Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold85
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: 1350895
ACGTcount: A:0.20, C:0.11, G:0.11, T:0.21
Warning! 487514 characters in sequence are not A, C, G, or T
File 5 of 6
Found at i:1077203 original size:9 final size:9
Alignment explanation
Indices: 1077189--1077249 Score: 74
Period size: 9 Copynumber: 7.1 Consensus size: 9
1077179 GGATGATAGG
1077189 AGGAGAGAT
1 AGGAGAGAT
1077198 AGGAGAGAT
1 AGGAGAGAT
*
1077207 AGTAGAGAT
1 AGGAGAGAT
*
1077216 AGGAGGGAT
1 AGGAGAGAT
*
1077225 --GATAGA-
1 AGGAGAGAT
1077231 AGGAGAGAT
1 AGGAGAGAT
1077240 AGGAGAGAT
1 AGGAGAGAT
1077249 A
1 A
1077250 ATAGAGAGAG
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
7 4 0.09
8 5 0.12
9 34 0.79
ACGTcount: A:0.44, C:0.00, G:0.43, T:0.13
Consensus pattern (9 bp):
AGGAGAGAT
Found at i:1077222 original size:42 final size:42
Alignment explanation
Indices: 1077176--1077278 Score: 170
Period size: 42 Copynumber: 2.5 Consensus size: 42
1077166 GAAGAGACAA
* *
1077176 GAGGGATGATAGGAGGAGAGATAGGAGAGATAGTAGAGATAG
1 GAGGGATGATAGGAGGAGAGATAGGAGAGATAATAGAGAGAG
*
1077218 GAGGGATGATAGAAGGAGAGATAGGAGAGATAATAGAGAGAG
1 GAGGGATGATAGGAGGAGAGATAGGAGAGATAATAGAGAGAG
*
1077260 GAGGGATGACAGGAGGAGA
1 GAGGGATGATAGGAGGAGA
1077279 AGAGAAGAAG
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.42, C:0.01, G:0.46, T:0.12
Consensus pattern (42 bp):
GAGGGATGATAGGAGGAGAGATAGGAGAGATAATAGAGAGAG
Found at i:1089143 original size:12 final size:11
Alignment explanation
Indices: 1089121--1089196 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
1089111 AGAGAAAGAA
*
1089121 GAGAGAGGAGG
1 GAGATAGGAGG
1089132 GATGATAGGAGG
1 GA-GATAGGAGG
*
1089144 AGAGACAGGA--
1 -GAGATAGGAGG
*
1089154 GAGATAGTA--
1 GAGATAGGAGG
1089163 GAGATAGGAGG
1 GAGATAGGAGG
1089174 GATGATAGGAGG
1 GA-GATAGGAGG
*
1089186 AGAGACAGGAG
1 -GAGATAGGAG
1089197 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:1089153 original size:24 final size:24
Alignment explanation
Indices: 1089120--1089205 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
1089110 AAGAGAAAGA
*
1089120 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
1089144 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
1089162 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
1089186 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
1089206 AGAGAGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:1089172 original size:42 final size:42
Alignment explanation
Indices: 1089111--1089229 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
1089101 TAGCCCTCAA
* *
1089111 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
1089153 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
1089195 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
1089230 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.43, C:0.03, G:0.46, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:1094830 original size:17 final size:18
Alignment explanation
Indices: 1094799--1094843 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
1094789 CAAATGCTGG
* *
1094799 TTTTTCTTTTTTTTCTT-
1 TTTTTCTATTATTTCTTC
*
1094816 TTTTTGTATTATTTCTTC
1 TTTTTCTATTATTTCTTC
1094834 TTTTTCTATT
1 TTTTTCTATT
1094844 TTTTTGAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.07, C:0.11, G:0.02, T:0.80
Consensus pattern (18 bp):
TTTTTCTATTATTTCTTC
Found at i:1101722 original size:11 final size:9
Alignment explanation
Indices: 1101697--1101728 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
1101687 GGATGATAGG
1101697 AGGAGAGAT
1 AGGAGAGAT
1101706 AGGAGAGAT
1 AGGAGAGAT
*
1101715 AGTAGAGAT
1 AGGAGAGAT
1101724 AGGAG
1 AGGAG
1101729 GGATGATAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.44, T:0.12
Consensus pattern (9 bp):
AGGAGAGAT
Found at i:1101731 original size:42 final size:42
Alignment explanation
Indices: 1101684--1101786 Score: 152
Period size: 42 Copynumber: 2.5 Consensus size: 42
1101674 AGCCCTCAAA
* * *
1101684 GAGGGATGATAGGAGGAGAGATAGGAGAGATAGTAGAGATAG
1 GAGGGATGATAGGAGGAGAGATAGGAGAAATAATAGAGAGAG
*
1101726 GAGGGATGATAGGAGAAGAGATAGGAGAAATAATAGAGAGAG
1 GAGGGATGATAGGAGGAGAGATAGGAGAAATAATAGAGAGAG
* *
1101768 GAGGGATTACAGGAGGAGA
1 GAGGGATGATAGGAGGAGA
1101787 AGAGAAAAAG
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.43, C:0.01, G:0.44, T:0.13
Consensus pattern (42 bp):
GAGGGATGATAGGAGGAGAGATAGGAGAAATAATAGAGAGAG
Found at i:1101761 original size:24 final size:25
Alignment explanation
Indices: 1101718--1101766 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
1101708 GAGAGATAGT
** *
1101718 AGAGATAGGAGGGATGATAG-GAGA
1 AGAGATAGGAGAAATAATAGAGAGA
1101742 AGAGATAGGAGAAATAATAGAGAGA
1 AGAGATAGGAGAAATAATAGAGAGA
1101767 GGAGGGATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.49, C:0.00, G:0.39, T:0.12
Consensus pattern (25 bp):
AGAGATAGGAGAAATAATAGAGAGA
Found at i:1109215 original size:158 final size:157
Alignment explanation
Indices: 1108863--1109477 Score: 450
Period size: 159 Copynumber: 3.9 Consensus size: 157
1108853 GGTTACTAAG
* * * * *
1108863 AGAATCCATG-TTGTTTCATTTGGGGGATGAACTTTGATTCTAAAGAAGATGAA-AGGAAGAAAA
1 AGAATCCATGTTTGTCTCA-TTGAGGGACGAACTTTGATTCTAAGGAA-ATTAATAGGAAGAAAA
* * * ** * * *
1108926 GCTTTTCCTATGAAGCCAAAGC-T---TATCATGTA-CCCAAAG-GGAAGAAAGTGTTTTGATTG
64 ACTTTTCTTGTGAAGATAAAGCATCAATATCATGTATCCTAAAGAGGAA-ACA-TGTTTTTATTG
* ** *
1108985 GCCAATCATGAAAAGAATGGAAATTATT--A
127 CCCAATCACAAAAAGAATGAAAATTATTACA
* * * * * *
1109014 TGATTACCTATG-TTGTCTTATTTGAGGGATGAACTTTGGTTCTAAGGAAATTAATAGGATGAAA
1 AGAAT-CC-ATGTTTGTCTCA-TTGAGGGACGAACTTTGATTCTAAGGAAATTAATAGGAAGAAA
* * *
1109078 AGCTTTTATTGTGAAGGTAAAGCATC-ATATCATGTATCCTAAAGAGGAGAACATGTTTTTATTG
63 AACTTTTCTTGTGAAGATAAAGCATCAATATCATGTATCCTAAAGAGGA-AACATGTTTTTATTG
* *
1109142 CCCAATCACAAAGAAG-ATGGAGATTATTACA
127 CCCAATCACAAA-AAGAATGAAAATTATTACA
*
1109173 AGAATCCAATGTTT-TCTCTATTGAGGGGCGAACTTTGATTCTAAGGAAATTAA-AGGGAAGAAA
1 AGAATCC-ATGTTTGTCTC-ATTGAGGGACGAACTTTGATTCTAAGGAAATTAATA-GGAAGAAA
* * * * * * * *
1109236 ATCTTCTCGTGTAAAAATAAAGCATCAATATCATGTATCCCAAAGAGGCAACTATGCTTTTATTG
63 AACTTTTCTTGTGAAGATAAAGCATCAATATCATGTATCCTAAAGAGGAAAC-ATGTTTTTATTG
* * ***
1109301 CCTAGTCACAAAAAGAATGAAAATTATTTTG
127 CCCAATCACAAAAAGAATGAAAATTATTACA
* * * * * * * *
1109332 AGAATCCATGTTTGTCTCATTTAGGAGACAAACATTGATCCTAGGGAAAATGATTGGAAGAAAAA
1 AGAATCCATGTTTGTCTCATTGAGG-GACGAACTTTGATTCTAAGGAAATTAATAGGAAGAAAAA
** * * * * ** *
1109397 CTTTTCTTGTGAAGCCATAGAATCAAAATCATGTATCCTAATGAGGAAATGTGTTTTGATTGCCC
65 CTTTTCTTGTGAAGATAAAGCATCAATATCATGTATCCTAAAGAGGAAACATGTTTTTATTGCCC
**
1109462 AATCATGAAAAGAATG
130 AATCACAAAAAGAATG
1109478 GAGAATGTTA
Statistics
Matches: 367, Mismatches: 76, Indels: 35
0.77 0.16 0.07
Matches are distributed among these distances:
151 3 0.01
152 6 0.02
153 61 0.17
154 1 0.00
156 9 0.02
157 37 0.10
158 114 0.31
159 136 0.37
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (157 bp):
AGAATCCATGTTTGTCTCATTGAGGGACGAACTTTGATTCTAAGGAAATTAATAGGAAGAAAAAC
TTTTCTTGTGAAGATAAAGCATCAATATCATGTATCCTAAAGAGGAAACATGTTTTTATTGCCCA
ATCACAAAAAGAATGAAAATTATTACA
Found at i:1113488 original size:159 final size:157
Alignment explanation
Indices: 1113017--1113967 Score: 599
Period size: 159 Copynumber: 6.0 Consensus size: 157
1113007 ACGTATCTCA
* * ** * *
1113017 ATTGCCCAATCAGGAAAAGAATGGAGAATATTATGAGAATAGA-TTTTATCTCATTTAAGGGATG
1 ATTGCCCAATCATGAAAAGAATGGAGATTATTATGAGAATCCATTTTTATCTCATTTGAGAGATG
* * * *
1113081 AACTTTGATTCTAAGGAAAATGATTGGAAGAAAAGCCTTTCTTGTGAAACCAAAGCATCAATAAT
66 AACTTTGATTCTAAGGAAAATAAAT-GAAGAAAAGCTTTTCATGTGAAACCAAAGCATCAAT-AT
*
1113146 -GTGTATCCCAATGAGAAGAAA-GTGTTTTG
129 CATGTATCCCAA--AGAAGAAATGTGTTTTG
* * * * ** * *
1113175 ATTGGCTAATAATGAAAAAGAATAGAGATTATTATGACTATCCATCTTTGTCTCATTTGAGAGAT
1 ATTGCCCAATCATG-AAAAGAATGGAGATTATTATGAGAATCCATTTTTATCTCATTTGAGAGAT
* * ** * *
1113240 GAACTTTGATTATGAGG-AAATTGATGGGAAGAAAAGCTGTT-ATTGTGAAGCCAAAGCATCAAT
65 GAACTTTGATTCTAAGGAAAATAAAT--GAAGAAAAGCTTTTCA-TGTGAAACCAAAGCATCAAT
* * *
1113303 ATCATGTATCCCTAAA-ACGTGAATGTGTTTTT
127 ATCATGTATCCC-AAAGAAG-AAATGTGTTTTG
* ** *
1113335 ATTGCCCAATCATGAAAACG-ATGGAGATTACTACAAGAATCCATTTTTTTCTCATTTGAGAGAT
1 ATTGCCCAATCATGAAAA-GAATGGAGATTATTATGAGAATCCATTTTTATCTCATTTGAGAGAT
* * * *
1113399 GAATTTTTATTCTAAGGAAACTAAAATGAAGAAAAGCTTTTCATGTAAAACCAAAGCATCAATAT
65 GAACTTTGATTCTAAGGAAAAT-AAATGAAGAAAAGCTTTTCATGTGAAACCAAAGCATCAATAT
* *
1113464 CATGCATCCCAAAGAGGCAAATGTGTTTTG
129 CATGTATCCCAAAGAAG-AAATGTGTTTTG
** ** * * * * * * *
1113494 ATTATCCAATCACCAAGAGAGTGGAAATTATT-TCGAGAAAT-CATGTTTGTCTCATTTAAGGGA
1 ATTGCCCAATCATGAAAAGAATGGAGATTATTAT-GAG-AATCCATTTTTATCTCATTTGAGAGA
* * ** * * * * ** *
1113557 TGAA-TATTGATTATAAGAAAAATGGTAGGAAGAAAA-ATTTTCTTTTGATGCTAAAGCATCAAT
64 TGAACT-TTGATTCTAAGGAAAAT-AAATGAAGAAAAGCTTTTCATGTGAAACCAAAGCATCAAT
* * * ** **
1113620 ATCATTTATCCTAATGGGGAAACATGTTTTG
127 ATCATGTATCCCAAAGAAGAAATGTGTTTTG
* * * * * * *
1113651 GTTGCCCAATCATAAAAAGAATGGAGAATATTATAAGAATCTATGTTTATCTCATTTGAGGGATG
1 ATTGCCCAATCATGAAAAGAATGGAGATTATTATGAGAATCCATTTTTATCTCATTTGAGAGATG
* * * * * * * *
1113716 AGCTTTGATTCTAAAGAAAAT-GATGGGAGGAAAAACTTTTCTTGTGAAAGCAAAGTATCAATAT
66 AACTTTGATTCTAAGGAAAATAAAT--GAAGAAAAGCTTTTCATGTGAAACCAAAGCATCAATAT
* * ** *
1113780 -AGTGTATCCCAATA-AGGATAACGCATTTTC
129 CA-TGTATCCCAA-AGAAGA-AATGTGTTTTG
* * ** * * * * *
1113810 ATTGCCCAATCATGAAAAGAATAGAGATTATTGTGATTATCCATGTTTGTCTTATTTAAGGGATG
1 ATTGCCCAATCATGAAAAGAATGGAGATTATTATGAGAATCCATTTTTATCTCATTTGAGAGATG
* * *
1113875 AACTTTGATTCTAAATGG-AAAT-GATGGAAAGAAAAGCTTTTC-T-TGCAATA-GAAAGTATCA
66 AACTTTGATTCT-AA-GGAAAATAAAT-G-AAGAAAAGCTTTTCATGTG-AA-ACCAAAGCATCA
* *
1113935 ATGTCATGTATCCCAAAGAACGGAATGTGTTTT
125 ATATCATGTATCCCAAAGAA-GAAATGTGTTTT
1113968 TGCCACCCAA
Statistics
Matches: 612, Mismatches: 147, Indels: 67
0.74 0.18 0.08
Matches are distributed among these distances:
155 1 0.00
156 3 0.00
157 79 0.13
158 89 0.15
159 314 0.51
160 121 0.20
161 5 0.01
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (157 bp):
ATTGCCCAATCATGAAAAGAATGGAGATTATTATGAGAATCCATTTTTATCTCATTTGAGAGATG
AACTTTGATTCTAAGGAAAATAAATGAAGAAAAGCTTTTCATGTGAAACCAAAGCATCAATATCA
TGTATCCCAAAGAAGAAATGTGTTTTG
Found at i:1113821 original size:316 final size:317
Alignment explanation
Indices: 1113017--1113884 Score: 806
Period size: 316 Copynumber: 2.7 Consensus size: 317
1113007 ACGTATCTCA
** * ** *
1113017 ATTGCCCAATCAGGAAAAGAATGGAGAATATTATGAGAATAGATTTTATCTCATTTAAGGGATGA
1 ATTGCCCAATCATAAAAAGAATGGAGAATATTATAAGAATCCATTTTATCTCATTTGAGGGATGA
* *
1113082 ACTTTGATTCTAAGGAAAATGATTGGAAGAAAAGCCTTTCTTGTGAAACCAAAGCATCAATA-AT
66 ACTTTGATTCTAAGGAAAATGATAGGAAGAAAAGCTTTTCTTGTGAAACCAAAGCATCAATATA-
* * * * * * *
1113146 GTGTATCCCAATGAGAAGAAAGTGTTTTGATTGGCTAATAATGAAAAAGAATAGAGATTATTATG
130 GTGTATCCCAATAAGGA-AAAGTGTTTTGATTGCCCAATCATCAAAAAGAATAGAAATTATTATG
** * * * * *
1113211 ACTATCCATCTTTGTCTCATTTGAGAGATGAACTTTGATTATGAGGAAATTGATGGGAAGAAAAG
194 AAAATCCATCTTTGTCTCATTTAAGAGATGAACTTTGATTATAAGAAAAATGATAGGAAGAAAAG
* * ** *
1113276 CTGTTATTGTGAAGCCAAAGCATCAATATCATGTATCCCTAAAACGTGAATGTGTTTTT
259 ATGTTATTGTGAAGCCAAAGCATCAATATCATGTATCCCTAAAACGGGAACATGTTTTG
* * * * * *
1113335 ATTGCCCAATCATGAAAACG-ATGGAGATTACTACAAGAATCCATTTTTTTCTCATTTGAGAGAT
1 ATTGCCCAATCAT-AAAAAGAATGGAGAATATTATAAGAATCCA-TTTTATCTCATTTGAGGGAT
* * * * * * * *
1113399 GAATTTTTATTCTAAGGAAACTAAAATGAAGAAAAGCTTTTCATGTAAAACCAAAGCATCAATAT
64 GAACTTTGATTCTAAGGAAAATGATAGGAAGAAAAGCTTTTCTTGTGAAACCAAAGCATCAATAT
* * ** * * * *
1113464 CA-TGCATCCCAA-AGAGGCAAATGTGTTTTGATTATCCAATCA-CCAAGAGAGTGGAAATTATT
129 -AGTGTATCCCAATA-AGG-AAAAGTGTTTTGATTGCCCAATCATCAAAAAGAATAGAAATTATT
* * *
1113526 -TCGAGAAAT-CATGTTTGTCTCATTTAAGGGATGAA-TATTGATTATAAGAAAAATGGTAGGAA
191 AT-GA-AAATCCATCTTTGTCTCATTTAAGAGATGAACT-TTGATTATAAGAAAAATGATAGGAA
* * * * * * **
1113588 GAAAA-ATTTTCTTTTGATGCTAAAGCATCAATATCATTTAT-CCT-AATGGGGAAACATGTTTT
253 GAAAAGATGTTATTGTGAAGCCAAAGCATCAATATCATGTATCCCTAAAACGGG-AACATGTTTT
1113650 G
317 G
* *
1113651 GTTGCCCAATCATAAAAAGAATGGAGAATATTATAAGAATCTATGTTTATCTCATTTGAGGGATG
1 ATTGCCCAATCATAAAAAGAATGGAGAATATTATAAGAATCCAT-TTTATCTCATTTGAGGGATG
* * * * * * *
1113716 AGCTTTGATTCTAAAGAAAATGATGGGAGGAAAAACTTTTCTTGTGAAAGCAAAGTATCAATATA
65 AACTTTGATTCTAAGGAAAATGATAGGAAGAAAAGCTTTTCTTGTGAAACCAAAGCATCAATATA
* ** * * * *
1113781 GTGTATCCCAATAAGGATAACGCATTTTCATTGCCCAATCAT-GAAAAGAATAGAGATTATTGTG
130 GTGTATCCCAATAAGGA-AAAGTGTTTTGATTGCCCAATCATCAAAAAGAATAGAAATTATTATG
** * * *
1113845 ATTATCCATGTTTGTCTTATTTAAGGGATGAACTTTGATT
194 AAAATCCATCTTTGTCTCATTTAAGAGATGAACTTTGATT
1113885 CTAAATGGAA
Statistics
Matches: 434, Mismatches: 97, Indels: 40
0.76 0.17 0.07
Matches are distributed among these distances:
315 14 0.03
316 185 0.43
317 34 0.08
318 93 0.21
319 106 0.24
320 1 0.00
321 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (317 bp):
ATTGCCCAATCATAAAAAGAATGGAGAATATTATAAGAATCCATTTTATCTCATTTGAGGGATGA
ACTTTGATTCTAAGGAAAATGATAGGAAGAAAAGCTTTTCTTGTGAAACCAAAGCATCAATATAG
TGTATCCCAATAAGGAAAAGTGTTTTGATTGCCCAATCATCAAAAAGAATAGAAATTATTATGAA
AATCCATCTTTGTCTCATTTAAGAGATGAACTTTGATTATAAGAAAAATGATAGGAAGAAAAGAT
GTTATTGTGAAGCCAAAGCATCAATATCATGTATCCCTAAAACGGGAACATGTTTTG
Found at i:1117674 original size:163 final size:163
Alignment explanation
Indices: 1117486--1117812 Score: 636
Period size: 163 Copynumber: 2.0 Consensus size: 163
1117476 CATGCTAGTC
1117486 CCCATTGATTGAGGTTAGCATGCTTAGCTTAGAGAGGTCTTTCAAAAACTAGTTTTGATAGCTTC
1 CCCATTGATTGAGGTTAGCATGCTTAGCTTAGAGAGGTCTTTCAAAAACTAGTTTTGATAGCTTC
* *
1117551 TAAACACATTTTGACAAGGAAAATGTAGAAAATAATCAATGAGATGACAAGTAGAATGTATGAAC
66 TAAACACATTTTGACAAGGAAAATGCAGAAAATAATCAAGGAGATGACAAGTAGAATGTATGAAC
1117616 AGATTAGCTTGATGAATGACATTATGATCATGA
131 AGATTAGCTTGATGAATGACATTATGATCATGA
1117649 CCCATTGATTGAGGTTAGCATGCTTAGCTTAGAGAGGTCTTTCAAAAACTAGTTTTGATAGCTTC
1 CCCATTGATTGAGGTTAGCATGCTTAGCTTAGAGAGGTCTTTCAAAAACTAGTTTTGATAGCTTC
1117714 TAAACACATTTTGACAAGGAAAATGCAGAAAATAATCAAGGAGATGACAAGTAGAATGTATGAAC
66 TAAACACATTTTGACAAGGAAAATGCAGAAAATAATCAAGGAGATGACAAGTAGAATGTATGAAC
1117779 AGATTAGCTTGATGAATGACATTATGATCATGA
131 AGATTAGCTTGATGAATGACATTATGATCATGA
1117812 C
1 C
1117813 AAGGAAAATG
Statistics
Matches: 162, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
163 162 1.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.29
Consensus pattern (163 bp):
CCCATTGATTGAGGTTAGCATGCTTAGCTTAGAGAGGTCTTTCAAAAACTAGTTTTGATAGCTTC
TAAACACATTTTGACAAGGAAAATGCAGAAAATAATCAAGGAGATGACAAGTAGAATGTATGAAC
AGATTAGCTTGATGAATGACATTATGATCATGA
Found at i:1122936 original size:23 final size:23
Alignment explanation
Indices: 1122906--1122961 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
1122896 TGGGTGGTTA
*
1122906 GTTGCTGCCAGCAGCTGAAAGTG
1 GTTGCTGCCAGCAGCTGAAAATG
1122929 GTTGCTGCCAGCAGCTGAAAATG
1 GTTGCTGCCAGCAGCTGAAAATG
1122952 GTTGCTGCCA
1 GTTGCTGCCA
1122962 TGGGAACCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.21, C:0.23, G:0.32, T:0.23
Consensus pattern (23 bp):
GTTGCTGCCAGCAGCTGAAAATG
Found at i:1130183 original size:9 final size:9
Alignment explanation
Indices: 1130169--1130225 Score: 57
Period size: 9 Copynumber: 6.7 Consensus size: 9
1130159 TCTTCCATCT
1130169 TCTCCTATC
1 TCTCCTATC
*
1130178 TCTCCT-CC
1 TCTCCTATC
*
1130186 TAT-C-ATC
1 TCTCCTATC
*
1130193 CCTCCTATC
1 TCTCCTATC
*
1130202 TCTACTATC
1 TCTCCTATC
1130211 TCTCCTATC
1 TCTCCTATC
1130220 TCTCCT
1 TCTCCT
1130226 CCTACCATCC
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
7 3 0.08
8 4 0.11
9 30 0.81
ACGTcount: A:0.12, C:0.46, G:0.00, T:0.42
Consensus pattern (9 bp):
TCTCCTATC
Found at i:1130201 original size:24 final size:24
Alignment explanation
Indices: 1130170--1130246 Score: 85
Period size: 24 Copynumber: 3.5 Consensus size: 24
1130160 CTTCCATCTT
1130170 CTCCTATCTCTCCTCCTATCATCC
1 CTCCTATCTCTCCTCCTATCATCC
*
1130194 CTCCTA--TCT-CTACTATC-T--
1 CTCCTATCTCTCCTCCTATCATCC
*
1130212 CTCCTATCTCTCCTCCTACCATCC
1 CTCCTATCTCTCCTCCTATCATCC
*
1130236 CTCTTATCTCT
1 CTCCTATCTCT
1130247 TCTTTCTCTT
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
18 6 0.14
20 4 0.09
21 13 0.30
22 4 0.09
24 16 0.37
ACGTcount: A:0.13, C:0.47, G:0.00, T:0.40
Consensus pattern (24 bp):
CTCCTATCTCTCCTCCTATCATCC
Found at i:1130217 original size:42 final size:42
Alignment explanation
Indices: 1130169--1130255 Score: 138
Period size: 42 Copynumber: 2.1 Consensus size: 42
1130159 TCTTCCATCT
*
1130169 TCTCCTATCTCTCCTCCTATCATCCCTCCTATCTCTACTATC
1 TCTCCTATCTCTCCTCCTACCATCCCTCCTATCTCTACTATC
* * *
1130211 TCTCCTATCTCTCCTCCTACCATCCCTCTTATCTCTTCTTTC
1 TCTCCTATCTCTCCTCCTACCATCCCTCCTATCTCTACTATC
1130253 TCT
1 TCT
1130256 TTGAGGGCTA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.11, C:0.45, G:0.00, T:0.44
Consensus pattern (42 bp):
TCTCCTATCTCTCCTCCTACCATCCCTCCTATCTCTACTATC
Found at i:1130229 original size:12 final size:12
Alignment explanation
Indices: 1130170--1130204 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
1130160 CTTCCATCTT
1130170 CTCCTATCTCTC
1 CTCCTATCTCTC
1130182 CTCCTATCATC-C
1 CTCCTATC-TCTC
1130194 CTCCTATCTCT
1 CTCCTATCTCT
1130205 ACTATCTCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.10
12 17 0.81
13 2 0.10
ACGTcount: A:0.11, C:0.49, G:0.00, T:0.40
Consensus pattern (12 bp):
CTCCTATCTCTC
Found at i:1131452 original size:24 final size:23
Alignment explanation
Indices: 1131419--1131510 Score: 79
Period size: 24 Copynumber: 4.2 Consensus size: 23
1131409 AAGAGAGAAA
*
1131419 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATA-GAGG
*
1131443 AGAGACAGGA--GA-GAT--AGT
1 AGAGACAGGAGGGATGATAGAGG
*
1131461 AGAGATAGGAGGGATGATAGAAGG
1 AGAGACAGGAGGGATGATAG-AGG
* *
1131485 AGAGACAGGAGAGATAATAGA-G
1 AGAGACAGGAGGGATGATAGAGG
1131507 AGAG
1 AGAG
1131511 GAGGGATGAC
Statistics
Matches: 55, Mismatches: 7, Indels: 14
0.72 0.09 0.18
Matches are distributed among these distances:
18 11 0.20
20 2 0.04
21 6 0.11
22 7 0.13
23 1 0.02
24 28 0.51
ACGTcount: A:0.43, C:0.02, G:0.45, T:0.10
Consensus pattern (23 bp):
AGAGACAGGAGGGATGATAGAGG
Found at i:1131471 original size:42 final size:42
Alignment explanation
Indices: 1131411--1131528 Score: 186
Period size: 42 Copynumber: 2.9 Consensus size: 42
1131401 AGCCCTCAAA
1131411 GAGAGA-AA-AGAGAGAGGAGGGATGATAGGAGGAGAGACAG
1 GAGAGATAATAGAGAGAGGAGGGATGATAGGAGGAGAGACAG
* * *
1131451 GAGAGATAGTAGAGATAGGAGGGATGATAGAAGGAGAGACAG
1 GAGAGATAATAGAGAGAGGAGGGATGATAGGAGGAGAGACAG
*
1131493 GAGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 GAGAGATAATAGAGAGAGGAGGGATGATAGGAGGAG
1131529 GAGAGAAGAA
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
40 6 0.09
41 1 0.01
42 62 0.90
ACGTcount: A:0.43, C:0.03, G:0.46, T:0.08
Consensus pattern (42 bp):
GAGAGATAATAGAGAGAGGAGGGATGATAGGAGGAGAGACAG
Found at i:1132148 original size:11 final size:12
Alignment explanation
Indices: 1132121--1132153 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1132111 TACGACTCTA
*
1132121 AAGGATGGAAGG
1 AAGGAGGGAAGG
1132133 AAGGAGGGAA-G
1 AAGGAGGGAAGG
1132144 AAGGAGGGAA
1 AAGGAGGGAA
1132154 CTTCAGCGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.45, C:0.00, G:0.52, T:0.03
Consensus pattern (12 bp):
AAGGAGGGAAGG
Found at i:1144215 original size:30 final size:29
Alignment explanation
Indices: 1144160--1144261 Score: 141
Period size: 30 Copynumber: 3.4 Consensus size: 29
1144150 ATCCCCAAGG
* *
1144160 CTTTTAATTCCTTTTTGTGTTTTAGTTGC
1 CTTTTAATTCCTTTTTGTTTTTTAGTTGA
*
1144189 CTTTTAATTCCTTTTTATATTTTTAGTTGA
1 CTTTTAATTCCTTTTTGT-TTTTTAGTTGA
*
1144219 CTTTTAATTCCTTTTTGTGTTTTTAGCTGA
1 CTTTTAATTCCTTTTTGT-TTTTTAGTTGA
*
1144249 CTTTCAATTCCTT
1 CTTTTAATTCCTT
1144262 AGCTTTATTT
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
29 17 0.26
30 48 0.74
ACGTcount: A:0.15, C:0.15, G:0.10, T:0.61
Consensus pattern (29 bp):
CTTTTAATTCCTTTTTGTTTTTTAGTTGA
Found at i:1144959 original size:157 final size:151
Alignment explanation
Indices: 1144708--1145082 Score: 380
Period size: 157 Copynumber: 2.4 Consensus size: 151
1144698 CTCCTTTGTC
** *
1144708 GGATGAACCTTGATTATAATAAAAATGATGGGAAGAAAAGCTTTTCTTGT-AAAGCCAAAGAATT
1 GGATGAACCTTGATTATAAGGAAAATGATGGGAAG-AAAGCTTTTCTTGTGAAA-CCAAAGCA-T
* * * **
1144772 AATTTCATGTATCCCATTGAGGTTTATGTTTCCATTGCCCAATCATGAAAATGACA-AA-GATTT
63 CATATCATGTATCCCAATGAGGAATATGTTTCCATTGCCCAATCATG-AAA-GA-ATAATGA-TT
* * *
1144835 TTAAAATGATTCATGTTTGTC-TCTTTAGAG
124 ATAAAA--ATTCATGTTTATCTTATTTA-AG
* * * *
1144865 GGATGAACCTTAATTCTAAGGAAAGTGATGCGAAGAAAGCTTTTCTTGTGAAACCAAAGCATCAT
1 GGATGAACCTTGATTATAAGGAAAATGATGGGAAGAAAGCTTTTCTTGTGAAACCAAAGCATCAT
* ** * *
1144930 ATCATGTATCCCAATGAGAAGAATGTGTTTTTATTGCCCAATCATGAAAGAATAATGATTATGAG
66 ATCATGTATCCCAATGAG--GAATATGTTTCCATTGCCCAATCATGAAAGAATAATGATTATAAA
*
1144995 AATTCTTGTTTATCTTATTTAAG
129 AATTCATGTTTATCTTATTTAAG
* * * *
1145018 GGATGAACTTTGATTTTAAGGAAAATGAAGAGGAAAAAAGCTTTTCTTGTGAAACCAAAGCATCA
1 GGATGAACCTTGATTATAAGGAAAATGATG-GGAAGAAAGCTTTTCTTGTGAAACCAAAGCATCA
1145083 ACATCTTGTA
Statistics
Matches: 183, Mismatches: 28, Indels: 17
0.80 0.12 0.07
Matches are distributed among these distances:
153 38 0.21
154 38 0.21
155 28 0.15
156 26 0.14
157 53 0.29
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (151 bp):
GGATGAACCTTGATTATAAGGAAAATGATGGGAAGAAAGCTTTTCTTGTGAAACCAAAGCATCAT
ATCATGTATCCCAATGAGGAATATGTTTCCATTGCCCAATCATGAAAGAATAATGATTATAAAAA
TTCATGTTTATCTTATTTAAG
Found at i:1145619 original size:19 final size:19
Alignment explanation
Indices: 1145595--1145631 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1145585 GCCAATCAGA
1145595 AAAAGAATGAAGATTATTG
1 AAAAGAATGAAGATTATTG
*
1145614 AAAAGAATGAATATTATT
1 AAAAGAATGAAGATTATT
1145632 ACGAGAATCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.16, T:0.30
Consensus pattern (19 bp):
AAAAGAATGAAGATTATTG
Found at i:1145731 original size:177 final size:177
Alignment explanation
Indices: 1145435--1145790 Score: 712
Period size: 177 Copynumber: 2.0 Consensus size: 177
1145425 TGCCCAACTA
1145435 TGAAAAGAATGAATATTATTACGAGAATCCATGTTTGTCTCATTTGAGGCATGAACTTTGATTCT
1 TGAAAAGAATGAATATTATTACGAGAATCCATGTTTGTCTCATTTGAGGCATGAACTTTGATTCT
1145500 AAGGAAAATGTTAGAAAAAAAGCTTTTCCTATAAAACCAAAGCATTAATATCATGTATCCCAATG
66 AAGGAAAATGTTAGAAAAAAAGCTTTTCCTATAAAACCAAAGCATTAATATCATGTATCCCAATG
1145565 ACAAAAAAGTGTTTTGACTAGCCAATCAGAAAAAGAATGAAGATTAT
131 ACAAAAAAGTGTTTTGACTAGCCAATCAGAAAAAGAATGAAGATTAT
1145612 TGAAAAGAATGAATATTATTACGAGAATCCATGTTTGTCTCATTTGAGGCATGAACTTTGATTCT
1 TGAAAAGAATGAATATTATTACGAGAATCCATGTTTGTCTCATTTGAGGCATGAACTTTGATTCT
1145677 AAGGAAAATGTTAGAAAAAAAGCTTTTCCTATAAAACCAAAGCATTAATATCATGTATCCCAATG
66 AAGGAAAATGTTAGAAAAAAAGCTTTTCCTATAAAACCAAAGCATTAATATCATGTATCCCAATG
1145742 ACAAAAAAGTGTTTTGACTAGCCAATCAGAAAAAGAATGAAGATTAT
131 ACAAAAAAGTGTTTTGACTAGCCAATCAGAAAAAGAATGAAGATTAT
1145789 TG
1 TG
1145791 TGATTATCCA
Statistics
Matches: 179, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
177 179 1.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (177 bp):
TGAAAAGAATGAATATTATTACGAGAATCCATGTTTGTCTCATTTGAGGCATGAACTTTGATTCT
AAGGAAAATGTTAGAAAAAAAGCTTTTCCTATAAAACCAAAGCATTAATATCATGTATCCCAATG
ACAAAAAAGTGTTTTGACTAGCCAATCAGAAAAAGAATGAAGATTAT
Found at i:1146342 original size:15 final size:14
Alignment explanation
Indices: 1146320--1146356 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
1146310 CAAGAATACA
1146320 AAAAAAAAAGAAAG
1 AAAAAAAAAGAAAG
*
1146334 AATAAAAAAAGAGAG
1 AA-AAAAAAAGAAAG
1146349 AAAAAAAA
1 AAAAAAAA
1146357 CAGCATTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.03
Consensus pattern (14 bp):
AAAAAAAAAGAAAG
Found at i:1147122 original size:9 final size:9
Alignment explanation
Indices: 1147110--1147169 Score: 63
Period size: 9 Copynumber: 7.0 Consensus size: 9
1147100 AAGAGATAGG
1147110 AGGAGAGAT
1 AGGAGAGAT
1147119 AGGAGAGAT
1 AGGAGAGAT
*
1147128 AGTAGAGAT
1 AGGAGAGAT
*
1147137 AGGAGGGAT
1 AGGAGAGAT
**
1147146 --GATTGA-
1 AGGAGAGAT
1147152 AGGAGAGAT
1 AGGAGAGAT
1147161 AGGAGAGAT
1 AGGAGAGAT
1147170 CATAGAGAGA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
7 4 0.10
8 4 0.10
9 33 0.80
ACGTcount: A:0.42, C:0.00, G:0.43, T:0.15
Consensus pattern (9 bp):
AGGAGAGAT
Found at i:1147198 original size:42 final size:42
Alignment explanation
Indices: 1147107--1147198 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
1147097 AAGAAGAGAT
* * ** *
1147107 AGGAGGAGAGATAGGAGAGATAGTAGAGATAGGAGGGATGAT
1 AGGAGGAGAGATAGGAGAGATAGTAGAGAGAAGAGGGACAAC
* *
1147149 TGAAGGAGAGATAGGAGAGATCA-TAGAGAGAAGAGGGACAAC
1 AGGAGGAGAGATAGGAGAGAT-AGTAGAGAGAAGAGGGACAAC
1147191 AGGAGGAG
1 AGGAGGAG
1147199 GAGAGAAGAA
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
42 39 0.98
43 1 0.03
ACGTcount: A:0.42, C:0.03, G:0.43, T:0.11
Consensus pattern (42 bp):
AGGAGGAGAGATAGGAGAGATAGTAGAGAGAAGAGGGACAAC
Found at i:1150635 original size:33 final size:33
Alignment explanation
Indices: 1150592--1150662 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 33
1150582 TTTTTCTCTC
* *
1150592 CTCCTCCTATCATCCCTCATCTCTCTATTATCT
1 CTCCTCCTATCATCCCTCATATCTCTACTATCT
* **
1150625 CTCCTTCTATCATCCCTTTTATCTCTACTATCT
1 CTCCTCCTATCATCCCTCATATCTCTACTATCT
1150658 CTCCT
1 CTCCT
1150663 ATCTCCCTTC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.14, C:0.41, G:0.00, T:0.45
Consensus pattern (33 bp):
CTCCTCCTATCATCCCTCATATCTCTACTATCT
Found at i:1150678 original size:42 final size:42
Alignment explanation
Indices: 1150620--1150701 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
1150610 ATCTCTCTAT
**
1150620 TATCTCTCCTTCTATCATCCCTTTTATCTCTACTATCTCTCC
1 TATCTCTCCTTCTATCATCCCTCCTATCTCTACTATCTCTCC
* *
1150662 TATCTC-CCTTCATATCATCCCTCCTATCTCTTCTTTCTCT
1 TATCTCTCCTTC-TATCATCCCTCCTATCTCTACTATCTCT
1150702 TTGAGGGCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 5 0.14
42 30 0.86
ACGTcount: A:0.13, C:0.39, G:0.00, T:0.48
Consensus pattern (42 bp):
TATCTCTCCTTCTATCATCCCTCCTATCTCTACTATCTCTCC
Found at i:1153732 original size:283 final size:283
Alignment explanation
Indices: 1153225--1153796 Score: 1135
Period size: 283 Copynumber: 2.0 Consensus size: 283
1153215 GCCTCAACAA
1153225 TGCATCTGCTACCACATTCATCTTGCGTTTCTTATGCTTAATAACATAAGGAAACTGTTCTAGGA
1 TGCATCTGCTACCACATTCATCTTGCGTTTCTTATGCTTAATAACATAAGGAAACTGTTCTAGGA
1153290 ACTCTACCCACTTAGCATGCCTTTTATTTAATTTCCCTTGACCCTTAAGATATTTCAATGATTCA
66 ACTCTACCCACTTAGCATGCCTTTTATTTAATTTCCCTTGACCCTTAAGATATTTCAATGATTCA
1153355 TGATCACTATGGATTACAAATTCTCGAGGTAAAAGGTAATGTTGCCAAGTTTGAAGTGCTCTAAT
131 TGATCACTATGGATTACAAATTCTCGAGGTAAAAGGTAATGTTGCCAAGTTTGAAGTGCTCTAAT
1153420 CAAAGCATACAGTTCTTTATCATAAGTAGGATACTTCAAACTAGCCCCATTAAGCTTTTCACTAA
196 CAAAGCATACAGTTCTTTATCATAAGTAGGATACTTCAAACTAGCCCCATTAAGCTTTTCACTAA
1153485 AGTAGGCAATGGGATGCCCTCCT
261 AGTAGGCAATGGGATGCCCTCCT
1153508 TGCATCTGCTACCACATTCATCTTGCGTTTCTTATGCTTAATAACATAAGGAAACTGTTCTAGGA
1 TGCATCTGCTACCACATTCATCTTGCGTTTCTTATGCTTAATAACATAAGGAAACTGTTCTAGGA
*
1153573 ACTCTACCCACTTAGCATGCCTTTTATTTAATTTCCCTTGACCCTTAAGATATTTTAATGATTCA
66 ACTCTACCCACTTAGCATGCCTTTTATTTAATTTCCCTTGACCCTTAAGATATTTCAATGATTCA
1153638 TGATCACTATGGATTACAAATTCTCGAGGTAAAAGGTAATGTTGCCAAGTTTGAAGTGCTCTAAT
131 TGATCACTATGGATTACAAATTCTCGAGGTAAAAGGTAATGTTGCCAAGTTTGAAGTGCTCTAAT
1153703 CAAAGCATACAGTTCTTTATCATAAGTAGGATACTTCAAACTAGCCCCATTAAGCTTTTCACTAA
196 CAAAGCATACAGTTCTTTATCATAAGTAGGATACTTCAAACTAGCCCCATTAAGCTTTTCACTAA
1153768 AGTAGGCAATGGGATGCCCTCCT
261 AGTAGGCAATGGGATGCCCTCCT
1153791 TGCATC
1 TGCATC
1153797 AAAACAGCCC
Statistics
Matches: 288, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
283 288 1.00
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.34
Consensus pattern (283 bp):
TGCATCTGCTACCACATTCATCTTGCGTTTCTTATGCTTAATAACATAAGGAAACTGTTCTAGGA
ACTCTACCCACTTAGCATGCCTTTTATTTAATTTCCCTTGACCCTTAAGATATTTCAATGATTCA
TGATCACTATGGATTACAAATTCTCGAGGTAAAAGGTAATGTTGCCAAGTTTGAAGTGCTCTAAT
CAAAGCATACAGTTCTTTATCATAAGTAGGATACTTCAAACTAGCCCCATTAAGCTTTTCACTAA
AGTAGGCAATGGGATGCCCTCCT
Found at i:1162175 original size:70 final size:70
Alignment explanation
Indices: 1162088--1162236 Score: 235
Period size: 70 Copynumber: 2.1 Consensus size: 70
1162078 AACCCAGAAT
* * *
1162088 GTATTGATATAATAAAAAATGTATCAATACAATTTTTCTAGAATGCAAAATTTTACCTTAACAAG
1 GTATTGATATAATAAAAAATGTACCAATACAATTTTTCTAGAATGCAAAATTTTACATCAACAAG
1162153 GTCTA
66 GTCTA
* * *
1162158 GTATCGATATAATAAAAAATGTACCGATACAATTTTTCTAGAATGCAAAATTTTACATCAACACG
1 GTATTGATATAATAAAAAATGTACCAATACAATTTTTCTAGAATGCAAAATTTTACATCAACAAG
*
1162223 GTTTA
66 GTCTA
1162228 GTATTGATA
1 GTATTGATA
1162237 CATTCACTTA
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (70 bp):
GTATTGATATAATAAAAAATGTACCAATACAATTTTTCTAGAATGCAAAATTTTACATCAACAAG
GTCTA
Found at i:1163470 original size:116 final size:116
Alignment explanation
Indices: 1163142--1163463 Score: 400
Period size: 116 Copynumber: 2.8 Consensus size: 116
1163132 CTTTTAAAAA
* * * * *
1163142 TGACAAGGTGCCAATGTGTTAATTCAAGGCTAGCGACATTGGG-CTTAGGAAAGAAGGTTTGATA
1 TGAC-AGGTGCCAATATGCTAATTCAAGGCTAGTGACATTGGGCCTGA-GAAAGAAGGTTTGACA
* * * *
1163206 AGTGCT-ATGTGCTAGTTCAAGACCAACAACATTGGGCTTGAGAGAAAAGGTT
64 AGTGCTAATGTGCTAATTCAAGGCCAGCAACATTGGGCCTGAGAGAAAAGGTT
* * * *
1163258 TGACAAGTGCCAATATGCTAATTTAAGGCTAGTGACATTGGGCTTGAGAAAGAAGGTTTGACAGG
1 TGACAGGTGCCAATATGCTAATTCAAGGCTAGTGACATTGGGCCTGAGAAAGAAGGTTTGACAAG
* * * *
1163323 TTCTAATGTGTTGATTCAAGGCTAGCAACATTGGGCCT-AG-GAAAGGAGGTT
66 TGCTAATGTGCTAATTCAAGGCCAGCAACATTGGGCCTGAGAGAAA--AGGTT
* * *
1163374 TGATAGGTGCCAATATGCTGATTCAAGGCTAGTGACATTGGGCCTGAGAAAGAAGATTTGACAAG
1 TGACAGGTGCCAATATGCTAATTCAAGGCTAGTGACATTGGGCCTGAGAAAGAAGGTTTGACAAG
1163439 TGCTAATGTGCTAATTCAAGGCCAG
66 TGCTAATGTGCTAATTCAAGGCCAG
1163464 TGACATTAGA
Statistics
Matches: 174, Mismatches: 28, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
114 4 0.02
115 54 0.31
116 116 0.67
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.26
Consensus pattern (116 bp):
TGACAGGTGCCAATATGCTAATTCAAGGCTAGTGACATTGGGCCTGAGAAAGAAGGTTTGACAAG
TGCTAATGTGCTAATTCAAGGCCAGCAACATTGGGCCTGAGAGAAAAGGTT
Found at i:1163492 original size:58 final size:58
Alignment explanation
Indices: 1163142--1163486 Score: 315
Period size: 58 Copynumber: 5.9 Consensus size: 58
1163132 CTTTTAAAAA
*
1163142 TGACAAGGTGCCAATGTGTTAATTCAAGGCTAGCGACATTGGGCTTAG-GAAAGAAGGTT
1 TGACAA-GTGCCAATGTGCTAATTCAAGGCTAGCGACATTGGGCTTAGAGAAAG-AGGTT
* * * * * * *
1163201 TGATAAGTG-CTATGTGCTAGTTCAAGACCAACAACATTGGGCTTGAGAGAAA-AGGTT
1 TGACAAGTGCCAATGTGCTAATTCAAGGCTAGCGACATTGGGCTT-AGAGAAAGAGGTT
* * *
1163258 TGACAAGTGCCAATATGCTAATTTAAGGCTAGTGACATTGGGCTT-GAGAAAGAAGGTT
1 TGACAAGTGCCAATGTGCTAATTCAAGGCTAGCGACATTGGGCTTAGAGAAAG-AGGTT
* * * * * * *
1163316 TGACAGGTTCTAATGTGTTGATTCAAGGCTAGCAACATTGGGCCTAG-GAAAGGAGGTT
1 TGACAAGTGCCAATGTGCTAATTCAAGGCTAGCGACATTGGGCTTAGAGAAA-GAGGTT
* * * * * * *
1163374 TGATAGGTGCCAATATGCTGATTCAAGGCTAGTGACATTGGGCCT-GAGAAAGAAGATT
1 TGACAAGTGCCAATGTGCTAATTCAAGGCTAGCGACATTGGGCTTAGAGAAAG-AGGTT
* * * * *
1163432 TGACAAGTGCTAATGTGCTAATTCAAGGCCAGTGACATTAGACTTAGAAGAAAGA
1 TGACAAGTGCCAATGTGCTAATTCAAGGCTAGCGACATTGGGCTTAG-AGAAAGA
1163487 TTTTGATAGA
Statistics
Matches: 230, Mismatches: 45, Indels: 22
0.77 0.15 0.07
Matches are distributed among these distances:
56 6 0.03
57 43 0.19
58 162 0.70
59 13 0.06
60 6 0.03
ACGTcount: A:0.32, C:0.14, G:0.28, T:0.26
Consensus pattern (58 bp):
TGACAAGTGCCAATGTGCTAATTCAAGGCTAGCGACATTGGGCTTAGAGAAAGAGGTT
Found at i:1163642 original size:136 final size:137
Alignment explanation
Indices: 1163381--1163691 Score: 330
Period size: 137 Copynumber: 2.3 Consensus size: 137
1163371 GTTTGATAGG
* * *
1163381 TGCCAATATGCTGATTCAAGGCTAGTGACATTGGGCCTGAGAAAGAAGATTTGACAAGTGCTAAT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGG-CTGAGAAAGAAGATTTGACAAGTGCTAAT
** **
1163446 GTGCTAATTCAAGGCCAGTGACATTAGACTTAGAAGAAAGATTTTGATAGATGACACATG-ACTA
65 GTGCTAATTCAAGGCCAGCAACATTAGACTTAGAAGAAAGATTGGGATAGATGACACATGAACTA
1163510 GGGC-AGAA
130 GGGCAAG-A
*
1163518 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTGAGAAAGAAGGTTTGACAAGTG-TCAAT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTGAGAAAGAAGATTTGACAAGTGCT-AAT
** * * * *
1163582 GTTTTGATTCAAGGCCAGCAACATTGGGCTTGAGAA-AGAAGATTGGGCA-AG-TG-CGTCATGA
65 GTGCTAATTCAAGGCCAGCAACATTAGACTT-AGAAGA-AAGATTGGG-ATAGATGAC-ACATGA
* *
1163643 ATTAGGGCAAGG
126 ACTAGGGCAAGA
* ** *
1163655 TGCTAATGTGCTGATTTGAGGCCAGCGACATTAGGCT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCT
1163692 TAAAAGGAGA
Statistics
Matches: 147, Mismatches: 20, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
135 2 0.01
136 57 0.39
137 85 0.58
138 3 0.02
ACGTcount: A:0.31, C:0.15, G:0.29, T:0.25
Consensus pattern (137 bp):
TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTGAGAAAGAAGATTTGACAAGTGCTAATG
TGCTAATTCAAGGCCAGCAACATTAGACTTAGAAGAAAGATTGGGATAGATGACACATGAACTAG
GGCAAGA
Found at i:1172291 original size:33 final size:35
Alignment explanation
Indices: 1172254--1172328 Score: 91
Period size: 33 Copynumber: 2.2 Consensus size: 35
1172244 AGAGTGATAC
* *
1172254 GAGAGATAGTAGAGATAAAAGGGATGAT-GGA-AG
1 GAGAGATAATAGAGAGAAAAGGGATGATAGGAGAG
**
1172287 GAGAGATAATAGAGAGATGAGGGATGATAGGAGGAG
1 GAGAGATAATAGAGAGAAAAGGGATGATAGGA-GAG
1172323 GAGAGA
1 GAGAGA
1172329 AAAAGATGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
33 24 0.69
34 3 0.09
36 8 0.23
ACGTcount: A:0.44, C:0.00, G:0.43, T:0.13
Consensus pattern (35 bp):
GAGAGATAATAGAGAGAAAAGGGATGATAGGAGAG
Found at i:1179846 original size:52 final size:52
Alignment explanation
Indices: 1179784--1179930 Score: 267
Period size: 52 Copynumber: 2.8 Consensus size: 52
1179774 AATATGAAAT
*
1179784 TTTGTCTGCATGTATCGATACAAAGATTAGTGTATCGATACATCTGGGCAAA
1 TTTGCCTGCATGTATCGATACAAAGATTAGTGTATCGATACATCTGGGCAAA
1179836 TTTGCCTGCATGTATCGATACAAAGATTAGTGTATCGATACATCTGGGCAAA
1 TTTGCCTGCATGTATCGATACAAAGATTAGTGTATCGATACATCTGGGCAAA
* *
1179888 TTTGCCTGCATATATCGATACAAAGATCAGTGTATCGATACAT
1 TTTGCCTGCATGTATCGATACAAAGATTAGTGTATCGATACAT
1179931 TTTCTTGGCA
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 92 1.00
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (52 bp):
TTTGCCTGCATGTATCGATACAAAGATTAGTGTATCGATACATCTGGGCAAA
Found at i:1179973 original size:19 final size:18
Alignment explanation
Indices: 1179949--1180016 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
1179939 CAGTAGCTAA
1179949 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1179968 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1179983 -T-TGTATCGATACAACAC
1 TTATGTATCGATACAA-AC
1180000 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1180017 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 2 0.05
19 27 0.63
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:1179989 original size:13 final size:13
Alignment explanation
Indices: 1179971--1179995 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1179961 ACAATACTTA
1179971 TGTATCGATACAT
1 TGTATCGATACAT
1179984 TGTATCGATACA
1 TGTATCGATACA
1179996 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1179993 original size:32 final size:32
Alignment explanation
Indices: 1179952--1180014 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1179942 TAGCTAATTA
*
1179952 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAACACTTATGTATCGATACAT
1179984 TGTATCGATACAACACTTATGTATCGATACA
1 TGTATCGATACAACACTTATGTATCGATACA
1180015 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAACACTTATGTATCGATACAT
Found at i:1181324 original size:159 final size:158
Alignment explanation
Indices: 1181107--1182414 Score: 649
Period size: 159 Copynumber: 8.4 Consensus size: 158
1181097 TTAAAGGGTG
* * * *
1181107 AACTTTAATTCTAAAGGAAAATGATGGG-AGAAAAAGCTTTTCTTGTGAAGCTAAAGTATCAATA
1 AACTTTGATTCT-AAGAAAAATGATGGGAAG-AAAAGCTTTTCTTGTGAAACCAAAGTATCAATA
* *
1181171 TCATGTATCCCAATGAGGAGAATGCATTTTGATTGCCCAATCATGAAAAGAATAGAGAAATATTA
64 TCGTGTATCCCAATGAGGAGAATGCATTTTGATTGCCCAATCATGAAAAGAATAGAG-ATTATTA
* *
1181236 AAGAATCCTTATTTATCTCATTTGAGGGAAA
128 AAGAATCCATATTTATCTCATTTGAGGGATA
* * *
1181267 AATTTTGATTCCAAGAAAAATGATGGGAAGAAAAGCTTTTCTTGTGAAAGCAAAGTATCAATATC
1 AACTTTGATTCTAAGAAAAATGATGGGAAGAAAAGCTTTTCTTGTGAAACCAAAGTATCAATATC
* * * * * * * * * * * *
1181332 GTCTA-CCGAAAGAAGAGAACGCATTTTCATTACCTAATCTTGAAAAGAACAAAGATTA-TCAA-
66 GTGTATCCCAATGAGGAGAATGCATTTTGATTGCCCAATCATGAAAAGAATAGAGATTATTAAAG
** * * * *
1181394 AATCCACCTATGTCTCATTTAAAGGATA
131 AATCCATATTTATCTCATTTGAGGGATA
* * * * **
1181422 AACTTTGATTCTAAAGGAAAATAAATGGGAAAAAAAGATTTTCTT-CCAATACCAAAGTATCAAT
1 AACTTTGATTCT-AAGAAAAAT-GATGGGAAGAAAAGCTTTTCTTGTGAA-ACCAAAGTATCAAT
* *** * ** * ** * * *
1181486 ATTGTGTATTATAAAGAGGAGAATGTGTTTTTCATCCCCCAATCATGATAACACTAGAGATTATT
63 ATCGTGTATCCCAATGAGGAGAATG-CATTTTGATTGCCCAATCATGAAAAGAATAGAGATTATT
* * *
1181551 AAAAGAATCCAT-TTCAGTCT-TTTTCATGGG---
127 -AAAGAATCCATATTTA-TCTCATTTGA-GGGATA
* * * *
1181581 AA----G-------G-AAAATGATAGGAAGAAAAACTTTTCTTGTGAATCCAAAGTATCAATTTC
1 AACTTTGATTCTAAGAAAAATGATGGGAAGAAAAGCTTTTCTTGTGAAACCAAAGTATCAATATC
** ** * *
1181634 GTGTATCCCAATGAGGAGAATGTGTTTTTG-TTGCCCAATCATGAAATTAATGGAGACTATTAAA
66 GTGTATCCCAATGAGGAGAATG-CATTTTGATTGCCCAATCATGAAAAGAATAGAGATTATT-AA
* * * ** * * *
1181698 ATAATCCATGTTCATCTTTTTTGAAGGCTG
129 AGAATCCATATTTATCTCATTTGAGGGATA
* * * *
1181728 AACCTTGATTCTAAGGAAAATGATGGGAAGAAAAGCTTTTCTTGTGAAACCAAAGCATCAATATT
1 AACTTTGATTCTAAGAAAAATGATGGGAAGAAAAGCTTTTCTTGTGAAACCAAAGTATCAATATC
* * * * * * * *
1181793 GTGTATCCCAATAAGGAGAA-ACTATTTTGACTGGCCAATCATGAAAAGAGTGGAGATTACT-AT
66 GTGTATCCCAATGAGGAGAATGC-ATTTTGATTGCCCAATCATGAAAAGAATAGAGATTATTAAA
* * * *
1181856 GATTATCCATGTTTATCACATTTGAGGGTTG
130 GA--ATCCATATTTATCTCATTTGAGGGATA
* * * * * * *
1181887 AACTTTGATTCTAACATAATTGATGGGAAGAAAAGCTTTTATTGTGAAACCAAAGCAACAATATT
1 AACTTTGATTCTAAGAAAAATGATGGGAAGAAAAGCTTTTCTTGTGAAACCAAAGTATCAATATC
* * ** * * ** * * * * *
1181952 ATGTATCCCAAAGAACAAAAAGTGTTTTTATTGCCTAATCATGAAAA-AGATATATATTTTTACA
66 GTGTATCCCAATGAGGAGAATGCATTTTGATTGCCCAATCATGAAAAGA-ATAGAGATTATTA-A
* * * *
1182016 AGAATCCATGTTT-TAATCATTTGAAGGACA
129 AGAATCCATATTTAT-CTCATTTGAGGGATA
* * * * *
1182046 AACTTTGATTCTAAGGAAATTAGA-GGGAAGAAAAGCTTTT-TCTATAAAACCAAAGCATCAATA
1 AACTTTGATTCTAAGAAAAAT-GATGGGAAGAAAAGCTTTTCT-TGTGAAACCAAAGTATCAATA
* * * * ** * * * *
1182109 TCTTGTTTCCTAAAGAGGCA-AATGTGTTTTTATTG-----T--TGAAAAAAATGGAAATTATTT
64 TCGTGTATCCCAATGAGG-AGAATGCATTTTGATTGCCCAATCATGAAAAGAATAGAGATTA-TT
* * * * *
1182166 AGAGAATCCATGTTTGTCTCATTTAAGGGATGC
127 AAAGAATCCATATTTATCTCATTTGAGGGAT-A
* ** * * * **
1182199 ACCAAT-ATTCTAAGGAAAATGATGGGAAGAAAAACTTTTCTTG-CAAAGCCAAACCATCAATAT
1 AACTTTGATTCTAAGAAAAATGATGGGAAGAAAAGCTTTTCTTGTGAAA-CCAAAGTATCAATAT
* * *
1182262 CATGTATCCCAATGAGGAGAA--CATGTTTTGATTG-CCAATCATGGAAAATACA-A-AGAATAT
65 CGTGTATCCCAATGAGGAGAATGCA--TTTTGATTGCCCAATCAT-GAAAAGA-ATAGAGATTAT
** *
1182322 TATGGGAAT--ATATGCTTATCTCATTTGAGGGGTA
126 TA-AAGAATCCATAT--TTATCTCATTTGAGGGATA
* * * * * * *
1182356 AACTTTGATAT-AAAGGAAGATTATGAGAGGAAAAGCTTTTCTTGTGAAAGCAAAGTATC
1 AACTTTGAT-TCTAAGAAAAATGATGGGAAGAAAAGCTTTTCTTGTGAAACCAAAGTATC
1182415 TGATGACAAC
Statistics
Matches: 874, Mismatches: 209, Indels: 132
0.72 0.17 0.11
Matches are distributed among these distances:
144 39 0.04
145 65 0.07
146 7 0.01
147 3 0.00
151 7 0.01
152 101 0.12
153 9 0.01
154 1 0.00
155 31 0.04
156 17 0.02
157 49 0.06
158 120 0.14
159 388 0.44
160 16 0.02
161 10 0.01
162 11 0.01
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (158 bp):
AACTTTGATTCTAAGAAAAATGATGGGAAGAAAAGCTTTTCTTGTGAAACCAAAGTATCAATATC
GTGTATCCCAATGAGGAGAATGCATTTTGATTGCCCAATCATGAAAAGAATAGAGATTATTAAAG
AATCCATATTTATCTCATTTGAGGGATA
Found at i:1184813 original size:42 final size:42
Alignment explanation
Indices: 1184764--1184869 Score: 142
Period size: 42 Copynumber: 2.5 Consensus size: 42
1184754 AAGAGAAAGA
*
1184764 AGAGATAGGAAGGATGATA-GAAGGAGAGATAGGAAAGATAGT
1 AGAGATAGGAAGGATGATAGGAA-GAGAGATAGGAAAGATAAT
* *
1184806 AGAGATAGGAAGGATGATAGGAAGAGAGATAGGAGAGGTAAT
1 AGAGATAGGAAGGATGATAGGAAGAGAGATAGGAAAGATAAT
* * *
1184848 AGAGAGAGGAGGGATGACAGGA
1 AGAGATAGGAAGGATGATAGGA
1184870 GAAGGAGAGA
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
42 54 0.95
43 3 0.05
ACGTcount: A:0.45, C:0.01, G:0.42, T:0.12
Consensus pattern (42 bp):
AGAGATAGGAAGGATGATAGGAAGAGAGATAGGAAAGATAAT
Found at i:1184826 original size:12 final size:11
Alignment explanation
Indices: 1184765--1184839 Score: 61
Period size: 12 Copynumber: 6.8 Consensus size: 11
1184755 AGAGAAAGAA
1184765 GAGATAGGAAG
1 GAGATAGGAAG
1184776 GATGATA-GAAGG
1 GA-GATAGGAA-G
1184788 AGAGATAGGAA-
1 -GAGATAGGAAG
*
1184799 -AGATA-GTA-
1 GAGATAGGAAG
1184807 GAGATAGGAAG
1 GAGATAGGAAG
1184818 GATGATAGGAAG
1 GA-GATAGGAAG
1184830 AGAGATAGGA
1 -GAGATAGGA
1184840 GAGGTAATAG
Statistics
Matches: 53, Mismatches: 2, Indels: 17
0.74 0.03 0.24
Matches are distributed among these distances:
8 2 0.04
9 10 0.19
10 2 0.04
11 7 0.13
12 25 0.47
13 7 0.13
ACGTcount: A:0.47, C:0.00, G:0.40, T:0.13
Consensus pattern (11 bp):
GAGATAGGAAG
Found at i:1184838 original size:24 final size:23
Alignment explanation
Indices: 1184764--1184855 Score: 90
Period size: 24 Copynumber: 4.2 Consensus size: 23
1184754 AAGAGAAAGA
1184764 AGAGATAGGAAGGATGATAGAAGG
1 AGAGATAGGAAGGATGATAGAA-G
*
1184788 AGAGATAGGAA--A-GATAG--T
1 AGAGATAGGAAGGATGATAGAAG
1184806 AGAGATAGGAAGGATGATAGGAAG
1 AGAGATAGGAAGGATGATA-GAAG
*
1184830 AGAGATAGGAGAGG-TAATAG-AG
1 AGAGATAGGA-AGGATGATAGAAG
1184852 AGAG
1 AGAG
1184856 GAGGGATGAC
Statistics
Matches: 58, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
18 11 0.19
20 1 0.02
21 9 0.16
22 8 0.14
23 1 0.02
24 25 0.43
25 3 0.05
ACGTcount: A:0.47, C:0.00, G:0.40, T:0.13
Consensus pattern (23 bp):
AGAGATAGGAAGGATGATAGAAG
Found at i:1189533 original size:16 final size:17
Alignment explanation
Indices: 1189512--1189547 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
1189502 TCTTTTTTAA
1189512 TTTC-TTTTTTGTATTC
1 TTTCTTTTTTTGTATTC
1189528 TTTCTTTTTTTTGTATTC
1 TTTC-TTTTTTTGTATTC
1189546 TT
1 TT
1189548 GAAAAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
18 14 0.78
ACGTcount: A:0.06, C:0.11, G:0.06, T:0.78
Consensus pattern (17 bp):
TTTCTTTTTTTGTATTC
Found at i:1190440 original size:36 final size:36
Alignment explanation
Indices: 1190400--1190473 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
1190390 CATATATCCT
1190400 AATGAGGAGAACATGTTTTCATTGCCCAATCATGAA
1 AATGAGGAGAACATGTTTTCATTGCCCAATCATGAA
1190436 AATGAGGAGAACATGTTTTCATTGCCCAATCATGAA
1 AATGAGGAGAACATGTTTTCATTGCCCAATCATGAA
1190472 AA
1 AA
1190474 GAACGAAGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (36 bp):
AATGAGGAGAACATGTTTTCATTGCCCAATCATGAA
Found at i:1191956 original size:21 final size:21
Alignment explanation
Indices: 1191916--1191957 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1191906 TTTTCTTCAG
*
1191916 GAATACAAAAAAGAAGGGAAA
1 GAATACAAAAAAGAAAGGAAA
1191937 GAATACAAAAATA-AAAGGAAA
1 GAATACAAAAA-AGAAAGGAAA
1191958 ACCCAGCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.69, C:0.05, G:0.19, T:0.07
Consensus pattern (21 bp):
GAATACAAAAAAGAAAGGAAA
Found at i:1192749 original size:42 final size:42
Alignment explanation
Indices: 1192692--1192831 Score: 149
Period size: 42 Copynumber: 3.3 Consensus size: 42
1192682 TAGCCCTCAC
* *
1192692 AGAGAAAGAAGAGATAGGAGGGATGATAGGATGAGAGATAAG
1 AGAGATAGAAGAGATAGGAGGGATGATAGGAGGAGAGATAAG
* * * * *
1192734 AGAGATAGTAGAGATAAGAGGGATAATAGGAGGAAAGATAGG
1 AGAGATAGAAGAGATAGGAGGGATGATAGGAGGAGAGATAAG
* * * *
1192776 AGAGATA-ATAGATAAAGGAGGGATGATAAGAGGAAGAGAGAAG
1 AGAGATAGA-AGAGATAGGAGGGATGATAGGAGG-AGAGATAAG
1192819 A-AGATAGAAGAGA
1 AGAGATAGAAGAGA
1192832 AAGAAAATGA
Statistics
Matches: 78, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
42 70 0.90
43 8 0.10
ACGTcount: A:0.50, C:0.00, G:0.38, T:0.12
Consensus pattern (42 bp):
AGAGATAGAAGAGATAGGAGGGATGATAGGAGGAGAGATAAG
Found at i:1196517 original size:13 final size:13
Alignment explanation
Indices: 1196499--1196524 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1196489 CATGGCACAT
1196499 TGTATCGATACAA
1 TGTATCGATACAA
1196512 TGTATCGATACAA
1 TGTATCGATACAA
1196525 GATGAATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1202645 original size:20 final size:20
Alignment explanation
Indices: 1202620--1202686 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
1202610 GATGTATTGA
1202620 TGATACAATGTTCTTTGTAT
1 TGATACAATGTTCTTTGTAT
1202640 TGATACAATGTTCTTTGTAT
1 TGATACAATGTTCTTTGTAT
*
1202660 TGATACAATGTTCTTGGTAT
1 TGATACAATGTTCTTTGTAT
*
1202680 CGATACA
1 TGATACA
1202687 TTATATCAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.45
Consensus pattern (20 bp):
TGATACAATGTTCTTTGTAT
Found at i:1205154 original size:15 final size:15
Alignment explanation
Indices: 1205134--1205171 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
1205124 CCCTTGTATA
1205134 TATCGATACACATTG
1 TATCGATACACATTG
*
1205149 TATCGAT--ATATTG
1 TATCGATACACATTG
1205162 TATCGATACA
1 TATCGATACA
1205172 TTATACTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
13 12 0.60
15 8 0.40
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (15 bp):
TATCGATACACATTG
Found at i:1205163 original size:13 final size:13
Alignment explanation
Indices: 1205145--1205202 Score: 56
Period size: 13 Copynumber: 4.9 Consensus size: 13
1205135 ATCGATACAC
1205145 ATTGTATCGATAT
1 ATTGTATCGATAT
*
1205158 ATTGTATCGATAC
1 ATTGTATCGATAT
*
1205171 A-T-TAT--A-CT
1 ATTGTATCGATAT
1205179 -TTGTATCGATAT
1 ATTGTATCGATAT
1205191 ATTGTATCGATA
1 ATTGTATCGATA
1205203 CATGTTCATT
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
8 1 0.03
9 4 0.11
11 4 0.11
12 2 0.06
13 24 0.69
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.45
Consensus pattern (13 bp):
ATTGTATCGATAT
Found at i:1205184 original size:33 final size:32
Alignment explanation
Indices: 1205144--1205221 Score: 122
Period size: 33 Copynumber: 2.4 Consensus size: 32
1205134 TATCGATACA
1205144 CATTGTATCGATATATTGTATCGATACAT-TAT
1 CATTGTATCGATATATTGTATCGATACATGT-T
*
1205176 ACTTTGTATCGATATATTGTATCGATACATGTT
1 -CATTGTATCGATATATTGTATCGATACATGTT
1205209 CATTGTATCGATA
1 CATTGTATCGATA
1205222 CATGCATAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
32 12 0.29
33 29 0.69
34 1 0.02
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.44
Consensus pattern (32 bp):
CATTGTATCGATATATTGTATCGATACATGTT
Found at i:1205215 original size:19 final size:20
Alignment explanation
Indices: 1205191--1205245 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
1205181 GTATCGATAT
* *
1205191 ATTGTATCGATACATG-TTC
1 ATTGTATCGATACATGCATA
1205210 ATTGTATCGATACATGCATA
1 ATTGTATCGATACATGCATA
*
1205230 ATTGTATCAATACATG
1 ATTGTATCGATACATG
1205246 AAACTGGCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (20 bp):
ATTGTATCGATACATGCATA
Found at i:1205235 original size:20 final size:19
Alignment explanation
Indices: 1205186--1205246 Score: 77
Period size: 20 Copynumber: 3.1 Consensus size: 19
1205176 ACTTTGTATC
1205186 GATATATTGTATCGATACAT
1 GATA-ATTGTATCGATACAT
* *
1205206 GTTCATTGTATCGATACAT
1 GATAATTGTATCGATACAT
*
1205225 GCATAATTGTATCAATACAT
1 G-ATAATTGTATCGATACAT
1205245 GA
1 GA
1205247 AACTGGCAGT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 17 0.49
20 18 0.51
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (19 bp):
GATAATTGTATCGATACAT
Found at i:1208260 original size:96 final size:96
Alignment explanation
Indices: 1208141--1208380 Score: 345
Period size: 96 Copynumber: 2.5 Consensus size: 96
1208131 ATTGAAAAAT
* * * *
1208141 GGGGTTGGAGTATCCCCTTGGAGGAATGGGGTTGGAGTGTCCTCGATGATGACAATTTAAGTGAG
1 GGGG-TGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTATCCCCGATGATGACAATTTAAGTGAA
1208206 AATAAGATTTAAACTTTGATGCGTTTAAAAGC
65 AATAAGATTTAAACTTTGATGCGTTTAAAAGC
* *
1208238 GGGGTGGAGTATCCCCTCGGAGGAATGGGGTTGAAGTATCCCCGATGGTGACAATTTAAGTGAAA
1 GGGGTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTATCCCCGATGATGACAATTTAAGTGAAA
*
1208303 ATAAGATTTAAACTTTGATGTGTTTAAAAGC
66 ATAAGATTTAAACTTTGATGCGTTTAAAAGC
* ** * * *
1208334 GAGGTTACAGTATCCCCTCGAAGAAATAGGGTTGGAGTATCCCCGAT
1 G-GGGTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTATCCCCGAT
1208381 AAATAAAATT
Statistics
Matches: 128, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
96 86 0.67
97 42 0.33
ACGTcount: A:0.29, C:0.14, G:0.30, T:0.28
Consensus pattern (96 bp):
GGGGTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTATCCCCGATGATGACAATTTAAGTGAAA
ATAAGATTTAAACTTTGATGCGTTTAAAAGC
Found at i:1210085 original size:11 final size:11
Alignment explanation
Indices: 1210052--1210107 Score: 55
Period size: 10 Copynumber: 5.3 Consensus size: 11
1210042 TTTCTACCTC
*
1210052 TTTCTTTCT-A
1 TTTCTTTCTCT
1210062 TTTCTTCTCTCT
1 TTTCTT-TCTCT
1210074 TTTCTTTCTCT
1 TTTCTTTCTCT
*
1210085 TTT-TTTTTCT
1 TTTCTTTCTCT
*
1210095 TTT-TTTTTCT
1 TTTCTTTCTCT
1210105 TTT
1 TTT
1210108 TTTAGTTGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
10 25 0.60
11 11 0.26
12 6 0.14
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTCTTTCTCT
Found at i:1210097 original size:10 final size:10
Alignment explanation
Indices: 1210071--1210110 Score: 62
Period size: 10 Copynumber: 3.9 Consensus size: 10
1210061 ATTTCTTCTC
*
1210071 TCTTTTCTTTC
1 TCTTTT-TTTT
1210082 TCTTTTTTTT
1 TCTTTTTTTT
1210092 TCTTTTTTTT
1 TCTTTTTTTT
1210102 TCTTTTTTT
1 TCTTTTTTT
1210111 AGTTGAAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
10 22 0.79
11 6 0.21
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (10 bp):
TCTTTTTTTT
Found at i:1210108 original size:16 final size:16
Alignment explanation
Indices: 1210056--1210108 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
1210046 TACCTCTTTC
*
1210056 TTTCTATTTCTTCTCTCT
1 TTTCTTTTTCTT-TCT-T
* *
1210074 TTTCTTTCTCTTTTTT
1 TTTCTTTTTCTTTCTT
*
1210090 TTTCTTTTTTTTTCTT
1 TTTCTTTTTCTTTCTT
1210106 TTT
1 TTT
1210109 TTAGTTGAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
16 17 0.59
17 2 0.07
18 10 0.34
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTCTTTTTCTTTCTT
Found at i:1211663 original size:28 final size:28
Alignment explanation
Indices: 1211604--1211914 Score: 315
Period size: 28 Copynumber: 10.9 Consensus size: 28
1211594 CACCAACTTG
* *
1211604 TGTGGGCTTTAAAAAGGGTTGCCACTGACT
1 TGTGGGCTTT-GAAA-GGATGCCACTGACT
*
1211634 TGTGGGCTTTGAAAAGG-TGCCATTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
** * *
1211662 TGTTGGATTTTGAAAATG-TGCCATTGACT
1 TG-TGGGCTTTG-AAAGGATGCCACTGACT
** *
1211691 TGTTAGCTTTTGAAAGG-TACCACTGACT
1 TGTGGGC-TTTGAAAGGATGCCACTGACT
* * * * *
1211719 TGTTGGCTTTTGAAATG-TGCTATTAACT
1 TGTGGGC-TTTGAAAGGATGCCACTGACT
1211747 TGTGGGCCTTTGAAAGGATGCCACTGACT
1 TGTGGG-CTTTGAAAGGATGCCACTGACT
1211776 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
1211804 TGTGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
1211832 TGTGGGTTTTAAAAAAGATGCCACTGACT
1 TGTGGGCTTT-GAAAGGATGCCACTGACT
* *
1211861 TGGGGGCTTCGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
1211889 TGTGGGGTTTGAAAGGATGCCACTGA
1 TGTGGGCTTTGAAAGGATGCCACTGA
1211915 TGAAAACCAA
Statistics
Matches: 239, Mismatches: 36, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
28 158 0.66
29 68 0.28
30 13 0.05
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.32
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:1211700 original size:57 final size:56
Alignment explanation
Indices: 1211623--1211914 Score: 322
Period size: 57 Copynumber: 5.2 Consensus size: 56
1211613 TAAAAAGGGT
* *
1211623 TGCCACTGACTTGTGGGCTTTGAAAAGG-TGCCATTGACTTGTTGGATTTTGAAAATG-
1 TGCCACTGACTTGTGGGCTTTG-AAAGGATGCCACTGACTTG-TGGGTTTTG-AAATGA
* ** * *
1211680 TGCCATTGACTTGTTAGCTTTTGAAAGG-TACCACTGACTTGTTGGCTTTTGAAATG-
1 TGCCACTGACTTGTGGGC-TTTGAAAGGATGCCACTGACTTG-TGGGTTTTGAAATGA
* * * * *
1211736 TGCTATTAACTTGTGGGCCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGA
1 TGCCACTGACTTGTGGG-CTTTGAAAGGATGCCACTGACTTGTGGGTTTTGAAATGA
* * *
1211793 TGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGTTTTAAAAAAGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGTTTT-GAAATGA
* * * *
1211850 TGCCACTGACTTGGGGGCTTCGAAAGGATGCCACTGACTTGTGGGGTTTGAAAGGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGTTTTGAAATGA
1211906 TGCCACTGA
1 TGCCACTGA
1211915 TGAAAACCAA
Statistics
Matches: 203, Mismatches: 27, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
56 82 0.40
57 117 0.58
58 4 0.02
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.32
Consensus pattern (56 bp):
TGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGTTTTGAAATGA
Found at i:1211721 original size:85 final size:86
Alignment explanation
Indices: 1211604--1211910 Score: 338
Period size: 85 Copynumber: 3.6 Consensus size: 86
1211594 CACCAACTTG
* * *
1211604 TGTGGGCTTTAAAAAGGGTTGCCACTGACTTGTGGGCTTTGAAAAGG-TGCCATTGACTTGTTGG
1 TGTGGGCTTT-GAAA-GGATGCCACTGACTTGTGGGCTTTG-AAAGGATGCCATTAACTTGTTGG
* *
1211668 ATTTTGAAAATG-TGCCATTGACT
63 ATTTTGAAAAAGATGCCACTGACT
** * * * * * *
1211691 TGTTAGCTTTTGAAAGG-TACCACTGACTTGTTGGCTTTTGAAATG-TGCTATTAACTTGTGGGC
1 TGTGGGC-TTTGAAAGGATGCCACTGACTTGTGGGC-TTTGAAAGGATGCCATTAACTTGTTGGA
* *
1211754 CTTTG-AAAGGATGCCACTGACT
64 TTTTGAAAAAGATGCCACTGACT
* *
1211776 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACTTG-TGGGTT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCATTAACTTGTTGGATT
*
1211840 TTAAAAAAGATGCCACTGACT
66 TTGAAAAAGATGCCACTGACT
* * *
1211861 TGGGGGCTTCGAAAGGATGCCACTGACTTGTGGGGTTTGAAAGGATGCCA
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCA
1211911 CTGATGAAAA
Statistics
Matches: 186, Mismatches: 28, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
84 26 0.14
85 143 0.77
86 6 0.03
87 8 0.04
88 3 0.02
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.32
Consensus pattern (86 bp):
TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCATTAACTTGTTGGATT
TTGAAAAAGATGCCACTGACT
Found at i:1213556 original size:12 final size:11
Alignment explanation
Indices: 1213537--1213643 Score: 68
Period size: 12 Copynumber: 10.0 Consensus size: 11
1213527 AGAGAAAGAA
1213537 GAGATAGGAGG
1 GAGATAGGAGG
1213548 GATGATAGGAGG
1 GA-GATAGGAGG
1213560 AGAGATAGGA--
1 -GAGATAGGAGG
**
1213570 GAGATA--ATA
1 GAGATAGGAGG
1213579 GAGATAGGAGG
1 GAGATAGGAGG
1213590 GATGATAGGAGG
1 GA-GATAGGAGG
1213602 AGAGATA-G-GG
1 -GAGATAGGAGG
**
1213612 GAGATA--ATA
1 GAGATAGGAGG
*
1213621 GAGAGAGGAGG
1 GAGATAGGAGG
1213632 GATGATAGGAGG
1 GA-GATAGGAGG
1213644 AGGAAAGAAG
Statistics
Matches: 76, Mismatches: 8, Indels: 23
0.71 0.07 0.21
Matches are distributed among these distances:
7 1 0.01
9 23 0.30
10 2 0.03
11 9 0.12
12 37 0.49
13 4 0.05
ACGTcount: A:0.40, C:0.00, G:0.47, T:0.13
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:1213583 original size:18 final size:18
Alignment explanation
Indices: 1213560--1213630 Score: 61
Period size: 18 Copynumber: 3.6 Consensus size: 18
1213550 TGATAGGAGG
1213560 AGAGATAGGAGAGATAAT
1 AGAGATAGGAGAGATAAT
*
1213578 AGAGATAGGAGGGATGATAGGAGG
1 AGAGATAGGA--GA-GATA--A-T
*
1213602 AGAGATAGGGGAGATAAT
1 AGAGATAGGAGAGATAAT
*
1213620 AGAGAGAGGAG
1 AGAGATAGGAG
1213631 GGATGATAGG
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
18 19 0.45
19 1 0.02
20 2 0.05
21 8 0.19
22 2 0.05
23 1 0.02
24 9 0.21
ACGTcount: A:0.44, C:0.00, G:0.44, T:0.13
Consensus pattern (18 bp):
AGAGATAGGAGAGATAAT
Found at i:1213586 original size:42 final size:42
Alignment explanation
Indices: 1213536--1213645 Score: 202
Period size: 42 Copynumber: 2.6 Consensus size: 42
1213526 AAGAGAAAGA
1213536 AGAGATAGGAGGGATGATAGGAGGAGAGATAGGAGAGATAAT
1 AGAGATAGGAGGGATGATAGGAGGAGAGATAGGAGAGATAAT
*
1213578 AGAGATAGGAGGGATGATAGGAGGAGAGATAGGGGAGATAAT
1 AGAGATAGGAGGGATGATAGGAGGAGAGATAGGAGAGATAAT
*
1213620 AGAGAGAGGAGGGATGATAGGAGGAG
1 AGAGATAGGAGGGATGATAGGAGGAG
1213646 GAAAGAAGAA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.41, C:0.00, G:0.46, T:0.13
Consensus pattern (42 bp):
AGAGATAGGAGGGATGATAGGAGGAGAGATAGGAGAGATAAT
Found at i:1213639 original size:18 final size:18
Alignment explanation
Indices: 1213560--1213639 Score: 52
Period size: 18 Copynumber: 4.1 Consensus size: 18
1213550 TGATAGGAGG
* *
1213560 AGAGATAGGAGAGATAAT
1 AGAGAGAGGAGGGATAAT
* *
1213578 AGAGATAGGAGGGATGAT
1 AGAGAGAGGAGGGATAAT
*
1213596 AGGAGGAGAGATAGGGGAGATAAT
1 A-GA-GAGAG---GAGG-GATAAT
*
1213620 AGAGAGAGGAGGGATGAT
1 AGAGAGAGGAGGGATAAT
1213638 AG
1 AG
1213640 GAGGAGGAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 24 0.49
19 5 0.10
20 4 0.08
22 5 0.10
23 5 0.10
24 6 0.12
ACGTcount: A:0.42, C:0.00, G:0.44, T:0.14
Consensus pattern (18 bp):
AGAGAGAGGAGGGATAAT
Found at i:1218630 original size:29 final size:29
Alignment explanation
Indices: 1218597--1218817 Score: 254
Period size: 29 Copynumber: 7.7 Consensus size: 29
1218587 GTTGTCATCA
*
1218597 GCCACTAACTTGT-GGCTTTTTGAAAGGAT
1 GCCACTGACTTGTGGGC-TTTTGAAAGGAT
* * *
1218626 GCCACTGACTTGTAGG-TTTTAAAAAGGGT
1 GCCACTGACTTGTGGGCTTTT-GAAAGGAT
* *
1218655 GCCACTGATTTGTGGGCCTTTGAAAGGAT
1 GCCACTGACTTGTGGGCTTTTGAAAGGAT
*
1218684 GCCACTGACTTGCGGGC-TTTGAAAGGAT
1 GCCACTGACTTGTGGGCTTTTGAAAGGAT
* *
1218712 GCCACTAACTTGCGGGC-TTTGAAAGGAT
1 GCCACTGACTTGTGGGCTTTTGAAAGGAT
1218740 GCCACTGACTTGTGGGCTTTTGAAAGGAT
1 GCCACTGACTTGTGGGCTTTTGAAAGGAT
* * * **
1218769 GCCACTAACTTGTAAGG-TATAAAAAGGAT
1 GCCACTGACTTGT-GGGCTTTTGAAAGGAT
1218798 GCCACTGACTTGTGGGCTTT
1 GCCACTGACTTGTGGGCTTT
1218818 AAAAAGGGTC
Statistics
Matches: 165, Mismatches: 21, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
28 59 0.36
29 99 0.60
30 7 0.04
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.29
Consensus pattern (29 bp):
GCCACTGACTTGTGGGCTTTTGAAAGGAT
Found at i:1218756 original size:85 final size:86
Alignment explanation
Indices: 1218597--1218824 Score: 246
Period size: 86 Copynumber: 2.6 Consensus size: 86
1218587 GTTGTCATCA
* * * * *
1218597 GCCACTAACTTG-TGGCTTTTTGAAAGGATGCCACTGACTTGTAGGTTTTAAAAAGGGTGCCACT
1 GCCACTAACTTGCGGGC--TTTGAAAGGATGCCACTAACTTGCAGGCTTTAAAAAGGATGCCACT
*
1218661 GATTTGTGGGCCTTTGAAAGGAT
64 GACTTGTGGGCCTTTGAAAGGAT
* * *
1218684 GCCACTGACTTGCGGGCTTTGAAAGGATGCCACTAACTTGCGGGCTTT-GAAAGGATGCCACTGA
1 GCCACTAACTTGCGGGCTTTGAAAGGATGCCACTAACTTGCAGGCTTTAAAAAGGATGCCACTGA
*
1218748 CTTGTGGGCTTTTGAAAGGAT
66 CTTGTGGGCCTTTGAAAGGAT
** ** * **
1218769 GCCACTAACTTGTAAGG-TATAAAAAGGATGCCACTGACTTGTGGGCTTTAAAAAGG
1 GCCACTAACTTG-CGGGCT-TTGAAAGGATGCCACTAACTTGCAGGCTTTAAAAAGG
1218825 GTCATATTGA
Statistics
Matches: 119, Mismatches: 18, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
85 45 0.38
86 55 0.46
87 16 0.13
88 3 0.03
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.29
Consensus pattern (86 bp):
GCCACTAACTTGCGGGCTTTGAAAGGATGCCACTAACTTGCAGGCTTTAAAAAGGATGCCACTGA
CTTGTGGGCCTTTGAAAGGAT
Found at i:1218815 original size:114 final size:113
Alignment explanation
Indices: 1218597--1218817 Score: 277
Period size: 114 Copynumber: 1.9 Consensus size: 113
1218587 GTTGTCATCA
* * *
1218597 GCCACTAACTTGTGGCTTTTTGAAAGGATGCCACTGACTTGTAGGTTTTAAAAAGGGTGCCACTG
1 GCCACTAACTTGGGGC-TTTTGAAAGGATGCCACTGACTTGTAGGTTTTAAAAAGGATGCCACTA
* * **
1218662 ATTTGTGGGCCTTTGAAAGGATGCCACTGACTTGCGGGCTTTGAAAGGAT
65 ACTTGTAGG-CTTAAAAAGGATGCCACTGACTTGCGGGCTTTGAAAGGAT
* *
1218712 GCCACTAACTTGCGGGC-TTTGAAAGGATGCCACTGACTTGTGGGCTTTT-GAAAGGATGCCACT
1 GCCACTAACTTG-GGGCTTTTGAAAGGATGCCACTGACTTGTAGG-TTTTAAAAAGGATGCCACT
*
1218775 AACTTGTAAGG-TATAAAAAGGATGCCACTGACTTGTGGGCTTT
64 AACTTGT-AGGCT-TAAAAAGGATGCCACTGACTTGCGGGCTTT
1218818 AAAAAGGGTC
Statistics
Matches: 92, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
113 1 0.01
114 70 0.76
115 18 0.20
116 3 0.03
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.29
Consensus pattern (113 bp):
GCCACTAACTTGGGGCTTTTGAAAGGATGCCACTGACTTGTAGGTTTTAAAAAGGATGCCACTAA
CTTGTAGGCTTAAAAAGGATGCCACTGACTTGCGGGCTTTGAAAGGAT
Found at i:1220123 original size:8 final size:8
Alignment explanation
Indices: 1220112--1220152 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
1220102 TTTTGTGTTT
1220112 TTTTTTTA
1 TTTTTTTA
*
1220120 TTTTTTTGG
1 TTTTTTT-A
1220129 TTTTTTTA
1 TTTTTTTA
*
1220137 TTTTTTTG
1 TTTTTTTA
1220145 TTTTTTTA
1 TTTTTTTA
1220153 AAGAAGGATG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
8 21 0.75
9 7 0.25
ACGTcount: A:0.07, C:0.00, G:0.07, T:0.85
Consensus pattern (8 bp):
TTTTTTTA
Found at i:1220134 original size:16 final size:17
Alignment explanation
Indices: 1220112--1220152 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
1220102 TTTTGTGTTT
1220112 TTTTTTTATTTTTTTGG
1 TTTTTTTATTTTTTTGG
1220129 TTTTTTTATTTTTTT-G
1 TTTTTTTATTTTTTTGG
1220145 TTTTTTTA
1 TTTTTTTA
1220153 AAGAAGGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 9 0.38
17 15 0.62
ACGTcount: A:0.07, C:0.00, G:0.07, T:0.85
Consensus pattern (17 bp):
TTTTTTTATTTTTTTGG
Found at i:1230398 original size:10 final size:10
Alignment explanation
Indices: 1230368--1230419 Score: 59
Period size: 10 Copynumber: 5.0 Consensus size: 10
1230358 CATCCTTTGT
1230368 ACCAAAAAAA
1 ACCAAAAAAA
*
1230378 ACCCAAAAAA
1 ACCAAAAAAA
1230388 ACCAAAAAAAA
1 ACC-AAAAAAA
*
1230399 ACAAATAAAAA
1 ACCAA-AAAAA
*
1230410 AACAAAAAAA
1 ACCAAAAAAA
1230420 GAAGGGTCCA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
10 19 0.54
11 16 0.46
ACGTcount: A:0.81, C:0.17, G:0.00, T:0.02
Consensus pattern (10 bp):
ACCAAAAAAA
Found at i:1230408 original size:12 final size:11
Alignment explanation
Indices: 1230382--1230419 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
1230372 AAAAAAACCC
*
1230382 AAAAAAACCAA
1 AAAAAAACAAA
1230393 AAAAAAACAAA
1 AAAAAAACAAA
1230404 TAAAAAAACAAA
1 -AAAAAAACAAA
1230416 AAAA
1 AAAA
1230420 GAAGGGTCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.87, C:0.11, G:0.00, T:0.03
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:1230408 original size:20 final size:20
Alignment explanation
Indices: 1230368--1230419 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
1230358 CATCCTTTGT
*
1230368 ACCAAAAAAAACCCAAAAAA
1 ACCAAAAAAAACACAAAAAA
*
1230388 ACCAAAAAAAAACAAATAAAAA
1 ACC-AAAAAAAACACA-AAAAA
*
1230410 AACAAAAAAA
1 ACCAAAAAAA
1230420 GAAGGGTCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.11
21 17 0.63
22 7 0.26
ACGTcount: A:0.81, C:0.17, G:0.00, T:0.02
Consensus pattern (20 bp):
ACCAAAAAAAACACAAAAAA
Found at i:1231667 original size:28 final size:28
Alignment explanation
Indices: 1231635--1232109 Score: 469
Period size: 28 Copynumber: 16.8 Consensus size: 28
1231625 TCATCTCTTG
*
1231635 AAAGCTCATAAGTCAGTGGCATCCTTTC
1 AAAGCCCATAAGTCAGTGGCATCCTTTC
* *
1231663 AAAGCCCACAAGTCAATGGCAT-CTCTTC
1 AAAGCCCATAAGTCAGTGGCATCCT-TTC
* * *
1231691 AAAGTCCACAGGTCAGTGGCATCCTTTC
1 AAAGCCCATAAGTCAGTGGCATCCTTTC
* * *
1231719 AAAGCCCACAACTCAGTGGCAT-TTCTTC
1 AAAGCCCATAAGTCAGTGGCATCCT-TTC
*
1231747 AAAGCCCATAGGTCAGTGGCATCCTTTC
1 AAAGCCCATAAGTCAGTGGCATCCTTTC
* *
1231775 AATGCCCATAAGTTAGTGGCAT-CTCTTC
1 AAAGCCCATAAGTCAGTGGCATCCT-TTC
*
1231803 AAAGCCCATAAGTCAGTGGCAACCCTTTTC
1 AAAGCCCATAAGTCAGTGGC-ATCC-TTTC
1231833 AAAGCCCATAAGTCAGTGGCAT-CTCTTC
1 AAAGCCCATAAGTCAGTGGCATCCT-TTC
* *
1231861 AAGGCCCATAGGTCAGTGGCATCCTTTC
1 AAAGCCCATAAGTCAGTGGCATCCTTTC
* *
1231889 AAAGCCCACAAGTCAGTGGCATCTTTTC
1 AAAGCCCATAAGTCAGTGGCATCCTTTC
*
1231917 AAAGCCCATAGGTCAGTGGCATCCTTTC
1 AAAGCCCATAAGTCAGTGGCATCCTTTC
* * * * * *
1231945 GAAGTCCACAAGTTAGTGGCACCCTTTT
1 AAAGCCCATAAGTCAGTGGCATCCTTTC
* * *
1231973 TAAGCCCACAAGTTAGTGGCA-CCTTTCC
1 AAAGCCCATAAGTCAGTGGCATCCTTT-C
* * *
1232001 AAAGCCCACAAG-CAAGTGGCACCCTTTT
1 AAAGCCCATAAGTC-AGTGGCATCCTTTC
*
1232029 TAAGCCCATAAGTCAGTGGCA-CCTTTCC
1 AAAGCCCATAAGTCAGTGGCATCCTTT-C
* *
1232057 AAAGCCCATAGGTCAGTGGCACCTCTTTTC
1 AAAGCCCATAAGTCAGTGGCA--TCCTTTC
* *
1232087 AAGGCCCACACAAGTCAGTGGCA
1 AAAG-CC-CATAAGTCAGTGGCA
1232110 ACCCTTTTCA
Statistics
Matches: 375, Mismatches: 52, Indels: 36
0.81 0.11 0.08
Matches are distributed among these distances:
27 16 0.04
28 298 0.79
29 13 0.03
30 28 0.07
31 7 0.02
32 13 0.03
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.24
Consensus pattern (28 bp):
AAAGCCCATAAGTCAGTGGCATCCTTTC
Found at i:1231706 original size:56 final size:56
Alignment explanation
Indices: 1231626--1232083 Score: 530
Period size: 56 Copynumber: 8.1 Consensus size: 56
1231616 CTAGAACATT
* * * *
1231626 CATCTCTTGAAAGCTCATAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAATGG
1 CATCTCTTCAAAGCCCATAGGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGG
* * *
1231682 CATCTCTTCAAAGTCCACAGGTCAGTGGCATCCTTTCAAAGCCCACAACTCAGTGG
1 CATCTCTTCAAAGCCCATAGGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGG
* * * *
1231738 CATTTCTTCAAAGCCCATAGGTCAGTGGCATCCTTTCAATGCCCATAAGTTAGTGG
1 CATCTCTTCAAAGCCCATAGGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGG
* * *
1231794 CATCTCTTCAAAGCCCATAAGTCAGTGGCAACCCTTTTCAAAGCCCATAAGTCAGTGG
1 CATCTCTTCAAAGCCCATAGGTCAGTGGC-ATCC-TTTCAAAGCCCACAAGTCAGTGG
*
1231852 CATCTCTTCAAGGCCCATAGGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGG
1 CATCTCTTCAAAGCCCATAGGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGG
* * * *
1231908 CATCTTTTCAAAGCCCATAGGTCAGTGGCATCCTTTCGAAGTCCACAAGTTAGTGG
1 CATCTCTTCAAAGCCCATAGGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGG
* ** * * *
1231964 CA-CCCTTTTTAAGCCCACAAGTTAGTGGCA-CCTTTCCAAAGCCCACAAG-CAAGTGG
1 CATCTC-TTCAAAGCCCATAGGTCAGTGGCATCCTTT-CAAAGCCCACAAGTC-AGTGG
* ** * * *
1232020 CA-CCCTTTTTAAGCCCATAAGTCAGTGGCA-CCTTTCCAAAGCCCATAGGTCAGTGG
1 CATCTC-TTCAAAGCCCATAGGTCAGTGGCATCCTTT-CAAAGCCCACAAGTCAGTGG
*
1232076 CACCTCTT
1 CATCTCTT
1232084 TTCAAGGCCC
Statistics
Matches: 352, Mismatches: 43, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
55 6 0.02
56 289 0.82
57 9 0.03
58 48 0.14
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (56 bp):
CATCTCTTCAAAGCCCATAGGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGG
Found at i:1233200 original size:97 final size:97
Alignment explanation
Indices: 1233066--1233286 Score: 325
Period size: 97 Copynumber: 2.3 Consensus size: 97
1233056 AATAGGGATA
* * * * *
1233066 GAGTACCCCCTCGGAGGAATAGGGTTGGAGTGTCCCCGATGATGACAGTTTAAGTGAAAATAAGA
1 GAGTATCCCCTCGGAGGAATAGGGTTGAAATGCCCCCGATGATGACAATTTAAGTGAAAATAAGA
1233131 TTTAAACTTTGATGTATTTAAAAGCGGGGTTG
66 TTTAAACTTTGATGTATTTAAAAGCGGGGTTG
* * * * **
1233163 GAGTATCCCCTCAGAGGAATGGGGTTGAAATGCCCCCGATGGTGACAATTTTAGTGAGGATAAGA
1 GAGTATCCCCTCGGAGGAATAGGGTTGAAATGCCCCCGATGATGACAATTTAAGTGAAAATAAGA
* *
1233228 TTTAAACTTTGATGTGTTTAAAAGTGGGGTTG
66 TTTAAACTTTGATGTATTTAAAAGCGGGGTTG
1233260 GAGTATCCCCTCGGAGGAATAGGGTTG
1 GAGTATCCCCTCGGAGGAATAGGGTTG
1233287 GAGTATCCCG
Statistics
Matches: 109, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
97 109 1.00
ACGTcount: A:0.28, C:0.14, G:0.30, T:0.28
Consensus pattern (97 bp):
GAGTATCCCCTCGGAGGAATAGGGTTGAAATGCCCCCGATGATGACAATTTAAGTGAAAATAAGA
TTTAAACTTTGATGTATTTAAAAGCGGGGTTG
Found at i:1235014 original size:21 final size:21
Alignment explanation
Indices: 1234980--1235037 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
1234970 CTAACGTTAT
*
1234980 TTTTTTCTACCTCTTTGTTTCTA
1 TTTTTTCT--CTCTTTCTTTCTA
*
1235003 TTTTTTCTCTCTTTTCTTTCTC
1 TTTTTTCTCTC-TTTCTTTCTA
1235025 TTTTTT-TCTCTTT
1 TTTTTTCTCTCTTT
1235038 TTTTTTTCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 3 0.09
21 7 0.22
22 14 0.44
23 8 0.25
ACGTcount: A:0.03, C:0.22, G:0.02, T:0.72
Consensus pattern (21 bp):
TTTTTTCTCTCTTTCTTTCTA
Found at i:1235024 original size:11 final size:10
Alignment explanation
Indices: 1234990--1235052 Score: 72
Period size: 11 Copynumber: 6.0 Consensus size: 10
1234980 TTTTTTCTAC
*
1234990 CTCTTTGTTT
1 CTCTTTTTTT
*
1235000 CTATTTTTTCT
1 CTCTTTTTT-T
1235011 CTCTTTTCTTT
1 CTCTTTT-TTT
1235022 CTCTTTTTTT
1 CTCTTTTTTT
1235032 CTCTTTTTTTT
1 CTC-TTTTTTT
*
1235043 TTCTTTTTTT
1 CTCTTTTTTT
1235053 AGTTGAACCT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
10 20 0.43
11 24 0.52
12 2 0.04
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.78
Consensus pattern (10 bp):
CTCTTTTTTT
Found at i:1235038 original size:21 final size:21
Alignment explanation
Indices: 1234979--1235052 Score: 76
Period size: 21 Copynumber: 3.3 Consensus size: 21
1234969 GCTAACGTTA
* *
1234979 TTTTTTTCTACCTCTTTGTTTCTA
1 TTTTTTTCT--CT-TTTCTTTCTC
1235003 TTTTTTCTCTCTTTTCTTTCTC
1 TTTTTT-TCTCTTTTCTTTCTC
* *
1235025 TTTTTTTCTCTTTTTTTTTTC
1 TTTTTTTCTCTTTTCTTTCTC
1235046 TTTTTTT
1 TTTTTTT
1235053 AGTTGAACCT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
21 20 0.44
22 14 0.31
23 2 0.04
24 6 0.13
25 3 0.07
ACGTcount: A:0.03, C:0.19, G:0.01, T:0.77
Consensus pattern (21 bp):
TTTTTTTCTCTTTTCTTTCTC
Found at i:1235775 original size:165 final size:166
Alignment explanation
Indices: 1235604--1235942 Score: 418
Period size: 166 Copynumber: 2.0 Consensus size: 166
1235594 GACATCATTA
* ** * * * *
1235604 GATGAATTCTAAAATTTTTAAACTGAAAAAAAAT-CCCTCCAAAAAA-TTACGGAGAAGAAAACT
1 GATGAATTCTAAAAATTGAAAACCG-AAAAAAATCCCCTCAAAAAAATTTACGAAGAAGAAAACA
* * * *
1235667 CGATTTTTTCCAAAAAAAGA-GATTTTCAAAGAAAAATTC-AAAACTCATGAAAATAAATGAATT
65 CCA-TATTT-CAAAAAAAGAGGAATTTCAAAGAAAAAATCAAAAACTCATGAAAATAAATGAATT
* *
1235730 TTTGAAAACTAAATTAATATG-AATCAAATGATGATGTTT
128 TTTGAAAACTAAATTAATATGAAAT-AAATGATAATATTT
* * **
1235769 GATGAATTTTAAAAATTGAAAACCGAGAAAAATCCCCTCAAAAAAATTTACGAAGTTGAAAACAC
1 GATGAATTCTAAAAATTGAAAACCGAAAAAAATCCCCTCAAAAAAATTTACGAAGAAGAAAACAC
* *
1235834 CATATTTCGAAAAAAGAGGAATTTCAAAGAAAAAATCAAAAACTCATGAAAATGAATGAATTTTT
66 CATATTTCAAAAAAAGAGGAATTTCAAAGAAAAAATCAAAAACTCATGAAAATAAATGAATTTTT
*
1235899 GAAAACTGAATTAATATGAAATAAATGATAATATTT
131 GAAAACTAAATTAATATGAAATAAATGATAATATTT
*
1235935 GATTAATT
1 GATGAATT
1235943 TTGATGTTTG
Statistics
Matches: 148, Mismatches: 21, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
164 16 0.11
165 52 0.35
166 77 0.52
167 3 0.02
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.28
Consensus pattern (166 bp):
GATGAATTCTAAAAATTGAAAACCGAAAAAAATCCCCTCAAAAAAATTTACGAAGAAGAAAACAC
CATATTTCAAAAAAAGAGGAATTTCAAAGAAAAAATCAAAAACTCATGAAAATAAATGAATTTTT
GAAAACTAAATTAATATGAAATAAATGATAATATTT
Found at i:1236541 original size:159 final size:159
Alignment explanation
Indices: 1236284--1236583 Score: 358
Period size: 159 Copynumber: 1.9 Consensus size: 159
1236274 TGTCTACACA
* ** * *
1236284 TCTCATTTGAGGGAAAAACTTTGATTCTATGGAACATGATGAGAAGAAAAGTTTTTCTTATGAAA
1 TCTCATTTAAGGGAAAAACTTTGATTCTAAAGAACATGATGAGAAGAAAAGCTTTTATTATGAAA
* * * *
1236349 CCAAAGCATCAATATCATGTATTCTAATAAGGAGAA-AGTGTTTTGATTGGCTAATCATAAAAAT
66 CCAAAGCATCAATATCAAGTATTCTAATAAGGAGAACA-TGTTTTGATTGCCCAATCATAAAAAC
*
1236413 ATTGGAGATTATTATAACAATCCACATTTG
130 AATGGAGATTATTATAACAATCCACATTTG
* * * *
1236443 TCTCATTTAAGGGATAAACTTTGATTTTAAAGAA-ATTGATGGGAAGAAAAGCTTTTATTGT-AA
1 TCTCATTTAAGGGAAAAACTTTGATTCTAAAGAACA-TGATGAGAAGAAAAGCTTTTATTATGAA
* * *
1236506 AGCCAAAGGATCAATATCAAGTA-TCTCAA-AGAGGAGAACATGTTTTTATTGCCCAATCATGAA
65 A-CCAAAGCATCAATATCAAGTATTCT-AATA-AGGAGAACATGTTTTGATTGCCCAATCATAAA
*
1236569 AGCAATGGAGATTAT
127 AACAATGGAGATTAT
1236584 CAAAGAATTT
Statistics
Matches: 118, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
158 8 0.07
159 109 0.92
160 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (159 bp):
TCTCATTTAAGGGAAAAACTTTGATTCTAAAGAACATGATGAGAAGAAAAGCTTTTATTATGAAA
CCAAAGCATCAATATCAAGTATTCTAATAAGGAGAACATGTTTTGATTGCCCAATCATAAAAACA
ATGGAGATTATTATAACAATCCACATTTG
Found at i:1241027 original size:19 final size:20
Alignment explanation
Indices: 1240982--1241031 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
1240972 CACCTTCAGA
*
1240982 TGTATCGATACATAATGCAC
1 TGTATCGATACATAATCCAC
* *
1241002 AGTATCGATACATGA-CCAC
1 TGTATCGATACATAATCCAC
1241021 TGTATCGATAC
1 TGTATCGATAC
1241032 TTGCAAAGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (20 bp):
TGTATCGATACATAATCCAC
Found at i:1241132 original size:13 final size:13
Alignment explanation
Indices: 1241114--1241138 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1241104 ACATACAAGA
1241114 TGTATCGATACAC
1 TGTATCGATACAC
1241127 TGTATCGATACA
1 TGTATCGATACA
1241139 TTGGCTTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:1249731 original size:13 final size:13
Alignment explanation
Indices: 1249713--1249737 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1249703 ATAATGCACA
1249713 GTATCGATACATT
1 GTATCGATACATT
1249726 GTATCGATACAT
1 GTATCGATACAT
1249738 GACCACTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1249855 original size:13 final size:13
Alignment explanation
Indices: 1249837--1249861 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1249827 ACATACAAGA
1249837 TGTATCGATACAC
1 TGTATCGATACAC
1249850 TGTATCGATACA
1 TGTATCGATACA
1249862 TGACCAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:1249859 original size:32 final size:34
Alignment explanation
Indices: 1249818--1249882 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
1249808 CTTAACTATT
*
1249818 TGTATCGATACAT-A-CAAGATGTATCGATACAC
1 TGTATCGATACATGACCAAAATGTATCGATACAC
1249850 TGTATCGATACATGACCAAAATGTATCGATACA
1 TGTATCGATACATGACCAAAATGTATCGATACA
1249883 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 13 0.43
33 1 0.03
34 16 0.53
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.28
Consensus pattern (34 bp):
TGTATCGATACATGACCAAAATGTATCGATACAC
Found at i:1256404 original size:22 final size:22
Alignment explanation
Indices: 1256379--1256420 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1256369 GCAATTTCAG
*
1256379 CTTCTTGTCTGTCCATTCTTAT
1 CTTCTTGTCTATCCATTCTTAT
*
1256401 CTTCTTGTTTATCCATTCTT
1 CTTCTTGTCTATCCATTCTT
1256421 TCAAACTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.10, C:0.26, G:0.07, T:0.57
Consensus pattern (22 bp):
CTTCTTGTCTATCCATTCTTAT
Found at i:1267005 original size:12 final size:12
Alignment explanation
Indices: 1266988--1267120 Score: 60
Period size: 12 Copynumber: 11.7 Consensus size: 12
1266978 GAAAGAACAT
1266988 ATAGGAGGGATG
1 ATAGGAGGGATG
1267000 ATAGGA-GGAGTG
1 ATAGGAGGGA-TG
1267012 ATAGGA--GA-G
1 ATAGGAGGGATG
*
1267021 ATAGTA--GA-G
1 ATAGGAGGGATG
1267030 ATAGGAGGGATG
1 ATAGGAGGGATG
1267042 ATAGGA-GGA-G
1 ATAGGAGGGATG
*
1267052 AGT-GTA--GA-G
1 A-TAGGAGGGATG
1267061 ATAGGAGGGATG
1 ATAGGAGGGATG
1267073 ATAGGAGGAGA-G
1 ATAGGAGG-GATG
* * *
1267085 ATAGAAGAGATA
1 ATAGGAGGGATG
1267097 ATAGAAAAGAGGGATG
1 ATAG----GAGGGATG
1267113 ATAGGAGG
1 ATAGGAGG
1267121 AGAAGAGAAA
Statistics
Matches: 96, Mismatches: 10, Indels: 30
0.71 0.07 0.22
Matches are distributed among these distances:
8 1 0.01
9 20 0.21
10 4 0.04
11 15 0.16
12 45 0.47
13 2 0.02
16 9 0.09
ACGTcount: A:0.41, C:0.00, G:0.44, T:0.15
Consensus pattern (12 bp):
ATAGGAGGGATG
Found at i:1267062 original size:31 final size:32
Alignment explanation
Indices: 1266999--1267096 Score: 141
Period size: 31 Copynumber: 3.1 Consensus size: 32
1266989 TAGGAGGGAT
1266999 GATAGGA-GGAGTGATAGGA-GAGA-TAGTAGA
1 GATAGGAGGGA-TGATAGGAGGAGAGTAGTAGA
1267029 GATAGGAGGGATGATAGGAGGAGAGT-GTAGA
1 GATAGGAGGGATGATAGGAGGAGAGTAGTAGA
*
1267060 GATAGGAGGGATGATAGGAGGAGAGATAGAAGA
1 GATAGGAGGGATGATAGGAGGAGAG-TAGTAGA
1267093 GATA
1 GATA
1267097 ATAGAAAAGA
Statistics
Matches: 62, Mismatches: 1, Indels: 7
0.89 0.01 0.10
Matches are distributed among these distances:
30 15 0.24
31 37 0.60
32 2 0.03
33 8 0.13
ACGTcount: A:0.40, C:0.00, G:0.45, T:0.15
Consensus pattern (32 bp):
GATAGGAGGGATGATAGGAGGAGAGTAGTAGA
Found at i:1267074 original size:73 final size:71
Alignment explanation
Indices: 1266988--1267123 Score: 218
Period size: 73 Copynumber: 1.9 Consensus size: 71
1266978 GAAAGAACAT
* * * *
1266988 ATAGGAGGGATGATAGGAGGAGTGATAGGAGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGA
1 ATAGGAGGGATGATAGGAGGAGAGATAGAAGAGATAATAGA-A-AAGAGGGATGATAGGAGGAGA
1267053 GTGTAGAG
64 GTGTAGAG
1267061 ATAGGAGGGATGATAGGAGGAGAGATAGAAGAGATAATAGAAAAGAGGGATGATAGGAGGAGA
1 ATAGGAGGGATGATAGGAGGAGAGATAGAAGAGATAATAGAAAAGAGGGATGATAGGAGGAGA
1267124 AGAGAAAAAG
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
71 20 0.34
72 1 0.02
73 38 0.64
ACGTcount: A:0.41, C:0.00, G:0.44, T:0.15
Consensus pattern (71 bp):
ATAGGAGGGATGATAGGAGGAGAGATAGAAGAGATAATAGAAAAGAGGGATGATAGGAGGAGAGT
GTAGAG
Found at i:1272712 original size:18 final size:18
Alignment explanation
Indices: 1272689--1272723 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1272679 ATCCCTCAAA
1272689 TGACACAAACATGGCTTT
1 TGACACAAACATGGCTTT
1272707 TGACACAAACATGGCTT
1 TGACACAAACATGGCTT
1272724 CTCGTAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (18 bp):
TGACACAAACATGGCTTT
Found at i:1276025 original size:13 final size:13
Alignment explanation
Indices: 1276007--1276031 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1275997 CAAAGATCAG
1276007 TGTATCGATACAA
1 TGTATCGATACAA
1276020 TGTATCGATACA
1 TGTATCGATACA
1276032 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1276109 original size:33 final size:33
Alignment explanation
Indices: 1276072--1276138 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1276062 AGTAGCTTAA
1276072 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1276105 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1276138 A
1 A
1276139 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1276112 original size:13 final size:13
Alignment explanation
Indices: 1276094--1276118 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1276084 CAAAAAAATA
1276094 TGTATCGATACAT
1 TGTATCGATACAT
1276107 TGTATCGATACA
1 TGTATCGATACA
1276119 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1276577 original size:28 final size:28
Alignment explanation
Indices: 1276545--1276603 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
1276535 AGAATCAAGG
*
1276545 TTCATCCCTCA-AAAGAGATGAATTTGGA
1 TTCATCACTCATAAA-AGATGAATTTGGA
*
1276573 TTCATCACTCATAAAAGATGGATTTGGA
1 TTCATCACTCATAAAAGATGAATTTGGA
1276601 TTC
1 TTC
1276604 TCATAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 25 0.89
29 3 0.11
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (28 bp):
TTCATCACTCATAAAAGATGAATTTGGA
Found at i:1277230 original size:13 final size:13
Alignment explanation
Indices: 1277212--1277237 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1277202 TACACCAAGT
1277212 ATGTATCGATACA
1 ATGTATCGATACA
1277225 ATGTATCGATACA
1 ATGTATCGATACA
1277238 CCAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1277256 original size:34 final size:32
Alignment explanation
Indices: 1277194--1277258 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
1277184 TAGCCAAACT
**
1277194 TGTATCGATACACCAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAATGTATCGATACAA
1277226 TGTATCGATACACCAAAAAATTGTATCGATACA
1 TGTATCGATACACC-AAAAA-TGTATCGATACA
1277259 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 14 0.48
33 3 0.10
34 12 0.41
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACCAAAAATGTATCGATACAA
Found at i:1281376 original size:13 final size:13
Alignment explanation
Indices: 1281358--1281383 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1281348 CAATTTTTTG
1281358 TGTATCGATACAT
1 TGTATCGATACAT
1281371 TGTATCGATACAT
1 TGTATCGATACAT
1281384 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1281398 original size:32 final size:33
Alignment explanation
Indices: 1281338--1281401 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1281328 TACAAGCCAA
** *
1281338 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
1281371 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
1281402 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:1282121 original size:21 final size:21
Alignment explanation
Indices: 1282080--1282123 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1282070 CTCCCCTTTA
* *
1282080 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
1282101 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
1282122 TC
1 TC
1282124 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:1283948 original size:13 final size:13
Alignment explanation
Indices: 1283930--1283968 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
1283920 ATAATTACCC
1283930 TGTATCGATACAA
1 TGTATCGATACAA
1283943 TGTATCGATACAA
1 TGTATCGATACAA
1283956 TGTATCGATACAA
1 TGTATCGATACAA
1283969 AAAAAAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1287909 original size:21 final size:21
Alignment explanation
Indices: 1287880--1287924 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1287870 AAGTTTTTAT
*
1287880 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1287900 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1287922 TTT
1 TTT
1287925 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1290163 original size:13 final size:13
Alignment explanation
Indices: 1290145--1290170 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1290135 CAATTTTTTG
1290145 TGTATCGATACAT
1 TGTATCGATACAT
1290158 TGTATCGATACAT
1 TGTATCGATACAT
1290171 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1290185 original size:32 final size:33
Alignment explanation
Indices: 1290125--1290188 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1290115 TACAAGCCAA
** *
1290125 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
1290158 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
1290189 AGTTTAGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:1295683 original size:21 final size:22
Alignment explanation
Indices: 1295646--1295698 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 22
1295636 CATCATTGTT
*
1295646 CATCACTGTTCATGTATCGATA
1 CATCACTGTTAATGTATCGATA
*
1295668 TATCACT-TTAATGTATCGATA
1 CATCACTGTTAATGTATCGATA
1295689 CATCACTGTT
1 CATCACTGTT
1295699 CATAACTGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 19 0.70
22 8 0.30
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (22 bp):
CATCACTGTTAATGTATCGATA
Found at i:1295791 original size:13 final size:13
Alignment explanation
Indices: 1295773--1295810 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1295763 TCACTATTCA
*
1295773 TGTATCGATATAG
1 TGTATCGATACAG
1295786 TGTATCGATACAG
1 TGTATCGATACAG
1295799 TGTATCGATACA
1 TGTATCGATACA
1295811 TTATGAATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1296324 original size:31 final size:31
Alignment explanation
Indices: 1296284--1296345 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
1296274 AAGAGATTGA
1296284 GAGGTTCTATCTTAGCC-CGTAAAAGATAGG
1 GAGGTTCTATCTTAGCCTCGTAAAAGATAGG
*
1296314 GAGGTTTCTATCTTAGCCTTTGTAAAAGATAG
1 GAGG-TTCTATCTTAGCC-TCGTAAAAGATAG
1296346 TGTTGTAAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 4 0.14
31 13 0.46
33 11 0.39
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (31 bp):
GAGGTTCTATCTTAGCCTCGTAAAAGATAGG
Found at i:1301594 original size:20 final size:22
Alignment explanation
Indices: 1301541--1301599 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 22
1301531 CCCTTTAATT
*
1301541 ATAAAAATTTT-TTCCCCCTTA
1 ATAAAAATTTTCCTCCCCCTTA
1301562 ATAAAAAATTTTCCTCCCCCTTA
1 AT-AAAAATTTTCCTCCCCCTTA
*
1301585 ATAAAATTTCTTCCT
1 ATAAAAATT-TTCCT
1301600 TTTTTAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 2 0.06
22 15 0.45
23 16 0.48
ACGTcount: A:0.34, C:0.25, G:0.00, T:0.41
Consensus pattern (22 bp):
ATAAAAATTTTCCTCCCCCTTA
Found at i:1301599 original size:23 final size:23
Alignment explanation
Indices: 1301528--1301590 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
1301518 CAAATTATAA
*
1301528 CTCCCCTTTAATTATAAAAATTTT-
1 CTCCCCCTTAA-TA-AAAAATTTTC
*
1301552 TTCCCCCTTAATAAAAAATTTTC
1 CTCCCCCTTAATAAAAAATTTTC
1301575 CTCCCCCTTAATAAAA
1 CTCCCCCTTAATAAAA
1301591 TTTCTTCCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
22 9 0.26
23 17 0.49
24 9 0.26
ACGTcount: A:0.35, C:0.27, G:0.00, T:0.38
Consensus pattern (23 bp):
CTCCCCCTTAATAAAAAATTTTC
Found at i:1307611 original size:15 final size:16
Alignment explanation
Indices: 1307587--1307628 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
1307577 CCTTTTCTAG
1307587 TTCAACAATTTTC-TT
1 TTCAACAATTTTCATT
*
1307602 TTCAAGAA-TTTCATT
1 TTCAACAATTTTCATT
1307617 TTCAACAATTTT
1 TTCAACAATTTT
1307629 TTATTTATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 4 0.17
15 16 0.70
16 3 0.13
ACGTcount: A:0.31, C:0.17, G:0.02, T:0.50
Consensus pattern (16 bp):
TTCAACAATTTTCATT
Found at i:1308064 original size:3 final size:3
Alignment explanation
Indices: 1308056--1308086 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1308046 CGAGTCAACT
*
1308056 TCA TCA TCA TCA TCA TCA TCA TCA TCT TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1308087 TATCTTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.39
Consensus pattern (3 bp):
TCA
Found at i:1308091 original size:9 final size:9
Alignment explanation
Indices: 1308054--1308092 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
1308044 TCCGAGTCAA
1308054 CTTCATCAT
1 CTTCATCAT
*
1308063 CATCATCAT
1 CTTCATCAT
*
1308072 CATCATCAT
1 CTTCATCAT
*
1308081 CTTCATTAT
1 CTTCATCAT
1308090 CTT
1 CTT
1308093 TGATAGTTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.26, C:0.31, G:0.00, T:0.44
Consensus pattern (9 bp):
CTTCATCAT
Found at i:1310210 original size:13 final size:13
Alignment explanation
Indices: 1310192--1310217 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1310182 ATATTTTTTG
1310192 TGTATCGATACAT
1 TGTATCGATACAT
1310205 TGTATCGATACAT
1 TGTATCGATACAT
1310218 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1310228 original size:32 final size:33
Alignment explanation
Indices: 1310171--1310235 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
1310161 TACAAGCCAA
1310171 TGTATCGATACATATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-TTTTTGTGTATCGATACAT
1310205 TGTATCGATACATA-TTTTGTGTATCGATACA
1 TGTATCGATACATATTTTTGTGTATCGATACA
1310236 AGTTTGGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 17 0.55
34 14 0.45
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATATTTTTGTGTATCGATACAT
Found at i:1310229 original size:19 final size:19
Alignment explanation
Indices: 1310171--1310235 Score: 70
Period size: 19 Copynumber: 3.6 Consensus size: 19
1310161 TACAAGCCAA
1310171 TGTATCGATACATATTTTTTG
1 TGTATCGATACATA--TTTTG
1310192 TGTATCGATAC--A---T-
1 TGTATCGATACATATTTTG
1310205 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
1310224 TGTATCGATACA
1 TGTATCGATACA
1310236 AGTTTGGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
15 1 0.03
18 1 0.03
19 13 0.34
21 11 0.29
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:1310883 original size:13 final size:13
Alignment explanation
Indices: 1310865--1310894 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1310855 ACTTTTCATT
1310865 ATGTATCGATACA
1 ATGTATCGATACA
*
1310878 ATGTATTGATACA
1 ATGTATCGATACA
1310891 ATGT
1 ATGT
1310895 CCCATGTATC
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:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1311002 original size:13 final size:13
Alignment explanation
Indices: 1310984--1311008 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1310974 ACCAAGATCA
1310984 TGTATCGATACAC
1 TGTATCGATACAC
1310997 TGTATCGATACA
1 TGTATCGATACA
1311009 AAGTAATATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:1312183 original size:18 final size:18
Alignment explanation
Indices: 1312160--1312252 Score: 116
Period size: 18 Copynumber: 5.7 Consensus size: 18
1312150 ATTGAGTATA
1312160 TATCGATACAATGACGTG
1 TATCGATACAATGACGTG
1312178 TATCGATAC-A--A--TG
1 TATCGATACAATGACGTG
1312191 TATCGATACAATGACGTG
1 TATCGATACAATGACGTG
1312209 TATCGATAC-A--A--TG
1 TATCGATACAATGACGTG
1312222 TATCGATACAATGACGTG
1 TATCGATACAATGACGTG
1312240 TATCGATACAATG
1 TATCGATACAATG
1312253 TATCAATACA
Statistics
Matches: 65, Mismatches: 0, Indels: 20
0.76 0.00 0.24
Matches are distributed among these distances:
13 22 0.34
14 2 0.03
15 2 0.03
16 2 0.03
17 2 0.03
18 35 0.54
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (18 bp):
TATCGATACAATGACGTG
Found at i:1312194 original size:13 final size:13
Alignment explanation
Indices: 1312176--1312263 Score: 77
Period size: 13 Copynumber: 6.0 Consensus size: 13
1312166 TACAATGACG
1312176 TGTATCGATACAA
1 TGTATCGATACAA
1312189 TGTATCGATACAATGA
1 TGTATCGATAC-A--A
1312205 CGTGTATCGATACAA
1 --TGTATCGATACAA
1312220 TGTATCGATACAATGA
1 TGTATCGATAC-A--A
1312236 CGTGTATCGATACAA
1 --TGTATCGATACAA
*
1312251 TGTATCAATACAA
1 TGTATCGATACAA
1312264 AGTAATATGT
Statistics
Matches: 64, Mismatches: 1, Indels: 20
0.75 0.01 0.24
Matches are distributed among these distances:
13 34 0.53
14 2 0.03
15 2 0.03
16 2 0.03
17 2 0.03
18 22 0.34
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.30
Consensus pattern (13 bp):
TGTATCGATACAA
Done.