explanation
Indices: 284938--284990 Score: 61
Period size: 5 Copynumber: 10.6 Consensus size: 5
284928 TTAAACAAAT
* * * * *
284938 TAATT TAATA TAATA AAATA TATTA TAATA TAACA TAATA TATTA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
284988 TAA
1 TAA
284991 CTTAAACCAA
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
TAATA
Found at i:284968 original size:20 final size:20
Alignment explanation
Indices: 284931--284991 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
284921 CAATAAATTA
*
284931 AACAAATTA-ATT-TAATAT
1 AACAAAATATATTATAATAT
*
284949 AATAAAATATATTATAATAT
1 AACAAAATATATTATAATAT
*
284969 AACATAATATATTATAATAT
1 AACAAAATATATTATAATAT
284989 AAC
1 AAC
284992 TTAAACCAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.19
19 3 0.08
20 27 0.73
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
AACAAAATATATTATAATAT
Found at i:285187 original size:43 final size:49
Alignment explanation
Indices: 285131--285244 Score: 123
Period size: 50 Copynumber: 2.4 Consensus size: 49
285121 TTAAACACAT
* *
285131 TAACAAATTAATTAAAT-ATTTTTT-TA-CAT-T-TA-ATAACTTAAAC
1 TAACAAACTAATTAAATAATTTTTTATATAATCTATATATAACTTAAAC
* *
285174 TAAGAAACTAATTAACTAATTTTTTATATAATCTAATATATAACTTAAAC
1 TAACAAACTAATTAAATAATTTTTTATATAATCT-ATATATAACTTAAAC
285224 TAACAAACTAATATAATATAA
1 TAACAAACTAAT-TAA-ATAA
285245 CTTAAACTAA
Statistics
Matches: 56, Mismatches: 6, Indels: 9
0.79 0.08 0.13
Matches are distributed among these distances:
43 14 0.25
44 7 0.12
45 2 0.04
46 2 0.04
47 1 0.02
49 2 0.04
50 22 0.39
51 3 0.05
52 3 0.05
ACGTcount: A:0.50, C:0.10, G:0.01, T:0.39
Consensus pattern (49 bp):
TAACAAACTAATTAAATAATTTTTTATATAATCTATATATAACTTAAAC
Found at i:285683 original size:19 final size:19
Alignment explanation
Indices: 285659--285696 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
285649 GTCTCGAAGC
285659 TATGGCACGAGGGAGCAGA
1 TATGGCACGAGGGAGCAGA
285678 TATGGCACGAGGGAGCAGA
1 TATGGCACGAGGGAGCAGA
285697 AGCTTGGTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.42, T:0.11
Consensus pattern (19 bp):
TATGGCACGAGGGAGCAGA
Found at i:285933 original size:47 final size:47
Alignment explanation
Indices: 285864--285957 Score: 152
Period size: 47 Copynumber: 2.0 Consensus size: 47
285854 CCTACAAACA
* * *
285864 AGGTCGCCTGGAAGGCATGGCGACCTACAAGGTCGCCTGGATGGCAT
1 AGGTCGCCTGGAAGACATGGCGACCTACAAGGTCGCCCGGAGGGCAT
*
285911 AGGTCGCCTGGATGACATGGCGACCTACAAGGTCGCCCGGAGGGCAT
1 AGGTCGCCTGGAAGACATGGCGACCTACAAGGTCGCCCGGAGGGCAT
285958 GTCGACCTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.21, C:0.27, G:0.36, T:0.16
Consensus pattern (47 bp):
AGGTCGCCTGGAAGACATGGCGACCTACAAGGTCGCCCGGAGGGCAT
Found at i:285958 original size:29 final size:29
Alignment explanation
Indices: 285911--285966 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
285901 TGGATGGCAT
* *
285911 AGGTCGCCTGGATGACATGGCGACCTACA
1 AGGTCGCCCGGAGGACATGGCGACCTACA
* *
285940 AGGTCGCCCGGAGGGCATGTCGACCTA
1 AGGTCGCCCGGAGGACATGGCGACCTA
285967 TGTTTTGCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.21, C:0.29, G:0.34, T:0.16
Consensus pattern (29 bp):
AGGTCGCCCGGAGGACATGGCGACCTACA
Found at i:286596 original size:34 final size:32
Alignment explanation
Indices: 286547--286623 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 32
286537 TTAATAATAA
* *
286547 TATTGAAAT-TTTTAAATATAAATATATAAAAACT
1 TATTAAAATATTTAAAATAT-AATAT-TAAAAA-T
*
286581 TATTAAAATATTTAAAATATACTATTAAAAAT
1 TATTAAAATATTTAAAATATAATATTAAAAAT
286613 TATTTAAAATA
1 TA-TTAAAATA
286624 AAATACTATT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
32 3 0.08
33 14 0.37
34 12 0.32
35 9 0.24
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.42
Consensus pattern (32 bp):
TATTAAAATATTTAAAATATAATATTAAAAAT
Found at i:286656 original size:20 final size:20
Alignment explanation
Indices: 286633--286671 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
286623 AAAATACTAT
286633 TAAATA-TAGTAAAAGTTAAG
1 TAAATACTA-TAAAAGTTAAG
*
286653 TAAATACTATAAAATTTAA
1 TAAATACTATAAAAGTTAA
286672 AAATAGCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.56, C:0.03, G:0.08, T:0.33
Consensus pattern (20 bp):
TAAATACTATAAAAGTTAAG
Found at i:287581 original size:23 final size:22
Alignment explanation
Indices: 287555--287597 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
287545 TAAACAACTA
*
287555 AAAGATATAATAAATCGTGTCTT
1 AAAGATAGAA-AAATCGTGTCTT
*
287578 AAAGGTAGAAAAATCGTGTC
1 AAAGATAGAAAAATCGTGTC
287598 ATATAAATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.44, C:0.09, G:0.19, T:0.28
Consensus pattern (22 bp):
AAAGATAGAAAAATCGTGTCTT
Found at i:290683 original size:108 final size:108
Alignment explanation
Indices: 290544--290760 Score: 382
Period size: 108 Copynumber: 2.0 Consensus size: 108
290534 GGTAGCTTGG
*
290544 TGCATAGGTGTTCTCCAAAGGCTTCAATAAATGAATTTTAAGAAAATCCTACTAAGATGTGGATA
1 TGCATAGGTGTTCTCCAAAGGCTTCAATAAATGAATTGTAAGAAAATCCTACTAAGATGTGGATA
* *
290609 GAGTCGCAGAGGAGTAACTTTCAATTGATTCTATACATTTCTA
66 AAGTCGCAGAGGAGTAACTTTCAATTGATTCTATACATATCTA
290652 TGCATAGGTCGTTCT-CAAAGGCTTCAATAAATGAATTGTAAGAAAATCCTACTAAGATGTGGAT
1 TGCATAGGT-GTTCTCCAAAGGCTTCAATAAATGAATTGTAAGAAAATCCTACTAAGATGTGGAT
*
290716 AAAGTCGCAGAGGAGTAGCTTTCAATTGATTCTATACATATCTA
65 AAAGTCGCAGAGGAGTAACTTTCAATTGATTCTATACATATCTA
290760 T
1 T
290761 TGTTTGGTGG
Statistics
Matches: 104, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
108 99 0.95
109 5 0.05
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.32
Consensus pattern (108 bp):
TGCATAGGTGTTCTCCAAAGGCTTCAATAAATGAATTGTAAGAAAATCCTACTAAGATGTGGATA
AAGTCGCAGAGGAGTAACTTTCAATTGATTCTATACATATCTA
Found at i:293117 original size:19 final size:19
Alignment explanation
Indices: 293095--293157 Score: 59
Period size: 19 Copynumber: 3.7 Consensus size: 19
293085 TTGTTTAGAA
*
293095 TCTATTTATCTATCACGAG
1 TCTATGTATCTATCACGAG
293114 TCTATGTATCTAT----A-
1 TCTATGTATCTATCACGAG
*
293128 --TATTTATCTATCACGAG
1 TCTATGTATCTATCACGAG
293145 TCTATGTATCTAT
1 TCTATGTATCTAT
293158 ATATTTATCT
Statistics
Matches: 34, Mismatches: 3, Indels: 14
0.67 0.06 0.27
Matches are distributed among these distances:
12 10 0.29
15 1 0.03
16 1 0.03
19 22 0.65
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.46
Consensus pattern (19 bp):
TCTATGTATCTATCACGAG
Found at i:293134 original size:31 final size:31
Alignment explanation
Indices: 293097--293170 Score: 148
Period size: 31 Copynumber: 2.4 Consensus size: 31
293087 GTTTAGAATC
293097 TATTTATCTATCACGAGTCTATGTATCTATA
1 TATTTATCTATCACGAGTCTATGTATCTATA
293128 TATTTATCTATCACGAGTCTATGTATCTATA
1 TATTTATCTATCACGAGTCTATGTATCTATA
293159 TATTTATCTATC
1 TATTTATCTATC
293171 CATCCATGTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.28, C:0.16, G:0.08, T:0.47
Consensus pattern (31 bp):
TATTTATCTATCACGAGTCTATGTATCTATA
Found at i:301799 original size:182 final size:181
Alignment explanation
Indices: 301517--302220 Score: 846
Period size: 182 Copynumber: 3.9 Consensus size: 181
301507 ATATCTCTCC
* * * * * *
301517 ATAACAATATTACAGGTAAAAATATGACAAAACCGGTCTCGAAATGATAAAACCGATAAA-ACGA
1 ATAACAATATAACAGGTAAAAATATGACAAAACAGATCTCAAAATGACAAAACCGATAAAGA-AA
301581 TACCGGATATGTTGAAAGTGTCAATAATTTAATATAAGTATCGACACTTTTAGAATTTAAAAGAG
65 TACCGGATATGTTGAAAGTGTCAATAATTTAATATAAGTATCGACACTTTT-GAATTTAAAAGAG
*
301646 AAGAAGTTATAGCGCCTATAAAA-TATCGATACTTTAAAAAAATGTATTGAT-T
129 AAGAAGTTATAGCGCCTA-AAAAGTATCGATACTTTAAAAAAATGTATCGATCT
* * *
301698 CATAACAATATAACAGGTAAAAATATGACAAAACATATCTTAAAAATGACAAAACCGGTAAA-AA
1 -ATAACAATATAACAGGTAAAAATATGACAAAACAGATC-TCAAAATGACAAAACCGATAAAGAA
* * * * ** * *
301762 ATATCGGATATGTTAAAAGTGTCGATAATTAAATATAAGTATATAAATTTTTTGGAATTTAAAAG
64 ATACCGGATATGTTGAAAGTGTCAATAATTTAATATAAGTATCGACA-CTTTT-GAATTTAAAAG
* * * *
301827 AAAATAAGTTATAGCGCCTATAAAGTGTCGATACTTTTAAAAAAA--TATCGATCT
127 AGAAGAAGTTATAGCGCCTAAAAAGTATCGATAC-TTTAAAAAAATGTATCGATCT
* * * ***
301881 ATAACAATATAACAGGTAAAAATATGACAAAACCA-ATCCCAAAATGACAAATCCGGTAAAGCGC
1 ATAACAATATAACAGGTAAAAATATGACAAAA-CAGATCTCAAAATGACAAAACCGATAAAGAAA
* *
301945 TACCAGATATGTTGAAAGTGTCAATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAATAG
65 TACCGGATATGTTGAAAGTGTCAATAATTTAATATAAGTATCGACACTTT-TGAATTTAAAAGAG
* **
302010 AAGAAGTTATAGCGCCTAAAAAGTATCAATACTTTATGAAAATGTATCGATCT
129 AAGAAGTTATAGCGCCTAAAAAGTATCGATACTTTAAAAAAATGTATCGATCT
** * * * * * * *
302063 ATAACAATATAACAACTAAAAATATGATAAAGCCGGTTTCAAAATGATAAAACCGATAAAGAACT
1 ATAACAATATAACAGGTAAAAATATGACAAAACAGATCTCAAAATGACAAAACCGATAAAGAAAT
* * *
302128 ACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCTACACTTTTGAAATTTAAAAGAGA
66 ACCGGATATGTTGAAAGTGTCAATAATTTAATATAAGTATCGACACTTTTG-AATTTAAAAGAGA
*
302193 ATAAGTTATAGCGCCTAAAAAGTATCGA
130 AGAAGTTATAGCGCCTAAAAAGTATCGA
302221 CACTCTTTAA
Statistics
Matches: 444, Mismatches: 66, Indels: 24
0.83 0.12 0.04
Matches are distributed among these distances:
180 8 0.02
181 64 0.14
182 299 0.67
183 63 0.14
184 10 0.02
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.28
Consensus pattern (181 bp):
ATAACAATATAACAGGTAAAAATATGACAAAACAGATCTCAAAATGACAAAACCGATAAAGAAAT
ACCGGATATGTTGAAAGTGTCAATAATTTAATATAAGTATCGACACTTTTGAATTTAAAAGAGAA
GAAGTTATAGCGCCTAAAAAGTATCGATACTTTAAAAAAATGTATCGATCT
Found at i:302615 original size:23 final size:23
Alignment explanation
Indices: 302582--302680 Score: 135
Period size: 23 Copynumber: 4.3 Consensus size: 23
302572 AAATAGGTCA
* *
302582 ATATAAACGCTATCTATTACATT
1 ATATAAGCACTATCTATTACATT
* *
302605 ATATAAGCGCTATCTATTATATT
1 ATATAAGCACTATCTATTACATT
*
302628 ATATAAGCACTATTTATTACATT
1 ATATAAGCACTATCTATTACATT
* *
302651 ATATAAACACTATTTATTACATT
1 ATATAAGCACTATCTATTACATT
302674 ATATAAG
1 ATATAAG
302681 TGTTACCTAA
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 69 1.00
ACGTcount: A:0.40, C:0.13, G:0.05, T:0.41
Consensus pattern (23 bp):
ATATAAGCACTATCTATTACATT
Found at i:302739 original size:110 final size:114
Alignment explanation
Indices: 302618--302828 Score: 295
Period size: 115 Copynumber: 1.9 Consensus size: 114
302608 TAAGCGCTAT
** *
302618 CTATTATATTATATAAGCACTATTTATTACATTATATAA-AC-AC-TATT-TATTACATTATATA
1 CTATTATATTATATAAGCACTACCTATTACATTATATAACACTACATATTACATTACATTATATA
* * *
302679 AGTGTTACCTAATATGTTATTGTACTTGGTAATATTTCTGGTTAAATGC
66 AGCGCTACCTAATATGTTATTGTACTTGATAATATTTCTGGTTAAATGC
* * *
302728 CTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACATATTACATTACATTATAT
1 CTATTATATTATATAAGCACTACCTATTACATTATATAA-CACTACATATTACATTACATTATAT
*
302793 AAGCGCTACCTAATATGTTATTGTGCTTGATAATAT
65 AAGCGCTACCTAATATGTTATTGTACTTGATAATAT
302829 ATTTAATAAT
Statistics
Matches: 86, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
110 35 0.41
112 1 0.01
113 2 0.02
114 4 0.05
115 44 0.51
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.43
Consensus pattern (114 bp):
CTATTATATTATATAAGCACTACCTATTACATTATATAACACTACATATTACATTACATTATATA
AGCGCTACCTAATATGTTATTGTACTTGATAATATTTCTGGTTAAATGC
Found at i:302753 original size:23 final size:23
Alignment explanation
Indices: 302727--302804 Score: 84
Period size: 23 Copynumber: 3.2 Consensus size: 23
302717 TGGTTAAATG
302727 CCTATTTTATTATATAAGCGCTA
1 CCTATTTTATTATATAAGCGCTA
**
302750 CCTATTACATTATATAAGCGCTA
1 CCTATTTTATTATATAAGCGCTA
*
302773 CATATTACATTACATTATATAAGCGCTA
1 CCTATT---TT--ATTATATAAGCGCTA
302801 CCTA
1 CCTA
302805 ATATGTTATT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
23 26 0.59
28 18 0.41
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.37
Consensus pattern (23 bp):
CCTATTTTATTATATAAGCGCTA
Found at i:302813 original size:23 final size:23
Alignment explanation
Indices: 302735--302807 Score: 83
Period size: 28 Copynumber: 3.0 Consensus size: 23
302725 TGCCTATTTT
*
302735 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
*
302758 ATTATATAAGCGCTACATATTACATTAC
1 ATTATATAAGCGCTAC---CTA-A-TAC
302786 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
302808 TGTTATTGTG
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
23 18 0.43
24 1 0.02
25 2 0.05
26 2 0.05
28 19 0.45
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.34
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:309880 original size:15 final size:15
Alignment explanation
Indices: 309862--309895 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
309852 GTGAAATTCT
309862 AATTATTTAAATAAA
1 AATTATTTAAATAAA
*
309877 AATTATTTATATAAA
1 AATTATTTAAATAAA
309892 AATT
1 AATT
309896 CATCGATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTATTTAAATAAA
Found at i:310230 original size:31 final size:32
Alignment explanation
Indices: 310168--310233 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 32
310158 ATTCCTCGAA
* *
310168 AGATGATTTCTACCGAGTCGGACACTTGTTAC
1 AGATGATTTCTACCGACTCAGACACTTGTTAC
*
310200 AGATGATTTCTA-CGACTCAGACTCTTGTTAC
1 AGATGATTTCTACCGACTCAGACACTTGTTAC
310231 AGA
1 AGA
310234 CGCTATGTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
31 19 0.61
32 12 0.39
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (32 bp):
AGATGATTTCTACCGACTCAGACACTTGTTAC
Found at i:311245 original size:31 final size:31
Alignment explanation
Indices: 311207--311270 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
311197 CTCCGTCTCC
311207 AAGCCAACCTGCATTATAAGAGCTTTAAATT
1 AAGCCAACCTGCATTATAAGAGCTTTAAATT
311238 AAGCCAACCTGCATTATAAGAGCTTTAAATT
1 AAGCCAACCTGCATTATAAGAGCTTTAAATT
311269 AA
1 AA
311271 TGTACGTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (31 bp):
AAGCCAACCTGCATTATAAGAGCTTTAAATT
Found at i:313167 original size:3 final size:3
Alignment explanation
Indices: 313159--313199 Score: 57
Period size: 3 Copynumber: 13.3 Consensus size: 3
313149 TTTATTTTAA
313159 ATT ATT ATT ATT ATT ATT ATT ATT ATTT ACTT -TT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A-TT A-TT ATT ATT ATT A
313200 CTAGTTGTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.80
4 5 0.14
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:316228 original size:31 final size:31
Alignment explanation
Indices: 316187--316313 Score: 164
Period size: 31 Copynumber: 4.1 Consensus size: 31
316177 AAGAGTTGAG
* *
316187 GGTTATCTATGCCCTTCGGGACATATGGACA
1 GGTTACCTATGTCCTTCGGGACATATGGACA
* *
316218 GGTTACCTATGTTCTTCGGGACGTATGGACA
1 GGTTACCTATGTCCTTCGGGACATATGGACA
* *
316249 TGTTACCTATATCCTTCGGGACATATGGACA
1 GGTTACCTATGTCCTTCGGGACATATGGACA
* ** *
316280 GGTCACCTATGTCCTTCAAGACATATAGACA
1 GGTTACCTATGTCCTTCGGGACATATGGACA
316311 GGT
1 GGT
316314 CCTTCGGGAC
Statistics
Matches: 82, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 82 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (31 bp):
GGTTACCTATGTCCTTCGGGACATATGGACA
Found at i:320399 original size:31 final size:31
Alignment explanation
Indices: 320361--320425 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
320351 AAGAGTCGAG
* *
320361 GGTTACCTATGTCCTTCGGGACATATGGACA
1 GGTTACCTATATCCTTCAGGACATATGGACA
*
320392 GGTTACCTATATCCTTCAGGACATATGGATA
1 GGTTACCTATATCCTTCAGGACATATGGACA
320423 GGT
1 GGT
320426 CCTTCGAGAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.31
Consensus pattern (31 bp):
GGTTACCTATATCCTTCAGGACATATGGACA
Found at i:321890 original size:15 final size:15
Alignment explanation
Indices: 321870--321904 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
321860 CCGTAGGACC
*
321870 ACTACGTCCCTAAGG
1 ACTACGTCCCGAAGG
321885 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
321900 ACTAC
1 ACTAC
321905 AATACCCTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.34, G:0.20, T:0.17
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:328733 original size:15 final size:15
Alignment explanation
Indices: 328713--328747 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
328703 CCGTAGGACC
328713 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
328728 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
328743 ACTAC
1 ACTAC
328748 AATACCCTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.29, C:0.34, G:0.23, T:0.14
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:329694 original size:12 final size:12
Alignment explanation
Indices: 329677--329701 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
329667 TGATGACAAG
329677 TCAAATTTAACT
1 TCAAATTTAACT
329689 TCAAATTTAACT
1 TCAAATTTAACT
329701 T
1 T
329702 ATCAACTCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (12 bp):
TCAAATTTAACT
Found at i:332382 original size:4 final size:4
Alignment explanation
Indices: 332373--332406 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
332363 TGTTCAGAAT
332373 ATCC ATCC ATCC ATCC ATCC ATCC ATCC ATCC AT
1 ATCC ATCC ATCC ATCC ATCC ATCC ATCC ATCC AT
332407 TATTTTCCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.26, C:0.47, G:0.00, T:0.26
Consensus pattern (4 bp):
ATCC
Found at i:334166 original size:16 final size:16
Alignment explanation
Indices: 334141--334183 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
334131 AACGTCTTTT
334141 AAAAACAATTTT-TAAG
1 AAAAA-AATTTTATAAG
334157 AAAAATAATTTTATAAG
1 AAAAA-AATTTTATAAG
*
334174 ACAAAAATTT
1 AAAAAAATTT
334184 GGTCTACGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.33
Consensus pattern (16 bp):
AAAAAAATTTTATAAG
Found at i:334881 original size:20 final size:20
Alignment explanation
Indices: 334858--334896 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
334848 ATGAACATCT
*
334858 AATAAATTAACAACAAAAAA
1 AATAAAATAACAACAAAAAA
*
334878 AATAAAATAACAATAAAAA
1 AATAAAATAACAACAAAAA
334897 TAATTTCTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (20 bp):
AATAAAATAACAACAAAAAA
Found at i:336435 original size:12 final size:12
Alignment explanation
Indices: 336410--336447 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
336400 AAAACTTTTC
336410 TTTTTTC-TCT-
1 TTTTTTCTTCTG
336420 TTTTTTCTTCTG
1 TTTTTTCTTCTG
*
336432 TTTTTTTTTCTG
1 TTTTTTCTTCTG
336444 TTTT
1 TTTT
336448 CGAAAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 7 0.28
11 3 0.12
12 15 0.60
ACGTcount: A:0.00, C:0.13, G:0.05, T:0.82
Consensus pattern (12 bp):
TTTTTTCTTCTG
Found at i:336853 original size:25 final size:25
Alignment explanation
Indices: 336825--336946 Score: 217
Period size: 25 Copynumber: 4.9 Consensus size: 25
336815 AGTTAGGGTT
*
336825 GGGTTTGAAACCCTAGTCTGATTTA
1 GGGTTTGAAACCCTAATCTGATTTA
*
336850 GGGTTTGAAACCCTAAACTGATTTA
1 GGGTTTGAAACCCTAATCTGATTTA
*
336875 GGGTTTGAAACCCTAAACTGATTTA
1 GGGTTTGAAACCCTAATCTGATTTA
336900 GGGTTTGAAACCCTAATCTGATTTA
1 GGGTTTGAAACCCTAATCTGATTTA
336925 GGGTTTGAAACCCTAATCTGAT
1 GGGTTTGAAACCCTAATCTGAT
336947 GGGTTGTTGG
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 94 1.00
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (25 bp):
GGGTTTGAAACCCTAATCTGATTTA
Found at i:337096 original size:3 final size:3
Alignment explanation
Indices: 337075--337116 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
337065 TAATTAATTT
* **
337075 ATA ATA AAA ATA ACG ATA ATA ATA ATA ATA ATA ATA A-A ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
337117 CAGAAAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (3 bp):
ATA
Found at i:337526 original size:141 final size:136
Alignment explanation
Indices: 337300--337585 Score: 430
Period size: 141 Copynumber: 2.1 Consensus size: 136
337290 CAATGAAGAG
* * * *
337300 GTCTGGTCGTCTAAGGGTGACACGGCTCCTACGTGATGAGGAAATCTGGTCATCTTTAGGAAGGG
1 GTCTGGTCGTCTAAGGGTGACACGGCTCATACATGATGAAGAAATCTGGCCATCTTTAGGAAGGG
337365 TGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCCTAATGTTGACACAGCTCCTACGTG
66 TGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCCTAATGTTGACAC-GCTCCTACGTG
337430 ATGAGGAA
130 ATGAGG-A
* * *
337438 GTCTGGTCGTCTAAGGGTAGATGACATGGTTCATACATGATGAAGAACTCTGGCCATC-TTAGGA
1 GTCTGGTCGTCTAA-GG--G-TGACACGGCTCATACATGATGAAGAAATCTGGCCATCTTTAGGA
*
337502 AGGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCCTAATGTTGACACTCTCCTAC
62 AGGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCCTAATGTTGACACGCTCCTAC
337567 GTGATGAGGA
127 GTGATGAGGA
337577 GATCTGGTC
1 G-TCTGGTC
337586 AGTTGATGTT
Statistics
Matches: 135, Mismatches: 8, Indels: 8
0.89 0.05 0.05
Matches are distributed among these distances:
138 14 0.10
139 4 0.03
140 23 0.17
141 64 0.47
142 30 0.22
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (136 bp):
GTCTGGTCGTCTAAGGGTGACACGGCTCATACATGATGAAGAAATCTGGCCATCTTTAGGAAGGG
TGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCCTAATGTTGACACGCTCCTACGTGA
TGAGGA
Found at i:349312 original size:16 final size:16
Alignment explanation
Indices: 349287--349329 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
349277 AACGTCTTTT
349287 AAAAACAATTTT-TAAG
1 AAAAA-AATTTTATAAG
349303 AAAAATAATTTTATAAG
1 AAAAA-AATTTTATAAG
*
349320 ACAAAAATTT
1 AAAAAAATTT
349330 GGTCTACGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.33
Consensus pattern (16 bp):
AAAAAAATTTTATAAG
Found at i:350499 original size:30 final size:31
Alignment explanation
Indices: 350420--350505 Score: 88
Period size: 30 Copynumber: 2.8 Consensus size: 31
350410 TAAACATACA
* *
350420 GGATTAAAATAATAAAAATAGCAA-TAAAAG
1 GGATTAAAATAGTAAAAATAGAAACTAAAAG
* * * *
350450 GGATCAAAAT-GGATGAAATAAAAACT-AAAG
1 GGATTAAAATAGTA-AAAATAGAAACTAAAAG
350480 GGATTAAAATAGTAAAAATAGAAACT
1 GGATTAAAATAGTAAAAATAGAAACT
350506 TATGAGTCTA
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
29 1 0.02
30 39 0.91
31 3 0.07
ACGTcount: A:0.59, C:0.05, G:0.16, T:0.20
Consensus pattern (31 bp):
GGATTAAAATAGTAAAAATAGAAACTAAAAG
Found at i:351587 original size:13 final size:13
Alignment explanation
Indices: 351562--351600 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
351552 AAAACTTTTC
*
351562 TTTT-TTCTCTTT
1 TTTTCTTCTGTTT
351574 TTTTCTTCTGTTT
1 TTTTCTTCTGTTT
351587 TTTTCTTCTGTTT
1 TTTTCTTCTGTTT
351600 T
1 T
351601 CGAAAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 4 0.16
13 21 0.84
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.79
Consensus pattern (13 bp):
TTTTCTTCTGTTT
Found at i:352022 original size:25 final size:25
Alignment explanation
Indices: 351994--352093 Score: 182
Period size: 25 Copynumber: 4.0 Consensus size: 25
351984 AGTTAGGGGA
*
351994 TTAGGGTTTGAAACCCTAGTCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
*
352019 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
352044 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
352069 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
352094 GGGTTGTTGG
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 72 1.00
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGAT
Found at i:352243 original size:3 final size:3
Alignment explanation
Indices: 352222--352263 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
352212 TAATTAATTT
* **
352222 ATA ATA AAA ATA ACG ATA ATA ATA ATA ATA ATA ATA A-A ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
352264 CGGAAAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (3 bp):
ATA
Found at i:353765 original size:3 final size:3
Alignment explanation
Indices: 353757--353785 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
353747 ATGCTCAAGT
353757 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
353786 TAATAAAGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:358030 original size:3 final size:3
Alignment explanation
Indices: 358022--358047 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
358012 CTTGAGTTGA
358022 TGC TGC TGC TGC TGC TGC TGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TG
358048 TGACTGTGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.35, T:0.35
Consensus pattern (3 bp):
TGC
Found at i:366286 original size:19 final size:19
Alignment explanation
Indices: 366262--366298 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
366252 TTTATGAGTA
366262 TTATTTT-ATTATTTTAATT
1 TTATTTTAATT-TTTTAATT
366281 TTATTTTAATTTTTTAAT
1 TTATTTTAATTTTTTAAT
366299 CAAGTTAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (19 bp):
TTATTTTAATTTTTTAATT
Found at i:368478 original size:39 final size:39
Alignment explanation
Indices: 368429--368551 Score: 183
Period size: 39 Copynumber: 3.2 Consensus size: 39
368419 TCACACCTTG
*
368429 ACTCAGCCTTGTCCTCTTCAACAGTCTTCTCCTCCACAA
1 ACTCACCCTTGTCCTCTTCAACAGTCTTCTCCTCCACAA
*
368468 ACTCGCCCTTGTCCTCTTCAACAGTCTTCTCCTCCACAA
1 ACTCACCCTTGTCCTCTTCAACAGTCTTCTCCTCCACAA
* * * * *
368507 ACTCATCCTTGTCTTCTCCAACACTCTTCTCTTCCACAA
1 ACTCACCCTTGTCCTCTTCAACAGTCTTCTCCTCCACAA
368546 ACTCAC
1 ACTCAC
368552 TGCATCTGGC
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 75 1.00
ACGTcount: A:0.20, C:0.42, G:0.06, T:0.32
Consensus pattern (39 bp):
ACTCACCCTTGTCCTCTTCAACAGTCTTCTCCTCCACAA
Found at i:371418 original size:181 final size:181
Alignment explanation
Indices: 370859--371590 Score: 936
Period size: 182 Copynumber: 4.0 Consensus size: 181
370849 TGTCGGTTTA
* * * **
370859 TGTCGATACTTTATAAAAATGTATCGATCCACATCAATATAATAGAAAAAAATATGACAAAACCG
1 TGTCGATACTTTATAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
* * * * *
370924 GTCACGAAAAGATAAAATCGGTAAAGTGCTACC-AGATATATTTAAAGTGTCGATACTTTAATAT
66 GT-ACTAAAAGATAAAACCGGTAAAGAGCGACCGA-ATATATTGAAAGTGTCGATACTTTAATAT
* * * * *
370988 AAGTATCGACACATTGTGAATTTAAAGGAGAAACAATTTTAGCGTTTATAAAG
129 AAGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGTCTATAAAG
* *
371041 TGTCGATTA-TTTATAAATATGTATCGATCCACAACGATATAACATGTAAAAATATGACAAAACC
1 TGTCGA-TACTTTATAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACC
* * *
371105 GAT-CTCGAAAAGATAAAACCGGTAAAGCGCTACCGAATATATTGAAAGTGTCGATACTTTAATA
65 GGTACT--AAAAGATAAAACCGGTAAAGAGCGACCGAATATATTGAAAGTGTCGATACTTTAATA
* *
371169 TAAGTATCGACACTTTGTGAATTTAAAATAG-AGCAGTTTTAGCTTCTATAAAG
128 TAAGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGTCTATAAAG
* * *
371222 TGTAGATATTTTATAACAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
1 TGTCGATACTTTATAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
* * * * * *
371287 GTACTAAAGGACAAAACCGTTATAGAGCGACCGGATATATTGAAAGTGTCGATACGTTAATATAA
66 GTACTAAAAGATAAAACCGGTAAAGAGCGACCGAATATATTGAAAGTGTCGATACTTTAATATAA
* * * * *
371352 GTATCGACACTTTGTAAATTTAAAAGAGAAGTATTTTTCGCGTCTATGAAG
131 GTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGTCTATAAAG
* * * *
371403 TGTCGATACTTTATAAAAATGTATCGATACATAACGATATAACAGGTAAAAATATGAAAAAATCG
1 TGTCGATACTTTATAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
* * * *
371468 GTATCTAAAGGATAAAATCGGTATAGAGCGACCGAATATATTTAAAGTGT-GAATACTTTAATAT
66 GTA-CTAAAAGATAAAACCGGTAAAGAGCGACCGAATATATTGAAAGTGTCG-ATACTTTAATAT
* *
371532 AAGTATCGACATTTTGTGAATTTAAAAGAGAAG-AGGTTTTAGCGCCTATAAAG
129 AAGTATCGACACTTTGTGAATTTAAAAGAGAAGCA-GTTTTAGCGTCTATAAAG
371585 TGTCGA
1 TGTCGA
371591 GTCCAAAACG
Statistics
Matches: 482, Mismatches: 58, Indels: 20
0.86 0.10 0.04
Matches are distributed among these distances:
180 81 0.17
181 157 0.33
182 241 0.50
183 3 0.01
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (181 bp):
TGTCGATACTTTATAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
GTACTAAAAGATAAAACCGGTAAAGAGCGACCGAATATATTGAAAGTGTCGATACTTTAATATAA
GTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGTCTATAAAG
Found at i:371534 original size:362 final size:364
Alignment explanation
Indices: 370863--371587 Score: 974
Period size: 362 Copynumber: 2.0 Consensus size: 364
370853 GGTTTATGTC
* *
370863 GATACTTTATAAAAATGTATCGATCCACATCAATATAATAGAAAAAAATATGACAAAACCGGTCA
1 GATACTTTATAAAAATGTATCGATCCACAACAATATAACAGAAAAAAATATGACAAAACCGGTCA
* * * * * *
370928 CGAAAAGATAAAATCGGTAAAGTGCTACCAGATATATTTAAAGTGTCGATACTTTAATATAAGTA
66 CGAAAAGACAAAACCGGTAAAGAGCGACCAGATATATTGAAAGTGTCGATACGTTAATATAAGTA
* * *
370993 TCGACACATTGTGAATTTAAAGGAGAAACAATTTTAGCGTTTATAAAGTGTCGATTATTTATAAA
131 TCGACACATTGTAAATTTAAAAGAGAAACAATTTTAGCGTCTATAAAGTGTCGATTATTTATAAA
* * * * *
371058 TATGTATCGATCCACAACGATATAACATGTAAAAATATGACAAAACCGATCTCGAAAAGATAAAA
196 AATGTATCGATACACAACGATATAACAGGTAAAAATATGAAAAAACCGATATCGAAAAGATAAAA
* *
371123 CCGGTAAAGCGCTACCGAATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTGTG
261 CCGGTAAAGAGCGACCGAATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTGTG
* **
371188 AATTTAAAATAG-AGCA-GTTTTAGCTTCTATAAAGTGTA
326 AATTTAAAAGAGAAG-AGGTTTTAGCGCCTATAAAGTGTA
* * * **
371226 GATATTTTATAACAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCGGT-A
1 GATACTTTATAAAAATGTATCGATCCACAACAATATAACAGAAAAAAATATGACAAAACCGGTCA
* * * * *
371290 CTAAAGGACAAAACCGTTATAGAGCGACCGGATATATTGAAAGTGTCGATACGTTAATATAAGTA
66 CGAAAAGACAAAACCGGTAAAGAGCGACCAGATATATTGAAAGTGTCGATACGTTAATATAAGTA
* ** * * *
371355 TCGACACTTTGTAAATTTAAAAGAGAAGTATTTTTCGCGTCTATGAAGTGTCGA-TACTTTATAA
131 TCGACACATTGTAAATTTAAAAGAGAAACAATTTTAGCGTCTATAAAGTGTCGATTA-TTTATAA
* * * * *
371419 AAATGTATCGATACATAACGATATAACAGGTAAAAATATGAAAAAATCGGTATCTAAAGGATAAA
195 AAATGTATCGATACACAACGATATAACAGGTAAAAATATGAAAAAACCGATATCGAAAAGATAAA
* * * *
371484 ATCGGTATAGAGCGACCGAATATATTTAAAGTGT-GAATACTTTAATATAAGTATCGACATTTTG
260 ACCGGTAAAGAGCGACCGAATATATTGAAAGTGTCG-ATACTTTAATATAAGTATCGACACTTTG
371548 TGAATTTAAAAGAGAAGAGGTTTTAGCGCCTATAAAGTGT
324 TGAATTTAAAAGAGAAGAGGTTTTAGCGCCTATAAAGTGT
371588 CGAGTCCAAA
Statistics
Matches: 312, Mismatches: 46, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
361 3 0.01
362 232 0.74
363 77 0.25
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.29
Consensus pattern (364 bp):
GATACTTTATAAAAATGTATCGATCCACAACAATATAACAGAAAAAAATATGACAAAACCGGTCA
CGAAAAGACAAAACCGGTAAAGAGCGACCAGATATATTGAAAGTGTCGATACGTTAATATAAGTA
TCGACACATTGTAAATTTAAAAGAGAAACAATTTTAGCGTCTATAAAGTGTCGATTATTTATAAA
AATGTATCGATACACAACGATATAACAGGTAAAAATATGAAAAAACCGATATCGAAAAGATAAAA
CCGGTAAAGAGCGACCGAATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTGTG
AATTTAAAAGAGAAGAGGTTTTAGCGCCTATAAAGTGTA
Found at i:372187 original size:20 final size:20
Alignment explanation
Indices: 372162--372295 Score: 124
Period size: 20 Copynumber: 6.6 Consensus size: 20
372152 TAGTTGGAAA
*
372162 TCGCGTTGCGATTTTTCATT
1 TCGCGTTGCGATTTTCCATT
*
372182 TCGCGTTGTGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
372202 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
372223 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* * ** **
372243 TCGCGTTGCTATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
372264 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
*
372284 TCGCATTGCGAT
1 TCGCGTTGCGAT
372296 AGTCTACAGT
Statistics
Matches: 86, Mismatches: 26, Indels: 4
0.74 0.22 0.03
Matches are distributed among these distances:
20 57 0.66
21 29 0.34
ACGTcount: A:0.16, C:0.20, G:0.22, T:0.41
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:372227 original size:41 final size:41
Alignment explanation
Indices: 372182--372298 Score: 207
Period size: 41 Copynumber: 2.9 Consensus size: 41
372172 ATTTTTCATT
*
372182 TCGCGTTGTGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
*
372223 TCGCGTTGCGATTTTCCATTTCGCGTTGCTATAGTTGAAAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
*
372264 TCGCGTTGCGATTTTCCATTTCGCATTGCGATAGT
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT
372299 CTACAGTTGT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 72 1.00
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
Found at i:372228 original size:21 final size:21
Alignment explanation
Indices: 372202--372275 Score: 87
Period size: 21 Copynumber: 3.6 Consensus size: 21
372192 ATTTTCCATT
372202 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
372223 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
*
372243 TCGCGTTGCTATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
372264 TCGCGTTGCGAT
1 TCGCGTTGCGAT
372276 TTTCCATTTC
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 14 0.35
21 26 0.65
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:372321 original size:22 final size:22
Alignment explanation
Indices: 372289--372338 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
372279 CCATTTCGCA
* * *
372289 TTGCGATAGTCTACAGTTGTTG
1 TTGCGAAAGTCTACAATTGTCG
372311 TTGCGAAAGTCTACAATTGTCG
1 TTGCGAAAGTCTACAATTGTCG
372333 TTGCGA
1 TTGCGA
372339 TTTTCCAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.22, C:0.16, G:0.26, T:0.36
Consensus pattern (22 bp):
TTGCGAAAGTCTACAATTGTCG
Found at i:373131 original size:20 final size:20
Alignment explanation
Indices: 373103--373157 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
373093 ACTGTAGACT
373103 ATCGCAACGCGATTTCAAAA
1 ATCGCAACGCGATTTCAAAA
* ** **
373123 ATCGTAACGCGAACTGGAAA
1 ATCGCAACGCGATTTCAAAA
373143 ATCGCAACGCGATTT
1 ATCGCAACGCGATTT
373158 TCGCAACGAA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGATTTCAAAA
Found at i:373138 original size:42 final size:40
Alignment explanation
Indices: 373078--373157 Score: 99
Period size: 40 Copynumber: 1.9 Consensus size: 40
373068 ACGAATATGG
**
373078 AAAATCGCAACGACAACTGTAGACTATCGCAACGCGATTTCA
1 AAAATCGCAACGACAACTG--GAAAATCGCAACGCGATTTCA
*
373120 AAAATCGTAACG-CGAACTGGAAAATCGCAACGCGATTT
1 AAAATCGCAACGAC-AACTGGAAAATCGCAACGCGATTT
373158 TCGCAACGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
40 17 0.50
41 1 0.03
42 16 0.47
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.19
Consensus pattern (40 bp):
AAAATCGCAACGACAACTGGAAAATCGCAACGCGATTTCA
Found at i:373223 original size:20 final size:20
Alignment explanation
Indices: 373170--373291 Score: 138
Period size: 20 Copynumber: 6.0 Consensus size: 20
373160 GCAACGAATT
373170 TGGAAAATCGCAACGAC-AAC
1 TGGAAAATCGCAACG-CGAAC
**
373190 TGTAGACTATCGCAACGCGAAC
1 TG--GAAAATCGCAACGCGAAC
373212 TGGAAAATCGCAACGCGAAC
1 TGGAAAATCGCAACGCGAAC
**
373232 TGGAAAATCGCAACGCGATT
1 TGGAAAATCGCAACGCGAAC
** *
373252 TTCAACTATCGCAACGCGAAC
1 TGGAA-AATCGCAACGCGAAC
373273 TGGAAAATCGCAACGCGAA
1 TGGAAAATCGCAACGCGAA
373292 ATGCAACTCG
Statistics
Matches: 84, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
20 52 0.62
21 16 0.19
22 16 0.19
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.15
Consensus pattern (20 bp):
TGGAAAATCGCAACGCGAAC
Found at i:373229 original size:95 final size:95
Alignment explanation
Indices: 373066--373254 Score: 324
Period size: 95 Copynumber: 2.0 Consensus size: 95
373056 TTAACTATCA
** *
373066 CAACGAATATGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGATTTCAAAAATCGTAAC
1 CAACGAATATGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAACTCAAAAATCGCAAC
373131 GCGAACTGGAAAATCGCAACGCGATTTTCG
66 GCGAACTGGAAAATCGCAACGCGATTTTCG
* **
373161 CAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAACTGGAAAATCGCAAC
1 CAACGAATATGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAACTCAAAAATCGCAAC
373226 GCGAACTGGAAAATCGCAACGCGATTTTC
66 GCGAACTGGAAAATCGCAACGCGATTTTC
373255 AACTATCGCA
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
95 88 1.00
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.18
Consensus pattern (95 bp):
CAACGAATATGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAACTCAAAAATCGCAAC
GCGAACTGGAAAATCGCAACGCGATTTTCG
Found at i:373233 original size:42 final size:40
Alignment explanation
Indices: 373170--373291 Score: 122
Period size: 41 Copynumber: 3.0 Consensus size: 40
373160 GCAACGAATT
**
373170 TGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAC
1 TGGAAAATCGCAACGACAACTG--GAAAATCGCAACGCGAAC
**
373212 TGGAAAATCGCAACG-CGAACTGGAAAATCGCAACGCGATT
1 TGGAAAATCGCAACGAC-AACTGGAAAATCGCAACGCGAAC
** *
373252 TTCAACTATCGCAACG-CGAACTGGAAAATCGCAACGCGAA
1 TGGAA-AATCGCAACGAC-AACTGGAAAATCGCAACGCGAA
373292 ATGCAACTCG
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
40 17 0.24
41 33 0.47
42 20 0.29
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.15
Consensus pattern (40 bp):
TGGAAAATCGCAACGACAACTGGAAAATCGCAACGCGAAC
Found at i:373299 original size:41 final size:41
Alignment explanation
Indices: 373198--373299 Score: 143
Period size: 41 Copynumber: 2.5 Consensus size: 41
373188 ACTGTAGACT
* * *
373198 ATCGCAACGCGAACTGGAA-AATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAAATGCAACTATCGCAACGCGAACTGGAAA
** *
373238 ATCGCAACGCGATTTTCAACTATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAAATGCAACTATCGCAACGCGAACTGGAAA
373279 ATCGCAACGCGAAATGCAACT
1 ATCGCAACGCGAAATGCAACT
373300 CGAAATGCAA
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 15 0.28
41 38 0.72
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (41 bp):
ATCGCAACGCGAAATGCAACTATCGCAACGCGAACTGGAAA
Found at i:373303 original size:12 final size:12
Alignment explanation
Indices: 373277--373315 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
373267 GCGAACTGGA
373277 AAATCGCAACGCG
1 AAAT-GCAACGCG
*
373290 AAATGCAACTCG
1 AAATGCAACGCG
373302 AAATGCAACGCG
1 AAATGCAACGCG
373314 AA
1 AA
373316 TTTGCGATAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 20 0.83
13 4 0.17
ACGTcount: A:0.44, C:0.26, G:0.21, T:0.10
Consensus pattern (12 bp):
AAATGCAACGCG
Found at i:375144 original size:22 final size:23
Alignment explanation
Indices: 375094--375148 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
375084 AACGTTTTTG
375094 TTTT-TTATATAAAATGATAATA
1 TTTTATTATATAAAATGATAATA
* *
375116 TAGTTATTATATAAAATTATAA-A
1 T-TTTATTATATAAAATGATAATA
375139 TTTTATTATA
1 TTTTATTATA
375149 AATGCATGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 9 0.32
23 4 0.14
24 15 0.54
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (23 bp):
TTTTATTATATAAAATGATAATA
Found at i:375550 original size:21 final size:21
Alignment explanation
Indices: 375526--375569 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
375516 AAGACAATCA
* *
375526 AGAGTCGAATAGAAACTTGAG
1 AGAGTCAAAGAGAAACTTGAG
* *
375547 AGAGTTAAAGAGACACTTGAG
1 AGAGTCAAAGAGAAACTTGAG
375568 AG
1 AG
375570 GCATAAGGGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.09, G:0.30, T:0.18
Consensus pattern (21 bp):
AGAGTCAAAGAGAAACTTGAG
Found at i:375640 original size:33 final size:33
Alignment explanation
Indices: 375603--375698 Score: 156
Period size: 33 Copynumber: 2.9 Consensus size: 33
375593 AAATAGATGG
* **
375603 AGTGGTGAAAGAAGTTGAGGTGTTGAATGTTGA
1 AGTGGTGAAAGAAGTTGAGGTGTTGAAGGGCGA
*
375636 AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGCGA
1 AGTGGTGAAAGAAGTTGAGGTGTTGAAGGGCGA
375669 AGTGGTGAAAGAAGTTGAGGTGTTGAAGGG
1 AGTGGTGAAAGAAGTTGAGGTGTTGAAGGG
375699 TGAACTTAAG
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.29, C:0.01, G:0.45, T:0.25
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTTGAGGTGTTGAAGGGCGA
Found at i:375652 original size:18 final size:18
Alignment explanation
Indices: 375603--375653 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 18
375593 AAATAGATGG
375603 AGTGGTGAAAGAAGTTGA
1 AGTGGTGAAAGAAGTTGA
* * *
375621 GGTGTTG--A-ATGTTGA
1 AGTGGTGAAAGAAGTTGA
375636 AGTGGTGAAAGAAGTTGA
1 AGTGGTGAAAGAAGTTGA
375654 GGTGTTGAGG
Statistics
Matches: 24, Mismatches: 6, Indels: 6
0.67 0.17 0.17
Matches are distributed among these distances:
15 11 0.46
16 1 0.04
17 1 0.04
18 11 0.46
ACGTcount: A:0.33, C:0.00, G:0.39, T:0.27
Consensus pattern (18 bp):
AGTGGTGAAAGAAGTTGA
Found at i:375921 original size:15 final size:15
Alignment explanation
Indices: 375887--375937 Score: 75
Period size: 15 Copynumber: 3.2 Consensus size: 15
375877 AAAATATGAA
375887 GAAGAAAAGAGTGAGGAG
1 GAAGAAAAGA-T--GGAG
375905 GAAGAAAAGATGGAG
1 GAAGAAAAGATGGAG
375920 GAAGAAAAGATGGAG
1 GAAGAAAAGATGGAG
375935 GAA
1 GAA
375938 ATGAGGAGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
15 22 0.67
17 1 0.03
18 10 0.30
ACGTcount: A:0.53, C:0.00, G:0.41, T:0.06
Consensus pattern (15 bp):
GAAGAAAAGATGGAG
Found at i:377516 original size:19 final size:19
Alignment explanation
Indices: 377492--377540 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
377482 AATGTAGAGT
*
377492 TAATTTTGTATAAGATTTG
1 TAATTTTGTATAAGATTTA
* *
377511 TAATTTTGAATATGATTTA
1 TAATTTTGTATAAGATTTA
377530 TAATTTTGTAT
1 TAATTTTGTAT
377541 GTGGATGTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:378730 original size:402 final size:397
Alignment explanation
Indices: 377890--379009 Score: 1448
Period size: 402 Copynumber: 2.8 Consensus size: 397
377880 GTAAGCATAT
* * * * *
377890 GTGTCGATACAGTTATAAAAAGTTTCGATCCCA-AAAAATCAAAACTCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGAT-CCAGAAACATCGAAACCCATAATTATAATGTAATA
* * * * *
377954 GGTAATTTTGTAATATAATC-AGTATAAATATATCAGTTTTATGTGAGAATAGGTCTA-TATAAT
65 GGTAATTTT-TAATGTAACCGA-TAT-AATATACCAGTTTTATGAGAGAATAGGTCTACAAT-AT
* * * * * * *
378017 GTATCGACACTT-TATCATTATGTGTCGATACTTTTTGTCCAGAATGAATGCTCAAAATGATGAA
126 GTATCGACACTTGTGTAATT-TGTGTCGATACTTTTTGTCCAGAAGGAATGCCCAAAAGGGTGCA
** * * * *
378081 CGCATTAAGTGTCGATACATTTATTGAAAGTGTCGATCTCAGAAACATCGAAACCCATAAATATA
190 C-CATTAAGTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCAAAACCCATAATTATA
* * * *
378146 ATGTAATATGTAAATTTACAATGTAACCGGTATAACTAAACCGATTTTATGAAAGAATAGGTCTA
254 ATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGAGAATAGGTCTA
*
378211 CATAATGTATCGACACTTATGGAATTTGTGTCGATATTGTTTGTCCAGAAGGAATGCCCAAAAAG
319 CATAATGTATCAACACTTATGGAATTTGTGTCGATATTGTTTGTCCAGAAGGAATGCCCAAAAAG
*
378276 GGTGCAAGCAACAA
384 GATGCAAGCAACAA
378290 GTGTCGATACATTTATAAACAAGTATCGATCTCAGAAACATCGAAACCCATAATTATAATGTAAT
1 GTGTCGATACATTTATAAA-AAGTATCGATC-CAGAAACATCGAAACCCATAATTATAATGTAAT
*
378355 AGATAATTTTTCAATGTAACCGATATACATATACCAGTTTTATGAGAGAATAGGTCTACAATATG
64 AGGTAATTTTT-AATGTAACCGATATA-ATATACCAGTTTTATGAGAGAATAGGTCTACAATATG
*
378420 TATCGACACTTGTGTAATTTGTGTCGATACTTTTGGTCCAGAAGGAATGCCCAAAAAGGGTGCAC
127 TATCGACACTTGTGTAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCC-AAAAGGGTGCAC
* *
378485 CATTAAGTGTCGATACATTTATAAAAAAAGTGTCGATCCCAAAAACTTCTAAACCCATAATTATA
191 CATTAAGTGTCGATACATTTAT--AAAAAGTGTCGATCCCAAAAACATCAAAACCCATAATTATA
* * ** * *
378550 ATATAATAGGTAATTTTGTAATATAACCGGTATAAATATACCGATTTTATGTGAGAATAGGTCTA
254 ATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGAGAATAGGTCTA
* ** * *
378615 CATAATGTATCAACACTTTTTTATTTTGTGTCGATACTT-TTTGTCCAGAATGAATGCCC-AAAA
319 CATAATGTATCAACACTTATGGAATTTGTGTCGATA-TTGTTTGTCCAGAAGGAATGCCCAAAAA
378678 GGATG-AACGCATA-AA
383 GGATGCAA-GCA-ACAA
* * *
378693 GTGTCGATATATTTATAAAAAGTGTCGATACCAGAAACATCGAAACCCATAAATATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGAT-CCAGAAACATCGAAACCCATAATTATAATGTAATA
** * * *
378758 GGTAAATTTAAAATGTAACCGGTATAACTATACCGGTTTTATGAGAGAATAGGTCTACAACATGT
65 GGT-AATTTTTAATGTAACCGATATAA-TATACCAGTTTTATGAGAGAATAGGTCTACAATATGT
* *
378823 ATCGACACTTGTGTAATTTGTGTCGATACTTTTTATCCAGAAGGAATG-CCAAAAGGGTTGCATG
128 ATCGACACTTGTGTAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCCAAAAGGG-TGCA-C
* * *
378887 CATAAAGTGTCGATACATTTTTAAAAAGTGTCGATCCCAAAAACATCAAAACCGATAATTATAAT
191 CATTAAGTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCAAAACCCATAATTATAAT
* *
378952 GTAATAGGTAAATTTCCAATGTAACCGGTATAAATATACCGATTTTATGAGAAAATAG
256 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGAGAATAG
379010 ATCATCATAA
Statistics
Matches: 634, Mismatches: 67, Indels: 38
0.86 0.09 0.05
Matches are distributed among these distances:
400 117 0.18
401 20 0.03
402 301 0.47
403 54 0.09
404 140 0.22
405 2 0.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (397 bp):
GTGTCGATACATTTATAAAAAGTATCGATCCAGAAACATCGAAACCCATAATTATAATGTAATAG
GTAATTTTTAATGTAACCGATATAATATACCAGTTTTATGAGAGAATAGGTCTACAATATGTATC
GACACTTGTGTAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCCAAAAGGGTGCACCATTA
AGTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCAAAACCCATAATTATAATGTAAT
AGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGAGAATAGGTCTACATAATG
TATCAACACTTATGGAATTTGTGTCGATATTGTTTGTCCAGAAGGAATGCCCAAAAAGGATGCAA
GCAACAA
Found at i:378825 original size:200 final size:200
Alignment explanation
Indices: 377890--379009 Score: 1389
Period size: 200 Copynumber: 5.6 Consensus size: 200
377880 GTAAGCATAT
* * * * *
377890 GTGTCGATACAGTTATAAAAAGTTTCGATCCCA-AAAAATCAAAACTCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
* ** * * * * * *
377954 GGTAATTTTGTAATATAATCAGTATAAATATATC-AGTTTTATGTGAGAATAGGTCTATATAATG
66 GGTAAATTTACAATGTAACCGGTATAAATATACCGA-TTTTATGAGAGAATAGGTCTACATAATG
* * * * *
378018 TATCGACACTT-TATCATTATGTGTCGATACTTTTTGTCCAGAATGAATGCTCAAAATGATGAAC
130 TATCGACACTTGTGTAATT-TGTGTCGATACTTTTTGTCCAGAAGGAATGCCCAAAAGGATGAAC
*
378082 GCATTAA
194 GCATAAA
** * *
378089 GTGTCGATACATTTATTGAAAGTGTCGATCTCAGAAACATCGAAACCCATAAATATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
* * * *
378154 TGTAAATTTACAATGTAACCGGTATAACTAAACCGATTTTATGAAAGAATAGGTCTACATAATGT
66 GGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGAGAATAGGTCTACATAATGT
* * *
378219 ATCGACACTTATGGAATTTGTGTCGATA-TTGTTTGTCCAGAAGGAATGCCCAAAAAGGGTGCAA
131 ATCGACACTTGTGTAATTTGTGTCGATACTT-TTTGTCCAGAAGGAATGCCC-AAAAGGATG-AA
378283 -GCA-ACAA
193 CGCATA-AA
* *
378290 GTGTCGATACATTTATAAACAAGTATCGATCTCAGAAACATCGAAACCCATAATTATAATGTAAT
1 GTGTCGATACATTTATAAA-AAGTGTCGATCCCAGAAACATCGAAACCCATAATTATAATGTAAT
* * * * *
378355 AGATAATTTTTCAATGTAACCGATATACATATACC-AGTTTTATGAGAGAATAGGTCTACA-ATA
65 AGGTAAATTTACAATGTAACCGGTATAAATATACCGA-TTTTATGAGAGAATAGGTCTACATA-A
* * *
378418 TGTATCGACACTTGTGTAATTTGTGTCGATACTTTTGGTCCAGAAGGAATGCCCAAAAAGGGTGC
128 TGTATCGACACTTGTGTAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCC-AAAAGGATGA
*
378483 AC-CATTAA
192 ACGCATAAA
* * * *
378491 GTGTCGATACATTTATAAAAAAAGTGTCGATCCCAAAAACTTCTAAACCCATAATTATAATATAA
1 GTGTCGATACATTTAT--AAAAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATAATGTAA
* ** * *
378556 TAGGTAATTTTGTAATATAACCGGTATAAATATACCGATTTTATGTGAGAATAGGTCTACATAAT
64 TAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGAGAATAGGTCTACATAAT
* * * * *
378621 GTATCAACACTTTTTTATTTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAAGGATGAAC
129 GTATCGACACTTGTGTAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCCAAAAGGATGAAC
378686 GCATAAA
194 GCATAAA
* * *
378693 GTGTCGATATATTTATAAAAAGTGTCGATACCAGAAACATCGAAACCCATAAATATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
* * *
378758 GGTAAATTTAAAATGTAACCGGTATAACTATACCGGTTTTATGAGAGAATAGGTCTACA-ACATG
66 GGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGAGAATAGGTCTACATA-ATG
* * * *
378822 TATCGACACTTGTGTAATTTGTGTCGATACTTTTTATCCAGAAGGAATG-CCAAAAGGGTTGCAT
130 TATCGACACTTGTGTAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCCAAAA-GGATGAAC
378886 GCATAAA
194 GCATAAA
* * * *
378893 GTGTCGATACATTTTTAAAAAGTGTCGATCCCAAAAACATCAAAACCGATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
* *
378958 GGTAAATTTCCAATGTAACCGGTATAAATATACCGATTTTATGAGAAAATAG
66 GGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGAGAATAG
379010 ATCATCATAA
Statistics
Matches: 796, Mismatches: 105, Indels: 39
0.85 0.11 0.04
Matches are distributed among these distances:
199 37 0.05
200 373 0.47
201 67 0.08
202 312 0.39
203 7 0.01
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (200 bp):
GTGTCGATACATTTATAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
GGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGAGAATAGGTCTACATAATGT
ATCGACACTTGTGTAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCCAAAAGGATGAACGC
ATAAA
Found at i:381865 original size:15 final size:15
Alignment explanation
Indices: 381845--381887 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
381835 TCTCCACAAC
381845 AAAGTTTTCATACAT
1 AAAGTTTTCATACAT
* * *
381860 AAAGTTTCCAAACTT
1 AAAGTTTTCATACAT
381875 AAAGTTTCTCATA
1 AAAGTTT-TCATA
381888 AAGTGTCGAT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
15 19 0.86
16 3 0.14
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.37
Consensus pattern (15 bp):
AAAGTTTTCATACAT
Found at i:382339 original size:179 final size:177
Alignment explanation
Indices: 382038--382583 Score: 587
Period size: 179 Copynumber: 3.1 Consensus size: 177
382028 TTCTAGAATT
* *
382038 TGTGTCGATA-TTGTTTGTCCAGAAGGAATGCCCAAAAAGGGTGCACCCATAAAGTATCGATACT
1 TGTGTCGATACTT-TTTATCCAGAA-GAATGCCC-AAAAGGGTGCA-CCATAAAGTGTCGATA-T
* * *
382102 TTTTA-AAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTG
61 ATTTATAAAACGTATCGATCCCAAAAACATCAAAACCCATAATTATAATGTAATAGGTAATTTTG
382166 TAATATAACCGGTATAAATATACCAGTTTTATGTGAGAATAGGTCTACATAA
126 TAATATAACCGGTATAAATATACCAGTTTTATGTGAGAATAGGTCTACATAA
* *
382218 TGTGTCGATACTTTTTATCCAGAATGAATGCCCAAAAGGGTGAACGCATAAAGTGTCGGTATATT
1 TGTGTCGATACTTTTTATCCAGAA-GAATGCCCAAAAGGGTGCAC-CATAAAGTGTCGATATATT
* * * **
382283 TATAAAACGTATCGATACCAAAAACATCAAAACCGATAATTATAATGTAATAGGTAAATTTACAA
64 TATAAAACGTATCGATCCCAAAAACATCAAAACCCATAATTATAATGTAATAGGTAATTTTGTAA
* * * * * * ** *
382348 TGTAATCGGTATAAATAAACC-GATTTTTTGAGAAAATATATATACATAA
129 TATAACCGGTATAAATATACCAG-TTTTATGTGAGAATAGGTCTACATAA
* ** * * *
382397 TGTATCG--AC--TCCA-CAAGGAA-AAT-CCAAAAAGGGTGCACCTATAAAGTGTCGATACATG
1 TGTGTCGATACTTTTTATCCA-GAAGAATGCCCAAAAGGGTGCACC-ATAAAGTGTCGATATAT-
* *
382455 TT-T-AAACAGTATCGATCCCTAAAACATCAAAACCCATAAATATAATGTAATAGGTAATTTTGT
63 TTATAAAAC-GTATCGATCCCAAAAACATCAAAACCCATAATTATAATGTAATAGGTAATTTTGT
* *
382518 AATATAACCGGTATAAATATA-CATATTTTATGTCAGAATAGGTCTACATAA
127 AATATAACCGGTATAAATATACCA-GTTTTATGTGAGAATAGGTCTACATAA
* *
382569 TATGTCGACACTTTT
1 TGTGTCGATACTTTT
382584 GAATGATGTG
Statistics
Matches: 301, Mismatches: 51, Indels: 32
0.78 0.13 0.08
Matches are distributed among these distances:
171 6 0.02
172 119 0.40
173 5 0.02
174 4 0.01
175 5 0.02
176 1 0.00
177 2 0.01
178 7 0.02
179 122 0.41
180 28 0.09
181 2 0.01
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (177 bp):
TGTGTCGATACTTTTTATCCAGAAGAATGCCCAAAAGGGTGCACCATAAAGTGTCGATATATTTA
TAAAACGTATCGATCCCAAAAACATCAAAACCCATAATTATAATGTAATAGGTAATTTTGTAATA
TAACCGGTATAAATATACCAGTTTTATGTGAGAATAGGTCTACATAA
Found at i:382769 original size:200 final size:198
Alignment explanation
Indices: 382423--383000 Score: 732
Period size: 200 Copynumber: 2.9 Consensus size: 198
382413 GGAAAATCCA
* ** * * *
382423 AAAAGGGTGCACCTATAAAGTGTCGATACATGTTTAAACAGTATCGATCCCTAAAACATCAAAAC
1 AAAAGGGTGAACGAATAAAGTGTCGATACAT-TTTAAAAAGTATCGATCCCAAAAACATCGAAAC
* * * ** * **
382488 CCATAAATATAATGTAATAGGTAATTTTGTAATATAACCGGTATAAATATACATATTTTATGTCA
65 CGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGTCA
* ** * * *
382553 GAATAGGTCTACATAATATGTCGACAC-TTTT-GAATGATGTGTCGATACGTTTTCTCCATAATG
130 AAATAGGTGAACATAATGTATCGACACGTTTTAG-AT-ATGTGTCGATACGTTTTCTCCAAAATG
382616 AATGCCC
193 AATG-CC
* *
382623 AAAAGGGTGAACGAATAAAGTATCGATACATTTATAAAAAGTAACGATCCCAAAAACATCGAAAC
1 AAAAGGGTGAACGAATAAAGTGTCGATACATTT-TAAAAAGTATCGATCCCAAAAACATCGAAAC
*
382688 CGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGTTA
65 CGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGTCA
* * ** *
382753 AAATAGGTGAACATAATGTATTGACACGTTTTAGATTTGTGTCGATATTTTTTTTCCAAAATGAA
130 AAATAGGTGAACATAATGTATCGACACGTTTTAGATATGTGTCGATACGTTTTCTCCAAAATGAA
382818 TGCC
195 TGCC
*
382822 AAAAGGGTTGCAA-GCATAAAGTGTCGATACATTTTTTAAAAAGTATCGATCCCAAAAACATCG-
1 AAAAGGG-TG-AACGAATAAAGTGTCGATACA--TTTTAAAAAGTATCGATCCCAAAAACATCGA
*
382885 AACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATGTACCGATTTTATG
62 AACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATG
** * * *
382950 AGAAAATATGTGAACATAATGTATCGACACGTTTTAGATTTTTGTCGATAC
127 TCAAAATAGGTGAACATAATGTATCGACACGTTTTAGATATGTGTCGATAC
383001 TTGTAAATAA
Statistics
Matches: 333, Mismatches: 38, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
199 11 0.03
200 284 0.85
201 34 0.10
202 4 0.01
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (198 bp):
AAAAGGGTGAACGAATAAAGTGTCGATACATTTTAAAAAGTATCGATCCCAAAAACATCGAAACC
GATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGTCAA
AATAGGTGAACATAATGTATCGACACGTTTTAGATATGTGTCGATACGTTTTCTCCAAAATGAAT
GCC
Found at i:389596 original size:55 final size:55
Alignment explanation
Indices: 389517--390052 Score: 616
Period size: 55 Copynumber: 9.7 Consensus size: 55
389507 TCTTCAAATG
*
389517 ACGGGTCTGCTCCCTATT-TCTTCAGGAAGTATAAGACTCGAACAATCTTCAACAA
1 ACGGGTCTGCTCCCTATTCT-TTCAGGGAGTATAAGACTCGAACAATCTTCAACAA
** * * *
389572 ACATGTCTGCTCCTTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTTAACAA
1 ACGGGTCTGCTCCCTATTCTTTCAGGGAGTATAAGACTCGAACAATCTTCAACAA
*
389627 ACGAGTCTGCTCCCTATTCTTTCAGGGAGTATAAGACTCGAACAATCTTCAACAA
1 ACGGGTCTGCTCCCTATTCTTTCAGGGAGTATAAGACTCGAACAATCTTCAACAA
* * * * * *
389682 ACAGATCCGTTGCCTATTCTTTCAGGCAGTATAAGACTCGAACAATCTTCAACAA
1 ACGGGTCTGCTCCCTATTCTTTCAGGGAGTATAAGACTCGAACAATCTTCAACAA
* * *
389737 ATGGGTCCGCTCCCTATTCTTTCAGGGAGTATAAGACTCGAACAATCTTCAGCAA
1 ACGGGTCTGCTCCCTATTCTTTCAGGGAGTATAAGACTCGAACAATCTTCAACAA
* * *
389792 ACGGGTCCGCTCCCTATTTTTTCAGGGAGTATCAGACTCGAACAATCTTCAGA-AA
1 ACGGGTCTGCTCCCTATTCTTTCAGGGAGTATAAGACTCGAACAATCTTCA-ACAA
* * * * *
389847 ACAGGT-TCGTTCCCTATTTTTTCAGGGAGTATAAGACTC-AAAATATCTTCAGCAA
1 ACGGGTCT-GCTCCCTATTCTTTCAGGGAGTATAAGACTCGAACA-ATCTTCAACAA
* * * ***
389902 GCGGGT-TCGCTCTCTATTCTTTTAGGGAGTAT-AGAACTCGAACAATCTTCAGTGA
1 ACGGGTCT-GCTCCCTATTCTTTCAGGGAGTATAAG-ACTCGAACAATCTTCAACAA
* * * ***
389957 ACGTGTATGCTCCCTATTCATTCAGGGAGTATAAGACTCGAACAATCTTCAATTT
1 ACGGGTCTGCTCCCTATTCTTTCAGGGAGTATAAGACTCGAACAATCTTCAACAA
* * * *
390012 ACGTGTCTGCTCCCTATTCCTTCAGAGAGTATATGACTCGA
1 ACGGGTCTGCTCCCTATTCTTTCAGGGAGTATAAGACTCGA
390053 TCTTCATAAA
Statistics
Matches: 416, Mismatches: 56, Indels: 18
0.85 0.11 0.04
Matches are distributed among these distances:
54 5 0.01
55 405 0.97
56 6 0.01
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.30
Consensus pattern (55 bp):
ACGGGTCTGCTCCCTATTCTTTCAGGGAGTATAAGACTCGAACAATCTTCAACAA
Found at i:390176 original size:37 final size:37
Alignment explanation
Indices: 390069--390176 Score: 155
Period size: 37 Copynumber: 2.9 Consensus size: 37
390059 TAAAATGAGT
* *
390069 TTGCTTCACTACTCTTCCATGAAGGCTTATAGA-TGAT
1 TTGCTTCACTACTCTTCCGTGAAGGCTTA-AGATTGAA
*
390106 TTGCTTCACTACTCTTCCGTGAAGGGTTAAGATTGAA
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAA
* *
390143 TTGCTTCACTTCTCTTTCGTGAAGGCTTAAGATT
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATT
390177 AACTTGTTTC
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
36 3 0.05
37 61 0.95
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (37 bp):
TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAA
Found at i:392740 original size:47 final size:47
Alignment explanation
Indices: 392634--392746 Score: 131
Period size: 47 Copynumber: 2.4 Consensus size: 47
392624 CCATGCTTTG
* *
392634 TTATTCACAAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGC
1 TTATTCAGAAAAAGAAATCCTAACCGCATGATATCTAATTCGCAAGC
* * *
392681 TTGTTCGAGAAAAATAAA-CCTAACCGCATGATATCTAGTTCGCAAGC
1 TTATTC-AGAAAAAGAAATCCTAACCGCATGATATCTAATTCGCAAGC
392728 ATTTATTC-GAAAAACGAAA
1 --TTATTCAGAAAAA-GAAA
392747 ATAAATGACT
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
47 38 0.69
48 12 0.22
49 5 0.09
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (47 bp):
TTATTCAGAAAAAGAAATCCTAACCGCATGATATCTAATTCGCAAGC
Found at i:396617 original size:23 final size:25
Alignment explanation
Indices: 396577--396622 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
396567 GTATTTTTAG
396577 TTTAATAAAAATATATATTTTGACC
1 TTTAATAAAAATATATATTTTGACC
*
396602 TTTAA-AATAATA-ATATTTTGA
1 TTTAATAAAAATATATATTTTGA
396623 TTTAATCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 6 0.30
25 5 0.25
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (25 bp):
TTTAATAAAAATATATATTTTGACC
Found at i:396633 original size:23 final size:24
Alignment explanation
Indices: 396568--396633 Score: 66
Period size: 23 Copynumber: 2.8 Consensus size: 24
396558 GTAGACAATG
* * *
396568 TATTTTTAGTTTAATAAAAATATA
1 TATTTTGACTTTAATAATAATATA
396592 TATTTTGACCTTTAA-AATAATA-A
1 TATTTTGA-CTTTAATAATAATATA
396615 TATTTTGA-TTTAATCAATA
1 TATTTTGACTTTAAT-AATA
396634 TAAAAATATA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
21 5 0.14
23 13 0.36
24 13 0.36
25 5 0.14
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.48
Consensus pattern (24 bp):
TATTTTGACTTTAATAATAATATA
Found at i:399736 original size:3 final size:3
Alignment explanation
Indices: 399723--399764 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
399713 GCTAACAACT
*
399723 ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
399765 TTGTCAGTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:401015 original size:120 final size:119
Alignment explanation
Indices: 400774--401472 Score: 608
Period size: 120 Copynumber: 5.8 Consensus size: 119
400764 CAATTAAAGA
* ** * * ** *
400774 TCAACAAAGCTTCAATGACAAG-CAAAGTCAATATGCATGGTAATCATCAAATCAAATGGGTAGC
1 TCAACAAAGCTTCAATGGC-AGTCAGGGCCAATATACATGGCCATCATCAAATCAAATGAGTAGC
* * * * * * *
400838 AATGTACATAATATAAATTCTATAAATACATTTAACCGAGAAACAAGAGTTGAAGG
65 AATGTCCATAACATGAATTCTACAAATGCATTTAACCTAGAAAC-ACAGTTGAAGG
* * * *
400894 TCAAAAAAACTT-AAGTGGCAGTCATGGCCAATATACATGGCCATCATCAAATCAAATG-GATAA
1 TCAACAAAGCTTCAA-TGGCAGTCAGGGCCAATATACATGGCCATCATCAAATCAAATGAG-TAG
* * * *
400957 CATTATCCATAACATGAATTCTACAAATGCATTTAA-TTATGAAACACTGATTGAAGG
64 CAATGTCCATAACATGAATTCTACAAATGCATTTAACCTA-GAAACACAG-TTGAAGG
* * * * ** * * * * *
401014 TCCATAAAGCTTCAATGGTAGGCAAAGCCAATATATATGCCCGTTATCAAATCATATGAGTAGCA
1 TCAACAAAGCTTCAATGGCAGTCAGGGCCAATATACATGGCCATCATCAAATCAAATGAGTAGCA
* * * * * * * *
401079 GA-GTTCATAATATAAATTCTGCACATGTATTTAACTTAGGAACAACAGTTGAAGG
66 -ATGTCCATAACATGAATTCTACAAATGCATTTAACCTAGAAAC-ACAGTTGAAGG
* * * * * * *
401134 TTAACAAAACTTCAATGGCAATCAGGACCAATATACATGGTCATCATCAAATCAAATTAGTAGTA
1 TCAACAAAGCTTCAATGGCAGTCAGGGCCAATATACATGGCCATCATCAAATCAAATGAGTAGCA
* * *
401199 GTGTCCATAACATGAATTTTACAAATGCATTTAACC-A-AAGAGCA-ATGGTTGAAGA
66 ATGTCCATAACATGAATTCTACAAATGCATTTAACCTAGAA-A-CACA--GTTGAAGG
* * * *
401254 TCAACAAAGCTTCAATGACAATCAGGGCTAATATACATGGTCATCATCAAATCAAATGAGTAGCA
1 TCAACAAAGCTTCAATGGCAGTCAGGGCCAATATACATGGCCATCATCAAATCAAATGAGTAGCA
* * *
401319 GTGTCCATAACATGAA-TCTACAAATGCATTTAACCAAGGAGAA-ACAGTTGAATG
66 ATGTCCATAACATGAATTCTACAAATGCATTTAACCTA-GA-AACACAGTTGAAGG
* * * *
401373 TCAATAAAGCTTCAATGGCAGTCAGGGTCAATATACATGACCATCATCAAATCAAATGGGTAGCA
1 TCAACAAAGCTTCAATGGCAGTCAGGGCCAATATACATGGCCATCATCAAATCAAATGAGTAGCA
* * *
401438 ATGTCCATAATATGAATTCTGCAAATACATTTAAC
66 ATGTCCATAACATGAATTCTACAAATGCATTTAAC
401473 TTTTTGTCCG
Statistics
Matches: 463, Mismatches: 95, Indels: 42
0.77 0.16 0.07
Matches are distributed among these distances:
118 2 0.00
119 106 0.23
120 342 0.74
121 10 0.02
122 2 0.00
123 1 0.00
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.26
Consensus pattern (119 bp):
TCAACAAAGCTTCAATGGCAGTCAGGGCCAATATACATGGCCATCATCAAATCAAATGAGTAGCA
ATGTCCATAACATGAATTCTACAAATGCATTTAACCTAGAAACACAGTTGAAGG
Found at i:401208 original size:240 final size:239
Alignment explanation
Indices: 400749--401472 Score: 733
Period size: 240 Copynumber: 3.0 Consensus size: 239
400739 CAAGGATTGG
* ** * * * *
400749 TTAATCAAAGAGCAACAATTAAAGATCAACAAAGCTTCAATGACAAGCAAAGTCAATATGCATGG
1 TTAACCAAAGAGCAATGATTGAAGATCAACAAAGCTTCAATGACAAGCAAAGCCAATATACATGC
** * * * *
400814 TAATCATCAAATCAAATGGGTAGCA-ATGTACATAATATAAATTCTATAAATACATTTAACCGAG
66 CCATCATCAAATCAAATGAGTAGCAGA-GTACATAATATAAATTCTACAAATGCATTTAACCAAG
* *
400878 AAACAAGAGTTGAAGGTCAAAAAAACTT-AAGTGGCAGTCATGGCCAATATACATGGCCATCATC
130 GAACAACAGTTGAAGGTCAAAAAAACTTCAA-TGGCAGTCA-GGCCAATATACATGGCCATCATC
* * *
400942 AAATCAAA-TGGATAACATTATCCATAACATGAATTCTACAAATGCAT
193 AAATCAAATTGG-TAGCAATGTCCATAACATGAATTCTACAAATGCAT
** * * * * ** * *
400989 TTAATTATGAA-A-CACTGATTGAAGGTCCATAAAGCTTCAATGGTAGGCAAAGCCAATATATAT
1 TTAACCA--AAGAGCAATGATTGAAGATCAACAAAGCTTCAATGACAAGCAAAGCCAATATACAT
* * * * * * * **
401052 GCCCGTTATCAAATCATATGAGTAGCAGAGTTCATAATATAAATTCTGCACATGTATTTAACTTA
64 GCCCATCATCAAATCAAATGAGTAGCAGAGTACATAATATAAATTCTACAAATGCATTTAACCAA
* * * *
401117 GGAACAACAGTTGAAGGTTAACAAAACTTCAATGGCAATCAGGACCAATATACATGGTCATCATC
129 GGAACAACAGTTGAAGGTCAAAAAAACTTCAATGGCAGTCAGG-CCAATATACATGGCCATCATC
* * * *
401182 AAATCAAATTAGTAGTAGTGTCCATAACATGAATTTTACAAATGCAT
193 AAATCAAATTGGTAGCAATGTCCATAACATGAATTCTACAAATGCAT
* * ** * *
401229 TTAACCAAAGAGCAATGGTTGAAGATCAACAAAGCTTCAATGACAATCAGGGCTAATATACATGG
1 TTAACCAAAGAGCAATGATTGAAGATCAACAAAGCTTCAATGACAAGCAAAGCCAATATACATGC
* * * * *
401294 TCATCATCAAATCAAATGAGTAGCAGTGTCCATAACATGAA-TCTACAAATGCATTTAACCAAGG
66 CCATCATCAAATCAAATGAGTAGCAGAGTACATAATATAAATTCTACAAATGCATTTAACCAAGG
* * * * *
401358 AGA-AACAGTTGAATGTCAATAAAGCTTCAATGGCAGTCAGGGTCAATATACATGACCATCATCA
131 A-ACAACAGTTGAAGGTCAAAAAAACTTCAATGGCAGTCA-GGCCAATATACATGGCCATCATCA
* * * *
401422 AATCAAATGGGTAGCAATGTCCATAATATGAATTCTGCAAATACAT
194 AATCAAATTGGTAGCAATGTCCATAACATGAATTCTACAAATGCAT
401468 TTAAC
1 TTAAC
401473 TTTTTGTCCG
Statistics
Matches: 388, Mismatches: 86, Indels: 21
0.78 0.17 0.04
Matches are distributed among these distances:
238 2 0.01
239 115 0.30
240 263 0.68
241 6 0.02
242 2 0.01
ACGTcount: A:0.42, C:0.17, G:0.16, T:0.26
Consensus pattern (239 bp):
TTAACCAAAGAGCAATGATTGAAGATCAACAAAGCTTCAATGACAAGCAAAGCCAATATACATGC
CCATCATCAAATCAAATGAGTAGCAGAGTACATAATATAAATTCTACAAATGCATTTAACCAAGG
AACAACAGTTGAAGGTCAAAAAAACTTCAATGGCAGTCAGGCCAATATACATGGCCATCATCAAA
TCAAATTGGTAGCAATGTCCATAACATGAATTCTACAAATGCAT
Found at i:402364 original size:22 final size:22
Alignment explanation
Indices: 402339--402455 Score: 207
Period size: 22 Copynumber: 5.3 Consensus size: 22
402329 GGCATGTGAA
402339 ATTTGTCCCGAATGACCTATGT
1 ATTTGTCCCGAATGACCTATGT
402361 ATTTGTCCCGAATGACCTATGT
1 ATTTGTCCCGAATGACCTATGT
402383 ATTTGTCCCGAATGACCTATGT
1 ATTTGTCCCGAATGACCTATGT
* *
402405 ATTTGTCCCGAAGGGCCTATGT
1 ATTTGTCCCGAATGACCTATGT
402427 ATTTGTCCCGAATGACCTATGT
1 ATTTGTCCCGAATGACCTATGT
402449 ATATTGT
1 AT-TTGT
402456 ATATGTAACA
Statistics
Matches: 90, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
22 86 0.96
23 4 0.04
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (22 bp):
ATTTGTCCCGAATGACCTATGT
Found at i:404058 original size:24 final size:26
Alignment explanation
Indices: 404016--404066 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
404006 AAGAATATAA
404016 TGATAATGAGTGCATATGTG-TTTTG
1 TGATAATGAGTGCATATGTGATTTTG
404041 TGATAA-GAGATG-ATATGTGATTTTG
1 TGATAATGAG-TGCATATGTGATTTTG
404066 T
1 T
404067 ATGATATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.27, C:0.02, G:0.27, T:0.43
Consensus pattern (26 bp):
TGATAATGAGTGCATATGTGATTTTG
Found at i:407029 original size:17 final size:17
Alignment explanation
Indices: 407001--407049 Score: 91
Period size: 17 Copynumber: 2.9 Consensus size: 17
406991 TTATATGAAA
407001 TTAGAC-AAACCCTGGT
1 TTAGACAAAACCCTGGT
407017 TTAGACAAAACCCTGGT
1 TTAGACAAAACCCTGGT
407034 TTAGACAAAACCCTGG
1 TTAGACAAAACCCTGG
407050 GAGTATATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 6 0.19
17 26 0.81
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.22
Consensus pattern (17 bp):
TTAGACAAAACCCTGGT
Found at i:417530 original size:30 final size:32
Alignment explanation
Indices: 417495--417562 Score: 95
Period size: 33 Copynumber: 2.2 Consensus size: 32
417485 ATAGTTATTA
417495 TATTTTATATT-AAT-ATATTTATATAAATAT
1 TATTTTATATTAAATAATATTTATATAAATAT
* *
417525 TATTTTTTATTAAAATAATATTTATATAATTAT
1 TATTTTATATT-AAATAATATTTATATAAATAT
417558 TATTT
1 TATTT
417563 ATTTAGAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 10 0.30
32 3 0.09
33 20 0.61
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (32 bp):
TATTTTATATTAAATAATATTTATATAAATAT
Found at i:417746 original size:17 final size:17
Alignment explanation
Indices: 417710--417748 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
417700 TAATGTTAAT
* * *
417710 ATTTAAATTTATTTTTA
1 ATTTAAAGTTATTATGA
417727 ATTTAAAGTTATTATGA
1 ATTTAAAGTTATTATGA
417744 ATTTA
1 ATTTA
417749 TATTAATTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (17 bp):
ATTTAAAGTTATTATGA
Done.