Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006400.1 Hibiscus syriacus cultivar Beakdansim tig00015426_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: 1412076
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 8
Found at i:195045 original size:12 final size:12
Alignment explanation
Indices: 195028--195052 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
195018 TCTTCGGGGA
195028 CTTTTTCTTCTT
1 CTTTTTCTTCTT
195040 CTTTTTCTTCTT
1 CTTTTTCTTCTT
195052 C
1 C
195053 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:195261 original size:24 final size:24
Alignment explanation
Indices: 195227--195273 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
195217 CTGAAACATC
195227 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
195251 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
195274 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:195983 original size:20 final size:20
Alignment explanation
Indices: 195955--196204 Score: 250
Period size: 20 Copynumber: 12.5 Consensus size: 20
195945 AAATTTCAGT
* * *
195955 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
195975 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
195995 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
196015 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* **
196035 GTTGCGATTTACAGATTATC
1 GTTGCGATTTACGGATTCGC
*
196055 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
196075 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
196095 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
196115 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
196135 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
196155 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
196175 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
196195 GTTGCGATTT
1 GTTGCGATTT
196205 TGGAAAATCG
Statistics
Matches: 200, Mismatches: 28, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 199 1.00
21 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:196221 original size:21 final size:21
Alignment explanation
Indices: 196191--196273 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
196181 ATTTTCATAT
*
196191 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
196212 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
196233 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
196254 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
196274 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:196264 original size:42 final size:43
Alignment explanation
Indices: 196171--196269 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
196161 ATTTATGTGT
* *
196171 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
196212 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
196254 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
196270 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:197286 original size:13 final size:13
Alignment explanation
Indices: 197268--197297 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
197258 ACCGGTCAAC
*
197268 GGTCAACGGGTCG
1 GGTCAACGGGCCG
197281 GGTCAACGGGCCG
1 GGTCAACGGGCCG
197294 GGTC
1 GGTC
197298 GGGTGAACGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.13, C:0.27, G:0.47, T:0.13
Consensus pattern (13 bp):
GGTCAACGGGCCG
Found at i:197297 original size:18 final size:18
Alignment explanation
Indices: 197274--197319 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
197264 CAACGGTCAA
197274 CGGGTCGGGTCAACGGGC
1 CGGGTCGGGTCAACGGGC
* *
197292 CGGGTCGGGTGAACGGGT
1 CGGGTCGGGTCAACGGGC
197310 CGGGTCGGGT
1 CGGGTCGGGT
197320 TGTGACCGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.09, C:0.22, G:0.54, T:0.15
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGC
Found at i:201594 original size:15 final size:15
Alignment explanation
Indices: 201563--201592 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
201553 TTCAATAATA
201563 TAAATTTCTACAATT
1 TAAATTTCTACAATT
201578 TAAATTT-TACAATT
1 TAAATTTCTACAATT
201592 T
1 T
201593 TATTTTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (15 bp):
TAAATTTCTACAATT
Found at i:202605 original size:15 final size:15
Alignment explanation
Indices: 202585--202617 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
202575 TTAGCTGAGT
*
202585 GGGCGGATGTGGGGC
1 GGGCGGATGCGGGGC
202600 GGGCGGATGCGGGGC
1 GGGCGGATGCGGGGC
202615 GGG
1 GGG
202618 TAATGTCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.15, G:0.70, T:0.09
Consensus pattern (15 bp):
GGGCGGATGCGGGGC
Found at i:204100 original size:19 final size:19
Alignment explanation
Indices: 204076--204114 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
204066 ACCCAAAACG
204076 TCAGTAATCCAACAATACT
1 TCAGTAATCCAACAATACT
204095 TCAGTAATCCAACAATACT
1 TCAGTAATCCAACAATACT
204114 T
1 T
204115 AAGGTTAGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.26, G:0.05, T:0.28
Consensus pattern (19 bp):
TCAGTAATCCAACAATACT
Found at i:205906 original size:19 final size:22
Alignment explanation
Indices: 205864--205908 Score: 69
Period size: 19 Copynumber: 2.2 Consensus size: 22
205854 TATTAGGTAG
205864 TATTAATATAATATAAAGTATA
1 TATTAATATAATATAAAGTATA
205886 TATTAA-ATAAT-TAAA-TATA
1 TATTAATATAATATAAAGTATA
205905 TATT
1 TATT
205909 TACTAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.35
20 4 0.17
21 5 0.22
22 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
TATTAATATAATATAAAGTATA
Found at i:205915 original size:19 final size:21
Alignment explanation
Indices: 205864--205917 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 21
205854 TATTAGGTAG
205864 TATTAATATAATATAAAGTATA
1 TATTAA-ATAATATAAAGTATA
205886 TATTAAATAAT-TAAA-TATA
1 TATTAAATAATATAAAGTATA
* *
205905 TATTTACTAATAT
1 TATTAAATAATAT
205918 TTTTATTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 13 0.45
20 5 0.17
21 5 0.17
22 6 0.21
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (21 bp):
TATTAAATAATATAAAGTATA
Found at i:210219 original size:35 final size:34
Alignment explanation
Indices: 210134--210220 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
210124 AAAATAATTT
*
210134 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
* *
210168 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAATGG
210206 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
210221 ACTTAAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 4 0.09
38 11 0.24
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:211371 original size:2 final size:2
Alignment explanation
Indices: 211366--211393 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
211356 TATTTTTTAA
211366 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
211394 TAAAACTCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:214875 original size:25 final size:25
Alignment explanation
Indices: 214829--214876 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
214819 AGGAGTGCAT
* * *
214829 AAATGATGTGGCAAATATTGAAGTG
1 AAATGATGTGACAAACAATGAAGTG
214854 AAATGATGTGACAAACAATGAAG
1 AAATGATGTGACAAACAATGAAG
214877 AATTTTGTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.46, C:0.06, G:0.25, T:0.23
Consensus pattern (25 bp):
AAATGATGTGACAAACAATGAAGTG
Found at i:225107 original size:20 final size:20
Alignment explanation
Indices: 225082--225132 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
225072 TAAGAAAATT
*
225082 GTGGATTCTAGCTCATTTTA
1 GTGGATTCAAGCTCATTTTA
225102 GTGGATTCAAGCTCATTTTA
1 GTGGATTCAAGCTCATTTTA
225122 GTGGATTCAAG
1 GTGGATTCAAG
225133 TTATATAAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.39
Consensus pattern (20 bp):
GTGGATTCAAGCTCATTTTA
Found at i:234701 original size:2 final size:2
Alignment explanation
Indices: 234694--234727 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
234684 ATGGTTTTTA
234694 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
234728 TGTTTTGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:234796 original size:16 final size:16
Alignment explanation
Indices: 234777--234852 Score: 68
Period size: 17 Copynumber: 4.7 Consensus size: 16
234767 ATATTTTTGA
234777 AAATATATATAGTTTT
1 AAATATATATAGTTTT
*
234793 AAATATATATA--TAT
1 AAATATATATAGTTTT
* *
234807 ATATATATATATTTTTT
1 AAATATATATA-GTTTT
234824 AAA-ACCTATATAGTTTT
1 AAATA--TATATAGTTTT
234841 GAAATATATATA
1 -AAATATATATA
234853 TATATATATA
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
14 12 0.25
16 12 0.25
17 14 0.29
18 9 0.19
19 1 0.02
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (16 bp):
AAATATATATAGTTTT
Found at i:234810 original size:49 final size:49
Alignment explanation
Indices: 234754--234867 Score: 158
Period size: 49 Copynumber: 2.3 Consensus size: 49
234744 AATTTTAAAA
* *
234754 ATATATATGTCAAATATTTTTGAAAATATATATAGTTTT-AAATATATAT
1 ATATATATAT-AAATATTTTTGAAAACATATATAGTTTTGAAATATATAT
* * *
234803 ATATATATATATATATTTTTTAAAACCTATATAGTTTTGAAATATATAT
1 ATATATATATAAATATTTTTGAAAACATATATAGTTTTGAAATATATAT
*
234852 ATATATATATATATAT
1 ATATATATATAAATAT
234868 ATATATATAT
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
48 24 0.41
49 35 0.59
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (49 bp):
ATATATATATAAATATTTTTGAAAACATATATAGTTTTGAAATATATAT
Found at i:234849 original size:2 final size:2
Alignment explanation
Indices: 234844--234879 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
234834 TAGTTTTGAA
234844 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
234880 TTAAAATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:234904 original size:61 final size:56
Alignment explanation
Indices: 234795--234936 Score: 153
Period size: 57 Copynumber: 2.5 Consensus size: 56
234785 ATAGTTTTAA
* **
234795 ATATATATATATATATATATATATTTTTTAAAACCTATATAGTTTTGAAATATATAT
1 ATATATATATATATATATATATATTATTTAAAACAAATATAGTTTTGAAA-ATATAT
* *
234852 ATATATATATATATATATATATATATATTTAAAATAAATATGGTTTTATTGAAAATATAT
1 ATATATATATATATATATATATAT-TATTTAAAACAAATATAG--TT-TTGAAAATATAT
* *
234912 -TATATGTCAAATAT-TATATATATTA
1 ATATATAT-ATATATATATATATATTA
234937 ATATTTTTAT
Statistics
Matches: 73, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
57 24 0.33
58 15 0.21
59 15 0.21
60 13 0.18
61 6 0.08
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (56 bp):
ATATATATATATATATATATATATTATTTAAAACAAATATAGTTTTGAAAATATAT
Found at i:235533 original size:77 final size:79
Alignment explanation
Indices: 235434--235582 Score: 178
Period size: 77 Copynumber: 1.9 Consensus size: 79
235424 TAATAAAAAA
* * **
235434 TCTTATTTAATTTATTTAAATTAGATATCCATT-AAAGACTTATAATCTGAATTACAATC-TTTA
1 TCTTATTTAATTTATTCAAATTAAATATCCATTAAAAGACTTATAATCAAAATTACAATCTTTTA
235497 ACGTTTATTTAAAC
66 ACGTTTATTTAAAC
* * * * *
235511 TCTTATTTAA-TTATTCCGAATTAAATATCGATTAAAAGAGTTGTAATCAAAATTACATTCTTTT
1 TCTTATTTAATTTATT-CAAATTAAATATCCATTAAAAGACTTATAATCAAAATTACAATCTTTT
*
235575 AATGTTTA
65 AACGTTTA
235583 CTTACTATAT
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
76 5 0.08
77 23 0.39
78 21 0.36
79 10 0.17
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.45
Consensus pattern (79 bp):
TCTTATTTAATTTATTCAAATTAAATATCCATTAAAAGACTTATAATCAAAATTACAATCTTTTA
ACGTTTATTTAAAC
Found at i:239256 original size:41 final size:41
Alignment explanation
Indices: 239190--239320 Score: 129
Period size: 41 Copynumber: 3.2 Consensus size: 41
239180 AACTTTAAAC
* ** *
239190 CTAAACCCTAAATTCTAAAGTTTAAATCTCAAACCCTAAGTT
1 CTAAACCCTAAA-TCCAAAACTTAAATCTCAAATCCTAAGTT
** * *
239232 CTAAACTTTAAA-CCAAAACCTTAAATCTCTAATCCTAAATT
1 CTAAACCCTAAATCCAAAA-CTTAAATCTCAAATCCTAAGTT
* * * *
239273 ATAAACCCTAAATCCTAAAGTTAAATCTCAAATCCTAAGTC
1 CTAAACCCTAAATCCAAAACTTAAATCTCAAATCCTAAGTT
239314 CTAAACC
1 CTAAACC
239321 TAACCTTAAA
Statistics
Matches: 70, Mismatches: 17, Indels: 5
0.76 0.18 0.05
Matches are distributed among these distances:
40 4 0.06
41 51 0.73
42 15 0.21
ACGTcount: A:0.43, C:0.25, G:0.03, T:0.29
Consensus pattern (41 bp):
CTAAACCCTAAATCCAAAACTTAAATCTCAAATCCTAAGTT
Found at i:239291 original size:14 final size:14
Alignment explanation
Indices: 239185--239291 Score: 51
Period size: 14 Copynumber: 7.8 Consensus size: 14
239175 TATCAAACTT
239185 TAAA-CCTAAACCC
1 TAAATCCTAAACCC
* ***
239198 TAAATTCTAAAGTT
1 TAAATCCTAAACCC
239212 TAAAT-CTCAAACCC
1 TAAATCCT-AAACCC
* * **
239226 TAAGTTCTAAACTT
1 TAAATCCTAAACCC
* *
239240 TAAA-CCAAAACCT
1 TAAATCCTAAACCC
*
239253 TAAATCTCT-AATCC
1 TAAATC-CTAAACCC
**
239267 TAAATTATAAACCC
1 TAAATCCTAAACCC
239281 TAAATCCTAAA
1 TAAATCCTAAA
239292 GTTAAATCTC
Statistics
Matches: 66, Mismatches: 22, Indels: 11
0.67 0.22 0.11
Matches are distributed among these distances:
13 17 0.26
14 46 0.70
15 3 0.05
ACGTcount: A:0.45, C:0.24, G:0.02, T:0.29
Consensus pattern (14 bp):
TAAATCCTAAACCC
Found at i:239297 original size:20 final size:21
Alignment explanation
Indices: 239253--239310 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
239243 ACCAAAACCT
* * *
239253 TAAATCTCTAATCCTAAATTA
1 TAAACCTCAAATCCTAAAGTA
239274 TAAACC-CTAAATCCTAAAGT-
1 TAAACCTC-AAATCCTAAAGTA
*
239294 TAAATCTCAAATCCTAA
1 TAAACCTCAAATCCTAA
239311 GTCCTAAACC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.45, C:0.22, G:0.02, T:0.31
Consensus pattern (21 bp):
TAAACCTCAAATCCTAAAGTA
Found at i:240636 original size:22 final size:20
Alignment explanation
Indices: 240585--240638 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 20
240575 CGAACCAAAA
*
240585 ATTAGTATCGATACTCCATC
1 ATTAGTATCGATACCCCATC
*
240605 A--AGTAGCGATACCCCATC
1 ATTAGTATCGATACCCCATC
240623 ACCTTAGTATCGATAC
1 A--TTAGTATCGATAC
240639 TCTACTAAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
18 16 0.59
20 1 0.04
22 10 0.37
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.28
Consensus pattern (20 bp):
ATTAGTATCGATACCCCATC
Found at i:240734 original size:20 final size:20
Alignment explanation
Indices: 240711--240756 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
240701 CAACAAGTGG
*
240711 GTATCGATACTAAAGGTTTA
1 GTATCGATACTAAAGGATTA
* *
240731 GTATCAATACTGAAGGATTA
1 GTATCGATACTAAAGGATTA
*
240751 ATATCG
1 GTATCG
240757 GTACCCATAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.33
Consensus pattern (20 bp):
GTATCGATACTAAAGGATTA
Found at i:248874 original size:29 final size:27
Alignment explanation
Indices: 248839--248919 Score: 110
Period size: 26 Copynumber: 2.9 Consensus size: 27
248829 AAATATTTAA
248839 AATATATTTATTAATATTTATAATAATAT
1 AATATATTT-TTAATA-TTATAATAATAT
248868 AATATATATTTTTAATATTATAATAATAT
1 -A-ATATATTTTTAATATTATAATAATAT
*
248897 AATAT-TTTTAAATATTATAATAA
1 AATATATTTTTAATATTATAATAA
248920 AATACTCAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
26 17 0.35
27 4 0.08
28 1 0.02
29 12 0.24
30 7 0.14
31 8 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
AATATATTTTTAATATTATAATAATAT
Found at i:248876 original size:21 final size:22
Alignment explanation
Indices: 248852--248897 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
248842 ATATTTATTA
248852 ATATTTATAATAATATAAT-AT
1 ATATTTATAATAATATAATAAT
* *
248873 ATATTTTTAATATTATAATAAT
1 ATATTTATAATAATATAATAAT
248895 ATA
1 ATA
248898 ATATTTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATATTTATAATAATATAATAAT
Found at i:248905 original size:26 final size:28
Alignment explanation
Indices: 248839--248919 Score: 112
Period size: 29 Copynumber: 2.9 Consensus size: 28
248829 AAATATTTAA
*
248839 AATATATTTATTAATATTTATAATAATAT
1 AATATATTTTTTAATA-TTATAATAATAT
248868 AATATATATTTTTAATATTATAATAATAT
1 AATATAT-TTTTTAATATTATAATAATAT
*
248897 -A-ATATTTTTAAATATTATAATAA
1 AATATATTTTTTAATATTATAATAA
248920 AATACTCAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
26 17 0.35
27 4 0.08
28 1 0.02
29 19 0.39
30 8 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
AATATATTTTTTAATATTATAATAATAT
Found at i:249105 original size:23 final size:23
Alignment explanation
Indices: 249078--249126 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
249068 ATAATAATCT
*
249078 AATATTTTAATAAAGATATTTAA
1 AATATATTAATAAAGATATTTAA
* * *
249101 AATATATTAATTAATATTTTTAA
1 AATATATTAATAAAGATATTTAA
249124 AAT
1 AAT
249127 GTAATATAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
AATATATTAATAAAGATATTTAA
Found at i:251378 original size:16 final size:17
Alignment explanation
Indices: 251359--251396 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
251349 AATAACGCAC
*
251359 TTTATTTTTT-TAAATT
1 TTTATTTTTTATAAAAT
251375 TTTATTTTTTATAAAAT
1 TTTATTTTTTATAAAAT
251392 TTTAT
1 TTTAT
251397 AAATTTATCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTATTTTTTATAAAAT
Found at i:255108 original size:7 final size:7
Alignment explanation
Indices: 255096--255120 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
255086 GAAAGTTAAT
255096 AAATTTA
1 AAATTTA
255103 AAATTTA
1 AAATTTA
255110 AAATTTA
1 AAATTTA
255117 AAAT
1 AAAT
255121 ATCCGATTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AAATTTA
Found at i:256565 original size:23 final size:23
Alignment explanation
Indices: 256522--256565 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
256512 TATATATATA
*
256522 TATATAAAATATTTTCCAAAACC
1 TATATAAAATATTTTCAAAAACC
*
256545 TATATAATATACTTTT-AAAAA
1 TATATAAAATA-TTTTCAAAAA
256566 TATTTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 14 0.78
24 4 0.22
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (23 bp):
TATATAAAATATTTTCAAAAACC
Found at i:256583 original size:34 final size:36
Alignment explanation
Indices: 256527--256618 Score: 109
Period size: 35 Copynumber: 2.6 Consensus size: 36
256517 ATATATATAT
**
256527 AAAATATTTTCCAAAA-CCTATATAATATAC-TTTTA
1 AAAATATTTT-CAAAATTATATATAATATACTTTTTA
*
256562 AAAATATTTT-AAAATTATATATTATATACTTTTTA
1 AAAATATTTTCAAAATTATATATAATATACTTTTTA
* *
256597 AACATGTTTTCAAAATTATATA
1 AAAATATTTTCAAAATTATATA
256619 GTTTTCAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
33 4 0.08
34 11 0.22
35 23 0.47
36 11 0.22
ACGTcount: A:0.46, C:0.09, G:0.01, T:0.45
Consensus pattern (36 bp):
AAAATATTTTCAAAATTATATATAATATACTTTTTA
Found at i:256632 original size:29 final size:29
Alignment explanation
Indices: 256582--256669 Score: 115
Period size: 29 Copynumber: 3.0 Consensus size: 29
256572 AAAATTATAT
* * *
256582 ATTATATACTTTTTAAACATGTTTTCAAA
1 ATTATATAGTTTTCAAAAATGTTTTCAAA
*
256611 ATTATATAGTTTTCAAAAATGTTTTTAAA
1 ATTATATAGTTTTCAAAAATGTTTTCAAA
*
256640 ATTATATATGTTTTC-AAAATGATTTCAAA
1 ATTATATA-GTTTTCAAAAATGTTTTCAAA
256669 A
1 A
256670 ACTATATAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
29 46 0.88
30 6 0.12
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.47
Consensus pattern (29 bp):
ATTATATAGTTTTCAAAAATGTTTTCAAA
Found at i:256719 original size:37 final size:34
Alignment explanation
Indices: 256615--256976 Score: 196
Period size: 37 Copynumber: 10.1 Consensus size: 34
256605 TTCAAAATTA
256615 TATAGTTTTCAAAAATGTTTTT-AAAA-T-TATA--
1 TATA-TTTTCAAA-ATGTTTTTAAAAACTATATATT
* * *
256646 TATGTTTTCAAAATGATTTCAAAAACTATATAATATATT
1 TATATTTTCAAAATGTTTTTAAAAAC----T-ATATATT
*
256685 TATGTTTTCAAAATGTTTTTTTTAAAAACTATATA--
1 TATATTTTCAAAATG---TTTTTAAAAACTATATATT
*
256720 TAT-TTTT-AAAATG-TTTTAAAAACTATATAATA
1 TATATTTTCAAAATGTTTTTAAAAACTATAT-ATT
*
256752 TGTATTTTCAAAAATG-TTTTAAAAACTATATATT
1 TATATTTTC-AAAATGTTTTTAAAAACTATATATT
256786 ATATTAATTTTCAAAATGTTTTTAAAAACTATATAATAT
1 -TA-T-ATTTTCAAAATGTTTTTAAAAACTATAT-AT-T
*
256825 ATATATTTTCAAAAATG-TTTTGAAAACTATATATT
1 -TATATTTTC-AAAATGTTTTTAAAAACTATATATT
* *
256860 ATATTAATTTTCAAAATG-TCTTAAGAACTATATAATAT
1 -TA-T-ATTTTCAAAATGTTTTTAAAAACTATAT-AT-T
* * * *
256898 ATAAATGTTTTCAAACATGCTTTTCAAAATTATATATTAT
1 -T--ATATTTTCAAA-ATGTTTTTAAAAACTATATA-T-T
* *
256938 ATATATTTTAAAAATG-TTTT-CAAACTATATATT
1 -TATATTTTCAAAATGTTTTTAAAAACTATATATT
256971 GTATAT
1 -TATAT
256977 ATATATATAT
Statistics
Matches: 274, Mismatches: 22, Indels: 68
0.75 0.06 0.19
Matches are distributed among these distances:
29 21 0.08
30 13 0.05
31 3 0.01
32 2 0.01
33 16 0.06
34 7 0.03
35 39 0.14
36 32 0.12
37 61 0.22
38 30 0.11
39 24 0.09
40 17 0.06
42 9 0.03
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (34 bp):
TATATTTTCAAAATGTTTTTAAAAACTATATATT
Found at i:256851 original size:74 final size:73
Alignment explanation
Indices: 256640--256978 Score: 333
Period size: 74 Copynumber: 4.6 Consensus size: 73
256630 TGTTTTTAAA
* * *
256640 ATTATATATGTTTTCAAAATGATTTCAAAAACTATATAATATATTTATGTTTTC-AAAATGTTTT
1 ATTATATA-ATTTTCAAAATG-TTTTAAAAACTATATAATATA--TATATTTTCAAAAATG---T
256704 TTTTAAAAAC--TAT
59 TTTTAAAAACTATAT
*
256717 A-TATAT--TTTT-AAAATGTTTTAAAAACTATAT-A-ATATGTATTTTCAAAAATG-TTTTAAA
1 ATTATATAATTTTCAAAATGTTTTAAAAACTATATAATATATATATTTTCAAAAATGTTTTTAAA
256775 AACTATAT
66 AACTATAT
*
256783 ATTATATTAATTTTCAAAATGTTTTTAAAAACTATATAATATATATATTTTCAAAAATG-TTTTG
1 ATTATA-TAATTTTCAAAATG-TTTTAAAAACTATATAATATATATATTTTCAAAAATGTTTTTA
256847 AAAACTATAT
64 AAAACTATAT
* * * * *
256857 ATTATATTAATTTTCAAAATGTCTTAAGAACTATATAATATATAAATGTTTTCAAACATGCTTTT
1 ATTATA-TAATTTTCAAAATGTTTTAAAAACTATATAATATAT--ATATTTTCAAAAATGTTTTT
* *
256922 CAAAATTATAT
63 AAAAACTATAT
* * * *
256933 ATTATATATATTTTAAAAATGTTTT-CAAACTATATATTGTATATAT
1 ATTATATA-ATTTTCAAAATGTTTTAAAAACTATATAATATATATAT
256979 ATATATATAT
Statistics
Matches: 229, Mismatches: 18, Indels: 34
0.81 0.06 0.12
Matches are distributed among these distances:
64 10 0.04
66 4 0.02
67 11 0.05
68 7 0.03
69 3 0.01
70 5 0.02
71 20 0.09
72 21 0.09
73 28 0.12
74 53 0.23
75 28 0.12
76 38 0.17
77 1 0.00
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (73 bp):
ATTATATAATTTTCAAAATGTTTTAAAAACTATATAATATATATATTTTCAAAAATGTTTTTAAA
AACTATAT
Found at i:256978 original size:37 final size:38
Alignment explanation
Indices: 256714--256980 Score: 270
Period size: 37 Copynumber: 7.2 Consensus size: 38
256704 TTTTAAAAAC
*
256714 TATATATATTTTTAAAATGTTTTAAAAACTATATA--A
1 TATATATATTTTAAAAATGTTTTAAAAACTATATATTA
* *
256750 TATGTAT-TTTCAAAAATGTTTTAAAAACTATATATTA
1 TATATATATTTTAAAAATGTTTTAAAAACTATATATTA
*
256787 TAT-TA-ATTTTCAAAATGTTTTTAAAAACTATATA--A
1 TATATATATTTTAAAAATG-TTTTAAAAACTATATATTA
*
256822 TATATATATTTTCAAAAATGTTTTGAAAACTATATATTA
1 TATATATATTTT-AAAAATGTTTTAAAAACTATATATTA
* * * *
256861 TAT-TA-ATTTTCAAAATGTCTTAAGAACTATATAATA
1 TATATATATTTTAAAAATGTTTTAAAAACTATATATTA
* * * * *
256897 TATAAATGTTTTCAAACATGCTTTTCAAAATTATATA-T-
1 TATATATATTTT-AAAAATG-TTTTAAAAACTATATATTA
* *
256935 TATATATATTTTAAAAATGTTTT-CAAACTATATATTG
1 TATATATATTTTAAAAATGTTTTAAAAACTATATATTA
256972 TATATATAT
1 TATATATAT
256981 ATATATATAT
Statistics
Matches: 191, Mismatches: 25, Indels: 29
0.78 0.10 0.12
Matches are distributed among these distances:
35 38 0.20
36 48 0.25
37 61 0.32
38 22 0.12
39 10 0.05
40 12 0.06
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.46
Consensus pattern (38 bp):
TATATATATTTTAAAAATGTTTTAAAAACTATATATTA
Found at i:257806 original size:84 final size:83
Alignment explanation
Indices: 257546--258616 Score: 1062
Period size: 84 Copynumber: 12.9 Consensus size: 83
257536 ATTTTATTGA
* * * * * * * *
257546 CAGATAGCCCTTCTCGCCTTAAGCTATGCTGTAAATGTTGTGCCTTTGAGCTGAGTGTAGTCGAC
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* * *
257611 CTCAAAGGTCTTCTGGTGA
66 CTCGAAGGTCTT-TGTTGG
* * * * * * * * * *
257630 CAGATAACCCTCCT-AACCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAGTTGAGTGTAATCG
1 CAGATAACCCTTCTCGA-CTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCG
* * **
257694 AATTAGGGGGTC--T-TTGG
64 AACTCGAAGGTCTTTGTTGG
* * * *
257711 CAGATAGCCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCTTGGAGCTGAACGTAG-CTGA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC-GA
*
257775 ACTCGAAGGTTTTTGGTTGG
65 ACTCGAAGGTCTTT-GTTGG
* *
257795 CAGATAACCCTTCTCGACTTAAGTTATGCAGCAAATGATGTGTCGTT-GAGCTGAGCGTAGTCGA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGA
*
257859 ACTCAAAGGTCTTTTGTTGG
65 ACTCGAAGGTC-TTTGTTGG
* * * * *
257879 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCAA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGA
**
257944 ACTCGGGGGTC--T-TTGG
65 ACTCGAAGGTCTTTGTTGG
** * *
257960 CAGATAGTCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTT-GAGCTGAGCGTAGTCAA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC-TTGGAGCTGAGCGTAGTCGA
* *
258024 ACTCGAAGGTCTTTGGGTGA
65 ACTCGAAGGTCTTT-GTTGG
* * * *
258044 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
258109 CTCGAAGGTCTTTGGTTGG
66 CTCGAAGGTCTTT-GTTGG
*
258128 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCGTT-GAGCTGGGCGTAGTCGA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC-TTGGAGCTGAGCGTAGTCGA
*
258192 ACTCAAAGGTCTTGTGTTGG
65 ACTCGAAGGTCTT-TGTTGG
* * * *
258212 CAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* *
258277 CTCGAAGGTCTTTGGTGA
66 CTCGAAGGTCTTTGTTGG
* * * * * * * *
258295 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAACGTAGTCGA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGA
*
258360 ACTCGAGGGTC--T-TTGG
65 ACTCGAAGGTCTTTGTTGG
* * *
258376 CAGATAGCCCTTCTCGACTTAAGTTATTCTACAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* * **
258441 CTCAAAGGTCTTTGCTAA
66 CTCGAAGGTCTTTGTTGG
* * * * * * ** * * *
258459 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTTAAGCTGAGTGTAATCAA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGA
*
258524 ACT-TAAGGGTC--T-TTGG
65 ACTCGAA-GGTCTTTGTTGG
* * * *
258540 CAGATATCTCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
258605 CTCGAAGGTCTT
66 CTCGAAGGTCTT
258617 GGTGGAAGGT
Statistics
Matches: 804, Mismatches: 153, Indels: 62
0.79 0.15 0.06
Matches are distributed among these distances:
79 1 0.00
80 97 0.12
81 151 0.19
82 8 0.01
83 81 0.10
84 413 0.51
85 53 0.07
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.30
Consensus pattern (83 bp):
CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
CTCGAAGGTCTTTGTTGG
Found at i:257866 original size:249 final size:247
Alignment explanation
Indices: 257543--258635 Score: 1077
Period size: 249 Copynumber: 4.4 Consensus size: 247
257533 ACAATTTTAT
* * * * * *
257543 TGACAGATAGCCCTTCTCGCCTTAAGCTATGCTGTAAATGTTGTGCCTTTGAGCTGAGTGTAGTC
1 TGACAGATAACCCTTCTAGCCTTAAGTTATGCTGTAAATGATGTGCCCTTGAGCTGAGCGTAGTC
* * * * * * *
257608 GACCTCAAAGGTCTTCTGGTGACAGATAACCCTCCT-AACCTTGAGTTATGTTGTAAATGATGTG
66 GAACTCAAAGGTCTT-TGGTGGCAGATAACCCTTCTCGA-CTTAAGTTATGCTGCAAATGATGTG
*
257672 CCCTCGAAGTTGAGTGTAATCGAATTAGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTA
129 CCCTCGAAGCTGAGTGTAATCGAATTAGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTA
* * *
257737 TGCTGTAAATGATGTGCCTTGGAGCTGAACGTAG-CTGAACTCGAAGGTTTTTGG
194 TGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC-GAACTCGAAGGTCTTTGG
* * * * * * *
257791 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCAGCAAATGATGTGTCGTTGAGCTGAGCGTAGT
1 -TGACAGATAACCCTTCTAGCCTTAAGTTATGCTGTAAATGATGTGCCCTTGAGCTGAGCGTAGT
*
257856 CGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
65 CGAACTCAAAGGTC-TTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
* * * *
257921 CCCTCGAAGCTGAGTGTAATCAAACTCGGGGGTCTTTGGCAGATAGTCCTTCTCGACTTAAGCTA
129 CCCTCGAAGCTGAGTGTAATCGAATTAGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTA
*
257986 TGCTGCAAATGATGTGCCGTT-GAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGG
194 TGCTGCAAATGATGTGCC-TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GG
*
258041 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG-CCTTGGAGCTGAGCGTAGT
1 TGACAGATAACCCTTCTAGCCTTAAGTTATGCTGTAAATGATGTGCCCTT-GAGCTGAGCGTAGT
*
258105 CGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
65 CGAACTCAAAGGTCTTTGG-TGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
* * * * * * ** * * *
258170 CCGTTG-AGCTGGGCGTAGTCGAACTCA-AAGGTCTTGTGTTGGCAGACAACCCTTCTAGACTTA
129 CCCTCGAAGCTGAGTGTAATCGAA-TTAGGGGGTC---T-TTGGCAGATAGCCCTTCTCGACTTA
* * *
258233 AGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
189 AGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
* * * *
258292 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAACGTAGT
1 TGACAGATAACCCTTCTAGCCTTAAGTTATGCTGTAAATGATGTGCCCTTG-AGCTGAGCGTAGT
* * * * *
258357 CGAACTCGAGGGTC-TT--TGGCAGATAGCCCTTCTCGACTTAAGTTATTCTACAAATGATGTG-
65 CGAACTCAAAGGTCTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGC
* * * * * ** * * * * *
258418 CCTTGGAGCTGAGCGTAGTCGAACTCA-AAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAG
130 CCTCGAAGCTGAGTGTAATCGAA-TTAGGGGGTCTTTG---GCAGATAGCCCTTCTCGACTTAAG
* * * * ** * * * *
258482 TTATGCTGTAAATGTTATGCCCTTTAAGCTGAGTGTAATCAAACT-TAAGGGTCTTT-G
191 CTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAA-GGTCTTTGG
* * * * * * *
258539 -G-CAGATATCTCTTCTCGACTTAAGCTATACTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGT
1 TGACAGATAACCCTTCTAGCCTTAAGTTATGCTGTAAATGATGTGCCCTT-GAGCTGAGCGTAGT
* * * *
258601 CGAACTCGAAGGTC-TTGGTGGAAGGTAGCCCTTCT
65 CGAACTCAAAGGTCTTTGGTGGCAGATAACCCTTCT
258636 GGCCTTGAGC
Statistics
Matches: 729, Mismatches: 91, Indels: 51
0.84 0.10 0.06
Matches are distributed among these distances:
244 33 0.05
245 35 0.05
246 16 0.02
247 43 0.06
248 119 0.16
249 324 0.44
250 8 0.01
251 52 0.07
252 99 0.14
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (247 bp):
TGACAGATAACCCTTCTAGCCTTAAGTTATGCTGTAAATGATGTGCCCTTGAGCTGAGCGTAGTC
GAACTCAAAGGTCTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC
CTCGAAGCTGAGTGTAATCGAATTAGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATG
CTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
Found at i:258436 original size:164 final size:163
Alignment explanation
Indices: 257546--258657 Score: 1149
Period size: 164 Copynumber: 6.7 Consensus size: 163
257536 ATTTTATTGA
* * * * * * * *
257546 CAGATAGCCCTTCTCGCCTTAAGCTATGCTGTAAATGTTGTGCCTTTGAGCTGAGTGTAGTCGAC
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* * * * *
257611 CTCAAAGGTCTTCTGGTGACAGATAACCCTCCTAACCTTGAGTTATGTTGTAAATGATGTGCCCT
66 CTCGAAGGTCTT-TGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCT
* * * * * **
257676 CGAAGTTGAGTGTAATCGAA-TTAGGGGGTCTTTGG
130 TG-AGCTGAGCGTAGTCGAACTCA-AAGGTCTTTGG
* * * *
257711 CAGATAGCCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCTTGGAGCTGAACGTAG-CTGA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC-GA
* * * * * * * *
257775 ACTCGAAGGTTTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCAGCAAATGATGTGTCG
65 ACTCGAAGGTCTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCC
257840 TTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGG
129 TTGAGCTGAGCGTAGTCGAACTCAAAGGTC---T-TTGG
* * * * *
257879 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCAA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGA
** ** * * * * *
257944 ACTCGGGGGTCTTT-G-G-CAGATAGTCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGT
65 ACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCT
* *
258006 TGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGGTG
130 TGAGCTGAGCGTAGTCGAACTCAAAGGTCTTT--G-G
* * * *
258043 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
1 -CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
* * * * *
258108 ACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCG
65 ACTCGAAGGTCTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCC
*
258173 TTGAGCTGGGCGTAGTCGAACTCAAAGGTCTTGTGTTGG
129 TTGAGCTGAGCGTAGTCGAACTCAAAGGTC---T-TTGG
* * * *
258212 CAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* * *
258277 CTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTC
66 CTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTT
* * *
258342 GAAGCTGAACGTAGTCGAACTCGAGGGTCTTTGG
131 G-AGCTGAGCGTAGTCGAACTCAAAGGTCTTTGG
* * *
258376 CAGATAGCCCTTCTCGACTTAAGTTATTCTACAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* * * * * *
258441 CTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTT
66 CTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCC-T
* * * * * *
258506 TAAGCTGAGTGTAATCAAACTTAAGGGTCTTTGG
130 TGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGG
* * * *
258540 CAGATATCTCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* * * * *
258605 CTCGAAGGTC-TTGGTGGA-AGGTAGCCCTTCTGGCCTTGAGCTAAGCTGCAAAT
66 CTCGAAGGTCTTTGGT-GACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAAT
258658 AGTTTGTTTA
Statistics
Matches: 810, Mismatches: 113, Indels: 50
0.83 0.12 0.05
Matches are distributed among these distances:
161 2 0.00
162 1 0.00
163 34 0.04
164 269 0.33
165 217 0.27
166 1 0.00
167 45 0.06
168 210 0.26
169 26 0.03
170 2 0.00
171 1 0.00
172 2 0.00
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (163 bp):
CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
CTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTT
GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGG
Found at i:262099 original size:19 final size:19
Alignment explanation
Indices: 262075--262122 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
262065 AGTTAATGTG
* *
262075 AATGCAAAGAAAATAACCA
1 AATGCAAAAAAAATAACAA
262094 AATGCAAAAAAAATAACAA
1 AATGCAAAAAAAATAACAA
262113 AATGCAAAAA
1 AATGCAAAAA
262123 GTCTAAATGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.69, C:0.12, G:0.08, T:0.10
Consensus pattern (19 bp):
AATGCAAAAAAAATAACAA
Found at i:265213 original size:2 final size:2
Alignment explanation
Indices: 265204--265249 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
265194 GGAAAAAATA
265204 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
265245 AT AT A
1 AT AT A
265250 AAATATTTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:265288 original size:36 final size:34
Alignment explanation
Indices: 265230--265691 Score: 133
Period size: 37 Copynumber: 13.2 Consensus size: 34
265220 TATATATATA
*
265230 TATATATATATATA-TATATAAAATATTTTCCAAAACC
1 TATATA-ATATATACT-TTTAAAATATTTT-CAAAA-C
*
265267 TATATAATATATACTTTTAAAAATATTTT-AAAAT
1 TATATAATATATACTTTT-AAAATATTTTCAAAAC
* *
265301 TATATATTATATACTTTTTAAACATGTTTTCAAAA-
1 TATATAATATATAC-TTTTAAA-ATATTTTCAAAAC
** * *
265336 T-TAT-ATAGT-T--TTCAAAAATGTTTTTAAAAC
1 TATATAATA-TATACTTTTAAAATATTTTCAAAAC
* *
265366 --TAT-ATATGT--TTTCAAAATGA-TTTCAAAAAC
1 TATATAATATATACTTTTAAAAT-ATTTTC-AAAAC
* * *
265396 TATATAATATATTTATGTTTTCAAAATGTTTTTTAAAA-
1 TATATAATATA--TA-CTTTT-AAAAT-ATTTTCAAAAC
* * *
265434 -A-ACT-ATATATATTTTTAAAATGTTTTAAAAAC
1 TATA-TAATATATACTTTTAAAATATTTTCAAAAC
* * *
265466 TATATAATATGTA-TTTTCAAAAATGTTTTAAAAAC
1 TATATAATATATACTTTT--AAAATATTTTCAAAAC
* * * *
265501 TATATATTATATTAATTTTCAAAATGTTTTTAAAAAC
1 TATATAATATA-TACTTTT-AAAAT-ATTTTCAAAAC
* *
265538 TATATAATATATA-TATATTCAAAAATGTTTTGAAAAC
1 TATATAATATATACT-T-TT--AAAATATTTTCAAAAC
* * * *
265575 TATATATTATATTAATTTTCAAAATGTCTT-AAGAAC
1 TATATAATATA-TACTTTT-AAAATATTTTCAA-AAC
* * *
265611 TATATAATATATAAATGTTTTCAAACATGCTTTTCAAAAT
1 TATATAATATAT--A-CTTTT-AAA-AT-ATTTTCAAAAC
*
265651 TATATATTATATATA-TTTTAAAAATGTTTTC-AAAC
1 TATATA--ATATATACTTTT-AAAATATTTTCAAAAC
265686 TATATA
1 TATATA
265692 CTGTATATAT
Statistics
Matches: 342, Mismatches: 39, Indels: 90
0.73 0.08 0.19
Matches are distributed among these distances:
28 1 0.00
29 28 0.08
30 10 0.03
31 8 0.02
32 8 0.02
33 17 0.05
34 29 0.08
35 54 0.16
36 56 0.16
37 69 0.20
38 26 0.08
39 13 0.04
40 15 0.04
41 2 0.01
42 6 0.02
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (34 bp):
TATATAATATATACTTTTAAAATATTTTCAAAAC
Found at i:265305 original size:34 final size:36
Alignment explanation
Indices: 265249--265342 Score: 120
Period size: 35 Copynumber: 2.6 Consensus size: 36
265239 ATATATATAT
*
265249 AAAATATTTTCCAAAACCTATATAATATATAC-TTTTA
1 AAAATATTTT-CAAAA-TTATATAATATATACTTTTTA
*
265286 AAAATATTTT-AAAATTATATATTATATACTTTTTA
1 AAAATATTTTCAAAATTATATAATATATACTTTTTA
* *
265321 AACATGTTTTCAAAATTATATA
1 AAAATATTTTCAAAATTATATA
265343 GTTTTCAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
34 13 0.25
35 17 0.33
36 11 0.22
37 10 0.20
ACGTcount: A:0.46, C:0.09, G:0.01, T:0.45
Consensus pattern (36 bp):
AAAATATTTTCAAAATTATATAATATATACTTTTTA
Found at i:265356 original size:29 final size:29
Alignment explanation
Indices: 265306--265393 Score: 106
Period size: 29 Copynumber: 3.0 Consensus size: 29
265296 AAAATTATAT
* * *
265306 ATTATATACTTTTTAAACATGTTTTCAAA
1 ATTATATAGTTTTCAAAAATGTTTTCAAA
*
265335 ATTATATAGTTTTCAAAAATGTTTTTAAA
1 ATTATATAGTTTTCAAAAATGTTTTCAAA
* *
265364 ACTATATATGTTTTC-AAAATGATTTCAAA
1 ATTATATA-GTTTTCAAAAATGTTTTCAAA
265393 A
1 A
265394 ACTATATAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 45 0.88
30 6 0.12
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (29 bp):
ATTATATAGTTTTCAAAAATGTTTTCAAA
Found at i:265407 original size:100 final size:103
Alignment explanation
Indices: 265302--265680 Score: 275
Period size: 105 Copynumber: 3.6 Consensus size: 103
265292 TTTTAAAATT
* * *
265302 ATATATTATATACTTTTTAAACATG-TTTT-CAAAA-T-TATATAGTTTTCAAAAATGTTTTTAA
1 ATATATTATAT-CTTTTCAAA-ATGTTTTTAAAAAACTATATATA-TTTT-AAAAATGTTTTAAA
265363 AAC-TAT-ATATG-TTTTC-AAAATGATTTCAAAAACTATATA
62 AACATATAATATGATTTTCAAAAATG-TTTCAAAAACTATATA
* *
265402 ATATATT-TATGTTTTCAAAATGTTTTTTAAAAAACTATATATATTTTTAAAATGTTTTAAAAAC
1 ATATATTATATCTTTTCAAAATG-TTTTTAAAAAACTATATATATTTTAAAAATGTTTTAAAAAC
*
265466 TATATAATATGTATTTTCAAAAATGTTTTAAAAACTATATA
65 -ATATAATATG-ATTTTCAAAAATGTTTCAAAAACTATATA
* *
265507 TTATATTA-A--TTTTCAAAATGTTTTTAAAAACTATATAATATATATATATTCAAAAATGTTTT
1 ATATATTATATCTTTTCAAAATGTTTTTAAAAA--A-CT-ATATATAT-T-TT-AAAAATGTTTT
* * *
265569 GAAAACTATATATTATATTAATTTTC-AAAATGTCTT-AAGAACTATATA
59 AAAAAC-ATATA--ATA-TGATTTTCAAAAATGT-TTCAAAAACTATATA
* * * *
265617 ATATA-TAAATGTTTTCAAACATGCTTTTCAAAATTATATATTATATATATTTTAAAAATGTTTT
1 ATATATTATATCTTTTCAAA-ATG-TTTT-TAAA--A-A-ACTATATATATTTTAAAAATGTTTT
265681 CAAACTATAT
Statistics
Matches: 232, Mismatches: 15, Indels: 52
0.78 0.05 0.17
Matches are distributed among these distances:
97 3 0.01
98 7 0.03
99 7 0.03
100 26 0.11
101 5 0.02
102 19 0.08
103 16 0.07
104 1 0.00
105 28 0.12
106 14 0.06
107 1 0.00
108 2 0.01
109 23 0.10
110 23 0.10
111 11 0.05
112 20 0.09
113 5 0.02
114 5 0.02
115 11 0.05
116 1 0.00
117 3 0.01
118 1 0.00
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (103 bp):
ATATATTATATCTTTTCAAAATGTTTTTAAAAAACTATATATATTTTAAAAATGTTTTAAAAACA
TATAATATGATTTTCAAAAATGTTTCAAAAACTATATA
Found at i:265519 original size:37 final size:37
Alignment explanation
Indices: 265450--265691 Score: 259
Period size: 37 Copynumber: 6.6 Consensus size: 37
265440 ATATATTTTT
265450 AAAATGTTTTAAAAACTATATA--ATATGT-ATTTTCA
1 AAAATGTTTTAAAAACTATATATTATAT-TAATTTTCA
265485 AAAATGTTTTAAAAACTATATATTATATTAATTTTC-
1 AAAATGTTTTAAAAACTATATATTATATTAATTTTCA
* *
265521 AAAATGTTTTTAAAAACTATATAATATA-TATATATTCA
1 AAAATG-TTTTAAAAACTATATATTATATTA-ATTTTCA
*
265559 AAAATGTTTTGAAAACTATATATTATATTAATTTTC-
1 AAAATGTTTTAAAAACTATATATTATATTAATTTTCA
* * * *
265595 AAAATGTCTTAAGAACTATATAATATATAAATGTTTTCA
1 AAAATGTTTTAAAAACTATATATTATATTAA--TTTTCA
* * *
265634 AACATGCTTTTCAAAATTATATATTATA-TATATTTT-A
1 AAAATG-TTTTAAAAACTATATATTATATTA-ATTTTCA
*
265671 AAAATGTTTT-CAAACTATATA
1 AAAATGTTTTAAAAACTATATA
265692 CTGTATATAT
Statistics
Matches: 175, Mismatches: 20, Indels: 24
0.80 0.09 0.11
Matches are distributed among these distances:
35 31 0.18
36 39 0.22
37 65 0.37
38 17 0.10
39 6 0.03
40 17 0.10
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.44
Consensus pattern (37 bp):
AAAATGTTTTAAAAACTATATATTATATTAATTTTCA
Found at i:265575 original size:74 final size:73
Alignment explanation
Indices: 265374--265703 Score: 324
Period size: 74 Copynumber: 4.5 Consensus size: 73
265364 ACTATATATG
* * * *
265374 TTTTCAAAATGATTTCAAAAACTATATAATATATTTATGTTTTC-AAAATGTTTTTTAAAAA--A
1 TTTTCAAAATG-TTTTAAAAACTATATAATATA--TATATATTCAAAAATG-CTTTTAAAAACTA
265436 CTATA-TATAT--
62 -TATATTATATAA
*
265446 TTTT-AAAATGTTTTAAAAACTATATAATATGTAT-T-TTCAAAAATG-TTTTAAAAACTATATA
1 TTTTCAAAATGTTTTAAAAACTATATAATATATATATATTCAAAAATGCTTTTAAAAACTATATA
265507 TTATATTAA
66 TTATA-TAA
*
265516 TTTTCAAAATGTTTTTAAAAACTATATAATATATATATATTCAAAAATG-TTTTGAAAACTATAT
1 TTTTCAAAATG-TTTTAAAAACTATATAATATATATATATTCAAAAATGCTTTTAAAAACTATAT
265580 ATTATATTAA
65 ATTATA-TAA
* * * * * * *
265590 TTTTCAAAATGTCTTAAGAACTATATAATATATAAATGTTTTCAAACATGCTTTTCAAAATTATA
1 TTTTCAAAATGTTTTAAAAACTATATAATATAT--ATATATTCAAAAATGCTTTTAAAAACTATA
265655 TATTATATATA
64 TATTATATA-A
* * * *
265666 TTTTAAAAATGTTTT-CAAACTATATACTGTATATATAT
1 TTTTCAAAATGTTTTAAAAACTATATAATATATATATAT
265704 ATATGTAGAA
Statistics
Matches: 224, Mismatches: 19, Indels: 29
0.82 0.07 0.11
Matches are distributed among these distances:
65 9 0.04
66 7 0.03
67 12 0.05
68 4 0.02
70 23 0.10
71 12 0.05
72 27 0.12
73 25 0.11
74 45 0.20
75 27 0.12
76 33 0.15
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.45
Consensus pattern (73 bp):
TTTTCAAAATGTTTTAAAAACTATATAATATATATATATTCAAAAATGCTTTTAAAAACTATATA
TTATATAA
Found at i:266015 original size:3 final size:3
Alignment explanation
Indices: 266009--266033 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
265999 AATGATGATG
266009 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
266034 ATATTTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:270799 original size:28 final size:28
Alignment explanation
Indices: 270762--270818 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
270752 GTCTCTGTTT
* * *
270762 ATATTTTGTCATCGAGTCAATGCTTGAA
1 ATATTATGTCATCAAATCAATGCTTGAA
* *
270790 ATATTATGTCGTCAAATCAATGTTTGAA
1 ATATTATGTCATCAAATCAATGCTTGAA
270818 A
1 A
270819 ACTCAAACGG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (28 bp):
ATATTATGTCATCAAATCAATGCTTGAA
Found at i:271678 original size:2 final size:2
Alignment explanation
Indices: 271671--271718 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
271661 TGTAAAACTA
271671 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
271713 AT AT AT
1 AT AT AT
271719 CGCAACCGTC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:273271 original size:13 final size:13
Alignment explanation
Indices: 273253--273281 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
273243 CTAAAAAAGA
273253 AAAGAAACAAAAT
1 AAAGAAACAAAAT
273266 AAAGAAACAAAAT
1 AAAGAAACAAAAT
273279 AAA
1 AAA
273282 TAAATAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.79, C:0.07, G:0.07, T:0.07
Consensus pattern (13 bp):
AAAGAAACAAAAT
Found at i:273290 original size:13 final size:13
Alignment explanation
Indices: 273261--273313 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
273251 GAAAAGAAAC
* *
273261 AAAATAAAGAAAC
1 AAAATAAATAAAT
273274 AAAATAAATAAAT
1 AAAATAAATAAAT
* *
273287 AAAAGAAACAAAT
1 AAAATAAATAAAT
273300 ATAATATAAATAAA
1 A-AA-ATAAATAAA
273314 ACTATATAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
13 23 0.72
14 2 0.06
15 7 0.22
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.17
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:273423 original size:36 final size:36
Alignment explanation
Indices: 273383--273747 Score: 323
Period size: 36 Copynumber: 10.2 Consensus size: 36
273373 AAAAAGTTAT
*
273383 AAAACTATATATTATATATATTTCAAAAATATTTTC
1 AAAACTATATAATATATATATTTCAAAAATATTTTC
273419 AAAAC--TAT-ATAT-TATA--T-----ATATTTTC
1 AAAACTATATAATATATATATTTCAAAAATATTTTC
* *
273444 AAAACTATATAATATATATT-TTCAAAAATTGTTTTC
1 AAAACTATATAATATATATATTTCAAAAA-TATTTTC
*
273480 AAAACTATATAATATATAT-TTTTAAAAAT-TGTTTC
1 AAAACTATATAATATATATATTTCAAAAATAT-TTTC
*
273515 AAAACTATATAATATATATATCTTCAAAAATTGTTTTC
1 AAAACTATATAATATATATAT-TTCAAAAA-TATTTTC
273553 AAAACTATATAATATATATA-TTCAAAAATCATTTTC
1 AAAACTATATAATATATATATTTCAAAAAT-ATTTTC
*
273589 AAAACTATATAATATATAT-TTTCAAAAACCATTTTC
1 AAAACTATATAATATATATATTTCAAAAA-TATTTTC
* *
273625 AAAACTATATAATATATAT-TTTCAAAAACCAATTTTTAAA
1 AAAACTATATAATATATATATTTCAAAAA--TA-TTTT--C
* * * * * * * *
273665 AAAAGTATATATTATATGTTTTTTAAACCATTTTTTA
1 AAAACTATATAATATATATATTTCAAA-AATATTTTC
* * *
273702 AAAACTATATATTATATTTTTTTCAAAAATATTTTC
1 AAAACTATATAATATATATATTTCAAAAATATTTTC
273738 AAAAACTATA
1 -AAAACTATA
273748 CTATATTAAT
Statistics
Matches: 280, Mismatches: 22, Indels: 53
0.79 0.06 0.15
Matches are distributed among these distances:
25 13 0.05
27 3 0.01
28 4 0.01
29 3 0.01
30 2 0.01
32 4 0.01
33 3 0.01
34 4 0.01
35 26 0.09
36 118 0.42
37 43 0.15
38 29 0.10
39 5 0.02
40 16 0.06
41 6 0.02
42 1 0.00
ACGTcount: A:0.46, C:0.09, G:0.01, T:0.43
Consensus pattern (36 bp):
AAAACTATATAATATATATATTTCAAAAATATTTTC
Found at i:273427 original size:25 final size:25
Alignment explanation
Indices: 273397--273470 Score: 80
Period size: 25 Copynumber: 3.0 Consensus size: 25
273387 CTATATATTA
273397 TATATATTTCAAAAATATTTTCAAAAC
1 TATATA-TT-AAAAATATTTTCAAAAC
* *
273424 TATATATTATATATATTTTCAAAAC
1 TATATATTAAAAATATTTTCAAAAC
* *
273449 TATATA--ATATATATTTTCAAAA
1 TATATATTAAAAATATTTTCAAAA
273471 ATTGTTTTCA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
23 16 0.36
25 21 0.47
26 2 0.04
27 6 0.13
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (25 bp):
TATATATTAAAAATATTTTCAAAAC
Found at i:273452 original size:23 final size:24
Alignment explanation
Indices: 273411--273470 Score: 95
Period size: 23 Copynumber: 2.5 Consensus size: 24
273401 TATTTCAAAA
*
273411 ATATTTTCAAAACTATATATTATAT
1 ATATTTTCAAAAC-ATATATAATAT
273436 ATATTTTCAAAAC-TATATAATAT
1 ATATTTTCAAAACATATATAATAT
273459 ATATTTTCAAAA
1 ATATTTTCAAAA
273471 ATTGTTTTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
23 21 0.62
25 13 0.38
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (24 bp):
ATATTTTCAAAACATATATAATAT
Found at i:273557 original size:109 final size:107
Alignment explanation
Indices: 273439--273652 Score: 340
Period size: 109 Copynumber: 2.0 Consensus size: 107
273429 ATTATATATA
* ** *
273439 TTTTCAAAACTATATAATATATATTTTCAAAAATTGTTTTCAAAACTATATAATATATATTTTTA
1 TTTTCAAAACTATATAATATATATATTCAAAAATCATTTTCAAAACTATATAATATATATTTTCA
*
273504 AAAA-TTGTTTCAAAACTATATAATATATATATCTTCAAAAATTG
66 AAAACAT-TTTCAAAACTATATAATATATAT-T-TTCAAAAATTG
273548 TTTTCAAAACTATATAATATATATATTCAAAAATCATTTTCAAAACTATATAATATATATTTTCA
1 TTTTCAAAACTATATAATATATATATTCAAAAATCATTTTCAAAACTATATAATATATATTTTCA
273613 AAAACCATTTTCAAAACTATATAATATATATTTTCAAAAA
66 AAAA-CATTTTCAAAACTATATAATATATATTTTCAAAAA
273653 CCAATTTTTA
Statistics
Matches: 98, Mismatches: 5, Indels: 5
0.91 0.05 0.05
Matches are distributed among these distances:
108 8 0.08
109 66 0.67
110 23 0.23
111 1 0.01
ACGTcount: A:0.47, C:0.10, G:0.01, T:0.42
Consensus pattern (107 bp):
TTTTCAAAACTATATAATATATATATTCAAAAATCATTTTCAAAACTATATAATATATATTTTCA
AAAACATTTTCAAAACTATATAATATATATTTTCAAAAATTG
Found at i:274800 original size:186 final size:186
Alignment explanation
Indices: 274486--275238 Score: 994
Period size: 186 Copynumber: 4.0 Consensus size: 186
274476 GAAACTTAAG
* * * ** ** * *
274486 TCAATCCATTTGGGCACGATATCCTTCTTTGTAAAGTTGAAATCGTAAATAACTCTTTCGTTGTG
1 TCAATCCATTTAGGCACGATATCCTTCTTCGTGAAGTTGAAATCGTGGATGGCTCCTTCATTGTG
* * *
274551 AAGTTGAGCATTGAATTGGATGTCCTTCATTGTGAAGTTGAAATCCAATATCGAGTTGTAGTGCT
66 AAGTTGAGCTTTGAATTGGATGTCCTTCATTGTGAAATTGAAATCCAATCTCGAGTTGTAGTGCT
*
274616 TCGCCAAATTGGCTTTGGGTTGGATAAT-CTTTGTTGTGAAGTTGAAATCCAATCAA
131 TCGCCAAATTGGCTTTGGGTTGGAT-ATCCTTCGTTGTGAAGTTGAAATCCAATCAA
*
274672 TCAATCCATTTAGGCATGATATCCTTCTTCGTGAAGTTGAAATCGTGGATGGCTCCTTCATTGTG
1 TCAATCCATTTAGGCACGATATCCTTCTTCGTGAAGTTGAAATCGTGGATGGCTCCTTCATTGTG
* **
274737 AAGTTGATCTTTGAATTGGATGTCCTTTGTTGTGAAATTGAAATCCAATCTCGAGTTGTAGTGCT
66 AAGTTGAGCTTTGAATTGGATGTCCTTCATTGTGAAATTGAAATCCAATCTCGAGTTGTAGTGCT
* *
274802 TCGTCAAATTGGCTTTGGGTTTGATATCCTTCGTTGGACAATCTTCGTTGTGAAGTTGAAATCCA
131 TCGCCAAATTGGCTTTGGGTTGGATA--------T---C---CTTCGTTGTGAAGTTGAAATCCA
274867 ATCAA
182 ATCAA
*
274872 TCAATCCATTTAGGCATGATATCCTTCTTCGTGAAGTTGAAATCGTGGATGGCTCCTTCATTGTG
1 TCAATCCATTTAGGCACGATATCCTTCTTCGTGAAGTTGAAATCGTGGATGGCTCCTTCATTGTG
* **
274937 AAGTTGATCTTTGAATTGGATGTCCTTTGTTGTGAAATTGAAATCCAATCTCGAGTTGTAGTGCT
66 AAGTTGAGCTTTGAATTGGATGTCCTTCATTGTGAAATTGAAATCCAATCTCGAGTTGTAGTGCT
* * *
275002 TCGCCAAATTGGCTTTGGGTTTGATATCCTTCATTGTGAAGTTGAAATCCAATCAG
131 TCGCCAAATTGGCTTTGGGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCAA
* * *
275058 TCAATCCATTTGGGCACAATATCCTTCTT-GTTGAAGTTGAAATCGTGGATGGCTCCTTCGTTGT
1 TCAATCCATTTAGGCACGATATCCTTCTTCG-TGAAGTTGAAATCGTGGATGGCTCCTTCATTGT
* * * *
275122 GAAGTTGAGCTTTGAATTGGATGTCATTCATTGTGACATTAAAATCCAATCTCGAGTTATAGTGC
65 GAAGTTGAGCTTTGAATTGGATGTCCTTCATTGTGAAATTGAAATCCAATCTCGAGTTGTAGTGC
* * * *
275187 TTTGTC---TTGGCTTTGGGTTTGATATCCTTCGTTGTAAAGTTGAAATCCAATC
130 TTCGCCAAATTGGCTTTGGGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATC
275239 TTGTATAAGT
Statistics
Matches: 514, Mismatches: 37, Indels: 35
0.88 0.06 0.06
Matches are distributed among these distances:
183 44 0.09
185 2 0.00
186 283 0.55
189 1 0.00
192 1 0.00
193 1 0.00
200 182 0.35
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (186 bp):
TCAATCCATTTAGGCACGATATCCTTCTTCGTGAAGTTGAAATCGTGGATGGCTCCTTCATTGTG
AAGTTGAGCTTTGAATTGGATGTCCTTCATTGTGAAATTGAAATCCAATCTCGAGTTGTAGTGCT
TCGCCAAATTGGCTTTGGGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCAA
Found at i:274991 original size:200 final size:199
Alignment explanation
Indices: 274634--275220 Score: 893
Period size: 200 Copynumber: 3.0 Consensus size: 199
274624 TTGGCTTTGG
*
274634 GTTGGATAATCTTTGTTGTGAAGTTGAAATCCAATCAATCAATCCATTTAGGCATGATATCCTTC
1 GTTGGACAATC-TTGTTGTGAAGTTGAAATCCAATCAATCAATCCATTTAGGCATGATATCCTTC
274699 TTCGTGAAGTTGAAATCGTGGATGGCTCCTTCATTGTGAAGTTGATCTTTGAATTGGATGTCCTT
65 TTCGTGAAGTTGAAATCGTGGATGGCTCCTTCATTGTGAAGTTGATCTTTGAATTGGATGTCCTT
274764 TGTTGTGAAATTGAAATCCAATCTCGAGTTGTAGTGCTTCGTCAAATTGGCTTTGGGTTTGATAT
130 TGTTGTGAAATTGAAATCCAATCTCGAGTTGTAGTGCTTCGTCAAATTGGCTTTGGGTTTGATAT
274829 CCTTC
195 CCTTC
274834 GTTGGACAATCTTCGTTGTGAAGTTGAAATCCAATCAATCAATCCATTTAGGCATGATATCCTTC
1 GTTGGACAATCTT-GTTGTGAAGTTGAAATCCAATCAATCAATCCATTTAGGCATGATATCCTTC
274899 TTCGTGAAGTTGAAATCGTGGATGGCTCCTTCATTGTGAAGTTGATCTTTGAATTGGATGTCCTT
65 TTCGTGAAGTTGAAATCGTGGATGGCTCCTTCATTGTGAAGTTGATCTTTGAATTGGATGTCCTT
*
274964 TGTTGTGAAATTGAAATCCAATCTCGAGTTGTAGTGCTTCGCCAAATTGGCTTTGGGTTTGATAT
130 TGTTGTGAAATTGAAATCCAATCTCGAGTTGTAGTGCTTCGTCAAATTGGCTTTGGGTTTGATAT
275029 -C--C
195 CCTTC
* * **
275031 -TT---C-A-----TTGTGAAGTTGAAATCCAATCAGTCAATCCATTTGGGCACAATATCCTTCT
1 GTTGGACAATCTTGTTGTGAAGTTGAAATCCAATCAATCAATCCATTTAGGCATGATATCCTTCT
* * *
275086 T-GTTGAAGTTGAAATCGTGGATGGCTCCTTCGTTGTGAAGTTGAGCTTTGAATTGGATGTCATT
66 TCG-TGAAGTTGAAATCGTGGATGGCTCCTTCATTGTGAAGTTGATCTTTGAATTGGATGTCCTT
** * * * *
275150 CATTGTGACATTAAAATCCAATCTCGAGTTATAGTGCTTTGTC---TTGGCTTTGGGTTTGATAT
130 TGTTGTGAAATTGAAATCCAATCTCGAGTTGTAGTGCTTCGTCAAATTGGCTTTGGGTTTGATAT
275212 CCTTC
195 CCTTC
275217 GTTG
1 GTTG
275221 TAAAGTTGAA
Statistics
Matches: 364, Mismatches: 16, Indels: 26
0.90 0.04 0.06
Matches are distributed among these distances:
183 19 0.05
184 1 0.00
185 1 0.00
186 143 0.39
187 2 0.01
192 1 0.00
193 1 0.00
196 2 0.01
197 1 0.00
199 3 0.01
200 190 0.52
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.38
Consensus pattern (199 bp):
GTTGGACAATCTTGTTGTGAAGTTGAAATCCAATCAATCAATCCATTTAGGCATGATATCCTTCT
TCGTGAAGTTGAAATCGTGGATGGCTCCTTCATTGTGAAGTTGATCTTTGAATTGGATGTCCTTT
GTTGTGAAATTGAAATCCAATCTCGAGTTGTAGTGCTTCGTCAAATTGGCTTTGGGTTTGATATC
CTTC
Found at i:276867 original size:99 final size:99
Alignment explanation
Indices: 276628--276907 Score: 411
Period size: 99 Copynumber: 2.8 Consensus size: 99
276618 GCCATTTTCT
* *
276628 GGCTAGCTGAATCTTATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCACA
1 GGCTAGCTGAATCTTATCCATAAAG-CCGGGAGTTTAACCAATTGCTCTAGAGGGACAACTCA-A
276693 -CTTTATTGTATACATATAATATTATAATCACCTTTATCA
64 GCTTTATTG--T--ATATAATATTATAATCACCTTTATCA
* * *
276732 AGCTAGCTAAATCTTATCCATAAAGACGGGGAGTTTAACCAATTGCTCTAGAGGGACAACTCAAG
1 GGCTAGCTGAATCTTATCCATAAAG-CCGGGAGTTTAACCAATTGCTCTAGAGGGACAACTCAAG
*
276797 CTTTATTGTATAT-GTATTATAATCACCTTTATCA
65 CTTTATTGTATATAATATTATAATCACCTTTATCA
*
276831 GGCTAGCTGAATCTTATCCATAAAGCCGGGATGTTTAACCAATTGCTCTAGAGGGACAGCTCAAG
1 GGCTAGCTGAATCTTATCCATAAAGCCGGGA-GTTTAACCAATTGCTCTAGAGGGACAACTCAAG
276896 CTTTATTGTATA
65 CTTTATTGTATA
276908 CATATAATAT
Statistics
Matches: 165, Mismatches: 9, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
98 5 0.03
99 87 0.53
100 4 0.02
102 1 0.01
103 1 0.01
104 67 0.41
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Consensus pattern (99 bp):
GGCTAGCTGAATCTTATCCATAAAGCCGGGAGTTTAACCAATTGCTCTAGAGGGACAACTCAAGC
TTTATTGTATATAATATTATAATCACCTTTATCA
Found at i:280839 original size:21 final size:23
Alignment explanation
Indices: 280809--280861 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 23
280799 ATTTCAAAAC
* *
280809 TATTTCCAAAACCATAT-AT-TA
1 TATTTTCAAAACCATATAATAAA
*
280830 TATTTTCAAAACTATATAATAAA
1 TATTTTCAAAACCATATAATAAA
280853 TATTTTCAA
1 TATTTTCAA
280862 TATTTGTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 15 0.56
22 2 0.07
23 10 0.37
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (23 bp):
TATTTTCAAAACCATATAATAAA
Found at i:280877 original size:36 final size:36
Alignment explanation
Indices: 280832--281009 Score: 220
Period size: 36 Copynumber: 4.9 Consensus size: 36
280822 ATATATTATA
* * * *
280832 TTTTCAAAACTATATAATAAATATTTTCAATATTTG
1 TTTTCAAAACTATATAATATATATTTTCAAAAATCG
*
280868 TTTTCAAAACTATATAATATATATTTTCAAAAATTG
1 TTTTCAAAACTATATAATATATATTTTCAAAAATCG
*
280904 TTTTCAAAACTATTAATATATATATATCTTT-AAAAATCA
1 TTTTCAAAACTA-T-ATA-ATATATAT-TTTCAAAAATCG
*
280943 TTTTCAAAACTATA-ATATATATATATTC--AAATCG
1 TTTTCAAAACTATATA-ATATATATTTTCAAAAATCG
280977 TTTTCAAAACTATATAATATATATTTTCAAAAA
1 TTTTCAAAACTATATAATATATATTTTCAAAAA
281010 CTGATTTTTT
Statistics
Matches: 126, Mismatches: 8, Indels: 16
0.84 0.05 0.11
Matches are distributed among these distances:
34 30 0.24
35 3 0.02
36 58 0.46
37 2 0.02
38 4 0.03
39 26 0.21
40 3 0.02
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.44
Consensus pattern (36 bp):
TTTTCAAAACTATATAATATATATTTTCAAAAATCG
Found at i:281060 original size:37 final size:37
Alignment explanation
Indices: 280837--281066 Score: 117
Period size: 36 Copynumber: 6.2 Consensus size: 37
280827 TTATATTTTC
* **
280837 AAAACTATATAATAAATA-TTTTCAATATTTGTTTTC--
1 AAAACTATATAATATATATTTTTCAA-A-CCGTTTTCTA
**
280873 AAAACTATATAATATATA-TTTTCAAAAATTGTTTTC--
1 AAAACTATATAATATATATTTTTC--AAACCGTTTTCTA
** * *
280909 AAAACTATTAATATATATATATCTTTAAAAATCATTTTC--
1 AAAACTA-T-ATA-ATATATAT-TTTTCAAACCGTTTTCTA
* *
280948 AAAAC--TATAATATATATATATTCAAATCGTTTTC--
1 AAAACTATATAATATATAT-TTTTCAAACCGTTTTCTA
* *
280982 AAAACTATATAATATATA-TTTTCAAAAACTGATTTTTTA
1 AAAACTATATAATATATATTTTTC--AAACCG-TTTTCTA
* *
281021 AAAAGTATATATTATATATTTTTCAAACCGTTTTCTA
1 AAAACTATATAATATATATTTTTCAAACCGTTTTCTA
*
281058 AAAATTATA
1 AAAACTATA
281067 CTATATTAAT
Statistics
Matches: 160, Mismatches: 19, Indels: 29
0.77 0.09 0.14
Matches are distributed among these distances:
34 29 0.18
35 3 0.02
36 53 0.33
37 20 0.12
38 10 0.06
39 37 0.23
40 5 0.03
41 3 0.02
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (37 bp):
AAAACTATATAATATATATTTTTCAAACCGTTTTCTA
Found at i:281123 original size:2 final size:2
Alignment explanation
Indices: 281116--281141 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
281106 GTGTCTACAA
281116 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
281142 TGTTAGGATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:285262 original size:5 final size:5
Alignment explanation
Indices: 285252--285500 Score: 498
Period size: 5 Copynumber: 49.8 Consensus size: 5
285242 TGATATTTGA
285252 AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC
1 AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC
285302 AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC
1 AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC
285352 AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC
1 AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC
285402 AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC
1 AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC
285452 AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACA
1 AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACAC AACA
285501 TAATATAATA
Statistics
Matches: 244, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 244 1.00
ACGTcount: A:0.60, C:0.40, G:0.00, T:0.00
Consensus pattern (5 bp):
AACAC
Found at i:287839 original size:28 final size:28
Alignment explanation
Indices: 287796--287873 Score: 129
Period size: 28 Copynumber: 2.8 Consensus size: 28
287786 TCATTTTGCC
* * *
287796 TCCTTTAATTAGTTTACAAATGTCCTTG
1 TCCTGTAATTAATTTACAAATGTCCATG
287824 TCCTGTAATTAATTTACAAATGTCCATG
1 TCCTGTAATTAATTTACAAATGTCCATG
287852 TCCTGTAATTAATTTACAAATG
1 TCCTGTAATTAATTTACAAATG
287874 ATTCAGCAGC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (28 bp):
TCCTGTAATTAATTTACAAATGTCCATG
Found at i:291857 original size:15 final size:15
Alignment explanation
Indices: 291837--291873 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
291827 TGAGACATTA
*
291837 CCCGCCCCGCATCCG
1 CCCGCCCCACATCCG
291852 CCCGCCCCACATCCG
1 CCCGCCCCACATCCG
291867 CCCGCCC
1 CCCGCCC
291874 AGCTAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.08, C:0.70, G:0.16, T:0.05
Consensus pattern (15 bp):
CCCGCCCCACATCCG
Found at i:295015 original size:20 final size:20
Alignment explanation
Indices: 294990--295043 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
294980 TTTGGTTTAC
294990 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
*
295010 GGAATGTAAGATTACCGGTG
1 GGAATGTAAGATTACCAGTG
*
295030 AGAATGTAAGATTA
1 GGAATGTAAGATTA
295044 TCAGGGAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.37, C:0.07, G:0.30, T:0.26
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:298839 original size:2 final size:2
Alignment explanation
Indices: 298827--298895 Score: 131
Period size: 2 Copynumber: 35.0 Consensus size: 2
298817 ATACAATACA
298827 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
298868 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
298896 GTCTTATCAA
Statistics
Matches: 66, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 65 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:299135 original size:32 final size:32
Alignment explanation
Indices: 299099--299168 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
299089 ATTTTGATCG
*
299099 AATTTAAGAG-TAAAATTAATATTTTTATTTAA
1 AATTTAAGAGCT-AAATTAATATTTTTATATAA
*
299131 AATTT-AGGGCTAAATTAATATTTTTATATAA
1 AATTTAAGAGCTAAATTAATATTTTTATATAA
*
299162 AGTTTAA
1 AATTTAA
299169 AATTAAACTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 26 0.79
32 7 0.21
ACGTcount: A:0.44, C:0.01, G:0.09, T:0.46
Consensus pattern (32 bp):
AATTTAAGAGCTAAATTAATATTTTTATATAA
Found at i:301240 original size:25 final size:25
Alignment explanation
Indices: 301204--301264 Score: 88
Period size: 25 Copynumber: 2.4 Consensus size: 25
301194 TATAGGCTTT
301204 CTTTCTTGCAAGCAAAATTACTAGA
1 CTTTCTTGCAAGCAAAATTACTAGA
* *
301229 -TATTCTTGCAAGCAAAGTTACTCGA
1 CT-TTCTTGCAAGCAAAATTACTAGA
301254 CTTTCTTGCAA
1 CTTTCTTGCAA
301265 ATAGAGTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 1 0.03
25 30 0.94
26 1 0.03
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.34
Consensus pattern (25 bp):
CTTTCTTGCAAGCAAAATTACTAGA
Found at i:305508 original size:14 final size:15
Alignment explanation
Indices: 305476--305509 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
305466 AACAATAATA
305476 AAAATGTTATGTCAT
1 AAAATGTTATGTCAT
*
305491 AAAATGTTAT-TGAT
1 AAAATGTTATGTCAT
305505 AAAAT
1 AAAAT
305510 AAACTAGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (15 bp):
AAAATGTTATGTCAT
Found at i:307670 original size:17 final size:17
Alignment explanation
Indices: 307644--307682 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
307634 TAAACTTAAT
307644 TAAAAAAAT-AAATAAA
1 TAAAAAAATAAAATAAA
307660 TAAAAAGAATAAAATAAA
1 TAAAAA-AATAAAATAAA
307678 -AAAAA
1 TAAAAA
307683 TAAGGACCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.29
17 8 0.38
18 7 0.33
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (17 bp):
TAAAAAAATAAAATAAA
Found at i:307674 original size:14 final size:14
Alignment explanation
Indices: 307647--307685 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
307637 ACTTAATTAA
307647 AAAAATAAAT-AAAT
1 AAAAA-AAATAAAAT
*
307661 AAAAAGAATAAAAT
1 AAAAAAAATAAAAT
307675 AAAAAAAATAA
1 AAAAAAAATAA
307686 GGACCTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 3 0.14
14 19 0.86
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (14 bp):
AAAAAAAATAAAAT
Found at i:315768 original size:20 final size:21
Alignment explanation
Indices: 315734--315773 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
315724 TTCTTTCCTA
* *
315734 TTTTATTATTTTCAATTAAAT
1 TTTTATTATTATCAAATAAAT
315755 TTTTATT-TTATCAAATAAA
1 TTTTATTATTATCAAATAAA
315774 AATTAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTATTATTATCAAATAAAT
Found at i:319370 original size:28 final size:30
Alignment explanation
Indices: 319330--319397 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
319320 TTAACGGTGG
*
319330 GATACTCAAATGAA-AAAA-TGAA-AGTTTA
1 GATACTAAAATGAACAAAACT-AATAGTTTA
319358 GATACTAAAATGAACCAAAACTAATAGTTTA
1 GATACTAAAATGAA-CAAAACTAATAGTTTA
*
319389 GGTACTAAA
1 GATACTAAA
319398 TGCATAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 13 0.38
30 6 0.18
31 15 0.44
ACGTcount: A:0.51, C:0.10, G:0.13, T:0.25
Consensus pattern (30 bp):
GATACTAAAATGAACAAAACTAATAGTTTA
Found at i:319629 original size:2 final size:2
Alignment explanation
Indices: 319622--319648 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
319612 GTATCAGTTC
319622 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
319649 ATTAAGTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:319894 original size:29 final size:29
Alignment explanation
Indices: 319862--319997 Score: 100
Period size: 29 Copynumber: 4.7 Consensus size: 29
319852 GGGGAAGTTA
*
319862 TTAGAATGTTCAAAAGTTTGGGGACTG-AT
1 TTAGAATGTTCAAAAGTTTGAGGA-TGAAT
* * *
319891 TTAGAATGAGGGTC-ATAGTTTGGGGATGAAT
1 TTAGAAT---GTTCAAAAGTTTGAGGATGAAT
* * *
319922 TTGGAATTTTCAAAAGTTTAAGGA-GAAGT
1 TTAGAATGTTCAAAAGTTTGAGGATGAA-T
* * *
319951 TTAGAATG-ACAATAGTTTGAGGATTAAT
1 TTAGAATGTTCAAAAGTTTGAGGATGAAT
*
319979 TTAGAATGTTTAAAAGTTT
1 TTAGAATGTTCAAAAGTTT
319998 CAAGACTAAT
Statistics
Matches: 82, Mismatches: 17, Indels: 16
0.71 0.15 0.14
Matches are distributed among these distances:
28 26 0.32
29 32 0.39
30 2 0.02
31 19 0.23
32 3 0.04
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.36
Consensus pattern (29 bp):
TTAGAATGTTCAAAAGTTTGAGGATGAAT
Found at i:321007 original size:32 final size:33
Alignment explanation
Indices: 320971--321042 Score: 96
Period size: 32 Copynumber: 2.2 Consensus size: 33
320961 TACATGTTGT
*
320971 TGATGTGAAACATATCACATA-ATTATTTTCTG
1 TGATGTGAAACATATAACATACATTATTTTCTG
*
321003 TGATGT--ATCATATAACATATCATTATTTTCTG
1 TGATGTGAAACATATAACATA-CATTATTTTCTG
321035 TGATGTGA
1 TGATGTGA
321043 TGTGTTACCA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
30 11 0.32
32 23 0.68
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (33 bp):
TGATGTGAAACATATAACATACATTATTTTCTG
Found at i:321690 original size:75 final size:75
Alignment explanation
Indices: 321591--321736 Score: 220
Period size: 75 Copynumber: 1.9 Consensus size: 75
321581 GACTCAGTGT
* * * * *
321591 CCACCCTGAAATCTGAATTTTCTTCGATTAGTCACCTATTTTATTGATGGTGCCCACCCTAAAAT
1 CCACCCTGAAATCTAAATTCTCTTCGATCAATCACATATTTTATTGATGGTGCCCACCCTAAAAT
321656 TTTATTGTGC
66 TTTATTGTGC
* * *
321666 CCACTCTGAAATTTAAATTCTCTTCGATCAATCACATATTTTATTGATGGTGCCCACCCTGAAAT
1 CCACCCTGAAATCTAAATTCTCTTCGATCAATCACATATTTTATTGATGGTGCCCACCCTAAAAT
321731 TTTATT
66 TTTATT
321737 TATGATCAAC
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
75 63 1.00
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.39
Consensus pattern (75 bp):
CCACCCTGAAATCTAAATTCTCTTCGATCAATCACATATTTTATTGATGGTGCCCACCCTAAAAT
TTTATTGTGC
Found at i:322030 original size:2 final size:2
Alignment explanation
Indices: 322018--322049 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
322008 TCCCCTAGTC
322018 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
322050 TCTTCCTATG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:324061 original size:15 final size:16
Alignment explanation
Indices: 324039--324075 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
324029 TATATTTCAC
324039 ATTATGTG-TTAT-TG
1 ATTATGTGATTATATG
324053 ATCTATGTGATTATATG
1 AT-TATGTGATTATATG
324070 ATTATG
1 ATTATG
324076 AGATACAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 2 0.10
15 6 0.30
16 8 0.40
17 4 0.20
ACGTcount: A:0.27, C:0.03, G:0.19, T:0.51
Consensus pattern (16 bp):
ATTATGTGATTATATG
Found at i:324202 original size:23 final size:23
Alignment explanation
Indices: 324175--324316 Score: 115
Period size: 23 Copynumber: 6.1 Consensus size: 23
324165 GGTTATACGC
* *
324175 GGTCCTTCGGGATAATTCTACGT
1 GGTCCTTCGGGACAATTCTACAT
* * * **
324198 AGTCCTTCAGGATAAATTCTACGC
1 GGTCCTTCGGGA-CAATTCTACAT
* * *
324222 GGTCCTCCGGGATAAATTCTACAC
1 GGTCCTTCGGGA-CAATTCTACAT
* *
324246 AGTCC-TCTGGGACATTTCTACAT
1 GGTCCTTC-GGGACAATTCTACAT
* *
324269 GGTCCTTCGAGACATTTCTACAT
1 GGTCCTTCGGGACAATTCTACAT
*
324292 GGTCCTTCGGGACATTTCTACAT
1 GGTCCTTCGGGACAATTCTACAT
324315 GG
1 GG
324317 CACTTCAGTG
Statistics
Matches: 100, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
23 61 0.61
24 39 0.39
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.32
Consensus pattern (23 bp):
GGTCCTTCGGGACAATTCTACAT
Found at i:324220 original size:24 final size:24
Alignment explanation
Indices: 324170--324251 Score: 103
Period size: 24 Copynumber: 3.5 Consensus size: 24
324160 TAGAAGGTTA
*
324170 TACGCGGTCCTTCGGGAT-AATTC
1 TACGCAGTCCTTCGGGATAAATTC
* *
324193 TACGTAGTCCTTCAGGATAAATTC
1 TACGCAGTCCTTCGGGATAAATTC
* *
324217 TACGCGGTCCTCCGGGATAAATTC
1 TACGCAGTCCTTCGGGATAAATTC
*
324241 TACACAGTCCT
1 TACGCAGTCCT
324252 CTGGGACATT
Statistics
Matches: 49, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 15 0.31
24 34 0.69
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (24 bp):
TACGCAGTCCTTCGGGATAAATTC
Found at i:324322 original size:23 final size:23
Alignment explanation
Indices: 324254--324316 Score: 117
Period size: 23 Copynumber: 2.7 Consensus size: 23
324244 ACAGTCCTCT
324254 GGGACATTTCTACATGGTCCTTC
1 GGGACATTTCTACATGGTCCTTC
*
324277 GAGACATTTCTACATGGTCCTTC
1 GGGACATTTCTACATGGTCCTTC
324300 GGGACATTTCTACATGG
1 GGGACATTTCTACATGG
324317 CACTTCAGTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.33
Consensus pattern (23 bp):
GGGACATTTCTACATGGTCCTTC
Found at i:324360 original size:23 final size:24
Alignment explanation
Indices: 324315--324360 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
324305 ATTTCTACAT
*
324315 GGCACTTCAGTGTATATTCTATGC
1 GGCACTTCAGTGCATATTCTATGC
*
324339 GGCACTTCGGTGCA-ATTCTATG
1 GGCACTTCAGTGCATATTCTATG
324361 TGGTAGTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.35
Consensus pattern (24 bp):
GGCACTTCAGTGCATATTCTATGC
Found at i:330384 original size:23 final size:23
Alignment explanation
Indices: 330357--330454 Score: 108
Period size: 23 Copynumber: 4.2 Consensus size: 23
330347 GAGTCGAGGG
330357 TTCTACGTGGTCCTTCGAGACAA
1 TTCTACGTGGTCCTTCGAGACAA
*
330380 TTCTACGTGGTCTTTC-AGGACAAA
1 TTCTACGTGGTCCTTCGA-GAC-AA
** * *
330404 TTCTACGCAGTCTTTCGAGACAT
1 TTCTACGTGGTCCTTCGAGACAA
* *
330427 TTCTACGTGGTCCTTCGGGACAT
1 TTCTACGTGGTCCTTCGAGACAA
330450 TTCTA
1 TTCTA
330455 TGAGGCACTT
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
22 1 0.02
23 43 0.67
24 19 0.30
25 1 0.02
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.35
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGAGACAA
Found at i:330465 original size:23 final size:23
Alignment explanation
Indices: 330357--330467 Score: 82
Period size: 23 Copynumber: 4.8 Consensus size: 23
330347 GAGTCGAGGG
* * *
330357 TTCTACGTGGTCCTTCGAGACAA
1 TTCTACGAGGTCCTTCGGGACAT
* * * *
330380 TTCTACGTGGTCTTTCAGGACAAA
1 TTCTACGAGGTCCTTCGGGAC-AT
* *
330404 TTCTACGCA-GTCTTTCGAGACAT
1 TTCTACG-AGGTCCTTCGGGACAT
*
330427 TTCTACGTGGTCCTTCGGGACAT
1 TTCTACGAGGTCCTTCGGGACAT
*
330450 TTCTATGAGG-CACTTCGG
1 TTCTACGAGGTC-CTTCGG
330468 TGTATATTCT
Statistics
Matches: 72, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
22 1 0.01
23 52 0.72
24 19 0.26
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.33
Consensus pattern (23 bp):
TTCTACGAGGTCCTTCGGGACAT
Found at i:335420 original size:12 final size:12
Alignment explanation
Indices: 335403--335435 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
335393 ATTTAATGTC
335403 GACCACAACCAT
1 GACCACAACCAT
335415 GACCACAACCAT
1 GACCACAACCAT
*
335427 GGCCACAAC
1 GACCACAAC
335436 AGCGGTGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.39, C:0.42, G:0.12, T:0.06
Consensus pattern (12 bp):
GACCACAACCAT
Found at i:336192 original size:29 final size:30
Alignment explanation
Indices: 336151--336226 Score: 102
Period size: 30 Copynumber: 2.6 Consensus size: 30
336141 AGAAATTTTA
* *
336151 GGGTT-TGTTAACGTACGCC-GCCCCTCTT
1 GGGTTCTGCTAACGTACGCCAGCCCCCCTT
*
336179 GGGTTCTGCTAACGTGCGCCAGCCCCCCTT
1 GGGTTCTGCTAACGTACGCCAGCCCCCCTT
*
336209 GGGTTCTGCTAACATACG
1 GGGTTCTGCTAACGTACG
336227 TCGTTAATGA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
28 5 0.12
29 12 0.29
30 24 0.59
ACGTcount: A:0.13, C:0.33, G:0.26, T:0.28
Consensus pattern (30 bp):
GGGTTCTGCTAACGTACGCCAGCCCCCCTT
Found at i:339229 original size:19 final size:18
Alignment explanation
Indices: 339197--339234 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
339187 TGGGGGGGTT
339197 TGGTAAAATGAAATTAAAA
1 TGGTAAAATGAAA-TAAAA
339216 TGGTAAAAAT-AAATAAAA
1 TGGT-AAAATGAAATAAAA
339234 T
1 T
339235 CAATTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 7 0.39
20 5 0.28
ACGTcount: A:0.61, C:0.00, G:0.13, T:0.26
Consensus pattern (18 bp):
TGGTAAAATGAAATAAAA
Found at i:339864 original size:30 final size:29
Alignment explanation
Indices: 339830--339889 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 29
339820 CTTAGCATTT
339830 TGAAAACAAAGCTTGAAAA-AAAAAGAAAAA
1 TGAAAA-AAA-CTTGAAAAGAAAAAGAAAAA
*
339860 TGAAAAGAACTTGAAAAGTAAAAAGAAAAA
1 TGAAAAAAACTTGAAAAG-AAAAAGAAAAA
339890 GCTTTTATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 8 0.30
29 2 0.07
30 17 0.63
ACGTcount: A:0.68, C:0.05, G:0.15, T:0.12
Consensus pattern (29 bp):
TGAAAAAAACTTGAAAAGAAAAAGAAAAA
Found at i:341709 original size:26 final size:27
Alignment explanation
Indices: 341680--341733 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
341670 CAAAAAAAAA
341680 TTTA-TTTTCTTTAAATATAGGATAAG
1 TTTATTTTTCTTTAAATATAGGATAAG
341706 TTTATTTTTCTTTAAATATAGGATAAG
1 TTTATTTTTCTTTAAATATAGGATAAG
341733 T
1 T
341734 CTCAACCTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 4 0.15
27 23 0.85
ACGTcount: A:0.33, C:0.04, G:0.11, T:0.52
Consensus pattern (27 bp):
TTTATTTTTCTTTAAATATAGGATAAG
Found at i:341971 original size:31 final size:29
Alignment explanation
Indices: 341936--342021 Score: 86
Period size: 29 Copynumber: 2.9 Consensus size: 29
341926 ATTTTTTAAT
**
341936 ATTCTAATTTCATCCTCAAACTAATATACTC
1 ATTCTAATTTCATCCTCAAACT-AT-TAAAC
*
341967 ATTCTAAATTT-GTCCTCAAACCT-TTAAAC
1 ATTCT-AATTTCATCCTCAAA-CTATTAAAC
*
341996 ATTCTAATTTCATCATCAAACTATTA
1 ATTCTAATTTCATCCTCAAACTATTA
342022 CACTTATTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
28 7 0.15
29 18 0.39
30 1 0.02
31 13 0.28
32 7 0.15
ACGTcount: A:0.36, C:0.23, G:0.01, T:0.40
Consensus pattern (29 bp):
ATTCTAATTTCATCCTCAAACTATTAAAC
Found at i:342332 original size:60 final size:60
Alignment explanation
Indices: 342268--342382 Score: 131
Period size: 60 Copynumber: 1.9 Consensus size: 60
342258 AGTTTGGGGA
* * * * * * *
342268 TGAAAATAAAATGTTCAAAAGTTTCATGACTAATTTAGAATGATAGTCATAGTTTAAGGG
1 TGAAAATAAAATATTCAAAAGTTTAAGGACCAATTTAGAACGAGAATCATAGTTTAAGGG
* * * *
342328 TGAAATTAGAATATTTAGAAGTTTAAGGACCAATTTAGAACGAGAATCATAGTTT
1 TGAAAATAAAATATTCAAAAGTTTAAGGACCAATTTAGAACGAGAATCATAGTTT
342383 GAGGACGTAT
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
60 44 1.00
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.33
Consensus pattern (60 bp):
TGAAAATAAAATATTCAAAAGTTTAAGGACCAATTTAGAACGAGAATCATAGTTTAAGGG
Found at i:343494 original size:12 final size:12
Alignment explanation
Indices: 343477--343501 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
343467 TCTCAAAAAG
343477 CCAATTCACCCC
1 CCAATTCACCCC
343489 CCAATTCACCCC
1 CCAATTCACCCC
343501 C
1 C
343502 TCTTGGCAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.60, G:0.00, T:0.16
Consensus pattern (12 bp):
CCAATTCACCCC
Found at i:343793 original size:16 final size:16
Alignment explanation
Indices: 343772--343822 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 16
343762 GGACGAGCAG
343772 CGATGAGCATCACTAA
1 CGATGAGCATCACTAA
*
343788 CGATGAG-----C-AG
1 CGATGAGCATCACTAA
343798 CGATGAGCATCACTAA
1 CGATGAGCATCACTAA
343814 CGATGAGCA
1 CGATGAGCA
343823 GCGATGAGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 12
0.66 0.05 0.29
Matches are distributed among these distances:
10 8 0.30
11 1 0.04
15 1 0.04
16 17 0.63
ACGTcount: A:0.35, C:0.24, G:0.25, T:0.16
Consensus pattern (16 bp):
CGATGAGCATCACTAA
Found at i:343797 original size:26 final size:26
Alignment explanation
Indices: 343766--343843 Score: 156
Period size: 26 Copynumber: 3.0 Consensus size: 26
343756 AATGTTGGAC
343766 GAGCAGCGATGAGCATCACTAACGAT
1 GAGCAGCGATGAGCATCACTAACGAT
343792 GAGCAGCGATGAGCATCACTAACGAT
1 GAGCAGCGATGAGCATCACTAACGAT
343818 GAGCAGCGATGAGCATCACTAACGAT
1 GAGCAGCGATGAGCATCACTAACGAT
343844 AAACACCATT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 52 1.00
ACGTcount: A:0.35, C:0.23, G:0.27, T:0.15
Consensus pattern (26 bp):
GAGCAGCGATGAGCATCACTAACGAT
Found at i:344934 original size:60 final size:60
Alignment explanation
Indices: 344870--344984 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 60
344860 AATTAAGGAT
** * * * *
344870 ATAGTTTGGGGATGAAACTAAAATGTTCAAAAGTTTCATGACTAATTTAGAATGATAGTC
1 ATAGTTTAAGGATGAAACTAAAATATTCAAAAGTTTAAGGACCAATTTAGAATGATAGTC
* * * *
344930 ATAGTTTAAGGATGAAATTAGAATATTTAGAAGTTTAAGGACCAATTTAGAATGA
1 ATAGTTTAAGGATGAAACTAAAATATTCAAAAGTTTAAGGACCAATTTAGAATGA
344985 GAATTATAGT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 45 1.00
ACGTcount: A:0.41, C:0.06, G:0.20, T:0.33
Consensus pattern (60 bp):
ATAGTTTAAGGATGAAACTAAAATATTCAAAAGTTTAAGGACCAATTTAGAATGATAGTC
Found at i:350127 original size:18 final size:17
Alignment explanation
Indices: 350077--350124 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 17
350067 ATTCTTGTTA
*
350077 ATTTAAATACAACTTATG
1 ATTTAAATAC-ACTTTTG
350095 ATTTAAAT--A-TTTTG
1 ATTTAAATACACTTTTG
350109 ATTTAAATACACTTTT
1 ATTTAAATACACTTTT
350125 TGAACTGGCG
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
14 12 0.46
15 1 0.04
16 1 0.04
17 4 0.15
18 8 0.31
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (17 bp):
ATTTAAATACACTTTTG
Found at i:354972 original size:36 final size:38
Alignment explanation
Indices: 354931--355003 Score: 105
Period size: 36 Copynumber: 2.0 Consensus size: 38
354921 TATTTTAACA
* * *
354931 TAAAAAATTATTTTACATAATTTTT-T-TTAAAATATT
1 TAAAAAATTATGTAAAATAATTTTTATGTTAAAATATT
354967 TAAAAAATTATGTAAAATAATTTTTATGTTAAAATAT
1 TAAAAAATTATGTAAAATAATTTTTATGTTAAAATAT
355004 AAGATATTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
36 22 0.69
37 1 0.03
38 9 0.28
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (38 bp):
TAAAAAATTATGTAAAATAATTTTTATGTTAAAATATT
Found at i:355031 original size:2 final size:2
Alignment explanation
Indices: 355024--355104 Score: 155
Period size: 2 Copynumber: 41.0 Consensus size: 2
355014 TATGTTTTTA
355024 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
355066 -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
355105 CAAGAACCAC
Statistics
Matches: 78, Mismatches: 0, Indels: 2
0.98 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 77 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:355537 original size:15 final size:15
Alignment explanation
Indices: 355507--355554 Score: 69
Period size: 15 Copynumber: 3.1 Consensus size: 15
355497 AACAGGTCAT
*
355507 TCGGATTGTATTTGGG
1 TCGGATTAT-TTTGGG
*
355523 TCGGGTTATTTTGGG
1 TCGGATTATTTTGGG
355538 TCGGATTATTTTGGG
1 TCGGATTATTTTGGG
355553 TC
1 TC
355555 TATATTGTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
15 22 0.76
16 7 0.24
ACGTcount: A:0.10, C:0.08, G:0.35, T:0.46
Consensus pattern (15 bp):
TCGGATTATTTTGGG
Found at i:355811 original size:32 final size:32
Alignment explanation
Indices: 355761--355821 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
355751 TAGATTTCGG
* **
355761 ATTAGGTCAACATAAAATCAGTTGATTTTTGA
1 ATTAGGTAAACATAAAATCAAATGATTTTTGA
* *
355793 ATTAGGTAAATATCAAATCAAATGATTTT
1 ATTAGGTAAACATAAAATCAAATGATTTT
355822 CGGTTTTGGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38
Consensus pattern (32 bp):
ATTAGGTAAACATAAAATCAAATGATTTTTGA
Found at i:356019 original size:16 final size:16
Alignment explanation
Indices: 356000--356046 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
355990 TTCGGTTCGA
*
356000 ATTATTTTCGGTTTGG
1 ATTATTTTCAGTTTGG
356016 ATTAATTTT-AGTTTGG
1 ATT-ATTTTCAGTTTGG
* *
356032 GTTACTTTCAGTTTG
1 ATTATTTTCAGTTTG
356047 AGTTAATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 4 0.15
16 17 0.65
17 5 0.19
ACGTcount: A:0.17, C:0.06, G:0.21, T:0.55
Consensus pattern (16 bp):
ATTATTTTCAGTTTGG
Found at i:358143 original size:33 final size:33
Alignment explanation
Indices: 358106--358180 Score: 105
Period size: 33 Copynumber: 2.3 Consensus size: 33
358096 AACACGCTGG
* *
358106 GCATCCGAGGCCATCTGACCGAGCTATGCGAGA
1 GCATCCGAGGCCATCCGAACGAGCTATGCGAGA
* *
358139 GCATCCGAGGTCATCCGAACGAGCTATGCGAGG
1 GCATCCGAGGCCATCCGAACGAGCTATGCGAGA
*
358172 GCAGCCGAG
1 GCATCCGAG
358181 CGAGCTATGC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.24, C:0.29, G:0.33, T:0.13
Consensus pattern (33 bp):
GCATCCGAGGCCATCCGAACGAGCTATGCGAGA
Found at i:358170 original size:23 final size:23
Alignment explanation
Indices: 358144--358195 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
358134 CGAGAGCATC
* *
358144 CGAGGTCATCCGAACGAGCTATG
1 CGAGGGCAGCCGAACGAGCTATG
*
358167 CGAGGGCAGCCGAGCGAGCTATG
1 CGAGGGCAGCCGAACGAGCTATG
358190 CGAGGG
1 CGAGGG
358196 AATCCGAGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.23, C:0.25, G:0.40, T:0.12
Consensus pattern (23 bp):
CGAGGGCAGCCGAACGAGCTATG
Found at i:358202 original size:23 final size:23
Alignment explanation
Indices: 358151--358203 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
358141 ATCCGAGGTC
* *
358151 ATCCGAACGAGCTATGCGAGGGC
1 ATCCGAGCGAGCTATGCGAGGGA
*
358174 AGCCGAGCGAGCTATGCGAGGGA
1 ATCCGAGCGAGCTATGCGAGGGA
358197 ATCCGAG
1 ATCCGAG
358204 GGCAGCCGAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.26, C:0.25, G:0.38, T:0.11
Consensus pattern (23 bp):
ATCCGAGCGAGCTATGCGAGGGA
Found at i:358204 original size:33 final size:33
Alignment explanation
Indices: 358167--358250 Score: 168
Period size: 33 Copynumber: 2.5 Consensus size: 33
358157 ACGAGCTATG
358167 CGAGGGCAGCCGAGCGAGCTATGCGAGGGAATC
1 CGAGGGCAGCCGAGCGAGCTATGCGAGGGAATC
358200 CGAGGGCAGCCGAGCGAGCTATGCGAGGGAATC
1 CGAGGGCAGCCGAGCGAGCTATGCGAGGGAATC
358233 CGAGGGCAGCCGAGCGAG
1 CGAGGGCAGCCGAGCGAG
358251 GGTAGGTCGC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.24, C:0.25, G:0.44, T:0.07
Consensus pattern (33 bp):
CGAGGGCAGCCGAGCGAGCTATGCGAGGGAATC
Found at i:358236 original size:56 final size:56
Alignment explanation
Indices: 358125--358236 Score: 161
Period size: 56 Copynumber: 2.0 Consensus size: 56
358115 GCCATCTGAC
* * * *
358125 CGAGCTATGCGAGAGCATCCGAGGTCATCCGAACGAGCTATGCGAGGGCAGCCGAG
1 CGAGCTATGCGAGAGAATCCGAGGGCAGCCGAACGAGCTATGCGAGGGAAGCCGAG
* * *
358181 CGAGCTATGCGAGGGAATCCGAGGGCAGCCGAGCGAGCTATGCGAGGGAATCCGAG
1 CGAGCTATGCGAGAGAATCCGAGGGCAGCCGAACGAGCTATGCGAGGGAAGCCGAG
358237 GGCAGCCGAG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.25, C:0.25, G:0.38, T:0.12
Consensus pattern (56 bp):
CGAGCTATGCGAGAGAATCCGAGGGCAGCCGAACGAGCTATGCGAGGGAAGCCGAG
Found at i:358287 original size:29 final size:29
Alignment explanation
Indices: 358254--358309 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
358244 GAGCGAGGGT
* *
358254 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCAGAGGGCATGGCGACCTACA
358283 AGGTCGCCCAGAGGGCATGGCGACCTA
1 AGGTCGCCCAGAGGGCATGGCGACCTA
358310 TGTGTTGGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.21, C:0.30, G:0.36, T:0.12
Consensus pattern (29 bp):
AGGTCGCCCAGAGGGCATGGCGACCTACA
Found at i:358413 original size:29 final size:29
Alignment explanation
Indices: 358368--358453 Score: 127
Period size: 29 Copynumber: 3.0 Consensus size: 29
358358 GAGCAAGGGT
*
358368 AGGTCGCCCGGAGTGCATGACGACCTACA
1 AGGTCGCCCGGAATGCATGACGACCTACA
*
358397 AGGTCGCCCGGAATGCATGTCGACCTACA
1 AGGTCGCCCGGAATGCATGACGACCTACA
* * *
358426 AGGTCGCCAGGAAGGCATGGCGACCTAC
1 AGGTCGCCCGGAATGCATGACGACCTAC
358454 GACCAACACT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.24, C:0.30, G:0.31, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGAATGCATGACGACCTACA
Found at i:360748 original size:2 final size:2
Alignment explanation
Indices: 360741--360770 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
360731 AACAACAGTG
360741 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
360771 CAGTGCGGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:370737 original size:15 final size:16
Alignment explanation
Indices: 370717--370747 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
370707 TAGTCCTTTA
370717 TGTATA-TATGTATTT
1 TGTATATTATGTATTT
370732 TGTATATTATGTATTT
1 TGTATATTATGTATTT
370748 ATTAAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.26, C:0.00, G:0.13, T:0.61
Consensus pattern (16 bp):
TGTATATTATGTATTT
Found at i:372553 original size:10 final size:10
Alignment explanation
Indices: 372538--372562 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
372528 TTCATTGTAT
372538 TCTTCTATTC
1 TCTTCTATTC
372548 TCTTCTATTC
1 TCTTCTATTC
372558 TCTTC
1 TCTTC
372563 GTCTTATTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.32, G:0.00, T:0.60
Consensus pattern (10 bp):
TCTTCTATTC
Found at i:374074 original size:136 final size:136
Alignment explanation
Indices: 373830--374622 Score: 836
Period size: 136 Copynumber: 5.8 Consensus size: 136
373820 ACCTTGAAGG
*
373830 CATTTCGAATCAGTGACACCTCGCTTGAGAGATTGACATTTCCAATGGAGAGTTCATAATGAGAA
1 CATTTCGAATCAGTGACACCTCGCTTGAGGGATTGACATTTCCAATGGAGAGTTCATAATGAGAA
* * * * *
373895 GAACTCATCAAACAAAGGAAGAAGAAGTTCAAAATGAGAAGAGCTTGTTCGACCTATCACTCGAT
66 GAACTCATCCAACAGAGGGAGAAAAAGTTCATAATGAGAAGAGCTTGTTCGACCTATCACTCGAT
373960 TCACGA
131 TCACGA
* * * *
373966 CATTTCGAATTAGTGACACCTCGCTTGAGTGATTGATATTTCCAATAGAGAGTTCATAATGAGAA
1 CATTTCGAATCAGTGACACCTCGCTTGAGGGATTGACATTTCCAATGGAGAGTTCATAATGAGAA
*
374031 GAACTCATCCGACAGAGGGAGAAAAAGTTCATAATGAGAAGAGCTTGTTCGACCTATCACTCGAT
66 GAACTCATCCAACAGAGGGAGAAAAAGTTCATAATGAGAAGAGCTTGTTCGACCTATCACTCGAT
*
374096 TCACGG
131 TCACGA
* * * * *
374102 TATTTTGAATCAGTGACGCCTCGCTTGAGCGATTGACATTTCTAATGGAGAGTTCATAATGAGAA
1 CATTTCGAATCAGTGACACCTCGCTTGAGGGATTGACATTTCCAATGGAGAGTTCATAATGAGAA
* * * ** ** *
374167 GAAATCATCCTA-A-A-GGAG--AAAGTTCATAATGAGAAGAACTTGTTCCTTTCAAATTCACCA
66 GAACTCATCCAACAGAGGGAGAAAAAGTTCATAATGAGAAGAGCTTGTT-C-GACCTA-TCA-CT
** *
374227 CAGAAGGAGGTGAACCAA
127 C-----GA--TTCA-CGA
* ** * * *
374245 CATTTCCAGAA-CAGT-TCA--T--AATGA--GA-AGA-ACTCGTCCTAAAGGAGAAAGTTCATA
1 CATTT-C-GAATCAGTGACACCTCGCTTGAGGGATTGACA-T-TTCC-AATGGAG--AGTTCATA
* * *
374300 ATGAGAAGAACTCATCCAAC-GAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGAACTATC
59 ATGAGAAGAACTCATCCAACAGAGGGAGAAAAAGTTCATAATGAGAAGAGCTTGTTCGACCTATC
374364 ACTCGATTCACGA
124 ACTCGATTCACGA
*
374377 CATTTCGAATCAGTGACACCTCGCTTGAGGGATTGACATTACCAATGGAGAGTTCATAATGAGAA
1 CATTTCGAATCAGTGACACCTCGCTTGAGGGATTGACATTTCCAATGGAGAGTTCATAATGAGAA
* * * *
374442 GAACTCATTCGACAGAGGGAGAAAAAGTTCATAATGAGAAGAGTTTGTTCGACCTATTACTCGAT
66 GAACTCATCCAACAGAGGGAGAAAAAGTTCATAATGAGAAGAGCTTGTTCGACCTATCACTCGAT
*
374507 TCACGG
131 TCACGA
* *
374513 CATTTCGAATCAGTGACGCCTCGCTTGAGGGATTGACATTTCTAATGGAGAGTTCATAATGAGAA
1 CATTTCGAATCAGTGACACCTCGCTTGAGGGATTGACATTTCCAATGGAGAGTTCATAATGAGAA
* * *
374578 GAACTCGTCCTA-A-A-GGAG--AAAGTTCATAATGAGAAGAACTTGTTC
66 GAACTCATCCAACAGAGGGAGAAAAAGTTCATAATGAGAAGAGCTTGTTC
374623 ATTTCAAATT
Statistics
Matches: 544, Mismatches: 78, Indels: 75
0.78 0.11 0.11
Matches are distributed among these distances:
130 3 0.01
131 55 0.10
132 10 0.02
133 12 0.02
134 6 0.01
135 33 0.06
136 320 0.59
137 10 0.02
138 10 0.02
139 6 0.01
140 30 0.06
141 5 0.01
142 6 0.01
143 7 0.01
144 28 0.05
145 3 0.01
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (136 bp):
CATTTCGAATCAGTGACACCTCGCTTGAGGGATTGACATTTCCAATGGAGAGTTCATAATGAGAA
GAACTCATCCAACAGAGGGAGAAAAAGTTCATAATGAGAAGAGCTTGTTCGACCTATCACTCGAT
TCACGA
Found at i:374303 original size:35 final size:36
Alignment explanation
Indices: 374252--374347 Score: 124
Period size: 35 Copynumber: 2.6 Consensus size: 36
374242 CAACATTTCC
*
374252 AGAACAGTTCATAATGAGAAGAACTCGTCCTAA-AGG-
1 AGAA-AGTTCATAATGAGAAGAACTCATCC-AACAGGA
374288 AGAAAGTTCATAATGAGAAGAACTCATCCAACGAGGA
1 AGAAAGTTCATAATGAGAAGAACTCATCCAAC-AGGA
374325 AGAAGAAGTTCATAATGAGAAGA
1 AG-A-AAGTTCATAATGAGAAGA
374348 GCTTGTTCGA
Statistics
Matches: 54, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
34 2 0.04
35 24 0.44
36 7 0.13
37 2 0.04
38 1 0.02
39 18 0.33
ACGTcount: A:0.46, C:0.14, G:0.23, T:0.18
Consensus pattern (36 bp):
AGAAAGTTCATAATGAGAAGAACTCATCCAACAGGA
Found at i:374674 original size:411 final size:411
Alignment explanation
Indices: 373880--374758 Score: 1524
Period size: 411 Copynumber: 2.1 Consensus size: 411
373870 TCCAATGGAG
* * *
373880 AGTTCATAATGAGAAGAACTCATCAAACAAAGGAAGAAGAAGTTCAAAATGAGAAGAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCATCCAAC-GAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
* * * * *
373945 GACCTATCACTCGATTCACGACATTTCGAATTAGTGACACCTCGCTTGAGTGATTGATATTTCCA
65 GAACTATCACTCGATTCACGACATTTCGAATCAGTGACACCTCGCTTGAGGGATTGACATTACCA
374010 ATAGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAAAAGTTCATAATGAGAAGAGC
130 ATAGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAAAAGTTCATAATGAGAAGAGC
* *
374075 TTGTTCGACCTATCACTCGATTCACGGTATTTTGAATCAGTGACGCCTCGCTTGAGCGATTGACA
195 TTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACGCCTCGCTTGAGCGATTGACA
374140 TTTCTAATGGAGAGTTCATAATGAGAAGAAATCATCCTAAAGGAGAAAGTTCATAATGAGAAGAA
260 TTTCTAATGGAGAGTTCATAATGAGAAGAAATCATCCTAAAGGAGAAAGTTCATAATGAGAAGAA
* * *
374205 CTTGTTCCTTTCAAATTCACCACAGAAGGAGGTGAACCAACATTTCCAGAACAGTTCATAATGAG
325 CTTGTTCATTTCAAATTCACCACAGAAGGAGGCGAACCAACATTTACAGAACAGTTCATAATGAG
*
374270 AAGAACTCGTCCTAAAGGAGAA
390 AAGAACTCGTCCTAAAAGAGAA
374292 AGTTCATAATGAGAAGAACTCATCCAACGAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCG
1 AGTTCATAATGAGAAGAACTCATCCAACGAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCG
374357 AACTATCACTCGATTCACGACATTTCGAATCAGTGACACCTCGCTTGAGGGATTGACATTACCAA
66 AACTATCACTCGATTCACGACATTTCGAATCAGTGACACCTCGCTTGAGGGATTGACATTACCAA
* * *
374422 TGGAGAGTTCATAATGAGAAGAACTCATTCGACAGAGGGAGAAAAAGTTCATAATGAGAAGAGTT
131 TAGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAAAAGTTCATAATGAGAAGAGCT
* *
374487 TGTTCGACCTATTACTCGATTCACGGCATTTCGAATCAGTGACGCCTCGCTTGAGGGATTGACAT
196 TGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACGCCTCGCTTGAGCGATTGACAT
* *
374552 TTCTAATGGAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATGAGAAGAAC
261 TTCTAATGGAGAGTTCATAATGAGAAGAAATCATCCTAAAGGAGAAAGTTCATAATGAGAAGAAC
* *
374617 TTGTTCATTTCAAATTCACCACAGAAGGAGGCGAACCAATATTTACAGAAGAGTTCATAATGAGA
326 TTGTTCATTTCAAATTCACCACAGAAGGAGGCGAACCAACATTTACAGAACAGTTCATAATGAGA
374682 AGAACTCGTCCTAAAAGAGAA
391 AGAACTCGTCCTAAAAGAGAA
* *
374703 AGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATAAGAAGA
1 AGTTCATAATGAGAAGAACTCATCCAACGAGGAAGAAGAAGTTCATAATGAGAAGA
374759 ACTCATCCAA
Statistics
Matches: 442, Mismatches: 25, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
411 415 0.94
412 27 0.06
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (411 bp):
AGTTCATAATGAGAAGAACTCATCCAACGAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCG
AACTATCACTCGATTCACGACATTTCGAATCAGTGACACCTCGCTTGAGGGATTGACATTACCAA
TAGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAAAAGTTCATAATGAGAAGAGCT
TGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACGCCTCGCTTGAGCGATTGACAT
TTCTAATGGAGAGTTCATAATGAGAAGAAATCATCCTAAAGGAGAAAGTTCATAATGAGAAGAAC
TTGTTCATTTCAAATTCACCACAGAAGGAGGCGAACCAACATTTACAGAACAGTTCATAATGAGA
AGAACTCGTCCTAAAAGAGAA
Done.