Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008504.1 Hibiscus syriacus cultivar Beakdansim tig00111356_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2056749
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 10
Found at i:1194287 original size:64 final size:65
Alignment explanation
Indices: 1194171--1194295 Score: 175
Period size: 64 Copynumber: 1.9 Consensus size: 65
1194161 GAATGCATTT
* * *
1194171 CATGCATCGATGCACTCAGAGTTTTATGAAAACATCGAATTCATTTGATGCATTGATGCACCAGC
1 CATGCATCGATGCACTCAGAGTTTTATGAAAACATCGAATGCATTTCATGCATCGATGCACCAGC
*
1194236 CATGCATCGATGCACTCTG-GCTATTT-TG-AAACATCGAATGCATTTCATGCATCGATGCAC
1 CATGCATCGATGCACTCAGAG-T-TTTATGAAAACATCGAATGCATTTCATGCATCGATGCAC
1194296 TCTTAGTACA
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
64 30 0.56
65 21 0.39
66 3 0.06
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (65 bp):
CATGCATCGATGCACTCAGAGTTTTATGAAAACATCGAATGCATTTCATGCATCGATGCACCAGC
Found at i:1202337 original size:2 final size:2
Alignment explanation
Indices: 1202330--1202364 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1202320 CAGCTTAAGC
1202330 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1202365 CAATTGGCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1202943 original size:65 final size:64
Alignment explanation
Indices: 1202826--1203034 Score: 221
Period size: 65 Copynumber: 3.2 Consensus size: 64
1202816 TTTCAAAGTG
* * * * * **
1202826 ATGCACCGATGCATCAATCCATGCATCGATGCACTATGGAATAAATTG-AACATCGAATGCATTT
1 ATGCATCGATGCA-CTAGCCATGCATCGATGCACTCTGG-CTATTTTGAAACATCGAATGCATTT
1202890 C
64 C
*
1202891 ATGCATCGATGCACATA-CTATGCATCGATGCACT-TAGAG-T-TTTATGAAAACATCGAATGCA
1 ATGCATCGATGCAC-TAGCCATGCATCGATGCACTCT-G-GCTATTT-TG-AAACATCGAATGCA
*
1202952 TTTG
61 TTTC
*
1202956 ATGCATCGATGCACTAGCCATGCATTGATGCACTCTGGCTATTTTGAAACATCGAATGCATTTC
1 ATGCATCGATGCACTAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCATTTC
*
1203020 ATGCATTGATGCACT
1 ATGCATCGATGCACT
1203035 CTTAGTGCAC
Statistics
Matches: 124, Mismatches: 10, Indels: 21
0.80 0.06 0.14
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 52 0.42
65 63 0.51
66 4 0.03
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.30
Consensus pattern (64 bp):
ATGCATCGATGCACTAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCATTTC
Found at i:1206382 original size:22 final size:20
Alignment explanation
Indices: 1206356--1206411 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
1206346 AATACTCAGG
1206356 AAAGTATCGATACCCTAGTAC
1 AAAGTATCGATACCC-AGTAC
* * *
1206377 AGAAGTATCAATACTCAGTTC
1 A-AAGTATCGATACCCAGTAC
1206398 AAGAGTATCGATAC
1 AA-AGTATCGATAC
1206412 TAAACTCCCA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 1 0.03
21 16 0.55
22 12 0.41
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (20 bp):
AAAGTATCGATACCCAGTAC
Found at i:1207801 original size:3 final size:3
Alignment explanation
Indices: 1207793--1207872 Score: 108
Period size: 3 Copynumber: 26.7 Consensus size: 3
1207783 GATTATATTG
* * * *
1207793 TAA TAA TAA TAA TAA AAA TAA AAA TAA AAA TAAA TAG TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
1207839 TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1207873 TAGGTGAAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.03
3 62 0.93
4 3 0.04
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:1209473 original size:24 final size:24
Alignment explanation
Indices: 1209440--1209536 Score: 87
Period size: 23 Copynumber: 4.2 Consensus size: 24
1209430 TATTTATTTC
*
1209440 TTTTCCTTTTTTTCCTCTTCTTC-T
1 TTTTCATTTTTTTCCT-TTCTTCAT
* *
1209464 TTTTCATTTTTTCCCTTT-TCTCTT
1 TTTTCATTTTTTTCCTTTCT-TCAT
*
1209488 TTTTCA-TTTTTTCATTT-TTCAT
1 TTTTCATTTTTTTCCTTTCTTCAT
* *
1209510 TTTTCA-TTTTTTCATTTTTTCAT
1 TTTTCATTTTTTTCCTTTCTTCAT
1209533 TTTT
1 TTTT
1209537 TCAATTTTCA
Statistics
Matches: 65, Mismatches: 5, Indels: 7
0.84 0.06 0.09
Matches are distributed among these distances:
22 21 0.32
23 23 0.35
24 21 0.32
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.73
Consensus pattern (24 bp):
TTTTCATTTTTTTCCTTTCTTCAT
Found at i:1209476 original size:8 final size:8
Alignment explanation
Indices: 1209463--1209592 Score: 120
Period size: 8 Copynumber: 17.4 Consensus size: 8
1209453 CCTCTTCTTC
1209463 TTTTTCAT
1 TTTTTCAT
*
1209471 TTTTTCCCT
1 TTTTT-CAT
*
1209480 TTTCTC-T
1 TTTTTCAT
1209487 TTTTTCAT
1 TTTTTCAT
1209495 TTTTTCA-
1 TTTTTCAT
1209502 TTTTTCA-
1 TTTTTCAT
1209509 TTTTTCAT
1 TTTTTCAT
1209517 TTTTTCAT
1 TTTTTCAT
1209525 TTTTTCAT
1 TTTTTCAT
1209533 TTTTTCA-
1 TTTTTCAT
*
1209540 ATTTTCA-
1 TTTTTCAT
1209547 TTTTTC--
1 TTTTTCAT
1209553 TTTTTCA-
1 TTTTTCAT
* *
1209560 -ATTTCCT
1 TTTTTCAT
1209567 TTTTTCTAT
1 TTTTTC-AT
1209576 TTTTTC--
1 TTTTTCAT
1209582 TTTTTCAT
1 TTTTTCAT
1209590 TTT
1 TTT
1209593 CTCTTTATTC
Statistics
Matches: 104, Mismatches: 9, Indels: 18
0.79 0.07 0.14
Matches are distributed among these distances:
6 16 0.15
7 31 0.30
8 44 0.42
9 13 0.12
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.73
Consensus pattern (8 bp):
TTTTTCAT
Found at i:1213142 original size:173 final size:172
Alignment explanation
Indices: 1212698--1213361 Score: 1058
Period size: 169 Copynumber: 3.8 Consensus size: 172
1212688 ATGGCTATCT
1212698 TAATCGTGATCTTACTTGTGTAGCATCACTACTGCCCTTATTTATTTTTATTTTTTTTGCAGTTT
1 TAATCGTGATCTTACTTGTGTAGCATCACTACTGCCC---TTTA----TATTTTTTTTGCAGTTT
1212763 CAGACTTGAATTCCTGACCTGTTAAACACCACCTCTTAAAAATGACTATATAAACCAACTTAGCT
59 CAGACTTGAATTCCTGACCTGTTAAACACCACCTCTTAAAAATGACTATATAAACCAACTTAGCT
*
1212828 AAATTCTTTGTTCACTACTGCCCAT---ACACACATATATATATATATA
124 AAATTCTGTGTTCACTACTGCCCATACAACACACATATATATATATATA
* * *
1212874 TAATCGTGATCTTACTTGTGTAGCATCACTATTGCCCTTTTTCTTTTTTTTGCAGTTTCAGACTT
1 TAATCGTGATCTTACTTGTGTAGCATCACTACTGCCCTTTATATTTTTTTTGCAGTTTCAGACTT
1212939 GAATTCCTGACCTGTTAAACACCACCTCTTAAAAATGACTATATAAACCAACTTAGCTAAATTCT
66 GAATTCCTGACCTGTTAAACACCACCTCTTAAAAATGACTATATAAACCAACTTAGCTAAATTCT
1213004 GTGTTCACTACTGCCCATACACACACACACATATATATATATATA
131 GTGTTCACTACTGCCCAT--ACA-ACACACATATATATATATATA
* *
1213049 TAATCGTGATCTTACTTGTGTAGCATCACTATTGCCC-TTAT-TTTTTTTTGCAATTTCAGACTT
1 TAATCGTGATCTTACTTGTGTAGCATCACTACTGCCCTTTATATTTTTTTTGCAGTTTCAGACTT
1213112 GAATTCCTGACCTGTTAAACACCACCTCTTAAAAATGACTATATAAACCAACTTAGCTAAATTCT
66 GAATTCCTGACCTGTTAAACACCACCTCTTAAAAATGACTATATAAACCAACTTAGCTAAATTCT
* * *
1213177 GTGTTCACTACTGCCCATACATATATATATATATATATATATA
131 GTGTTCACTACTGCCCATACA-ACACACATATATATATATATA
*
1213220 TAATCGTGATCTTACGTGTGTAGCATCACTACTGCCC--T-TATTTTTTTTGCAGTTTCAGACTT
1 TAATCGTGATCTTACTTGTGTAGCATCACTACTGCCCTTTATATTTTTTTTGCAGTTTCAGACTT
* *
1213282 GAAATCCTGACCTGTTAAACACCACCTCTTAAAAATGACTATATAAACC-ACTTAGTTAAATTCT
66 GAATTCCTGACCTGTTAAACACCACCTCTTAAAAATGACTATATAAACCAACTTAGCTAAATTCT
1213346 GTGTTCACTACTGCCC
131 GTGTTCACTACTGCCC
1213362 TTATTATTTT
Statistics
Matches: 466, Mismatches: 15, Indels: 21
0.93 0.03 0.04
Matches are distributed among these distances:
169 136 0.29
170 70 0.15
171 56 0.12
173 107 0.23
174 3 0.01
175 58 0.12
176 36 0.08
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38
Consensus pattern (172 bp):
TAATCGTGATCTTACTTGTGTAGCATCACTACTGCCCTTTATATTTTTTTTGCAGTTTCAGACTT
GAATTCCTGACCTGTTAAACACCACCTCTTAAAAATGACTATATAAACCAACTTAGCTAAATTCT
GTGTTCACTACTGCCCATACAACACACATATATATATATATA
Found at i:1213204 original size:2 final size:2
Alignment explanation
Indices: 1213197--1213221 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1213187 CTGCCCATAC
1213197 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1213222 ATCGTGATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1213344 original size:342 final size:343
Alignment explanation
Indices: 1212698--1213361 Score: 1095
Period size: 342 Copynumber: 1.9 Consensus size: 343
1212688 ATGGCTATCT
*
1212698 TAATCGTGATCTTACTTGTGTAGCATCACTACTGCCCTTATTTATTTTTATTTTTTTTGCAGTTT
1 TAATCGTGATCTTACTTGTGTAGCATCACTACTGCCC---TTTA---TTATTTTTTTTGCAATTT
1212763 CAGACTTGAATTCCTGACCTGTTAAACACCACCTCTTAAAAATGACTATATAAACCAACTTAGCT
60 CAGACTTGAATTCCTGACCTGTTAAACACCACCTCTTAAAAATGACTATATAAACCAACTTAGCT
* *
1212828 AAATTCTTTGTTCACTACTGCCCATACACACATATATATATATATATAATCGTGATCTTACTTGT
125 AAATTCTGTGTTCACTACTGCCCATACACACATATATATATATATATAATCGTGATCTTACGTGT
* * *
1212893 GTAGCATCACTATTGCCCTTTTTCTTTTTTTTGCAGTTTCAGACTTGAATTCCTGACCTGTTAAA
190 GTAGCATCACTACTGCCC--TTTATTTTTTTTGCAGTTTCAGACTTGAAATCCTGACCTGTTAAA
1212958 CACCACCTCTTAAAAATGACTATATAAACCAACTTAGCTAAATTCTGTGTTCACTACTGCCCATA
253 CACCACCTCTTAAAAATGACTATATAAACCAACTTAGCTAAATTCTGTGTTCACTACTGCCCATA
1213023 CACACACACACATATATATATATATA
318 CACACACACACATATATATATATATA
*
1213049 TAATCGTGATCTTACTTGTGTAGCATCACTATTGCCC-TTA-T-TTTTTTTTGCAATTTCAGACT
1 TAATCGTGATCTTACTTGTGTAGCATCACTACTGCCCTTTATTATTTTTTTTGCAATTTCAGACT
1213111 TGAATTCCTGACCTGTTAAACACCACCTCTTAAAAATGACTATATAAACCAACTTAGCTAAATTC
66 TGAATTCCTGACCTGTTAAACACCACCTCTTAAAAATGACTATATAAACCAACTTAGCTAAATTC
* *
1213176 TGTGTTCACTACTGCCCATACATATATATATATATATATATATATAATCGTGATCTTACGTGTGT
131 TGTGTTCACTACTGCCCATAC----ACACATATATATATATATATAATCGTGATCTTACGTGTGT
1213241 AGCATCACTACTGCCC-TTATTTTTTTTGCAGTTTCAGACTTGAAATCCTGACCTGTTAAACACC
192 AGCATCACTACTGCCCTTTATTTTTTTTGCAGTTTCAGACTTGAAATCCTGACCTGTTAAACACC
*
1213305 ACCTCTTAAAAATGACTATATAAACC-ACTTAGTTAAATTCTGTGTTCACTACTGCCC
257 ACCTCTTAAAAATGACTATATAAACCAACTTAGCTAAATTCTGTGTTCACTACTGCCC
1213362 TTATTATTTT
Statistics
Matches: 299, Mismatches: 10, Indels: 17
0.92 0.03 0.05
Matches are distributed among these distances:
342 135 0.45
343 73 0.24
346 52 0.17
347 3 0.01
351 36 0.12
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38
Consensus pattern (343 bp):
TAATCGTGATCTTACTTGTGTAGCATCACTACTGCCCTTTATTATTTTTTTTGCAATTTCAGACT
TGAATTCCTGACCTGTTAAACACCACCTCTTAAAAATGACTATATAAACCAACTTAGCTAAATTC
TGTGTTCACTACTGCCCATACACACATATATATATATATATAATCGTGATCTTACGTGTGTAGCA
TCACTACTGCCCTTTATTTTTTTTGCAGTTTCAGACTTGAAATCCTGACCTGTTAAACACCACCT
CTTAAAAATGACTATATAAACCAACTTAGCTAAATTCTGTGTTCACTACTGCCCATACACACACA
CACATATATATATATATA
Found at i:1215004 original size:15 final size:15
Alignment explanation
Indices: 1214984--1215012 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1214974 GTTCCAAATG
1214984 GATTTACTTCTTGAA
1 GATTTACTTCTTGAA
1214999 GATTTACTTCTTGA
1 GATTTACTTCTTGA
1215013 TTTATTACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.48
Consensus pattern (15 bp):
GATTTACTTCTTGAA
Found at i:1215155 original size:218 final size:217
Alignment explanation
Indices: 1214773--1215197 Score: 823
Period size: 218 Copynumber: 2.0 Consensus size: 217
1214763 GTTAATTCAG
1214773 CTTCTGAAGATTTACTTCTTGATTTATTACAACAAACATCCAAAATGGTAAGCCCGAATGGATTG
1 CTTCTGAAGATTTACTTCTTGATTTATTACAACAAACATCCAAAATGGTAAGCCCGAATGGATTG
*
1214838 TCTGAGCAAAAGGTTCCAAAAGCTGCTTGGGAGAACAATATTCAGTTTTCATCCTCACAACAGGT
66 TCTGAGCAAAAGGTTCCAAAAGCTGCTTGGGAGAACAATATTCAGTCTTCATCCTCACAACAGGT
1214903 CACAAAGTCAAAAGTCTTGGATGATTTCGATTCATGGTTGGATACTATTTGATGGTTTGTAATAA
131 CACAAAGTCAAAAGTCTTGGATGATTTCGATTCATGGTTGGATACTATTTGATGGTTTGTAATAA
1214968 AAGGAAGTTCCAAATGGATTTA
196 AAGGAAGTTCCAAATGGATTTA
1214990 CTTCTTGAAGATTTACTTCTTGATTTATTACAACAAACATCCAAAATGGTAAGCCCGAATGGATT
1 CTTC-TGAAGATTTACTTCTTGATTTATTACAACAAACATCCAAAATGGTAAGCCCGAATGGATT
1215055 GTCTGAGCAAAAGGTTCCAAAAGCTGCTTGGGAGAACAATATTCAGTCTTCATCCTCACAACAGG
65 GTCTGAGCAAAAGGTTCCAAAAGCTGCTTGGGAGAACAATATTCAGTCTTCATCCTCACAACAGG
1215120 TCACAAAGTCAAAAGTCTTGGATGATTTCGATTCATGGTTGGATACTATTTGATGGTTTGTAATA
130 TCACAAAGTCAAAAGTCTTGGATGATTTCGATTCATGGTTGGATACTATTTGATGGTTTGTAATA
*
1215185 CAAGGAAGTTCCA
195 AAAGGAAGTTCCA
1215198 CTCATTGAAT
Statistics
Matches: 205, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
217 4 0.02
218 201 0.98
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (217 bp):
CTTCTGAAGATTTACTTCTTGATTTATTACAACAAACATCCAAAATGGTAAGCCCGAATGGATTG
TCTGAGCAAAAGGTTCCAAAAGCTGCTTGGGAGAACAATATTCAGTCTTCATCCTCACAACAGGT
CACAAAGTCAAAAGTCTTGGATGATTTCGATTCATGGTTGGATACTATTTGATGGTTTGTAATAA
AAGGAAGTTCCAAATGGATTTA
Found at i:1215700 original size:22 final size:22
Alignment explanation
Indices: 1215675--1215723 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
1215665 TGGTTAATGT
1215675 AGAGACCCTTACTCCTTACTGG
1 AGAGACCCTTACTCCTTACTGG
1215697 AGAGACCCTTACTCCTTACTGG
1 AGAGACCCTTACTCCTTACTGG
1215719 AGAGA
1 AGAGA
1215724 GATGTACATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (22 bp):
AGAGACCCTTACTCCTTACTGG
Found at i:1219849 original size:18 final size:18
Alignment explanation
Indices: 1219826--1219861 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1219816 GACTGACTTC
1219826 CAGTTAGCCAACTTAAGA
1 CAGTTAGCCAACTTAAGA
1219844 CAGTTAGCCAACTTAAGA
1 CAGTTAGCCAACTTAAGA
1219862 GGCTGCCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (18 bp):
CAGTTAGCCAACTTAAGA
Found at i:1223038 original size:20 final size:21
Alignment explanation
Indices: 1223013--1223052 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1223003 TCAATAAATC
1223013 AAATATAATT-TAAAATTATA
1 AAATATAATTATAAAATTATA
*
1223033 AAATATAATTATAATATTAT
1 AAATATAATTATAAAATTAT
1223053 TTTTCAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AAATATAATTATAAAATTATA
Found at i:1223112 original size:19 final size:19
Alignment explanation
Indices: 1223090--1223126 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1223080 AGTATGGATG
1223090 AGAGAATAAGGAAATTAAT
1 AGAGAATAAGGAAATTAAT
1223109 AGAGAATAAGGAAATTAA
1 AGAGAATAAGGAAATTAA
1223127 GGAATTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.19
Consensus pattern (19 bp):
AGAGAATAAGGAAATTAAT
Found at i:1223156 original size:16 final size:16
Alignment explanation
Indices: 1223135--1223166 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1223125 AAGGAATTAA
*
1223135 TATAAAAGAAATAGTT
1 TATAAAAGAAAAAGTT
1223151 TATAAAAGAAAAAGTT
1 TATAAAAGAAAAAGTT
1223167 ACAGTCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.28
Consensus pattern (16 bp):
TATAAAAGAAAAAGTT
Found at i:1229783 original size:13 final size:13
Alignment explanation
Indices: 1229767--1229791 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1229757 ATATATTATA
1229767 AGAAGAAAAAAAC
1 AGAAGAAAAAAAC
1229780 AGAAGAAAAAAA
1 AGAAGAAAAAAA
1229792 ATAATAGAAA
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:0.80, C:0.04, G:0.16, T:0.00
Consensus pattern (13 bp):
AGAAGAAAAAAAC
Found at i:1229829 original size:27 final size:26
Alignment explanation
Indices: 1229799--1229867 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 26
1229789 AAAATAATAG
1229799 AAAAAGAAAATGA-AAACGAAGAAGAAA
1 AAAAAGAAAATGAGAAA-GAA-AAGAAA
*
1229826 AAAATGAAAATGAGAAAGAAAAGAAA
1 AAAAAGAAAATGAGAAAGAAAAGAAA
1229852 AAGAGAA-AAAATGAGA
1 AA-A-AAGAAAATGAGA
1229868 GATGAAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
26 8 0.22
27 25 0.68
28 4 0.11
ACGTcount: A:0.72, C:0.01, G:0.20, T:0.06
Consensus pattern (26 bp):
AAAAAGAAAATGAGAAAGAAAAGAAA
Found at i:1229851 original size:17 final size:17
Alignment explanation
Indices: 1229821--1229862 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
1229811 AAAACGAAGA
*
1229821 AGAAAAAAATGAAAATG
1 AGAAAAAAATGAAAAAG
1229838 AGAAAGAAAA-GAAAAAG
1 AGAAA-AAAATGAAAAAG
1229855 AGAAAAAA
1 AGAAAAAA
1229863 TGAGAGATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 3 0.13
17 16 0.70
18 4 0.17
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (17 bp):
AGAAAAAAATGAAAAAG
Found at i:1229852 original size:38 final size:38
Alignment explanation
Indices: 1229780--1229852 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
1229770 AGAAAAAAAC
*
1229780 AGAAGAAAAAAAATAATAGAAAAAGAAAATGAAAACGA
1 AGAAGAAAAAAAAAAATAGAAAAAGAAAATGAAAACGA
*
1229818 AGAAGAAAAAAATGAAAAT-GAGAAAGAAAA-GAAAA
1 AGAAGAAAAAAA--AAAATAGAAAAAGAAAATGAAAA
1229853 AGAGAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
38 17 0.55
39 10 0.32
40 4 0.13
ACGTcount: A:0.74, C:0.01, G:0.18, T:0.07
Consensus pattern (38 bp):
AGAAGAAAAAAAAAAATAGAAAAAGAAAATGAAAACGA
Found at i:1230251 original size:13 final size:13
Alignment explanation
Indices: 1230233--1230261 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1230223 CTACCCTAAA
1230233 AATTAGGGTTATG
1 AATTAGGGTTATG
1230246 AATTAGGGTTATG
1 AATTAGGGTTATG
1230259 AAT
1 AAT
1230262 ATACAATGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.28, T:0.38
Consensus pattern (13 bp):
AATTAGGGTTATG
Found at i:1232658 original size:47 final size:45
Alignment explanation
Indices: 1232565--1232689 Score: 175
Period size: 47 Copynumber: 2.8 Consensus size: 45
1232555 GTAAGTATGC
*
1232565 AAATAAGCTTACGAGCTTAT-GAAT-AATGGCAAGTATATTGATA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGATA
*
1232608 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTAGT-TTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTA-TATTGATA
*
1232655 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
1232690 AGATTTTATA
Statistics
Matches: 74, Mismatches: 3, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
43 20 0.27
44 3 0.04
45 11 0.15
46 1 0.01
47 38 0.51
48 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.30
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGATA
Found at i:1236769 original size:201 final size:202
Alignment explanation
Indices: 1236383--1236791 Score: 644
Period size: 201 Copynumber: 2.0 Consensus size: 202
1236373 GATAAAAGGT
* ** * *
1236383 TTACACTTTGAAACTAAATTTTCTCTGCTTCCTCCCGTTGTCTTCTTTACTTTTTACTTTGGTTG
1 TTACACGTTGAAACTAAATTTTCTCTGCTTCCTCCCGTTACCTTCTTTACTTCTTACTTTGATTG
*
1236448 TGAATTTCTTTTAATATTTTGATTTTTAAATTCATTTTTTTCAATTATTTTTAACACGACCAAAC
66 TGAATTTCTTTTAATATTTTGATTTTTAAATTCATTTTTTTCAATTATTTTTAACACGACCAAAA
* *
1236513 AAATTTTCTACTATTTGCTTTAGTACTTTCTTACACACCTACATCATCTACTACATGCTTTACTA
131 AAATTATCTACTATTTGCTTTAGTACTTTCTTACACACCTACATCATCTACTACATGATTTACTA
1236578 CTTTTAC
196 CTTTTAC
* * *
1236585 TTACACGTTGAAACTAGA-TTTC-CATGCTTCTTCCTGTTACCTTCTTTACTTCTTACTTTGATT
1 TTACACGTTGAAACTAAATTTTCTC-TGCTTCCTCCCGTTACCTTCTTTACTTCTTACTTTGATT
* * **
1236648 GTGAATTT-TTTTAATATTTTGATTTTTAACTTCATTTTTTTTAATTATTTTTAACACTTCCAAA
65 GTGAATTTCTTTTAATATTTTGATTTTTAAATTCATTTTTTTCAATTATTTTTAACACGACC-AA
1236712 AAAAATTATCTACTATTTGCTTTAGTACTTTCTTACACACCTACATCATCTACTACATGATTTAC
129 AAAAATTATCTACTATTTGCTTTAGTACTTTCTTACACACCTACATCATCTACTACATGATTTAC
1236777 TACTTTTAC
194 TACTTTTAC
1236786 TTACAC
1 TTACAC
1236792 CCTTTTTTTT
Statistics
Matches: 190, Mismatches: 15, Indels: 5
0.90 0.07 0.02
Matches are distributed among these distances:
200 50 0.26
201 124 0.65
202 16 0.08
ACGTcount: A:0.25, C:0.20, G:0.06, T:0.49
Consensus pattern (202 bp):
TTACACGTTGAAACTAAATTTTCTCTGCTTCCTCCCGTTACCTTCTTTACTTCTTACTTTGATTG
TGAATTTCTTTTAATATTTTGATTTTTAAATTCATTTTTTTCAATTATTTTTAACACGACCAAAA
AAATTATCTACTATTTGCTTTAGTACTTTCTTACACACCTACATCATCTACTACATGATTTACTA
CTTTTAC
Found at i:1236886 original size:23 final size:23
Alignment explanation
Indices: 1236828--1236886 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
1236818 CCAAGAATCA
*
1236828 TATTATTTTAT-TTTACTTATAT
1 TATTATTTTATATTTACATATAT
*
1236850 TATTATTGTT-TATTTACATGTAT
1 TATTATT-TTATATTTACATATAT
*
1236873 TTTTATTTTATATT
1 TATTATTTTATATT
1236887 ATTTTGTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 10 0.32
23 21 0.68
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.68
Consensus pattern (23 bp):
TATTATTTTATATTTACATATAT
Found at i:1238022 original size:12 final size:12
Alignment explanation
Indices: 1237997--1238090 Score: 91
Period size: 12 Copynumber: 7.8 Consensus size: 12
1237987 ACGGATATAT
* *
1237997 CAGAAATCAAAA
1 CAGAATTCAGAA
1238009 CAGAATTCAGAA
1 CAGAATTCAGAA
*
1238021 CAG-ATATCATAA
1 CAGAAT-TCAGAA
* *
1238033 CAGAATCCAGAT
1 CAGAATTCAGAA
*
1238045 CAGAAATCAGAA
1 CAGAATTCAGAA
* *
1238057 CAGAATCCAGAT
1 CAGAATTCAGAA
*
1238069 CAGAAATCAGAA
1 CAGAATTCAGAA
1238081 CAGAATTCAG
1 CAGAATTCAG
1238091 GTCATATATC
Statistics
Matches: 64, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
11 2 0.03
12 60 0.94
13 2 0.03
ACGTcount: A:0.51, C:0.19, G:0.15, T:0.15
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:1238024 original size:24 final size:24
Alignment explanation
Indices: 1237995--1238127 Score: 151
Period size: 24 Copynumber: 5.5 Consensus size: 24
1237985 AAACGGATAT
* *
1237995 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATCCAG
* * *
1238019 AACAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATCCAG
1238043 ATCAGAAATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATCCAG
*
1238067 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATCCAG
* * * * *
1238091 GTCATATATCAGAACAAAATTCA-
1 ATCAGAAATCAGAACAGAATCCAG
1238114 AGTCAGAAATCAGA
1 A-TCAGAAATCAGA
1238128 TAAAATATTT
Statistics
Matches: 93, Mismatches: 15, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
24 93 1.00
ACGTcount: A:0.50, C:0.18, G:0.14, T:0.17
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATCCAG
Found at i:1238049 original size:36 final size:36
Alignment explanation
Indices: 1237997--1238090 Score: 111
Period size: 36 Copynumber: 2.6 Consensus size: 36
1237987 ACGGATATAT
* *
1237997 CAGAAATCAAAACAGAATTCAGAACAGATAT-CATAA
1 CAGAAATCAGAACAGAATTCAGAACAGA-ATCCAGAA
* * *
1238033 CAG-AATCCAGATCAGAAATCAGAACAGAATCCAGAT
1 CAGAAAT-CAGAACAGAATTCAGAACAGAATCCAGAA
1238069 CAGAAATCAGAACAGAATTCAG
1 CAGAAATCAGAACAGAATTCAG
1238091 GTCATATATC
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
35 5 0.10
36 40 0.83
37 3 0.06
ACGTcount: A:0.51, C:0.19, G:0.15, T:0.15
Consensus pattern (36 bp):
CAGAAATCAGAACAGAATTCAGAACAGAATCCAGAA
Found at i:1238053 original size:7 final size:6
Alignment explanation
Indices: 1237995--1238086 Score: 54
Period size: 5 Copynumber: 15.3 Consensus size: 6
1237985 AAACGGATAT
* *
1237995 ATCAGAA ATCA-A AACAGA ATTCAGA A-CAGA TATCATA A-CAGA ATCCAG-
1 ATCAG-A ATCAGA ATCAGA A-TCAGA ATCAGA -ATCAGA ATCAGA AT-CAGA
1238043 ATCAGAA ATCAGA A-CAGA ATCCAG- ATCAGAA ATCAGA A-CAGA AT
1 ATCAG-A ATCAGA ATCAGA AT-CAGA ATCAG-A ATCAGA ATCAGA AT
1238087 TCAGGTCATA
Statistics
Matches: 68, Mismatches: 4, Indels: 27
0.69 0.04 0.27
Matches are distributed among these distances:
5 28 0.41
6 12 0.18
7 28 0.41
ACGTcount: A:0.52, C:0.18, G:0.14, T:0.15
Consensus pattern (6 bp):
ATCAGA
Found at i:1240618 original size:13 final size:13
Alignment explanation
Indices: 1240608--1240642 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
1240598 ACGGTCAATG
1240608 GGTCGGGTCAACA
1 GGTCGGGTCAACA
1240621 GGTCGGGTCAACA
1 GGTCGGGTCAACA
1240634 GGTCGGGTC
1 GGTCGGGTC
1240643 GGGTAAACGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.17, C:0.23, G:0.43, T:0.17
Consensus pattern (13 bp):
GGTCGGGTCAACA
Found at i:1240642 original size:18 final size:18
Alignment explanation
Indices: 1240621--1240666 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
1240611 CGGGTCAACA
1240621 GGTCGGGTCAACAGGTCG
1 GGTCGGGTCAACAGGTCG
* *
1240639 GGTCGGGTAAACGGGTCG
1 GGTCGGGTCAACAGGTCG
*
1240657 AGTCGGGTCA
1 GGTCGGGTCA
1240667 GGTTATGACC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.17, C:0.20, G:0.46, T:0.17
Consensus pattern (18 bp):
GGTCGGGTCAACAGGTCG
Found at i:1242760 original size:12 final size:12
Alignment explanation
Indices: 1242735--1242804 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
1242725 ACGGAGATAT
* *
1242735 CAGAAATCAAAA
1 CAGAATTCAGAA
1242747 CAGAATTCAGAA
1 CAGAATTCAGAA
1242759 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* * *
1242771 CAGAATCCATAT
1 CAGAATTCAGAA
*
1242783 CAGAAATCAGAA
1 CAGAATTCAGAA
1242795 CAGAATTCAG
1 CAGAATTCAG
1242805 GTCATATATC
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
11 2 0.04
12 42 0.91
13 2 0.04
ACGTcount: A:0.51, C:0.19, G:0.14, T:0.16
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:1242762 original size:24 final size:24
Alignment explanation
Indices: 1242735--1242841 Score: 99
Period size: 24 Copynumber: 4.5 Consensus size: 24
1242725 ACGGAGATAT
*
1242735 CAGAAATCAAAACAGAATTCAGAA
1 CAGAAATCAGAACAGAATTCAGAA
* * * *
1242759 CAGATATCAGAACAGAATCCATAT
1 CAGAAATCAGAACAGAATTCAGAA
**
1242783 CAGAAATCAGAACAGAATTCAGGT
1 CAGAAATCAGAACAGAATTCAGAA
* * * *
1242807 CATATATCAGAACAAAATTCA-AGT
1 CAGAAATCAGAACAGAATTCAGA-A
1242831 CAGAAATCAGA
1 CAGAAATCAGA
1242842 TAAAATATTT
Statistics
Matches: 67, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
24 67 1.00
ACGTcount: A:0.50, C:0.18, G:0.14, T:0.18
Consensus pattern (24 bp):
CAGAAATCAGAACAGAATTCAGAA
Found at i:1242802 original size:48 final size:48
Alignment explanation
Indices: 1242731--1242841 Score: 152
Period size: 48 Copynumber: 2.3 Consensus size: 48
1242721 TTAAACGGAG
* *
1242731 ATATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCC
1 ATATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAAAATCC
** * *
1242779 ATATCAGAAATCAGAACAGAATTCAGGTCATATATCAGAACAAAATTC
1 ATATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAAAATCC
1242827 A-AGTCAGAAATCAGA
1 ATA-TCAGAAATCAGA
1242842 TAAAATATTT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
47 1 0.02
48 55 0.98
ACGTcount: A:0.50, C:0.17, G:0.14, T:0.19
Consensus pattern (48 bp):
ATATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAAAATCC
Found at i:1245256 original size:15 final size:16
Alignment explanation
Indices: 1245226--1245259 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
1245216 GGTCAACAGT
1245226 GGTCAACGTTGGTCAAC
1 GGTCAACG-TGGTCAAC
1245243 GGTCAACG-GGTCAAC
1 GGTCAACGTGGTCAAC
1245258 GG
1 GG
1245260 GTCGGGTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.24, C:0.24, G:0.35, T:0.18
Consensus pattern (16 bp):
GGTCAACGTGGTCAAC
Found at i:1245267 original size:13 final size:13
Alignment explanation
Indices: 1245249--1245280 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1245239 CAACGGTCAA
*
1245249 CGGGTCAACGGGT
1 CGGGTCAACAGGT
1245262 CGGGTCAACAGGT
1 CGGGTCAACAGGT
1245275 CGGGTC
1 CGGGTC
1245281 GGGTAAACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.25, G:0.44, T:0.16
Consensus pattern (13 bp):
CGGGTCAACAGGT
Found at i:1245275 original size:8 final size:8
Alignment explanation
Indices: 1245216--1245262 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 8
1245206 TCAAAGTTTT
1245216 GGTCAACAG
1 GGTCAAC-G
1245225 TGGTCAACG
1 -GGTCAACG
1245234 TTGGTCAAC-
1 --GGTCAACG
1245243 GGTCAACG
1 GGTCAACG
1245251 GGTCAACG
1 GGTCAACG
1245259 GGTC
1 GGTC
1245263 GGGTCAACAG
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
7 7 0.20
8 12 0.34
9 1 0.03
10 15 0.43
ACGTcount: A:0.23, C:0.23, G:0.34, T:0.19
Consensus pattern (8 bp):
GGTCAACG
Found at i:1245280 original size:5 final size:5
Alignment explanation
Indices: 1245272--1245312 Score: 55
Period size: 5 Copynumber: 7.6 Consensus size: 5
1245262 CGGGTCAACA
1245272 GGTCG GGTCG GGTAAACG GGTCG GGTCG GGTCG GGTCG GGT
1 GGTCG GGTCG GGT---CG GGTCG GGTCG GGTCG GGTCG GGT
1245313 TATGACTGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 28 0.85
8 5 0.15
ACGTcount: A:0.07, C:0.17, G:0.56, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:1245280 original size:18 final size:18
Alignment explanation
Indices: 1245257--1245303 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
1245247 AACGGGTCAA
1245257 CGGGTCGGGTCAACAGGT
1 CGGGTCGGGTCAACAGGT
* *
1245275 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTCAACAGGT
1245293 CGGGTCGGGTC
1 CGGGTCGGGTC
1245304 GGGTCGGGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.13, C:0.21, G:0.49, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACAGGT
Found at i:1248087 original size:4 final size:4
Alignment explanation
Indices: 1248074--1248127 Score: 101
Period size: 4 Copynumber: 13.8 Consensus size: 4
1248064 TAAATATTAG
1248074 AAAT -AAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1248121 AAAT AAA
1 AAAT AAA
1248128 CAATGGTTAG
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 3 0.06
4 46 0.94
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:1260854 original size:22 final size:21
Alignment explanation
Indices: 1260805--1260872 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 21
1260795 AGACTTTGGA
**
1260805 GTATCGATACC-CT-TAGGAG
1 GTATCGATACCACTCTATTAG
*
1260824 GTACCGATACCACTCTATTAG
1 GTATCGATACCACTCTATTAG
1260845 AGTATCGATACCA-TC--TTAG
1 -GTATCGATACCACTCTATTAG
1260864 GTATCGATA
1 GTATCGATA
1260873 TTGGTTTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
18 9 0.21
19 14 0.33
20 2 0.05
21 6 0.14
22 11 0.26
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (21 bp):
GTATCGATACCACTCTATTAG
Found at i:1260869 original size:18 final size:20
Alignment explanation
Indices: 1260822--1260872 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
1260812 TACCCTTAGG
*
1260822 AGGTACCGATACCACTCTATT
1 AGGTATCGATACCACTC-ATT
1260843 AGAGTATCGATACCA-TC-TT
1 AG-GTATCGATACCACTCATT
1260862 AGGTATCGATA
1 AGGTATCGATA
1260873 TTGGTTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 9 0.32
19 4 0.14
21 4 0.14
22 11 0.39
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (20 bp):
AGGTATCGATACCACTCATT
Found at i:1263854 original size:22 final size:22
Alignment explanation
Indices: 1263829--1263889 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 22
1263819 CAATGTTACT
1263829 AAAGTGCCTCAACACTAATACA
1 AAAGTGCCTCAACACTAATACA
* * *
1263851 AAAGT-CCATTC-GCACTGATACT
1 AAAGTGCC--TCAACACTAATACA
*
1263873 AAAGTGCCTTAACACTA
1 AAAGTGCCTCAACACTA
1263890 CAAACACATA
Statistics
Matches: 29, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
21 3 0.10
22 22 0.76
23 4 0.14
ACGTcount: A:0.39, C:0.26, G:0.11, T:0.23
Consensus pattern (22 bp):
AAAGTGCCTCAACACTAATACA
Found at i:1267145 original size:2 final size:2
Alignment explanation
Indices: 1267138--1267166 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1267128 TTGTTTTTAA
1267138 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1267167 ATTATTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1268721 original size:12 final size:13
Alignment explanation
Indices: 1268688--1268721 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
1268678 TTTGAATTAA
1268688 TAATTAAATATTT
1 TAATTAAATATTT
1268701 TAATATAAAT-TTT
1 TAAT-TAAATATTT
1268714 TAATTAAA
1 TAATTAAA
1268722 ATTGAGTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.20
13 11 0.55
14 5 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TAATTAAATATTT
Found at i:1273429 original size:11 final size:11
Alignment explanation
Indices: 1273405--1273438 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
1273395 TGTTAAAAAA
1273405 ATTAACACTAAT
1 ATTAACA-TAAT
1273417 ATTAACATAAT
1 ATTAACATAAT
1273428 ATTAAGCATAA
1 ATTAA-CATAA
1273439 ATGAAGTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.32
Consensus pattern (11 bp):
ATTAACATAAT
Found at i:1274252 original size:23 final size:23
Alignment explanation
Indices: 1274221--1274291 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
1274211 TAAGCTACCA
* *
1274221 AAAGACAGAGAAAAACGTGTCAT
1 AAAGGCAGAGAAAAACATGTCAT
* *
1274244 AAAGGCAGATATAAACATGTCAT
1 AAAGGCAGAGAAAAACATGTCAT
1274267 AAAGGC--AG-AAAACATGTCAT
1 AAAGGCAGAGAAAAACATGTCAT
1274287 AAAGG
1 AAAGG
1274292 TAAAAAACAT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
20 16 0.38
21 1 0.02
23 25 0.60
ACGTcount: A:0.51, C:0.13, G:0.21, T:0.15
Consensus pattern (23 bp):
AAAGGCAGAGAAAAACATGTCAT
Found at i:1274281 original size:20 final size:20
Alignment explanation
Indices: 1274232--1274305 Score: 94
Period size: 20 Copynumber: 3.5 Consensus size: 20
1274222 AAGACAGAGA
*
1274232 AAAACGTGTCATAAAGGCAG
1 AAAACATGTCATAAAGGCAG
1274252 ATATAAACATGTCATAAAGGCAG
1 --A-AAACATGTCATAAAGGCAG
* *
1274275 AAAACATGTCATAAAGGTAA
1 AAAACATGTCATAAAGGCAG
1274295 AAAACATGTCA
1 AAAACATGTCA
1274306 CAAAAACATA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
20 28 0.58
21 1 0.02
22 1 0.02
23 18 0.38
ACGTcount: A:0.50, C:0.14, G:0.18, T:0.19
Consensus pattern (20 bp):
AAAACATGTCATAAAGGCAG
Found at i:1276348 original size:15 final size:16
Alignment explanation
Indices: 1276299--1276350 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
1276289 TTCAAAGCTA
* *
1276299 ATTCATACATCTGAATA
1 ATTCA-ACATTTGAATC
1276316 ATTCAACATTTGAATC
1 ATTCAACATTTGAATC
*
1276332 ATTCAACGTTT-AATC
1 ATTCAACATTTGAATC
1276347 ATTC
1 ATTC
1276351 TGAAACAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
15 8 0.25
16 19 0.59
17 5 0.16
ACGTcount: A:0.37, C:0.19, G:0.06, T:0.38
Consensus pattern (16 bp):
ATTCAACATTTGAATC
Found at i:1279287 original size:17 final size:16
Alignment explanation
Indices: 1279262--1279313 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
1279252 CCTGAAAAAC
*
1279262 AAAACAAAATAAATAA
1 AAAATAAAATAAATAA
*
1279278 GAAAATAAAAATAGATAA
1 -AAAAT-AAAATAAATAA
*
1279296 AAAATAAAAAAAATAA
1 AAAATAAAATAAATAA
1279312 AA
1 AA
1279314 GTAAATAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 11 0.37
17 9 0.30
18 10 0.33
ACGTcount: A:0.81, C:0.02, G:0.04, T:0.13
Consensus pattern (16 bp):
AAAATAAAATAAATAA
Found at i:1279287 original size:22 final size:21
Alignment explanation
Indices: 1279257--1279330 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 21
1279247 TTGGACCTGA
* *
1279257 AAAACAAAACAAAATAAATAAG
1 AAAATAAAA-AAAATAAATAAT
* *
1279279 AAAATAAAAATAGATAAAAAAT
1 AAAATAAAAA-AAATAAATAAT
1279301 AAAA-AAAATAAAAGTAAATAAT
1 AAAATAAAA-AAAA-TAAATAAT
1279323 AATAATAA
1 AA-AATAA
1279331 TATAGTATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
21 7 0.17
22 30 0.73
23 2 0.05
24 2 0.05
ACGTcount: A:0.77, C:0.03, G:0.04, T:0.16
Consensus pattern (21 bp):
AAAATAAAAAAAATAAATAAT
Found at i:1279290 original size:18 final size:17
Alignment explanation
Indices: 1279267--1279313 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
1279257 AAAACAAAAC
1279267 AAAATAAATAAGAAAATA
1 AAAATAAATAA-AAAATA
*
1279285 AAAATAGATAAAAAATA
1 AAAATAAATAAAAAATA
1279302 AAAA-AAATAAAA
1 AAAATAAATAAAA
1279314 GTAAATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 7 0.26
17 10 0.37
18 10 0.37
ACGTcount: A:0.81, C:0.00, G:0.04, T:0.15
Consensus pattern (17 bp):
AAAATAAATAAAAAATA
Found at i:1279321 original size:26 final size:28
Alignment explanation
Indices: 1279279--1279330 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 28
1279269 AATAAATAAG
*
1279279 AAAATAAAAATAGATAA-AA-AATAAAA
1 AAAATAAAAATAAATAATAATAATAAAA
*
1279305 AAAATAAAAGTAAATAATAATAATAA
1 AAAATAAAAATAAATAATAATAATAA
1279331 TATAGTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 15 0.68
27 2 0.09
28 5 0.23
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (28 bp):
AAAATAAAAATAAATAATAATAATAAAA
Found at i:1281736 original size:42 final size:42
Alignment explanation
Indices: 1281591--1281789 Score: 166
Period size: 43 Copynumber: 4.7 Consensus size: 42
1281581 TAATAGTTCA
* * * * * * * *
1281591 AGATTTATAGCGGTGTTTTTGGAACAAACGCTGTAAAATGTTG
1 AGATCTATAGCAGCGTTTTTGGAACAAACACCGCAAAA-GGTC
* * *
1281634 AGATATATAGC-GACATTTTTGGAATAAACACCGCAAAAGGTC
1 AGATCTATAGCAG-CGTTTTTGGAACAAACACCGCAAAAGGTC
* *
1281676 GAGATCTATAGCAACGTTTTTGGAACAAACACTGCAAAAGGTC
1 -AGATCTATAGCAGCGTTTTTGGAACAAACACCGCAAAAGGTC
* * ** * *
1281719 AGATCTATAGTAGCGTTTTTTGAACAAATGCCGCAAAAGATT
1 AGATCTATAGCAGCGTTTTTGGAACAAACACCGCAAAAGGTC
* *
1281761 AGATCTATAGCGGCATTTTTGGATACAAA
1 AGATCTATAGCAGCGTTTTTGGA-ACAAA
1281790 TGCCGCTAAT
Statistics
Matches: 126, Mismatches: 26, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
42 56 0.44
43 70 0.56
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.29
Consensus pattern (42 bp):
AGATCTATAGCAGCGTTTTTGGAACAAACACCGCAAAAGGTC
Found at i:1282370 original size:3 final size:3
Alignment explanation
Indices: 1282356--1282419 Score: 85
Period size: 3 Copynumber: 21.0 Consensus size: 3
1282346 TTTCTCCATT
*
1282356 TTA TTCA TTA TTA TTA TTTA TTA TTA TT- CTA TTA TTA TTA TTA TTA
1 TTA TT-A TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
1282402 ATA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
1282420 CATGCCCAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
2 1 0.02
3 47 0.87
4 6 0.11
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1283234 original size:14 final size:14
Alignment explanation
Indices: 1283215--1283250 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1283205 TTCTCTCCAA
1283215 CGAGAGAAATATTT
1 CGAGAGAAATATTT
1283229 CGAGAGAAATATTT
1 CGAGAGAAATATTT
*
1283243 AGAGAGAA
1 CGAGAGAA
1283251 GGGAGAGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.47, C:0.06, G:0.25, T:0.22
Consensus pattern (14 bp):
CGAGAGAAATATTT
Found at i:1284091 original size:142 final size:144
Alignment explanation
Indices: 1283910--1284299 Score: 343
Period size: 148 Copynumber: 2.7 Consensus size: 144
1283900 TTAAATAATA
* * * *
1283910 ATATTTATTT-ATTATTAAATACTCAGAAA-GGG-TAGTCTTAAAATAACAAGATGTCATATTCT
1 ATATTTATTTAATT-TT-AATATTAAGAAAGGGGCT-GTCTTAAAACAACAAGAAGTCATATTCT
* * * **
1283972 GGTATTTTAAAA-ATAATAAATATCATGCTTATA-AAATATATATTTTCTTTAATTTTATATAAA
63 GATATTTTAAAATA-AATAAATATCATACTTATATAAAT-TATATATAATTT-ATTTT-T-TAAA
**
1284035 TTA-TTTT-AATCA-TTTT-TT
123 TTATTTTTAAAAAAGTTTTATT
* * *
1284053 -TATTTATTTAATTTTAATATTAAGAAAGGGGCTGTCTTAAAGCAACTAGAAGTCATTTTCTGAT
1 ATATTTATTTAATTTTAATATTAAGAAAGGGGCTGTCTTAAAACAACAAGAAGTCATATTCTGAT
* * * *
1284117 ATTTTTAAATAAATAAATATCCTACTTTTATAAATTATATATAATTTATTTTTTTAATTATTTTT
66 ATTTTAAAATAAATAAATATCATACTTATATAAATTATATATAATTTATTTTTTAAATTATTTTT
1284182 AGAAAAATGTTTTATT
131 A-AAAAA-GTTTTATT
* * * * *
1284198 GATATTTATTTATTTTTTAATATTAAGAAAGGGGCTGTCTTAAAGCAACTAGAAGTCATTTTCTA
1 -ATATTTATTTA-ATTTTAATATTAAGAAAGGGGCTGTCTTAAAACAACAAGAAGTCATATTCTG
* * * *
1284263 ATATTTCT-AAGTAAATAAATATCTTATTTATAAAAAT
64 ATATTT-TAAAATAAATAAATATCATACTTATATAAAT
1284300 ATAAAAAATA
Statistics
Matches: 207, Mismatches: 25, Indels: 25
0.81 0.10 0.10
Matches are distributed among these distances:
139 6 0.03
140 5 0.02
141 15 0.07
142 75 0.36
143 9 0.04
144 4 0.02
145 2 0.01
147 10 0.05
148 80 0.39
149 1 0.00
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (144 bp):
ATATTTATTTAATTTTAATATTAAGAAAGGGGCTGTCTTAAAACAACAAGAAGTCATATTCTGAT
ATTTTAAAATAAATAAATATCATACTTATATAAATTATATATAATTTATTTTTTAAATTATTTTT
AAAAAAGTTTTATT
Found at i:1284330 original size:16 final size:17
Alignment explanation
Indices: 1284299--1284332 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1284289 TTTATAAAAA
1284299 TATAAAAAATATATATT
1 TATAAAAAATATATATT
*
1284316 TATAAAAATTA-ATATT
1 TATAAAAAATATATATT
1284332 T
1 T
1284333 TTTCTTGGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TATAAAAAATATATATT
Found at i:1285541 original size:9 final size:9
Alignment explanation
Indices: 1285512--1285550 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
1285502 GTACTAACCA
1285512 TTTTATTTT
1 TTTTATTTT
* *
1285521 TTTTCTTAT
1 TTTTATTTT
1285530 TTTTATTTT
1 TTTTATTTT
1285539 TTTTATTTT
1 TTTTATTTT
1285548 TTT
1 TTT
1285551 ACATTGCTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.10, C:0.03, G:0.00, T:0.87
Consensus pattern (9 bp):
TTTTATTTT
Found at i:1285544 original size:15 final size:16
Alignment explanation
Indices: 1285519--1285548 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1285509 CCATTTTATT
1285519 TTTTTTCTTATTTTTA
1 TTTTTTCTTATTTTTA
1285535 TTTTTT-TTATTTTT
1 TTTTTTCTTATTTTT
1285549 TTACATTGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.10, C:0.03, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTTTTCTTATTTTTA
Found at i:1286381 original size:7 final size:7
Alignment explanation
Indices: 1286365--1286397 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
1286355 TTTTCATACA
1286365 TGCA-TT
1 TGCATTT
1286371 TGCATTT
1 TGCATTT
1286378 TGCATTT
1 TGCATTT
1286385 T-CATTT
1 TGCATTT
1286391 TGCATTT
1 TGCATTT
1286398 GTACTTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 10 0.40
7 15 0.60
ACGTcount: A:0.15, C:0.15, G:0.12, T:0.58
Consensus pattern (7 bp):
TGCATTT
Found at i:1286383 original size:13 final size:13
Alignment explanation
Indices: 1286365--1286398 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
1286355 TTTTCATACA
1286365 TGCATTTGCATTT
1 TGCATTTGCATTT
*
1286378 TGCATTTTCATTT
1 TGCATTTGCATTT
1286391 TGCATTTG
1 TGCATTTG
1286399 TACTTTTATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.56
Consensus pattern (13 bp):
TGCATTTGCATTT
Found at i:1293163 original size:36 final size:36
Alignment explanation
Indices: 1293112--1293384 Score: 153
Period size: 36 Copynumber: 7.5 Consensus size: 36
1293102 TTCAAATAGT
1293112 AATTTATCTCACTTGAGATTATTTTTCTTCAAACAA
1 AATTTATCTCACTTGAGATTATTTTTCTTCAAACAA
* * * * *
1293148 AATTTGTCTCGCTTGAGA-CA-GTTTCACTCGAAACAA
1 AATTTATCTCACTTGAGATTATTTTTC-TTC-AAACAA
* *
1293184 CAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
1 -AATTTATCTCACTTGAGATTATTTTTCTTCAAACAA
* ** * * * * *
1293221 AATTTGTCTTGCATGAGA-CA-GTTTCACTCGAAATAA
1 AATTTATCTCACTTGAGATTATTTTTC-TTC-AAACAA
* *
1293257 CAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
1 -AATTTATCTCACTTGAGATTATTTTTCTTCAAACAA
* * * * * * *
1293294 ACTGTGTCTCGCTTGAGA-CA-GTTTCACTCGAAACAAA
1 AATTTATCTCACTTGAGATTATTTTTC-TTC-AAAC-AA
* *
1293331 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
1 AATTTATCTCACTTGAGATTATTTTTCTTCAAACAA
* ** *
1293367 GATTCGTCTCGCTTGAGA
1 AATTTATCTCACTTGAGA
1293385 CAGTTTCACT
Statistics
Matches: 168, Mismatches: 54, Indels: 30
0.67 0.21 0.12
Matches are distributed among these distances:
34 12 0.07
35 5 0.03
36 75 0.45
37 61 0.36
38 3 0.02
39 12 0.07
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (36 bp):
AATTTATCTCACTTGAGATTATTTTTCTTCAAACAA
Found at i:1293365 original size:37 final size:37
Alignment explanation
Indices: 1293112--1293366 Score: 192
Period size: 37 Copynumber: 7.0 Consensus size: 37
1293102 TTCAAATAGT
* *
1293112 AATTTATCTCACTTGAGATTATTTTTCTTCAAAC-AA
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA
* * ** ** ** *
1293148 AATTTGTCTCGCTTGAGACAGTTTCACTCGAAACAAC
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA
1293185 AATTTATCTCACTTGAGATTGTTTTTCTTAAAAC-AA
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA
* ** * ** ** ** * *
1293221 AATTTGTCTTGCATGAGACAGTTTCACTCGAAATAAC
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA
1293258 AATTTATCTCACTTGAGATTGTTTTTCTTAAAAC-AA
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA
* * * * ** ** **
1293294 ACTGTGTCTCGCTTGAGACAGTTTCACTCGAAACAAA
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA
1293331 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
1293367 GATTCGTCTC
Statistics
Matches: 153, Mismatches: 63, Indels: 5
0.69 0.29 0.02
Matches are distributed among these distances:
36 74 0.48
37 79 0.52
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (37 bp):
AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA
Found at i:1293416 original size:73 final size:73
Alignment explanation
Indices: 1293112--1293408 Score: 477
Period size: 73 Copynumber: 4.1 Consensus size: 73
1293102 TTCAAATAGT
* *
1293112 AATTTATCTCACTTGAGATTATTTTTCTTCAAACAAAATTTGTCTCGCTTGAGACAGTTTCACTC
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCACTC
*
1293177 GAAACAAC
66 GAAACAAA
* *
1293185 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTTGCATGAGACAGTTTCACTC
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCACTC
* *
1293250 GAAATAAC
66 GAAACAAA
* *
1293258 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTGTGTCTCGCTTGAGACAGTTTCACTC
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCACTC
1293323 GAAACAAA
66 GAAACAAA
* * *
1293331 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGATTCGTCTCGCTTGAGACAGTTTCACTA
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCACTC
*
1293396 GAAATAAA
66 GAAACAAA
1293404 AATTT
1 AATTT
1293409 CCATCACTCG
Statistics
Matches: 207, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 207 1.00
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.37
Consensus pattern (73 bp):
AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCACTC
GAAACAAA
Found at i:1293883 original size:122 final size:122
Alignment explanation
Indices: 1293423--1293873 Score: 719
Period size: 122 Copynumber: 3.7 Consensus size: 122
1293413 CACTCGATGA
*
1293423 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGATGAAGTTCATAA
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
* * *
1293488 TGAGAAGAATCTGTTCAACCTTTTGCTCGATTCTATCACAGAAAGAGATAAATCAGC
66 TGAGAAGAATTTGTTCAACCTTTTGCTCGATTCTATCACAGAAGGAGATAGATCAGC
* * * *
1293545 ATCAACATTTCTAGAGGAATTCATAACGAGAAGAACTCATCTGAAGA-G--GAAGAAGTTCATAA
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
* * *
1293607 TGAGAAGAATTTGTACAACCTTTTGCTCGATTCTATCACAAAAGGAGATAGATCAAC
66 TGAGAAGAATTTGTTCAACCTTTTGCTCGATTCTATCACAGAAGGAGATAGATCAGC
* *
1293664 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAGGAATAAGAAGTTCATAA
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
* *
1293729 TGAGAAGAACTTGCTCAACCTTTTGCTCGATTCTATCACAGAAGGAGATAGATCAGC
66 TGAGAAGAATTTGTTCAACCTTTTGCTCGATTCTATCACAGAAGGAGATAGATCAGC
*
1293786 ATCAACATTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGATGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGA-AGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
*
1293851 ATGAGAAGAATTTGTTCGACCTT
65 ATGAGAAGAATTTGTTCAACCTT
1293874 AGATTGATTC
Statistics
Matches: 297, Mismatches: 28, Indels: 7
0.89 0.08 0.02
Matches are distributed among these distances:
119 106 0.36
120 1 0.00
121 1 0.00
122 123 0.41
123 66 0.22
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (122 bp):
ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
TGAGAAGAATTTGTTCAACCTTTTGCTCGATTCTATCACAGAAGGAGATAGATCAGC
Found at i:1293953 original size:139 final size:135
Alignment explanation
Indices: 1293786--1294149 Score: 480
Period size: 139 Copynumber: 2.6 Consensus size: 135
1293776 ATAGATCAGC
1293786 ATCAACATTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGATGAAGAAGAAGTTCATA
1 ATCAACATTT-CAGA-AGAGTTCATAATGAGAAGAACTCATCTGAAGATGAAGAAGAAGTTCATA
* * * * * *
1293851 ATGAGAAGAATTTGTTCGACCTTAG-ATTGATTCATCACCTATGGAGTTAAATGAAAGAAGAACC
64 ATGAGAAGAACTTGTTCAACCTT-GCATTAATTCATCACATATGAAGTTAAATCAAAG-A-AACC
*
1293915 TCTCTTGAGG
126 TCTCTTGAGA
* *
1293925 ATCAACATTATCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACATT-TCAGA-AGAGTTCATAATGAGAAGAACTCATCTGAAGATGAAGAAGAAGTTCATA
* * * *
1293990 ATGAGAAGAACTTGTTCAACCTTGCCTTAATTCATCACATATGAAGTTGAATCAATGACACCTCT
64 ATGAGAAGAACTTGTTCAACCTTGCATTAATTCATCACATATGAAGTTAAATCAAAGAAACCTCT
*
1294055 TTTGAGA
129 CTTGAGA
*
1294062 ATCAACATGTCCAGAAGGAGTTCATAATGAGTAA-AACTCATCTGAAGATGAAGAAGAAGTTCAT
1 ATCAACAT-TTCAGAA-GAGTTCATAATGAG-AAGAACTCATCTGAAGATGAAGAAGAAGTTCAT
*
1294126 AATGAGAAAAACTTGTTCAACCTT
63 AATGAGAAGAACTTGTTCAACCTT
1294150 TTGCTAGATT
Statistics
Matches: 201, Mismatches: 19, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
136 1 0.00
137 88 0.44
138 5 0.02
139 106 0.53
140 1 0.00
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.27
Consensus pattern (135 bp):
ATCAACATTTCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGATGAAGAAGAAGTTCATAAT
GAGAAGAACTTGTTCAACCTTGCATTAATTCATCACATATGAAGTTAAATCAAAGAAACCTCTCT
TGAGA
Found at i:1294367 original size:3 final size:3
Alignment explanation
Indices: 1294349--1294433 Score: 70
Period size: 3 Copynumber: 28.7 Consensus size: 3
1294339 GTTTTTTCTC
*
1294349 TAT T-T TAT TCAT TAT TAT TATT TAT TAT TAT T-C TAT TAT TAT TAT
1 TAT TAT TAT T-AT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
1294394 TAT T-T TAAT TA- TAA TAA TAA TAA TAT TAT TAT TAT TAT TA
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1294434 CAGGCCCAAA
Statistics
Matches: 72, Mismatches: 3, Indels: 14
0.81 0.03 0.16
Matches are distributed among these distances:
2 7 0.10
3 57 0.79
4 8 0.11
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:1294374 original size:17 final size:16
Alignment explanation
Indices: 1294352--1294432 Score: 69
Period size: 17 Copynumber: 5.1 Consensus size: 16
1294342 TTTTCTCTAT
1294352 TTTATTCATTATTATTA
1 TTTATT-ATTATTATTA
*
1294369 TTTATTATTATT-CTA
1 TTTATTATTATTATTA
1294384 -TTATTATTATTATT-
1 TTTATTATTATTATTA
* * * *
1294398 TTAATTATAATAATAA
1 TTTATTATTATTATTA
*
1294414 TAATATTATTATTATTA
1 T-TTATTATTATTATTA
1294431 TT
1 TT
1294433 ACAGGCCCAA
Statistics
Matches: 48, Mismatches: 12, Indels: 9
0.70 0.17 0.13
Matches are distributed among these distances:
14 11 0.23
15 13 0.27
16 7 0.15
17 17 0.35
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTATTATTATTATTA
Found at i:1294391 original size:24 final size:22
Alignment explanation
Indices: 1294349--1294400 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 22
1294339 GTTTTTTCTC
1294349 TATTTTATTCATTATTATTATT
1 TATTTTATTCATTATTATTATT
1294371 TATTATTATTCTATTATTATTA-T
1 TATT-TTATTC-ATTATTATTATT
1294394 TATTTTA
1 TATTTTA
1294401 ATTATAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.25
23 11 0.39
24 10 0.36
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (22 bp):
TATTTTATTCATTATTATTATT
Found at i:1301924 original size:21 final size:21
Alignment explanation
Indices: 1301898--1301961 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
1301888 TTTTGGTGCA
*
1301898 GAGGGAATCGATCCCCCCCAT
1 GAGGGAACCGATCCCCCCCAT
* **
1301919 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATCCCCCCCAT
*
1301940 GAAGGGGAACCGATTCCCCCCA
1 G-A-GGGAACCGATCCCCCCCA
1301962 CAGGGGAATC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 18 0.51
22 1 0.03
23 16 0.46
ACGTcount: A:0.23, C:0.36, G:0.25, T:0.16
Consensus pattern (21 bp):
GAGGGAACCGATCCCCCCCAT
Found at i:1301968 original size:21 final size:21
Alignment explanation
Indices: 1301900--1301980 Score: 60
Period size: 21 Copynumber: 3.8 Consensus size: 21
1301890 TTGGTGCAGA
*
1301900 GGGAATCGA-TCCCCCC-CATG
1 GGGAACCGATTCCCCCCACA-G
*
1301920 AGGGAACCGATTCCCCCTTTGA-AG
1 -GGGAACCGATTCCCCC---CACAG
1301944 GGGAACCGATTCCCCCCACAG
1 GGGAACCGATTCCCCCCACAG
* *
1301965 GGGAATCGATACCCCC
1 GGGAACCGATTCCCCC
1301981 TGGGGTTCTG
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
20 1 0.02
21 24 0.49
22 6 0.12
23 16 0.33
24 1 0.02
25 1 0.02
ACGTcount: A:0.23, C:0.37, G:0.25, T:0.15
Consensus pattern (21 bp):
GGGAACCGATTCCCCCCACAG
Found at i:1304303 original size:13 final size:14
Alignment explanation
Indices: 1304285--1304314 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1304275 TAAGGGGGAG
1304285 TAATTTCAAAA-CT
1 TAATTTCAAAATCT
1304298 TAATTTCAAAATCT
1 TAATTTCAAAATCT
1304312 TAA
1 TAA
1304315 AATTACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (14 bp):
TAATTTCAAAATCT
Found at i:1309042 original size:21 final size:22
Alignment explanation
Indices: 1309015--1309076 Score: 81
Period size: 21 Copynumber: 2.8 Consensus size: 22
1309005 TGCTAGATAA
1309015 AATGTCCCGAAGGACCACATA-
1 AATGTCCCGAAGGACCACATAG
* *
1309036 TATGTCCCGAAGGACCGCATAG
1 AATGTCCCGAAGGACCACATAG
*
1309058 AATTGCCCCGAAGGACCAC
1 AA-TGTCCCGAAGGACCAC
1309077 GTGGAACCCT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 19 0.56
22 1 0.03
23 14 0.41
ACGTcount: A:0.32, C:0.31, G:0.23, T:0.15
Consensus pattern (22 bp):
AATGTCCCGAAGGACCACATAG
Found at i:1314193 original size:6 final size:6
Alignment explanation
Indices: 1314182--1314234 Score: 88
Period size: 6 Copynumber: 8.8 Consensus size: 6
1314172 TTTATTTCTT
* *
1314182 CCTCTA CCTCTA CCTCTA CCTCTA CCTCTA CCTCTA CCTCTT CCTCTT
1 CCTCTA CCTCTA CCTCTA CCTCTA CCTCTA CCTCTA CCTCTA CCTCTA
1314230 CCTCT
1 CCTCT
1314235 CTGGGATATC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.11, C:0.51, G:0.00, T:0.38
Consensus pattern (6 bp):
CCTCTA
Found at i:1316139 original size:23 final size:24
Alignment explanation
Indices: 1316094--1316139 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
1316084 CACAATAGCT
* * *
1316094 CGTATAAATTGCACTGAAGTGCCG
1 CGTAGAAATTGCACCGAAATGCCG
1316118 CGTAGAAA-TGCACCGAAATGCC
1 CGTAGAAATTGCACCGAAATGCC
1316140 ACATAAAATG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.20
Consensus pattern (24 bp):
CGTAGAAATTGCACCGAAATGCCG
Found at i:1316155 original size:22 final size:22
Alignment explanation
Indices: 1316130--1316182 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
1316120 TAGAAATGCA
*
1316130 CCGAAATG-CCACATAAAATGTC
1 CCGAAAGGACCACAT-AAATGTC
*
1316152 CCG-AAGGACCACATATATGTC
1 CCGAAAGGACCACATAAATGTC
1316173 CCG-AAGGACC
1 CCGAAAGGACC
1316183 GCGTAGAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 19 0.68
22 9 0.32
ACGTcount: A:0.36, C:0.30, G:0.19, T:0.15
Consensus pattern (22 bp):
CCGAAAGGACCACATAAATGTC
Found at i:1316173 original size:21 final size:22
Alignment explanation
Indices: 1316138--1316182 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
1316128 CACCGAAATG
1316138 CCACATAAAATGTCCCGAAGGA
1 CCACATAAAATGTCCCGAAGGA
*
1316160 CCACAT-ATATGTCCCGAAGGA
1 CCACATAAAATGTCCCGAAGGA
1316181 CC
1 CC
1316183 GCGTAGAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.36, C:0.31, G:0.18, T:0.16
Consensus pattern (22 bp):
CCACATAAAATGTCCCGAAGGA
Found at i:1317986 original size:42 final size:44
Alignment explanation
Indices: 1317873--1317993 Score: 129
Period size: 44 Copynumber: 2.8 Consensus size: 44
1317863 ATTGCGGCAT
* * * * *
1317873 TTATAATAAAAGCGCCACTAAGGTACATAAGTGTTGTAGCGTTTA
1 TTATAA-AAAAACGCCACTAAGGTACATGACTATTATAGCGTTTA
** * *
1317918 TTATAAAAAAACGCCACTAAATTACATGATTATTATGGCGTTTA
1 TTATAAAAAAACGCCACTAAGGTACATGACTATTATAGCGTTTA
*
1317962 -T-TACAAAAACGCCACTAAGGTACATGACTATT
1 TTATAAAAAAACGCCACTAAGGTACATGACTATT
1317994 GCGACGTTTG
Statistics
Matches: 64, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
42 27 0.42
43 1 0.02
44 30 0.47
45 6 0.09
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.31
Consensus pattern (44 bp):
TTATAAAAAAACGCCACTAAGGTACATGACTATTATAGCGTTTA
Found at i:1318002 original size:42 final size:42
Alignment explanation
Indices: 1317924--1318064 Score: 126
Period size: 41 Copynumber: 3.4 Consensus size: 42
1317914 TTTATTATAA
* * ** *
1317924 AAAAACGCCACTAAATTACATGATTATTATGGCGTTTATTAC
1 AAAAACGCCACTAAAGTACATGACTATTGCGACGTTTATTAC
* *
1317966 AAAAACGCCACTAAGGTACATGACTATTGCGACGTTTGA--AT
1 AAAAACGCCACTAAAGTACATGACTATTGCGACGTTT-ATTAC
* * * * *
1318007 AAAAACGCCACTAAAGTATAAGTCTATAGCGACGTTTGTT-C
1 AAAAACGCCACTAAAGTACATGACTATTGCGACGTTTATTAC
* *
1318048 ACAAACGCCACAAAAGT
1 AAAAACGCCACTAAAGT
1318065 CTGAGTCTTT
Statistics
Matches: 80, Mismatches: 16, Indels: 7
0.78 0.16 0.07
Matches are distributed among these distances:
41 48 0.60
42 31 0.39
43 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.26
Consensus pattern (42 bp):
AAAAACGCCACTAAAGTACATGACTATTGCGACGTTTATTAC
Found at i:1318039 original size:41 final size:40
Alignment explanation
Indices: 1317966--1318106 Score: 131
Period size: 41 Copynumber: 3.5 Consensus size: 40
1317956 CGTTTATTAC
* * * * *
1317966 AAAAACGCCACTAAGGTACATGACTATTGCGACGTTTGAAT
1 AAAAACGCCACTAAAGTATAAGTCTATAGCGACGTTTG-AT
*
1318007 AAAAACGCCACTAAAGTATAAGTCTATAGCGACGTTTGTT
1 AAAAACGCCACTAAAGTATAAGTCTATAGCGACGTTTGAT
* * * * *
1318047 CACAAACGCCACAAAAGTCTGAGTCTTTCA-CGACGTTTGTAT
1 -AAAAACGCCACTAAAGTATAAGTCTAT-AGCGACGTTTG-AT
*
1318089 ACAAACGCCACTAAAGTA
1 AAAAACGCCACTAAAGTA
1318107 AGAGTATTTT
Statistics
Matches: 83, Mismatches: 14, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
40 1 0.01
41 80 0.96
42 2 0.02
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (40 bp):
AAAAACGCCACTAAAGTATAAGTCTATAGCGACGTTTGAT
Found at i:1318125 original size:41 final size:41
Alignment explanation
Indices: 1317992--1318126 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
1317982 TACATGACTA
* * *
1317992 TTGCGACGTTTGAATAAAAACGCCACTAAAGTATA-AGTCTA
1 TTGCGACGTTTGTATACAAACGCCACTAAAGTA-AGAGTCTT
* * **
1318033 TAGCGACGTTTGT-TCACAAACGCCACAAAAGTCTGAGTCTT
1 TTGCGACGTTTGTAT-ACAAACGCCACTAAAGTAAGAGTCTT
** *
1318074 TCACGACGTTTGTATACAAACGCCACTAAAGTAAGAGTATT
1 TTGCGACGTTTGTATACAAACGCCACTAAAGTAAGAGTCTT
*
1318115 TTGCGGCGTTTG
1 TTGCGACGTTTG
1318127 ATCAAAAACA
Statistics
Matches: 75, Mismatches: 16, Indels: 6
0.77 0.16 0.06
Matches are distributed among these distances:
40 1 0.01
41 73 0.97
42 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (41 bp):
TTGCGACGTTTGTATACAAACGCCACTAAAGTAAGAGTCTT
Found at i:1318512 original size:14 final size:14
Alignment explanation
Indices: 1318475--1318513 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1318465 GGCATTTTAT
*
1318475 ATGTATATAATAAA
1 ATGTATATCATAAA
* *
1318489 ATATAAATCATAAA
1 ATGTATATCATAAA
1318503 ATGTATATCAT
1 ATGTATATCAT
1318514 GTAATAAAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (14 bp):
ATGTATATCATAAA
Found at i:1322532 original size:484 final size:484
Alignment explanation
Indices: 1321624--1322591 Score: 1882
Period size: 484 Copynumber: 2.0 Consensus size: 484
1321614 TGCTTGATAA
1321624 CTATTATTATAAGAAAAATCAGGCAAAGGCAAGTACTTTTCCCATGATCCTTAGATTTTATTCAC
1 CTATTATTATAAGAAAAATCAGGCAAAGGCAAGTACTTTTCCCATGATCCTTAGATTTTATTCAC
1321689 ACATGCTCTTAGCATATCTTTCAAAATTTGAATAATTCGTTCGAATTACCCATCCGTCTGAGGAT
66 ACATGCTCTTAGCATATCTTTCAAAATTTGAATAATTCGTTCGAATTACCCATCCGTCTGAGGAT
* *
1321754 GAAAAGCAATGTTGAAGTTAAGTCGAGTCCTCAAGGCTTTATGCAAAGATTTCAAAAATCTCGAA
131 GAAAAGCAATGCTGAAGTTAAGTCAAGTCCTCAAGGCTTTATGCAAAGATTTCAAAAATCTCGAA
1321819 GTGAACCTTGGGTCTCTTTCAGATACTATCGAGACATTCATTCCATGTATTCGAACAATATCTGT
196 GTGAACCTTGGGTCTCTTTCAGATACTATCGAGACATTCATTCCATGTATTCGAACAATATCTGT
1321884 AATGTATAATGCAACATACTTATCCATAGAGTAATTAGTTCGAACTTGGATGAAGTGCGCTGACC
261 AATGTATAATGCAACATACTTATCCATAGAGTAATTAGTTCGAACTTGGATGAAGTGCGCTGACC
1321949 TGGTCAATCTATCCATAATCACCCAAATTAAATCAATTTTATTGGATGTAAAAGGTAATCATGTG
326 TGGTCAATCTATCCATAATCACCCAAATTAAATCAATTTTATTGGATGTAAAAGGTAATCATGTG
1322014 ACAAAATCCATTTCAACTTTTTCTAATTTCCATTGAGGAAAGTAAATCAGTTGTGATGATCCGAA
391 ACAAAATCCATTTCAACTTTTTCTAATTTCCATTGAGGAAAGTAAATCAGTTGTGATGATCCGAA
1322079 GGGCACTTGATGTTCTACTTTAACTTGAT
456 GGGCACTTGATGTTCTACTTTAACTTGAT
1322108 CTATTATTATAAGAAAAATCAGGCAAAGGCAAGTACTTTTCCCATGATCCTTAGATTTTATTCAC
1 CTATTATTATAAGAAAAATCAGGCAAAGGCAAGTACTTTTCCCATGATCCTTAGATTTTATTCAC
*
1322173 ACATGCTCTTAGCATATCTTTCAAAATTTGAATAATTCGTTCGAATTGCCCATCCGTCTGAGGAT
66 ACATGCTCTTAGCATATCTTTCAAAATTTGAATAATTCGTTCGAATTACCCATCCGTCTGAGGAT
*
1322238 GAAAAGCAATGCTGAAGTTAAGTCAAGTCCTCAAGGCTTTATTCAAAGATTTCAAAAATCTCGAA
131 GAAAAGCAATGCTGAAGTTAAGTCAAGTCCTCAAGGCTTTATGCAAAGATTTCAAAAATCTCGAA
*
1322303 GTGAACCTTGGGTCTCTTTCAGATACTATCGAGACATTCATTCCATGTATTCGAACAATCTCTGT
196 GTGAACCTTGGGTCTCTTTCAGATACTATCGAGACATTCATTCCATGTATTCGAACAATATCTGT
1322368 AATGTATAATGCAACATACTTATCCATAGAGTAATTAGTTCGAACTTGGATGAAGTGCGCTGACC
261 AATGTATAATGCAACATACTTATCCATAGAGTAATTAGTTCGAACTTGGATGAAGTGCGCTGACC
1322433 TGGTCAATCTATCCATAATCACCCAAATTAAATCAATTTTATTGGATGTAAAAGGTAATCATGTG
326 TGGTCAATCTATCCATAATCACCCAAATTAAATCAATTTTATTGGATGTAAAAGGTAATCATGTG
*
1322498 ACAAAATCCATTTTAACTTTTTCTAATTTCCATTGAGGAAAGTAAATCAGTTGTGATGATCCGAA
391 ACAAAATCCATTTCAACTTTTTCTAATTTCCATTGAGGAAAGTAAATCAGTTGTGATGATCCGAA
1322563 GGGCACTTGATGTTCTACTTTAACTTGAT
456 GGGCACTTGATGTTCTACTTTAACTTGAT
1322592 GACATGTCAG
Statistics
Matches: 478, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
484 478 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (484 bp):
CTATTATTATAAGAAAAATCAGGCAAAGGCAAGTACTTTTCCCATGATCCTTAGATTTTATTCAC
ACATGCTCTTAGCATATCTTTCAAAATTTGAATAATTCGTTCGAATTACCCATCCGTCTGAGGAT
GAAAAGCAATGCTGAAGTTAAGTCAAGTCCTCAAGGCTTTATGCAAAGATTTCAAAAATCTCGAA
GTGAACCTTGGGTCTCTTTCAGATACTATCGAGACATTCATTCCATGTATTCGAACAATATCTGT
AATGTATAATGCAACATACTTATCCATAGAGTAATTAGTTCGAACTTGGATGAAGTGCGCTGACC
TGGTCAATCTATCCATAATCACCCAAATTAAATCAATTTTATTGGATGTAAAAGGTAATCATGTG
ACAAAATCCATTTCAACTTTTTCTAATTTCCATTGAGGAAAGTAAATCAGTTGTGATGATCCGAA
GGGCACTTGATGTTCTACTTTAACTTGAT
Found at i:1328297 original size:34 final size:35
Alignment explanation
Indices: 1328249--1328317 Score: 122
Period size: 34 Copynumber: 2.0 Consensus size: 35
1328239 TCAAAATATA
1328249 ATTTTTTTTAAAAACCTAATCCAATAGATGTTGTG
1 ATTTTTTTTAAAAACCTAATCCAATAGATGTTGTG
*
1328284 ATTTTTTTT-AAAACCTAATCCAATAGTTGTTGTG
1 ATTTTTTTTAAAAACCTAATCCAATAGATGTTGTG
1328318 CCCATCTCTA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 24 0.73
35 9 0.27
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.45
Consensus pattern (35 bp):
ATTTTTTTTAAAAACCTAATCCAATAGATGTTGTG
Found at i:1330030 original size:27 final size:27
Alignment explanation
Indices: 1329996--1330053 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
1329986 ACTCAAAATA
* * *
1329996 ATATTATTTTTTTTAATTAATATTAAT
1 ATATTATTTTATTAAAATAATATTAAT
1330023 ATATTATTTTATTAAAATAATATTAAT
1 ATATTATTTTATTAAAATAATATTAAT
1330050 -TATT
1 ATATT
1330054 TAAAATAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 4 0.14
27 24 0.86
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (27 bp):
ATATTATTTTATTAAAATAATATTAAT
Found at i:1334422 original size:3 final size:3
Alignment explanation
Indices: 1334414--1334456 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
1334404 TACCAAATAA
* *
1334414 TCT TCT TCT TCT TCT TCT TC- TCT TCT TTT TCA TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1334457 AAAGATAGTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:1334439 original size:20 final size:20
Alignment explanation
Indices: 1334414--1334454 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1334404 TACCAAATAA
*
1334414 TCTTCTTCTTCTTCTTCTTC
1 TCTTCTTCTTCATCTTCTTC
*
1334434 TCTTCTTTTTCATCTTCTTC
1 TCTTCTTCTTCATCTTCTTC
1334454 T
1 T
1334455 TCAAAGATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (20 bp):
TCTTCTTCTTCATCTTCTTC
Found at i:1336260 original size:15 final size:14
Alignment explanation
Indices: 1336229--1336280 Score: 63
Period size: 14 Copynumber: 3.7 Consensus size: 14
1336219 TATAAATAAA
1336229 AATATTA-TTATTT
1 AATATTATTTATTT
1336242 AATATTATTTATGTT
1 AATATTATTTAT-TT
*
1336257 AATATTA-TTATTGA
1 AATATTATTTATT-T
1336271 AATATTATTT
1 AATATTATTT
1336281 CTACAACTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
13 8 0.24
14 15 0.44
15 11 0.32
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (14 bp):
AATATTATTTATTT
Found at i:1336274 original size:14 final size:14
Alignment explanation
Indices: 1336228--1336279 Score: 54
Period size: 15 Copynumber: 3.7 Consensus size: 14
1336218 CTATAAATAA
1336228 AAATATTATTATT-
1 AAATATTATTATTG
*
1336241 TAATATTATT-TATG
1 AAATATTATTAT-TG
*
1336255 TTAATATTATTATTG
1 -AAATATTATTATTG
1336270 AAATATTATT
1 AAATATTATT
1336280 TCTACAACTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
12 1 0.03
13 10 0.30
14 9 0.27
15 12 0.36
16 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (14 bp):
AAATATTATTATTG
Found at i:1336339 original size:19 final size:18
Alignment explanation
Indices: 1336315--1336381 Score: 57
Period size: 19 Copynumber: 3.6 Consensus size: 18
1336305 TAAGACTAAT
1336315 ATATTATATTGAAATAAAA
1 ATATTATATT-AAATAAAA
*
1336334 ATATTATAAATTATAT-AAA
1 ATATTAT--ATTAAATAAAA
* *
1336353 TTATT-TATTAAAATAAGA
1 ATATTATATT-AAATAAAA
1336371 ATATTATATTA
1 ATATTATATTA
1336382 TATTTTAGTA
Statistics
Matches: 38, Mismatches: 5, Indels: 11
0.70 0.09 0.20
Matches are distributed among these distances:
16 3 0.08
17 3 0.08
18 8 0.21
19 18 0.47
20 3 0.08
21 3 0.08
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (18 bp):
ATATTATATTAAATAAAA
Found at i:1336356 original size:35 final size:36
Alignment explanation
Indices: 1336293--1336378 Score: 90
Period size: 37 Copynumber: 2.4 Consensus size: 36
1336283 ACAACTTTAT
* *
1336293 AAAT-AAAA-ATTATAAGACTAATATATTA-TATTG
1 AAATAAAAATATTATAAGACTAATAAATTATTATTA
*
1336326 AAATAAAAATATTATAA-ATTATATAAATTATTTATTA
1 AAATAAAAATATTATAAGACTA-ATAAATTA-TTATTA
*
1336363 AAATAAGAATATTATA
1 AAATAAAAATATTATA
1336379 TTATATTTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
33 4 0.09
34 7 0.16
35 14 0.32
37 19 0.43
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.38
Consensus pattern (36 bp):
AAATAAAAATATTATAAGACTAATAAATTATTATTA
Found at i:1342448 original size:43 final size:43
Alignment explanation
Indices: 1342387--1342472 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
1342377 ATAAACCGTA
* *
1342387 TATATGTGTGTGTGTGTTGACATGAGTGGTTGTTTTTTGAGGG
1 TATATATGTGTGTGTGTTGACATGAGTGGATGTTTTTTGAGGG
1342430 TATATATGTGTGTGTGTTGACATGAGTGGATGTTTTTTGAGGG
1 TATATATGTGTGTGTGTTGACATGAGTGGATGTTTTTTGAGGG
1342473 GGGAAATTGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.16, C:0.02, G:0.36, T:0.45
Consensus pattern (43 bp):
TATATATGTGTGTGTGTTGACATGAGTGGATGTTTTTTGAGGG
Found at i:1343875 original size:45 final size:45
Alignment explanation
Indices: 1343805--1343905 Score: 114
Period size: 45 Copynumber: 2.2 Consensus size: 45
1343795 TAATCTTAAA
* *
1343805 TTATTTTTTCTCCTAAAAATATTAATATTAGACGTTA-CTTAAAATG
1 TTATTTTTT-TACTAAAAATATTAATATCAGACGTTATC-TAAAATG
* * * **
1343851 TTATTTTTTTACTTAAAATGTTAATATCGGTTGTTATCTAAAATG
1 TTATTTTTTTACTAAAAATATTAATATCAGACGTTATCTAAAATG
1343896 TTATTTTTTT
1 TTATTTTTTT
1343906 TATTTTAATA
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
45 37 0.79
46 10 0.21
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (45 bp):
TTATTTTTTTACTAAAAATATTAATATCAGACGTTATCTAAAATG
Found at i:1345469 original size:14 final size:14
Alignment explanation
Indices: 1345470--1345509 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1345460 AATAATGATT
* *
1345470 TAATGATTTATTAC
1 TAATGATTTAATAA
*
1345484 TAATTATTTAATAA
1 TAATGATTTAATAA
1345498 TAATGATTTAAT
1 TAATGATTTAAT
1345510 GTTTTTTGTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (14 bp):
TAATGATTTAATAA
Found at i:1345492 original size:22 final size:22
Alignment explanation
Indices: 1345436--1345495 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
1345426 AAAACTCAAT
*
1345436 TTAATAAT-ATTGATATGATTTA
1 TTAATAATGATTTA-ATGATTTA
1345458 TTAATAATGATTTAATGATTTA
1 TTAATAATGATTTAATGATTTA
* *
1345480 TTACTAATTATTTAAT
1 TTAATAATGATTTAAT
1345496 AATAATGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 30 0.88
23 4 0.12
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.52
Consensus pattern (22 bp):
TTAATAATGATTTAATGATTTA
Found at i:1346160 original size:84 final size:84
Alignment explanation
Indices: 1346002--1346161 Score: 275
Period size: 84 Copynumber: 1.9 Consensus size: 84
1345992 CCAGAATCAC
*
1346002 CAAACACTTGATTAAATGATCTTGTGTGACCAAAAGATTCTAGTGGGATATTACCCTAAACCCTA
1 CAAACACTTGATTAAATAATCTTGTGTGACCAAAAGATTCTAGTGGGATATTACCCTAAACCCTA
*
1346067 AACCCTAAACCATAATAAA
66 AACACTAAACCATAATAAA
* *
1346086 CAAACACTTGATTAAATAATCTTGTGTGATCAAAAGATTCTAGTTGGATATTACCCTAAACCCTA
1 CAAACACTTGATTAAATAATCTTGTGTGACCAAAAGATTCTAGTGGGATATTACCCTAAACCCTA
*
1346151 AACATTAAACC
66 AACACTAAACC
1346162 TTAAACCCTA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 71 1.00
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.28
Consensus pattern (84 bp):
CAAACACTTGATTAAATAATCTTGTGTGACCAAAAGATTCTAGTGGGATATTACCCTAAACCCTA
AACACTAAACCATAATAAA
Found at i:1346166 original size:21 final size:21
Alignment explanation
Indices: 1346142--1346181 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1346132 GATATTACCC
1346142 TAAACCCT-AAACATTAAACCT
1 TAAACCCTAAAACA-TAAACCT
1346163 TAAACCCTAAAACATAAAC
1 TAAACCCTAAAACATAAAC
1346182 AACAATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.53, C:0.28, G:0.00, T:0.20
Consensus pattern (21 bp):
TAAACCCTAAAACATAAACCT
Found at i:1346924 original size:24 final size:24
Alignment explanation
Indices: 1346897--1346959 Score: 72
Period size: 27 Copynumber: 2.5 Consensus size: 24
1346887 TTTTTTTTAC
1346897 TATTAAATCATTATTAGTAATAAT
1 TATTAAATCATTATTAGTAATAAT
**
1346921 TATTATAATTTCATTATTAGTAATCTT
1 TATTA-AA--TCATTATTAGTAATAAT
*
1346948 TACTAAATCATT
1 TATTAAATCATT
1346960 TGTATCAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
24 10 0.30
25 2 0.06
26 2 0.06
27 19 0.58
ACGTcount: A:0.40, C:0.08, G:0.03, T:0.49
Consensus pattern (24 bp):
TATTAAATCATTATTAGTAATAAT
Found at i:1347075 original size:14 final size:11
Alignment explanation
Indices: 1346897--1347090 Score: 83
Period size: 11 Copynumber: 16.3 Consensus size: 11
1346887 TTTTTTTTAC
1346897 TATTAAATCAT
1 TATTAAATCAT
*
1346908 TATTAGTAATAAT
1 TATTA--AATCAT
1346921 TATTATAATTTCAT
1 TATTA-AA--TCAT
*
1346935 TATTAGTAATCTT
1 TATTA--AATCAT
*
1346948 TACTAAATCATTT
1 TATTAAATCA--T
*
1346961 GTATCAAATCAT
1 -TATTAAATCAT
* *
1346973 TA--AATATTAA
1 TATTAA-ATCAT
* *
1346983 TAATAAAACAT
1 TATTAAATCAT
1346994 TATTACTAATCAT
1 TATTA--AATCAT
1347007 TATTAAATCAT
1 TATTAAATCAT
1347018 TAAAGTTCAAATCAT
1 T--A-TT-AAATCAT
*
1347033 TA--AAATTAT
1 TATTAAATCAT
*
1347042 TAGT-AATCAT
1 TATTAAATCAT
1347052 TATTAAATCAT
1 TATTAAATCAT
1347063 TATTATCAGATCAT
1 TATTA--A-ATCAT
1347077 TATTAAATCAT
1 TATTAAATCAT
1347088 TAT
1 TAT
1347091 CCACAAAAAT
Statistics
Matches: 143, Mismatches: 17, Indels: 46
0.69 0.08 0.22
Matches are distributed among these distances:
9 10 0.07
10 13 0.09
11 43 0.30
12 7 0.05
13 31 0.22
14 28 0.20
15 11 0.08
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (11 bp):
TATTAAATCAT
Found at i:1356595 original size:94 final size:94
Alignment explanation
Indices: 1356434--1356623 Score: 380
Period size: 94 Copynumber: 2.0 Consensus size: 94
1356424 CAGTTTTAGC
1356434 GTTGAGTACTGATAACCTCGTAAAAAGGCTGTATTTTGTGCCTTTTTACTTAGGTTGTTGTTTGT
1 GTTGAGTACTGATAACCTCGTAAAAAGGCTGTATTTTGTGCCTTTTTACTTAGGTTGTTGTTTGT
1356499 TTTAAAGCCCATGTCATAGCATTTAGAGT
66 TTTAAAGCCCATGTCATAGCATTTAGAGT
1356528 GTTGAGTACTGATAACCTCGTAAAAAGGCTGTATTTTGTGCCTTTTTACTTAGGTTGTTGTTTGT
1 GTTGAGTACTGATAACCTCGTAAAAAGGCTGTATTTTGTGCCTTTTTACTTAGGTTGTTGTTTGT
1356593 TTTAAAGCCCATGTCATAGCATTTAGAGT
66 TTTAAAGCCCATGTCATAGCATTTAGAGT
1356622 GT
1 GT
1356624 ATTTAGCTCT
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 96 1.00
ACGTcount: A:0.23, C:0.14, G:0.22, T:0.42
Consensus pattern (94 bp):
GTTGAGTACTGATAACCTCGTAAAAAGGCTGTATTTTGTGCCTTTTTACTTAGGTTGTTGTTTGT
TTTAAAGCCCATGTCATAGCATTTAGAGT
Found at i:1367800 original size:155 final size:155
Alignment explanation
Indices: 1367518--1367827 Score: 548
Period size: 155 Copynumber: 2.0 Consensus size: 155
1367508 TATGTTTTTT
*
1367518 GTTGGGATATACGGTGAAGCTCAATCGATCAACCAAATCATTGCCAAGAGGGGTTGAGTTGGTTT
1 GTTGGGATATACGGTGAAGCTCAATCGATCAACCAAATCATTGCCAAGAGGGGTTAAGTTGGTTT
* *
1367583 TCGAGATTAGTGAGTAAGGAGATTAAAAAGATAGGAAAATTGGAACAAGGATTTATAGTGGTTCG
66 TCGAGATTAGGGAGTAAGGAGATTAAAAAGATAAGAAAATTGGAACAAGGATTTATAGTGGTTCG
1367648 ACTTCTCAACCAAGTCTACATCCAC
131 ACTTCTCAACCAAGTCTACATCCAC
* * *
1367673 GTTGGGATATACGGTGAAGCTCAATCGATCAACCGAATGATTTCCAAGAGGGGTTAAGTTGGTTT
1 GTTGGGATATACGGTGAAGCTCAATCGATCAACCAAATCATTGCCAAGAGGGGTTAAGTTGGTTT
* *
1367738 TCGAGATTAGGGAGTAAGGAGATTAAAAATATAAGAAAATTGGCACAAGGATTTATAGTGGTTCG
66 TCGAGATTAGGGAGTAAGGAGATTAAAAAGATAAGAAAATTGGAACAAGGATTTATAGTGGTTCG
1367803 ACTTCTCAACCAAGTCTACATCCAC
131 ACTTCTCAACCAAGTCTACATCCAC
1367828 TGCCTTAGCT
Statistics
Matches: 147, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
155 147 1.00
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.27
Consensus pattern (155 bp):
GTTGGGATATACGGTGAAGCTCAATCGATCAACCAAATCATTGCCAAGAGGGGTTAAGTTGGTTT
TCGAGATTAGGGAGTAAGGAGATTAAAAAGATAAGAAAATTGGAACAAGGATTTATAGTGGTTCG
ACTTCTCAACCAAGTCTACATCCAC
Found at i:1369991 original size:15 final size:15
Alignment explanation
Indices: 1369971--1370019 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
1369961 TTTTCATAAT
*
1369971 CCAAACATCATAACC
1 CCAAACCTCATAACC
1369986 CCAAACCTCATAACC
1 CCAAACCTCATAACC
*
1370001 TCAAACCTCA-AACC
1 CCAAACCTCATAACC
*
1370015 TCAAA
1 CCAAA
1370020 GACCTAAACC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
14 9 0.28
15 23 0.72
ACGTcount: A:0.45, C:0.41, G:0.00, T:0.14
Consensus pattern (15 bp):
CCAAACCTCATAACC
Found at i:1370007 original size:7 final size:7
Alignment explanation
Indices: 1369972--1370019 Score: 60
Period size: 7 Copynumber: 6.6 Consensus size: 7
1369962 TTTCATAATC
*
1369972 CAAACAT
1 CAAACCT
*
1369979 CATAACCC
1 CA-AACCT
1369987 CAAACCT
1 CAAACCT
1369994 CATAACCT
1 CA-AACCT
1370002 CAAACCT
1 CAAACCT
1370009 CAAACCT
1 CAAACCT
1370016 CAAA
1 CAAA
1370020 GACCTAAACC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
7 24 0.67
8 12 0.33
ACGTcount: A:0.46, C:0.40, G:0.00, T:0.15
Consensus pattern (7 bp):
CAAACCT
Found at i:1370028 original size:22 final size:22
Alignment explanation
Indices: 1369973--1370031 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
1369963 TTCATAATCC
*
1369973 AAACATCATAACCCCAAACCTCA
1 AAACCTCA-AACCCCAAACCTCA
* *
1369996 TAACCTCAAACCTCAAACCTCA
1 AAACCTCAAACCCCAAACCTCA
1370018 AAGACCT-AAACCCC
1 AA-ACCTCAAACCCC
1370032 TTTAAACCCC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 20 0.67
23 10 0.33
ACGTcount: A:0.44, C:0.41, G:0.02, T:0.14
Consensus pattern (22 bp):
AAACCTCAAACCCCAAACCTCA
Found at i:1374524 original size:11 final size:11
Alignment explanation
Indices: 1374508--1374532 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1374498 CTAAATTTTA
1374508 AAAAAAAAATT
1 AAAAAAAAATT
1374519 AAAAAAAAATT
1 AAAAAAAAATT
1374530 AAA
1 AAA
1374533 TACTAAAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAAAAAATT
Found at i:1384873 original size:35 final size:35
Alignment explanation
Indices: 1384824--1384891 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
1384814 GTAACTTAAT
* *
1384824 GACGGCATCGATAGTATGCCCTCATTATCCATAAC
1 GACGGCATCAATAGTATGCCCTCAGTATCCATAAC
* *
1384859 GACGGTATCAATAGTATGCCCTTAGTATCCATA
1 GACGGCATCAATAGTATGCCCTCAGTATCCATA
1384892 CCTTATAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (35 bp):
GACGGCATCAATAGTATGCCCTCAGTATCCATAAC
Found at i:1385646 original size:15 final size:15
Alignment explanation
Indices: 1385617--1385655 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
1385607 AGAACTTACA
*
1385617 AGAGAAAGA-AGAAG
1 AGAGAAAAAGAGAAG
1385631 AGAGAAAAAGAGAAG
1 AGAGAAAAAGAGAAG
1385646 AG-GAAAAAGA
1 AGAGAAAAAGA
1385656 TATGATGAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 16 0.70
15 7 0.30
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (15 bp):
AGAGAAAAAGAGAAG
Found at i:1392241 original size:61 final size:59
Alignment explanation
Indices: 1392116--1392245 Score: 149
Period size: 61 Copynumber: 2.2 Consensus size: 59
1392106 AAAATGCTCT
* * * *
1392116 AATTTCAT-CCCTAAACTATGACTCATTCTAAATTGTTCCTCAAACTTTTGAATATTTC
1 AATTTCATCCCCAAAACTATGACTAATTCTAAATTGTTCCCCAAACTTTTGAACATTTC
* *
1392174 ATTTTCATCCCCAAAAC-ATGACCTTAATTCTAAATTAG-TCCCCAGACTTTTTGAACATTTC
1 AATTTCATCCCCAAAACTATGA-C-TAATTCTAAATT-GTTCCCCAAAC-TTTTGAACATTTC
1392235 AATTTCATCCC
1 AATTTCATCCC
1392246 AAATTATGCA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
58 11 0.18
59 8 0.13
60 18 0.30
61 23 0.38
ACGTcount: A:0.31, C:0.25, G:0.05, T:0.38
Consensus pattern (59 bp):
AATTTCATCCCCAAAACTATGACTAATTCTAAATTGTTCCCCAAACTTTTGAACATTTC
Found at i:1392247 original size:60 final size:58
Alignment explanation
Indices: 1392116--1392248 Score: 153
Period size: 60 Copynumber: 2.2 Consensus size: 58
1392106 AAAATGCTCT
* * * *
1392116 AATTTCATCCCTAAACTATGACTCATTCTAAATTGTTCCTCAAACTTTTGAATATTTC
1 AATTTCATCCCAAAACTATGACTAATTCTAAATTGTTCCCCAAACTTTTGAACATTTC
* *
1392174 ATTTTCATCCCCAAAAC-ATGACCTTAATTCTAAATTAG-TCCCCAGACTTTTTGAACATTTC
1 AATTTCAT-CCCAAAACTATGA-C-TAATTCTAAATT-GTTCCCCAAAC-TTTTGAACATTTC
1392235 AATTTCATCCCAAA
1 AATTTCATCCCAAA
1392249 TTATGCATAT
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
58 11 0.17
59 8 0.13
60 24 0.38
61 20 0.32
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (58 bp):
AATTTCATCCCAAAACTATGACTAATTCTAAATTGTTCCCCAAACTTTTGAACATTTC
Found at i:1393733 original size:3 final size:3
Alignment explanation
Indices: 1393719--1393790 Score: 85
Period size: 3 Copynumber: 23.7 Consensus size: 3
1393709 AATTTTTTCA
*
1393719 TAT TAT TTT TAT TAT TAT TAT T-T TCAT TAT T-T TCAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT T-AT TAT TAT TAT
*
1393764 TAT TAT TAA TAT ATAT TAT TAT TAT TA
1 TAT TAT TAT TAT -TAT TAT TAT TAT TA
1393791 AATAAATAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
2 4 0.07
3 49 0.82
4 7 0.12
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1393803 original size:19 final size:19
Alignment explanation
Indices: 1393762--1393803 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
1393752 CATTATTATT
* *
1393762 ATTATTATTAATATATATT
1 ATTATTATTAATAAATATA
1393781 ATTATTATTAAATAAATA-A
1 ATTATTATT-AATAAATATA
1393800 ATTA
1 ATTA
1393804 CAAGACCCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTATTATTAATAAATATA
Found at i:1393803 original size:22 final size:22
Alignment explanation
Indices: 1393756--1393803 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1393746 TATTTTCATT
* *
1393756 ATTATTATTATTATTAATATAT
1 ATTATTATTATTAATAATATAA
1393778 ATTATTATTATTAAATAA-ATAA
1 ATTATTATTATT-AATAATATAA
1393800 ATTA
1 ATTA
1393804 CAAGACCCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATTATTATTATTAATAATATAA
Found at i:1394148 original size:35 final size:35
Alignment explanation
Indices: 1394097--1394177 Score: 135
Period size: 35 Copynumber: 2.3 Consensus size: 35
1394087 ACCTGCCGCT
*
1394097 GCCATGCTGCTACGATGCCAACCGAAGCCTCCAGAA
1 GCCA-GCTGCCACGATGCCAACCGAAGCCTCCAGAA
1394133 GCCAGCTGCCACGATGCCAACCGAAGCCTCCAGAA
1 GCCAGCTGCCACGATGCCAACCGAAGCCTCCAGAA
*
1394168 GCTAGCTGCC
1 GCCAGCTGCC
1394178 CCTCCACGTC
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
35 39 0.91
36 4 0.09
ACGTcount: A:0.26, C:0.38, G:0.23, T:0.12
Consensus pattern (35 bp):
GCCAGCTGCCACGATGCCAACCGAAGCCTCCAGAA
Found at i:1394623 original size:20 final size:20
Alignment explanation
Indices: 1394598--1394639 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1394588 AAATCCGGCC
1394598 ACCATCGGCAGTGGCTGACG
1 ACCATCGGCAGTGGCTGACG
1394618 ACCATCGGCAGTGGCTGACG
1 ACCATCGGCAGTGGCTGACG
1394638 AC
1 AC
1394640 GGCGATTGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.21, C:0.31, G:0.33, T:0.14
Consensus pattern (20 bp):
ACCATCGGCAGTGGCTGACG
Found at i:1400430 original size:22 final size:22
Alignment explanation
Indices: 1400402--1400456 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
1400392 ACATCGACAA
*
1400402 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTATC
*
1400424 TCTTCAAAGATGATATATTATC
1 TCTTCAAAGATGATAGATTATC
*
1400446 TTTTCAAAGAT
1 TCTTCAAAGAT
1400457 AATCGCTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.40
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTATC
Found at i:1401282 original size:76 final size:74
Alignment explanation
Indices: 1401151--1401293 Score: 205
Period size: 76 Copynumber: 1.9 Consensus size: 74
1401141 ATTCAGTGCA
*
1401151 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACATGCAGTGCAGGATGTTTTCAAAAAGCCTT
1 TGATATTTTCAAAACCTTCGGGTCATCCATAAGACATGCAGTGCAGGATGTTTTC-AAAA-CCTT
1401216 CGGGAGCTTTT
64 CGGGAGCTTTT
** * * * *
1401227 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
1 TGATATTTTCAAAACCTTCGGGTCATCCATAAGACATGCAGTGCAGGATGTTTTCAAAACCTTCG
1401292 GG
66 GG
1401294 TCATCTGTAA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
74 8 0.13
75 4 0.07
76 48 0.80
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (74 bp):
TGATATTTTCAAAACCTTCGGGTCATCCATAAGACATGCAGTGCAGGATGTTTTCAAAACCTTCG
GGAGCTTTT
Found at i:1401315 original size:45 final size:45
Alignment explanation
Indices: 1401227--1401316 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 45
1401217 GGGAGCTTTT
*
1401227 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
*
1401272 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTAT-AGTGCA
1 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGACCT-TCAGTGCA
1401317 AAATGATAGG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
45 41 0.98
46 1 0.02
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (45 bp):
TGATATTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
Found at i:1401489 original size:3 final size:3
Alignment explanation
Indices: 1401469--1401531 Score: 83
Period size: 3 Copynumber: 20.7 Consensus size: 3
1401459 AATTTTTTCA
* *
1401469 TAT TAT TTT TAT TTT TAT TAT T-T TCAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT
1401514 ATAT TAT TAT TAT TAT TA
1 -TAT TAT TAT TAT TAT TA
1401532 AATAAATAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
2 2 0.04
3 46 0.87
4 5 0.09
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1402636 original size:13 final size:13
Alignment explanation
Indices: 1402618--1402644 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1402608 TCATGCATTT
1402618 TAATTTTGTTTTA
1 TAATTTTGTTTTA
1402631 TAATTTTGTTTTA
1 TAATTTTGTTTTA
1402644 T
1 T
1402645 TTATATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.70
Consensus pattern (13 bp):
TAATTTTGTTTTA
Done.